docs(docs): asdded and cleaned up docs

README.md

@@ -5,175 +5,10 @@
 
 ---
 
-GridFire is a C++ library designed to preform general nuclear network evolution using the reaclib library. It is a
+GridFire is a C++ library designed to perform general nuclear network evolution using the Reaclib library. It is part of the larger SERiF project within the 4D-STAR collaboration.
-part of the larger SERiF project which is itself a part of the 4D-STAR collaboration. 
 
-> Note that GridFire is still very early in development and is not ready for scientific use. The API is not stable and
+**Design Philosophy and Workflow:**
-> the reults are not yet validated. We are actively working on improving the library and once it is tested and validated
+GridFire is architected to balance physical fidelity, computational efficiency, and extensibility when simulating complex nuclear reaction networks. Users begin by defining a composition, which is used to construct a full GraphEngine representation of the reaction network. To manage the inherent stiffness and multi-scale nature of these networks, GridFire employs a layered view strategy: partitioning algorithms isolate fast and slow processes, adaptive culling removes negligible reactions at runtime, and implicit solvers stably integrate the remaining stiff system. This modular pipeline allows researchers to tailor accuracy versus performance trade-offs, reuse common engine components, and extend screening or partitioning models without modifying core integration routines.
-> we will release a stable version.
-
-## Design
-
-GridFire uses a "graph-first" design to represent the nuclear network. Specifically, internally the network is
-represented as a directed hypergraph where nodes are nuclides and edges are reactions. This design allows for very straightforward
-and efficient evolution of the network topology. 
-
-## Current Features
-- **Reaclib Support**: GridFire uses reaclib coefficients statically compiled into the binary to evaluate reation rates. We bundle a script which can be used to generate the header files where these are stored. 
-- **Auto Differentiation**: GridFire uses [CppAD](https://github.com/coin-or/CppAD) to generate analytic Jacobians for stiff network evaluation.
-- **Dynamic Network Topology**: GridFire supports dynamic network topology, allowing for the addition and removal of nuclides and reactions during runtime.
-- **Dynamic Stiff Detection**: GridFire uses a heuristic stiff detection algorithm to determine the stiffness of the network at runtime.
-
-## Planned Features
-### High Priority
-- **Reverse Reactions**: Currently, GridFire only supports forward reactions. Very soon we will add support for reverse reactions.
-- **Weak Reactions**: GridFire will eventually support weak reactions, allowing for a more complete nuclear network evolution.
-- **Python Bindings**: We plan to add Python bindings to GridFire, allowing for easy integration with Python-based workflows.
-
-### Low Priority
-- **GPU and Multi-Core Support**: We plan to add support for GPU and multi-core execution, allowing for faster network evolution.
-- **Topology Optimization**: We plan to add support for topology optimization, allowing for more efficient network evolution.
-- **Real-Time Network Visualization**: We plan to add support for real-time network visualization, allowing for better understanding of the network evolution.
-
-## Building
-GridFire uses meson as its build system. The minimum required version is 1.5.0. To build GridFire, you will need to have the following dependencies installed:
-
-- C++ compiler supporting at least C++20 (though we test against C++23, and it is **strongly** recommended to use C++23)
-- [Meson](https://mesonbuild.com/) build system (`apt install meson` or `brew install meson` or `pip install "meson>=1.5.0"`)
-- [Ninja](https://ninja-build.org/) build system (`apt install ninja-build` or `brew install ninja` or `pip install ninja`)
-- (_optional to have preinstalled_) [Boost](https://www.boost.org/) libraries (`apt install libboost-all-dev` or `brew install boost`)
-
-Boost is labeled as optional because if GridFire cannot find boost during installation it will ask the user if they want
-to install it, and then it will take care of that insallation. 
-
-Once at least the C++ compiler, meson, and ninja are installed, you can build GridFire by running the following commands in the root directory of the repository:
-
-```bash
-meson setup build --buildtype=release
-meson compile -C build
-meson install -C build
-```
-
-Running the first command will create a `build` directory in the root of the repository, which will contain all the
-build files. The second command will compile the library and the third command will install it to your system.
-When installing GridFire it will generate a `pkg-config` file which can be used to link against the library in other
-projects.
-
-### Linking Against GridFire
-The easiest way, by far, to link against GridFire is to use `pkg-config`. This will automatically handle all the
-library and include flags for you. Further, the `pkg-config` file will also include the required information on
-the libcomposition library so that you do not need to also manually link against it.
-
-```bash
-g++ -o main.cpp $(pkg-config --cflags --libs gridfire)
-```
-
-### Meson Wrap Installed Dependencies
-Aside from Boost, GridFire dependes on a few other libraries which are not required to be installed on the system, but
-are instead downloaded and built as part of the GridFire build process. These are:
-- [CppAD](https://github.com/coin-or/CppAD): Used for automatic differentiation.
-- [libcomposition](https://github.com/4d-star/libcomposition): Used for composition of networks.
-- [libconfig](https://github.com/4d-star/libconfig): Used for configuration management.
-- [libconstants](https://github.com/4d-star/libconstants): Used for physical constants.
-- [liblogging](https://github.com/4d-star/liblogging): Used for logging.
-
-These will all be downloaded and build automatically by meson when you run the `meson setup` and `meson compile` commands.
-
-## Usage
-
-> All code in GridFire is within the `gridfire` namespace. This means that you will need to use `gridfire::` prefix when
-> using any of the classes or functions in GridFire.
-
-> All code in lib* libraries is within the `fourdst::` namespace or subnamespaces of this (`fourdst::composition`,
-`fourdst::config`, etc...). This means that you will need to use `fourdst::` prefix when using any of the classes or
-> functions in these libraries.
-
-GridFire is designed to primarily interface with `fourdst::composition::Composition` objects (provided by libcomposition).
-The idea is that you create a composition object which tracks some set of species and either their mass fractions or number
-fractions. You then initialize a network from this composition object. 
-
-When evaluating the network you pass the current state of the composition object, the temperature, the density, and the 
-current energy of the system (along with some other parmeters such as the maximum time and the initial time step). Any
-network implemented in GridFire will then use this information to evolve the network and return a `gridfire::NetOut` object
-which contains the updated state of the composition object, the new energy of the system, and the number of steps the
-solver took to reach the final state.
-
-There are a few networks currently implemented in GridFire.
-
-| Network Name               | Description                                                                                                                                                                             | Network Format Enum |
-|----------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------|
-| `gridfire::GraphNetwork`   | A general nuclear network which uses a directed hypergraph to represent the network topology. This is the main network implemented in GridFire and is the one you will most likely use. | `REACLIB`         |
-| `gridfire::StaticGraphNetwork` |  A less general version of `gridfire::GraphNetwork` which uses a static graph to represent the network topology. That is to say that new species cannot be added or removed after instatiation of the network. | `REACLIB_STATIC`  |
-| `gridfire::Approx8Network` | A specialized network for the approximate 8 species network used in stellar nucleosynthesis. This is a reimplimentation of the network developed by Frank Timmes' for MESA              | `APPROX8`          |
-| `gridfire::Network`        | A virtual base class for all networks in GridFire. This is not meant to be used directly; rather, all networks in GridFire should subclass `gridfire::Network` and implement the required `evaluate` method. | `DEFAULT`         |
-
-Regardless of the network you chose, the interface is the same. You will need to create a `gridfire::NetIn` object
-which contains the initial state of the network, including the composition, temperature, density, energy, initial time
-step, and maximum time. You will then pass this object to the `evaluate` method of the network you chose. The `evaluate`
-method will return a `gridfire::NetOut` object which contains the updated state of the network.
-
-A simple example of how to use `gridfire::GraphNetwork` is shown below (note that `composition.h` is a header file
-provided by libcomposition, which means your compiler must be able to find its header and library files. The pkg-config
-file generated during the installation of GridFire will take care of this for you, so you can use `pkg-config` to
-compile this example):
-
-```c++
-#include <gridfire/netgraph.h>
-#include <fourdst/composition/composition.h>
-
-#include <iostream>
-#include <vector>
-#include <string>
-
-int main() {
-    const std::vector<double> comp = {0.708, 2.94e-5, 0.276, 0.003, 0.0011, 9.62e-3, 1.62e-3, 5.16e-4};
-    const std::vector<std::string> symbols = {"H-1", "He-3", "He-4", "C-12", "N-14", "O-16", "Ne-20", "Mg-24"};
-
-    fourdst::composition::Composition composition;
-    
-    // true puts this in mass fraction mode. false would mean you must provide number fractions instead.
-    composition.registerSymbol(symbols, true); 
-    
-    composition.setMassFraction(symbols, comp);
-    composition.finalize(true);
-
-    gridfire::NetIn netIn;
-    netIn.composition = composition;
-    netIn.temperature = 1e7; // In Kelvin
-    netIn.density = 1e2;     // In g/cm^3
-    netIn.energy = 0.0;      // Initial energy in erg
-
-    netIn.tMax = 3.15e17;    // In seconds
-    netIn.dt0 = 1e12;        // Initial time step in seconds
-
-    gridfire::GraphNetwork network(composition);
-    network.exportToDot("Network.dot");
-    gridfire::NetOut netOut;
-    netOut = network.evaluate(netIn);
-    std::cout << netOut << std::endl;    
-}
-
-```
-Save that file to `main.cpp` and compile it with the following command:
-```bash
-clang++ main.cpp $(pkg-config --cflags --libs gridfire) -I/opt/homebrew/include -o main -std=c++23
-./main
-```
-> Note that here I have included the `-I/opt/homebrew/include` flag to specify the header location for boost
-> on my system. This very well may already be in your compiler's include path, or if not it might be in a different
-> location. That is all very system dependent. You can try to get a sense of where the boost headers are located
-> by looking at the `build/compile-commmands.json` file generate by meson after running `meson setup build`.
-
- 
-> -std=c++23 or -std=c++20 is required as we use some C++20 feature in GridFire (specifically concepts). Compiling with
-> C++23 is **strongly** recommended.
-
-Using a different network is as simple as changing the type of the `network` variable to the desired network type. For
-example, if you wanted to use the `gridfire::Approx8Network`, you would change the line
-`gridfire::GraphNetwork network(composition);` to `gridfire::Approx8Network network(composition);`. The rest of the code
-would remain the same.
-
-For more details on how to use the composition library please refer to the libcomposition documentation.
 
 ## Funding
 GridFire is a part of the 4D-STAR collaboration.
@@ -182,3 +17,246 @@ GridFire is a part of the 4D-STAR collaboration.
 101071505: 4D-STAR)
 Work for this project is funded by the European Union. Views and opinions expressed are however those of the author(s)
 only and do not necessarily reflect those of the European Union or the European Research.
+
+## Build and Installation Instructions
+
+### Prerequisites
+- C++ compiler supporting C++23 standard
+- Meson build system (>= 1.5.0)
+- Python 3.10 or newer
+- Python packages: `meson-python>=0.15.0`
+- Boost libraries (>= 1.75.0) installed system-wide
+
+> Note: Boost is the only external library dependency; no additional libraries are required beyond a C++ compiler, Meson, Python, and Boost.
+> 
+> Windows is not supported at this time.
+
+### Dependency Installation on Common Platforms
+
+- **Ubuntu/Debian:**
+  ```bash
+  sudo apt-get update && \
+    sudo apt-get install -y build-essential meson python3 python3-pip libboost-all-dev
+  ```
+
+- **Fedora/CentOS/RHEL:**
+  ```bash
+  sudo dnf install -y gcc-c++ meson python3 python3-pip boost-devel
+  ```
+
+- **macOS (Homebrew):**
+  ```bash
+  brew update && \
+    brew install boost meson python
+  ```
+
+### Building the C++ Library
+```bash
+meson setup build
+meson compile -C build
+```
+
+### Installing the Library
+```bash
+meson install -C build
+```
+
+### Python Bindings and Installation
+The Python interface is provided via `meson-python` and `pybind11`. To install the Python package:
+```bash
+pip install .
+```
+
+### Developer Workflow
+1. Clone the repository and install dependencies listed in `pyproject.toml`.
+2. Configure and build with Meson:
+   ```bash
+   meson setup build
+   meson compile -C build
+   ```
+3. Run the unit tests:
+   ```bash
+   meson test -C build
+   ```
+4. Iterate on code, rebuild, and rerun tests.
+
+## Code Architecture and Logical Flow
+
+GridFire is organized into modular components that collaborate to simulate nuclear reaction networks with high fidelity:
+
+- **Engine Module:** Core interfaces and implementations (e.g., `GraphEngine`) that evaluate reaction network rate equations and energy generation.
+- **Screening Module:** Implements nuclear reaction screening corrections (`WeakScreening`, `BareScreening`, etc.) affecting reaction rates.
+- **Rates Module:** Parses and manages Reaclib reaction rate data, providing temperature- and density-dependent rate evaluations.
+- **Python Interface:** Exposes C++ functionality to Python, enabling rapid prototyping and integration into workflows.
+
+### GraphEngine Configuration Options
+
+GraphEngine exposes runtime configuration methods to tailor network construction and rate evaluations:
+
+- **Constructor Parameters:**
+  - `BuildDepthType` (`Full`/`Reduced`/`Minimal`): controls network build depth, trading startup time for network completeness.
+  - `partition::PartitionFunction`: custom functor for network partitioning based on `Z`, `A`, and `T9`.
+
+- **setPrecomputation(bool precompute):**
+  - Enable/disable caching of reaction rates and stoichiometric data at initialization.
+  - *Effect:* Reduces per-step overhead; increases memory and setup time.
+
+- **setScreeningModel(ScreeningType type):**
+  - Choose plasma screening (models: `BARE`, `WEAK`).
+  - *Effect:* Alters rate enhancement under dense/low-T conditions, impacting stiffness.
+
+- **setUseReverseReactions(bool useReverse):**
+  - Toggle inclusion of reverse (detailed balance) reactions.
+  - *Effect:* Improves equilibrium fidelity; increases network size and stiffness.
+
+### Available Partition Functions
+
+| Function Name                         | Identifier               | Description                                                     |
+|---------------------------------------|--------------------------|-----------------------------------------------------------------|
+| `GroundStatePartitionFunction`        | "GroundState"          | Weights using nuclear ground-state spin factors.               |
+| `RauscherThielemannPartitionFunction` | "RauscherThielemann"   | Interpolates normalized g-factors per Rauscher & Thielemann.   |
+
+These functions implement:
+```cpp
+double evaluate(int Z, int A, double T9) const;
+double evaluateDerivative(int Z, int A, double T9) const;
+bool supports(int Z, int A) const;
+std::string type() const;
+```
+
+## Engine Views
+
+The GridFire engine supports multiple engine view strategies to adapt or restrict network topology. Each view implements a specific algorithm:
+
+| View Name                             | Purpose                                                                          | Algorithm / Reference                                                                                   | When to Use                                                     |
+|---------------------------------------|----------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------|
+| AdaptiveEngineView                    | Dynamically culls low-flow species and reactions during runtime                 | Iterative flux thresholding to remove reactions below a flow threshold                                   | Large networks to reduce computational cost                     |
+| DefinedEngineView                     | Restricts the network to a user-specified subset of species and reactions        | Static network masking based on user-provided species/reaction lists                                      | Targeted pathway studies or code-to-code comparisons            |
+| MultiscalePartitioningEngineView      | Partitions the network into fast and slow subsets based on reaction timescales   | Network partitioning following Hix & Thielemann Silicon Burning I & II (DOI:10.1086/177016,10.1086/306692)| Stiff, multi-scale networks requiring tailored integration      |
+| NetworkPrimingEngineView              | Primes the network with an initial species or set of species for ignition studies| Single-species injection with transient flow analysis                                                     | Investigations of ignition triggers or initial seed sensitivities|
+
+These engine views implement the common Engine interface and may be composed in any order to build complex network pipelines. New view types can be added by deriving from the `EngineView` base class, and linked into the composition chain without modifying core engine code.
+
+**Python Extensibility:**
+Through the Python bindings, users can subclass engine view classes directly in Python, override methods like `evaluate` or `generateStoichiometryMatrix`, and pass instances back into C++ solvers. This enables rapid prototyping of custom view strategies without touching C++ sources.
+
+## Numerical Solver Strategies
+
+GridFire defines a flexible solver architecture through the `networkfire::solver::NetworkSolverStrategy` interface, enabling multiple ODE integration algorithms to be used interchangeably with any engine that implements the `Engine` or `DynamicEngine` contract.
+
+- **NetworkSolverStrategy&lt;EngineT&gt;**: Abstract strategy templated on an engine type. Requires implementation of:
+  ```cpp
+  NetOut evaluate(const NetIn& netIn);
+  ```
+  which integrates the network over one timestep and returns updated abundances, temperature, density, and diagnostics.
+
+### DirectNetworkSolver (Implicit Rosenbrock Method)
+
+- **Integrator:** Implicit Rosenbrock4 scheme (order 4) via Boost.Odeint’s `rosenbrock4<double>`, optimized for stiff reaction networks with adaptive step size control using configurable absolute and relative tolerances.
+- **Jacobian Assembly:** Employs the `JacobianFunctor` to assemble the Jacobian matrix (∂f/∂Y) at each step, enabling stable implicit integration.
+- **RHS Evaluation:** Continues to use the `RHSManager` to compute and cache derivative evaluations and specific energy rates, minimizing redundant computations.
+- **Linear Algebra:** Utilizes Boost.uBLAS for state vectors and dense Jacobian matrices, with sparse access patterns supported via coordinate lists of nonzero entries.
+- **Error Control and Logging:** Absolute and relative tolerance parameters (`absTol`, `relTol`) are read from configuration; Quill logger captures integration diagnostics and step statistics.
+
+### Algorithmic Workflow in DirectNetworkSolver
+1. **Initialization:** Convert input temperature to T9 units, retrieve tolerances, and initialize state vector `Y` from equilibrated composition.
+2. **Integrator Setup:** Construct the controlled Rosenbrock4 stepper and bind `RHSManager` and `JacobianFunctor`.
+3. **Adaptive Integration Loop:**
+   - Perform `integrate_adaptive` advancing until `tMax`, catching any `StaleEngineTrigger` to repartition the network and update composition.
+   - On each substep, observe states and log via `RHSManager::observe`.
+4. **Finalization:** Assemble final mass fractions, compute accumulated energy, and populate `NetOut` with updated composition and diagnostics.
+
+### Future Solver Implementations
+- **Operator Splitting Solvers:** Strategies to decouple thermodynamics, screening, and reaction substeps for performance on stiff, multi-scale networks.
+- **GPU-Accelerated Solvers:** Planned use of CUDA/OpenCL backends for large-scale network integration.
+
+These strategies can be developed by inheriting from `NetworkSolverStrategy` and registering against the same engine types without modifying existing engine code.
+
+## Usage Examples
+
+### C++ Example: GraphEngine Initialization
+```cpp
+#include "gridfire/engine/engine_graph.h"
+#include "fourdst/composition/composition.h"
+
+// Define a composition and initialize the engine
+fourdst::composition::Composition comp;
+gridfire::GraphEngine engine(comp);
+```
+
+### C++ Example: Adaptive Network View
+```cpp
+#include "gridfire/engine/views/engine_adaptive.h"
+#include "gridfire/engine/engine_graph.h"
+
+fourdst::composition::Composition comp;
+gridfire::GraphEngine baseEngine(comp);
+// Dynamically adapt network topology based on reaction flows
+gridfire::AdaptiveEngineView adaptiveView(baseEngine);
+```
+
+### Python Example
+```python
+import gridfire
+# Initialize GraphEngine with predefined composition
+engine = gridfire.GraphEngine(composition="example_composition")
+# Perform one integration step
+engine.step(dt=1e-3)
+print(engine.abundances)
+```
+
+## Common Workflow Example
+
+A representative workflow often composes multiple engine views to balance accuracy, stability, and performance when integrating stiff nuclear networks:
+
+```cpp
+#include "gridfire/engine/engine_graph.h"
+#include "gridfire/engine/views/engine_multiscale.h"
+#include "gridfire/engine/views/engine_adaptive.h"
+#include "gridfire/solver/solver.h"
+#include "fourdst/composition/composition.h"
+
+// 1. Define initial composition
+fourdst::composition::Composition comp;
+// 2. Create base network engine (full reaction graph)
+gridfire::GraphEngine baseEngine(comp);
+
+// 3. Partition network into fast/slow subsets (reduces stiffness)
+gridfire::MultiscalePartitioningEngineView msView(baseEngine);
+
+// 4. Adaptively cull negligible flux pathways (reduces dimension & stiffness)
+gridfire::AdaptiveEngineView adaptView(msView);
+
+// 5. Construct implicit solver (handles remaining stiffness)
+gridfire::DirectNetworkSolver solver(adaptView);
+
+// 6. Prepare input conditions
+NetIn input{
+    comp,     // composition
+    1.5e7,      // temperature [K]
+    1.5e2,      // density [g/cm^3]
+    1e-12,     // initial timestep [s]
+    3e17      // integration end time [s]
+};
+
+// 7. Execute integration
+NetOut output = solver.evaluate(input);
+```
+
+**Workflow Components and Effects:**
+- **GraphEngine** constructs the full reaction network, capturing all species and reactions.
+- **MultiscalePartitioningEngineView** segregates reactions by characteristic timescales (Hix & Thielemann), reducing the effective stiffness by treating fast processes separately.
+- **AdaptiveEngineView** prunes low-flux species/reactions at runtime, decreasing dimensionality and improving computational efficiency.
+- **DirectNetworkSolver** employs an implicit Rosenbrock method to stably integrate the remaining stiff system with adaptive step control.
+
+This layered approach enhances stability for stiff networks while maintaining accuracy and performance.
+
+## Related Projects
+
+GridFire integrates with and builds upon several key 4D-STAR libraries:
+
+- [fourdst](https://github.com/4D-STAR/fourdst): hub module managing versioning of `libcomposition`, `libconfig`, `liblogging`, and `libconstants`
+- [libcomposition](https://github.com/4D-STAR/libcomposition) ([docs](https://4d-star.github.io/libcomposition/)): Composition management toolkit.
+- [libconfig](https://github.com/4D-STAR/libconfig): Configuration file parsing utilities.
+- [liblogging](https://github.com/4D-STAR/liblogging): Flexible logging framework.
+- [libconstants](https://github.com/4D-STAR/libconstants): Physical constants

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+  <div class="headertitle"><div class="title">/Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h</div></div>
+</div><!--header-->
+<div class="contents">
+<p>Multiplies two arrays and sums the resulting elements.</p>
+<p>Multiplies two arrays and sums the resulting elements.</p><dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">a</td><td>First array. </td></tr>
+    <tr><td class="paramname">b</td><td>Second array. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns</dt><dd>Sum of the product of the arrays.</dd></dl>
+<div class="fragment"><div class="line">vec7 a = {1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0};</div>
+<div class="line">vec7 b = {0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5};</div>
+<div class="line"><span class="keywordtype">double</span> result = <a class="code hl_function" href="namespacegridfire_1_1approx8.html#aafd24448743672021dd4507316060817">sum_product</a>(a, b);</div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_aafd24448743672021dd4507316060817"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#aafd24448743672021dd4507316060817">gridfire::approx8::sum_product</a></div><div class="ttdeci">double sum_product(const vec7 &amp;a, const vec7 &amp;b)</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00082">engine_approx8.cpp:82</a></div></div>
+</div><!-- fragment --><div class="fragment"><div class="line"><span class="comment">/* ***********************************************************************</span></div>
+<div class="line"><span class="comment">//</span></div>
+<div class="line"><span class="comment">//   Copyright (C) 2025 -- The 4D-STAR Collaboration</span></div>
+<div class="line"><span class="comment">//   File Author: Emily Boudreaux</span></div>
+<div class="line"><span class="comment">//   Last Modified: March 21, 2025</span></div>
+<div class="line"><span class="comment">//</span></div>
+<div class="line"><span class="comment">//   4DSSE is free software; you can use it and/or modify</span></div>
+<div class="line"><span class="comment">//   it under the terms and restrictions the GNU General Library Public</span></div>
+<div class="line"><span class="comment">//   License version 3 (GPLv3) as published by the Free Software Foundation.</span></div>
+<div class="line"><span class="comment">//</span></div>
+<div class="line"><span class="comment">//   4DSSE is distributed in the hope that it will be useful,</span></div>
+<div class="line"><span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div>
+<div class="line"><span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</span></div>
+<div class="line"><span class="comment">//   See the GNU Library General Public License for more details.</span></div>
+<div class="line"><span class="comment">//</span></div>
+<div class="line"><span class="comment">//   You should have received a copy of the GNU Library General Public License</span></div>
+<div class="line"><span class="comment">//   along with this software; if not, write to the Free Software</span></div>
+<div class="line"><span class="comment">//   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA</span></div>
+<div class="line"><span class="comment">//</span></div>
+<div class="line"><span class="comment">// *********************************************************************** */</span></div>
+<div class="line"><span class="preprocessor">#pragma once</span></div>
+<div class="line"> </div>
+<div class="line"><span class="preprocessor">#include &lt;array&gt;</span></div>
+<div class="line"> </div>
+<div class="line"><span class="preprocessor">#include &lt;boost/numeric/odeint.hpp&gt;</span></div>
+<div class="line"> </div>
+<div class="line"><span class="preprocessor">#include &quot;<a class="code" href="network_8h.html">gridfire/network.h</a>&quot;</span></div>
+<div class="line"></div>
+<div class="line"> </div>
+<div class="line"> </div>
+<div class="line"><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacegridfire_1_1approx8.html">gridfire::approx8</a>{</div>
+<div class="line"></div>
+<div class="line">    <span class="keyword">typedef</span> boost::numeric::ublas::vector&lt; double &gt; <a id="a0" name="a0"></a><a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aa04f907d4ef6a1b6b2a9a28d4bb53882">vector_type</a>;</div>
+<div class="line"></div>
+<div class="line">    <span class="keyword">typedef</span> boost::numeric::ublas::matrix&lt; double &gt; <a id="a1" name="a1"></a><a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#a275aecf94e3145c2ff3d1756deda54ce">matrix_type</a>;</div>
+<div class="line"></div>
+<div class="line">    <span class="keyword">typedef</span> std::array&lt;double,7&gt; <a id="a2" name="a2"></a><a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a>;</div>
+<div class="line"></div>
+<div class="line">    <span class="keyword">struct </span>Approx8Net{</div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a3" name="a3"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#acc735a17e005f7e25c68a86d9735ec4c">ih1</a>=0;</div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a4" name="a4"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#ab0a43fee658efcaacfe7e6fb4870569b">ihe3</a>=1;</div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a5" name="a5"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a82977ad3df7f620e80a6235b3fe64731">ihe4</a>=2;</div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a6" name="a6"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a95b9a07e29285884e6de523f8132f653">ic12</a>=3;</div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a7" name="a7"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a1af9135867aa3786721b89dbfdc4aee0">in14</a>=4;</div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a8" name="a8"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#ab4e95622dc0414ad7e636ef811e600af">io16</a>=5;</div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a9" name="a9"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#ad43418fd8c536ebc814d5e6de555256c">ine20</a>=6;</div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a10" name="a10"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a9647205f52fb0fa21316be39c3a6d709">img24</a>=7;</div>
+<div class="line"> </div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a11" name="a11"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a010df59d40b3bc8a802224968922ebde">iTemp</a>=<a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a9647205f52fb0fa21316be39c3a6d709">img24</a>+1;</div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a12" name="a12"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a562c2383f585d3e9984225584d61c037">iDensity</a> =<a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a010df59d40b3bc8a802224968922ebde">iTemp</a>+1;</div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a13" name="a13"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a18501627dceb5d084bc7ba19f119826f">iEnergy</a>=<a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a562c2383f585d3e9984225584d61c037">iDensity</a>+1;</div>
+<div class="line"> </div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a14" name="a14"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a31928b4041479da6515a90569322fc02">nIso</a>=<a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a9647205f52fb0fa21316be39c3a6d709">img24</a>+1; <span class="comment">// number of isotopes</span></div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> <span class="keywordtype">int</span> <a id="a15" name="a15"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a7218aa9b3dbe7c6eca52119e115692db">nVar</a>=<a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a18501627dceb5d084bc7ba19f119826f">iEnergy</a>+1; <span class="comment">// number of variables</span></div>
+<div class="line"> </div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> std::array&lt;int,nIso&gt; <a id="a16" name="a16"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a296e54c1b22f0c5d4d07a13577c6e069">aIon</a> = {</div>
+<div class="line">            1,</div>
+<div class="line">            3,</div>
+<div class="line">            4,</div>
+<div class="line">            12,</div>
+<div class="line">            14,</div>
+<div class="line">            16,</div>
+<div class="line">            20,</div>
+<div class="line">            24</div>
+<div class="line">        };</div>
+<div class="line"> </div>
+<div class="line">        <span class="keyword">static</span> <span class="keyword">constexpr</span> std::array&lt;double,nIso&gt; <a id="a17" name="a17"></a><a class="code hl_variable" href="structgridfire_1_1approx8_1_1_approx8_net.html#a928b7810cb2993d59d40aa73c2faef18">mIon</a> = {</div>
+<div class="line">            1.67262164e-24, </div>
+<div class="line">            5.00641157e-24, </div>
+<div class="line">            6.64465545e-24, </div>
+<div class="line">            1.99209977e-23,</div>
+<div class="line">            2.32462686e-23,</div>
+<div class="line">            2.65528858e-23,</div>
+<div class="line">            3.31891077e-23,</div>
+<div class="line">            3.98171594e-23</div>
+<div class="line">        };</div>
+<div class="line"> </div>
+<div class="line">    };</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a18" name="a18"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#aafd24448743672021dd4507316060817">sum_product</a>( <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;a, <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;b);</div>
+<div class="line"></div>
+<div class="line">    <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> <a id="a19" name="a19"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a20f9c48e60a5abf0b6868d1d05080222">get_T9_array</a>(<span class="keyword">const</span> <span class="keywordtype">double</span> &amp;T);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a20" name="a20"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#aed8175751b4920a53922f87f8c0e63c4">rate_fit</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9, <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;coef);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a21" name="a21"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a16739298c01e56967ce784a9a957439f">pp_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a22" name="a22"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a51d139de74680c8437d20a3fa622200c">dp_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a23" name="a23"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a12cb71ba6ed03750af9e7659464197ea">he3he3_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a24" name="a24"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a593cd66c1eadae4da233ae73b4aad4a3">he3he4_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a25" name="a25"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a2715e1a6421717991814892046b896e3">triple_alpha_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a26" name="a26"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a890ad24c2cdb15fb76a3ff8a7b8d77db">c12p_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a27" name="a27"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#af7d9b901dbb3c88c151d927912d5121f">c12a_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a28" name="a28"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a34f18b2345a8fd8d96bbe1a9825c1f21">n14p_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a29" name="a29"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a3a9861a77093effdfc061743eb13fcdb">n14a_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a30" name="a30"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a9a90b83dd4aa2dcc928bd14f4678dcef">n15pa_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a31" name="a31"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#acdbb3ee2ef22bfd9c836324285d0da98">n15pg_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a32" name="a32"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#ac309c160c806208bf01bebeb29c23896">n15pg_frac</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a33" name="a33"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a62c2f567dc1ada3816843c8586aad0dc">o16p_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a34" name="a34"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a7387008e672ea12d277e2194745a4c93">o16a_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a35" name="a35"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#ad7a6f894fa4bdeebb4cae0eba3b2c210">ne20a_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a36" name="a36"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a70eb18e9706ac28a308dcb4fcec7421f">c12c12_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keywordtype">double</span> <a id="a37" name="a37"></a><a class="code hl_function" href="namespacegridfire_1_1approx8.html#a8c30b7e6099c5fc2aa94f9c68fd075dc">c12o16_rate</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">vec7</a> &amp;T9);</div>
+<div class="line"></div>
+<div class="line">    <span class="keyword">struct </span>Jacobian {</div>
+<div class="line">        <span class="keywordtype">void</span> <a id="a38" name="a38"></a><a class="code hl_function" href="structgridfire_1_1approx8_1_1_jacobian.html#a548431915b5895082eb96ce66d5494fa">operator() </a>( <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aa04f907d4ef6a1b6b2a9a28d4bb53882">vector_type</a> &amp;y, <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#a275aecf94e3145c2ff3d1756deda54ce">matrix_type</a> &amp;J, <span class="keywordtype">double</span> <span class="comment">/* t */</span>, <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aa04f907d4ef6a1b6b2a9a28d4bb53882">vector_type</a> &amp;dfdt ) <span class="keyword">const</span>;</div>
+<div class="line">    };</div>
+<div class="line"></div>
+<div class="line">    <span class="keyword">struct </span>ODE {</div>
+<div class="line">        <span class="keywordtype">void</span> <a id="a39" name="a39"></a><a class="code hl_function" href="structgridfire_1_1approx8_1_1_o_d_e.html#a2e1eb1ce2aa7949c225d45ce4edf03d0">operator() </a>( <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aa04f907d4ef6a1b6b2a9a28d4bb53882">vector_type</a> &amp;y, <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aa04f907d4ef6a1b6b2a9a28d4bb53882">vector_type</a> &amp;dydt, <span class="keywordtype">double</span> <span class="comment">/* t */</span>) <span class="keyword">const</span>;</div>
+<div class="line">    };</div>
+<div class="line"></div>
+<div class="line">    <span class="keyword">class </span>Approx8Network final : <span class="keyword">public</span> Network {</div>
+<div class="line">    <span class="keyword">public</span>:</div>
+<div class="line">        <a id="a40" name="a40"></a><a class="code hl_function" href="classgridfire_1_1approx8_1_1_approx8_network.html#a65066078081c544be4e56e25eb407c8b">Approx8Network</a>();</div>
+<div class="line"></div>
+<div class="line">        NetOut <a id="a41" name="a41"></a><a class="code hl_function" href="classgridfire_1_1approx8_1_1_approx8_network.html#a888734a3cdde4259e921e2efece411ee">evaluate</a>(<span class="keyword">const</span> NetIn &amp;netIn) <span class="keyword">override</span>;</div>
+<div class="line"></div>
+<div class="line">        <span class="keywordtype">void</span> <a id="a42" name="a42"></a><a class="code hl_function" href="classgridfire_1_1approx8_1_1_approx8_network.html#aefed972081514c29cdaaa1efd857ad8d">setStiff</a>(<span class="keywordtype">bool</span> stiff) <span class="keyword">override</span>;</div>
+<div class="line"></div>
+<div class="line">        <span class="keywordtype">bool</span> <a id="a43" name="a43"></a><a class="code hl_function" href="classgridfire_1_1approx8_1_1_approx8_network.html#a5b17b2831389829533385900ce19a37a">isStiff</a>()<span class="keyword"> const override </span>{ <span class="keywordflow">return</span> <a id="a44" name="a44"></a><a class="code hl_variable" href="classgridfire_1_1approx8_1_1_approx8_network.html#a697cb49bebc8d0659eb791500c451c67">m_stiff</a>; }</div>
+<div class="line">    <span class="keyword">private</span>:</div>
+<div class="line">        <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aa04f907d4ef6a1b6b2a9a28d4bb53882">vector_type</a> <a id="a45" name="a45"></a><a class="code hl_variable" href="classgridfire_1_1approx8_1_1_approx8_network.html#abf9f13ff532917ddac4a7d987698836d">m_y</a>;</div>
+<div class="line">        <span class="keywordtype">double</span> <a id="a46" name="a46"></a><a class="code hl_variable" href="classgridfire_1_1approx8_1_1_approx8_network.html#a6fadf388f07c160f1887a3cb72eaa869">m_tMax</a> = 0;</div>
+<div class="line">        <span class="keywordtype">double</span> <a id="a47" name="a47"></a><a class="code hl_variable" href="classgridfire_1_1approx8_1_1_approx8_network.html#a6ed8022834e9541b3e547dd867648b0f">m_dt0</a> = 0;</div>
+<div class="line">        <span class="keywordtype">bool</span> <a class="code hl_variable" href="classgridfire_1_1approx8_1_1_approx8_network.html#a697cb49bebc8d0659eb791500c451c67">m_stiff</a> = <span class="keyword">false</span>;</div>
+<div class="line"></div>
+<div class="line">        <span class="keyword">static</span> <a class="code hl_typedef" href="namespacegridfire_1_1approx8.html#aa04f907d4ef6a1b6b2a9a28d4bb53882">vector_type</a> <a id="a48" name="a48"></a><a class="code hl_function" href="classgridfire_1_1approx8_1_1_approx8_network.html#a56426da6f1af7eb8a6d1cc70bc8e742a">convert_netIn</a>(<span class="keyword">const</span> NetIn &amp;netIn);</div>
+<div class="line">    };</div>
+<div class="line"> </div>
+<div class="line"> </div>
+<div class="line">} <span class="comment">// namespace nnApprox8</span></div>
+<div class="ttc" id="aclassgridfire_1_1approx8_1_1_approx8_network_html_a56426da6f1af7eb8a6d1cc70bc8e742a"><div class="ttname"><a href="classgridfire_1_1approx8_1_1_approx8_network.html#a56426da6f1af7eb8a6d1cc70bc8e742a">gridfire::approx8::Approx8Network::convert_netIn</a></div><div class="ttdeci">static vector_type convert_netIn(const NetIn &amp;netIn)</div><div class="ttdoc">Converts the input parameters to the internal state vector.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00509">engine_approx8.cpp:509</a></div></div>
+<div class="ttc" id="aclassgridfire_1_1approx8_1_1_approx8_network_html_a5b17b2831389829533385900ce19a37a"><div class="ttname"><a href="classgridfire_1_1approx8_1_1_approx8_network.html#a5b17b2831389829533385900ce19a37a">gridfire::approx8::Approx8Network::isStiff</a></div><div class="ttdeci">bool isStiff() const override</div><div class="ttdoc">Checks if the solver is using a stiff method.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00315">engine_approx8.h:315</a></div></div>
+<div class="ttc" id="aclassgridfire_1_1approx8_1_1_approx8_network_html_a65066078081c544be4e56e25eb407c8b"><div class="ttname"><a href="classgridfire_1_1approx8_1_1_approx8_network.html#a65066078081c544be4e56e25eb407c8b">gridfire::approx8::Approx8Network::Approx8Network</a></div><div class="ttdeci">Approx8Network()</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00443">engine_approx8.cpp:443</a></div></div>
+<div class="ttc" id="aclassgridfire_1_1approx8_1_1_approx8_network_html_a697cb49bebc8d0659eb791500c451c67"><div class="ttname"><a href="classgridfire_1_1approx8_1_1_approx8_network.html#a697cb49bebc8d0659eb791500c451c67">gridfire::approx8::Approx8Network::m_stiff</a></div><div class="ttdeci">bool m_stiff</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00320">engine_approx8.h:320</a></div></div>
+<div class="ttc" id="aclassgridfire_1_1approx8_1_1_approx8_network_html_a6ed8022834e9541b3e547dd867648b0f"><div class="ttname"><a href="classgridfire_1_1approx8_1_1_approx8_network.html#a6ed8022834e9541b3e547dd867648b0f">gridfire::approx8::Approx8Network::m_dt0</a></div><div class="ttdeci">double m_dt0</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00319">engine_approx8.h:319</a></div></div>
+<div class="ttc" id="aclassgridfire_1_1approx8_1_1_approx8_network_html_a6fadf388f07c160f1887a3cb72eaa869"><div class="ttname"><a href="classgridfire_1_1approx8_1_1_approx8_network.html#a6fadf388f07c160f1887a3cb72eaa869">gridfire::approx8::Approx8Network::m_tMax</a></div><div class="ttdeci">double m_tMax</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00318">engine_approx8.h:318</a></div></div>
+<div class="ttc" id="aclassgridfire_1_1approx8_1_1_approx8_network_html_a888734a3cdde4259e921e2efece411ee"><div class="ttname"><a href="classgridfire_1_1approx8_1_1_approx8_network.html#a888734a3cdde4259e921e2efece411ee">gridfire::approx8::Approx8Network::evaluate</a></div><div class="ttdeci">NetOut evaluate(const NetIn &amp;netIn) override</div><div class="ttdoc">Evaluates the nuclear network.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00445">engine_approx8.cpp:445</a></div></div>
+<div class="ttc" id="aclassgridfire_1_1approx8_1_1_approx8_network_html_abf9f13ff532917ddac4a7d987698836d"><div class="ttname"><a href="classgridfire_1_1approx8_1_1_approx8_network.html#abf9f13ff532917ddac4a7d987698836d">gridfire::approx8::Approx8Network::m_y</a></div><div class="ttdeci">vector_type m_y</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00317">engine_approx8.h:317</a></div></div>
+<div class="ttc" id="aclassgridfire_1_1approx8_1_1_approx8_network_html_aefed972081514c29cdaaa1efd857ad8d"><div class="ttname"><a href="classgridfire_1_1approx8_1_1_approx8_network.html#aefed972081514c29cdaaa1efd857ad8d">gridfire::approx8::Approx8Network::setStiff</a></div><div class="ttdeci">void setStiff(bool stiff) override</div><div class="ttdoc">Sets whether the solver should use a stiff method.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00505">engine_approx8.cpp:505</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html"><div class="ttname"><a href="namespacegridfire_1_1approx8.html">gridfire::approx8</a></div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00039">engine_approx8.h:39</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a12cb71ba6ed03750af9e7659464197ea"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a12cb71ba6ed03750af9e7659464197ea">gridfire::approx8::he3he3_rate</a></div><div class="ttdeci">double he3he3_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction he3 + he3 -&gt; he4 + 2p.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00129">engine_approx8.cpp:129</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a16739298c01e56967ce784a9a957439f"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a16739298c01e56967ce784a9a957439f">gridfire::approx8::pp_rate</a></div><div class="ttdeci">double pp_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction p + p -&gt; d.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00115">engine_approx8.cpp:115</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a20f9c48e60a5abf0b6868d1d05080222"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a20f9c48e60a5abf0b6868d1d05080222">gridfire::approx8::get_T9_array</a></div><div class="ttdeci">vec7 get_T9_array(const double &amp;T)</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00093">engine_approx8.cpp:93</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a2715e1a6421717991814892046b896e3"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a2715e1a6421717991814892046b896e3">gridfire::approx8::triple_alpha_rate</a></div><div class="ttdeci">double triple_alpha_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction he4 + he4 + he4 -&gt; c12.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00142">engine_approx8.cpp:142</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a275aecf94e3145c2ff3d1756deda54ce"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a275aecf94e3145c2ff3d1756deda54ce">gridfire::approx8::matrix_type</a></div><div class="ttdeci">boost::numeric::ublas::matrix&lt; double &gt; matrix_type</div><div class="ttdoc">Alias for a matrix of doubles using Boost uBLAS.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00051">engine_approx8.h:51</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a34f18b2345a8fd8d96bbe1a9825c1f21"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a34f18b2345a8fd8d96bbe1a9825c1f21">gridfire::approx8::n14p_rate</a></div><div class="ttdeci">double n14p_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction n14(p,g)o15 - o15 + p -&gt; c12 + he4.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00164">engine_approx8.cpp:164</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a3a9861a77093effdfc061743eb13fcdb"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a3a9861a77093effdfc061743eb13fcdb">gridfire::approx8::n14a_rate</a></div><div class="ttdeci">double n14a_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction n14(a,g)f18 assumed to go on to ne20.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00173">engine_approx8.cpp:173</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a51d139de74680c8437d20a3fa622200c"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a51d139de74680c8437d20a3fa622200c">gridfire::approx8::dp_rate</a></div><div class="ttdeci">double dp_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction p + d -&gt; he3.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00122">engine_approx8.cpp:122</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a593cd66c1eadae4da233ae73b4aad4a3"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a593cd66c1eadae4da233ae73b4aad4a3">gridfire::approx8::he3he4_rate</a></div><div class="ttdeci">double he3he4_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction he3(he3,2p)he4.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00135">engine_approx8.cpp:135</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a62c2f567dc1ada3816843c8586aad0dc"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a62c2f567dc1ada3816843c8586aad0dc">gridfire::approx8::o16p_rate</a></div><div class="ttdeci">double o16p_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction o16(p,g)f17 then f17 -&gt; o17(p,a)n14.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00204">engine_approx8.cpp:204</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a70eb18e9706ac28a308dcb4fcec7421f"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a70eb18e9706ac28a308dcb4fcec7421f">gridfire::approx8::c12c12_rate</a></div><div class="ttdeci">double c12c12_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction c12(c12,a)ne20.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00227">engine_approx8.cpp:227</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a7387008e672ea12d277e2194745a4c93"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a7387008e672ea12d277e2194745a4c93">gridfire::approx8::o16a_rate</a></div><div class="ttdeci">double o16a_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction o16(a,g)ne20.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00210">engine_approx8.cpp:210</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a890ad24c2cdb15fb76a3ff8a7b8d77db"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a890ad24c2cdb15fb76a3ff8a7b8d77db">gridfire::approx8::c12p_rate</a></div><div class="ttdeci">double c12p_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction c12 + p -&gt; n13.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00150">engine_approx8.cpp:150</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a8c30b7e6099c5fc2aa94f9c68fd075dc"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a8c30b7e6099c5fc2aa94f9c68fd075dc">gridfire::approx8::c12o16_rate</a></div><div class="ttdeci">double c12o16_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction c12(o16,a)mg24.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00233">engine_approx8.cpp:233</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_a9a90b83dd4aa2dcc928bd14f4678dcef"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#a9a90b83dd4aa2dcc928bd14f4678dcef">gridfire::approx8::n15pa_rate</a></div><div class="ttdeci">double n15pa_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction n15(p,a)c12 (CNO I).</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00181">engine_approx8.cpp:181</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_aa04f907d4ef6a1b6b2a9a28d4bb53882"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#aa04f907d4ef6a1b6b2a9a28d4bb53882">gridfire::approx8::vector_type</a></div><div class="ttdeci">boost::numeric::ublas::vector&lt; double &gt; vector_type</div><div class="ttdoc">Alias for a vector of doubles using Boost uBLAS.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00045">engine_approx8.h:45</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_aaa49cb0c9ad4b0b9dd0f9b5e192ca12a"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#aaa49cb0c9ad4b0b9dd0f9b5e192ca12a">gridfire::approx8::vec7</a></div><div class="ttdeci">std::array&lt; double, 7 &gt; vec7</div><div class="ttdoc">Alias for a std::array of 7 doubles.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00057">engine_approx8.h:57</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_ac309c160c806208bf01bebeb29c23896"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#ac309c160c806208bf01bebeb29c23896">gridfire::approx8::n15pg_frac</a></div><div class="ttdeci">double n15pg_frac(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the fraction for the reaction n15(p,g)o16.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00197">engine_approx8.cpp:197</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_acdbb3ee2ef22bfd9c836324285d0da98"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#acdbb3ee2ef22bfd9c836324285d0da98">gridfire::approx8::n15pg_rate</a></div><div class="ttdeci">double n15pg_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction n15(p,g)o16 (CNO II).</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00190">engine_approx8.cpp:190</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_ad7a6f894fa4bdeebb4cae0eba3b2c210"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#ad7a6f894fa4bdeebb4cae0eba3b2c210">gridfire::approx8::ne20a_rate</a></div><div class="ttdeci">double ne20a_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction ne20(a,g)mg24.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00218">engine_approx8.cpp:218</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_aed8175751b4920a53922f87f8c0e63c4"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#aed8175751b4920a53922f87f8c0e63c4">gridfire::approx8::rate_fit</a></div><div class="ttdeci">double rate_fit(const vec7 &amp;T9, const vec7 &amp;coef)</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00110">engine_approx8.cpp:110</a></div></div>
+<div class="ttc" id="anamespacegridfire_1_1approx8_html_af7d9b901dbb3c88c151d927912d5121f"><div class="ttname"><a href="namespacegridfire_1_1approx8.html#af7d9b901dbb3c88c151d927912d5121f">gridfire::approx8::c12a_rate</a></div><div class="ttdeci">double c12a_rate(const vec7 &amp;T9)</div><div class="ttdoc">Calculates the rate for the reaction c12 + he4 -&gt; o16.</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8cpp_source.html#l00157">engine_approx8.cpp:157</a></div></div>
+<div class="ttc" id="anetwork_8h_html"><div class="ttname"><a href="network_8h.html">network.h</a></div></div>
+<div class="ttc" id="astructgridfire_1_1approx8_1_1_approx8_net_html_a010df59d40b3bc8a802224968922ebde"><div class="ttname"><a href="structgridfire_1_1approx8_1_1_approx8_net.html#a010df59d40b3bc8a802224968922ebde">gridfire::approx8::Approx8Net::iTemp</a></div><div class="ttdeci">static constexpr int iTemp</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00073">engine_approx8.h:73</a></div></div>
+<div class="ttc" id="astructgridfire_1_1approx8_1_1_approx8_net_html_a18501627dceb5d084bc7ba19f119826f"><div class="ttname"><a href="structgridfire_1_1approx8_1_1_approx8_net.html#a18501627dceb5d084bc7ba19f119826f">gridfire::approx8::Approx8Net::iEnergy</a></div><div class="ttdeci">static constexpr int iEnergy</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00075">engine_approx8.h:75</a></div></div>
+<div class="ttc" id="astructgridfire_1_1approx8_1_1_approx8_net_html_a1af9135867aa3786721b89dbfdc4aee0"><div class="ttname"><a href="structgridfire_1_1approx8_1_1_approx8_net.html#a1af9135867aa3786721b89dbfdc4aee0">gridfire::approx8::Approx8Net::in14</a></div><div class="ttdeci">static constexpr int in14</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00068">engine_approx8.h:68</a></div></div>
+<div class="ttc" id="astructgridfire_1_1approx8_1_1_approx8_net_html_a296e54c1b22f0c5d4d07a13577c6e069"><div class="ttname"><a href="structgridfire_1_1approx8_1_1_approx8_net.html#a296e54c1b22f0c5d4d07a13577c6e069">gridfire::approx8::Approx8Net::aIon</a></div><div class="ttdeci">static constexpr std::array&lt; int, nIso &gt; aIon</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00080">engine_approx8.h:80</a></div></div>
+<div class="ttc" id="astructgridfire_1_1approx8_1_1_approx8_net_html_a31928b4041479da6515a90569322fc02"><div class="ttname"><a href="structgridfire_1_1approx8_1_1_approx8_net.html#a31928b4041479da6515a90569322fc02">gridfire::approx8::Approx8Net::nIso</a></div><div class="ttdeci">static constexpr int nIso</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00077">engine_approx8.h:77</a></div></div>
+<div class="ttc" id="astructgridfire_1_1approx8_1_1_approx8_net_html_a562c2383f585d3e9984225584d61c037"><div class="ttname"><a href="structgridfire_1_1approx8_1_1_approx8_net.html#a562c2383f585d3e9984225584d61c037">gridfire::approx8::Approx8Net::iDensity</a></div><div class="ttdeci">static constexpr int iDensity</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00074">engine_approx8.h:74</a></div></div>
+<div class="ttc" id="astructgridfire_1_1approx8_1_1_approx8_net_html_a7218aa9b3dbe7c6eca52119e115692db"><div class="ttname"><a href="structgridfire_1_1approx8_1_1_approx8_net.html#a7218aa9b3dbe7c6eca52119e115692db">gridfire::approx8::Approx8Net::nVar</a></div><div class="ttdeci">static constexpr int nVar</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00078">engine_approx8.h:78</a></div></div>
+<div class="ttc" id="astructgridfire_1_1approx8_1_1_approx8_net_html_a82977ad3df7f620e80a6235b3fe64731"><div class="ttname"><a href="structgridfire_1_1approx8_1_1_approx8_net.html#a82977ad3df7f620e80a6235b3fe64731">gridfire::approx8::Approx8Net::ihe4</a></div><div class="ttdeci">static constexpr int ihe4</div><div class="ttdef"><b>Definition</b> <a href="engine__approx8_8h_source.html#l00066">engine_approx8.h:66</a></div></div>
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+</div><!-- fragment --> </div><!-- contents -->
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+<tr id="row_0_13_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_engine_view.html" target="_self">EngineView</a></td><td class="desc">Abstract base class for a "view" of a reaction network engine </td></tr>
+<tr id="row_0_14_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_file_defined_engine_view.html" target="_self">FileDefinedEngineView</a></td><td class="desc"></td></tr>
+<tr id="row_0_15_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_15_" class="arrow" onclick="dynsection.toggleFolder('0_15_')">&#9660;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_graph_engine.html" target="_self">GraphEngine</a></td><td class="desc">A reaction network engine that uses a graph-based representation </td></tr>
+<tr id="row_0_15_0_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html" target="_self">AtomicReverseRate</a></td><td class="desc"></td></tr>
+<tr id="row_0_15_1_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_graph_engine_1_1constants.html" target="_self">constants</a></td><td class="desc"></td></tr>
+<tr id="row_0_15_2_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html" target="_self">PrecomputedReaction</a></td><td class="desc"></td></tr>
+<tr id="row_0_16_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_16_" class="arrow" onclick="dynsection.toggleFolder('0_16_')">&#9660;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html" target="_self">MultiscalePartitioningEngineView</a></td><td class="desc">An engine view that partitions the reaction network into multiple groups based on timescales </td></tr>
+<tr id="row_0_16_0_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html" target="_self">CacheStats</a></td><td class="desc">Struct for tracking cache statistics </td></tr>
+<tr id="row_0_16_1_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html" target="_self">EigenFunctor</a></td><td class="desc">Functor for solving QSE abundances using Eigen's nonlinear optimization </td></tr>
+<tr id="row_0_16_2_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html" target="_self">QSEGroup</a></td><td class="desc">Struct representing a QSE group </td></tr>
+<tr id="row_0_17_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_net_in.html" target="_self">NetIn</a></td><td class="desc"></td></tr>
+<tr id="row_0_18_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_net_out.html" target="_self">NetOut</a></td><td class="desc"></td></tr>
+<tr id="row_0_19_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_network.html" target="_self">Network</a></td><td class="desc"></td></tr>
+<tr id="row_0_20_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_network_priming_engine_view.html" target="_self">NetworkPrimingEngineView</a></td><td class="desc">Provides a view of a <a class="el" href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> filtered to reactions involving a specified priming species </td></tr>
+<tr id="row_0_21_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_priming_report.html" target="_self">PrimingReport</a></td><td class="desc">Captures the result of a network priming operation </td></tr>
+<tr id="row_0_22_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_q_s_e_cache_config.html" target="_self">QSECacheConfig</a></td><td class="desc">Configuration struct for the QSE cache </td></tr>
+<tr id="row_0_23_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_q_s_e_cache_key.html" target="_self">QSECacheKey</a></td><td class="desc">Key struct for the QSE abundance cache </td></tr>
+<tr id="row_0_24_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_reaction.html" target="_self">Reaction</a></td><td class="desc">Represents a single nuclear reaction from a specific data source </td></tr>
+<tr id="row_0_25_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_step_derivatives.html" target="_self">StepDerivatives</a></td><td class="desc">Structure holding derivatives and energy generation for a network step </td></tr>
+<tr id="row_1_" class="even"><td class="entry"><span style="width:0px;display:inline-block;">&#160;</span><span id="arr_1_" class="arrow" onclick="dynsection.toggleFolder('1_')">&#9660;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacestd.html" target="_self">std</a></td><td class="desc">STL namespace </td></tr>
+<tr id="row_1_0_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structstd_1_1hash_3_01gridfire_1_1_q_s_e_cache_key_01_4.html" target="_self">hash&lt; gridfire::QSECacheKey &gt;</a></td><td class="desc"></td></tr>
+<tr id="row_1_1_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structstd_1_1hash_3_01gridfire_1_1reaction_1_1_logical_reaction_set_01_4.html" target="_self">hash&lt; gridfire::reaction::LogicalReactionSet &gt;</a></td><td class="desc"></td></tr>
+<tr id="row_1_2_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_01_4.html" target="_self">hash&lt; gridfire::reaction::Reaction &gt;</a></td><td class="desc"></td></tr>
+<tr id="row_1_3_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_set_01_4.html" target="_self">hash&lt; gridfire::reaction::ReactionSet &gt;</a></td><td class="desc"></td></tr>
+<tr id="row_2_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_dynamic_engine.html" target="_self">PyDynamicEngine</a></td><td class="desc"></td></tr>
+<tr id="row_3_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_dynamic_engine_view.html" target="_self">PyDynamicEngineView</a></td><td class="desc"></td></tr>
+<tr id="row_4_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_dynamic_network_solver_strategy.html" target="_self">PyDynamicNetworkSolverStrategy</a></td><td class="desc"></td></tr>
+<tr id="row_5_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_engine.html" target="_self">PyEngine</a></td><td class="desc"></td></tr>
+<tr id="row_6_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_engine_view.html" target="_self">PyEngineView</a></td><td class="desc"></td></tr>
+<tr id="row_7_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_network_file_parser.html" target="_self">PyNetworkFileParser</a></td><td class="desc"></td></tr>
+<tr id="row_8_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_partition_function.html" target="_self">PyPartitionFunction</a></td><td class="desc"></td></tr>
+<tr id="row_9_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_screening.html" target="_self">PyScreening</a></td><td class="desc"></td></tr>
+<tr id="row_10_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_r_h_s_functor.html" target="_self">RHSFunctor</a></td><td class="desc">Functor for calculating the right-hand side of the ODEs </td></tr>
 </table>
 </div><!-- directory -->
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docs/html/annotated_dup.js

