diff --git a/Doxyfile b/Doxyfile index 177be146..ef765de8 100644 --- a/Doxyfile +++ b/Doxyfile @@ -1238,7 +1238,7 @@ FORTRAN_COMMENT_AFTER = 72 # also VERBATIM_HEADERS is set to NO. # The default value is: NO. -SOURCE_BROWSER = YES +SOURCE_BROWSER = NO # Setting the INLINE_SOURCES tag to YES will include the body of functions, # multi-line macros, enums or list initialized variables directly into the @@ -1312,7 +1312,7 @@ USE_HTAGS = NO # See also: Section \class. # The default value is: YES. -VERBATIM_HEADERS = YES +VERBATIM_HEADERS = NO #--------------------------------------------------------------------------- # Configuration options related to the alphabetical class index @@ -2036,7 +2036,7 @@ LATEX_OUTPUT = latex # the output language. # This tag requires that the tag GENERATE_LATEX is set to YES. -LATEX_CMD_NAME = pdflatex +LATEX_CMD_NAME = xelatex # The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate # index for LaTeX. @@ -2073,7 +2073,7 @@ COMPACT_LATEX = NO # The default value is: a4. # This tag requires that the tag GENERATE_LATEX is set to YES. -PAPER_TYPE = a4 +PAPER_TYPE = letter # The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names # that should be included in the LaTeX output. The package can be specified just @@ -2264,7 +2264,7 @@ RTF_EXTRA_FILES = # classes and files. # The default value is: NO. -GENERATE_MAN = NO +GENERATE_MAN = YES # The MAN_OUTPUT tag is used to specify where the man pages will be put. If a # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of diff --git a/README.md b/README.md index 8d8c9f06..2c146eaf 100644 --- a/README.md +++ b/README.md @@ -5,31 +5,44 @@ --- -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. GridFire is primarily focused on modeling the most -relevant burning stages for stellar evolution modeling. Currently, there is limited support for inverse reactions. -Therefore, GridFire has a limited set of tools to evolves a fusing plasma in NSE; however, -this is not the primary focus of the library and has therefor not had significant development. For those interested in -modeling super nova, neutron star mergers, or other -high-energy astrophysical phenomena, we **strongly** recomment -using [SkyNet](https://bitbucket.org/jlippuner/skynet/src/master/). +# Introduction +GridFire is a C++ library designed to perform general nuclear network +evolution. It is part of the larger SERiF project within the 4D-STAR +collaboration. GridFire is primarily focused on modeling the most relevant +burning stages for stellar evolution modeling. Currently, there is limited +support for inverse reactions. Therefore, GridFire has a limited set of tools +to evolves a fusing plasma in NSE; however, this is not the primary focus of +the library and has therefor not had significant development. For those +interested in modeling super nova, neutron star mergers, or other high-energy +astrophysical phenomena, we **strongly** recomment using +[SkyNet](https://bitbucket.org/jlippuner/skynet/src/master/). -**Design Philosophy and Workflow:** -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 multiscale 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. +## Design Philosophy and Workflow +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. A GraphNetwork uses [JINA +Reaclib](https://reaclib.jinaweb.org/index.php) reaction rates ([Cyburt et al., ApJS 189 +(2010) 240.](https://iopscience.iop.org/article/10.1088/0067-0049/189/1/240)) along +with a dynamically constructed network topology. To manage the inherent +stiffness and multiscale 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. ## Funding GridFire is a part of the 4D-STAR collaboration. -4D-STAR is funded by European Research Council (ERC) under the Horizon Europe programme (Synergy Grant agreement No. -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 Council. +4D-STAR is funded by European Research Council (ERC) under the Horizon Europe +programme (Synergy Grant agreement No. 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 Council. + +# Usage ## Python installation By far the easiest way to install is with pip. This will install either @@ -44,70 +57,191 @@ Installing from pip is as simple as pip install gridfire ``` -If you want the most recent version follow the instructions below to build the python bindings from source... +These wheels have been compiled on many systems + +| Version | Platform | Architecture | CPython Versions | PyPy Versions | +| ------- | -------- | ------------ | ---------------------------------------------------------- | ------------- | +| 0.5.0 | macOS | arm64 | 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) | 3.10, 3.11 | +| 0.5.0 | Linux | aarch64 | 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) | 3.10, 3.11 | +| 0.5.0 | Linux | x86\_64 | 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) | 3.10, 3.11 | + +> **Note**: Currently macOS x86\_64 does **not** have a precompiled wheel. Due +> to that platform being phased out it is likely that there will never be +> precompiled wheels or releases for it. + +> **Note:** macOS wheels were targeted to MacOS 12 Monterey and should work on +> any version more recent than that (at least as of August 2025). + +> **Note:** Linux wheels were compiled using manylinux_2_28 and are expected to +> work on Debian 10+, Ubuntu 18.10+, Fedora 29+, or CentOS/RHEL 8+ + +> **Note:** If your system does not have a prebuilt wheel the source +> distribution will download from pypi and try to build. This may simply not +> work if you do not have the correct system dependencies installed. If it +> fails the best bet is to try to build boost >= 1.83.0 from source and install +> (https://www.boost.org/) as that is the most common broken dependency. + +### source +The user may also build the python bindings directly from source + +```bash +git clone https://github.com/4D-STAR/GridFire +cd GridFire +pip install . +``` + +> **Note:** that if you do not have all system dependencies installed this will +> fail, the steps in further sections address these in more detail. + +### source for developers +If you are a developer and would like an editable and incrimental python +install `meson-python` makes this very easy + +```bash +git clone https://github.com/4D-STAR/GridFire +cd GridFire +pip install -e . --no-build-isolation -vv +``` + +This will generate incrimental builds whenever source code changes and you run +a python script automartically (note that since `meson setup` must run for each +of these it does still take a few seconds to recompile regardless of how small +a source code change you have made). It is **strongly** reccomended that +developers use this approach and end users *do not*. + ## Automatic Build and Installation ### Script Build and Installation Instructions -The easiest way to build GridFire is using the `install.sh` or `install-tui.sh` scripts in the root directory. To use -these scripts, simply run: +The easiest way to build GridFire is using the `install.sh` or `install-tui.sh` +scripts in the root directory. To use these scripts, simply run: ```bash ./install.sh # or ./install-tui.sh ``` -The regular installation script will select a standard "ideal" set of build options for you. If you want more control -over the build options, you can use the `install-tui.sh` script, which will provide a text-based user interface to +The regular installation script will select a standard "ideal" set of build +options