@@ -7,12 +7,33 @@ var annotated_dup =
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+      [ "NetworkPrimingEngineView", "classgridfire_1_1_network_priming_engine_view.html", "classgridfire_1_1_network_priming_engine_view" ],
+      [ "PrimingReport", "structgridfire_1_1_priming_report.html", "structgridfire_1_1_priming_report" ],
+      [ "QSECacheConfig", "structgridfire_1_1_q_s_e_cache_config.html", "structgridfire_1_1_q_s_e_cache_config" ],
+      [ "QSECacheKey", "structgridfire_1_1_q_s_e_cache_key.html", "structgridfire_1_1_q_s_e_cache_key" ],
+      [ "Reaction", "classgridfire_1_1_reaction.html", "classgridfire_1_1_reaction" ],
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+    [ "PyDynamicEngineView", "class_py_dynamic_engine_view.html", "class_py_dynamic_engine_view" ],
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+    [ "PyEngine", "class_py_engine.html", "class_py_engine" ],
+    [ "PyEngineView", "class_py_engine_view.html", "class_py_engine_view" ],
+    [ "PyNetworkFileParser", "class_py_network_file_parser.html", "class_py_network_file_parser" ],
+    [ "PyPartitionFunction", "class_py_partition_function.html", "class_py_partition_function" ],
+    [ "PyScreening", "class_py_screening.html", "class_py_screening" ],
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+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle"><div class="title">bindings.cpp File Reference</div></div>
+</div><!--header-->
+<div class="contents">
+<div class="textblock"><code>#include &lt;pybind11/pybind11.h&gt;</code><br />
+<code>#include &lt;pybind11/stl.h&gt;</code><br />
+<code>#include &lt;string&gt;</code><br />
+<code>#include &quot;<a class="el" href="types_2bindings_8h_source.html">types/bindings.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="partition_2bindings_8h_source.html">partition/bindings.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="expectations_2bindings_8h_source.html">expectations/bindings.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="engine_2bindings_8h_source.html">engine/bindings.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="exceptions_2bindings_8h_source.html">exceptions/bindings.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="io_2bindings_8h_source.html">io/bindings.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="reaction_2bindings_8h_source.html">reaction/bindings.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="screening_2bindings_8h_source.html">screening/bindings.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="solver_2bindings_8h_source.html">solver/bindings.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="utils_2bindings_8h_source.html">utils/bindings.h</a>&quot;</code><br />
+</div>
+<p><a href="bindings_8cpp_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:aa8955e3a8d1ea2d94e8a2c941a12c03f" id="r_aa8955e3a8d1ea2d94e8a2c941a12c03f"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa8955e3a8d1ea2d94e8a2c941a12c03f">PYBIND11_MODULE</a> (gridfire, m)</td></tr>
+<tr class="separator:aa8955e3a8d1ea2d94e8a2c941a12c03f"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<h2 class="groupheader">Function Documentation</h2>
+<a id="aa8955e3a8d1ea2d94e8a2c941a12c03f" name="aa8955e3a8d1ea2d94e8a2c941a12c03f"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#aa8955e3a8d1ea2d94e8a2c941a12c03f">&#9670;&#160;</a></span>PYBIND11_MODULE()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PYBIND11_MODULE </td>
+          <td>(</td>
+          <td class="paramtype">gridfire</td>          <td class="paramname"><span class="paramname"><em></em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">m</td>          <td class="paramname"><span class="paramname"><em></em></span>&#160;)</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="bindings_8cpp_source.html#l00017">17</a> of file <a class="el" href="bindings_8cpp_source.html">bindings.cpp</a>.</p>
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docs/html/bindings_8cpp.js

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+[
+    [ "PYBIND11_MODULE", "bindings_8cpp.html#aa8955e3a8d1ea2d94e8a2c941a12c03f", null ]
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docs/html/bindings_8cpp_source.html

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+  <div class="headertitle"><div class="title">bindings.cpp</div></div>
+</div><!--header-->
+<div class="contents">
+<a href="bindings_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span><span class="preprocessor">#include &lt;pybind11/pybind11.h&gt;</span></div>
+<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span><span class="preprocessor">#include &lt;pybind11/stl.h&gt;</span></div>
+<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span> </div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span><span class="preprocessor">#include &lt;string&gt;</span></div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span> </div>
+<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span><span class="preprocessor">#include &quot;<a class="code" href="types_2bindings_8h.html">types/bindings.h</a>&quot;</span></div>
+<div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span><span class="preprocessor">#include &quot;<a class="code" href="partition_2bindings_8h.html">partition/bindings.h</a>&quot;</span></div>
+<div class="line"><a id="l00008" name="l00008"></a><span class="lineno">    8</span><span class="preprocessor">#include &quot;<a class="code" href="expectations_2bindings_8h.html">expectations/bindings.h</a>&quot;</span></div>
+<div class="line"><a id="l00009" name="l00009"></a><span class="lineno">    9</span><span class="preprocessor">#include &quot;<a class="code" href="engine_2bindings_8h.html">engine/bindings.h</a>&quot;</span></div>
+<div class="line"><a id="l00010" name="l00010"></a><span class="lineno">   10</span><span class="preprocessor">#include &quot;<a class="code" href="exceptions_2bindings_8h.html">exceptions/bindings.h</a>&quot;</span></div>
+<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span><span class="preprocessor">#include &quot;<a class="code" href="io_2bindings_8h.html">io/bindings.h</a>&quot;</span></div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span><span class="preprocessor">#include &quot;<a class="code" href="reaction_2bindings_8h.html">reaction/bindings.h</a>&quot;</span></div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="preprocessor">#include &quot;<a class="code" href="screening_2bindings_8h.html">screening/bindings.h</a>&quot;</span></div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="preprocessor">#include &quot;<a class="code" href="solver_2bindings_8h.html">solver/bindings.h</a>&quot;</span></div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="preprocessor">#include &quot;<a class="code" href="utils_2bindings_8h.html">utils/bindings.h</a>&quot;</span></div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span> </div>
+<div class="foldopen" id="foldopen00017" data-start="{" data-end="}">
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"><a class="line" href="bindings_8cpp.html#aa8955e3a8d1ea2d94e8a2c941a12c03f">   17</a></span><a class="code hl_function" href="bindings_8cpp.html#aa8955e3a8d1ea2d94e8a2c941a12c03f">PYBIND11_MODULE</a>(<a class="code hl_namespace" href="namespacegridfire.html">gridfire</a>, m) {</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>    m.doc() = <span class="stringliteral">&quot;Python bindings for the fourdst utility modules which are a part of the 4D-STAR project.&quot;</span>;</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span> </div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>    pybind11::module::import(<span class="stringliteral">&quot;fourdst.constants&quot;</span>);</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>    pybind11::module::import(<span class="stringliteral">&quot;fourdst.composition&quot;</span>);</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>    pybind11::module::import(<span class="stringliteral">&quot;fourdst.config&quot;</span>);</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>    pybind11::module::import(<span class="stringliteral">&quot;fourdst.atomic&quot;</span>);</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span> </div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>    <span class="keyword">auto</span> typeMod  = m.def_submodule(<span class="stringliteral">&quot;type&quot;</span>, <span class="stringliteral">&quot;GridFire type bindings&quot;</span>);</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>    <a class="code hl_function" href="types_2bindings_8cpp.html#a37d2e0b6a2605d063eec5e2a64e9bcc5">register_type_bindings</a>(typeMod);</div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span> </div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>    <span class="keyword">auto</span> partitionMod  = m.def_submodule(<span class="stringliteral">&quot;partition&quot;</span>, <span class="stringliteral">&quot;GridFire partition function bindings&quot;</span>);</div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span>    <a class="code hl_function" href="partition_2bindings_8cpp.html#a2806baaec82e0e6d66b80348584e08fd">register_partition_bindings</a>(partitionMod);</div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span> </div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>    <span class="keyword">auto</span> expectationMod  = m.def_submodule(<span class="stringliteral">&quot;expectations&quot;</span>, <span class="stringliteral">&quot;GridFire expectations bindings&quot;</span>);</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>    <a class="code hl_function" href="expectations_2bindings_8cpp.html#ac6720822f6ad76636adbc1ae6febc2c2">register_expectation_bindings</a>(expectationMod);</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span> </div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span>    <span class="keyword">auto</span> reactionMod  = m.def_submodule(<span class="stringliteral">&quot;reaction&quot;</span>, <span class="stringliteral">&quot;GridFire reaction bindings&quot;</span>);</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>    <a class="code hl_function" href="reaction_2bindings_8cpp.html#ae174b115814ec42920a799881cef1efa">register_reaction_bindings</a>(reactionMod);</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span> </div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span>    <span class="keyword">auto</span> screeningMod  = m.def_submodule(<span class="stringliteral">&quot;screening&quot;</span>, <span class="stringliteral">&quot;GridFire plasma screening bindings&quot;</span>);</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>    <a class="code hl_function" href="screening_2bindings_8cpp.html#a4fcef69d9382bfbc315cb061038627f4">register_screening_bindings</a>(screeningMod);</div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span> </div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>    <span class="keyword">auto</span> ioMod  = m.def_submodule(<span class="stringliteral">&quot;io&quot;</span>, <span class="stringliteral">&quot;GridFire io bindings&quot;</span>);</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>    <a class="code hl_function" href="io_2bindings_8cpp.html#a7f552627cbe94906e0ee98b121e77862">register_io_bindings</a>(ioMod);</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span> </div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>    <span class="keyword">auto</span> exceptionMod  = m.def_submodule(<span class="stringliteral">&quot;exceptions&quot;</span>, <span class="stringliteral">&quot;GridFire exceptions bindings&quot;</span>);</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>    <a class="code hl_function" href="exceptions_2bindings_8cpp.html#a15a0d54e4fe015a87d9f7a63284c2958">register_exception_bindings</a>(exceptionMod);</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span> </div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>    <span class="keyword">auto</span> engineMod  = m.def_submodule(<span class="stringliteral">&quot;engine&quot;</span>, <span class="stringliteral">&quot;Engine and Engine View bindings&quot;</span>);</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>    <a class="code hl_function" href="engine_2bindings_8cpp.html#ac2df9cd0e71d39b97ddd47b3e7024b0c">register_engine_bindings</a>(engineMod);</div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span> </div>
+<div class="line"><a id="l00049" name="l00049"></a><span class="lineno">   49</span>    <span class="keyword">auto</span> solverMod  = m.def_submodule(<span class="stringliteral">&quot;solver&quot;</span>, <span class="stringliteral">&quot;GridFire numerical solver bindings&quot;</span>);</div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>    <a class="code hl_function" href="solver_2bindings_8cpp.html#a8b1a9e2faca389d99c0b5feaa4262630">register_solver_bindings</a>(solverMod);</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span> </div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span>    <span class="keyword">auto</span> utilsMod  = m.def_submodule(<span class="stringliteral">&quot;utils&quot;</span>, <span class="stringliteral">&quot;GridFire utility method bindings&quot;</span>);</div>
+<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span>    <a class="code hl_function" href="utils_2bindings_8cpp.html#a7af842f50ca4a721518e716d0229697c">register_utils_bindings</a>(utilsMod);</div>
+<div class="line"><a id="l00054" name="l00054"></a><span class="lineno">   54</span>}</div>
+</div>
+<div class="ttc" id="abindings_8cpp_html_aa8955e3a8d1ea2d94e8a2c941a12c03f"><div class="ttname"><a href="bindings_8cpp.html#aa8955e3a8d1ea2d94e8a2c941a12c03f">PYBIND11_MODULE</a></div><div class="ttdeci">PYBIND11_MODULE(gridfire, m)</div><div class="ttdef"><b>Definition</b> <a href="#l00017">bindings.cpp:17</a></div></div>
+<div class="ttc" id="aengine_2bindings_8cpp_html_ac2df9cd0e71d39b97ddd47b3e7024b0c"><div class="ttname"><a href="engine_2bindings_8cpp.html#ac2df9cd0e71d39b97ddd47b3e7024b0c">register_engine_bindings</a></div><div class="ttdeci">void register_engine_bindings(py::module &amp;m)</div><div class="ttdef"><b>Definition</b> <a href="engine_2bindings_8cpp_source.html#l00114">bindings.cpp:114</a></div></div>
+<div class="ttc" id="aengine_2bindings_8h_html"><div class="ttname"><a href="engine_2bindings_8h.html">bindings.h</a></div></div>
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+<div class="ttc" id="aio_2bindings_8h_html"><div class="ttname"><a href="io_2bindings_8h.html">bindings.h</a></div></div>
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+<div class="textblock"><code>#include &lt;variant&gt;</code><br />
+</div>
+<p><a href="building_8h_source.html">Go to the source code of this file.</a></p>
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+  <div class="headertitle"><div class="title">building.h</div></div>
+</div><!--header-->
+<div class="contents">
+<a href="building_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span><span class="preprocessor">#pragma once</span></div>
+<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span> </div>
+<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span><span class="preprocessor">#include &lt;variant&gt;</span></div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span> </div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacegridfire.html">gridfire</a> {</div>
+<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span></div>
+<div class="foldopen" id="foldopen00021" data-start="{" data-end="};">
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"><a class="line" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57">   21</a></span>    <span class="keyword">enum class</span> <a class="code hl_enumeration" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57">NetworkBuildDepth</a> {</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"><a class="line" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57abbd47109890259c0127154db1af26c75">   22</a></span>        <a class="code hl_enumvalue" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57abbd47109890259c0127154db1af26c75">Full</a> = -1,</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"><a class="line" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a928d0f1285ee7d36c1c2fa1b1b7a164c">   23</a></span>        <a class="code hl_enumvalue" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a928d0f1285ee7d36c1c2fa1b1b7a164c">Shallow</a> = 1,</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"><a class="line" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a264572d66aed5373d19dc80c7cde1f46">   24</a></span>        <a class="code hl_enumvalue" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a264572d66aed5373d19dc80c7cde1f46">SecondOrder</a> = 2,</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"><a class="line" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a3fc719e07f9f63e7f11a3d4fb74b476f">   25</a></span>        <a class="code hl_enumvalue" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a3fc719e07f9f63e7f11a3d4fb74b476f">ThirdOrder</a> = 3,</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"><a class="line" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a100e3bf0197221c19b222badf42aa964">   26</a></span>        <a class="code hl_enumvalue" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a100e3bf0197221c19b222badf42aa964">FourthOrder</a> = 4,</div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"><a class="line" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a5105376c2b90747e00bed5bf2953dd56">   27</a></span>        <a class="code hl_enumvalue" href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a5105376c2b90747e00bed5bf2953dd56">FifthOrder</a> = 5</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>    };</div>
+</div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span></div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"><a class="line" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">   37</a></span>    <span class="keyword">using </span><a class="code hl_typedef" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a> = std::variant&lt;NetworkBuildDepth, int&gt;;</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span> </div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span>}</div>
+<div class="ttc" id="anamespacegridfire_html"><div class="ttname"><a href="namespacegridfire.html">gridfire</a></div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00031">engine_abstract.h:31</a></div></div>
+<div class="ttc" id="anamespacegridfire_html_a0210bd2e07538932135a56b62b8ddb57"><div class="ttname"><a href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57">gridfire::NetworkBuildDepth</a></div><div class="ttdeci">NetworkBuildDepth</div><div class="ttdoc">Specifies supported depths for building the reaction network.</div><div class="ttdef"><b>Definition</b> <a href="#l00021">building.h:21</a></div></div>
+<div class="ttc" id="anamespacegridfire_html_a0210bd2e07538932135a56b62b8ddb57a100e3bf0197221c19b222badf42aa964"><div class="ttname"><a href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a100e3bf0197221c19b222badf42aa964">gridfire::NetworkBuildDepth::FourthOrder</a></div><div class="ttdeci">@ FourthOrder</div><div class="ttdef"><b>Definition</b> <a href="#l00026">building.h:26</a></div></div>
+<div class="ttc" id="anamespacegridfire_html_a0210bd2e07538932135a56b62b8ddb57a264572d66aed5373d19dc80c7cde1f46"><div class="ttname"><a href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a264572d66aed5373d19dc80c7cde1f46">gridfire::NetworkBuildDepth::SecondOrder</a></div><div class="ttdeci">@ SecondOrder</div><div class="ttdef"><b>Definition</b> <a href="#l00024">building.h:24</a></div></div>
+<div class="ttc" id="anamespacegridfire_html_a0210bd2e07538932135a56b62b8ddb57a3fc719e07f9f63e7f11a3d4fb74b476f"><div class="ttname"><a href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a3fc719e07f9f63e7f11a3d4fb74b476f">gridfire::NetworkBuildDepth::ThirdOrder</a></div><div class="ttdeci">@ ThirdOrder</div><div class="ttdef"><b>Definition</b> <a href="#l00025">building.h:25</a></div></div>
+<div class="ttc" id="anamespacegridfire_html_a0210bd2e07538932135a56b62b8ddb57a5105376c2b90747e00bed5bf2953dd56"><div class="ttname"><a href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a5105376c2b90747e00bed5bf2953dd56">gridfire::NetworkBuildDepth::FifthOrder</a></div><div class="ttdeci">@ FifthOrder</div><div class="ttdef"><b>Definition</b> <a href="#l00027">building.h:27</a></div></div>
+<div class="ttc" id="anamespacegridfire_html_a0210bd2e07538932135a56b62b8ddb57a928d0f1285ee7d36c1c2fa1b1b7a164c"><div class="ttname"><a href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57a928d0f1285ee7d36c1c2fa1b1b7a164c">gridfire::NetworkBuildDepth::Shallow</a></div><div class="ttdeci">@ Shallow</div><div class="ttdef"><b>Definition</b> <a href="#l00023">building.h:23</a></div></div>
+<div class="ttc" id="anamespacegridfire_html_a0210bd2e07538932135a56b62b8ddb57abbd47109890259c0127154db1af26c75"><div class="ttname"><a href="namespacegridfire.html#a0210bd2e07538932135a56b62b8ddb57abbd47109890259c0127154db1af26c75">gridfire::NetworkBuildDepth::Full</a></div><div class="ttdeci">@ Full</div><div class="ttdef"><b>Definition</b> <a href="#l00022">building.h:22</a></div></div>
+<div class="ttc" id="anamespacegridfire_html_a3b1f70dc7ff5b501809330a97079e4f6"><div class="ttname"><a href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">gridfire::BuildDepthType</a></div><div class="ttdeci">std::variant&lt; NetworkBuildDepth, int &gt; BuildDepthType</div><div class="ttdoc">Variant specifying either a predefined NetworkBuildDepth or a custom integer depth.</div><div class="ttdef"><b>Definition</b> <a href="#l00037">building.h:37</a></div></div>
+</div><!-- fragment --></div><!-- contents -->
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+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
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docs/html/class_py_dynamic_engine-members.html

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+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
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+</div>
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+<div class="header">
+  <div class="headertitle"><div class="title">PyDynamicEngine Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a6224f546ba66b1257506b1fc9f47195a">calculateMolarReactionFlow</a>(const gridfire::reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a5b7f0cfe327c634ec125303256de8b9a">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a5bd40c752db1badcd600797c9113121d">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#aa0f1fd3f0c0185395193d1b6897d64c5">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const gridfire::SparsityPattern &amp;sparsityPattern) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2066649ca11a869c054079ea12d8d0e9">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#adba68716d832b6100e08d32fbc36f13c">getDepth</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a1c888bbc0618f1ae02d9a53e45f3c159">getJacobianMatrixEntry</a>(int i, int j) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a5988cfba247631ba6c00795cafda9a38">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#afc745e7ab5da5d8b3cf916044515cd7d">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ab4cfdca5e15957c5cef75ffa6dedeee5">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a020044829e0146427ed4830e5b02c4f3">getSpeciesDestructionTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2ee1d745c1c21b9fcb652c96c42f1091">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a02a4c86c9637a3c9c9ca8ddd82ecff22">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ab48ef6db18da20024aa563a91fa16f83">getStoichiometryMatrixEntry</a>(int speciesIndex, int reactionIndex) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a55bf19ed7534a312a36faf74753f7b14">isStale</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2246382b1c98ba69cdb419bba63a6d03">m_species_cache</a></td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a61bb4b430fe740cfb2c24e5cc673e4ac">mapNetInToMolarAbundanceVector</a>(const gridfire::NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ac22a10412be6649bf379e6d61113c878">primeEngine</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a3d30a9116825ab2c5c209bc2712126bc">rebuild</a>(const fourdst::composition::Composition &amp;comp, gridfire::BuildDepthType depth) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#afd818c408c64d207e71b1a90426328d6">setNetworkReactions</a>(const gridfire::reaction::LogicalReactionSet &amp;reactions) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#afa3abfd612033336a656f092721c14ac">setScreeningModel</a>(gridfire::screening::ScreeningType model) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#af8e6a8cd44f278535d7bcc9a896d6da8">update</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
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docs/html/class_py_dynamic_engine_view-members.html

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+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>GridFire: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+/* @license-end */
+</script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() { codefold.init(0); });
+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
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+      <div id="nav-sync" class="sync"></div>
+    </div>
+  </div>
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+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function(){initNavTree('class_py_dynamic_engine_view.html',''); initResizable(true); });
+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
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+<!-- iframe showing the search results (closed by default) -->
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+<div id="MSearchResults">
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+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">PyDynamicEngineView Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_py_dynamic_engine_view.html">PyDynamicEngineView</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine_view.html#a51680b135cfc3eea40daf9ef5aa903e0">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine_view.html">PyDynamicEngineView</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; gridfire::DynamicEngine &gt;</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
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docs/html/class_py_dynamic_engine_view.html

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+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=11"/>
+<meta name="generator" content="Doxygen 1.13.2"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>GridFire: PyDynamicEngineView Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<script type="text/javascript" src="clipboard.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="navtreedata.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="cookie.js"></script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/searchdata.js"></script>
+<script type="text/javascript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+var searchBox = new SearchBox("searchBox", "search/",'.html');
+/* @license-end */
+</script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() { codefold.init(0); });
+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
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+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
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+      <div id="nav-sync" class="sync"></div>
+    </div>
+  </div>
+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function(){initNavTree('class_py_dynamic_engine_view.html',''); initResizable(true); });
+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
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+<!-- iframe showing the search results (closed by default) -->
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+<div id="MSearchResults">
+<div class="SRPage">
+<div id="SRIndex">
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+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="summary">
+<a href="#pri-methods">Private Member Functions</a> &#124;
+<a href="class_py_dynamic_engine_view-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">PyDynamicEngineView Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
+</div><!--header-->
+<div class="contents">
+
+<p><code>#include &lt;<a class="el" href="py__engine_8h_source.html">py_engine.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for PyDynamicEngineView:</div>
+<div class="dyncontent">
+ <div class="center">
+  <img src="class_py_dynamic_engine_view.png" usemap="#PyDynamicEngineView_map" alt=""/>
+  <map id="PyDynamicEngineView_map" name="PyDynamicEngineView_map">
+<area href="classgridfire_1_1_engine_view.html" alt="gridfire::EngineView&lt; gridfire::DynamicEngine &gt;" shape="rect" coords="0,0,285,24"/>
+  </map>
+</div></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
+Private Member Functions</h2></td></tr>
+<tr class="memitem:a51680b135cfc3eea40daf9ef5aa903e0" id="r_a51680b135cfc3eea40daf9ef5aa903e0"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a51680b135cfc3eea40daf9ef5aa903e0">getBaseEngine</a> () const override</td></tr>
+<tr class="memdesc:a51680b135cfc3eea40daf9ef5aa903e0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Access the underlying engine instance.  <br /></td></tr>
+<tr class="separator:a51680b135cfc3eea40daf9ef5aa903e0"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="inherited" name="inherited"></a>
+Additional Inherited Members</h2></td></tr>
+<tr class="inherit_header pub_methods_classgridfire_1_1_engine_view"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine_view')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; gridfire::DynamicEngine &gt;</a></td></tr>
+<tr class="memitem:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view" id="r_a994660f2d553f3a123512dc5eb421e74"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a> ()=default</td></tr>
+<tr class="memdesc:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor.  <br /></td></tr>
+<tr class="separator:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="py__engine_8h_source.html#l00057">57</a> of file <a class="el" href="py__engine_8h_source.html">py_engine.h</a>.</p>
+</div><h2 class="groupheader">Member Function Documentation</h2>
+<a id="a51680b135cfc3eea40daf9ef5aa903e0" name="a51680b135cfc3eea40daf9ef5aa903e0"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a51680b135cfc3eea40daf9ef5aa903e0">&#9670;&#160;</a></span>getBaseEngine()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">const <a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a> &amp; PyDynamicEngineView::getBaseEngine </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Access the underlying engine instance. </p>
+<dl class="section return"><dt>Returns</dt><dd>Const reference to the underlying engine.</dd></dl>
+<p>This method must be implemented by derived classes to provide access to the base engine. The returned reference should remain valid for the lifetime of the EngineView.</p>
+<p>Example: </p><div class="fragment"><div class="line"><span class="keyword">const</span> DynamicEngine&amp; engine = myView.getBaseEngine();</div>
+</div><!-- fragment --> 
+<p>Implements <a class="el" href="classgridfire_1_1_engine_view.html#ad294227f8b5cf6d970c349eabf5447a6">gridfire::EngineView&lt; gridfire::DynamicEngine &gt;</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__engine_8cpp_source.html#l00237">237</a> of file <a class="el" href="py__engine_8cpp_source.html">py_engine.cpp</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/python/engine/trampoline/<a class="el" href="py__engine_8h_source.html">py_engine.h</a></li>
+<li>src/python/engine/trampoline/<a class="el" href="py__engine_8cpp_source.html">py_engine.cpp</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="class_py_dynamic_engine_view.html">PyDynamicEngineView</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
+</body>
+</html>

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+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
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+ </tr>
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+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
+<script type="text/javascript">
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+  <div class="headertitle"><div class="title">PyDynamicNetworkSolverStrategy Member List</div></div>
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+<p>This is the complete list of members for <a class="el" href="class_py_dynamic_network_solver_strategy.html">PyDynamicNetworkSolverStrategy</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_network_solver_strategy.html#a2095abb83ed6229ebb27b4883cec51c4">evaluate</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_network_solver_strategy.html">PyDynamicNetworkSolverStrategy</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
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+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_network_solver_strategy.html#a4a3fce2a9853e7192354834bf2b36159">PyDynamicNetworkSolverStrategy</a>(gridfire::DynamicEngine &amp;engine)</td><td class="entry"><a class="el" href="class_py_dynamic_network_solver_strategy.html">PyDynamicNetworkSolverStrategy</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">explicit</span><span class="mlabel">private</span></td></tr>
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+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
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+<div class="header">
+  <div class="summary">
+<a href="#pri-methods">Private Member Functions</a> &#124;
+<a href="class_py_dynamic_network_solver_strategy-members.html">List of all members</a>  </div>
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+<p><code>#include &lt;<a class="el" href="py__solver_8h_source.html">py_solver.h</a>&gt;</code></p>
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+<tr class="memitem:a01cbbec0eb5c3a60f50da38cdaf66505 inherit pub_methods_classgridfire_1_1solver_1_1_network_solver_strategy" id="r_a01cbbec0eb5c3a60f50da38cdaf66505"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a01cbbec0eb5c3a60f50da38cdaf66505">NetworkSolverStrategy</a> (<a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;engine)</td></tr>
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+<tr class="memitem:a724924d94eaf82b67d9988a55c3261e8 inherit pro_attribs_classgridfire_1_1solver_1_1_network_solver_strategy" id="r_a724924d94eaf82b67d9988a55c3261e8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a724924d94eaf82b67d9988a55c3261e8">m_engine</a></td></tr>
+<tr class="memdesc:a724924d94eaf82b67d9988a55c3261e8 inherit pro_attribs_classgridfire_1_1solver_1_1_network_solver_strategy"><td class="mdescLeft">&#160;</td><td class="mdescRight">The engine used by this solver strategy.  <br /></td></tr>
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+<tr class="memitem:a724924d94eaf82b67d9988a55c3261e8 inherit pro_attribs_classgridfire_1_1solver_1_1_network_solver_strategy" id="r_a724924d94eaf82b67d9988a55c3261e8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a724924d94eaf82b67d9988a55c3261e8">m_engine</a></td></tr>
+<tr class="memdesc:a724924d94eaf82b67d9988a55c3261e8 inherit pro_attribs_classgridfire_1_1solver_1_1_network_solver_strategy"><td class="mdescLeft">&#160;</td><td class="mdescRight">The engine used by this solver strategy.  <br /></td></tr>
+<tr class="separator:a724924d94eaf82b67d9988a55c3261e8 inherit pro_attribs_classgridfire_1_1solver_1_1_network_solver_strategy"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="py__solver_8h_source.html#l00007">7</a> of file <a class="el" href="py__solver_8h_source.html">py_solver.h</a>.</p>
+</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
+<a id="a4a3fce2a9853e7192354834bf2b36159" name="a4a3fce2a9853e7192354834bf2b36159"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a4a3fce2a9853e7192354834bf2b36159">&#9670;&#160;</a></span>PyDynamicNetworkSolverStrategy()</h2>
+
+<div class="memitem">
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+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">PyDynamicNetworkSolverStrategy::PyDynamicNetworkSolverStrategy </td>
+          <td>(</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>engine</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel explicit">explicit</span><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="py__solver_8h_source.html#l00008">8</a> of file <a class="el" href="py__solver_8h_source.html">py_solver.h</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Function Documentation</h2>
+<a id="a2095abb83ed6229ebb27b4883cec51c4" name="a2095abb83ed6229ebb27b4883cec51c4"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a2095abb83ed6229ebb27b4883cec51c4">&#9670;&#160;</a></span>evaluate()</h2>
+
+<div class="memitem">
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+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="structgridfire_1_1_net_out.html">gridfire::NetOut</a> PyDynamicNetworkSolverStrategy::evaluate </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">gridfire::NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Evaluates the network for a given timestep. </p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">netIn</td><td>The input conditions for the network. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns</dt><dd>The output conditions after the timestep. </dd></dl>
+
+<p>Implements <a class="el" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#ace539b0482db171845ff1bd38d76b70f">gridfire::solver::NetworkSolverStrategy&lt; DynamicEngine &gt;</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__solver_8cpp_source.html#l00014">14</a> of file <a class="el" href="py__solver_8cpp_source.html">py_solver.cpp</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/python/solver/trampoline/<a class="el" href="py__solver_8h_source.html">py_solver.h</a></li>
+<li>src/python/solver/trampoline/<a class="el" href="py__solver_8cpp_source.html">py_solver.cpp</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
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+  <ul>
+    <li class="navelem"><a class="el" href="class_py_dynamic_network_solver_strategy.html">PyDynamicNetworkSolverStrategy</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
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+    [ "evaluate", "class_py_dynamic_network_solver_strategy.html#a2095abb83ed6229ebb27b4883cec51c4", null ]
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+<div class="header">
+  <div class="headertitle"><div class="title">PyEngine Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_py_engine.html">PyEngine</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="class_py_engine.html#a2f92602ecf210414b46838fc0a9ae26d">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_engine.html">PyEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_engine.html#a2d240423899e039c2ca688e96f8af1f2">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="class_py_engine.html">PyEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_engine.html#a73caaa7606e2cdfd1aa82729a78ebb73">m_species_cache</a></td><td class="entry"><a class="el" href="class_py_engine.html">PyEngine</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
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+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
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+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
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+/* @license-end */
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+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pri-attribs">Private Attributes</a> &#124;
+<a href="class_py_engine-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">PyEngine Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
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+
+<p><code>#include &lt;<a class="el" href="py__engine_8h_source.html">py_engine.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for PyEngine:</div>
+<div class="dyncontent">
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+  <map id="PyEngine_map" name="PyEngine_map">
+<area href="classgridfire_1_1_engine.html" title="Abstract base class for a reaction network engine." alt="gridfire::Engine" shape="rect" coords="0,0,98,24"/>
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+<tr class="separator:a2d240423899e039c2ca688e96f8af1f2"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="memdesc:a2f92602ecf210414b46838fc0a9ae26d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation.  <br /></td></tr>
+<tr class="separator:a2f92602ecf210414b46838fc0a9ae26d"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="inherit_header pub_methods_classgridfire_1_1_engine"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td></tr>
+<tr class="memitem:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" id="r_a2e7970bed2100699f226f4141d5db037"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a> ()=default</td></tr>
+<tr class="memdesc:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor.  <br /></td></tr>
+<tr class="separator:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
+Private Attributes</h2></td></tr>
+<tr class="memitem:a73caaa7606e2cdfd1aa82729a78ebb73" id="r_a73caaa7606e2cdfd1aa82729a78ebb73"><td class="memItemLeft" align="right" valign="top">std::vector&lt; fourdst::atomic::Species &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a73caaa7606e2cdfd1aa82729a78ebb73">m_species_cache</a></td></tr>
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+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="py__engine_8h_source.html#l00012">12</a> of file <a class="el" href="py__engine_8h_source.html">py_engine.h</a>.</p>
+</div><h2 class="groupheader">Member Function Documentation</h2>
+<a id="a2f92602ecf210414b46838fc0a9ae26d" name="a2f92602ecf210414b46838fc0a9ae26d"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a2f92602ecf210414b46838fc0a9ae26d">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">gridfire::StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">gridfire::expectations::StaleEngineError</a> &gt; PyEngine::calculateRHSAndEnergy </td>
+          <td>(</td>
+          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Calculate the right-hand side (dY/dt) and energy generation. </p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">Y</td><td>Vector of current abundances for all species. </td></tr>
+    <tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
+    <tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns</dt><dd>StepDerivatives&lt;double&gt; containing dY/dt and energy generation rate.</dd></dl>
+<p>This function must be implemented by derived classes to compute the time derivatives of all species and the specific nuclear energy generation rate for the current state. </p>
+
+<p>Implements <a class="el" href="classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb">gridfire::Engine</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__engine_8cpp_source.html#l00037">37</a> of file <a class="el" href="py__engine_8cpp_source.html">py_engine.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a2d240423899e039c2ca688e96f8af1f2" name="a2d240423899e039c2ca688e96f8af1f2"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a2d240423899e039c2ca688e96f8af1f2">&#9670;&#160;</a></span>getNetworkSpecies()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">const std::vector&lt; fourdst::atomic::Species &gt; &amp; PyEngine::getNetworkSpecies </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Get the list of species in the network. </p>
+<dl class="section return"><dt>Returns</dt><dd>Vector of Species objects representing all network species. </dd></dl>
+
+<p>Implements <a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">gridfire::Engine</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__engine_8cpp_source.html#l00016">16</a> of file <a class="el" href="py__engine_8cpp_source.html">py_engine.cpp</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Data Documentation</h2>
+<a id="a73caaa7606e2cdfd1aa82729a78ebb73" name="a73caaa7606e2cdfd1aa82729a78ebb73"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a73caaa7606e2cdfd1aa82729a78ebb73">&#9670;&#160;</a></span>m_species_cache</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::vector&lt;fourdst::atomic::Species&gt; PyEngine::m_species_cache</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel mutable">mutable</span><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="py__engine_8h_source.html#l00017">17</a> of file <a class="el" href="py__engine_8h_source.html">py_engine.h</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/python/engine/trampoline/<a class="el" href="py__engine_8h_source.html">py_engine.h</a></li>
+<li>src/python/engine/trampoline/<a class="el" href="py__engine_8cpp_source.html">py_engine.cpp</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="class_py_engine.html">PyEngine</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/html/class_py_engine.js

@@ -0,0 +1,6 @@
+var class_py_engine =
+[
+    [ "calculateRHSAndEnergy", "class_py_engine.html#a2f92602ecf210414b46838fc0a9ae26d", null ],
+    [ "getNetworkSpecies", "class_py_engine.html#a2d240423899e039c2ca688e96f8af1f2", null ],
+    [ "m_species_cache", "class_py_engine.html#a73caaa7606e2cdfd1aa82729a78ebb73", null ]
+];

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+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>GridFire: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<script type="text/javascript" src="clipboard.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="navtreedata.js"></script>
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+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+var searchBox = new SearchBox("searchBox", "search/",'.html');
+/* @license-end */
+</script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() { codefold.init(0); });
+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
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+      <div id="nav-sync" class="sync"></div>
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+  </div>
+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function(){initNavTree('class_py_engine_view.html',''); initResizable(true); });
+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+</div>
+
+<!-- iframe showing the search results (closed by default) -->
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+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">PyEngineView Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_py_engine_view.html">PyEngineView</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="class_py_engine_view.html#a3cd83dc57b521c65a14edf70357a8845">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="class_py_engine_view.html">PyEngineView</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; gridfire::Engine &gt;</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/html/class_py_engine_view.html

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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
+<head>
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+<meta name="generator" content="Doxygen 1.13.2"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>GridFire: PyEngineView Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<script type="text/javascript" src="clipboard.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="navtreedata.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="cookie.js"></script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/searchdata.js"></script>
+<script type="text/javascript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
+<script type="text/javascript">
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+/* @license-end */
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+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
+    <div id="nav-tree-contents">
+      <div id="nav-sync" class="sync"></div>
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+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
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+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<div id="MSearchResults">
+<div class="SRPage">
+<div id="SRIndex">
+<div id="SRResults"></div>
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="summary">
+<a href="#pri-methods">Private Member Functions</a> &#124;
+<a href="class_py_engine_view-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">PyEngineView Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
+</div><!--header-->
+<div class="contents">
+
+<p><code>#include &lt;<a class="el" href="py__engine_8h_source.html">py_engine.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for PyEngineView:</div>
+<div class="dyncontent">
+ <div class="center">
+  <img src="class_py_engine_view.png" usemap="#PyEngineView_map" alt=""/>
+  <map id="PyEngineView_map" name="PyEngineView_map">
+<area href="classgridfire_1_1_engine_view.html" alt="gridfire::EngineView&lt; gridfire::Engine &gt;" shape="rect" coords="0,0,236,24"/>
+  </map>
+</div></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
+Private Member Functions</h2></td></tr>
+<tr class="memitem:a3cd83dc57b521c65a14edf70357a8845" id="r_a3cd83dc57b521c65a14edf70357a8845"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a3cd83dc57b521c65a14edf70357a8845">getBaseEngine</a> () const override</td></tr>
+<tr class="memdesc:a3cd83dc57b521c65a14edf70357a8845"><td class="mdescLeft">&#160;</td><td class="mdescRight">Access the underlying engine instance.  <br /></td></tr>
+<tr class="separator:a3cd83dc57b521c65a14edf70357a8845"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="inherited" name="inherited"></a>
+Additional Inherited Members</h2></td></tr>
+<tr class="inherit_header pub_methods_classgridfire_1_1_engine_view"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine_view')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; gridfire::Engine &gt;</a></td></tr>
+<tr class="memitem:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view" id="r_a994660f2d553f3a123512dc5eb421e74"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a> ()=default</td></tr>
+<tr class="memdesc:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor.  <br /></td></tr>
+<tr class="separator:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="py__engine_8h_source.html#l00053">53</a> of file <a class="el" href="py__engine_8h_source.html">py_engine.h</a>.</p>
+</div><h2 class="groupheader">Member Function Documentation</h2>
+<a id="a3cd83dc57b521c65a14edf70357a8845" name="a3cd83dc57b521c65a14edf70357a8845"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a3cd83dc57b521c65a14edf70357a8845">&#9670;&#160;</a></span>getBaseEngine()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">const <a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a> &amp; PyEngineView::getBaseEngine </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Access the underlying engine instance. </p>
+<dl class="section return"><dt>Returns</dt><dd>Const reference to the underlying engine.</dd></dl>
+<p>This method must be implemented by derived classes to provide access to the base engine. The returned reference should remain valid for the lifetime of the EngineView.</p>
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+
+<p class="definition">Definition at line <a class="el" href="py__engine_8cpp_source.html#l00229">229</a> of file <a class="el" href="py__engine_8cpp_source.html">py_engine.cpp</a>.</p>
+
+</div>
+</div>
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+<li>src/python/engine/trampoline/<a class="el" href="py__engine_8h_source.html">py_engine.h</a></li>
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+
+<div class="header">
+  <div class="headertitle"><div class="title">PyNetworkFileParser Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_py_network_file_parser.html">PyNetworkFileParser</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="class_py_network_file_parser.html#afe09d1e5b07110e62cf4c6ec713cff54">parse</a>(const std::string &amp;filename) const override</td><td class="entry"><a class="el" href="class_py_network_file_parser.html">PyNetworkFileParser</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html#a9b4095d06fad5df3805c92ae97b3eab3">~NetworkFileParser</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">gridfire::io::NetworkFileParser</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+</table></div><!-- contents -->
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+<!-- start footer part -->
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+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="summary">
+<a href="#pri-methods">Private Member Functions</a> &#124;
+<a href="class_py_network_file_parser-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">PyNetworkFileParser Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
+</div><!--header-->
+<div class="contents">
+
+<p><code>#include &lt;<a class="el" href="py__io_8h_source.html">py_io.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for PyNetworkFileParser:</div>
+<div class="dyncontent">
+ <div class="center">
+  <img src="class_py_network_file_parser.png" usemap="#PyNetworkFileParser_map" alt=""/>
+  <map id="PyNetworkFileParser_map" name="PyNetworkFileParser_map">
+<area href="classgridfire_1_1io_1_1_network_file_parser.html" title="An abstract base class for network file parsers." alt="gridfire::io::NetworkFileParser" shape="rect" coords="0,0,180,24"/>
+  </map>
+</div></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
+Private Member Functions</h2></td></tr>
+<tr class="memitem:afe09d1e5b07110e62cf4c6ec713cff54" id="r_afe09d1e5b07110e62cf4c6ec713cff54"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1io.html#abcbdcbd13cfa8c9fbe1b48e8ee2cc352">gridfire::io::ParsedNetworkData</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#afe09d1e5b07110e62cf4c6ec713cff54">parse</a> (const std::string &amp;filename) const override</td></tr>
+<tr class="memdesc:afe09d1e5b07110e62cf4c6ec713cff54"><td class="mdescLeft">&#160;</td><td class="mdescRight">Parses a network file and returns the parsed data.  <br /></td></tr>
+<tr class="separator:afe09d1e5b07110e62cf4c6ec713cff54"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="inherited" name="inherited"></a>
+Additional Inherited Members</h2></td></tr>
+<tr class="inherit_header pub_methods_classgridfire_1_1io_1_1_network_file_parser"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1io_1_1_network_file_parser')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">gridfire::io::NetworkFileParser</a></td></tr>
+<tr class="memitem:a9b4095d06fad5df3805c92ae97b3eab3 inherit pub_methods_classgridfire_1_1io_1_1_network_file_parser" id="r_a9b4095d06fad5df3805c92ae97b3eab3"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html#a9b4095d06fad5df3805c92ae97b3eab3">~NetworkFileParser</a> ()=default</td></tr>
+<tr class="memdesc:a9b4095d06fad5df3805c92ae97b3eab3 inherit pub_methods_classgridfire_1_1io_1_1_network_file_parser"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor for the base class.  <br /></td></tr>
+<tr class="separator:a9b4095d06fad5df3805c92ae97b3eab3 inherit pub_methods_classgridfire_1_1io_1_1_network_file_parser"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="py__io_8h_source.html#l00005">5</a> of file <a class="el" href="py__io_8h_source.html">py_io.h</a>.</p>
+</div><h2 class="groupheader">Member Function Documentation</h2>
+<a id="afe09d1e5b07110e62cf4c6ec713cff54" name="afe09d1e5b07110e62cf4c6ec713cff54"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#afe09d1e5b07110e62cf4c6ec713cff54">&#9670;&#160;</a></span>parse()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="namespacegridfire_1_1io.html#abcbdcbd13cfa8c9fbe1b48e8ee2cc352">gridfire::io::ParsedNetworkData</a> PyNetworkFileParser::parse </td>
+          <td>(</td>
+          <td class="paramtype">const std::string &amp;</td>          <td class="paramname"><span class="paramname"><em>filename</em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Parses a network file and returns the parsed data. </p>
+<p>This is a pure virtual function that must be implemented by derived classes. It takes a filename as input and returns a <code>ParsedNetworkData</code> struct containing the information extracted from the file.</p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">filename</td><td>The path to the network file to parse. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns</dt><dd>A <code>ParsedNetworkData</code> struct containing the parsed reaction data.</dd></dl>
+<dl class="exception"><dt>Exceptions</dt><dd>
+  <table class="exception">
+    <tr><td class="paramname">std::runtime_error</td><td>If the file cannot be opened or a parsing error occurs.</td></tr>
+  </table>
+  </dd>
+</dl>
+<p><b>Usage</b> </p><div class="fragment"><div class="line">std::unique_ptr&lt;NetworkFileParser&gt; parser = std::make_unique&lt;SimpleReactionListFileParser&gt;();</div>
+<div class="line"><span class="keywordflow">try</span> {</div>
+<div class="line">    ParsedNetworkData data = parser-&gt;parse(<span class="stringliteral">&quot;my_reactions.txt&quot;</span>);</div>
+<div class="line">    <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>&amp; reaction_name : data.reactionPENames) {</div>
+<div class="line">        <span class="comment">// ... process reaction name</span></div>
+<div class="line">    }</div>
+<div class="line">} <span class="keywordflow">catch</span> (<span class="keyword">const</span> std::runtime_error&amp; e) {</div>
+<div class="line">    <span class="comment">// ... handle error</span></div>
+<div class="line">}</div>
+</div><!-- fragment --> 
+<p>Implements <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html#a66e8e724c903d6ef4dd1c8103276bdbf">gridfire::io::NetworkFileParser</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__io_8cpp_source.html#l00008">8</a> of file <a class="el" href="py__io_8cpp_source.html">py_io.cpp</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/python/io/trampoline/<a class="el" href="py__io_8h_source.html">py_io.h</a></li>
+<li>src/python/io/trampoline/<a class="el" href="py__io_8cpp_source.html">py_io.cpp</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
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+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="class_py_network_file_parser.html">PyNetworkFileParser</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
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+  <div class="headertitle"><div class="title">PyPartitionFunction Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_py_partition_function.html">PyPartitionFunction</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="class_py_partition_function.html#af918b357e38fb82499ad53584557c43d">clone</a>() const override</td><td class="entry"><a class="el" href="class_py_partition_function.html">PyPartitionFunction</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_partition_function.html#a83aca0bc261734b7d3df8269f730c69b">evaluate</a>(int z, int a, double T9) const override</td><td class="entry"><a class="el" href="class_py_partition_function.html">PyPartitionFunction</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_partition_function.html#a260df9689bf698970ebf5104977a3dcf">evaluateDerivative</a>(int z, int a, double T9) const override</td><td class="entry"><a class="el" href="class_py_partition_function.html">PyPartitionFunction</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_partition_function.html#a0f288a01a3ed7fb92fff5d9fd7d56aa8">supports</a>(int z, int a) const override</td><td class="entry"><a class="el" href="class_py_partition_function.html">PyPartitionFunction</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_partition_function.html#a07f4d0ff83822dd2800897161d2a3717">type</a>() const override</td><td class="entry"><a class="el" href="class_py_partition_function.html">PyPartitionFunction</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1partition_1_1_partition_function.html#a197a0663dcfb4ab4be3b0e14b98391db">~PartitionFunction</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1partition_1_1_partition_function.html">gridfire::partition::PartitionFunction</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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docs/html/class_py_partition_function.html

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+   <div id="projectbrief">General Purpose Nuclear Network</div>
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+<div class="header">
+  <div class="summary">
+<a href="#pri-methods">Private Member Functions</a> &#124;
+<a href="class_py_partition_function-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">PyPartitionFunction Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
+</div><!--header-->
+<div class="contents">
+
+<p><code>#include &lt;<a class="el" href="py__partition_8h_source.html">py_partition.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for PyPartitionFunction:</div>
+<div class="dyncontent">
+ <div class="center">
+  <img src="class_py_partition_function.png" usemap="#PyPartitionFunction_map" alt=""/>
+  <map id="PyPartitionFunction_map" name="PyPartitionFunction_map">
+<area href="classgridfire_1_1partition_1_1_partition_function.html" title="Abstract interface for evaluating nuclear partition functions." alt="gridfire::partition::PartitionFunction" shape="rect" coords="0,0,205,24"/>
+  </map>
+</div></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
+Private Member Functions</h2></td></tr>
+<tr class="memitem:a83aca0bc261734b7d3df8269f730c69b" id="r_a83aca0bc261734b7d3df8269f730c69b"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a83aca0bc261734b7d3df8269f730c69b">evaluate</a> (int z, int a, double T9) const override</td></tr>
+<tr class="memdesc:a83aca0bc261734b7d3df8269f730c69b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Evaluate the partition function for a given isotope.  <br /></td></tr>
+<tr class="separator:a83aca0bc261734b7d3df8269f730c69b"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a260df9689bf698970ebf5104977a3dcf" id="r_a260df9689bf698970ebf5104977a3dcf"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a260df9689bf698970ebf5104977a3dcf">evaluateDerivative</a> (int z, int a, double T9) const override</td></tr>
+<tr class="memdesc:a260df9689bf698970ebf5104977a3dcf"><td class="mdescLeft">&#160;</td><td class="mdescRight">Evaluate the temperature derivative of the partition function.  <br /></td></tr>
+<tr class="separator:a260df9689bf698970ebf5104977a3dcf"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a0f288a01a3ed7fb92fff5d9fd7d56aa8" id="r_a0f288a01a3ed7fb92fff5d9fd7d56aa8"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0f288a01a3ed7fb92fff5d9fd7d56aa8">supports</a> (int z, int a) const override</td></tr>
+<tr class="memdesc:a0f288a01a3ed7fb92fff5d9fd7d56aa8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Check if this partition function supports an isotope.  <br /></td></tr>
+<tr class="separator:a0f288a01a3ed7fb92fff5d9fd7d56aa8"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a07f4d0ff83822dd2800897161d2a3717" id="r_a07f4d0ff83822dd2800897161d2a3717"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a07f4d0ff83822dd2800897161d2a3717">type</a> () const override</td></tr>
+<tr class="memdesc:a07f4d0ff83822dd2800897161d2a3717"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the human-readable type of this partition function.  <br /></td></tr>
+<tr class="separator:a07f4d0ff83822dd2800897161d2a3717"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:af918b357e38fb82499ad53584557c43d" id="r_af918b357e38fb82499ad53584557c43d"><td class="memItemLeft" align="right" valign="top">std::unique_ptr&lt; <a class="el" href="classgridfire_1_1partition_1_1_partition_function.html">gridfire::partition::PartitionFunction</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#af918b357e38fb82499ad53584557c43d">clone</a> () const override</td></tr>
+<tr class="memdesc:af918b357e38fb82499ad53584557c43d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Create a deep copy of this PartitionFunction.  <br /></td></tr>
+<tr class="separator:af918b357e38fb82499ad53584557c43d"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="inherited" name="inherited"></a>
+Additional Inherited Members</h2></td></tr>
+<tr class="inherit_header pub_methods_classgridfire_1_1partition_1_1_partition_function"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1partition_1_1_partition_function')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1partition_1_1_partition_function.html">gridfire::partition::PartitionFunction</a></td></tr>
+<tr class="memitem:a197a0663dcfb4ab4be3b0e14b98391db inherit pub_methods_classgridfire_1_1partition_1_1_partition_function" id="r_a197a0663dcfb4ab4be3b0e14b98391db"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1partition_1_1_partition_function.html#a197a0663dcfb4ab4be3b0e14b98391db">~PartitionFunction</a> ()=default</td></tr>
+<tr class="memdesc:a197a0663dcfb4ab4be3b0e14b98391db inherit pub_methods_classgridfire_1_1partition_1_1_partition_function"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor.  <br /></td></tr>
+<tr class="separator:a197a0663dcfb4ab4be3b0e14b98391db inherit pub_methods_classgridfire_1_1partition_1_1_partition_function"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="py__partition_8h_source.html#l00009">9</a> of file <a class="el" href="py__partition_8h_source.html">py_partition.h</a>.</p>
+</div><h2 class="groupheader">Member Function Documentation</h2>
+<a id="af918b357e38fb82499ad53584557c43d" name="af918b357e38fb82499ad53584557c43d"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#af918b357e38fb82499ad53584557c43d">&#9670;&#160;</a></span>clone()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::unique_ptr&lt; <a class="el" href="classgridfire_1_1partition_1_1_partition_function.html">gridfire::partition::PartitionFunction</a> &gt; PyPartitionFunction::clone </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Create a deep copy of this PartitionFunction. </p>
+<dl class="section return"><dt>Returns</dt><dd>Unique pointer to a new PartitionFunction instance with identical state. </dd></dl>
+<dl class="section post"><dt>Postcondition</dt><dd>The caller owns the returned object and must manage its lifetime. </dd></dl>
+
+<p>Implements <a class="el" href="classgridfire_1_1partition_1_1_partition_function.html#a677a90f992fd56b8718e36655c33ce6d">gridfire::partition::PartitionFunction</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__partition_8cpp_source.html#l00050">50</a> of file <a class="el" href="py__partition_8cpp_source.html">py_partition.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a83aca0bc261734b7d3df8269f730c69b" name="a83aca0bc261734b7d3df8269f730c69b"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a83aca0bc261734b7d3df8269f730c69b">&#9670;&#160;</a></span>evaluate()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">double PyPartitionFunction::evaluate </td>
+          <td>(</td>
+          <td class="paramtype">int</td>          <td class="paramname"><span class="paramname"><em>z</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int</td>          <td class="paramname"><span class="paramname"><em>a</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>T9</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Evaluate the partition function for a given isotope. </p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">z</td><td>Proton number (atomic number) of the isotope; must be &gt;= 1. </td></tr>
+    <tr><td class="paramname">a</td><td>Mass number of the isotope; must be &gt;= z. </td></tr>
+    <tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K; must be &gt; 0. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns</dt><dd>Partition function value (dimensionless) at the specified temperature. </dd></dl>
+<dl class="section pre"><dt>Precondition</dt><dd>Derived implementation supports (z, a) and T9 &gt; 0. </dd></dl>
+<dl class="section post"><dt>Postcondition</dt><dd>No side effects; pure function. </dd></dl>
+
+<p>Implements <a class="el" href="classgridfire_1_1partition_1_1_partition_function.html#a08ee79b7d8723b4e00ee1fc9cdfbe817">gridfire::partition::PartitionFunction</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__partition_8cpp_source.html#l00015">15</a> of file <a class="el" href="py__partition_8cpp_source.html">py_partition.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a260df9689bf698970ebf5104977a3dcf" name="a260df9689bf698970ebf5104977a3dcf"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a260df9689bf698970ebf5104977a3dcf">&#9670;&#160;</a></span>evaluateDerivative()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">double PyPartitionFunction::evaluateDerivative </td>
+          <td>(</td>
+          <td class="paramtype">int</td>          <td class="paramname"><span class="paramname"><em>z</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int</td>          <td class="paramname"><span class="paramname"><em>a</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>T9</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Evaluate the temperature derivative of the partition function. </p>
+<p>Computes d/dT (partition function) at the given parameters.</p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">z</td><td>Proton number (atomic number) of the isotope; must be &gt;= 1. </td></tr>
+    <tr><td class="paramname">a</td><td>Mass number of the isotope; must be &gt;= z. </td></tr>
+    <tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K; must be &gt; 0. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns</dt><dd>Temperature derivative of the partition function. </dd></dl>
+<dl class="section pre"><dt>Precondition</dt><dd>Derived implementation supports (z, a) and T9 &gt; 0. </dd></dl>
+<dl class="section post"><dt>Postcondition</dt><dd>No side effects; pure function. </dd></dl>
+
+<p>Implements <a class="el" href="classgridfire_1_1partition_1_1_partition_function.html#a14009bdaca47f3eddf2c6c023845db5a">gridfire::partition::PartitionFunction</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__partition_8cpp_source.html#l00024">24</a> of file <a class="el" href="py__partition_8cpp_source.html">py_partition.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a0f288a01a3ed7fb92fff5d9fd7d56aa8" name="a0f288a01a3ed7fb92fff5d9fd7d56aa8"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a0f288a01a3ed7fb92fff5d9fd7d56aa8">&#9670;&#160;</a></span>supports()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool PyPartitionFunction::supports </td>
+          <td>(</td>
+          <td class="paramtype">int</td>          <td class="paramname"><span class="paramname"><em>z</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int</td>          <td class="paramname"><span class="paramname"><em>a</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Check if this partition function supports an isotope. </p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">z</td><td>Proton number of the isotope. </td></tr>
+    <tr><td class="paramname">a</td><td>Mass number of the isotope. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns</dt><dd>true if evaluate and evaluateDerivative can be called for this isotope; false otherwise. </dd></dl>
+<dl class="section post"><dt>Postcondition</dt><dd>No side effects. </dd></dl>
+
+<p>Implements <a class="el" href="classgridfire_1_1partition_1_1_partition_function.html#a6df4191d10516477371a0384e1e55bf5">gridfire::partition::PartitionFunction</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__partition_8cpp_source.html#l00033">33</a> of file <a class="el" href="py__partition_8cpp_source.html">py_partition.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a07f4d0ff83822dd2800897161d2a3717" name="a07f4d0ff83822dd2800897161d2a3717"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a07f4d0ff83822dd2800897161d2a3717">&#9670;&#160;</a></span>type()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::string PyPartitionFunction::type </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Get the human-readable type of this partition function. </p>
+<dl class="section return"><dt>Returns</dt><dd>String identifier for the partition function implementation. </dd></dl>
+<dl class="section post"><dt>Postcondition</dt><dd>No side effects. </dd></dl>
+
+<p>Implements <a class="el" href="classgridfire_1_1partition_1_1_partition_function.html#ab0c67985a972707eac0ebc64417dfb97">gridfire::partition::PartitionFunction</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__partition_8cpp_source.html#l00042">42</a> of file <a class="el" href="py__partition_8cpp_source.html">py_partition.cpp</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/python/partition/trampoline/<a class="el" href="py__partition_8h_source.html">py_partition.h</a></li>
+<li>src/python/partition/trampoline/<a class="el" href="py__partition_8cpp_source.html">py_partition.cpp</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="class_py_partition_function.html">PyPartitionFunction</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
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+    [ "evaluateDerivative", "class_py_partition_function.html#a260df9689bf698970ebf5104977a3dcf", null ],
+    [ "supports", "class_py_partition_function.html#a0f288a01a3ed7fb92fff5d9fd7d56aa8", null ],
+    [ "type", "class_py_partition_function.html#a07f4d0ff83822dd2800897161d2a3717", null ]
+];