for you. If you want more control over the build options, you can use +the `install-tui.sh` script, which will provide a text-based user interface to select the build options you want. -Generally, both are intended to be easy to use and will prompt you automatically to install any missing dependencies. +Generally, both are intended to be easy to use and will prompt you +automatically to install any missing dependencies. ### Currently known good platforms -The installation script has been tested and found to work on clean installations of the following platforms: +The installation script has been tested and found to work on clean +installations of the following platforms: - MacOS 15.3.2 (Apple Silicon + brew installed) - Fedora 42.0 (aarch64) - Ubuntu 25.04 (aarch64) - Ubuntu 22.04 (X86_64) -> **Note:** On Ubuntu 22.04 the user needs to install boost libraries manually as the versions in the Ubuntu repositories -are too old. The installer automatically detects this and will instruct the user in how to do this. +> **Note:** On Ubuntu 22.04 the user needs to install boost libraries manually +> as the versions in the Ubuntu repositories +> are too old. The installer automatically detects this and will instruct the +> user in how to do this. ## Manual Build Instructions ### Prerequisites -These only need to be manually installed if the user is not making use of the `install.sh` or `install-tui.sh` +These only need to be manually installed if the user is not making use of the +`install.sh` or `install-tui.sh` +#### Required - C++ compiler supporting C++23 standard - Meson build system (>= 1.5.0) -- Python 3.10 or newer +- Python 3.8 or newer - CMake 3.20 or newer +- ninja 1.10.0 or newer - Python packages: `meson-python>=0.15.0` -- Boost libraries (>= 1.75.0) installed system-wide +- Boost libraries (>= 1.83.0) installed system-wide (or at least findable by +meson with pkg-config) -> **Note:** Boost is the only external library dependency; no additional libraries are required beyond a C++ compiler, Meson, Python, CMake, and Boost. - -> **Note:** Windows is not supported at this time and *there are no plans to support it in the future*. Windows users are encouraged to use WSL2 or a Linux VM. +#### Optional +- dialog (used by the `install.sh` script, not needed if using pip or meson +directly) +- pip (used by the `install.sh` script or by calling pip directly, not needed +if using meson directly) + +> **Note:** Boost is the only external library dependency used by GridFire directly. + +> **Note:** Windows is not supported at this time and *there are no plans to +> support it in the future*. Windows users are encouraged to use WSL2 or a +> Linux VM. + +> **Note:** If `install-tui.sh` is not able to find a usable version of boost +> it will provide directions to fetch, compile, and install a usable version. + +### Install Scripts +GridFire ships with an installer (`install.sh`) which is intended to make the +process of installation both easier and more repetable. + +#### Ease of Installation +Both scripts are intended to automate installation more or less completly. This +includes dependency checking. In the event that a dependency cannot be found +they try to install (after explicitly asking for user permission). If that does +not work they will provide a clear message as to what went wrong. + +#### Reproducibility +The TUI mode provides easy modification of meson build system and compiler +settings which can then be saved to a config file. This config file can then be +loaded by either tui mode or cli mode (with the `--config`) flag meaning that +build configurations can be made and reused. Note that this is **not** a +deterministicly reproducible build system as it does not interact with any +system dependencies or settings, only meson and compiler settings. + +#### Examples + +##### TUI config and saving +[![asciicast](https://asciinema.org/a/ahIrQPL71ErZv5EKKujfO1ZEW.svg)](https://asciinema.org/a/ahIrQPL71ErZv5EKKujfO1ZEW) + +##### TUI config loading and meson setup +[![asciicast](https://asciinema.org/a/zGdzt9kYsETltG0TJKC50g3BK.svg)](https://asciinema.org/a/zGdzt9kYsETltG0TJKC50g3BK) + +##### CLI config loading, setup, and build +[![asciicast](https://asciinema.org/a/GYaWTXZbDJRD4ohde0s3DkFMC.svg)](https://asciinema.org/a/GYaWTXZbDJRD4ohde0s3DkFMC) + + +> **Note:** `install-tui.sh` is simply a script which calles `install.sh` with +> the `--tui` flag. You can get the exact same results by running `install.sh +> --tui`. + +> **Note:** Call `install.sh` with the `--help` or `--h` flag to see command +> line options + +> **Note:** `clang` tends to compile GridFire much faster than `gcc` thus why I +> select it in the above asciinema recording. ### 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 - ``` +```bash +sudo apt-get update +sudo apt-get install -y build-essential meson python3 python3-pip libboost-all-dev +``` + +> **Note:** Depending on the ubuntu version you have the libboost-all-dev +> libraries may be too old. If this is the case refer to the boost +> documentation for how to download and install a version `>=1.83.0` + +> **Note:** On recent versions of ubuntu python has switched to being +> externally managed by the system. We **strongly** recomend that if you +> install manaully all python pacakges are installed inside some kind of +> virtual enviroment (e.g. `pyenv`, `conda`, `python-venv`, etc...). When using +> the installer script this is handled automatically using `python-venv`. - **Fedora/CentOS/RHEL:** - ```bash - sudo dnf install -y gcc-c++ meson python3 python3-pip boost-devel - ``` +```bash +sudo dnf install -y gcc-c++ meson python3 python3-pip boost-devel +``` - **macOS (Homebrew):** - ```bash - brew update && \ - brew install boost meson python - ``` +```bash +brew update +brew install boost meson python +``` ### Building the C++ Library ```bash @@ -115,54 +249,104 @@ meson setup build meson compile -C build ``` +#### Clang vs. GCC +As noted above `clang` tends to compile GridFire much faster than `gcc`. If +your system has both `clang` and `gcc` installed you may force meson to use +clang via enviromental variables + +```bash +CC=clang CXX=clang++ meson setup build_clang +meson compile -C build_clang +``` + ### 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 . -``` +### Minimum compiler versions +GridFire uses C++23 features and therefore only compilers and standard library +implimentations which support C++23 are supported. Generally we have found that +`gcc >= 13.0.0` or `clang >= 16.0.0` work well. -### 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 a series of composable modules, each responsible for a specific aspect of nuclear reaction network modeling. The core components include: +GridFire is organized into a series of composable modules, each responsible for +a specific aspect of nuclear reaction network modeling. The core components +include: -- **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. -- **Reaction Module:** Parses and manages Reaclib reaction rate data, providing temperature- and density-dependent rate evaluations. -- **Partition Module:** Implements partition functions (e.g., `GroundStatePartitionFunction`, `RauscherThielemannPartitionFunction`) to weight reaction rates based on nuclear properties. -- **Solver Module:** Defines numerical integration strategies (e.g., `DirectNetworkSolver`) for solving the stiff ODE systems arising from reaction