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+<meta name="generator" content="Doxygen 1.13.2"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
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+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+/* @license-end */
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+$(function() { codefold.init(0); });
+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function(){initNavTree('class_py_screening.html',''); initResizable(true); });
+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
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+
+<!-- iframe showing the search results (closed by default) -->
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+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">PyScreening Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_py_screening.html">PyScreening</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1screening_1_1_screening_model.html">gridfire::screening::ScreeningModel</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_screening.html#a2b8756c197eb89e77cb6dd231c979315">calculateScreeningFactors</a>(const gridfire::reaction::LogicalReactionSet &amp;reactions, const std::vector&lt; fourdst::atomic::Species &gt; &amp;species, const std::vector&lt; double &gt; &amp;Y, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="class_py_screening.html">PyScreening</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_screening.html#a5539d59311c778cf7f0006acc8f84ade">calculateScreeningFactors</a>(const gridfire::reaction::LogicalReactionSet &amp;reactions, const std::vector&lt; fourdst::atomic::Species &gt; &amp;species, const std::vector&lt; ADDouble &gt; &amp;Y, const ADDouble T9, const ADDouble rho) const override</td><td class="entry"><a class="el" href="class_py_screening.html">PyScreening</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#adef175acdbd911527f56a1f1592579a7">~ScreeningModel</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1screening_1_1_screening_model.html">gridfire::screening::ScreeningModel</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
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+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
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+<script type="text/javascript">
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+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="summary">
+<a href="#pri-methods">Private Member Functions</a> &#124;
+<a href="class_py_screening-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">PyScreening Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
+</div><!--header-->
+<div class="contents">
+
+<p><code>#include &lt;<a class="el" href="py__screening_8h_source.html">py_screening.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for PyScreening:</div>
+<div class="dyncontent">
+ <div class="center">
+  <img src="class_py_screening.png" usemap="#PyScreening_map" alt=""/>
+  <map id="PyScreening_map" name="PyScreening_map">
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+</div></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
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+<tr class="memitem:a2b8756c197eb89e77cb6dd231c979315" id="r_a2b8756c197eb89e77cb6dd231c979315"><td class="memItemLeft" align="right" valign="top">std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a2b8756c197eb89e77cb6dd231c979315">calculateScreeningFactors</a> (const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a> &amp;reactions, const std::vector&lt; fourdst::atomic::Species &gt; &amp;species, const std::vector&lt; double &gt; &amp;Y, const double T9, const double rho) const override</td></tr>
+<tr class="memdesc:a2b8756c197eb89e77cb6dd231c979315"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates screening factors for a set of reactions.  <br /></td></tr>
+<tr class="separator:a2b8756c197eb89e77cb6dd231c979315"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a5539d59311c778cf7f0006acc8f84ade" id="r_a5539d59311c778cf7f0006acc8f84ade"><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a5539d59311c778cf7f0006acc8f84ade">calculateScreeningFactors</a> (const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a> &amp;reactions, const std::vector&lt; fourdst::atomic::Species &gt; &amp;species, const std::vector&lt; <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> &gt; &amp;Y, const <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> T9, const <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> rho) const override</td></tr>
+<tr class="memdesc:a5539d59311c778cf7f0006acc8f84ade"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates screening factors using CppAD types for automatic differentiation.  <br /></td></tr>
+<tr class="separator:a5539d59311c778cf7f0006acc8f84ade"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
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+Additional Inherited Members</h2></td></tr>
+<tr class="inherit_header pub_types_classgridfire_1_1screening_1_1_screening_model"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_types_classgridfire_1_1screening_1_1_screening_model')"><img src="closed.png" alt="-"/>&#160;Public Types inherited from <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html">gridfire::screening::ScreeningModel</a></td></tr>
+<tr class="memitem:a107ff2897f040d6f27f69d56a0bdd28d inherit pub_types_classgridfire_1_1screening_1_1_screening_model" id="r_a107ff2897f040d6f27f69d56a0bdd28d"><td class="memItemLeft" align="right" valign="top">using&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> = CppAD::AD&lt;double&gt;</td></tr>
+<tr class="memdesc:a107ff2897f040d6f27f69d56a0bdd28d inherit pub_types_classgridfire_1_1screening_1_1_screening_model"><td class="mdescLeft">&#160;</td><td class="mdescRight">Alias for CppAD Automatic Differentiation type for double precision.  <br /></td></tr>
+<tr class="separator:a107ff2897f040d6f27f69d56a0bdd28d inherit pub_types_classgridfire_1_1screening_1_1_screening_model"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="inherit_header pub_methods_classgridfire_1_1screening_1_1_screening_model"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1screening_1_1_screening_model')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html">gridfire::screening::ScreeningModel</a></td></tr>
+<tr class="memitem:adef175acdbd911527f56a1f1592579a7 inherit pub_methods_classgridfire_1_1screening_1_1_screening_model" id="r_adef175acdbd911527f56a1f1592579a7"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#adef175acdbd911527f56a1f1592579a7">~ScreeningModel</a> ()=default</td></tr>
+<tr class="memdesc:adef175acdbd911527f56a1f1592579a7 inherit pub_methods_classgridfire_1_1screening_1_1_screening_model"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor.  <br /></td></tr>
+<tr class="separator:adef175acdbd911527f56a1f1592579a7 inherit pub_methods_classgridfire_1_1screening_1_1_screening_model"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="py__screening_8h_source.html#l00013">13</a> of file <a class="el" href="py__screening_8h_source.html">py_screening.h</a>.</p>
+</div><h2 class="groupheader">Member Function Documentation</h2>
+<a id="a5539d59311c778cf7f0006acc8f84ade" name="a5539d59311c778cf7f0006acc8f84ade"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a5539d59311c778cf7f0006acc8f84ade">&#9670;&#160;</a></span>calculateScreeningFactors() <span class="overload">[1/2]</span></h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::vector&lt; <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> &gt; PyScreening::calculateScreeningFactors </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>reactions</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const std::vector&lt; fourdst::atomic::Species &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>species</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const std::vector&lt; <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a></td>          <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a></td>          <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Calculates screening factors using CppAD types for automatic differentiation. </p>
+<p>This is a pure virtual function that provides an overload of <code>calculateScreeningFactors</code> for use with CppAD. It allows the derivatives of the screening factors with respect to abundances, temperature, and density to be computed automatically.</p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">reactions</td><td>The set of logical reactions in the network. </td></tr>
+    <tr><td class="paramname">species</td><td>A vector of all atomic species involved in the network. </td></tr>
+    <tr><td class="paramname">Y</td><td>A vector of the molar abundances (mol/g) for each species, as AD types. </td></tr>
+    <tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K, as an AD type. </td></tr>
+    <tr><td class="paramname">rho</td><td>The plasma density in g/cm^3, as an AD type. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns</dt><dd>A vector of screening factors (dimensionless), as AD types.</dd></dl>
+<p><b>Note</b> This method is essential for including the effects of screening in the Jacobian matrix of the reaction network. </p>
+
+<p>Implements <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a6c381a823cb9c1680d3e9c846da4ae22">gridfire::screening::ScreeningModel</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__screening_8cpp_source.html#l00025">25</a> of file <a class="el" href="py__screening_8cpp_source.html">py_screening.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a2b8756c197eb89e77cb6dd231c979315" name="a2b8756c197eb89e77cb6dd231c979315"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a2b8756c197eb89e77cb6dd231c979315">&#9670;&#160;</a></span>calculateScreeningFactors() <span class="overload">[2/2]</span></h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::vector&lt; double &gt; PyScreening::calculateScreeningFactors </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>reactions</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const std::vector&lt; fourdst::atomic::Species &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>species</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const double</td>          <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Calculates screening factors for a set of reactions. </p>
+<p>This is a pure virtual function that must be implemented by derived classes. It computes the screening enhancement factor for each reaction in the provided set based on the given plasma conditions.</p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">reactions</td><td>The set of logical reactions in the network. </td></tr>
+    <tr><td class="paramname">species</td><td>A vector of all atomic species involved in the network. </td></tr>
+    <tr><td class="paramname">Y</td><td>A vector of the molar abundances (mol/g) for each species. </td></tr>
+    <tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
+    <tr><td class="paramname">rho</td><td>The plasma density in g/cm^3. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns</dt><dd>A vector of screening factors (dimensionless), one for each reaction in the <code>reactions</code> set, in the same order.</dd></dl>
+<p><b>Pre-conditions</b> </p><ul>
+<li>The size of the <code>Y</code> vector must match the size of the <code>species</code> vector.</li>
+<li><code>T9</code> and <code>rho</code> must be positive.</li>
+</ul>
+<p><b>Post-conditions</b> </p><ul>
+<li>The returned vector will have the same size as the <code>reactions</code> set.</li>
+<li>Each element in the returned vector will be &gt;= 1.0.</li>
+</ul>
+<p><b>Usage</b> </p><div class="fragment"><div class="line"><span class="comment">// Assume &#39;model&#39; is a std::unique_ptr&lt;ScreeningModel&gt; to a concrete implementation</span></div>
+<div class="line"><span class="comment">// and other parameters (reactions, species, Y, T9, rho) are initialized.</span></div>
+<div class="line">std::vector&lt;double&gt; screening_factors = model-&gt;calculateScreeningFactors(</div>
+<div class="line">    reactions, species, Y, T9, rho</div>
+<div class="line">);</div>
+<div class="line"><span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; reactions.size(); ++i) {</div>
+<div class="line">    <span class="comment">// ... use screening_factors[i] ...</span></div>
+<div class="line">}</div>
+</div><!-- fragment --> 
+<p>Implements <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#aaec9184d80c86a2d8674e395dad81bde">gridfire::screening::ScreeningModel</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="py__screening_8cpp_source.html#l00016">16</a> of file <a class="el" href="py__screening_8cpp_source.html">py_screening.cpp</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/python/screening/trampoline/<a class="el" href="py__screening_8h_source.html">py_screening.h</a></li>
+<li>src/python/screening/trampoline/<a class="el" href="py__screening_8cpp_source.html">py_screening.cpp</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="class_py_screening.html">PyScreening</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/html/class_py_screening.js

@@ -0,0 +1,5 @@
+var class_py_screening =
+[
+    [ "calculateScreeningFactors", "class_py_screening.html#a5539d59311c778cf7f0006acc8f84ade", null ],
+    [ "calculateScreeningFactors", "class_py_screening.html#a2b8756c197eb89e77cb6dd231c979315", null ]
+];

docs/html/classes.html

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-<dd><a class="el" href="classgridfire_1_1_graph_engine.html">GraphEngine</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd></dl>
+<dd><a class="el" href="classgridfire_1_1_graph_engine.html">GraphEngine</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="classgridfire_1_1partition_1_1_ground_state_partition_function.html">GroundStatePartitionFunction</a> (<a class="el" href="namespacegridfire_1_1partition.html">gridfire::partition</a>)</dd></dl>
 <dl class="classindex odd">
 <dt class="alphachar"><a id="letter_H" name="letter_H">H</a></dt>
-<dd><a class="el" href="structstd_1_1hash_3_01gridfire_1_1reaction_1_1_logical_reaction_set_01_4.html">hash&lt; gridfire::reaction::LogicalReactionSet &gt;</a> (<a class="el" href="namespacestd.html">std</a>)</dd><dd><a class="el" href="structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_01_4.html">hash&lt; gridfire::reaction::Reaction &gt;</a> (<a class="el" href="namespacestd.html">std</a>)</dd><dd><a class="el" href="structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_set_01_4.html">hash&lt; gridfire::reaction::ReactionSet &gt;</a> (<a class="el" href="namespacestd.html">std</a>)</dd></dl>
+<dd><a class="el" href="structstd_1_1hash_3_01gridfire_1_1_q_s_e_cache_key_01_4.html">hash&lt; gridfire::QSECacheKey &gt;</a> (<a class="el" href="namespacestd.html">std</a>)</dd><dd><a class="el" href="structstd_1_1hash_3_01gridfire_1_1reaction_1_1_logical_reaction_set_01_4.html">hash&lt; gridfire::reaction::LogicalReactionSet &gt;</a> (<a class="el" href="namespacestd.html">std</a>)</dd><dd><a class="el" href="structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_01_4.html">hash&lt; gridfire::reaction::Reaction &gt;</a> (<a class="el" href="namespacestd.html">std</a>)</dd><dd><a class="el" href="structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_set_01_4.html">hash&lt; gridfire::reaction::ReactionSet &gt;</a> (<a class="el" href="namespacestd.html">std</a>)</dd></dl>
 <dl class="classindex even">
-<dt class="alphachar"><a id="letter_J" name="letter_J">J</a></dt>
+<dt class="alphachar"><a id="letter_I" name="letter_I">I</a></dt>
-<dd><a class="el" href="structgridfire_1_1approx8_1_1_jacobian.html">Jacobian</a> (<a class="el" href="namespacegridfire_1_1approx8.html">gridfire::approx8</a>)</dd><dd><a class="el" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html">DirectNetworkSolver::JacobianFunctor</a> (<a class="el" href="namespacegridfire_1_1solver.html">gridfire::solver</a>)</dd><dd><a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html">QSENetworkSolver::JacobianFunctor</a> (<a class="el" href="namespacegridfire_1_1solver.html">gridfire::solver</a>)</dd></dl>
+<dd><a class="el" href="structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_identified_isotope.html">RauscherThielemannPartitionFunction::IdentifiedIsotope</a> (<a class="el" href="namespacegridfire_1_1partition.html">gridfire::partition</a>)</dd><dd><a class="el" href="structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_interpolation_points.html">RauscherThielemannPartitionFunction::InterpolationPoints</a> (<a class="el" href="namespacegridfire_1_1partition.html">gridfire::partition</a>)</dd><dd><a class="el" href="structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_isotope_data.html">RauscherThielemannPartitionFunction::IsotopeData</a> (<a class="el" href="namespacegridfire_1_1partition.html">gridfire::partition</a>)</dd></dl>
 <dl class="classindex odd">
+<dt class="alphachar"><a id="letter_J" name="letter_J">J</a></dt>
+<dd><a class="el" href="structgridfire_1_1approx8_1_1_jacobian.html">Jacobian</a> (<a class="el" href="namespacegridfire_1_1approx8.html">gridfire::approx8</a>)</dd><dd><a class="el" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html">DirectNetworkSolver::JacobianFunctor</a> (<a class="el" href="namespacegridfire_1_1solver.html">gridfire::solver</a>)</dd></dl>
+<dl class="classindex even">
 <dt class="alphachar"><a id="letter_L" name="letter_L">L</a></dt>
 <dd><a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html">LogicalReaction</a> (<a class="el" href="namespacegridfire_1_1reaction.html">gridfire::reaction</a>)</dd></dl>
-<dl class="classindex even">
-<dt class="alphachar"><a id="letter_M" name="letter_M">M</a></dt>
-<dd><a class="el" href="classgridfire_1_1io_1_1_m_e_s_a_network_file_parser.html">MESANetworkFileParser</a> (<a class="el" href="namespacegridfire_1_1io.html">gridfire::io</a>)</dd></dl>
 <dl class="classindex odd">
-<dt class="alphachar"><a id="letter_N" name="letter_N">N</a></dt>
+<dt class="alphachar"><a id="letter_M" name="letter_M">M</a></dt>
-<dd><a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="structgridfire_1_1_net_out.html">NetOut</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="classgridfire_1_1_network.html">Network</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">NetworkFileParser</a> (<a class="el" href="namespacegridfire_1_1io.html">gridfire::io</a>)</dd><dd><a class="el" href="classgridfire_1_1solver_1_1_network_solver_strategy.html">NetworkSolverStrategy</a> (<a class="el" href="namespacegridfire_1_1solver.html">gridfire::solver</a>)</dd></dl>
+<dd><a class="el" href="classgridfire_1_1io_1_1_m_e_s_a_network_file_parser.html">MESANetworkFileParser</a> (<a class="el" href="namespacegridfire_1_1io.html">gridfire::io</a>)</dd><dd><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">MultiscalePartitioningEngineView</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd></dl>
 <dl class="classindex even">
+<dt class="alphachar"><a id="letter_N" name="letter_N">N</a></dt>
+<dd><a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="structgridfire_1_1_net_out.html">NetOut</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="classgridfire_1_1_network.html">Network</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">NetworkFileParser</a> (<a class="el" href="namespacegridfire_1_1io.html">gridfire::io</a>)</dd><dd><a class="el" href="classgridfire_1_1_network_priming_engine_view.html">NetworkPrimingEngineView</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="classgridfire_1_1exceptions_1_1_network_resized_error.html">NetworkResizedError</a> (<a class="el" href="namespacegridfire_1_1exceptions.html">gridfire::exceptions</a>)</dd><dd><a class="el" href="classgridfire_1_1solver_1_1_network_solver_strategy.html">NetworkSolverStrategy</a> (<a class="el" href="namespacegridfire_1_1solver.html">gridfire::solver</a>)</dd></dl>
+<dl class="classindex odd">
 <dt class="alphachar"><a id="letter_O" name="letter_O">O</a></dt>
 <dd><a class="el" href="structgridfire_1_1approx8_1_1_o_d_e.html">ODE</a> (<a class="el" href="namespacegridfire_1_1approx8.html">gridfire::approx8</a>)</dd></dl>
-<dl class="classindex odd">
+<dl class="classindex even">
 <dt class="alphachar"><a id="letter_P" name="letter_P">P</a></dt>
-<dd><a class="el" href="structgridfire_1_1io_1_1_parsed_network_data.html">ParsedNetworkData</a> (<a class="el" href="namespacegridfire_1_1io.html">gridfire::io</a>)</dd><dd><a class="el" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html">GraphEngine::PrecomputedReaction</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd></dl>
+<dd><a class="el" href="classgridfire_1_1partition_1_1_partition_function.html">PartitionFunction</a> (<a class="el" href="namespacegridfire_1_1partition.html">gridfire::partition</a>)</dd><dd><a class="el" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html">GraphEngine::PrecomputedReaction</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="structgridfire_1_1_priming_report.html">PrimingReport</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></dd><dd><a class="el" href="class_py_dynamic_engine_view.html">PyDynamicEngineView</a></dd><dd><a class="el" href="class_py_dynamic_network_solver_strategy.html">PyDynamicNetworkSolverStrategy</a></dd><dd><a class="el" href="class_py_engine.html">PyEngine</a></dd><dd><a class="el" href="class_py_engine_view.html">PyEngineView</a></dd><dd><a class="el" href="class_py_network_file_parser.html">PyNetworkFileParser</a></dd><dd><a class="el" href="class_py_partition_function.html">PyPartitionFunction</a></dd><dd><a class="el" href="class_py_screening.html">PyScreening</a></dd></dl>
-<dl class="classindex even">
+<dl class="classindex odd">
 <dt class="alphachar"><a id="letter_Q" name="letter_Q">Q</a></dt>
-<dd><a class="el" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html">QSENetworkSolver</a> (<a class="el" href="namespacegridfire_1_1solver.html">gridfire::solver</a>)</dd></dl>
+<dd><a class="el" href="structgridfire_1_1_q_s_e_cache_config.html">QSECacheConfig</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="structgridfire_1_1_q_s_e_cache_key.html">QSECacheKey</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html">MultiscalePartitioningEngineView::QSEGroup</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd></dl>
-<dl class="classindex odd">
-<dt class="alphachar"><a id="letter_R" name="letter_R">R</a></dt>
-<dd><a class="el" href="structgridfire_1_1reaction_1_1_rate_coefficient_set.html">RateCoefficientSet</a> (<a class="el" href="namespacegridfire_1_1reaction.html">gridfire::reaction</a>)</dd><dd><a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">Reaction</a> (<a class="el" href="namespacegridfire_1_1reaction.html">gridfire::reaction</a>)</dd><dd><a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html">AdaptiveEngineView::ReactionFlow</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="structgridfire_1_1reaclib_1_1_reaction_record.html">ReactionRecord</a> (<a class="el" href="namespacegridfire_1_1reaclib.html">gridfire::reaclib</a>)</dd><dd><a class="el" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html">DirectNetworkSolver::RHSFunctor</a> (<a class="el" href="namespacegridfire_1_1solver.html">gridfire::solver</a>)</dd><dd><a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html">QSENetworkSolver::RHSFunctor</a> (<a class="el" href="namespacegridfire_1_1solver.html">gridfire::solver</a>)</dd></dl>
 <dl class="classindex even">
-<dt class="alphachar"><a id="letter_S" name="letter_S">S</a></dt>
+<dt class="alphachar"><a id="letter_R" name="letter_R">R</a></dt>
-<dd><a class="el" href="classgridfire_1_1screening_1_1_screening_model.html">ScreeningModel</a> (<a class="el" href="namespacegridfire_1_1screening.html">gridfire::screening</a>)</dd><dd><a class="el" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html">SimpleReactionListFileParser</a> (<a class="el" href="namespacegridfire_1_1io.html">gridfire::io</a>)</dd><dd><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd></dl>
+<dd><a class="el" href="structgridfire_1_1reaction_1_1_rate_coefficient_set.html">RateCoefficientSet</a> (<a class="el" href="namespacegridfire_1_1reaction.html">gridfire::reaction</a>)</dd><dd><a class="el" href="structgridfire_1_1partition_1_1record_1_1_rauscher_thielemann_partition_data_record.html">RauscherThielemannPartitionDataRecord</a> (<a class="el" href="namespacegridfire_1_1partition_1_1record.html">gridfire::partition::record</a>)</dd><dd><a class="el" href="classgridfire_1_1partition_1_1_rauscher_thielemann_partition_function.html">RauscherThielemannPartitionFunction</a> (<a class="el" href="namespacegridfire_1_1partition.html">gridfire::partition</a>)</dd><dd><a class="el" href="classgridfire_1_1_reaction.html">Reaction</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">Reaction</a> (<a class="el" href="namespacegridfire_1_1reaction.html">gridfire::reaction</a>)</dd><dd><a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html">AdaptiveEngineView::ReactionFlow</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd><dd><a class="el" href="structgridfire_1_1reaclib_1_1_reaction_record.html">ReactionRecord</a> (<a class="el" href="namespacegridfire_1_1reaclib.html">gridfire::reaclib</a>)</dd><dd><a class="el" href="struct_r_h_s_functor.html">RHSFunctor</a></dd><dd><a class="el" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_manager.html">DirectNetworkSolver::RHSManager</a> (<a class="el" href="namespacegridfire_1_1solver.html">gridfire::solver</a>)</dd></dl>
 <dl class="classindex odd">
+<dt class="alphachar"><a id="letter_S" name="letter_S">S</a></dt>
+<dd><a class="el" href="classgridfire_1_1screening_1_1_screening_model.html">ScreeningModel</a> (<a class="el" href="namespacegridfire_1_1screening.html">gridfire::screening</a>)</dd><dd><a class="el" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html">SimpleReactionListFileParser</a> (<a class="el" href="namespacegridfire_1_1io.html">gridfire::io</a>)</dd><dd><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_error.html">StaleEngineError</a> (<a class="el" href="namespacegridfire_1_1exceptions.html">gridfire::exceptions</a>)</dd><dd><a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">StaleEngineError</a> (<a class="el" href="namespacegridfire_1_1expectations.html">gridfire::expectations</a>)</dd><dd><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">StaleEngineTrigger</a> (<a class="el" href="namespacegridfire_1_1exceptions.html">gridfire::exceptions</a>)</dd><dd><a class="el" href="structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html">StaleEngineTrigger::state</a> (<a class="el" href="namespacegridfire_1_1exceptions.html">gridfire::exceptions</a>)</dd><dd><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a> (<a class="el" href="namespacegridfire.html">gridfire</a>)</dd></dl>
+<dl class="classindex even">
 <dt class="alphachar"><a id="letter_T" name="letter_T">T</a></dt>
 <dd><a class="el" href="classgridfire_1_1reaction_1_1_templated_reaction_set.html">TemplatedReactionSet</a> (<a class="el" href="namespacegridfire_1_1reaction.html">gridfire::reaction</a>)</dd></dl>
+<dl class="classindex odd">
+<dt class="alphachar"><a id="letter_U" name="letter_U">U</a></dt>
+<dd><a class="el" href="classgridfire_1_1exceptions_1_1_unable_to_set_network_reactions_error.html">UnableToSetNetworkReactionsError</a> (<a class="el" href="namespacegridfire_1_1exceptions.html">gridfire::exceptions</a>)</dd></dl>
 <dl class="classindex even">
 <dt class="alphachar"><a id="letter_W" name="letter_W">W</a></dt>
 <dd><a class="el" href="classgridfire_1_1screening_1_1_weak_screening_model.html">WeakScreeningModel</a> (<a class="el" href="namespacegridfire_1_1screening.html">gridfire::screening</a>)</dd></dl>

docs/html/classgridfire_1_1_adaptive_engine_view-members.html

@@ -108,40 +108,51 @@ $(function(){initNavTree('classgridfire_1_1_adaptive_engine_view.html',''); init
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ad599363cdd457e72e2e2937b0222c455">AdaptiveEngineView</a>(DynamicEngine &amp;baseEngine)</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#abdbaf4b87629efe43ac1255dad424c0c">calculateAllReactionFlows</a>(const NetIn &amp;netIn, std::vector&lt; double &gt; &amp;out_Y_Full) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a048d4b1d41ecb4125a558d1b9ed7cb31">calculateMolarReactionFlow</a>(const reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y_culled, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7b276b7210be588263395bdb0497fc6d">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y_culled, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#af703ad17ea65ffff4b75bf8ccc00e5d5">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y_culled, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#afec39b2faa34ea65c5488dd8e11ba3c3">Config</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a89614f4a48f60c4170a0197f45303e7c">constructReactionIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a896d29325b4233e83d9298850b617a2d">constructSpeciesIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a42417e96fe9fd623458af109401daf08">cullReactionsByFlow</a>(const std::vector&lt; ReactionFlow &gt; &amp;allFlows, const std::unordered_set&lt; fourdst::atomic::Species &gt; &amp;reachableSpecies, const std::vector&lt; double &gt; &amp;Y_full, double maxFlow) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aa79fb382c98461b02a2c30668491e6c5">finalizeActiveSet</a>(const std::vector&lt; const reaction::LogicalReaction * &gt; &amp;finalReactions)</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a0ed21f7e7c1034fc87b40d4116c4221b">findReachableSpecies</a>(const NetIn &amp;netIn) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac9aab6f60e80a9228b2b19b1b10449ef">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_culled, const double T9, const double rho) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a03fc187d3d306b9058103b9522cbbaeb">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a231193a61ba5a31e8eb92b0d4ce69111">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">gridfire::DynamicEngine::generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const SparsityPattern &amp;sparsityPattern) const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aee095b30a9dce5fcb5ae2fa1d2aa192c">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a231193a61ba5a31e8eb92b0d4ce69111">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aee095b30a9dce5fcb5ae2fa1d2aa192c">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4710d218c8a0fd161e994ecd60b48e58">getJacobianMatrixEntry</a>(const int i_culled, const int j_culled) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a12cc2f352678fba9688363ba1876ab9c">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac83a8efe25c0e5b9bf7756ac3a500bb1">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a0ab1199f900a58f309c3c36532c9164f">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a93b38d0fdc4647f6f7340172dae17872">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y_culled, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a522e78bce9ff062939572248d57f8cea">getSpeciesDestructionTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a9055feb245524a5a9549ace935f059ff">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4e856d6d4d2fc220952bbb7e6b2f85d9">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y_culled, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a67b4ea8cad115394bb4a42cc39d696f9">getStoichiometryMatrixEntry</a>(const int speciesIndex_culled, const int reactionIndex_culled) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a5eaf7c3a4e28cd3a4f34979b88a80103">LogManager</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ad268c9942655e5c9605148fe07718e88">isStale</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a19fc7e02e216b797aa643fa35e429800">m_activeReactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a5eaf7c3a4e28cd3a4f34979b88a80103">LogManager</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#af4bc9fc6e4afcd6a53c49ca6e2a95940">m_activeSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a19fc7e02e216b797aa643fa35e429800">m_activeReactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4d38b46be9f25c7afe7ddd2b284253f8">m_baseEngine</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#af4bc9fc6e4afcd6a53c49ca6e2a95940">m_activeSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a14171a9ccc45a63996a967c72983de30">m_config</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4d38b46be9f25c7afe7ddd2b284253f8">m_baseEngine</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a63580db57e0f48f508906a11ccfd465e">m_isStale</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a14171a9ccc45a63996a967c72983de30">m_config</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a63580db57e0f48f508906a11ccfd465e">m_isStale</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a21c6e33bbf8c18fd5b5eaabb469054de">m_reactionIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a5f66204a0ff5b27eed243afddecb0093">m_speciesIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a21c6e33bbf8c18fd5b5eaabb469054de">m_reactionIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a68695f056b660e91285b7e5a931612e1">mapCulledToFull</a>(const std::vector&lt; double &gt; &amp;culled) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a5f66204a0ff5b27eed243afddecb0093">m_speciesIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a91e742642d8a8d9ec0620779927e5101">mapCulledToFullReactionIndex</a>(size_t culledReactionIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a68695f056b660e91285b7e5a931612e1">mapCulledToFull</a>(const std::vector&lt; double &gt; &amp;culled) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a256d14a333f9401039b826cc889761a8">mapCulledToFullSpeciesIndex</a>(size_t culledSpeciesIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a91e742642d8a8d9ec0620779927e5101">mapCulledToFullReactionIndex</a>(size_t culledReactionIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a3d9d8e862d1c2f0a8ba460c57f6a7f44">mapFullToCulled</a>(const std::vector&lt; double &gt; &amp;full) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a256d14a333f9401039b826cc889761a8">mapCulledToFullSpeciesIndex</a>(size_t culledSpeciesIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b">setScreeningModel</a>(screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a3d9d8e862d1c2f0a8ba460c57f6a7f44">mapFullToCulled</a>(const std::vector&lt; double &gt; &amp;full) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d61e73f5158f1574cda3edc90c51f7e">update</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d0237956bf3ec7230bc51d88e7f8019">mapNetInToMolarAbundanceVector</a>(const NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aedc0dedb51c81e03f253cc409a5d5c40">validateState</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a70005361262bc180d4417b608661e3c3">primeEngine</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a>(const fourdst::composition::Composition &amp;comp, BuildDepthType depth)</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; DynamicEngine &gt;</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a823c665ba89452aa2b3d5422fa5d313f">rescueEdgeSpeciesDestructionChannel</a>(const std::vector&lt; double &gt; &amp;Y_full, const double T9, const double rho, const std::vector&lt; fourdst::atomic::Species &gt; &amp;activeSpecies, const reaction::LogicalReactionSet &amp;activeReactions) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4ff60b5214ec0bdaf683feb6615573a5">RescueSet</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7b3a6b3ab0a52f0f84d2b142e74ea672">setNetworkReactions</a>(const reaction::LogicalReactionSet &amp;reactions) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b">setScreeningModel</a>(screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a2a7ecf985a326b4bea43e00cf9ee43dd">update</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aedc0dedb51c81e03f253cc409a5d5c40">validateState</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; DynamicEngine &gt;</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 </table></div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->

docs/html/classgridfire_1_1_adaptive_engine_view.html

@@ -137,18 +137,20 @@ Public Member Functions</h2></td></tr>
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-<tr class="separator:a7d61e73f5158f1574cda3edc90c51f7e"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="separator:a2a7ecf985a326b4bea43e00cf9ee43dd"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ad268c9942655e5c9605148fe07718e88" id="r_ad268c9942655e5c9605148fe07718e88"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad268c9942655e5c9605148fe07718e88">isStale</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) override</td></tr>
+<tr class="separator:ad268c9942655e5c9605148fe07718e88"><td class="memSeparator" colspan="2">&#160;</td></tr>
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-<tr class="separator:ac9aab6f60e80a9228b2b19b1b10449ef"><td class="memSeparator" colspan="2">&#160;</td></tr>
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@@ -164,9 +166,13 @@ Public Member Functions</h2></td></tr>
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-<tr class="memdesc:a93b38d0fdc4647f6f7340172dae17872"><td class="mdescLeft">&#160;</td><td class="mdescRight">Computes timescales for all active species in the network.  <br /></td></tr>
+<tr class="separator:a7b3a6b3ab0a52f0f84d2b142e74ea672"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="separator:a93b38d0fdc4647f6f7340172dae17872"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="memdesc:a4e856d6d4d2fc220952bbb7e6b2f85d9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Computes timescales for all active species in the network.  <br /></td></tr>
+<tr class="separator:a4e856d6d4d2fc220952bbb7e6b2f85d9"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="separator:a522e78bce9ff062939572248d57f8cea"><td class="memSeparator" colspan="2">&#160;</td></tr>
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 <tr class="memdesc:aee095b30a9dce5fcb5ae2fa1d2aa192c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the base engine.  <br /></td></tr>
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@@ -176,6 +182,19 @@ Public Member Functions</h2></td></tr>
 <tr class="memitem:a0ab1199f900a58f309c3c36532c9164f" id="r_a0ab1199f900a58f309c3c36532c9164f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0ab1199f900a58f309c3c36532c9164f">getScreeningModel</a> () const override</td></tr>
 <tr class="memdesc:a0ab1199f900a58f309c3c36532c9164f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the screening model from the base engine.  <br /></td></tr>
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+<tr class="separator:a9055feb245524a5a9549ace935f059ff"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="separator:a7d0237956bf3ec7230bc51d88e7f8019"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="separator:a70005361262bc180d4417b608661e3c3"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="memitem:a818d942efa843959393e4eed3263b7e7 inherit pub_methods_classgridfire_1_1_dynamic_engine" id="r_a818d942efa843959393e4eed3263b7e7"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">generateJacobianMatrix</a> (const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const <a class="el" href="namespacegridfire.html#a898dfe22579e649935645cbd6f073178">SparsityPattern</a> &amp;sparsityPattern) const</td></tr>
+<tr class="separator:a818d942efa843959393e4eed3263b7e7 inherit pub_methods_classgridfire_1_1_dynamic_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a04317b66ef14d519264bc30ee69f5bf9 inherit pub_methods_classgridfire_1_1_dynamic_engine" id="r_a04317b66ef14d519264bc30ee69f5bf9"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a> () const</td></tr>
+<tr class="separator:a04317b66ef14d519264bc30ee69f5bf9 inherit pub_methods_classgridfire_1_1_dynamic_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="separator:a4e2c8b896661b7a89beffe0066cb21cf inherit pub_methods_classgridfire_1_1_dynamic_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
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 <tr class="memitem:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" id="r_a2e7970bed2100699f226f4141d5db037"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a> ()=default</td></tr>
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 <tr class="separator:afec39b2faa34ea65c5488dd8e11ba3c3"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a5eaf7c3a4e28cd3a4f34979b88a80103" id="r_a5eaf7c3a4e28cd3a4f34979b88a80103"><td class="memItemLeft" align="right" valign="top">using&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a5eaf7c3a4e28cd3a4f34979b88a80103">LogManager</a> = fourdst::logging::LogManager</td></tr>
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 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
 Private Member Functions</h2></td></tr>
@@ -224,6 +245,8 @@ Private Member Functions</h2></td></tr>
 <tr class="memitem:a42417e96fe9fd623458af109401daf08" id="r_a42417e96fe9fd623458af109401daf08"><td class="memItemLeft" align="right" valign="top">std::vector&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html">reaction::LogicalReaction</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a42417e96fe9fd623458af109401daf08">cullReactionsByFlow</a> (const std::vector&lt; <a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html">ReactionFlow</a> &gt; &amp;allFlows, const std::unordered_set&lt; fourdst::atomic::Species &gt; &amp;reachableSpecies, const std::vector&lt; double &gt; &amp;Y_full, double maxFlow) const</td></tr>
 <tr class="memdesc:a42417e96fe9fd623458af109401daf08"><td class="mdescLeft">&#160;</td><td class="mdescRight">Culls reactions from the network based on their flow rates.  <br /></td></tr>
 <tr class="separator:a42417e96fe9fd623458af109401daf08"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a823c665ba89452aa2b3d5422fa5d313f" id="r_a823c665ba89452aa2b3d5422fa5d313f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="#a4ff60b5214ec0bdaf683feb6615573a5">RescueSet</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a823c665ba89452aa2b3d5422fa5d313f">rescueEdgeSpeciesDestructionChannel</a> (const std::vector&lt; double &gt; &amp;Y_full, const double T9, const double rho, const std::vector&lt; fourdst::atomic::Species &gt; &amp;activeSpecies, const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;activeReactions) const</td></tr>
+<tr class="separator:a823c665ba89452aa2b3d5422fa5d313f"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:aa79fb382c98461b02a2c30668491e6c5" id="r_aa79fb382c98461b02a2c30668491e6c5"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa79fb382c98461b02a2c30668491e6c5">finalizeActiveSet</a> (const std::vector&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html">reaction::LogicalReaction</a> * &gt; &amp;finalReactions)</td></tr>
 <tr class="memdesc:aa79fb382c98461b02a2c30668491e6c5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Finalizes the set of active species and reactions.  <br /></td></tr>
 <tr class="separator:aa79fb382c98461b02a2c30668491e6c5"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -259,9 +282,9 @@ Private Attributes</h2></td></tr>
 <div class="textblock"><p>An engine view that dynamically adapts the reaction network based on runtime conditions. </p>
 <p>This class implements an <a class="el" href="classgridfire_1_1_engine_view.html" title="Abstract base class for a &quot;view&quot; of a reaction network engine.">EngineView</a> that dynamically culls species and reactions from the full reaction network based on their reaction flow rates and connectivity. This allows for efficient simulation of reaction networks by focusing computational effort on the most important species and reactions.</p>
 <p>The <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> maintains a subset of "active" species and reactions, and maps between the full network indices and the active subset indices. This allows the base engine to operate on the full network data, while the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> provides a reduced view for external clients.</p>
-<p>The adaptation process is driven by the <code><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">update()</a></code> method, which performs the following steps:</p><ol type="1">
+<p>The adaptation process is driven by the <code><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">update()</a></code> method, which performs the following steps:</p><ol type="1">
-<li><b>Reaction Flow Calculation:</b> Calculates the molar reaction flow rate for each reaction in the full network based on the current temperature, density, and composition.</li>
+<li><b><a class="el" href="classgridfire_1_1_reaction.html" title="Represents a single nuclear reaction from a specific data source.">Reaction</a> Flow Calculation:</b> Calculates the molar reaction flow rate for each reaction in the full network based on the current temperature, density, and composition.</li>
-<li><b>Reaction Culling:</b> Culls reactions with flow rates below a threshold, determined by a relative culling threshold multiplied by the maximum flow rate.</li>
+<li><b><a class="el" href="classgridfire_1_1_reaction.html" title="Represents a single nuclear reaction from a specific data source.">Reaction</a> Culling:</b> Culls reactions with flow rates below a threshold, determined by a relative culling threshold multiplied by the maximum flow rate.</li>
 <li><b>Connectivity Analysis:</b> Performs a connectivity analysis to identify species that are reachable from the initial fuel species through the culled reaction network.</li>
 <li><b>Species Culling:</b> Culls species that are not reachable from the initial fuel.</li>
 <li><b>Index Map Construction:</b> Constructs index maps to map between the full network indices and the active subset indices for species and reactions.</li>
@@ -271,9 +294,9 @@ Private Attributes</h2></td></tr>
 <dd>
 <a class="el" href="engine__view__abstract_8h.html" title="Abstract interfaces for engine &quot;views&quot; in GridFire.">engine_view_abstract.h</a> </dd>
 <dd>
-<a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
+<a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00047">47</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00050">50</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 </div><h2 class="groupheader">Member Typedef Documentation</h2>
 <a id="afec39b2faa34ea65c5488dd8e11ba3c3" name="afec39b2faa34ea65c5488dd8e11ba3c3"></a>
 <h2 class="memtitle"><span class="permalink"><a href="#afec39b2faa34ea65c5488dd8e11ba3c3">&#9670;&#160;</a></span>Config</h2>
@@ -295,7 +318,7 @@ Private Attributes</h2></td></tr>
 </table>
 </div><div class="memdoc">
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00260">260</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00279">279</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 
 </div>
 </div>
@@ -319,7 +342,31 @@ Private Attributes</h2></td></tr>
 </table>
 </div><div class="memdoc">
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00261">261</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00280">280</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+
+</div>
+</div>
+<a id="a4ff60b5214ec0bdaf683feb6615573a5" name="a4ff60b5214ec0bdaf683feb6615573a5"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a4ff60b5214ec0bdaf683feb6615573a5">&#9670;&#160;</a></span>RescueSet</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">typedef std::pair&lt;std::unordered_set&lt;const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html">reaction::LogicalReaction</a>*&gt;, std::unordered_set&lt;fourdst::atomic::Species&gt; &gt; <a class="el" href="#a4ff60b5214ec0bdaf683feb6615573a5">gridfire::AdaptiveEngineView::RescueSet</a></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00452">452</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 
 </div>
 </div>
@@ -356,7 +403,7 @@ Private Attributes</h2></td></tr>
 </dl>
 <p>Initializes the active species and reactions to the full network, and constructs the initial index maps. </p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00013">13</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00016">16</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -409,7 +456,7 @@ Private Attributes</h2></td></tr>
 </ol>
 </dd></dl>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00268">268</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00368">368</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -464,7 +511,7 @@ Private Attributes</h2></td></tr>
 <p>This method maps the culled abundances to the full network abundances and calls the base engine to calculate the molar reaction flow.</p>
 <dl class="exception"><dt>Exceptions</dt><dd>
   <table class="exception">
-    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
+    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
     <tr><td class="paramname">std::runtime_error</td><td>If the reaction is not part of the active reactions in the adaptive engine view. </td></tr>
   </table>
   </dd>
@@ -472,12 +519,12 @@ Private Attributes</h2></td></tr>
 
 <p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00175">175</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00212">212</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
-<a id="a7b276b7210be588263395bdb0497fc6d" name="a7b276b7210be588263395bdb0497fc6d"></a>
+<a id="af703ad17ea65ffff4b75bf8ccc00e5d5" name="af703ad17ea65ffff4b75bf8ccc00e5d5"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a7b276b7210be588263395bdb0497fc6d">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#af703ad17ea65ffff4b75bf8ccc00e5d5">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -486,7 +533,7 @@ Private Attributes</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt; gridfire::AdaptiveEngineView::calculateRHSAndEnergy </td>
+          <td class="memname">std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::AdaptiveEngineView::calculateRHSAndEnergy </td>
           <td>(</td>
           <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y_culled</em></span>, </td>
         </tr>
@@ -521,15 +568,15 @@ Private Attributes</h2></td></tr>
 <p>This method maps the culled abundances to the full network abundances, calls the base engine to calculate the RHS and energy generation, and then maps the full network derivatives back to the culled derivatives.</p>
 <dl class="exception"><dt>Exceptions</dt><dd>
   <table class="exception">
-    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
+    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
   </table>
   </dd>
 </dl>
-<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
+<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
 
-<p>Implements <a class="el" href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">gridfire::Engine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb">gridfire::Engine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00120">120</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00152">152</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -559,9 +606,9 @@ Private Attributes</h2></td></tr>
 <p>Constructs the reaction index map. </p>
 <dl class="section return"><dt>Returns</dt><dd>A vector mapping culled reaction indices to full reaction indices.</dd></dl>
 <p>This method creates a map from the indices of the active reactions to the indices of the corresponding reactions in the full network.</p>
-<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
+<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00053">53</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00056">56</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -591,9 +638,9 @@ Private Attributes</h2></td></tr>
 <p>Constructs the species index map. </p>
 <dl class="section return"><dt>Returns</dt><dd>A vector mapping culled species indices to full species indices.</dd></dl>
 <p>This method creates a map from the indices of the active species to the indices of the corresponding species in the full network.</p>
-<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
+<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00024">24</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00027">27</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -655,7 +702,7 @@ Private Attributes</h2></td></tr>
 </ol>
 </dd></dl>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00342">342</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00442">442</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -697,7 +744,7 @@ Private Attributes</h2></td></tr>
 </ul>
 </dd></dl>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00385">385</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00641">641</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
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@@ -742,12 +789,12 @@ Private Attributes</h2></td></tr>
 </ol>
 </dd></dl>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00299">299</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00399">399</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
-<a id="ac9aab6f60e80a9228b2b19b1b10449ef" name="ac9aab6f60e80a9228b2b19b1b10449ef"></a>
+<a id="a03fc187d3d306b9058103b9522cbbaeb" name="a03fc187d3d306b9058103b9522cbbaeb"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#ac9aab6f60e80a9228b2b19b1b10449ef">&#9670;&#160;</a></span>generateJacobianMatrix()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a03fc187d3d306b9058103b9522cbbaeb">&#9670;&#160;</a></span>generateJacobianMatrix()</h2>
 
 <div class="memitem">
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@@ -758,7 +805,7 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="memname">void gridfire::AdaptiveEngineView::generateJacobianMatrix </td>
           <td>(</td>
-          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y_culled</em></span>, </td>
+          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y_dynamic</em></span>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
@@ -768,7 +815,7 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">const double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;)</td>
+          <td class="paramtype">const double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
         </tr>
       </table>
   </td>
@@ -781,7 +828,7 @@ Private Attributes</h2></td></tr>
 <p>Generates the Jacobian matrix for the active species. </p>
 <dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
-    <tr><td class="paramname">Y_culled</td><td>A vector of abundances for the active species. </td></tr>
+    <tr><td class="paramname">Y_dynamic</td><td>A vector of abundances for the active species. </td></tr>
     <tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
     <tr><td class="paramname">rho</td><td>The density in g/cm^3.</td></tr>
   </table>
@@ -790,15 +837,15 @@ Private Attributes</h2></td></tr>
 <p>This method maps the culled abundances to the full network abundances and calls the base engine to generate the Jacobian matrix.</p>
 <dl class="exception"><dt>Exceptions</dt><dd>
   <table class="exception">
-    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
+    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
   </table>
   </dd>
 </dl>
-<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
+<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
 
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f">gridfire::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a29bdd4231c29c3a4e524ad6ca66a127d">gridfire::DynamicEngine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00138">138</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00175">175</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -829,7 +876,7 @@ Private Attributes</h2></td></tr>
 <p>This method calls the base engine to generate the stoichiometry matrix.</p>
 <dl class="exception"><dt>Exceptions</dt><dd>
   <table class="exception">
-    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
+    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
   </table>
   </dd>
 </dl>
@@ -837,7 +884,7 @@ Private Attributes</h2></td></tr>
 
 <p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">gridfire::DynamicEngine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00160">160</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00197">197</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -869,7 +916,7 @@ Private Attributes</h2></td></tr>
 
 <p>Implements <a class="el" href="classgridfire_1_1_engine_view.html#ad294227f8b5cf6d970c349eabf5447a6">gridfire::EngineView&lt; DynamicEngine &gt;</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00226">226</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00239">239</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 
 </div>
 </div>
@@ -912,16 +959,16 @@ Private Attributes</h2></td></tr>
 <p>This method maps the culled indices to the full network indices and calls the base engine to get the Jacobian matrix entry.</p>
 <dl class="exception"><dt>Exceptions</dt><dd>
   <table class="exception">
-    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
+    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
     <tr><td class="paramname">std::out_of_range</td><td>If the culled index is out of bounds for the species index map. </td></tr>
   </table>
   </dd>
 </dl>
-<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
+<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
 
 <p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">gridfire::DynamicEngine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00149">149</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00186">186</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -949,11 +996,11 @@ Private Attributes</h2></td></tr>
 </div><div class="memdoc">
 
 <p>Gets the set of active logical reactions in the network. </p>
-<dl class="section return"><dt>Returns</dt><dd>Reference to the LogicalReactionSet containing all active reactions. </dd></dl>
+<dl class="section return"><dt>Returns</dt><dd>Reference to the <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" title="A set of logical reactions.">LogicalReactionSet</a> containing all active reactions. </dd></dl>
 
 <p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">gridfire::DynamicEngine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00192">192</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00229">229</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -985,7 +1032,7 @@ Private Attributes</h2></td></tr>
 
 <p>Implements <a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">gridfire::Engine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00116">116</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00148">148</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -1017,18 +1064,18 @@ Private Attributes</h2></td></tr>
 <dl class="section return"><dt>Returns</dt><dd>The current screening model type.</dd></dl>
 <dl class="section user"><dt>Usage Example:</dt><dd><div class="fragment"><div class="line"><a class="code hl_function" href="#ad599363cdd457e72e2e2937b0222c455">AdaptiveEngineView</a> engineView(...);</div>
 <div class="line"><a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model = engineView.getScreeningModel();</div>
-<div class="ttc" id="aclassgridfire_1_1_adaptive_engine_view_html_ad599363cdd457e72e2e2937b0222c455"><div class="ttname"><a href="#ad599363cdd457e72e2e2937b0222c455">gridfire::AdaptiveEngineView::AdaptiveEngineView</a></div><div class="ttdeci">AdaptiveEngineView(DynamicEngine &amp;baseEngine)</div><div class="ttdoc">Constructs an AdaptiveEngineView.</div><div class="ttdef"><b>Definition</b> <a href="engine__adaptive_8cpp_source.html#l00013">engine_adaptive.cpp:13</a></div></div>
+<div class="ttc" id="aclassgridfire_1_1_adaptive_engine_view_html_ad599363cdd457e72e2e2937b0222c455"><div class="ttname"><a href="#ad599363cdd457e72e2e2937b0222c455">gridfire::AdaptiveEngineView::AdaptiveEngineView</a></div><div class="ttdeci">AdaptiveEngineView(DynamicEngine &amp;baseEngine)</div><div class="ttdoc">Constructs an AdaptiveEngineView.</div><div class="ttdef"><b>Definition</b> <a href="engine__adaptive_8cpp_source.html#l00016">engine_adaptive.cpp:16</a></div></div>
 <div class="ttc" id="anamespacegridfire_1_1screening_html_aa82aafbc4f8c28d0a75b60798e3a7d25"><div class="ttname"><a href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">gridfire::screening::ScreeningType</a></div><div class="ttdeci">ScreeningType</div><div class="ttdoc">Enumerates the available plasma screening models.</div><div class="ttdef"><b>Definition</b> <a href="screening__types_8h_source.html#l00015">screening_types.h:15</a></div></div>
 </div><!-- fragment --> </dd></dl>
 
 <p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">gridfire::DynamicEngine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00220">220</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00296">296</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
-<a id="a93b38d0fdc4647f6f7340172dae17872" name="a93b38d0fdc4647f6f7340172dae17872"></a>
+<a id="a522e78bce9ff062939572248d57f8cea" name="a522e78bce9ff062939572248d57f8cea"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a93b38d0fdc4647f6f7340172dae17872">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a522e78bce9ff062939572248d57f8cea">&#9670;&#160;</a></span>getSpeciesDestructionTimescales()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -1037,7 +1084,74 @@ Private Attributes</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">std::unordered_map&lt; Species, double &gt; gridfire::AdaptiveEngineView::getSpeciesTimescales </td>
+          <td class="memname">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::AdaptiveEngineView::getSpeciesDestructionTimescales </td>
+          <td>(</td>
+          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6ca0f315f75252ca505507a61556dda6">gridfire::DynamicEngine</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00266">266</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a9055feb245524a5a9549ace935f059ff" name="a9055feb245524a5a9549ace935f059ff"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a9055feb245524a5a9549ace935f059ff">&#9670;&#160;</a></span>getSpeciesIndex()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">int gridfire::AdaptiveEngineView::getSpeciesIndex </td>
+          <td>(</td>
+          <td class="paramtype">const fourdst::atomic::Species &amp;</td>          <td class="paramname"><span class="paramname"><em>species</em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">gridfire::DynamicEngine</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00312">312</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a4e856d6d4d2fc220952bbb7e6b2f85d9" name="a4e856d6d4d2fc220952bbb7e6b2f85d9"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a4e856d6d4d2fc220952bbb7e6b2f85d9">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::expected&lt; std::unordered_map&lt; Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::AdaptiveEngineView::getSpeciesTimescales </td>
           <td>(</td>
           <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y_culled</em></span>, </td>
         </tr>
@@ -1072,14 +1186,14 @@ Private Attributes</h2></td></tr>
 <p>This method maps the culled abundances to the full network abundances and calls the base engine to compute the species timescales.</p>
 <dl class="exception"><dt>Exceptions</dt><dd>
   <table class="exception">
-    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
+    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
   </table>
   </dd>
 </dl>
 
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15">gridfire::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6772ac384b4c3d3e91712041e4aaa813">gridfire::DynamicEngine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00196">196</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00238">238</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -1122,16 +1236,45 @@ Private Attributes</h2></td></tr>
 <p>This method maps the culled indices to the full network indices and calls the base engine to get the stoichiometry matrix entry.</p>
 <dl class="exception"><dt>Exceptions</dt><dd>
   <table class="exception">
-    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
+    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
     <tr><td class="paramname">std::out_of_range</td><td>If the culled index is out of bounds for the species or reaction index map. </td></tr>
   </table>
   </dd>
 </dl>
-<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
+<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
 
 <p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">gridfire::DynamicEngine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00165">165</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00202">202</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+
+</div>
+</div>
+<a id="ad268c9942655e5c9605148fe07718e88" name="ad268c9942655e5c9605148fe07718e88"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ad268c9942655e5c9605148fe07718e88">&#9670;&#160;</a></span>isStale()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool gridfire::AdaptiveEngineView::isStale </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a942e65ced17ca602482cc42e469d6398">gridfire::DynamicEngine</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00144">144</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -1167,7 +1310,7 @@ Private Attributes</h2></td></tr>
 </dl>
 <dl class="section return"><dt>Returns</dt><dd>A vector of abundances for the full network, with the abundances of the active species copied from the culled vector. </dd></dl>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00224">224</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00323">323</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -1209,7 +1352,7 @@ Private Attributes</h2></td></tr>
   </dd>
 </dl>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00251">251</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00350">350</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -1251,7 +1394,7 @@ Private Attributes</h2></td></tr>
   </dd>
 </dl>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00242">242</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00341">341</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -1287,6 +1430,139 @@ Private Attributes</h2></td></tr>
 </dl>
 <dl class="section return"><dt>Returns</dt><dd>A vector of abundances for the active species, with the abundances of the active species copied from the full vector. </dd></dl>
 
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00332">332</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a7d0237956bf3ec7230bc51d88e7f8019" name="a7d0237956bf3ec7230bc51d88e7f8019"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a7d0237956bf3ec7230bc51d88e7f8019">&#9670;&#160;</a></span>mapNetInToMolarAbundanceVector()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::vector&lt; double &gt; gridfire::AdaptiveEngineView::mapNetInToMolarAbundanceVector </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a55f1b7e5ebe2840e1d7c54665ca5411a">gridfire::DynamicEngine</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00300">300</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a70005361262bc180d4417b608661e3c3" name="a70005361262bc180d4417b608661e3c3"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a70005361262bc180d4417b608661e3c3">&#9670;&#160;</a></span>primeEngine()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="structgridfire_1_1_priming_report.html">PrimingReport</a> gridfire::AdaptiveEngineView::primeEngine </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a21c34f59c080a853fafa38a25175124e">gridfire::DynamicEngine</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00308">308</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a823c665ba89452aa2b3d5422fa5d313f" name="a823c665ba89452aa2b3d5422fa5d313f"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a823c665ba89452aa2b3d5422fa5d313f">&#9670;&#160;</a></span>rescueEdgeSpeciesDestructionChannel()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="#a4ff60b5214ec0bdaf683feb6615573a5">AdaptiveEngineView::RescueSet</a> gridfire::AdaptiveEngineView::rescueEdgeSpeciesDestructionChannel </td>
+          <td>(</td>
+          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y_full</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const double</td>          <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const std::vector&lt; fourdst::atomic::Species &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>activeSpecies</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>activeReactions</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00485">485</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a7b3a6b3ab0a52f0f84d2b142e74ea672" name="a7b3a6b3ab0a52f0f84d2b142e74ea672"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a7b3a6b3ab0a52f0f84d2b142e74ea672">&#9670;&#160;</a></span>setNetworkReactions()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">void gridfire::AdaptiveEngineView::setNetworkReactions </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>reactions</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afb2ec904d88fc8aab516db4059d0e00f">gridfire::DynamicEngine</a>.</p>
+
 <p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00233">233</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
@@ -1330,12 +1606,12 @@ Private Attributes</h2></td></tr>
 
 <p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">gridfire::DynamicEngine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00216">216</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00292">292</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
-<a id="a7d61e73f5158f1574cda3edc90c51f7e" name="a7d61e73f5158f1574cda3edc90c51f7e"></a>
+<a id="a2a7ecf985a326b4bea43e00cf9ee43dd" name="a2a7ecf985a326b4bea43e00cf9ee43dd"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a7d61e73f5158f1574cda3edc90c51f7e">&#9670;&#160;</a></span>update()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a2a7ecf985a326b4bea43e00cf9ee43dd">&#9670;&#160;</a></span>update()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -1344,7 +1620,7 @@ Private Attributes</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">void gridfire::AdaptiveEngineView::update </td>
+          <td class="memname">fourdst::composition::Composition gridfire::AdaptiveEngineView::update </td>
           <td>(</td>
           <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
           <td></td>
@@ -1381,9 +1657,9 @@ Private Attributes</h2></td></tr>
 <dd>
 <a class="el" href="#a89614f4a48f60c4170a0197f45303e7c" title="Constructs the reaction index map.">AdaptiveEngineView::constructReactionIndexMap()</a> </dd></dl>
 
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f">gridfire::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aa799ff785e7e79bf35b11efd55f6282a">gridfire::DynamicEngine</a>.</p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00085">85</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00088">88</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -1413,12 +1689,12 @@ Private Attributes</h2></td></tr>
 <p>Validates that the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is not stale. </p>
 <dl class="exception"><dt>Exceptions</dt><dd>
   <table class="exception">
-    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
+    <tr><td class="paramname">std::runtime_error</td><td>If the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is stale (i.e., <code><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">update()</a></code> has not been called). </td></tr>
   </table>
   </dd>
 </dl>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00260">260</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8cpp_source.html#l00359">359</a> of file <a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a>.</p>
 
 </div>
 </div>
@@ -1445,7 +1721,7 @@ Private Attributes</h2></td></tr>
 
 <p>The set of reactions that are currently active in the network. </p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00273">273</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00292">292</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 
 </div>
 </div>
@@ -1471,7 +1747,7 @@ Private Attributes</h2></td></tr>
 
 <p>The set of species that are currently active in the network. </p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00271">271</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00290">290</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 
 </div>
 </div>
@@ -1497,7 +1773,7 @@ Private Attributes</h2></td></tr>
 
 <p>The underlying engine to which this view delegates calculations. </p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00268">268</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00287">287</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 
 </div>
 </div>
@@ -1523,7 +1799,7 @@ Private Attributes</h2></td></tr>
 
 <p>A reference to the singleton <a class="el" href="#afec39b2faa34ea65c5488dd8e11ba3c3">Config</a> instance, used for retrieving configuration parameters. </p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00263">263</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00282">282</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 
 </div>
 </div>
@@ -1549,7 +1825,7 @@ Private Attributes</h2></td></tr>
 
 <p>A flag indicating whether the view is stale and needs to be updated. </p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00281">281</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00300">300</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 
 </div>
 </div>
@@ -1575,7 +1851,7 @@ Private Attributes</h2></td></tr>
 
 <p>A pointer to the logger instance, used for logging messages. </p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00265">265</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00284">284</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 
 </div>
 </div>
@@ -1601,7 +1877,7 @@ Private Attributes</h2></td></tr>
 
 <p>A map from the indices of the active reactions to the indices of the corresponding reactions in the full network. </p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00278">278</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00297">297</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 
 </div>
 </div>
@@ -1627,13 +1903,13 @@ Private Attributes</h2></td></tr>
 
 <p>A map from the indices of the active species to the indices of the corresponding species in the full network. </p>
 
-<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00276">276</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__adaptive_8h_source.html#l00295">295</a> of file <a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a>.</p>
 
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>src/network/include/gridfire/engine/views/<a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a></li>
+<li>src/include/gridfire/engine/views/<a class="el" href="engine__adaptive_8h_source.html">engine_adaptive.h</a></li>
-<li>src/network/lib/engine/views/<a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a></li>
+<li>src/lib/engine/views/<a class="el" href="engine__adaptive_8cpp_source.html">engine_adaptive.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classgridfire_1_1_adaptive_engine_view.js

@@ -3,30 +3,38 @@ var classgridfire_1_1_adaptive_engine_view =
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     [ "LogManager", "classgridfire_1_1_adaptive_engine_view.html#a5eaf7c3a4e28cd3a4f34979b88a80103", null ],
+    [ "RescueSet", "classgridfire_1_1_adaptive_engine_view.html#a4ff60b5214ec0bdaf683feb6615573a5", null ],
     [ "AdaptiveEngineView", "classgridfire_1_1_adaptive_engine_view.html#ad599363cdd457e72e2e2937b0222c455", null ],
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     [ "calculateMolarReactionFlow", "classgridfire_1_1_adaptive_engine_view.html#a048d4b1d41ecb4125a558d1b9ed7cb31", null ],
-    [ "calculateRHSAndEnergy", "classgridfire_1_1_adaptive_engine_view.html#a7b276b7210be588263395bdb0497fc6d", null ],
+    [ "calculateRHSAndEnergy", "classgridfire_1_1_adaptive_engine_view.html#af703ad17ea65ffff4b75bf8ccc00e5d5", null ],
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     [ "findReachableSpecies", "classgridfire_1_1_adaptive_engine_view.html#a0ed21f7e7c1034fc87b40d4116c4221b", null ],
-    [ "generateJacobianMatrix", "classgridfire_1_1_adaptive_engine_view.html#ac9aab6f60e80a9228b2b19b1b10449ef", null ],
+    [ "generateJacobianMatrix", "classgridfire_1_1_adaptive_engine_view.html#a03fc187d3d306b9058103b9522cbbaeb", null ],
     [ "generateStoichiometryMatrix", "classgridfire_1_1_adaptive_engine_view.html#a231193a61ba5a31e8eb92b0d4ce69111", null ],
     [ "getBaseEngine", "classgridfire_1_1_adaptive_engine_view.html#aee095b30a9dce5fcb5ae2fa1d2aa192c", null ],
     [ "getJacobianMatrixEntry", "classgridfire_1_1_adaptive_engine_view.html#a4710d218c8a0fd161e994ecd60b48e58", null ],
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+    [ "getSpeciesDestructionTimescales", "classgridfire_1_1_adaptive_engine_view.html#a522e78bce9ff062939572248d57f8cea", null ],
+    [ "getSpeciesIndex", "classgridfire_1_1_adaptive_engine_view.html#a9055feb245524a5a9549ace935f059ff", null ],
+    [ "getSpeciesTimescales", "classgridfire_1_1_adaptive_engine_view.html#a4e856d6d4d2fc220952bbb7e6b2f85d9", null ],
     [ "getStoichiometryMatrixEntry", "classgridfire_1_1_adaptive_engine_view.html#a67b4ea8cad115394bb4a42cc39d696f9", null ],
+    [ "isStale", "classgridfire_1_1_adaptive_engine_view.html#ad268c9942655e5c9605148fe07718e88", null ],
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     [ "mapCulledToFullReactionIndex", "classgridfire_1_1_adaptive_engine_view.html#a91e742642d8a8d9ec0620779927e5101", null ],
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     [ "mapFullToCulled", "classgridfire_1_1_adaptive_engine_view.html#a3d9d8e862d1c2f0a8ba460c57f6a7f44", null ],
+    [ "mapNetInToMolarAbundanceVector", "classgridfire_1_1_adaptive_engine_view.html#a7d0237956bf3ec7230bc51d88e7f8019", null ],
+    [ "primeEngine", "classgridfire_1_1_adaptive_engine_view.html#a70005361262bc180d4417b608661e3c3", null ],
+    [ "rescueEdgeSpeciesDestructionChannel", "classgridfire_1_1_adaptive_engine_view.html#a823c665ba89452aa2b3d5422fa5d313f", null ],
+    [ "setNetworkReactions", "classgridfire_1_1_adaptive_engine_view.html#a7b3a6b3ab0a52f0f84d2b142e74ea672", null ],
     [ "setScreeningModel", "classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b", null ],
-    [ "update", "classgridfire_1_1_adaptive_engine_view.html#a7d61e73f5158f1574cda3edc90c51f7e", null ],
+    [ "update", "classgridfire_1_1_adaptive_engine_view.html#a2a7ecf985a326b4bea43e00cf9ee43dd", null ],
     [ "validateState", "classgridfire_1_1_adaptive_engine_view.html#aedc0dedb51c81e03f253cc409a5d5c40", null ],
     [ "m_activeReactions", "classgridfire_1_1_adaptive_engine_view.html#a19fc7e02e216b797aa643fa35e429800", null ],
     [ "m_activeSpecies", "classgridfire_1_1_adaptive_engine_view.html#af4bc9fc6e4afcd6a53c49ca6e2a95940", null ],

docs/html/classgridfire_1_1_defined_engine_view-members.html

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+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
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+<div class="header">
+  <div class="headertitle"><div class="title">gridfire::DefinedEngineView Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032">calculateMolarReactionFlow</a>(const reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e">collect</a>(const std::vector&lt; std::string &gt; &amp;peNames)</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ab2514984afaaf8590c28ab71943fbe68">constructReactionIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a9ea4812bc697fe43f8aded14f8aa0985">constructSpeciesIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92">DefinedEngineView</a>(const std::vector&lt; std::string &gt; &amp;peNames, DynamicEngine &amp;baseEngine)</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">gridfire::DynamicEngine::generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const SparsityPattern &amp;sparsityPattern) const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a69b9a5812ad8bda13f956acd0da24484">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b">getJacobianMatrixEntry</a>(const int i_defined, const int j_defined) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491">getSpeciesDestructionTimescales</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2">getStoichiometryMatrixEntry</a>(const int speciesIndex_defined, const int reactionIndex_defined) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a7d9e738dd28efb4d6127de7379169c87">isStale</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965">m_activeReactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae">m_activeSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195">m_baseEngine</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a217d541f3fa777b1552f652fbb520382">m_isStale</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd">m_reactionIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e">m_speciesIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a2f59af6fb3516911de2a3e3ff0ed8873">mapFullToView</a>(const std::vector&lt; double &gt; &amp;full) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2">mapNetInToMolarAbundanceVector</a>(const NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843">mapViewToFull</a>(const std::vector&lt; double &gt; &amp;defined) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#aadf373d69a22fcd171a6c251466d53d1">mapViewToFullReactionIndex</a>(size_t definedReactionIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a">mapViewToFullSpeciesIndex</a>(size_t definedSpeciesIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a13033abd3b44904f98b58c93e22da460">primeEngine</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a>(const fourdst::composition::Composition &amp;comp, BuildDepthType depth)</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d">setNetworkReactions</a>(const reaction::LogicalReactionSet &amp;reactions) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258">setScreeningModel</a>(screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae">update</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0">validateNetworkState</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; DynamicEngine &gt;</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/html/classgridfire_1_1_defined_engine_view.js

@@ -0,0 +1,38 @@
+var classgridfire_1_1_defined_engine_view =
+[
+    [ "DefinedEngineView", "classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92", null ],
+    [ "calculateMolarReactionFlow", "classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032", null ],
+    [ "calculateRHSAndEnergy", "classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d", null ],
+    [ "collect", "classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e", null ],
+    [ "constructReactionIndexMap", "classgridfire_1_1_defined_engine_view.html#ab2514984afaaf8590c28ab71943fbe68", null ],
+    [ "constructSpeciesIndexMap", "classgridfire_1_1_defined_engine_view.html#a9ea4812bc697fe43f8aded14f8aa0985", null ],
+    [ "generateJacobianMatrix", "classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae", null ],
+    [ "generateStoichiometryMatrix", "classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6", null ],
+    [ "getBaseEngine", "classgridfire_1_1_defined_engine_view.html#a69b9a5812ad8bda13f956acd0da24484", null ],
+    [ "getJacobianMatrixEntry", "classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b", null ],
+    [ "getNetworkReactions", "classgridfire_1_1_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d", null ],
+    [ "getNetworkSpecies", "classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211", null ],
+    [ "getScreeningModel", "classgridfire_1_1_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c", null ],
+    [ "getSpeciesDestructionTimescales", "classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491", null ],
+    [ "getSpeciesIndex", "classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3", null ],
+    [ "getSpeciesTimescales", "classgridfire_1_1_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72", null ],
+    [ "getStoichiometryMatrixEntry", "classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2", null ],
+    [ "isStale", "classgridfire_1_1_defined_engine_view.html#a7d9e738dd28efb4d6127de7379169c87", null ],
+    [ "mapFullToView", "classgridfire_1_1_defined_engine_view.html#a2f59af6fb3516911de2a3e3ff0ed8873", null ],
+    [ "mapNetInToMolarAbundanceVector", "classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2", null ],
+    [ "mapViewToFull", "classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843", null ],
+    [ "mapViewToFullReactionIndex", "classgridfire_1_1_defined_engine_view.html#aadf373d69a22fcd171a6c251466d53d1", null ],
+    [ "mapViewToFullSpeciesIndex", "classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a", null ],
+    [ "primeEngine", "classgridfire_1_1_defined_engine_view.html#a13033abd3b44904f98b58c93e22da460", null ],
+    [ "setNetworkReactions", "classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d", null ],
+    [ "setScreeningModel", "classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258", null ],
+    [ "update", "classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae", null ],
+    [ "validateNetworkState", "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0", null ],
+    [ "m_activeReactions", "classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965", null ],
+    [ "m_activeSpecies", "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae", null ],
+    [ "m_baseEngine", "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195", null ],
+    [ "m_isStale", "classgridfire_1_1_defined_engine_view.html#a217d541f3fa777b1552f652fbb520382", null ],
+    [ "m_logger", "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3", null ],
+    [ "m_reactionIndexMap", "classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd", null ],
+    [ "m_speciesIndexMap", "classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e", null ]
+];

docs/html/classgridfire_1_1_dynamic_engine-members.html

@@ -106,18 +106,27 @@ $(function(){initNavTree('classgridfire_1_1_dynamic_engine.html',''); initResiza
 <p>This is the complete list of members for <a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a>, including all inherited members.</p>
 <table class="directory">
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">calculateMolarReactionFlow</a>(const reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a29bdd4231c29c3a4e524ad6ca66a127d">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">generateStoichiometryMatrix</a>()=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const SparsityPattern &amp;sparsityPattern) const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">generateStoichiometryMatrix</a>()=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">getJacobianMatrixEntry</a>(int i, int j) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">getNetworkReactions</a>() const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">getNetworkSpecies</a>() const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">getScreeningModel</a>() const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a6ca0f315f75252ca505507a61556dda6">getSpeciesDestructionTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a6772ac384b4c3d3e91712041e4aaa813">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">getStoichiometryMatrixEntry</a>(int speciesIndex, int reactionIndex) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">setScreeningModel</a>(screening::ScreeningType model)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a942e65ced17ca602482cc42e469d6398">isStale</a>(const NetIn &amp;netIn)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f">update</a>(const NetIn &amp;netIn)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a55f1b7e5ebe2840e1d7c54665ca5411a">mapNetInToMolarAbundanceVector</a>(const NetIn &amp;netIn) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a21c34f59c080a853fafa38a25175124e">primeEngine</a>(const NetIn &amp;netIn)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a>(const fourdst::composition::Composition &amp;comp, BuildDepthType depth)</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#afb2ec904d88fc8aab516db4059d0e00f">setNetworkReactions</a>(const reaction::LogicalReactionSet &amp;reactions)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">setScreeningModel</a>(screening::ScreeningType model)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#aa799ff785e7e79bf35b11efd55f6282a">update</a>(const NetIn &amp;netIn)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 </table></div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->

docs/html/classgridfire_1_1_dynamic_engine.html

@@ -116,18 +116,24 @@ Inheritance diagram for gridfire::DynamicEngine:</div>
  <div class="center">
   <img src="classgridfire_1_1_dynamic_engine.png" usemap="#gridfire::DynamicEngine_map" alt=""/>
   <map id="gridfire::DynamicEngine_map" name="gridfire::DynamicEngine_map">
-<area href="classgridfire_1_1_engine.html" title="Abstract base class for a reaction network engine." alt="gridfire::Engine" shape="rect" coords="201,0,392,24"/>
+<area href="classgridfire_1_1_engine.html" title="Abstract base class for a reaction network engine." alt="gridfire::Engine" shape="rect" coords="512,0,758,24"/>
-<area href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions." alt="gridfire::AdaptiveEngineView" shape="rect" coords="0,112,191,136"/>
+<area href="class_py_dynamic_engine.html" alt="PyDynamicEngine" shape="rect" coords="0,112,246,136"/>
-<area href="classgridfire_1_1_file_defined_engine_view.html" title="An engine view that uses a user-defined reaction network from a file." alt="gridfire::FileDefinedEngineView" shape="rect" coords="201,112,392,136"/>
+<area href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions." alt="gridfire::AdaptiveEngineView" shape="rect" coords="256,112,502,136"/>
-<area href="classgridfire_1_1_graph_engine.html" title="A reaction network engine that uses a graph-based representation." alt="gridfire::GraphEngine" shape="rect" coords="402,112,593,136"/>
+<area href="classgridfire_1_1_defined_engine_view.html" alt="gridfire::DefinedEngineView" shape="rect" coords="512,112,758,136"/>
+<area href="classgridfire_1_1_graph_engine.html" title="A reaction network engine that uses a graph-based representation." alt="gridfire::GraphEngine" shape="rect" coords="768,112,1014,136"/>
+<area href="classgridfire_1_1_multiscale_partitioning_engine_view.html" title="An engine view that partitions the reaction network into multiple groups based on timescales." alt="gridfire::MultiscalePartitioningEngineView" shape="rect" coords="1024,112,1270,136"/>
+<area href="classgridfire_1_1_file_defined_engine_view.html" alt="gridfire::FileDefinedEngineView" shape="rect" coords="384,168,630,192"/>
+<area href="classgridfire_1_1_network_priming_engine_view.html" title="Provides a view of a DynamicEngine filtered to reactions involving a specified priming species." alt="gridfire::NetworkPrimingEngineView" shape="rect" coords="640,168,886,192"/>
   </map>
 </div></div>
 <table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
 Public Member Functions</h2></td></tr>
-<tr class="memitem:a0a2fb3435ee3271ab9c806f225c61a7f" id="r_a0a2fb3435ee3271ab9c806f225c61a7f"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0a2fb3435ee3271ab9c806f225c61a7f">generateJacobianMatrix</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho)=0</td></tr>
+<tr class="memitem:a29bdd4231c29c3a4e524ad6ca66a127d" id="r_a29bdd4231c29c3a4e524ad6ca66a127d"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a29bdd4231c29c3a4e524ad6ca66a127d">generateJacobianMatrix</a> (const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho) const =0</td></tr>
-<tr class="memdesc:a0a2fb3435ee3271ab9c806f225c61a7f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate the Jacobian matrix for the current state.  <br /></td></tr>
+<tr class="memdesc:a29bdd4231c29c3a4e524ad6ca66a127d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate the Jacobian matrix for the current state.  <br /></td></tr>
-<tr class="separator:a0a2fb3435ee3271ab9c806f225c61a7f"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="separator:a29bdd4231c29c3a4e524ad6ca66a127d"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="separator:a818d942efa843959393e4eed3263b7e7"><td class="memSeparator" colspan="2">&#160;</td></tr>
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 <tr class="memdesc:a05d15ff35a6bc06a2fa7eda19838bd07"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get an entry from the previously generated Jacobian matrix.  <br /></td></tr>
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@@ -143,18 +149,34 @@ Public Member Functions</h2></td></tr>
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-<tr class="memdesc:a5d8ba98b230d2849035ee2507728fa15"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute timescales for all species in the network.  <br /></td></tr>
+<tr class="separator:afb2ec904d88fc8aab516db4059d0e00f"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="separator:a5d8ba98b230d2849035ee2507728fa15"><td class="memSeparator" colspan="2">&#160;</td></tr>
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-<tr class="memitem:acd500e1cd788df1dc105d28a20dc5f4f" id="r_acd500e1cd788df1dc105d28a20dc5f4f"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#acd500e1cd788df1dc105d28a20dc5f4f">update</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn)=0</td></tr>
+<tr class="memdesc:a6772ac384b4c3d3e91712041e4aaa813"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute timescales for all species in the network.  <br /></td></tr>
-<tr class="memdesc:acd500e1cd788df1dc105d28a20dc5f4f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Update the internal state of the engine.  <br /></td></tr>
+<tr class="separator:a6772ac384b4c3d3e91712041e4aaa813"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="separator:acd500e1cd788df1dc105d28a20dc5f4f"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a6ca0f315f75252ca505507a61556dda6" id="r_a6ca0f315f75252ca505507a61556dda6"><td class="memItemLeft" align="right" valign="top">virtual std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a6ca0f315f75252ca505507a61556dda6">getSpeciesDestructionTimescales</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
+<tr class="separator:a6ca0f315f75252ca505507a61556dda6"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aa799ff785e7e79bf35b11efd55f6282a" id="r_aa799ff785e7e79bf35b11efd55f6282a"><td class="memItemLeft" align="right" valign="top">virtual fourdst::composition::Composition&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa799ff785e7e79bf35b11efd55f6282a">update</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn)=0</td></tr>
+<tr class="memdesc:aa799ff785e7e79bf35b11efd55f6282a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Update the internal state of the engine.  <br /></td></tr>
+<tr class="separator:aa799ff785e7e79bf35b11efd55f6282a"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="separator:a942e65ced17ca602482cc42e469d6398"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a3fb44b6f55563a2f590f31916528f2bd" id="r_a3fb44b6f55563a2f590f31916528f2bd"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a3fb44b6f55563a2f590f31916528f2bd">setScreeningModel</a> (<a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model)=0</td></tr>
 <tr class="memdesc:a3fb44b6f55563a2f590f31916528f2bd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Set the electron screening model.  <br /></td></tr>
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 <tr class="memitem:a7a203f8e0f3a6744ddc912dfbcfdbcc0" id="r_a7a203f8e0f3a6744ddc912dfbcfdbcc0"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a7a203f8e0f3a6744ddc912dfbcfdbcc0">getScreeningModel</a> () const =0</td></tr>
 <tr class="memdesc:a7a203f8e0f3a6744ddc912dfbcfdbcc0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the current electron screening model.  <br /></td></tr>
 <tr class="separator:a7a203f8e0f3a6744ddc912dfbcfdbcc0"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ad3d56a8b9161b9cc7f4da51f6bf7e8c9" id="r_ad3d56a8b9161b9cc7f4da51f6bf7e8c9"><td class="memItemLeft" align="right" valign="top">virtual int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">getSpeciesIndex</a> (const fourdst::atomic::Species &amp;species) const =0</td></tr>
+<tr class="separator:ad3d56a8b9161b9cc7f4da51f6bf7e8c9"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a55f1b7e5ebe2840e1d7c54665ca5411a" id="r_a55f1b7e5ebe2840e1d7c54665ca5411a"><td class="memItemLeft" align="right" valign="top">virtual std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a55f1b7e5ebe2840e1d7c54665ca5411a">mapNetInToMolarAbundanceVector</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) const =0</td></tr>
+<tr class="separator:a55f1b7e5ebe2840e1d7c54665ca5411a"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a21c34f59c080a853fafa38a25175124e" id="r_a21c34f59c080a853fafa38a25175124e"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="structgridfire_1_1_priming_report.html">PrimingReport</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a21c34f59c080a853fafa38a25175124e">primeEngine</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn)=0</td></tr>
+<tr class="separator:a21c34f59c080a853fafa38a25175124e"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a04317b66ef14d519264bc30ee69f5bf9" id="r_a04317b66ef14d519264bc30ee69f5bf9"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a> () const</td></tr>
+<tr class="separator:a04317b66ef14d519264bc30ee69f5bf9"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a4e2c8b896661b7a89beffe0066cb21cf" id="r_a4e2c8b896661b7a89beffe0066cb21cf"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a> (const fourdst::composition::Composition &amp;comp, <a class="el" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a> depth)</td></tr>
+<tr class="separator:a4e2c8b896661b7a89beffe0066cb21cf"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="inherit_header pub_methods_classgridfire_1_1_engine"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td></tr>
 <tr class="memitem:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" id="r_a2e7970bed2100699f226f4141d5db037"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a> ()=default</td></tr>
 <tr class="memdesc:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor.  <br /></td></tr>
@@ -162,9 +184,9 @@ Public Member Functions</h2></td></tr>
 <tr class="memitem:a020e1b493d6964cafdad08fde697ceb3 inherit pub_methods_classgridfire_1_1_engine" id="r_a020e1b493d6964cafdad08fde697ceb3"><td class="memItemLeft" align="right" valign="top">virtual const std::vector&lt; fourdst::atomic::Species &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">getNetworkSpecies</a> () const =0</td></tr>
 <tr class="memdesc:a020e1b493d6964cafdad08fde697ceb3 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the list of species in the network.  <br /></td></tr>
 <tr class="separator:a020e1b493d6964cafdad08fde697ceb3 inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:ac8b56124b6b49cd1802addb74a9a47c2 inherit pub_methods_classgridfire_1_1_engine" id="r_ac8b56124b6b49cd1802addb74a9a47c2"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
+<tr class="memitem:a89f714d19b84a93a004a7afbb487a6cb inherit pub_methods_classgridfire_1_1_engine" id="r_a89f714d19b84a93a004a7afbb487a6cb"><td class="memItemLeft" align="right" valign="top">virtual std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
-<tr class="memdesc:ac8b56124b6b49cd1802addb74a9a47c2 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation.  <br /></td></tr>
+<tr class="memdesc:a89f714d19b84a93a004a7afbb487a6cb inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation.  <br /></td></tr>
-<tr class="separator:ac8b56124b6b49cd1802addb74a9a47c2 inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="separator:a89f714d19b84a93a004a7afbb487a6cb inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Abstract class for engines supporting Jacobian and stoichiometry operations. </p>
@@ -177,7 +199,7 @@ Public Member Functions</h2></td></tr>
 </ul>
 <p>Intended usage: Derive from this class to implement engines that support advanced solver features such as implicit integration, sensitivity analysis, QSE (Quasi-Steady-State Equilibrium) handling, and more. </p>
 
-<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00121">121</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00130">130</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
 </div><h2 class="groupheader">Member Function Documentation</h2>
 <a id="a6633b1757c41dd9e1c397333f4f9e785" name="a6633b1757c41dd9e1c397333f4f9e785"></a>
 <h2 class="memtitle"><span class="permalink"><a href="#a6633b1757c41dd9e1c397333f4f9e785">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
@@ -229,12 +251,12 @@ Public Member Functions</h2></td></tr>
 <dl class="section return"><dt>Returns</dt><dd>Molar flow rate for the reaction (e.g., mol/g/s).</dd></dl>
 <p>This method computes the net rate at which the given reaction proceeds under the current state. </p>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a048d4b1d41ecb4125a558d1b9ed7cb31">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ac371fb66fd0a76a04df204c9dd9a05ef">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a048d4b1d41ecb4125a558d1b9ed7cb31">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a79eb9c108d694a27ec913ed0143aa044">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a6224f546ba66b1257506b1fc9f47195a">PyDynamicEngine</a>.</p>
 