networks. -- **Python Interface:** Exposes *almost* all C++ functionality to Python, allowing users to define compositions, configure engines, and run simulations directly from Python scripts. +- **Engine Module:** Core interfaces and implementations (e.g., `GraphEngine`) +that evaluate reaction network rate equations and energy generation. Also +implimented `Views` submodule. +- **Engine::Views Module:** Composable engine optimization and modification +(e.g. `MultiscalePartitioningEngineView`) which can be used to make a problem +more tractable or applicable. +- **Screening Module:** Implements nuclear reaction screening corrections (e.g. +`WeakScreening` ([Salpeter, +1954](https://adsabs.harvard.edu/full/1954AuJPh...7..373S)), `BareScreening`) +affecting reaction rates. +- **Reaction Module:** Parses and manages Reaclib reaction rate data, providing +temperature- and density-dependent rate evaluations. +- **Partition Module:** Implements partition functions (e.g., +`GroundStatePartitionFunction`, `RauscherThielemannPartitionFunction` +([Rauscher & Thielemann, +2000](https://www.sciencedirect.com/science/article/pii/S0092640X00908349?via%3Dihub])) +to weight reaction rates based on nuclear properties. +- **Solver Module:** Defines numerical integration strategies (e.g., +`DirectNetworkSolver`) for solving the stiff ODE systems arising from reaction +networks. +- **Python Interface:** Exposes *almost* all C++ functionality to Python, +allowing users to define compositions, configure engines, and run simulations +directly from Python scripts. -Generally a user will start by selecting a base engine (currently we only offer `GraphEngine`), which constructs the -full reaction network graph from a given composition. The user can then apply various engine views to adapt the network -topology, such as partitioning fast and slow reactions, adaptively culling low-flow pathways, or priming the network -with specific species. Finally, a numerical solver is selected to integrate the network over time, producing updated +Generally a user will start by selecting a base engine (currently we only offer +`GraphEngine`), which constructs the full reaction network graph from a given +composition. The user can then apply various engine views to adapt the network +topology, such as partitioning fast and slow reactions, adaptively culling +low-flow pathways, or priming the network with specific species. Finally, a +numerical solver is selected to integrate the network over time, producing +updated abundances and diagnostics. +## Engines +GridFire is, at its core, based on a series of `Engines`. These are constructs +which know how to report information on series of ODEs which need to be solved +to evolver abundnances. The important thing to understand about `Engines` is +that they contain all of the detailed physics GridFire uses. For example a +`Solver` takes an `Engine` but does not compute physics itself. Rather, it asks +the `Engine` for stuff like the jacobian matrix, stoichiometry, nuclear energy +generation rate, and change in abundance with time. + +Refer to the API documentation for the exact interface which an `Engine` must +impliment to be compatible with GridFire solvers. + +Currently we only impliment `GraphEngine` which is intended to be a very general and +adaptable `Engine`. + +### GraphEngine +In GridFire the `GraphEngine` will generally be the most fundamental building +block of a nuclear network. A `GraphEngine` represents a directional hypergraph +connecting some set of atomic species through reactions listed in the [JINA +Reaclib database](https://reaclib.jinaweb.org/index.php). + +`GraphEngine`s are constructed from a seed composition of species from which +they recursivley expand their topology outward, following known reaction +pathways and adding new species to the tracked list as they expand. + + ### GraphEngine Configuration Options -GraphEngine exposes runtime configuration methods to tailor network construction and rate evaluations: +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`. + - `composition`: The initial seed composition to start network construction from. + - `BuildDepthType` (`Full`, `Shallow`, `SecondOrder`, etc...): controls + number of recursions used to construct the network topology. Can either be an + member of the `NetworkBuildDepth` enum or an integerl. + - `partition::PartitionFunction`: Partition function used when evlauating + detailed balance for inverse rates. - **setPrecomputation(bool precompute):** - Enable/disable caching of reaction rates and stoichiometric data at initialization. @@ -178,70 +362,175 @@ GraphEngine exposes runtime configuration methods to tailor network construction ### Available Partition Functions -| Function Name | Identifier | Description | +| Function Name | Identifier / Enum | Description | |---------------------------------------|--------------------------|-----------------------------------------------------------------| -| `GroundStatePartitionFunction` | "GroundState" | Weights using nuclear ground-state spin factors. | -| `RauscherThielemannPartitionFunction` | "RauscherThielemann" | Interpolates normalized g-factors per Rauscher & Thielemann. | +| `GroundStatePartitionFunction` | "GroundState" | Weights using nuclear ground-state spin factors. | +| `RauscherThielemannPartitionFunction` | "RauscherThielemann" | Interpolates normalized g-factors per Rauscher & Thielemann. | +| `CompositePartitionFunction` | "Composite" | Combines multiple partition functions for situations where different partitions functions are used for different domains | + +### AutoDiff +One of the primary tasks any engine must accomplish is to report the jacobian +matrix of the system to the solver. `GraphEngine` uses `CppAD`, a C++ auto +differentiation library, to generate analytic jacobian matricies very +efficiently. + + +## Reaclib in GridFire +All reactions in JINA Reaclib which only include reactants iron and lighter +were downloaded on June 17th, 2025 where the most recent documented change on +the JINA Reaclib site was on June 24th, 2021. + +All of thes reactions have been compiled into a header file which is then +statically compiled into the gridfire binaries (specifically into +lib_reaction_reaclib.cpp.o). This does increase the binary size by a few MB; +however, the benafit is faster load times and more importantly no need for end +users to manage resource files. + +If a developer wants to add new reaclib reactions we include a script at +`utils/reaclib/format.py` which can injest a reaclib data file and produce the +needed header file. More details on this process are included in +`utils/reaclib/readme.md` -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: +The GridFire engine supports multiple engine view strategies to adapt or +restrict network topology. Generally when extending GridFire the approach is +likely to be one of adding new `EngineViews`. | 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 | +| FileDefinedEngineView | Load a defined engine view from a file using some parser | Same as DefinedEngineView but loads from a file | Same as DefinedEngineView | 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| +| NetworkPrimingEngineView | Primes the network with an initial species or set of species for ignition studies| Single-species ignition and network priming | 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. +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. +### A Note about composability +There are certain functions for which it is expected that a call to an engine +view will propegate the result down the chain of engine views, eventually +reaching the base engine (e.g. `DynamicEngine::update`). We do not strongly +enforce this as it is not hard to contrive a situation where that is not the +mose useful behavior; however, we do strongly encorage developers to think +carefully about passing along calls to base engine methods when implimenting +new views. ## 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. +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<EngineT>: +All GridFire solvers impliment the abstract strategy templated by +`NetworkSolverStrategy` which enforces only that there is some `evaluate` +method with the following signature + +```cpp +NetOut evaluate(const NetIn& netIn); +``` +Which is intended to integrate some network over some time and returns updated +abundances, temperature, density, and diagnostics. + +### NetIn and NetOut +GridFire solvers use a unified input and output type for their public interface +(though as developers will quickly learn, internally these are immediatly +broken down into simpler data structures). All solvers expect a `NetIn` struct +for the input type to the `evaluate` method and return a `NetOut` struct. + +#### NetIn +A `NetIn` struct contains +- The composition to start the timestep at. (`NetIn::composition`) +- The temperature in Kelvin (`NetIn::temperature`) +- The density in g/cm^3 (`NetIn::density`) +- The max time to evolve the network too in seconds (`NetIn::tMax`) +- The initial timestep to use in seconds (`NetIn::dt0`) +- The initial energy in the system in ergs (`NetIn::energy`) + +>**Note:** It is often useful to set `NetIn::dt0` to something *very* small and +>let an iterative timestepper push the timestep up. Often for main sequence +>burning I use ~1e-12 for dt0 + +>**Note:** The composition must be a `fourdst::composition::Composition` +>object. This is made avalible through the `foursdt` library and the +>`fourdst/composition/Composition.h` header. `fourdst` is installed +>automatically with GridFire + +>**Note:** In Python composition comes from `fourdst.composition.Composition` +>and similarly is installed automatically when building GridFire python +>bindings. + +#### NetOut +A `NetOut` struct contains +- The final composition after evolving to `tMax` (`NetOut::composition`) +- The number of steps the solver took to evolve to `tmax` (`NetOut::num_steps`) +- The final energy generated by the network while evolving to `tMax` +(`NetOut::energy`) + +>**Note:** Currently `GraphEngine` only considers energy due to nuclear mass +>defect and not neutrino loss. -- **NetworkSolverStrategy<EngineT>**: 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`, 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. +- **Integrator:** Implicit Rosenbrock4 scheme (order 4) via `Boost.Odeint`’s +`rosenbrock4`, optimized for stiff reaction networks with adaptive step +size control using configurable absolute and relative tolerances. +- **Jacobian Assembly:** Asks the base engine for the Jacobian Matrix +- **RHS Evaluation:** Assk the base engine for RHS of the abundance evolution +equations +- **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 loggers, which run in a +seperate non blocking thread, capture 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`. +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. + - 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. +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. +- **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. +- **Callback observer support:** Currently we use an observer built into our +`RHSManager` (`RHSManager::observe`); however, we intend to inlucde support for +custom, user defined, observer method. -These strategies can be developed by inheriting from `NetworkSolverStrategy` and registering against the same engine types without modifying existing engine code. +These strategies can be developed by inheriting from `NetworkSolverStrategy` +and registering against the same engine types without modifying existing engine +code. -## Usage Examples +## 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. -### C++ Example: GraphEngine Initialization + +# Usage Examples + +## C++ + +### GraphEngine Initialization ```cpp #include "gridfire/engine/engine_graph.h" #include "fourdst/composition/composition.h" @@ -251,7 +540,7 @@ fourdst::composition::Composition comp; gridfire::GraphEngine engine(comp); ``` -### C++ Example: Adaptive Network View +### Adaptive Network View ```cpp #include "gridfire/engine/views/engine_adaptive.h" #include "gridfire/engine/engine_graph.h" @@ -262,49 +551,49 @@ gridfire::GraphEngine baseEngine(comp); gridfire::AdaptiveEngineView adaptiveView(baseEngine); ``` -### Python Example -```python -import gridfire +### Composition Initialization +```cpp +#include "fourdst/composition/composition.h" +#include +#include +#include -from fourdst.composition import Composition +fourdst::composition::Composition comp; -symbols = ["H-1", ...] -X = [0.708, ...] +std::vector symbols = {"H-1", "He-4", "C-12"}; +std::vector massFractions = {0.7, 0.29, 0.01}; -comp = Composition() -comp.registerSymbols(symbols) -comp.setMassFraction(X) -comp.finalize(true) -# Initialize GraphEngine with predefined composition -engine = gridfire.GraphEngine(comp) -netIn = gridfire.types.NetIn -netIn.composition = comp -netIn.tMax = 1e-3 -netIn.temperature = 1.5e7 -netIn.density = 1.6e2 -netIn.dt0 = 1e-12 +comp.registerSymbols(symbols); +comp.setMassFraction(symbols, massFractions); -# Perform one integration step -netOut = engine.evaluate(netIn) -print(netOut) +comp.finalize(true); + +std::cout << comp << std::endl; ``` -## Common Workflow Example +### Common Workflow Example -A representative workflow often composes multiple engine views to balance accuracy, stability, and performance when integrating stiff nuclear networks: +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 "gridfire/engine/engine.h" // Unified header for real usage #include "fourdst/composition/composition.h" // 1. Define initial composition fourdst::composition::Composition comp; + +std::vector symbols = {"H-1", "He-4", "C-12"}; +std::vector massFractions = {0.7, 0.29, 0.01}; + +comp.registerSymbols(symbols); +comp.setMassFraction(symbols, massFractions); + +comp.finalize(true); + // 2. Create base network engine (full reaction graph) -gridfire::GraphEngine baseEngine(comp); +gridfire::GraphEngine baseEngine(comp, NetworkBuildDepth::SecondOrder) // 3. Partition network into fast/slow subsets (reduces stiffness) gridfire::MultiscalePartitioningEngineView msView(baseEngine); @@ -326,22 +615,73 @@ NetIn input{ // 7. Execute integration NetOut output = solver.evaluate(input); +std::cout << "Final results are: " << output << std::endl; ``` -**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. +#### 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. +This layered approach enhances stability for stiff networks while maintaining +accuracy and performance. -## Related Projects +## Python +The python bindings intentionally look **very** similar to the C++ code. +Generally all examples can be adapted to python by replacing includes of paths +with imports of modules such that + +`#include "gridfire/engine/GraphEngine.h` becomes `import