 </div>
 </div>
-<a id="a0a2fb3435ee3271ab9c806f225c61a7f" name="a0a2fb3435ee3271ab9c806f225c61a7f"></a>
+<a id="a29bdd4231c29c3a4e524ad6ca66a127d" name="a29bdd4231c29c3a4e524ad6ca66a127d"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a0a2fb3435ee3271ab9c806f225c61a7f">&#9670;&#160;</a></span>generateJacobianMatrix()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a29bdd4231c29c3a4e524ad6ca66a127d">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[1/2]</span></h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -245,7 +267,7 @@ Public Member Functions</h2></td></tr>
         <tr>
           <td class="memname">virtual void gridfire::DynamicEngine::generateJacobianMatrix </td>
           <td>(</td>
-          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
+          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y_dynamic</em></span>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
@@ -255,7 +277,7 @@ Public Member Functions</h2></td></tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;)</td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
         </tr>
       </table>
   </td>
@@ -268,7 +290,7 @@ Public Member Functions</h2></td></tr>
 <p>Generate the Jacobian matrix for the current state. </p>
 <dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
-    <tr><td class="paramname">Y</td><td>Vector of current abundances. </td></tr>
+    <tr><td class="paramname">Y_dynamic</td><td>Vector of current abundances. </td></tr>
     <tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
     <tr><td class="paramname">rho</td><td>Density in g/cm^3.</td></tr>
   </table>
@@ -276,7 +298,50 @@ Public Member Functions</h2></td></tr>
 </dl>
 <p>This method must compute and store the Jacobian matrix (∂(dY/dt)_i/∂Y_j) for the current state. The matrix can then be accessed via <a class="el" href="#a05d15ff35a6bc06a2fa7eda19838bd07" title="Get an entry from the previously generated Jacobian matrix.">getJacobianMatrixEntry()</a>. </p>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac9aab6f60e80a9228b2b19b1b10449ef">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a48b2451f96b8f5511ffc4071519c0810">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#ae347ff0316e532e0298ec8c913908105">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a03fc187d3d306b9058103b9522cbbaeb">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#acdf5ad8765290ea2b78170235aea391d">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a5bd40c752db1badcd600797c9113121d">PyDynamicEngine</a>.</p>
+
+</div>
+</div>
+<a id="a818d942efa843959393e4eed3263b7e7" name="a818d942efa843959393e4eed3263b7e7"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a818d942efa843959393e4eed3263b7e7">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[2/2]</span></h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual void gridfire::DynamicEngine::generateJacobianMatrix </td>
+          <td>(</td>
+          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y_dynamic</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const <a class="el" href="namespacegridfire.html#a898dfe22579e649935645cbd6f073178">SparsityPattern</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>sparsityPattern</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Reimplemented in <a class="el" href="classgridfire_1_1_graph_engine.html#a9687eef88c97eeb7f8680acb230f8ac1">gridfire::GraphEngine</a>, and <a class="el" href="class_py_dynamic_engine.html#aa0f1fd3f0c0185395193d1b6897d64c5">PyDynamicEngine</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00148">148</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
 
 </div>
 </div>
@@ -306,7 +371,36 @@ Public Member Functions</h2></td></tr>
 <p>Generate the stoichiometry matrix for the network. </p>
 <p>This method must compute and store the stoichiometry matrix, which encodes the net change of each species in each reaction. </p>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a231193a61ba5a31e8eb92b0d4ce69111">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a27a5163157cc15c4cb3b99a5d3564dbd">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a231193a61ba5a31e8eb92b0d4ce69111">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#abe76a46784b1ebc8ad67a9eec40d369a">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a2066649ca11a869c054079ea12d8d0e9">PyDynamicEngine</a>.</p>
+
+</div>
+</div>
+<a id="a04317b66ef14d519264bc30ee69f5bf9" name="a04317b66ef14d519264bc30ee69f5bf9"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a04317b66ef14d519264bc30ee69f5bf9">&#9670;&#160;</a></span>getDepth()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual <a class="el" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a> gridfire::DynamicEngine::getDepth </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel nodiscard">nodiscard</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Reimplemented in <a class="el" href="classgridfire_1_1_graph_engine.html#a166a5f4349580f9aa0b930afec73fcc4">gridfire::GraphEngine</a>, and <a class="el" href="class_py_dynamic_engine.html#adba68716d832b6100e08d32fbc36f13c">PyDynamicEngine</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00305">305</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
 
 </div>
 </div>
@@ -346,9 +440,9 @@ Public Member Functions</h2></td></tr>
   </dd>
 </dl>
 <dl class="section return"><dt>Returns</dt><dd>Value of the Jacobian matrix at (i, j).</dd></dl>
-<p>The Jacobian must have been generated by <a class="el" href="#a0a2fb3435ee3271ab9c806f225c61a7f" title="Generate the Jacobian matrix for the current state.">generateJacobianMatrix()</a> before calling this. </p>
+<p>The Jacobian must have been generated by <a class="el" href="#a29bdd4231c29c3a4e524ad6ca66a127d" title="Generate the Jacobian matrix for the current state.">generateJacobianMatrix()</a> before calling this. </p>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4710d218c8a0fd161e994ecd60b48e58">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a0ef8804780d13bbfce0856237bb00470">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4710d218c8a0fd161e994ecd60b48e58">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ac961484383e86d9712a424728e068633">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a1c888bbc0618f1ae02d9a53e45f3c159">PyDynamicEngine</a>.</p>
 
 </div>
 </div>
@@ -376,9 +470,9 @@ Public Member Functions</h2></td></tr>
 </div><div class="memdoc">
 
 <p>Get the set of logical reactions in the network. </p>
-<dl class="section return"><dt>Returns</dt><dd>Reference to the LogicalReactionSet containing all reactions. </dd></dl>
+<dl class="section return"><dt>Returns</dt><dd>Reference to the <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" title="A set of logical reactions.">LogicalReactionSet</a> containing all reactions. </dd></dl>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a12cc2f352678fba9688363ba1876ab9c">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a5bbea17b69cc8f81bc251a04f4435a0c">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a12cc2f352678fba9688363ba1876ab9c">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ad751f2c1306895ee74a61f2071ca96eb">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a5988cfba247631ba6c00795cafda9a38">PyDynamicEngine</a>.</p>
 
 </div>
 </div>
@@ -411,12 +505,12 @@ Public Member Functions</h2></td></tr>
 <div class="ttc" id="anamespacegridfire_1_1screening_html_aa82aafbc4f8c28d0a75b60798e3a7d25"><div class="ttname"><a href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">gridfire::screening::ScreeningType</a></div><div class="ttdeci">ScreeningType</div><div class="ttdoc">Enumerates the available plasma screening models.</div><div class="ttdef"><b>Definition</b> <a href="screening__types_8h_source.html#l00015">screening_types.h:15</a></div></div>
 </div><!-- fragment --> </dd></dl>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a0ab1199f900a58f309c3c36532c9164f">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#adbc50f397445f92b810d80cf329b8626">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a0ab1199f900a58f309c3c36532c9164f">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a7bfb4e6fec2f337a1dea69e3d4f1fc82">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#ab4cfdca5e15957c5cef75ffa6dedeee5">PyDynamicEngine</a>.</p>
 
 </div>
 </div>
-<a id="a5d8ba98b230d2849035ee2507728fa15" name="a5d8ba98b230d2849035ee2507728fa15"></a>
+<a id="a6ca0f315f75252ca505507a61556dda6" name="a6ca0f315f75252ca505507a61556dda6"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a5d8ba98b230d2849035ee2507728fa15">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a6ca0f315f75252ca505507a61556dda6">&#9670;&#160;</a></span>getSpeciesDestructionTimescales()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -425,7 +519,70 @@ Public Member Functions</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">virtual std::unordered_map&lt; fourdst::atomic::Species, double &gt; gridfire::DynamicEngine::getSpeciesTimescales </td>
+          <td class="memname">virtual std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::DynamicEngine::getSpeciesDestructionTimescales </td>
+          <td>(</td>
+          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel pure-virtual">pure virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a522e78bce9ff062939572248d57f8cea">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#aef8f6bde24d27345067b71084330c7da">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aa38c367ef3c74d012ccd10521cd5a727">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a020044829e0146427ed4830e5b02c4f3">PyDynamicEngine</a>.</p>
+
+</div>
+</div>
+<a id="ad3d56a8b9161b9cc7f4da51f6bf7e8c9" name="ad3d56a8b9161b9cc7f4da51f6bf7e8c9"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">&#9670;&#160;</a></span>getSpeciesIndex()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual int gridfire::DynamicEngine::getSpeciesIndex </td>
+          <td>(</td>
+          <td class="paramtype">const fourdst::atomic::Species &amp;</td>          <td class="paramname"><span class="paramname"><em>species</em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel pure-virtual">pure virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a9055feb245524a5a9549ace935f059ff">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a91d32b7197fcb27ee697d5bfde960f3f">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a2ee1d745c1c21b9fcb652c96c42f1091">PyDynamicEngine</a>.</p>
+
+</div>
+</div>
+<a id="a6772ac384b4c3d3e91712041e4aaa813" name="a6772ac384b4c3d3e91712041e4aaa813"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a6772ac384b4c3d3e91712041e4aaa813">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::DynamicEngine::getSpeciesTimescales </td>
           <td>(</td>
           <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
         </tr>
@@ -459,7 +616,7 @@ Public Member Functions</h2></td></tr>
 <dl class="section return"><dt>Returns</dt><dd>Map from Species to their characteristic timescales (s).</dd></dl>
 <p>This method estimates the timescale for abundance change of each species, which can be used for timestep control, diagnostics, and reaction network culling. </p>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a93b38d0fdc4647f6f7340172dae17872">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ace3c6ea4841318c08695973ab3dcddc6">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a26215593544c3a52597194602e4e25dd">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4e856d6d4d2fc220952bbb7e6b2f85d9">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a65f9f33cddb0bbd1da7c9d0cff23d581">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a560612347bbd5b7b380e990624d01105">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a02a4c86c9637a3c9c9ca8ddd82ecff22">PyDynamicEngine</a>.</p>
 
 </div>
 </div>
@@ -501,7 +658,148 @@ Public Member Functions</h2></td></tr>
 <dl class="section return"><dt>Returns</dt><dd>Stoichiometric coefficient for the species in the reaction.</dd></dl>
 <p>The stoichiometry matrix must have been generated by <a class="el" href="#aeae6d84ef74d88fd2cdf07b82e98a16f" title="Generate the stoichiometry matrix for the network.">generateStoichiometryMatrix()</a>. </p>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a67b4ea8cad115394bb4a42cc39d696f9">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a9da9224f5c99a5068f3d8cbf066e4693">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a67b4ea8cad115394bb4a42cc39d696f9">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a510b920dea726aef859ac1f6d051807e">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#ab48ef6db18da20024aa563a91fa16f83">PyDynamicEngine</a>.</p>
+
+</div>
+</div>
+<a id="a942e65ced17ca602482cc42e469d6398" name="a942e65ced17ca602482cc42e469d6398"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a942e65ced17ca602482cc42e469d6398">&#9670;&#160;</a></span>isStale()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual bool gridfire::DynamicEngine::isStale </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel pure-virtual">pure virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ad268c9942655e5c9605148fe07718e88">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a7d9e738dd28efb4d6127de7379169c87">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#af04a9f8a629d6f6c58c477af0f1ab9e5">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ae7847959fc5af2b83f5446dd73567b46">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a55bf19ed7534a312a36faf74753f7b14">PyDynamicEngine</a>.</p>
+
+</div>
+</div>
+<a id="a55f1b7e5ebe2840e1d7c54665ca5411a" name="a55f1b7e5ebe2840e1d7c54665ca5411a"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a55f1b7e5ebe2840e1d7c54665ca5411a">&#9670;&#160;</a></span>mapNetInToMolarAbundanceVector()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual std::vector&lt; double &gt; gridfire::DynamicEngine::mapNetInToMolarAbundanceVector </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel pure-virtual">pure virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d0237956bf3ec7230bc51d88e7f8019">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a27f3a928e1f6bbe7e847cffed6db729f">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aada497e8df74a295fdf5df7d7cdf64e0">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a61bb4b430fe740cfb2c24e5cc673e4ac">PyDynamicEngine</a>.</p>
+
+</div>
+</div>
+<a id="a21c34f59c080a853fafa38a25175124e" name="a21c34f59c080a853fafa38a25175124e"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a21c34f59c080a853fafa38a25175124e">&#9670;&#160;</a></span>primeEngine()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual <a class="el" href="structgridfire_1_1_priming_report.html">PrimingReport</a> gridfire::DynamicEngine::primeEngine </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel pure-virtual">pure virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a70005361262bc180d4417b608661e3c3">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a13033abd3b44904f98b58c93e22da460">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#ae7a371be61ab09b3fa4a93f05bd44e5e">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a05730ced13ac5331060ca011f0da6235">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#ac22a10412be6649bf379e6d61113c878">PyDynamicEngine</a>.</p>
+
+</div>
+</div>
+<a id="a4e2c8b896661b7a89beffe0066cb21cf" name="a4e2c8b896661b7a89beffe0066cb21cf"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a4e2c8b896661b7a89beffe0066cb21cf">&#9670;&#160;</a></span>rebuild()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual void gridfire::DynamicEngine::rebuild </td>
+          <td>(</td>
+          <td class="paramtype">const fourdst::composition::Composition &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a></td>          <td class="paramname"><span class="paramname"><em>depth</em></span>&#160;)</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Reimplemented in <a class="el" href="classgridfire_1_1_graph_engine.html#ad9d6c70ace5cbbf7f3aa7b31fce39490">gridfire::GraphEngine</a>, and <a class="el" href="class_py_dynamic_engine.html#a3d30a9116825ab2c5c209bc2712126bc">PyDynamicEngine</a>.</p>
+
+<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00309">309</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
+
+</div>
+</div>
+<a id="afb2ec904d88fc8aab516db4059d0e00f" name="afb2ec904d88fc8aab516db4059d0e00f"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#afb2ec904d88fc8aab516db4059d0e00f">&#9670;&#160;</a></span>setNetworkReactions()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual void gridfire::DynamicEngine::setNetworkReactions </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>reactions</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel pure-virtual">pure virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7b3a6b3ab0a52f0f84d2b142e74ea672">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a371ba0881d6903ddb2d586faa61805d0">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#acb5fa7f03cd89b8c1b6b9ffdf3abb12e">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#afd818c408c64d207e71b1a90426328d6">PyDynamicEngine</a>.</p>
 
 </div>
 </div>
@@ -541,12 +839,12 @@ Public Member Functions</h2></td></tr>
 </div><!-- fragment --></dd></dl>
 <dl class="section post"><dt>Postcondition</dt><dd>The engine will use the specified screening model for subsequent rate calculations. </dd></dl>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ad96bbee6d3d37b50d9236a975ef704c0">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1a0c0a0ade632eb10f0eecab828a059f">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#afa3abfd612033336a656f092721c14ac">PyDynamicEngine</a>.</p>
 
 </div>
 </div>
-<a id="acd500e1cd788df1dc105d28a20dc5f4f" name="acd500e1cd788df1dc105d28a20dc5f4f"></a>
+<a id="aa799ff785e7e79bf35b11efd55f6282a" name="aa799ff785e7e79bf35b11efd55f6282a"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#acd500e1cd788df1dc105d28a20dc5f4f">&#9670;&#160;</a></span>update()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#aa799ff785e7e79bf35b11efd55f6282a">&#9670;&#160;</a></span>update()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -555,7 +853,7 @@ Public Member Functions</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">virtual void gridfire::DynamicEngine::update </td>
+          <td class="memname">virtual fourdst::composition::Composition gridfire::DynamicEngine::update </td>
           <td>(</td>
           <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
           <td></td>
@@ -582,12 +880,12 @@ Public Member Functions</h2></td></tr>
 </div><!-- fragment --></dd></dl>
 <dl class="section post"><dt>Postcondition</dt><dd>The internal state of the engine is updated to reflect the new conditions. </dd></dl>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d61e73f5158f1574cda3edc90c51f7e">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ace3568eadaba69e7357b4386c5ca3eb0">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a51b4cedf9b00de79fb6eef243631b04d">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a2a7ecf985a326b4bea43e00cf9ee43dd">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a5ac7cff23e70bd07ba7e510b753e2ab6">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a6bee75b5a6e508e6eebf83f0d48c50b8">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#af8e6a8cd44f278535d7bcc9a896d6da8">PyDynamicEngine</a>.</p>
 
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following file:<ul>
-<li>src/network/include/gridfire/engine/<a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a></li>
+<li>src/include/gridfire/engine/<a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classgridfire_1_1_dynamic_engine.js

@@ -1,13 +1,22 @@
 var classgridfire_1_1_dynamic_engine =
 [
     [ "calculateMolarReactionFlow", "classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785", null ],
-    [ "generateJacobianMatrix", "classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f", null ],
+    [ "generateJacobianMatrix", "classgridfire_1_1_dynamic_engine.html#a29bdd4231c29c3a4e524ad6ca66a127d", null ],
+    [ "generateJacobianMatrix", "classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7", null ],
     [ "generateStoichiometryMatrix", "classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f", null ],
+    [ "getDepth", "classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9", null ],
     [ "getJacobianMatrixEntry", "classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07", null ],
     [ "getNetworkReactions", "classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037", null ],
     [ "getScreeningModel", "classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0", null ],
-    [ "getSpeciesTimescales", "classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15", null ],
+    [ "getSpeciesDestructionTimescales", "classgridfire_1_1_dynamic_engine.html#a6ca0f315f75252ca505507a61556dda6", null ],
+    [ "getSpeciesIndex", "classgridfire_1_1_dynamic_engine.html#ad3d56a8b9161b9cc7f4da51f6bf7e8c9", null ],
+    [ "getSpeciesTimescales", "classgridfire_1_1_dynamic_engine.html#a6772ac384b4c3d3e91712041e4aaa813", null ],
     [ "getStoichiometryMatrixEntry", "classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f", null ],
+    [ "isStale", "classgridfire_1_1_dynamic_engine.html#a942e65ced17ca602482cc42e469d6398", null ],
+    [ "mapNetInToMolarAbundanceVector", "classgridfire_1_1_dynamic_engine.html#a55f1b7e5ebe2840e1d7c54665ca5411a", null ],
+    [ "primeEngine", "classgridfire_1_1_dynamic_engine.html#a21c34f59c080a853fafa38a25175124e", null ],
+    [ "rebuild", "classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf", null ],
+    [ "setNetworkReactions", "classgridfire_1_1_dynamic_engine.html#afb2ec904d88fc8aab516db4059d0e00f", null ],
     [ "setScreeningModel", "classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd", null ],
-    [ "update", "classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f", null ]
+    [ "update", "classgridfire_1_1_dynamic_engine.html#aa799ff785e7e79bf35b11efd55f6282a", null ]
 ];

docs/html/classgridfire_1_1_engine-members.html

@@ -105,7 +105,7 @@ $(function(){initNavTree('classgridfire_1_1_engine.html',''); initResizable(true
 
 <p>This is the complete list of members for <a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a>, including all inherited members.</p>
 <table class="directory">
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">getNetworkSpecies</a>() const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 </table></div><!-- contents -->

docs/html/classgridfire_1_1_engine.html

@@ -116,10 +116,15 @@ Inheritance diagram for gridfire::Engine:</div>
  <div class="center">
   <img src="classgridfire_1_1_engine.png" usemap="#gridfire::Engine_map" alt=""/>
   <map id="gridfire::Engine_map" name="gridfire::Engine_map">
-<area href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations." alt="gridfire::DynamicEngine" shape="rect" coords="201,56,392,80"/>
+<area href="class_py_engine.html" alt="PyEngine" shape="rect" coords="0,56,246,80"/>
-<area href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions." alt="gridfire::AdaptiveEngineView" shape="rect" coords="0,112,191,136"/>
+<area href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations." alt="gridfire::DynamicEngine" shape="rect" coords="512,56,758,80"/>
-<area href="classgridfire_1_1_file_defined_engine_view.html" title="An engine view that uses a user-defined reaction network from a file." alt="gridfire::FileDefinedEngineView" shape="rect" coords="201,112,392,136"/>
+<area href="class_py_dynamic_engine.html" alt="PyDynamicEngine" shape="rect" coords="0,112,246,136"/>
-<area href="classgridfire_1_1_graph_engine.html" title="A reaction network engine that uses a graph-based representation." alt="gridfire::GraphEngine" shape="rect" coords="402,112,593,136"/>
+<area href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions." alt="gridfire::AdaptiveEngineView" shape="rect" coords="256,112,502,136"/>
+<area href="classgridfire_1_1_defined_engine_view.html" alt="gridfire::DefinedEngineView" shape="rect" coords="512,112,758,136"/>
+<area href="classgridfire_1_1_graph_engine.html" title="A reaction network engine that uses a graph-based representation." alt="gridfire::GraphEngine" shape="rect" coords="768,112,1014,136"/>
+<area href="classgridfire_1_1_multiscale_partitioning_engine_view.html" title="An engine view that partitions the reaction network into multiple groups based on timescales." alt="gridfire::MultiscalePartitioningEngineView" shape="rect" coords="1024,112,1270,136"/>
+<area href="classgridfire_1_1_file_defined_engine_view.html" alt="gridfire::FileDefinedEngineView" shape="rect" coords="384,168,630,192"/>
+<area href="classgridfire_1_1_network_priming_engine_view.html" title="Provides a view of a DynamicEngine filtered to reactions involving a specified priming species." alt="gridfire::NetworkPrimingEngineView" shape="rect" coords="640,168,886,192"/>
   </map>
 </div></div>
 <table class="memberdecls">
@@ -131,9 +136,9 @@ Public Member Functions</h2></td></tr>
 <tr class="memitem:a020e1b493d6964cafdad08fde697ceb3" id="r_a020e1b493d6964cafdad08fde697ceb3"><td class="memItemLeft" align="right" valign="top">virtual const std::vector&lt; fourdst::atomic::Species &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a020e1b493d6964cafdad08fde697ceb3">getNetworkSpecies</a> () const =0</td></tr>
 <tr class="memdesc:a020e1b493d6964cafdad08fde697ceb3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the list of species in the network.  <br /></td></tr>
 <tr class="separator:a020e1b493d6964cafdad08fde697ceb3"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:ac8b56124b6b49cd1802addb74a9a47c2" id="r_ac8b56124b6b49cd1802addb74a9a47c2"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ac8b56124b6b49cd1802addb74a9a47c2">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
+<tr class="memitem:a89f714d19b84a93a004a7afbb487a6cb" id="r_a89f714d19b84a93a004a7afbb487a6cb"><td class="memItemLeft" align="right" valign="top">virtual std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a89f714d19b84a93a004a7afbb487a6cb">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
-<tr class="memdesc:ac8b56124b6b49cd1802addb74a9a47c2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation.  <br /></td></tr>
+<tr class="memdesc:a89f714d19b84a93a004a7afbb487a6cb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation.  <br /></td></tr>
-<tr class="separator:ac8b56124b6b49cd1802addb74a9a47c2"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="separator:a89f714d19b84a93a004a7afbb487a6cb"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Abstract base class for a reaction network engine. </p>
@@ -142,9 +147,9 @@ Public Member Functions</h2></td></tr>
 <p>Example: </p><div class="fragment"><div class="line"><span class="keyword">class </span>MyEngine : <span class="keyword">public</span> <a class="code hl_class" href="classgridfire_1_1_engine.html">gridfire::Engine</a> {</div>
 <div class="line">    <span class="comment">// Implement required methods...</span></div>
 <div class="line">};</div>
-<div class="ttc" id="aclassgridfire_1_1_engine_html"><div class="ttname"><a href="classgridfire_1_1_engine.html">gridfire::Engine</a></div><div class="ttdoc">Abstract base class for a reaction network engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00075">engine_abstract.h:75</a></div></div>
+<div class="ttc" id="aclassgridfire_1_1_engine_html"><div class="ttname"><a href="classgridfire_1_1_engine.html">gridfire::Engine</a></div><div class="ttdoc">Abstract base class for a reaction network engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00084">engine_abstract.h:84</a></div></div>
 </div><!-- fragment --> 
-<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00075">75</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
+<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00084">84</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
 </div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
 <a id="a2e7970bed2100699f226f4141d5db037" name="a2e7970bed2100699f226f4141d5db037"></a>
 <h2 class="memtitle"><span class="permalink"><a href="#a2e7970bed2100699f226f4141d5db037">&#9670;&#160;</a></span>~Engine()</h2>
@@ -174,8 +179,8 @@ Public Member Functions</h2></td></tr>
 </div>
 </div>
 <h2 class="groupheader">Member Function Documentation</h2>
-<a id="ac8b56124b6b49cd1802addb74a9a47c2" name="ac8b56124b6b49cd1802addb74a9a47c2"></a>
+<a id="a89f714d19b84a93a004a7afbb487a6cb" name="a89f714d19b84a93a004a7afbb487a6cb"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#ac8b56124b6b49cd1802addb74a9a47c2">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a89f714d19b84a93a004a7afbb487a6cb">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -184,7 +189,7 @@ Public Member Functions</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">virtual <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt; gridfire::Engine::calculateRHSAndEnergy </td>
+          <td class="memname">virtual std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::Engine::calculateRHSAndEnergy </td>
           <td>(</td>
           <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
         </tr>
@@ -218,7 +223,7 @@ Public Member Functions</h2></td></tr>
 <dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives&lt;double&gt;</a> containing dY/dt and energy generation rate.</dd></dl>
 <p>This function must be implemented by derived classes to compute the time derivatives of all species and the specific nuclear energy generation rate for the current state. </p>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7b276b7210be588263395bdb0497fc6d">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a2c1d88b06568f9ea4c65e794d012ebfb">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a8b3baf29829c7ae0a61430ea70632bbf">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#af703ad17ea65ffff4b75bf8ccc00e5d5">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#aaed3743a52246b0f7bf03995e1c12081">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a716d7357e944e8394d8b8e0b5e7625eb">gridfire::MultiscalePartitioningEngineView</a>, <a class="el" href="class_py_dynamic_engine.html#a5b7f0cfe327c634ec125303256de8b9a">PyDynamicEngine</a>, and <a class="el" href="class_py_engine.html#a2f92602ecf210414b46838fc0a9ae26d">PyEngine</a>.</p>
 
 </div>
 </div>
@@ -248,12 +253,12 @@ Public Member Functions</h2></td></tr>
 <p>Get the list of species in the network. </p>
 <dl class="section return"><dt>Returns</dt><dd>Vector of Species objects representing all network species. </dd></dl>
 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac83a8efe25c0e5b9bf7756ac3a500bb1">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a8bb583e039b49608272997ed2d3387fa">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">gridfire::GraphEngine</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac83a8efe25c0e5b9bf7756ac3a500bb1">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a696f74f5135bbd62169b6577f92fee80">gridfire::MultiscalePartitioningEngineView</a>, <a class="el" href="class_py_dynamic_engine.html#afc745e7ab5da5d8b3cf916044515cd7d">PyDynamicEngine</a>, and <a class="el" href="class_py_engine.html#a2d240423899e039c2ca688e96f8af1f2">PyEngine</a>.</p>
 
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following file:<ul>
-<li>src/network/include/gridfire/engine/<a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a></li>
+<li>src/include/gridfire/engine/<a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classgridfire_1_1_engine.js

@@ -1,6 +1,6 @@
 var classgridfire_1_1_engine =
 [
     [ "~Engine", "classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037", null ],
-    [ "calculateRHSAndEnergy", "classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2", null ],
+    [ "calculateRHSAndEnergy", "classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb", null ],
     [ "getNetworkSpecies", "classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3", null ]
 ];

docs/html/classgridfire_1_1_engine_view.html

@@ -139,7 +139,7 @@ class gridfire::EngineView&lt; EngineT &gt;</div><p>Abstract base class for a "v
 <div class="line"><span class="keyword">private</span>:</div>
 <div class="line">    DynamicEngine&amp; engine_;</div>
 <div class="line">};</div>
-<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00121">engine_abstract.h:121</a></div></div>
+<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00130">engine_abstract.h:130</a></div></div>
 <div class="ttc" id="aclassgridfire_1_1_engine_view_html"><div class="ttname"><a href="classgridfire_1_1_engine_view.html">gridfire::EngineView</a></div><div class="ttdoc">Abstract base class for a &quot;view&quot; of a reaction network engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__view__abstract_8h_source.html#l00074">engine_view_abstract.h:74</a></div></div>
 <div class="ttc" id="aclassgridfire_1_1_engine_view_html_ad294227f8b5cf6d970c349eabf5447a6"><div class="ttname"><a href="#ad294227f8b5cf6d970c349eabf5447a6">gridfire::EngineView::getBaseEngine</a></div><div class="ttdeci">virtual const EngineT &amp; getBaseEngine() const =0</div><div class="ttdoc">Access the underlying engine instance.</div></div>
 </div><!-- fragment --><dl class="section see"><dt>See also</dt><dd><a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">gridfire::AdaptiveEngineView</a> for a concrete example of dynamic culling. </dd></dl>
@@ -206,12 +206,12 @@ template&lt;EngineType EngineT&gt; </div>
 <p>This method must be implemented by derived classes to provide access to the base engine. The returned reference should remain valid for the lifetime of the <a class="el" href="classgridfire_1_1_engine_view.html" title="Abstract base class for a &quot;view&quot; of a reaction network engine.">EngineView</a>.</p>
 <p>Example: </p><div class="fragment"><div class="line"><span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>&amp; engine = myView.getBaseEngine();</div>
 </div><!-- fragment --> 
-<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aee095b30a9dce5fcb5ae2fa1d2aa192c">gridfire::AdaptiveEngineView</a>, and <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a4c8b273c5cb3d470567c5691b68493a3">gridfire::FileDefinedEngineView</a>.</p>
+<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aee095b30a9dce5fcb5ae2fa1d2aa192c">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a69b9a5812ad8bda13f956acd0da24484">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a22bd1f0e821ed415611d75bac67063d1">gridfire::MultiscalePartitioningEngineView</a>, <a class="el" href="class_py_dynamic_engine_view.html#a51680b135cfc3eea40daf9ef5aa903e0">PyDynamicEngineView</a>, and <a class="el" href="class_py_engine_view.html#a3cd83dc57b521c65a14edf70357a8845">PyEngineView</a>.</p>
 
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following file:<ul>
-<li>src/network/include/gridfire/engine/views/<a class="el" href="engine__view__abstract_8h_source.html">engine_view_abstract.h</a></li>
+<li>src/include/gridfire/engine/views/<a class="el" href="engine__view__abstract_8h_source.html">engine_view_abstract.h</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classgridfire_1_1_file_defined_engine_view-members.html

@@ -105,43 +105,54 @@ $(function(){initNavTree('classgridfire_1_1_file_defined_engine_view.html','');
 
 <p>This is the complete list of members for <a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a>, including all inherited members.</p>
 <table class="directory">
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a3b5162b7be35405285ef9f825ec2663b">buildFromFile</a>(const std::string &amp;fileName)</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032">calculateMolarReactionFlow</a>(const reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ac371fb66fd0a76a04df204c9dd9a05ef">calculateMolarReactionFlow</a>(const reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a2c1d88b06568f9ea4c65e794d012ebfb">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e">collect</a>(const std::vector&lt; std::string &gt; &amp;peNames)</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a63f8f85e75ecaab6fa39d48d7a846187">Config</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#aebb3f3548f8781506f31580706810a4e">constructReactionIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ab2514984afaaf8590c28ab71943fbe68">constructReactionIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a51ba09ff01fdcac1125d42f276c9a0a7">constructSpeciesIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a9ea4812bc697fe43f8aded14f8aa0985">constructSpeciesIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd">FileDefinedEngineView</a>(DynamicEngine &amp;baseEngine, const std::string &amp;fileName, const io::NetworkFileParser &amp;parser)</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92">DefinedEngineView</a>(const std::vector&lt; std::string &gt; &amp;peNames, DynamicEngine &amp;baseEngine)</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a48b2451f96b8f5511ffc4071519c0810">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd">FileDefinedEngineView</a>(DynamicEngine &amp;baseEngine, const std::string &amp;fileName, const io::NetworkFileParser &amp;parser)</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a27a5163157cc15c4cb3b99a5d3564dbd">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a4c8b273c5cb3d470567c5691b68493a3">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">gridfire::DynamicEngine::generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const SparsityPattern &amp;sparsityPattern) const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a0ef8804780d13bbfce0856237bb00470">getJacobianMatrixEntry</a>(const int i_defined, const int j_defined) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a5bbea17b69cc8f81bc251a04f4435a0c">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a69b9a5812ad8bda13f956acd0da24484">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a8bb583e039b49608272997ed2d3387fa">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#adbc50f397445f92b810d80cf329b8626">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b">getJacobianMatrixEntry</a>(const int i_defined, const int j_defined) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ace3c6ea4841318c08695973ab3dcddc6">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ae0c35d8963b6ed05aeb88089ce301718">getNetworkFile</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a9da9224f5c99a5068f3d8cbf066e4693">getStoichiometryMatrixEntry</a>(const int speciesIndex_defined, const int reactionIndex_defined) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#aea834dc382ff1d663040db4532ea928f">getParser</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491">getSpeciesDestructionTimescales</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2">getStoichiometryMatrixEntry</a>(const int speciesIndex_defined, const int reactionIndex_defined) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a7d9e738dd28efb4d6127de7379169c87">isStale</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#acbb1a9bcb775e6d50de512a333afed08">LogManager</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ae012da2b1f6169cb13e6075a73353ab2">m_activeReactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965">m_activeReactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a299a0c61aa4f26029c770013c9feff5e">m_activeSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae">m_activeSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">m_baseEngine</a></td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195">m_baseEngine</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a7a80966c023ae722239491af58609362">m_config</a></td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a1b343998b93955025a589b2b4541e33b">m_fileName</a></td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a6e421bc748933be31bed9ff53f12b595">m_isStale</a></td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a217d541f3fa777b1552f652fbb520382">m_isStale</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500">m_parser</a></td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#af0a77a4749a15aae87bdecfccbd1736e">m_reactionIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd">m_reactionIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#aebd4a1a584f2784f1df3d503645be03b">m_speciesIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e">m_speciesIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a97e5ee4651dbe6754678fe96e4702fee">mapFullToView</a>(const std::vector&lt; double &gt; &amp;full) const</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a2f59af6fb3516911de2a3e3ff0ed8873">mapFullToView</a>(const std::vector&lt; double &gt; &amp;full) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#adba3c11b11a04b2907c1635210d73dee">mapViewToFull</a>(const std::vector&lt; double &gt; &amp;defined) const</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2">mapNetInToMolarAbundanceVector</a>(const NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a74217a1f8fd8e6daff969cb17885315c">mapViewToFullReactionIndex</a>(size_t definedReactionIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843">mapViewToFull</a>(const std::vector&lt; double &gt; &amp;defined) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#aa2373955ef5b0eabf7a57c7208e38bb1">mapViewToFullSpeciesIndex</a>(size_t definedSpeciesIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#aadf373d69a22fcd171a6c251466d53d1">mapViewToFullReactionIndex</a>(size_t definedReactionIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a92f14da849e99d07c1ff1347addb9263">setNetworkFile</a>(const std::string &amp;fileName)</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a">mapViewToFullSpeciesIndex</a>(size_t definedSpeciesIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ad96bbee6d3d37b50d9236a975ef704c0">setScreeningModel</a>(screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a13033abd3b44904f98b58c93e22da460">primeEngine</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ace3568eadaba69e7357b4386c5ca3eb0">update</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a>(const fourdst::composition::Composition &amp;comp, BuildDepthType depth)</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ae3f99002ab2c56a5bcdec00839f8628f">validateNetworkState</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">gridfire::FileDefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d">setNetworkReactions</a>(const reaction::LogicalReactionSet &amp;reactions) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258">setScreeningModel</a>(screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; DynamicEngine &gt;</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae">update</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0">validateNetworkState</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; DynamicEngine &gt;</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 </table></div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->

docs/html/classgridfire_1_1_file_defined_engine_view.js

@@ -3,36 +3,10 @@ var classgridfire_1_1_file_defined_engine_view =
     [ "Config", "classgridfire_1_1_file_defined_engine_view.html#a63f8f85e75ecaab6fa39d48d7a846187", null ],
     [ "LogManager", "classgridfire_1_1_file_defined_engine_view.html#acbb1a9bcb775e6d50de512a333afed08", null ],
     [ "FileDefinedEngineView", "classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd", null ],
-    [ "buildFromFile", "classgridfire_1_1_file_defined_engine_view.html#a3b5162b7be35405285ef9f825ec2663b", null ],
+    [ "getNetworkFile", "classgridfire_1_1_file_defined_engine_view.html#ae0c35d8963b6ed05aeb88089ce301718", null ],
-    [ "calculateMolarReactionFlow", "classgridfire_1_1_file_defined_engine_view.html#ac371fb66fd0a76a04df204c9dd9a05ef", null ],
+    [ "getParser", "classgridfire_1_1_file_defined_engine_view.html#aea834dc382ff1d663040db4532ea928f", null ],
-    [ "calculateRHSAndEnergy", "classgridfire_1_1_file_defined_engine_view.html#a2c1d88b06568f9ea4c65e794d012ebfb", null ],
-    [ "constructReactionIndexMap", "classgridfire_1_1_file_defined_engine_view.html#aebb3f3548f8781506f31580706810a4e", null ],
-    [ "constructSpeciesIndexMap", "classgridfire_1_1_file_defined_engine_view.html#a51ba09ff01fdcac1125d42f276c9a0a7", null ],
-    [ "generateJacobianMatrix", "classgridfire_1_1_file_defined_engine_view.html#a48b2451f96b8f5511ffc4071519c0810", null ],
-    [ "generateStoichiometryMatrix", "classgridfire_1_1_file_defined_engine_view.html#a27a5163157cc15c4cb3b99a5d3564dbd", null ],
-    [ "getBaseEngine", "classgridfire_1_1_file_defined_engine_view.html#a4c8b273c5cb3d470567c5691b68493a3", null ],
-    [ "getJacobianMatrixEntry", "classgridfire_1_1_file_defined_engine_view.html#a0ef8804780d13bbfce0856237bb00470", null ],
-    [ "getNetworkReactions", "classgridfire_1_1_file_defined_engine_view.html#a5bbea17b69cc8f81bc251a04f4435a0c", null ],
-    [ "getNetworkSpecies", "classgridfire_1_1_file_defined_engine_view.html#a8bb583e039b49608272997ed2d3387fa", null ],
-    [ "getScreeningModel", "classgridfire_1_1_file_defined_engine_view.html#adbc50f397445f92b810d80cf329b8626", null ],
-    [ "getSpeciesTimescales", "classgridfire_1_1_file_defined_engine_view.html#ace3c6ea4841318c08695973ab3dcddc6", null ],
-    [ "getStoichiometryMatrixEntry", "classgridfire_1_1_file_defined_engine_view.html#a9da9224f5c99a5068f3d8cbf066e4693", null ],
-    [ "mapFullToView", "classgridfire_1_1_file_defined_engine_view.html#a97e5ee4651dbe6754678fe96e4702fee", null ],
-    [ "mapViewToFull", "classgridfire_1_1_file_defined_engine_view.html#adba3c11b11a04b2907c1635210d73dee", null ],
-    [ "mapViewToFullReactionIndex", "classgridfire_1_1_file_defined_engine_view.html#a74217a1f8fd8e6daff969cb17885315c", null ],
-    [ "mapViewToFullSpeciesIndex", "classgridfire_1_1_file_defined_engine_view.html#aa2373955ef5b0eabf7a57c7208e38bb1", null ],
-    [ "setNetworkFile", "classgridfire_1_1_file_defined_engine_view.html#a92f14da849e99d07c1ff1347addb9263", null ],
-    [ "setScreeningModel", "classgridfire_1_1_file_defined_engine_view.html#ad96bbee6d3d37b50d9236a975ef704c0", null ],
-    [ "update", "classgridfire_1_1_file_defined_engine_view.html#ace3568eadaba69e7357b4386c5ca3eb0", null ],
-    [ "validateNetworkState", "classgridfire_1_1_file_defined_engine_view.html#ae3f99002ab2c56a5bcdec00839f8628f", null ],
-    [ "m_activeReactions", "classgridfire_1_1_file_defined_engine_view.html#ae012da2b1f6169cb13e6075a73353ab2", null ],
-    [ "m_activeSpecies", "classgridfire_1_1_file_defined_engine_view.html#a299a0c61aa4f26029c770013c9feff5e", null ],
-    [ "m_baseEngine", "classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81", null ],
     [ "m_config", "classgridfire_1_1_file_defined_engine_view.html#a7a80966c023ae722239491af58609362", null ],
     [ "m_fileName", "classgridfire_1_1_file_defined_engine_view.html#a1b343998b93955025a589b2b4541e33b", null ],
-    [ "m_isStale", "classgridfire_1_1_file_defined_engine_view.html#a6e421bc748933be31bed9ff53f12b595", null ],
     [ "m_logger", "classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432", null ],
-    [ "m_parser", "classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500", null ],
+    [ "m_parser", "classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500", null ]
-    [ "m_reactionIndexMap", "classgridfire_1_1_file_defined_engine_view.html#af0a77a4749a15aae87bdecfccbd1736e", null ],
-    [ "m_speciesIndexMap", "classgridfire_1_1_file_defined_engine_view.html#aebd4a1a584f2784f1df3d503645be03b", null ]
 ];