gridfire.engine.GraphEngine` + +All GridFire C++ types have been bound and can be passed around as one would expect. + +### Common Workflow Examople +This example impliments the same logic as the above C++ example +```python +import gridfire + + +from fourdst.composition import Composition + +symbols = ["H-1", ...] +X = [0.7, ...] + +comp = Composition() +comp.registerSymbols(symbols) +comp.setMassFraction(X) +comp.finalize(true) +# Initialize GraphEngine with predefined composition +engine = gridfire.GraphEngine(comp) +netIn = gridfire.types.NetIn +netIn.composition = comp +netIn.tMax = 1e-3 +netIn.temperature = 1.5e7 +netIn.density = 1.6e2 +netIn.dt0 = 1e-12 + +# Perform one integration step +netOut = engine.evaluate(netIn) +print(netOut) +``` + + + +# 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. +- [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 diff --git a/docs/html/_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html b/docs/html/_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html index 62bb7312..9aeb8635 100644 --- a/docs/html/_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html +++ b/docs/html/_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid_fire_2src_2include_2gridfire_2engine_2engine_approx8_8h-example.html @@ -114,7 +114,7 @@ $(function(){initNavTree('_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid
vec7 a = {1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0};
vec7 b = {0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5};
double result = sum_product(a, b);
-
gridfire::approx8::sum_product
double sum_product(const vec7 &a, const vec7 &b)
Definition engine_approx8.cpp:82
+
gridfire::approx8::sum_product
double sum_product(const vec7 &a, const vec7 &b)
Definition engine_approx8.cpp:82
/* ***********************************************************************
//
// Copyright (C) 2025 -- The 4D-STAR Collaboration
@@ -262,56 +262,56 @@ $(function(){initNavTree('_2_users_2tboudreaux_2_programming_24_d_s_t_a_r_2_grid
} // namespace nnApprox8
-
gridfire::approx8::Approx8Network::convert_netIn
static vector_type convert_netIn(const NetIn &netIn)
Converts the input parameters to the internal state vector.
Definition engine_approx8.cpp:509
-
gridfire::approx8::Approx8Network::isStiff
bool isStiff() const override
Checks if the solver is using a stiff method.
Definition engine_approx8.h:315
- - - - -
gridfire::approx8::Approx8Network::evaluate
NetOut evaluate(const NetIn &netIn) override
Evaluates the nuclear network.
Definition engine_approx8.cpp:445
- -
gridfire::approx8::Approx8Network::setStiff
void setStiff(bool stiff) override
Sets whether the solver should use a stiff method.
Definition engine_approx8.cpp:505
- -
gridfire::approx8::he3he3_rate
double he3he3_rate(const vec7 &T9)
Calculates the rate for the reaction he3 + he3 -> he4 + 2p.
Definition engine_approx8.cpp:129
-
gridfire::approx8::pp_rate
double pp_rate(const vec7 &T9)
Calculates the rate for the reaction p + p -> d.
Definition engine_approx8.cpp:115
-
gridfire::approx8::get_T9_array
vec7 get_T9_array(const double &T)
Definition engine_approx8.cpp:93
-
gridfire::approx8::triple_alpha_rate
double triple_alpha_rate(const vec7 &T9)
Calculates the rate for the reaction he4 + he4 + he4 -> c12.
Definition engine_approx8.cpp:142
-
gridfire::approx8::matrix_type
boost::numeric::ublas::matrix< double > matrix_type
Alias for a matrix of doubles using Boost uBLAS.
Definition engine_approx8.h:51
-
gridfire::approx8::n14p_rate
double n14p_rate(const vec7 &T9)
Calculates the rate for the reaction n14(p,g)o15 - o15 + p -> c12 + he4.
Definition engine_approx8.cpp:164
-
gridfire::approx8::n14a_rate
double n14a_rate(const vec7 &T9)
Calculates the rate for the reaction n14(a,g)f18 assumed to go on to ne20.
Definition engine_approx8.cpp:173
-
gridfire::approx8::dp_rate
double dp_rate(const vec7 &T9)
Calculates the rate for the reaction p + d -> he3.
Definition engine_approx8.cpp:122
-
gridfire::approx8::he3he4_rate
double he3he4_rate(const vec7 &T9)
Calculates the rate for the reaction he3(he3,2p)he4.
Definition engine_approx8.cpp:135
-
gridfire::approx8::o16p_rate
double o16p_rate(const vec7 &T9)
Calculates the rate for the reaction o16(p,g)f17 then f17 -> o17(p,a)n14.
Definition engine_approx8.cpp:204
-
gridfire::approx8::c12c12_rate
double c12c12_rate(const vec7 &T9)
Calculates the rate for the reaction c12(c12,a)ne20.
Definition engine_approx8.cpp:227
-
gridfire::approx8::o16a_rate
double o16a_rate(const vec7 &T9)
Calculates the rate for the reaction o16(a,g)ne20.
Definition engine_approx8.cpp:210
-
gridfire::approx8::c12p_rate
double c12p_rate(const vec7 &T9)
Calculates the rate for the reaction c12 + p -> n13.
Definition engine_approx8.cpp:150
-
gridfire::approx8::c12o16_rate
double c12o16_rate(const vec7 &T9)
Calculates the rate for the reaction c12(o16,a)mg24.
Definition engine_approx8.cpp:233
-
gridfire::approx8::n15pa_rate
double n15pa_rate(const vec7 &T9)
Calculates the rate for the reaction n15(p,a)c12 (CNO I).
Definition engine_approx8.cpp:181
-
gridfire::approx8::vector_type
boost::numeric::ublas::vector< double > vector_type
Alias for a vector of doubles using Boost uBLAS.
Definition engine_approx8.h:45
-
gridfire::approx8::vec7
std::array< double, 7 > vec7
Alias for a std::array of 7 doubles.
Definition engine_approx8.h:57
-
gridfire::approx8::n15pg_frac
double n15pg_frac(const vec7 &T9)
Calculates the fraction for the reaction n15(p,g)o16.
Definition engine_approx8.cpp:197
-
gridfire::approx8::n15pg_rate
double n15pg_rate(const vec7 &T9)
Calculates the rate for the reaction n15(p,g)o16 (CNO II).
Definition engine_approx8.cpp:190
-
gridfire::approx8::ne20a_rate
double ne20a_rate(const vec7 &T9)
Calculates the rate for the reaction ne20(a,g)mg24.
Definition engine_approx8.cpp:218
-
gridfire::approx8::rate_fit
double rate_fit(const vec7 &T9, const vec7 &coef)
Definition engine_approx8.cpp:110
-
gridfire::approx8::c12a_rate
double c12a_rate(const vec7 &T9)
Calculates the rate for the reaction c12 + he4 -> o16.
Definition engine_approx8.cpp:157
+
gridfire::approx8::Approx8Network::convert_netIn
static vector_type convert_netIn(const NetIn &netIn)
Converts the input parameters to the internal state vector.
Definition engine_approx8.cpp:509
+
gridfire::approx8::Approx8Network::isStiff
bool isStiff() const override
Checks if the solver is using a stiff method.
Definition engine_approx8.h:315
+
gridfire::approx8::Approx8Network::Approx8Network
Approx8Network()
Definition engine_approx8.cpp:443
+
gridfire::approx8::Approx8Network::m_stiff
bool m_stiff
Definition engine_approx8.h:320
+
gridfire::approx8::Approx8Network::m_dt0
double m_dt0
Definition engine_approx8.h:319
+
gridfire::approx8::Approx8Network::m_tMax
double m_tMax
Definition engine_approx8.h:318
+
gridfire::approx8::Approx8Network::evaluate
NetOut evaluate(const NetIn &netIn) override
Evaluates the nuclear network.
Definition engine_approx8.cpp:445
+
gridfire::approx8::Approx8Network::m_y
vector_type m_y
Definition engine_approx8.h:317
+
gridfire::approx8::Approx8Network::setStiff
void setStiff(bool stiff) override
Sets whether the solver should use a stiff method.
Definition engine_approx8.cpp:505
+
gridfire::approx8
Definition engine_approx8.h:39
+
gridfire::approx8::he3he3_rate
double he3he3_rate(const vec7 &T9)
Calculates the rate for the reaction he3 + he3 -> he4 + 2p.
Definition engine_approx8.cpp:129
+
gridfire::approx8::pp_rate
double pp_rate(const vec7 &T9)
Calculates the rate for the reaction p + p -> d.
Definition engine_approx8.cpp:115
+
gridfire::approx8::get_T9_array
vec7 get_T9_array(const double &T)
Definition engine_approx8.cpp:93
+
gridfire::approx8::triple_alpha_rate
double triple_alpha_rate(const vec7 &T9)
Calculates the rate for the reaction he4 + he4 + he4 -> c12.
Definition engine_approx8.cpp:142
+
gridfire::approx8::matrix_type
boost::numeric::ublas::matrix< double > matrix_type
Alias for a matrix of doubles using Boost uBLAS.
Definition engine_approx8.h:51
+
gridfire::approx8::n14p_rate
double n14p_rate(const vec7 &T9)
Calculates the rate for the reaction n14(p,g)o15 - o15 + p -> c12 + he4.
Definition engine_approx8.cpp:164
+
gridfire::approx8::n14a_rate
double n14a_rate(const vec7 &T9)
Calculates the rate for the reaction n14(a,g)f18 assumed to go on to ne20.
Definition engine_approx8.cpp:173
+
gridfire::approx8::dp_rate
double dp_rate(const vec7 &T9)
Calculates the rate for the reaction p + d -> he3.
Definition engine_approx8.cpp:122
+
gridfire::approx8::he3he4_rate
double he3he4_rate(const vec7 &T9)
Calculates the rate for the reaction he3(he3,2p)he4.
Definition engine_approx8.cpp:135
+
gridfire::approx8::o16p_rate
double o16p_rate(const vec7 &T9)
Calculates the rate for the reaction o16(p,g)f17 then f17 -> o17(p,a)n14.
Definition engine_approx8.cpp:204
+
gridfire::approx8::c12c12_rate
double c12c12_rate(const vec7 &T9)
Calculates the rate for the reaction c12(c12,a)ne20.
Definition engine_approx8.cpp:227
+
gridfire::approx8::o16a_rate
double o16a_rate(const vec7 &T9)
Calculates the rate for the reaction o16(a,g)ne20.
Definition engine_approx8.cpp:210
+
gridfire::approx8::c12p_rate
double c12p_rate(const vec7 &T9)
Calculates the rate for the reaction c12 + p -> n13.
Definition engine_approx8.cpp:150
+
gridfire::approx8::c12o16_rate
double c12o16_rate(const vec7 &T9)
Calculates the rate for the reaction c12(o16,a)mg24.
Definition engine_approx8.cpp:233
+
gridfire::approx8::n15pa_rate
double n15pa_rate(const vec7 &T9)
Calculates the rate for the reaction n15(p,a)c12 (CNO I).
Definition engine_approx8.cpp:181
+
gridfire::approx8::vector_type
boost::numeric::ublas::vector< double > vector_type
Alias for a vector of doubles using Boost uBLAS.
Definition engine_approx8.h:45
+
gridfire::approx8::vec7
std::array< double, 7 > vec7
Alias for a std::array of 7 doubles.
Definition engine_approx8.h:57
+
gridfire::approx8::n15pg_frac
double n15pg_frac(const vec7 &T9)
Calculates the fraction for the reaction n15(p,g)o16.
Definition engine_approx8.cpp:197
+
gridfire::approx8::n15pg_rate
double n15pg_rate(const vec7 &T9)
Calculates the rate for the reaction n15(p,g)o16 (CNO II).
Definition engine_approx8.cpp:190
+
gridfire::approx8::ne20a_rate
double ne20a_rate(const vec7 &T9)
Calculates the rate for the reaction ne20(a,g)mg24.
Definition engine_approx8.cpp:218
+
gridfire::approx8::rate_fit
double rate_fit(const vec7 &T9, const vec7 &coef)
Definition engine_approx8.cpp:110
+
gridfire::approx8::c12a_rate
double c12a_rate(const vec7 &T9)
Calculates the rate for the reaction c12 + he4 -> o16.
Definition engine_approx8.cpp:157
-
gridfire::approx8::Approx8Net::iTemp
static constexpr int iTemp
Definition engine_approx8.h:73
-
gridfire::approx8::Approx8Net::iEnergy
static constexpr int iEnergy
Definition engine_approx8.h:75
-
gridfire::approx8::Approx8Net::in14
static constexpr int in14
Definition engine_approx8.h:68
-
gridfire::approx8::Approx8Net::aIon
static constexpr std::array< int, nIso > aIon
Definition engine_approx8.h:80
-
gridfire::approx8::Approx8Net::nIso
static constexpr int nIso
Definition engine_approx8.h:77
-
gridfire::approx8::Approx8Net::iDensity
static constexpr int iDensity
Definition engine_approx8.h:74
-
gridfire::approx8::Approx8Net::nVar
static constexpr int nVar
Definition engine_approx8.h:78
-
gridfire::approx8::Approx8Net::ihe4
static constexpr int ihe4
Definition engine_approx8.h:66
-
gridfire::approx8::Approx8Net::mIon
static constexpr std::array< double, nIso > mIon
Definition engine_approx8.h:91
-
gridfire::approx8::Approx8Net::ic12
static constexpr int ic12
Definition engine_approx8.h:67
-
gridfire::approx8::Approx8Net::img24
static constexpr int img24
Definition engine_approx8.h:71
-
gridfire::approx8::Approx8Net::ihe3
static constexpr int ihe3
Definition engine_approx8.h:65
-
gridfire::approx8::Approx8Net::io16
static constexpr int io16
Definition engine_approx8.h:69
- -
gridfire::approx8::Approx8Net::ine20
static constexpr int ine20
Definition engine_approx8.h:70
-
gridfire::approx8::Jacobian::operator()
void operator()(const vector_type &y, matrix_type &J, double, vector_type &dfdt) const
Calculates the Jacobian matrix.
Definition engine_approx8.cpp:243
-
gridfire::approx8::ODE::operator()
void operator()(const vector_type &y, vector_type &dydt, double) const
Calculates the derivatives of the state vector.
Definition engine_approx8.cpp:348
+
gridfire::approx8::Approx8Net::iTemp
static constexpr int iTemp
Definition engine_approx8.h:73
+
gridfire::approx8::Approx8Net::iEnergy
static constexpr int iEnergy
Definition engine_approx8.h:75
+
gridfire::approx8::Approx8Net::in14
static constexpr int in14
Definition engine_approx8.h:68
+
gridfire::approx8::Approx8Net::aIon
static constexpr std::array< int, nIso > aIon
Definition engine_approx8.h:80
+
gridfire::approx8::Approx8Net::nIso
static constexpr int nIso
Definition engine_approx8.h:77
+
gridfire::approx8::Approx8Net::iDensity
static constexpr int iDensity
Definition engine_approx8.h:74
+
gridfire::approx8::Approx8Net::nVar
static constexpr int nVar
Definition engine_approx8.h:78
+
gridfire::approx8::Approx8Net::ihe4
static constexpr int ihe4
Definition engine_approx8.h:66
+
gridfire::approx8::Approx8Net::mIon
static constexpr std::array< double, nIso > mIon
Definition engine_approx8.h:91
+
gridfire::approx8::Approx8Net::ic12
static constexpr int ic12
Definition engine_approx8.h:67
+
gridfire::approx8::Approx8Net::img24
static constexpr int img24
Definition engine_approx8.h:71
+
gridfire::approx8::Approx8Net::ihe3
static constexpr int ihe3
Definition engine_approx8.h:65
+
gridfire::approx8::Approx8Net::io16
static constexpr int io16
Definition engine_approx8.h:69
+
gridfire::approx8::Approx8Net::ih1
static constexpr int ih1
Definition engine_approx8.h:64
+
gridfire::approx8::Approx8Net::ine20
static constexpr int ine20
Definition engine_approx8.h:70
+
gridfire::approx8::Jacobian::operator()
void operator()(const vector_type &y, matrix_type &J, double, vector_type &dfdt) const
Calculates the Jacobian matrix.
Definition engine_approx8.cpp:243
+
gridfire::approx8::ODE::operator()
void operator()(const vector_type &y, vector_type &dydt, double) const
Calculates the derivatives of the state vector.
Definition engine_approx8.cpp:348
diff --git a/docs/html/bindings_8cpp.html b/docs/html/bindings_8cpp.html index 32e720c1..7328ef32 100644 --- a/docs/html/bindings_8cpp.html +++ b/docs/html/bindings_8cpp.html @@ -107,19 +107,17 @@ $(function(){initNavTree('bindings_8cpp.html',''); initResizable(true); });
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
#include <string>
-#include "types/bindings.h"
-#include "partition/bindings.h"
-#include "expectations/bindings.h"
-#include "engine/bindings.h"
-#include "exceptions/bindings.h"
-#include "io/bindings.h"
-#include "reaction/bindings.h"
-#include "screening/bindings.h"
-#include "solver/bindings.h"
-#include "utils/bindings.h"
-
-