docs/html/classgridfire_1_1_graph_engine-members.html

@@ -108,50 +108,74 @@ $(function(){initNavTree('classgridfire_1_1_graph_engine.html',''); initResizabl
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives</a>(const std::vector&lt; T &gt; &amp;Y_in, T T9, T rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aaf4d54e4b774ab8ec8eabec006579d31">calculateAllDerivatives</a>(const std::vector&lt; double &gt; &amp;Y_in, const double T9, const double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a71a3d1181b90c3becdc5d9a3da05b9c9">calculateAllDerivatives</a>(const std::vector&lt; ADDouble &gt; &amp;Y_in, const ADDouble &amp;T9, const ADDouble &amp;rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a63639f4430d0889605c10839a6f32af9">calculateAllDerivativesUsingPrecomputation</a>(const std::vector&lt; double &gt; &amp;Y_in, const std::vector&lt; double &gt; &amp;bare_rates, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a97f98706b51fbe0d167ed81ffe58c438">calculateAllDerivativesUsingPrecomputation</a>(const std::vector&lt; double &gt; &amp;Y_in, const std::vector&lt; double &gt; &amp;bare_rates, const std::vector&lt; double &gt; &amp;bare_reverse_rates, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">calculateMolarReactionFlow</a>(const reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a5e96b5a0b34c8932f0e14eabda57f1a4">calculateMolarReactionFlow</a>(const reaction::Reaction &amp;reaction, const std::vector&lt; T &gt; &amp;Y, const T T9, const T rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a8b3baf29829c7ae0a61430ea70632bbf">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a17774cd9ffcf1ba94019df766a0984a0">calculateReverseMolarReactionFlow</a>(T T9, T rho, std::vector&lt; T &gt; screeningFactors, std::vector&lt; T &gt; Y, size_t reactionIndex, const reaction::LogicalReaction &amp;reaction) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa">collectNetworkSpecies</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28">calculateReverseRate</a>(const reaction::Reaction &amp;reaction, double T9) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95">exportToCSV</a>(const std::string &amp;filename) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755">calculateReverseRateTwoBody</a>(const reaction::Reaction &amp;reaction, const double T9, const double forwardRate, const double expFactor) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929">exportToDot</a>(const std::string &amp;filename) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#af28950c5af3a92eb03a1a64ed0f913e7">calculateReverseRateTwoBodyDerivative</a>(const reaction::Reaction &amp;reaction, const double T9, const double reverseRate) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ae347ff0316e532e0298ec8c913908105">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y, const double T9, const double rho) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aaed3743a52246b0f7bf03995e1c12081">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a29b338630c959449c15881935ac30746">collectAtomicReverseRateAtomicBases</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa">collectNetworkSpecies</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95">exportToCSV</a>(const std::string &amp;filename) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929">exportToDot</a>(const std::string &amp;filename) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a9687eef88c97eeb7f8680acb230f8ac1">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const SparsityPattern &amp;sparsityPattern) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c">getJacobianMatrixEntry</a>(const int i, const int j) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a166a5f4349580f9aa0b930afec73fcc4">getDepth</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">getNetReactionStoichiometry</a>(const reaction::Reaction &amp;reaction)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c">getJacobianMatrixEntry</a>(const int i, const int j) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">getNetReactionStoichiometry</a>(const reaction::Reaction &amp;reaction)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#add98ece49ec5c538bddf3cc77004fe44">getPartitionFunction</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a26215593544c3a52597194602e4e25dd">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aef8f6bde24d27345067b71084330c7da">getSpeciesDestructionTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a65f9f33cddb0bbd1da7c9d0cff23d581">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">getStoichiometryMatrixEntry</a>(const int speciesIndex, const int reactionIndex) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a9f74786ff930ab72664b31f29d05a30c">GraphEngine</a>(const fourdst::composition::Composition &amp;composition)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5">GraphEngine</a>(const fourdst::composition::Composition &amp;composition, const BuildDepthType=NetworkBuildDepth::Full)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a1e7e851dfa21d41c2dc533ba56fc4c7b">GraphEngine</a>(const reaction::LogicalReactionSet &amp;reactions)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a39d9838ed40bea71ee6c552bb5969026">GraphEngine</a>(const fourdst::composition::Composition &amp;composition, const partition::PartitionFunction &amp;partitionFunction, const BuildDepthType buildDepth=NetworkBuildDepth::Full)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b">involvesSpecies</a>(const fourdst::atomic::Species &amp;species) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a1e7e851dfa21d41c2dc533ba56fc4c7b">GraphEngine</a>(const reaction::LogicalReactionSet &amp;reactions)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f">isPrecomputationEnabled</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b">involvesSpecies</a>(const fourdst::atomic::Species &amp;species) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f">isPrecomputationEnabled</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#af04a9f8a629d6f6c58c477af0f1ab9e5">isStale</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ae7a210d9ab13ad5fb0c612f027acabd0">isUsingReverseReactions</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a816797b1d656d416844489692af44cf6">m_atomicReverseRates</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a3b17102b143435ddfdc015d7a50c4b18">m_config</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">m_constants</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01">m_depth</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a19b2eea0e8d05ac90f9fd7120bdc6e06">m_full_jacobian_sparsity_pattern</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a250cc6350dc052fbdfdf9a02066e7891">m_jac_work</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e">m_partitionFunction</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#af17cf3762abac3efcab9a8e87c961210">m_screeningModel</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80">m_screeningType</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de">m_usePrecomputation</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc">m_useReverseReactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a27f3a928e1f6bbe7e847cffed6db729f">mapNetInToMolarAbundanceVector</a>(const NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567">populateReactionIDMap</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391">populateSpeciesToIndexMap</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd">precomputeNetwork</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ae7a371be61ab09b3fa4a93f05bd44e5e">primeEngine</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ad9d6c70ace5cbbf7f3aa7b31fce39490">rebuild</a>(const fourdst::composition::Composition &amp;comp, const BuildDepthType depth) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889">recordADTape</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a5a5458ed01923124f2d7e1f04f32f138">reserveJacobianMatrix</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a8d0c0bd54a2908cff62dae7af0c149b5">reserveJacobianMatrix</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1">setPrecomputation</a>(bool precompute)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a371ba0881d6903ddb2d586faa61805d0">setNetworkReactions</a>(const reaction::LogicalReactionSet &amp;reactions) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">setScreeningModel</a>(screening::ScreeningType) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1">setPrecomputation</a>(bool precompute)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">setScreeningModel</a>(screening::ScreeningType) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197">setUseReverseReactions</a>(bool useReverse)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a51b4cedf9b00de79fb6eef243631b04d">update</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a5ac7cff23e70bd07ba7e510b753e2ab6">update</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aeeafeab40a5f4dbfae78bdc87e25e93f">validateComposition</a>(const fourdst::composition::Composition &amp;composition, double culling, double T9)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be">validateConservation</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>

docs/html/classgridfire_1_1_graph_engine.js

@@ -1,47 +1,71 @@
 var classgridfire_1_1_graph_engine =
 [
+    [ "AtomicReverseRate", "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html", "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate" ],
     [ "constants", "structgridfire_1_1_graph_engine_1_1constants.html", "structgridfire_1_1_graph_engine_1_1constants" ],
     [ "PrecomputedReaction", "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html", "structgridfire_1_1_graph_engine_1_1_precomputed_reaction" ],
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+    [ "GraphEngine", "classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5", null ],
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+    [ "setUseReverseReactions", "classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197", null ],
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     [ "validateConservation", "classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be", null ],
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     [ "m_constants", "classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e", null ],
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+    [ "m_jac_work", "classgridfire_1_1_graph_engine.html#a250cc6350dc052fbdfdf9a02066e7891", null ],
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     [ "m_networkSpeciesMap", "classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827", null ],
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docs/html/classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate-members.html

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+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>GridFire: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<script type="text/javascript" src="navtreedata.js"></script>
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+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
+ </tr>
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+</table>
+</div>
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+<script type="text/javascript">
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+/* @license-end */
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+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">gridfire::GraphEngine::AtomicReverseRate Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html">gridfire::GraphEngine::AtomicReverseRate</a>, including all inherited members.</p>
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+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#aec41632c2a362be33a1f7ff04204cbf4">for_sparse_jac</a>(size_t q, const CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;r, CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;s) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html">gridfire::GraphEngine::AtomicReverseRate</a></td><td class="entry"></td></tr>
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+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a75d355a0bef27217165644affd0cca4d">m_engine</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html">gridfire::GraphEngine::AtomicReverseRate</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a98ed8b450f7868f55e8362a848a4710d">m_reaction</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html">gridfire::GraphEngine::AtomicReverseRate</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a881d4daf2b973d523548cd8d4021bdc4">rev_sparse_jac</a>(size_t q, const CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;rt, CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;st) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html">gridfire::GraphEngine::AtomicReverseRate</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a4e8ff268c4377599c8798c7929ec2d5e">reverse</a>(size_t q, const CppAD::vector&lt; double &gt; &amp;tx, const CppAD::vector&lt; double &gt; &amp;ty, CppAD::vector&lt; double &gt; &amp;px, const CppAD::vector&lt; double &gt; &amp;py) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html">gridfire::GraphEngine::AtomicReverseRate</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
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docs/html/classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html

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+<meta name="viewport" content="width=device-width, initial-scale=1"/>
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+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
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+   <div id="projectbrief">General Purpose Nuclear Network</div>
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+/* @license-end */
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+</div>
+
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pri-attribs">Private Attributes</a> &#124;
+<a href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">gridfire::GraphEngine::AtomicReverseRate Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
+</div><!--header-->
+<div class="contents">
+<div class="dynheader">
+Inheritance diagram for gridfire::GraphEngine::AtomicReverseRate:</div>
+<div class="dyncontent">
+ <div class="center">
+  <img src="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.png" alt=""/>
+ </div></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a20d8e668f0af5fad5b7eda12564dc7cf" id="r_a20d8e668f0af5fad5b7eda12564dc7cf"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a20d8e668f0af5fad5b7eda12564dc7cf">AtomicReverseRate</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;reaction, const <a class="el" href="classgridfire_1_1_graph_engine.html">GraphEngine</a> &amp;engine)</td></tr>
+<tr class="separator:a20d8e668f0af5fad5b7eda12564dc7cf"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ad9b8dd0e8ba9c7745e33acc9a649d2e0" id="r_ad9b8dd0e8ba9c7745e33acc9a649d2e0"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad9b8dd0e8ba9c7745e33acc9a649d2e0">forward</a> (size_t p, size_t q, const CppAD::vector&lt; bool &gt; &amp;vx, CppAD::vector&lt; bool &gt; &amp;vy, const CppAD::vector&lt; double &gt; &amp;tx, CppAD::vector&lt; double &gt; &amp;ty) override</td></tr>
+<tr class="separator:ad9b8dd0e8ba9c7745e33acc9a649d2e0"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a4e8ff268c4377599c8798c7929ec2d5e" id="r_a4e8ff268c4377599c8798c7929ec2d5e"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a4e8ff268c4377599c8798c7929ec2d5e">reverse</a> (size_t q, const CppAD::vector&lt; double &gt; &amp;tx, const CppAD::vector&lt; double &gt; &amp;ty, CppAD::vector&lt; double &gt; &amp;px, const CppAD::vector&lt; double &gt; &amp;py) override</td></tr>
+<tr class="separator:a4e8ff268c4377599c8798c7929ec2d5e"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aec41632c2a362be33a1f7ff04204cbf4" id="r_aec41632c2a362be33a1f7ff04204cbf4"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aec41632c2a362be33a1f7ff04204cbf4">for_sparse_jac</a> (size_t q, const CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;r, CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;s) override</td></tr>
+<tr class="separator:aec41632c2a362be33a1f7ff04204cbf4"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a881d4daf2b973d523548cd8d4021bdc4" id="r_a881d4daf2b973d523548cd8d4021bdc4"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a881d4daf2b973d523548cd8d4021bdc4">rev_sparse_jac</a> (size_t q, const CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;rt, CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;st) override</td></tr>
+<tr class="separator:a881d4daf2b973d523548cd8d4021bdc4"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
+Private Attributes</h2></td></tr>
+<tr class="memitem:a98ed8b450f7868f55e8362a848a4710d" id="r_a98ed8b450f7868f55e8362a848a4710d"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a98ed8b450f7868f55e8362a848a4710d">m_reaction</a></td></tr>
+<tr class="separator:a98ed8b450f7868f55e8362a848a4710d"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a75d355a0bef27217165644affd0cca4d" id="r_a75d355a0bef27217165644affd0cca4d"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1_graph_engine.html">GraphEngine</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a75d355a0bef27217165644affd0cca4d">m_engine</a></td></tr>
+<tr class="separator:a75d355a0bef27217165644affd0cca4d"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00407">407</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
+</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
+<a id="a20d8e668f0af5fad5b7eda12564dc7cf" name="a20d8e668f0af5fad5b7eda12564dc7cf"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a20d8e668f0af5fad5b7eda12564dc7cf">&#9670;&#160;</a></span>AtomicReverseRate()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">gridfire::GraphEngine::AtomicReverseRate::AtomicReverseRate </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>reaction</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const <a class="el" href="classgridfire_1_1_graph_engine.html">GraphEngine</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>engine</em></span>&#160;)</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00409">409</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Function Documentation</h2>
+<a id="aec41632c2a362be33a1f7ff04204cbf4" name="aec41632c2a362be33a1f7ff04204cbf4"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#aec41632c2a362be33a1f7ff04204cbf4">&#9670;&#160;</a></span>for_sparse_jac()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool gridfire::GraphEngine::AtomicReverseRate::for_sparse_jac </td>
+          <td>(</td>
+          <td class="paramtype">size_t</td>          <td class="paramname"><span class="paramname"><em>q</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>r</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>s</em></span>&#160;)</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l01091">1091</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
+
+</div>
+</div>
+<a id="ad9b8dd0e8ba9c7745e33acc9a649d2e0" name="ad9b8dd0e8ba9c7745e33acc9a649d2e0"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ad9b8dd0e8ba9c7745e33acc9a649d2e0">&#9670;&#160;</a></span>forward()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool gridfire::GraphEngine::AtomicReverseRate::forward </td>
+          <td>(</td>
+          <td class="paramtype">size_t</td>          <td class="paramname"><span class="paramname"><em>p</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">size_t</td>          <td class="paramname"><span class="paramname"><em>q</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const CppAD::vector&lt; bool &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>vx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">CppAD::vector&lt; bool &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>vy</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const CppAD::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>tx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">CppAD::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>ty</em></span>&#160;)</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l01051">1051</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a881d4daf2b973d523548cd8d4021bdc4" name="a881d4daf2b973d523548cd8d4021bdc4"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a881d4daf2b973d523548cd8d4021bdc4">&#9670;&#160;</a></span>rev_sparse_jac()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool gridfire::GraphEngine::AtomicReverseRate::rev_sparse_jac </td>
+          <td>(</td>
+          <td class="paramtype">size_t</td>          <td class="paramname"><span class="paramname"><em>q</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>rt</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">CppAD::vector&lt; std::set&lt; size_t &gt; &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>st</em></span>&#160;)</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l01100">1100</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a4e8ff268c4377599c8798c7929ec2d5e" name="a4e8ff268c4377599c8798c7929ec2d5e"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a4e8ff268c4377599c8798c7929ec2d5e">&#9670;&#160;</a></span>reverse()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool gridfire::GraphEngine::AtomicReverseRate::reverse </td>
+          <td>(</td>
+          <td class="paramtype">size_t</td>          <td class="paramname"><span class="paramname"><em>q</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const CppAD::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>tx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const CppAD::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>ty</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">CppAD::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>px</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const CppAD::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>py</em></span>&#160;)</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l01073">1073</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Data Documentation</h2>
+<a id="a75d355a0bef27217165644affd0cca4d" name="a75d355a0bef27217165644affd0cca4d"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a75d355a0bef27217165644affd0cca4d">&#9670;&#160;</a></span>m_engine</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">const <a class="el" href="classgridfire_1_1_graph_engine.html">GraphEngine</a>&amp; gridfire::GraphEngine::AtomicReverseRate::m_engine</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00445">445</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
+
+</div>
+</div>
+<a id="a98ed8b450f7868f55e8362a848a4710d" name="a98ed8b450f7868f55e8362a848a4710d"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a98ed8b450f7868f55e8362a848a4710d">&#9670;&#160;</a></span>m_reaction</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a>&amp; gridfire::GraphEngine::AtomicReverseRate::m_reaction</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00444">444</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/include/gridfire/engine/<a class="el" href="engine__graph_8h_source.html">engine_graph.h</a></li>
+<li>src/lib/engine/<a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="namespacegridfire.html">gridfire</a></li><li class="navelem"><a class="el" href="classgridfire_1_1_graph_engine.html">GraphEngine</a></li><li class="navelem"><a class="el" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html">AtomicReverseRate</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/html/classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.js

@@ -0,0 +1,10 @@
+var classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate =
+[
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+    [ "for_sparse_jac", "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#aec41632c2a362be33a1f7ff04204cbf4", null ],
+    [ "forward", "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#ad9b8dd0e8ba9c7745e33acc9a649d2e0", null ],
+    [ "rev_sparse_jac", "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a881d4daf2b973d523548cd8d4021bdc4", null ],
+    [ "reverse", "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a4e8ff268c4377599c8798c7929ec2d5e", null ],
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docs/html/classgridfire_1_1_multiscale_partitioning_engine_view-members.html

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+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
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+  <div class="headertitle"><div class="title">gridfire::MultiscalePartitioningEngineView Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#af13e764c118a6cc51847384e9c70e05b">analyzeTimescalePoolConnectivity</a>(const std::vector&lt; std::vector&lt; size_t &gt; &gt; &amp;timescale_pools, const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aae0865e361dfeb23984d70409fdd9f39">buildConnectivityGraph</a>(const std::unordered_set&lt; size_t &gt; &amp;fast_reaction_indices) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ae3875c61dc916c0982ed122c2e272d94">buildConnectivityGraph</a>(const std::vector&lt; size_t &gt; &amp;species_pool) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a79eb9c108d694a27ec913ed0143aa044">calculateMolarReactionFlow</a>(const reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y_full, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a716d7357e944e8394d8b8e0b5e7625eb">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y_full, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ac206840057bac65b7f7738e6dfd1047a">constructCandidateGroups</a>(const std::vector&lt; std::vector&lt; size_t &gt; &gt; &amp;candidate_pools, const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a4bc879246c6fbd8633b05052858df51d">equilibrateNetwork</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b17f94386882ea1524147782b7a1ddc">equilibrateNetwork</a>(const NetIn &amp;netIn)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#acff59a15abac30eee16e9fa7b355fb18">exportToDot</a>(const std::string &amp;filename, const std::vector&lt; double &gt; &amp;Y, const double T9, const double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#acdf5ad8765290ea2b78170235aea391d">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_full, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">gridfire::DynamicEngine::generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const SparsityPattern &amp;sparsityPattern) const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#abe76a46784b1ebc8ad67a9eec40d369a">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a22bd1f0e821ed415611d75bac67063d1">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1e04e8cb8c84b1bd033ac599accf0888">getDynamicSpecies</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c82e4e082d1c82b1b090ac9847c7c5e">getFastSpecies</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ac961484383e86d9712a424728e068633">getJacobianMatrixEntry</a>(int i_full, int j_full) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ad751f2c1306895ee74a61f2071ca96eb">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a696f74f5135bbd62169b6577f92fee80">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a7bfb4e6fec2f337a1dea69e3d4f1fc82">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aa38c367ef3c74d012ccd10521cd5a727">getSpeciesDestructionTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a91d32b7197fcb27ee697d5bfde960f3f">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a560612347bbd5b7b380e990624d01105">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a510b920dea726aef859ac1f6d051807e">getStoichiometryMatrixEntry</a>(int speciesIndex, int reactionIndex) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a54ca8004fbd8d6d3ea6f67efeb5dbc8d">identifyMeanSlowestPool</a>(const std::vector&lt; std::vector&lt; size_t &gt; &gt; &amp;pools, const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ae7847959fc5af2b83f5446dd73567b46">isStale</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a445d7447f2cf18f755fc8b8b288e68cb">m_activeReactionIndices</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a57d97b11e80fa78ab5f509fce1f156b8">m_activeSpeciesIndices</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a4656c05b8235dbf4ec698b03a716a8c8">m_algebraic_species</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655">m_algebraic_species_indices</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93">m_baseEngine</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a">m_cacheStats</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aec6126b5c4a397d090790d7b75f9f70f">m_dynamic_species</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a38b4f0373c3bd81503889650c0bb69bb">m_dynamic_species_indices</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e">m_qse_abundance_cache</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b4aa04a1e641204e4fd82361b0e39c6">m_qse_groups</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aada497e8df74a295fdf5df7d7cdf64e0">mapNetInToMolarAbundanceVector</a>(const NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a0df457c0f0f6f403a295335c84fd828f">MultiscalePartitioningEngineView</a>(GraphEngine &amp;baseEngine)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ad4d29ee55f89384807616d1068797067">partitionByTimescale</a>(const std::vector&lt; double &gt; &amp;Y_full, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d26945df5395b9317552a3989c42d1c">partitionNetwork</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a98b11ffe498846f5a3a72f08504346b7">partitionNetwork</a>(const NetIn &amp;netIn)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a05730ced13ac5331060ca011f0da6235">primeEngine</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a34b5fdb2078e748edfbe6846ecadd681">QSEPartition</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a>(const fourdst::composition::Composition &amp;comp, BuildDepthType depth)</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#acb5fa7f03cd89b8c1b6b9ffdf3abb12e">setNetworkReactions</a>(const reaction::LogicalReactionSet &amp;reactions) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1a0c0a0ade632eb10f0eecab828a059f">setScreeningModel</a>(screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c5fcb8e3396d74359fd601554c9ffa9">solveQSEAbundances</a>(const std::vector&lt; double &gt; &amp;Y_full, double T9, double rho)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a6bee75b5a6e508e6eebf83f0d48c50b8">update</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aa55ed182301d216264daae3e6dfd8917">validateGroupsWithFluxAnalysis</a>(const std::vector&lt; QSEGroup &gt; &amp;candidate_groups, const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; DynamicEngine &gt;</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/html/classgridfire_1_1_multiscale_partitioning_engine_view.js

@@ -0,0 +1,53 @@
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+[
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+    [ "EigenFunctor", "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html", "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor" ],
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+    [ "QSEPartition", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a34b5fdb2078e748edfbe6846ecadd681", null ],
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+    [ "analyzeTimescalePoolConnectivity", "classgridfire_1_1_multiscale_partitioning_engine_view.html#af13e764c118a6cc51847384e9c70e05b", null ],
+    [ "buildConnectivityGraph", "classgridfire_1_1_multiscale_partitioning_engine_view.html#aae0865e361dfeb23984d70409fdd9f39", null ],
+    [ "buildConnectivityGraph", "classgridfire_1_1_multiscale_partitioning_engine_view.html#ae3875c61dc916c0982ed122c2e272d94", null ],
+    [ "calculateMolarReactionFlow", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a79eb9c108d694a27ec913ed0143aa044", null ],
+    [ "calculateRHSAndEnergy", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a716d7357e944e8394d8b8e0b5e7625eb", null ],
+    [ "constructCandidateGroups", "classgridfire_1_1_multiscale_partitioning_engine_view.html#ac206840057bac65b7f7738e6dfd1047a", null ],
+    [ "equilibrateNetwork", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b17f94386882ea1524147782b7a1ddc", null ],
+    [ "equilibrateNetwork", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4bc879246c6fbd8633b05052858df51d", null ],
+    [ "exportToDot", "classgridfire_1_1_multiscale_partitioning_engine_view.html#acff59a15abac30eee16e9fa7b355fb18", null ],
+    [ "generateJacobianMatrix", "classgridfire_1_1_multiscale_partitioning_engine_view.html#acdf5ad8765290ea2b78170235aea391d", null ],
+    [ "generateStoichiometryMatrix", "classgridfire_1_1_multiscale_partitioning_engine_view.html#abe76a46784b1ebc8ad67a9eec40d369a", null ],
+    [ "getBaseEngine", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a22bd1f0e821ed415611d75bac67063d1", null ],
+    [ "getDynamicSpecies", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1e04e8cb8c84b1bd033ac599accf0888", null ],
+    [ "getFastSpecies", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c82e4e082d1c82b1b090ac9847c7c5e", null ],
+    [ "getJacobianMatrixEntry", "classgridfire_1_1_multiscale_partitioning_engine_view.html#ac961484383e86d9712a424728e068633", null ],
+    [ "getNetworkReactions", "classgridfire_1_1_multiscale_partitioning_engine_view.html#ad751f2c1306895ee74a61f2071ca96eb", null ],
+    [ "getNetworkSpecies", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a696f74f5135bbd62169b6577f92fee80", null ],
+    [ "getScreeningModel", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7bfb4e6fec2f337a1dea69e3d4f1fc82", null ],
+    [ "getSpeciesDestructionTimescales", "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa38c367ef3c74d012ccd10521cd5a727", null ],
+    [ "getSpeciesIndex", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a91d32b7197fcb27ee697d5bfde960f3f", null ],
+    [ "getSpeciesTimescales", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a560612347bbd5b7b380e990624d01105", null ],
+    [ "getStoichiometryMatrixEntry", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a510b920dea726aef859ac1f6d051807e", null ],
+    [ "identifyMeanSlowestPool", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a54ca8004fbd8d6d3ea6f67efeb5dbc8d", null ],
+    [ "isStale", "classgridfire_1_1_multiscale_partitioning_engine_view.html#ae7847959fc5af2b83f5446dd73567b46", null ],
+    [ "mapNetInToMolarAbundanceVector", "classgridfire_1_1_multiscale_partitioning_engine_view.html#aada497e8df74a295fdf5df7d7cdf64e0", null ],
+    [ "partitionByTimescale", "classgridfire_1_1_multiscale_partitioning_engine_view.html#ad4d29ee55f89384807616d1068797067", null ],
+    [ "partitionNetwork", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a98b11ffe498846f5a3a72f08504346b7", null ],
+    [ "partitionNetwork", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d26945df5395b9317552a3989c42d1c", null ],
+    [ "primeEngine", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a05730ced13ac5331060ca011f0da6235", null ],
+    [ "setNetworkReactions", "classgridfire_1_1_multiscale_partitioning_engine_view.html#acb5fa7f03cd89b8c1b6b9ffdf3abb12e", null ],
+    [ "setScreeningModel", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1a0c0a0ade632eb10f0eecab828a059f", null ],
+    [ "solveQSEAbundances", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c5fcb8e3396d74359fd601554c9ffa9", null ],
+    [ "update", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a6bee75b5a6e508e6eebf83f0d48c50b8", null ],
+    [ "validateGroupsWithFluxAnalysis", "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa55ed182301d216264daae3e6dfd8917", null ],
+    [ "m_activeReactionIndices", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a445d7447f2cf18f755fc8b8b288e68cb", null ],
+    [ "m_activeSpeciesIndices", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a57d97b11e80fa78ab5f509fce1f156b8", null ],
+    [ "m_algebraic_species", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4656c05b8235dbf4ec698b03a716a8c8", null ],
+    [ "m_algebraic_species_indices", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655", null ],
+    [ "m_baseEngine", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93", null ],
+    [ "m_cacheStats", "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a", null ],
+    [ "m_dynamic_species", "classgridfire_1_1_multiscale_partitioning_engine_view.html#aec6126b5c4a397d090790d7b75f9f70f", null ],
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+    [ "m_logger", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a", null ],
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+    [ "m_qse_groups", "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b4aa04a1e641204e4fd82361b0e39c6", null ]
+];

docs/html/classgridfire_1_1_network.html

@@ -509,8 +509,8 @@ Protected Attributes</h2></td></tr>
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>src/network/include/gridfire/<a class="el" href="network_8h_source.html">network.h</a></li>
+<li>src/include/gridfire/<a class="el" href="network_8h_source.html">network.h</a></li>
-<li>src/network/lib/<a class="el" href="network_8cpp_source.html">network.cpp</a></li>
+<li>src/lib/<a class="el" href="network_8cpp_source.html">network.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classgridfire_1_1_network_priming_engine_view-members.html