Go to the source code of this file.

- +#include "types/bindings.h"
+#include "partition/bindings.h"
+#include "expectations/bindings.h"
+#include "engine/bindings.h"
+#include "exceptions/bindings.h"
+#include "io/bindings.h"
+#include "reaction/bindings.h"
+#include "screening/bindings.h"
+#include "solver/bindings.h"
+#include "utils/bindings.h"
+
@@ -145,8 +143,6 @@ Functions

Functions

 PYBIND11_MODULE (gridfire, m)
-

Definition at line 17 of file bindings.cpp.

-
diff --git a/docs/html/building_8h.html b/docs/html/building_8h.html index 344e1517..5361aafd 100644 --- a/docs/html/building_8h.html +++ b/docs/html/building_8h.html @@ -107,9 +107,7 @@ $(function(){initNavTree('building_8h.html',''); initResizable(true); });
#include <variant>
-
-

Go to the source code of this file.

- +
diff --git a/docs/html/class_py_dynamic_engine.html b/docs/html/class_py_dynamic_engine.html index a871d0e7..8329085e 100644 --- a/docs/html/class_py_dynamic_engine.html +++ b/docs/html/class_py_dynamic_engine.html @@ -107,7 +107,7 @@ $(function(){initNavTree('class_py_dynamic_engine.html',''); initResizable(true)
-

#include <py_engine.h>

+

#include <py_engine.h>

Inheritance diagram for PyDynamicEngine:
@@ -185,10 +185,7 @@ Private Attributes

Namespaces

namespace  gridfire
std::vector< fourdst::atomic::Species > m_species_cache
 
-

Detailed Description

-
-

Definition at line 20 of file py_engine.h.

-

Member Function Documentation

+

Member Function Documentation

◆ calculateMolarReactionFlow()

@@ -241,8 +238,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 123 of file py_engine.cpp.

-
@@ -291,8 +286,6 @@ Private Attributes

Implements gridfire::Engine.

-

Definition at line 70 of file py_engine.cpp.

- @@ -340,8 +333,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 79 of file py_engine.cpp.

- @@ -383,8 +374,6 @@ Private Attributes

Reimplemented from gridfire::DynamicEngine.

-

Definition at line 88 of file py_engine.cpp.

- @@ -415,8 +404,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 106 of file py_engine.cpp.

- @@ -444,8 +431,6 @@ Private Attributes

Reimplemented from gridfire::DynamicEngine.

-

Definition at line 41 of file py_engine.h.

- @@ -488,8 +473,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 97 of file py_engine.cpp.

- @@ -520,8 +503,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 132 of file py_engine.cpp.

- @@ -551,8 +532,6 @@ Private Attributes

Implements gridfire::Engine.

-

Definition at line 50 of file py_engine.cpp.

- @@ -585,8 +564,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 194 of file py_engine.cpp.

- @@ -623,8 +600,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 158 of file py_engine.cpp.

- @@ -652,8 +627,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 202 of file py_engine.cpp.

- @@ -702,8 +675,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 149 of file py_engine.cpp.

- @@ -746,8 +717,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 114 of file py_engine.cpp.

- @@ -775,8 +744,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 176 of file py_engine.cpp.

- @@ -804,8 +771,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 211 of file py_engine.cpp.

- @@ -833,8 +798,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 220 of file py_engine.cpp.

- @@ -866,8 +829,6 @@ Private Attributes

Reimplemented from gridfire::DynamicEngine.

-

Definition at line 44 of file py_engine.h.

- @@ -895,8 +856,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 140 of file py_engine.cpp.

- @@ -936,8 +895,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 185 of file py_engine.cpp.

- @@ -978,8 +935,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 167 of file py_engine.cpp.

-

Member Data Documentation

@@ -1003,13 +958,11 @@ Private Attributes
-

Definition at line 48 of file py_engine.h.

-
The documentation for this class was generated from the following files: diff --git a/docs/html/class_py_dynamic_engine_view.html b/docs/html/class_py_dynamic_engine_view.html index 7d84f014..84ac4c71 100644 --- a/docs/html/class_py_dynamic_engine_view.html +++ b/docs/html/class_py_dynamic_engine_view.html @@ -106,7 +106,7 @@ $(function(){initNavTree('class_py_dynamic_engine_view.html',''); initResizable(
-

#include <py_engine.h>

+

#include <py_engine.h>

Inheritance diagram for PyDynamicEngineView:
@@ -130,10 +130,7 @@ Additional Inherited Members  Virtual destructor.
  -

Detailed Description

-
-

Definition at line 57 of file py_engine.h.

-

Member Function Documentation

+

Member Function Documentation

◆ getBaseEngine()

@@ -164,13 +161,11 @@ Additional Inherited Members

Implements gridfire::EngineView< gridfire::DynamicEngine >.

-

Definition at line 237 of file py_engine.cpp.

-
The documentation for this class was generated from the following files: diff --git a/docs/html/class_py_dynamic_network_solver_strategy.html b/docs/html/class_py_dynamic_network_solver_strategy.html index 929b3ded..1ffe797b 100644 --- a/docs/html/class_py_dynamic_network_solver_strategy.html +++ b/docs/html/class_py_dynamic_network_solver_strategy.html @@ -106,7 +106,7 @@ $(function(){initNavTree('class_py_dynamic_network_solver_strategy.html',''); in
-

#include <py_solver.h>

+

#include <py_solver.h>

Inheritance diagram for PyDynamicNetworkSolverStrategy:
@@ -148,10 +148,7 @@ Additional Inherited Members  The engine used by this solver strategy.
  -

Detailed Description

-
-

Definition at line 7 of file py_solver.h.