@@ -0,0 +1,161 @@
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+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=11"/>
+<meta name="generator" content="Doxygen 1.13.2"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>GridFire: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<script type="text/javascript" src="clipboard.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="navtreedata.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="cookie.js"></script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/searchdata.js"></script>
+<script type="text/javascript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+/* @license-end */
+</script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+       class="ui-resizable-handle">
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+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function(){initNavTree('classgridfire_1_1_network_priming_engine_view.html',''); initResizable(true); });
+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
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+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+</div>
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+<!-- iframe showing the search results (closed by default) -->
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+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">gridfire::NetworkPrimingEngineView Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="classgridfire_1_1_network_priming_engine_view.html">gridfire::NetworkPrimingEngineView</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032">calculateMolarReactionFlow</a>(const reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e">collect</a>(const std::vector&lt; std::string &gt; &amp;peNames)</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_network_priming_engine_view.html#a91f60d8a6bd92dc5d5f6fcda8e89408f">constructPrimingReactionSet</a>(const fourdst::atomic::Species &amp;primingSpecies, const DynamicEngine &amp;baseEngine) const</td><td class="entry"><a class="el" href="classgridfire_1_1_network_priming_engine_view.html">gridfire::NetworkPrimingEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ab2514984afaaf8590c28ab71943fbe68">constructReactionIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a9ea4812bc697fe43f8aded14f8aa0985">constructSpeciesIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92">DefinedEngineView</a>(const std::vector&lt; std::string &gt; &amp;peNames, DynamicEngine &amp;baseEngine)</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">gridfire::DynamicEngine::generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const SparsityPattern &amp;sparsityPattern) const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a69b9a5812ad8bda13f956acd0da24484">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b">getJacobianMatrixEntry</a>(const int i_defined, const int j_defined) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491">getSpeciesDestructionTimescales</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2">getStoichiometryMatrixEntry</a>(const int speciesIndex_defined, const int reactionIndex_defined) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a7d9e738dd28efb4d6127de7379169c87">isStale</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965">m_activeReactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae">m_activeSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195">m_baseEngine</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a217d541f3fa777b1552f652fbb520382">m_isStale</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_network_priming_engine_view.html#a1eed366e916c4e9b7847ae52836f3c7d">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_network_priming_engine_view.html">gridfire::NetworkPrimingEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_network_priming_engine_view.html#aeb8f25d97e2459037cc999b974823cf5">m_primingSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_network_priming_engine_view.html">gridfire::NetworkPrimingEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd">m_reactionIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e">m_speciesIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a2f59af6fb3516911de2a3e3ff0ed8873">mapFullToView</a>(const std::vector&lt; double &gt; &amp;full) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2">mapNetInToMolarAbundanceVector</a>(const NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843">mapViewToFull</a>(const std::vector&lt; double &gt; &amp;defined) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#aadf373d69a22fcd171a6c251466d53d1">mapViewToFullReactionIndex</a>(size_t definedReactionIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a">mapViewToFullSpeciesIndex</a>(size_t definedSpeciesIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_network_priming_engine_view.html#ad13ec8d4974421c72cffd88558d71177">NetworkPrimingEngineView</a>(const std::string &amp;primingSymbol, DynamicEngine &amp;baseEngine)</td><td class="entry"><a class="el" href="classgridfire_1_1_network_priming_engine_view.html">gridfire::NetworkPrimingEngineView</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_network_priming_engine_view.html#a96751b66dd11f1155d0c488f39f9f6a6">NetworkPrimingEngineView</a>(const fourdst::atomic::Species &amp;primingSpecies, DynamicEngine &amp;baseEngine)</td><td class="entry"><a class="el" href="classgridfire_1_1_network_priming_engine_view.html">gridfire::NetworkPrimingEngineView</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a13033abd3b44904f98b58c93e22da460">primeEngine</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a>(const fourdst::composition::Composition &amp;comp, BuildDepthType depth)</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d">setNetworkReactions</a>(const reaction::LogicalReactionSet &amp;reactions) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258">setScreeningModel</a>(screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae">update</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0">validateNetworkState</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; DynamicEngine &gt;</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
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+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pri-methods">Private Member Functions</a> &#124;
+<a href="#pri-attribs">Private Attributes</a> &#124;
+<a href="classgridfire_1_1_network_priming_engine_view-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">gridfire::NetworkPrimingEngineView Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>Provides a view of a <a class="el" href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> filtered to reactions involving a specified priming species.  
+ <a href="#details">More...</a></p>
+
+<p><code>#include &lt;<a class="el" href="engine__priming_8h_source.html">engine_priming.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for gridfire::NetworkPrimingEngineView:</div>
+<div class="dyncontent">
+ <div class="center">
+  <img src="classgridfire_1_1_network_priming_engine_view.png" usemap="#gridfire::NetworkPrimingEngineView_map" alt=""/>
+  <map id="gridfire::NetworkPrimingEngineView_map" name="gridfire::NetworkPrimingEngineView_map">
+<area href="classgridfire_1_1_defined_engine_view.html" alt="gridfire::DefinedEngineView" shape="rect" coords="124,112,362,136"/>
+<area href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations." alt="gridfire::DynamicEngine" shape="rect" coords="0,56,238,80"/>
+<area href="classgridfire_1_1_engine_view.html" alt="gridfire::EngineView&lt; DynamicEngine &gt;" shape="rect" coords="248,56,486,80"/>
+<area href="classgridfire_1_1_engine.html" title="Abstract base class for a reaction network engine." alt="gridfire::Engine" shape="rect" coords="0,0,238,24"/>
+  </map>
+</div></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:ad13ec8d4974421c72cffd88558d71177" id="r_ad13ec8d4974421c72cffd88558d71177"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad13ec8d4974421c72cffd88558d71177">NetworkPrimingEngineView</a> (const std::string &amp;primingSymbol, <a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;baseEngine)</td></tr>
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+<tr class="separator:a4e2c8b896661b7a89beffe0066cb21cf inherit pub_methods_classgridfire_1_1_dynamic_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="inherit_header pub_methods_classgridfire_1_1_engine"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td></tr>
+<tr class="memitem:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" id="r_a2e7970bed2100699f226f4141d5db037"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a> ()=default</td></tr>
+<tr class="memdesc:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor.  <br /></td></tr>
+<tr class="separator:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="inherit_header pub_methods_classgridfire_1_1_engine_view"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine_view')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; DynamicEngine &gt;</a></td></tr>
+<tr class="memitem:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view" id="r_a994660f2d553f3a123512dc5eb421e74"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a> ()=default</td></tr>
+<tr class="memdesc:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor.  <br /></td></tr>
+<tr class="separator:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
+Private Member Functions</h2></td></tr>
+<tr class="memitem:a91f60d8a6bd92dc5d5f6fcda8e89408f" id="r_a91f60d8a6bd92dc5d5f6fcda8e89408f"><td class="memItemLeft" align="right" valign="top">std::vector&lt; std::string &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a91f60d8a6bd92dc5d5f6fcda8e89408f">constructPrimingReactionSet</a> (const fourdst::atomic::Species &amp;primingSpecies, const <a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;baseEngine) const</td></tr>
+<tr class="memdesc:a91f60d8a6bd92dc5d5f6fcda8e89408f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructs the set of reaction names that involve the priming species.  <br /></td></tr>
+<tr class="separator:a91f60d8a6bd92dc5d5f6fcda8e89408f"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
+Private Attributes</h2></td></tr>
+<tr class="memitem:a1eed366e916c4e9b7847ae52836f3c7d" id="r_a1eed366e916c4e9b7847ae52836f3c7d"><td class="memItemLeft" align="right" valign="top">quill::Logger *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a1eed366e916c4e9b7847ae52836f3c7d">m_logger</a> = fourdst::logging::LogManager::getInstance().getLogger(&quot;log&quot;)</td></tr>
+<tr class="separator:a1eed366e916c4e9b7847ae52836f3c7d"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aeb8f25d97e2459037cc999b974823cf5" id="r_aeb8f25d97e2459037cc999b974823cf5"><td class="memItemLeft" align="right" valign="top">fourdst::atomic::Species&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aeb8f25d97e2459037cc999b974823cf5">m_primingSpecies</a></td></tr>
+<tr class="memdesc:aeb8f25d97e2459037cc999b974823cf5"><td class="mdescLeft">&#160;</td><td class="mdescRight">The priming species, if specified.  <br /></td></tr>
+<tr class="separator:aeb8f25d97e2459037cc999b974823cf5"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="inherited" name="inherited"></a>
+Additional Inherited Members</h2></td></tr>
+<tr class="inherit_header pro_attribs_classgridfire_1_1_defined_engine_view"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pro_attribs_classgridfire_1_1_defined_engine_view')"><img src="closed.png" alt="-"/>&#160;Protected Attributes inherited from <a class="el" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></td></tr>
+<tr class="memitem:a217d541f3fa777b1552f652fbb520382 inherit pro_attribs_classgridfire_1_1_defined_engine_view" id="r_a217d541f3fa777b1552f652fbb520382"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a217d541f3fa777b1552f652fbb520382">m_isStale</a> = true</td></tr>
+<tr class="separator:a217d541f3fa777b1552f652fbb520382 inherit pro_attribs_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a6e3243a8a8bcdce3282a8f82c5f98195 inherit pro_attribs_classgridfire_1_1_defined_engine_view" id="r_a6e3243a8a8bcdce3282a8f82c5f98195"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195">m_baseEngine</a></td></tr>
+<tr class="separator:a6e3243a8a8bcdce3282a8f82c5f98195 inherit pro_attribs_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><p>Provides a view of a <a class="el" href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> filtered to reactions involving a specified priming species. </p>
+<p>This view constructs a subset of the network reactions from the base engine that contain the given priming species and delegates all engine operations to the underlying engine.</p>
+<p>See implementation in <a class="el" href="engine__priming_8cpp.html">engine_priming.cpp</a> for details on reaction set construction.</p>
+<dl class="section note"><dt>Note</dt><dd>Throws std::runtime_error if no priming reactions are found for the species. </dd></dl>
+
+<p class="definition">Definition at line <a class="el" href="engine__priming_8h_source.html#l00030">30</a> of file <a class="el" href="engine__priming_8h_source.html">engine_priming.h</a>.</p>
+</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
+<a id="ad13ec8d4974421c72cffd88558d71177" name="ad13ec8d4974421c72cffd88558d71177"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ad13ec8d4974421c72cffd88558d71177">&#9670;&#160;</a></span>NetworkPrimingEngineView() <span class="overload">[1/2]</span></h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">gridfire::NetworkPrimingEngineView::NetworkPrimingEngineView </td>
+          <td>(</td>
+          <td class="paramtype">const std::string &amp;</td>          <td class="paramname"><span class="paramname"><em>primingSymbol</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>baseEngine</em></span>&#160;)</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Constructs the view by looking up the priming species by symbol. </p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">primingSymbol</td><td>Symbol string of the species to prime. </td></tr>
+    <tr><td class="paramname">baseEngine</td><td>Reference to the base <a class="el" href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> to wrap. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section pre"><dt>Precondition</dt><dd>primingSymbol must correspond to a valid species in atomic::species registry. </dd></dl>
+<dl class="section post"><dt>Postcondition</dt><dd>The view will contain only reactions that involve the priming species. </dd></dl>
+<dl class="exception"><dt>Exceptions</dt><dd>
+  <table class="exception">
+    <tr><td class="paramname">std::out_of_range</td><td>If primingSymbol is not found in the species registry. </td></tr>
+    <tr><td class="paramname">std::runtime_error</td><td>If no reactions contain the priming species. </td></tr>
+  </table>
+  </dd>
+</dl>
+
+<p class="definition">Definition at line <a class="el" href="engine__priming_8cpp_source.html#l00023">23</a> of file <a class="el" href="engine__priming_8cpp_source.html">engine_priming.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a96751b66dd11f1155d0c488f39f9f6a6" name="a96751b66dd11f1155d0c488f39f9f6a6"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a96751b66dd11f1155d0c488f39f9f6a6">&#9670;&#160;</a></span>NetworkPrimingEngineView() <span class="overload">[2/2]</span></h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">gridfire::NetworkPrimingEngineView::NetworkPrimingEngineView </td>
+          <td>(</td>
+          <td class="paramtype">const fourdst::atomic::Species &amp;</td>          <td class="paramname"><span class="paramname"><em>primingSpecies</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>baseEngine</em></span>&#160;)</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Constructs the view using an existing Species object. </p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">primingSpecies</td><td>The species object to prime. </td></tr>
+    <tr><td class="paramname">baseEngine</td><td>Reference to the base <a class="el" href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> to wrap. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section pre"><dt>Precondition</dt><dd>primingSpecies must be valid and present in the network of baseEngine. </dd></dl>
+<dl class="section post"><dt>Postcondition</dt><dd>The view will contain only reactions that involve the priming species. </dd></dl>
+<dl class="exception"><dt>Exceptions</dt><dd>
+  <table class="exception">
+    <tr><td class="paramname">std::runtime_error</td><td>If no reactions contain the priming species. </td></tr>
+  </table>
+  </dd>
+</dl>
+
+<p class="definition">Definition at line <a class="el" href="engine__priming_8cpp_source.html#l00036">36</a> of file <a class="el" href="engine__priming_8cpp_source.html">engine_priming.cpp</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Function Documentation</h2>
+<a id="a91f60d8a6bd92dc5d5f6fcda8e89408f" name="a91f60d8a6bd92dc5d5f6fcda8e89408f"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a91f60d8a6bd92dc5d5f6fcda8e89408f">&#9670;&#160;</a></span>constructPrimingReactionSet()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::vector&lt; std::string &gt; gridfire::NetworkPrimingEngineView::constructPrimingReactionSet </td>
+          <td>(</td>
+          <td class="paramtype">const fourdst::atomic::Species &amp;</td>          <td class="paramname"><span class="paramname"><em>primingSpecies</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const <a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>baseEngine</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Constructs the set of reaction names that involve the priming species. </p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">primingSpecies</td><td>Species for which to collect priming reactions. </td></tr>
+    <tr><td class="paramname">baseEngine</td><td>Base engine containing the full network of reactions. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section pre"><dt>Precondition</dt><dd>baseEngine.getNetworkReactions() returns a valid iterable set of reactions. </dd></dl>
+<dl class="section post"><dt>Postcondition</dt><dd>Returns a vector of unique reaction name strings containing the priming species. </dd></dl>
+<dl class="section return"><dt>Returns</dt><dd>Vector of reaction name strings containing the priming species. </dd></dl>
+<dl class="exception"><dt>Exceptions</dt><dd>
+  <table class="exception">
+    <tr><td class="paramname">std::runtime_error</td><td>If no reactions involve the priming species. </td></tr>
+  </table>
+  </dd>
+</dl>
+
+<p class="definition">Definition at line <a class="el" href="engine__priming_8cpp_source.html#l00051">51</a> of file <a class="el" href="engine__priming_8cpp_source.html">engine_priming.cpp</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Data Documentation</h2>
+<a id="a1eed366e916c4e9b7847ae52836f3c7d" name="a1eed366e916c4e9b7847ae52836f3c7d"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a1eed366e916c4e9b7847ae52836f3c7d">&#9670;&#160;</a></span>m_logger</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">quill::Logger* gridfire::NetworkPrimingEngineView::m_logger = fourdst::logging::LogManager::getInstance().getLogger(&quot;log&quot;)</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="engine__priming_8h_source.html#l00056">56</a> of file <a class="el" href="engine__priming_8h_source.html">engine_priming.h</a>.</p>
+
+</div>
+</div>
+<a id="aeb8f25d97e2459037cc999b974823cf5" name="aeb8f25d97e2459037cc999b974823cf5"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#aeb8f25d97e2459037cc999b974823cf5">&#9670;&#160;</a></span>m_primingSpecies</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">fourdst::atomic::Species gridfire::NetworkPrimingEngineView::m_primingSpecies</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>The priming species, if specified. </p>
+
+<p class="definition">Definition at line <a class="el" href="engine__priming_8h_source.html#l00057">57</a> of file <a class="el" href="engine__priming_8h_source.html">engine_priming.h</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/include/gridfire/engine/views/<a class="el" href="engine__priming_8h_source.html">engine_priming.h</a></li>
+<li>src/lib/engine/views/<a class="el" href="engine__priming_8cpp_source.html">engine_priming.cpp</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
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+  <ul>
+    <li class="navelem"><a class="el" href="namespacegridfire.html">gridfire</a></li><li class="navelem"><a class="el" href="classgridfire_1_1_network_priming_engine_view.html">NetworkPrimingEngineView</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
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+    [ "NetworkPrimingEngineView", "classgridfire_1_1_network_priming_engine_view.html#a96751b66dd11f1155d0c488f39f9f6a6", null ],
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+   <div id="projectbrief">General Purpose Nuclear Network</div>
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+<div class="header">
+  <div class="headertitle"><div class="title">gridfire::Reaction Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a7dc8fda87e0581fde6da0a81cf4d7224">all_species</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a3a8ba9212d76d5ce51f20df6892c6061">calculate_forward_rate_log_derivative</a>(const double T9) const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#ad81e9b2a1773470059ca6989c60556ec">calculate_rate</a>(const double T9) const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a735192a42f72cd68f289493753e1a616">calculate_rate</a>(const CppAD::AD&lt; double &gt; T9) const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a648b9ed6108bed2469dc028fb7e351af">calculate_rate</a>(const T T9) const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a5cb438adfefb640e4bc58e09053bd629">chapter</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#ab92785f331a446e51a0960b75d60b37b">contains</a>(const fourdst::atomic::Species &amp;species) const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a074d3cd2421fd5d0133e47f0522403e2">contains_product</a>(const fourdst::atomic::Species &amp;species) const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#abbe243affa61ba9b2cd2a7b905cd5e45">contains_reactant</a>(const fourdst::atomic::Species &amp;species) const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#aa1d71e38fc55ae691dbb9ec459a612a5">excess_energy</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#af6c20e6d03a2d9f87632f71a90b88cb5">hash</a>(uint64_t seed=0) const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a084c38181408ed5e6fa2a2dd4d0ec905">id</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#aa67d05dfabf007c1acad34052d9a1dba">is_reverse</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a16f9cbb6269817099d3dc07d4e63da7b">m_chapter</a></td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a5c685e5a736b51799e5b9f6746c4126b">m_id</a></td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a7044d0a1d59d85502ce554e4ec2167e4">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a6124aa9fc2306349e1dd879a37923248">m_peName</a></td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a4b5607ed413acdf29539b8a57461e49e">m_products</a></td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a59122a2898bb9af640cc3e9aeb49028b">m_qValue</a></td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#aa61a9a024d7c4ff66a351ccd0277ec72">m_rateCoefficients</a></td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a87a065b3c7806bcdb5eadb7de2978a11">m_reactants</a></td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a0b0b9ac498080aae91ffd466d1ae85a9">m_reverse</a></td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a0185c6be5465d113f25e00aee1297cd6">m_sourceLabel</a></td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a1d3c8ab6d55155f9a21ad80ed8b9ef97">num_species</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a2f1c115a99bc7c477a2e858ff18b1b51">operator!=</a>(const Reaction &amp;other) const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a2b05ab608187216fc751bd2e42e8b7d8">operator&lt;&lt;</a>(std::ostream &amp;os, const Reaction &amp;r)</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#ac426457cf0a54a15b206549422083bac">operator==</a>(const Reaction &amp;other) const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a78f42664cc957e266b6cf15fda09be97">peName</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a01c67726efbaa2ff8e4d6f2c965f485c">product_species</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a6e2ff61b9e8409f2a561663628b8ce02">products</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#abda0b4e4313e6d4ba57acf37d5976fb8">qValue</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a85968076e686e67763f4fdf4f72a892e">rateCoefficients</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a855ea65e4b62fb0cddc550424a4bc923">reactant_species</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a0b543e9b0bb4a21efe4b29780d9bdf5b">reactants</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a7dff19d387e771d96c26e98d75ee9d5c">Reaction</a>(const std::string_view id, const std::string_view peName, const int chapter, const std::vector&lt; fourdst::atomic::Species &gt; &amp;reactants, const std::vector&lt; fourdst::atomic::Species &gt; &amp;products, const double qValue, const std::string_view label, const RateCoefficientSet &amp;sets, const bool reverse=false)</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#a410e2ab0784ad751f82bbe55be603db0">sourceLabel</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#aaf0c94db6536b4a9ac1ec08a5c8f01ac">stoichiometry</a>(const fourdst::atomic::Species &amp;species) const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#ad359c06d7196c1a7a955a7b66a51dbe3">stoichiometry</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html#ab1860df84843be70f97469761e11ab6a">~Reaction</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_reaction.html">gridfire::Reaction</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/html/classgridfire_1_1_reaction.js

@@ -0,0 +1,42 @@
+var classgridfire_1_1_reaction =
+[
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+    [ "Reaction", "classgridfire_1_1_reaction.html#a7dff19d387e771d96c26e98d75ee9d5c", null ],
+    [ "all_species", "classgridfire_1_1_reaction.html#a7dc8fda87e0581fde6da0a81cf4d7224", null ],
+    [ "calculate_forward_rate_log_derivative", "classgridfire_1_1_reaction.html#a3a8ba9212d76d5ce51f20df6892c6061", null ],
+    [ "calculate_rate", "classgridfire_1_1_reaction.html#a735192a42f72cd68f289493753e1a616", null ],
+    [ "calculate_rate", "classgridfire_1_1_reaction.html#ad81e9b2a1773470059ca6989c60556ec", null ],
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+    [ "contains_reactant", "classgridfire_1_1_reaction.html#abbe243affa61ba9b2cd2a7b905cd5e45", null ],
+    [ "excess_energy", "classgridfire_1_1_reaction.html#aa1d71e38fc55ae691dbb9ec459a612a5", null ],
+    [ "hash", "classgridfire_1_1_reaction.html#af6c20e6d03a2d9f87632f71a90b88cb5", null ],
+    [ "id", "classgridfire_1_1_reaction.html#a084c38181408ed5e6fa2a2dd4d0ec905", null ],
+    [ "is_reverse", "classgridfire_1_1_reaction.html#aa67d05dfabf007c1acad34052d9a1dba", null ],
+    [ "num_species", "classgridfire_1_1_reaction.html#a1d3c8ab6d55155f9a21ad80ed8b9ef97", null ],
+    [ "operator!=", "classgridfire_1_1_reaction.html#a2f1c115a99bc7c477a2e858ff18b1b51", null ],
+    [ "operator==", "classgridfire_1_1_reaction.html#ac426457cf0a54a15b206549422083bac", null ],
+    [ "peName", "classgridfire_1_1_reaction.html#a78f42664cc957e266b6cf15fda09be97", null ],
+    [ "product_species", "classgridfire_1_1_reaction.html#a01c67726efbaa2ff8e4d6f2c965f485c", null ],
+    [ "products", "classgridfire_1_1_reaction.html#a6e2ff61b9e8409f2a561663628b8ce02", null ],
+    [ "qValue", "classgridfire_1_1_reaction.html#abda0b4e4313e6d4ba57acf37d5976fb8", null ],
+    [ "rateCoefficients", "classgridfire_1_1_reaction.html#a85968076e686e67763f4fdf4f72a892e", null ],
+    [ "reactant_species", "classgridfire_1_1_reaction.html#a855ea65e4b62fb0cddc550424a4bc923", null ],
+    [ "reactants", "classgridfire_1_1_reaction.html#a0b543e9b0bb4a21efe4b29780d9bdf5b", null ],
+    [ "sourceLabel", "classgridfire_1_1_reaction.html#a410e2ab0784ad751f82bbe55be603db0", null ],
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+    [ "stoichiometry", "classgridfire_1_1_reaction.html#aaf0c94db6536b4a9ac1ec08a5c8f01ac", null ],
+    [ "operator<<", "classgridfire_1_1_reaction.html#a2b05ab608187216fc751bd2e42e8b7d8", null ],
+    [ "m_chapter", "classgridfire_1_1_reaction.html#a16f9cbb6269817099d3dc07d4e63da7b", null ],
+    [ "m_id", "classgridfire_1_1_reaction.html#a5c685e5a736b51799e5b9f6746c4126b", null ],
+    [ "m_logger", "classgridfire_1_1_reaction.html#a7044d0a1d59d85502ce554e4ec2167e4", null ],
+    [ "m_peName", "classgridfire_1_1_reaction.html#a6124aa9fc2306349e1dd879a37923248", null ],
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+];

docs/html/classgridfire_1_1approx8_1_1_approx8_network.html

@@ -185,7 +185,7 @@ Additional Inherited Members</h2></td></tr>
 </table>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Class for the Approx8 nuclear reaction network. </p>
-<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2network_2include_2gridfire_2engine_2engine_approx8_8h-example.html#_a3">/Users/tboudreaux/Programming/4DSTAR/GridFire/src/network/include/gridfire/engine/engine_approx8.h</a>.</dd>
+<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html#_a3">/Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h</a>.</dd>
 </dl>
 
 <p class="definition">Definition at line <a class="el" href="engine__approx8_8h_source.html#l00294">294</a> of file <a class="el" href="engine__approx8_8h_source.html">engine_approx8.h</a>.</p>
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+<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html#a40">/Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h</a>.</dd>
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 <p class="definition">Definition at line <a class="el" href="engine__approx8_8cpp_source.html#l00443">443</a> of file <a class="el" href="engine__approx8_8cpp_source.html">engine_approx8.cpp</a>.</p>
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+<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html#a48">/Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h</a>.</dd>
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 <p class="definition">Definition at line <a class="el" href="engine__approx8_8cpp_source.html#l00509">509</a> of file <a class="el" href="engine__approx8_8cpp_source.html">engine_approx8.cpp</a>.</p>
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+<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html#a41">/Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h</a>.</dd>
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+<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html#a43">/Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h</a>.</dd>
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 <p class="definition">Definition at line <a class="el" href="engine__approx8_8h_source.html#l00315">315</a> of file <a class="el" href="engine__approx8_8h_source.html">engine_approx8.h</a>.</p>
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+<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html#a42">/Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h</a>.</dd>
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+<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html#a47">/Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h</a>.</dd>
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 <p class="definition">Definition at line <a class="el" href="engine__approx8_8h_source.html#l00319">319</a> of file <a class="el" href="engine__approx8_8h_source.html">engine_approx8.h</a>.</p>
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+<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html#a44">/Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h</a>.</dd>
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 <p class="definition">Definition at line <a class="el" href="engine__approx8_8h_source.html#l00320">320</a> of file <a class="el" href="engine__approx8_8h_source.html">engine_approx8.h</a>.</p>
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+<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html#a46">/Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h</a>.</dd>
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 <p class="definition">Definition at line <a class="el" href="engine__approx8_8h_source.html#l00318">318</a> of file <a class="el" href="engine__approx8_8h_source.html">engine_approx8.h</a>.</p>
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 <p class="definition">Definition at line <a class="el" href="engine__approx8_8h_source.html#l00317">317</a> of file <a class="el" href="engine__approx8_8h_source.html">engine_approx8.h</a>.</p>
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docs/html/classgridfire_1_1exceptions_1_1_engine_error.html

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+  <div class="headertitle"><div class="title">gridfire::exceptions::EngineError Class Reference</div></div>
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+<li>src/include/gridfire/exceptions/<a class="el" href="error__engine_8h_source.html">error_engine.h</a></li>
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+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">gridfire::exceptions::FailedToPartitionEngineError Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html">gridfire::exceptions::FailedToPartitionEngineError</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html#a9b9e8752798876d34a444f61fc2f509a">FailedToPartitionEngineError</a>(const std::string &amp;message)</td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html">gridfire::exceptions::FailedToPartitionEngineError</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">explicit</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html#a77c9a660a2748c2e3a1c7e94edad1cf0">m_message</a></td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html">gridfire::exceptions::FailedToPartitionEngineError</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html#afe87ef508f5b20ca99ec70510747caff">what</a>() const noexcept override</td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html">gridfire::exceptions::FailedToPartitionEngineError</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
+<script type="text/javascript">
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+/* @license-end */
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+</div>
+
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pri-attribs">Private Attributes</a> &#124;
+<a href="classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">gridfire::exceptions::FailedToPartitionEngineError Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
+</div><!--header-->
+<div class="contents">
+
+<p><code>#include &lt;<a class="el" href="error__engine_8h_source.html">error_engine.h</a>&gt;</code></p>
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+Inheritance diagram for gridfire::exceptions::FailedToPartitionEngineError:</div>
+<div class="dyncontent">
+ <div class="center">
+  <img src="classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.png" usemap="#gridfire::exceptions::FailedToPartitionEngineError_map" alt=""/>
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+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
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+<tr class="memitem:a9b9e8752798876d34a444f61fc2f509a" id="r_a9b9e8752798876d34a444f61fc2f509a"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a9b9e8752798876d34a444f61fc2f509a">FailedToPartitionEngineError</a> (const std::string &amp;message)</td></tr>
+<tr class="separator:a9b9e8752798876d34a444f61fc2f509a"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:afe87ef508f5b20ca99ec70510747caff" id="r_afe87ef508f5b20ca99ec70510747caff"><td class="memItemLeft" align="right" valign="top">const char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#afe87ef508f5b20ca99ec70510747caff">what</a> () const noexcept override</td></tr>
+<tr class="separator:afe87ef508f5b20ca99ec70510747caff"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
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+<tr class="memitem:a77c9a660a2748c2e3a1c7e94edad1cf0" id="r_a77c9a660a2748c2e3a1c7e94edad1cf0"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a77c9a660a2748c2e3a1c7e94edad1cf0">m_message</a></td></tr>
+<tr class="separator:a77c9a660a2748c2e3a1c7e94edad1cf0"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00075">75</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
+<a id="a9b9e8752798876d34a444f61fc2f509a" name="a9b9e8752798876d34a444f61fc2f509a"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a9b9e8752798876d34a444f61fc2f509a">&#9670;&#160;</a></span>FailedToPartitionEngineError()</h2>
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+<div class="memitem">
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+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
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+          <td>(</td>
+          <td class="paramtype">const std::string &amp;</td>          <td class="paramname"><span class="paramname"><em>message</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel explicit">explicit</span></span>  </td>
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+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00077">77</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
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+<h2 class="groupheader">Member Function Documentation</h2>
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+<h2 class="memtitle"><span class="permalink"><a href="#afe87ef508f5b20ca99ec70510747caff">&#9670;&#160;</a></span>what()</h2>
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+      <table class="memname">
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+          <td class="memname">const char * gridfire::exceptions::FailedToPartitionEngineError::what </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel override">override</span><span class="mlabel noexcept">noexcept</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
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+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00080">80</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Data Documentation</h2>
+<a id="a77c9a660a2748c2e3a1c7e94edad1cf0" name="a77c9a660a2748c2e3a1c7e94edad1cf0"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a77c9a660a2748c2e3a1c7e94edad1cf0">&#9670;&#160;</a></span>m_message</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
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+          <td class="memname">std::string gridfire::exceptions::FailedToPartitionEngineError::m_message</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
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+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00084">84</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>src/include/gridfire/exceptions/<a class="el" href="error__engine_8h_source.html">error_engine.h</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
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+  <ul>
+    <li class="navelem"><a class="el" href="namespacegridfire.html">gridfire</a></li><li class="navelem"><a class="el" href="namespacegridfire_1_1exceptions.html">exceptions</a></li><li class="navelem"><a class="el" href="classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html">FailedToPartitionEngineError</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
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docs/html/classgridfire_1_1exceptions_1_1_network_resized_error-members.html

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+<script type="text/javascript">
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+/* @license-end */
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+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">gridfire::exceptions::NetworkResizedError Member List</div></div>
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+<div class="contents">
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+<p>This is the complete list of members for <a class="el" href="classgridfire_1_1exceptions_1_1_network_resized_error.html">gridfire::exceptions::NetworkResizedError</a>, including all inherited members.</p>
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+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
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docs/html/classgridfire_1_1exceptions_1_1_network_resized_error.html

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+<title>GridFire: gridfire::exceptions::NetworkResizedError Class Reference</title>
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+<div id="titlearea">
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+ <tbody>
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+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
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+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
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+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pri-attribs">Private Attributes</a> &#124;
+<a href="classgridfire_1_1exceptions_1_1_network_resized_error-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">gridfire::exceptions::NetworkResizedError Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
+</div><!--header-->
+<div class="contents">
+
+<p><code>#include &lt;<a class="el" href="error__engine_8h_source.html">error_engine.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for gridfire::exceptions::NetworkResizedError:</div>
+<div class="dyncontent">
+ <div class="center">
+  <img src="classgridfire_1_1exceptions_1_1_network_resized_error.png" usemap="#gridfire::exceptions::NetworkResizedError_map" alt=""/>
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+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
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+<tr class="separator:a80f09d037fff3c55a9b937b37d101cc1"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
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+<tr class="memitem:a581527fc03fdd84a8309c147259ec09d" id="r_a581527fc03fdd84a8309c147259ec09d"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a581527fc03fdd84a8309c147259ec09d">m_message</a></td></tr>
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+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00087">87</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
+<a id="a80c0adb088e8083309591d24051b056b" name="a80c0adb088e8083309591d24051b056b"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a80c0adb088e8083309591d24051b056b">&#9670;&#160;</a></span>NetworkResizedError()</h2>
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+      <table class="memname">
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+          <td class="memname">gridfire::exceptions::NetworkResizedError::NetworkResizedError </td>
+          <td>(</td>
+          <td class="paramtype">const std::string &amp;</td>          <td class="paramname"><span class="paramname"><em>message</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel explicit">explicit</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00089">89</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
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+<h2 class="groupheader">Member Function Documentation</h2>
+<a id="a80f09d037fff3c55a9b937b37d101cc1" name="a80f09d037fff3c55a9b937b37d101cc1"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a80f09d037fff3c55a9b937b37d101cc1">&#9670;&#160;</a></span>what()</h2>
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+  <tr>
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+      <table class="memname">
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+          <td class="memname">const char * gridfire::exceptions::NetworkResizedError::what </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel override">override</span><span class="mlabel noexcept">noexcept</span></span>  </td>
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+</table>
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+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00092">92</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Data Documentation</h2>
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+<h2 class="memtitle"><span class="permalink"><a href="#a581527fc03fdd84a8309c147259ec09d">&#9670;&#160;</a></span>m_message</h2>
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+<div class="memitem">
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+  <td class="mlabels-left">
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+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
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+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00096">96</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>src/include/gridfire/exceptions/<a class="el" href="error__engine_8h_source.html">error_engine.h</a></li>
+</ul>
+</div><!-- contents -->
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+  <ul>
+    <li class="navelem"><a class="el" href="namespacegridfire.html">gridfire</a></li><li class="navelem"><a class="el" href="namespacegridfire_1_1exceptions.html">exceptions</a></li><li class="navelem"><a class="el" href="classgridfire_1_1exceptions_1_1_network_resized_error.html">NetworkResizedError</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
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docs/html/classgridfire_1_1exceptions_1_1_stale_engine_error-members.html

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+<script type="text/javascript" src="dynsections.js"></script>
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+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
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+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
+<script type="text/javascript">
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+/* @license-end */
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+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
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+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+  $(function() { init_search(); });
+});
+/* @license-end */
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+<div id="main-nav"></div>
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+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">gridfire::exceptions::StaleEngineError Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_error.html">gridfire::exceptions::StaleEngineError</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_error.html#a4eb62e3842302997e44e05d0770d77bb">m_message</a></td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_error.html">gridfire::exceptions::StaleEngineError</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
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docs/html/classgridfire_1_1exceptions_1_1_stale_engine_error.html

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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
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+</table>
+</div>
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+/* @license-end */
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+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
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+<!-- iframe showing the search results (closed by default) -->
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+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pri-attribs">Private Attributes</a> &#124;
+<a href="classgridfire_1_1exceptions_1_1_stale_engine_error-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">gridfire::exceptions::StaleEngineError Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
+</div><!--header-->
+<div class="contents">
+
+<p><code>#include &lt;<a class="el" href="error__engine_8h_source.html">error_engine.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for gridfire::exceptions::StaleEngineError:</div>
+<div class="dyncontent">
+ <div class="center">
+  <img src="classgridfire_1_1exceptions_1_1_stale_engine_error.png" usemap="#gridfire::exceptions::StaleEngineError_map" alt=""/>
+  <map id="gridfire::exceptions::StaleEngineError_map" name="gridfire::exceptions::StaleEngineError_map">
+<area href="classgridfire_1_1exceptions_1_1_engine_error.html" alt="gridfire::exceptions::EngineError" shape="rect" coords="0,56,222,80"/>
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+</div></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a6672e4c3f42260bba25d78e14ebd5a50" id="r_a6672e4c3f42260bba25d78e14ebd5a50"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a6672e4c3f42260bba25d78e14ebd5a50">StaleEngineError</a> (const std::string &amp;message)</td></tr>
+<tr class="separator:a6672e4c3f42260bba25d78e14ebd5a50"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a15c1b625e8e58a457e7bc5dbb464eff4" id="r_a15c1b625e8e58a457e7bc5dbb464eff4"><td class="memItemLeft" align="right" valign="top">const char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a15c1b625e8e58a457e7bc5dbb464eff4">what</a> () const noexcept override</td></tr>
+<tr class="separator:a15c1b625e8e58a457e7bc5dbb464eff4"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
+Private Attributes</h2></td></tr>
+<tr class="memitem:a4eb62e3842302997e44e05d0770d77bb" id="r_a4eb62e3842302997e44e05d0770d77bb"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a4eb62e3842302997e44e05d0770d77bb">m_message</a></td></tr>
+<tr class="separator:a4eb62e3842302997e44e05d0770d77bb"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00062">62</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
+<a id="a6672e4c3f42260bba25d78e14ebd5a50" name="a6672e4c3f42260bba25d78e14ebd5a50"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a6672e4c3f42260bba25d78e14ebd5a50">&#9670;&#160;</a></span>StaleEngineError()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">gridfire::exceptions::StaleEngineError::StaleEngineError </td>
+          <td>(</td>
+          <td class="paramtype">const std::string &amp;</td>          <td class="paramname"><span class="paramname"><em>message</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel explicit">explicit</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00064">64</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Function Documentation</h2>
+<a id="a15c1b625e8e58a457e7bc5dbb464eff4" name="a15c1b625e8e58a457e7bc5dbb464eff4"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a15c1b625e8e58a457e7bc5dbb464eff4">&#9670;&#160;</a></span>what()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">const char * gridfire::exceptions::StaleEngineError::what </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel override">override</span><span class="mlabel noexcept">noexcept</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00067">67</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Data Documentation</h2>
+<a id="a4eb62e3842302997e44e05d0770d77bb" name="a4eb62e3842302997e44e05d0770d77bb"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a4eb62e3842302997e44e05d0770d77bb">&#9670;&#160;</a></span>m_message</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::string gridfire::exceptions::StaleEngineError::m_message</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00072">72</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>src/include/gridfire/exceptions/<a class="el" href="error__engine_8h_source.html">error_engine.h</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="namespacegridfire.html">gridfire</a></li><li class="navelem"><a class="el" href="namespacegridfire_1_1exceptions.html">exceptions</a></li><li class="navelem"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_error.html">StaleEngineError</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
+</body>
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+    [ "m_message", "classgridfire_1_1exceptions_1_1_stale_engine_error.html#a4eb62e3842302997e44e05d0770d77bb", null ]
+];

docs/html/classgridfire_1_1exceptions_1_1_stale_engine_trigger-members.html

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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
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+<title>GridFire: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<script type="text/javascript" src="clipboard.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="navtreedata.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript" src="resize.js"></script>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
+<script type="text/javascript">
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+/* @license-end */
+</script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() { codefold.init(0); });
+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
+    <div id="nav-tree-contents">
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+    </div>
+  </div>
+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+</div>
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+<!-- iframe showing the search results (closed by default) -->
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+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">gridfire::exceptions::StaleEngineTrigger Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">gridfire::exceptions::StaleEngineTrigger</a>, including all inherited members.</p>
+<table class="directory">
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html#ae8156ed7e659cb629da24a5b6734e2dc">density</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">gridfire::exceptions::StaleEngineTrigger</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html#aeebfb529118f8dfcaf1422ae1768f2bf">energy</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">gridfire::exceptions::StaleEngineTrigger</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html#a3183a0030b14253eb49d8304fb6665ea">getMolarAbundance</a>(const size_t index) const</td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">gridfire::exceptions::StaleEngineTrigger</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html#a06eb9eb03750038c193c23c7f53668f5">getState</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">gridfire::exceptions::StaleEngineTrigger</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html#a7f9fa2e34da3772714723ef7d5083be5">m_state</a></td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">gridfire::exceptions::StaleEngineTrigger</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html#a44ac2f7510ecf86cd5b556a842eee30c">numSpecies</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">gridfire::exceptions::StaleEngineTrigger</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html#afb50f1694a806e8bcaf99111d99aeb5d">StaleEngineTrigger</a>(const state &amp;s)</td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">gridfire::exceptions::StaleEngineTrigger</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">explicit</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html#a2f5925b67562cebd08568fce76c739e9">temperature</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">gridfire::exceptions::StaleEngineTrigger</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html#a0b7c627c3e69390808bef352b3875408">totalSteps</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">gridfire::exceptions::StaleEngineTrigger</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html#aac4899d001338688def2b809b55bb2ba">what</a>() const noexcept override</td><td class="entry"><a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html">gridfire::exceptions::StaleEngineTrigger</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/html/classgridfire_1_1exceptions_1_1_stale_engine_trigger.html

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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
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+<div class="header">
+  <div class="summary">
+<a href="#nested-classes">Classes</a> &#124;
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pri-attribs">Private Attributes</a> &#124;
+<a href="classgridfire_1_1exceptions_1_1_stale_engine_trigger-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">gridfire::exceptions::StaleEngineTrigger Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
+</div><!--header-->
+<div class="contents">
+
+<p><code>#include &lt;<a class="el" href="error__engine_8h_source.html">error_engine.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for gridfire::exceptions::StaleEngineTrigger:</div>
+<div class="dyncontent">
+ <div class="center">
+  <img src="classgridfire_1_1exceptions_1_1_stale_engine_trigger.png" usemap="#gridfire::exceptions::StaleEngineTrigger_map" alt=""/>
+  <map id="gridfire::exceptions::StaleEngineTrigger_map" name="gridfire::exceptions::StaleEngineTrigger_map">
+<area href="classgridfire_1_1exceptions_1_1_engine_error.html" alt="gridfire::exceptions::EngineError" shape="rect" coords="0,56,233,80"/>
+  </map>
+</div></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="nested-classes" name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html">state</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:afb50f1694a806e8bcaf99111d99aeb5d" id="r_afb50f1694a806e8bcaf99111d99aeb5d"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#afb50f1694a806e8bcaf99111d99aeb5d">StaleEngineTrigger</a> (const <a class="el" href="structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html">state</a> &amp;s)</td></tr>
+<tr class="separator:afb50f1694a806e8bcaf99111d99aeb5d"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aac4899d001338688def2b809b55bb2ba" id="r_aac4899d001338688def2b809b55bb2ba"><td class="memItemLeft" align="right" valign="top">const char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aac4899d001338688def2b809b55bb2ba">what</a> () const noexcept override</td></tr>
+<tr class="separator:aac4899d001338688def2b809b55bb2ba"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a06eb9eb03750038c193c23c7f53668f5" id="r_a06eb9eb03750038c193c23c7f53668f5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html">state</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a06eb9eb03750038c193c23c7f53668f5">getState</a> () const</td></tr>
+<tr class="separator:a06eb9eb03750038c193c23c7f53668f5"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a44ac2f7510ecf86cd5b556a842eee30c" id="r_a44ac2f7510ecf86cd5b556a842eee30c"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a44ac2f7510ecf86cd5b556a842eee30c">numSpecies</a> () const</td></tr>
+<tr class="separator:a44ac2f7510ecf86cd5b556a842eee30c"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a0b7c627c3e69390808bef352b3875408" id="r_a0b7c627c3e69390808bef352b3875408"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0b7c627c3e69390808bef352b3875408">totalSteps</a> () const</td></tr>
+<tr class="separator:a0b7c627c3e69390808bef352b3875408"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aeebfb529118f8dfcaf1422ae1768f2bf" id="r_aeebfb529118f8dfcaf1422ae1768f2bf"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aeebfb529118f8dfcaf1422ae1768f2bf">energy</a> () const</td></tr>
+<tr class="separator:aeebfb529118f8dfcaf1422ae1768f2bf"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a3183a0030b14253eb49d8304fb6665ea" id="r_a3183a0030b14253eb49d8304fb6665ea"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a3183a0030b14253eb49d8304fb6665ea">getMolarAbundance</a> (const size_t index) const</td></tr>
+<tr class="separator:a3183a0030b14253eb49d8304fb6665ea"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a2f5925b67562cebd08568fce76c739e9" id="r_a2f5925b67562cebd08568fce76c739e9"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a2f5925b67562cebd08568fce76c739e9">temperature</a> () const</td></tr>
+<tr class="separator:a2f5925b67562cebd08568fce76c739e9"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ae8156ed7e659cb629da24a5b6734e2dc" id="r_ae8156ed7e659cb629da24a5b6734e2dc"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ae8156ed7e659cb629da24a5b6734e2dc">density</a> () const</td></tr>
+<tr class="separator:ae8156ed7e659cb629da24a5b6734e2dc"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
+Private Attributes</h2></td></tr>
+<tr class="memitem:a7f9fa2e34da3772714723ef7d5083be5" id="r_a7f9fa2e34da3772714723ef7d5083be5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html">state</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a7f9fa2e34da3772714723ef7d5083be5">m_state</a></td></tr>
+<tr class="separator:a7f9fa2e34da3772714723ef7d5083be5"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock">
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00010">10</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
+<a id="afb50f1694a806e8bcaf99111d99aeb5d" name="afb50f1694a806e8bcaf99111d99aeb5d"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#afb50f1694a806e8bcaf99111d99aeb5d">&#9670;&#160;</a></span>StaleEngineTrigger()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">gridfire::exceptions::StaleEngineTrigger::StaleEngineTrigger </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html">state</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>s</em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel explicit">explicit</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00020">20</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Function Documentation</h2>
+<a id="ae8156ed7e659cb629da24a5b6734e2dc" name="ae8156ed7e659cb629da24a5b6734e2dc"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ae8156ed7e659cb629da24a5b6734e2dc">&#9670;&#160;</a></span>density()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">double gridfire::exceptions::StaleEngineTrigger::density </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00054">54</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<a id="aeebfb529118f8dfcaf1422ae1768f2bf" name="aeebfb529118f8dfcaf1422ae1768f2bf"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#aeebfb529118f8dfcaf1422ae1768f2bf">&#9670;&#160;</a></span>energy()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">double gridfire::exceptions::StaleEngineTrigger::energy </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00039">39</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<a id="a3183a0030b14253eb49d8304fb6665ea" name="a3183a0030b14253eb49d8304fb6665ea"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a3183a0030b14253eb49d8304fb6665ea">&#9670;&#160;</a></span>getMolarAbundance()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">double gridfire::exceptions::StaleEngineTrigger::getMolarAbundance </td>
+          <td>(</td>
+          <td class="paramtype">const size_t</td>          <td class="paramname"><span class="paramname"><em>index</em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00043">43</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<a id="a06eb9eb03750038c193c23c7f53668f5" name="a06eb9eb03750038c193c23c7f53668f5"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a06eb9eb03750038c193c23c7f53668f5">&#9670;&#160;</a></span>getState()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html">state</a> gridfire::exceptions::StaleEngineTrigger::getState </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00027">27</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<a id="a44ac2f7510ecf86cd5b556a842eee30c" name="a44ac2f7510ecf86cd5b556a842eee30c"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a44ac2f7510ecf86cd5b556a842eee30c">&#9670;&#160;</a></span>numSpecies()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">size_t gridfire::exceptions::StaleEngineTrigger::numSpecies </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00031">31</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<a id="a2f5925b67562cebd08568fce76c739e9" name="a2f5925b67562cebd08568fce76c739e9"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a2f5925b67562cebd08568fce76c739e9">&#9670;&#160;</a></span>temperature()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">double gridfire::exceptions::StaleEngineTrigger::temperature </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00050">50</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<a id="a0b7c627c3e69390808bef352b3875408" name="a0b7c627c3e69390808bef352b3875408"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a0b7c627c3e69390808bef352b3875408">&#9670;&#160;</a></span>totalSteps()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">size_t gridfire::exceptions::StaleEngineTrigger::totalSteps </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00035">35</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<a id="aac4899d001338688def2b809b55bb2ba" name="aac4899d001338688def2b809b55bb2ba"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#aac4899d001338688def2b809b55bb2ba">&#9670;&#160;</a></span>what()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">const char * gridfire::exceptions::StaleEngineTrigger::what </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel override">override</span><span class="mlabel noexcept">noexcept</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00023">23</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Data Documentation</h2>
+<a id="a7f9fa2e34da3772714723ef7d5083be5" name="a7f9fa2e34da3772714723ef7d5083be5"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a7f9fa2e34da3772714723ef7d5083be5">&#9670;&#160;</a></span>m_state</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html">state</a> gridfire::exceptions::StaleEngineTrigger::m_state</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="error__engine_8h_source.html#l00058">58</a> of file <a class="el" href="error__engine_8h_source.html">error_engine.h</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>src/include/gridfire/exceptions/<a class="el" href="error__engine_8h_source.html">error_engine.h</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
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