-

Constructor & Destructor Documentation

+

Constructor & Destructor Documentation

◆ PyDynamicNetworkSolverStrategy()

@@ -175,8 +172,6 @@ Additional Inherited Members
-

Definition at line 8 of file py_solver.h.

-

Member Function Documentation

@@ -214,13 +209,11 @@ Additional Inherited Members

Implements gridfire::solver::NetworkSolverStrategy< DynamicEngine >.

-

Definition at line 14 of file py_solver.cpp.

-
The documentation for this class was generated from the following files: diff --git a/docs/html/class_py_engine.html b/docs/html/class_py_engine.html index 465c2a7b..625dac78 100644 --- a/docs/html/class_py_engine.html +++ b/docs/html/class_py_engine.html @@ -107,7 +107,7 @@ $(function(){initNavTree('class_py_engine.html',''); initResizable(true); });
-

#include <py_engine.h>

+

#include <py_engine.h>

Inheritance diagram for PyEngine:
@@ -136,10 +136,7 @@ Private Attributes std::vector< fourdst::atomic::Species > m_species_cache   -

Detailed Description

-
-

Definition at line 12 of file py_engine.h.

-

Member Function Documentation

+

Member Function Documentation

◆ calculateRHSAndEnergy()

@@ -186,8 +183,6 @@ Private Attributes

Implements gridfire::Engine.

-

Definition at line 37 of file py_engine.cpp.

-
@@ -218,8 +213,6 @@ Private Attributes

Implements gridfire::Engine.

-

Definition at line 16 of file py_engine.cpp.

-

Member Data Documentation

@@ -243,13 +236,11 @@ Private Attributes
-

Definition at line 17 of file py_engine.h.

-
The documentation for this class was generated from the following files: diff --git a/docs/html/class_py_engine_view.html b/docs/html/class_py_engine_view.html index addaf25f..c97cc40a 100644 --- a/docs/html/class_py_engine_view.html +++ b/docs/html/class_py_engine_view.html @@ -106,7 +106,7 @@ $(function(){initNavTree('class_py_engine_view.html',''); initResizable(true); }
-

#include <py_engine.h>

+

#include <py_engine.h>

Inheritance diagram for PyEngineView:
@@ -130,10 +130,7 @@ Additional Inherited Members  Virtual destructor.
  -

Detailed Description

-
-

Definition at line 53 of file py_engine.h.

-

Member Function Documentation

+

Member Function Documentation

◆ getBaseEngine()

@@ -164,13 +161,11 @@ Additional Inherited Members

Implements gridfire::EngineView< gridfire::Engine >.

-

Definition at line 229 of file py_engine.cpp.

-
The documentation for this class was generated from the following files: diff --git a/docs/html/class_py_network_file_parser.html b/docs/html/class_py_network_file_parser.html index 9073db0d..f588aa65 100644 --- a/docs/html/class_py_network_file_parser.html +++ b/docs/html/class_py_network_file_parser.html @@ -106,7 +106,7 @@ $(function(){initNavTree('class_py_network_file_parser.html',''); initResizable(
-

#include <py_io.h>

+

#include <py_io.h>

Inheritance diagram for PyNetworkFileParser:
@@ -130,10 +130,7 @@ Additional Inherited Members  Virtual destructor for the base class.
  -

Detailed Description

-
-

Definition at line 5 of file py_io.h.

-

Member Function Documentation

+

Member Function Documentation

◆ parse()

@@ -184,13 +181,11 @@ Additional Inherited Members

Implements gridfire::io::NetworkFileParser.

-

Definition at line 8 of file py_io.cpp.

-
The documentation for this class was generated from the following files: diff --git a/docs/html/class_py_partition_function.html b/docs/html/class_py_partition_function.html index 69e583ab..3a5ae893 100644 --- a/docs/html/class_py_partition_function.html +++ b/docs/html/class_py_partition_function.html @@ -106,7 +106,7 @@ $(function(){initNavTree('class_py_partition_function.html',''); initResizable(t
-

#include <py_partition.h>

+

#include <py_partition.h>

Inheritance diagram for PyPartitionFunction:
@@ -142,10 +142,7 @@ Additional Inherited Members  Virtual destructor.
  -

Detailed Description

-
-

Definition at line 9 of file py_partition.h.

-

Member Function Documentation

+

Member Function Documentation

◆ clone()

@@ -175,8 +172,6 @@ Additional Inherited Members

Implements gridfire::partition::PartitionFunction.

-

Definition at line 50 of file py_partition.cpp.

-
@@ -226,8 +221,6 @@ Additional Inherited Members

Implements gridfire::partition::PartitionFunction.

-

Definition at line 15 of file py_partition.cpp.

- @@ -278,8 +271,6 @@ Additional Inherited Members

Implements gridfire::partition::PartitionFunction.

-

Definition at line 24 of file py_partition.cpp.

- @@ -322,8 +313,6 @@ Additional Inherited Members

Implements gridfire::partition::PartitionFunction.

-

Definition at line 33 of file py_partition.cpp.

- @@ -355,13 +344,11 @@ Additional Inherited Members

Implements gridfire::partition::PartitionFunction.

-

Definition at line 42 of file py_partition.cpp.

-
The documentation for this class was generated from the following files: diff --git a/docs/html/class_py_screening.html b/docs/html/class_py_screening.html index 2b8e8502..886594d3 100644 --- a/docs/html/class_py_screening.html +++ b/docs/html/class_py_screening.html @@ -106,7 +106,7 @@ $(function(){initNavTree('class_py_screening.html',''); initResizable(true); });
-

#include <py_screening.h>

+

#include <py_screening.h>

Inheritance diagram for PyScreening:
@@ -137,10 +137,7 @@ Additional Inherited Members  Virtual destructor.
  -

Detailed Description

-
-

Definition at line 13 of file py_screening.h.

-

Member Function Documentation

+

Member Function Documentation

◆ calculateScreeningFactors() [1/2]

@@ -200,8 +197,6 @@ Additional Inherited Members

Implements gridfire::screening::ScreeningModel.

-

Definition at line 25 of file py_screening.cpp.

-
@@ -278,13 +273,11 @@ Additional Inherited Members

Implements gridfire::screening::ScreeningModel.

-

Definition at line 16 of file py_screening.cpp.

-
The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1_adaptive_engine_view.html b/docs/html/classgridfire_1_1_adaptive_engine_view.html index d24612d9..2fee8f9f 100644 --- a/docs/html/classgridfire_1_1_adaptive_engine_view.html +++ b/docs/html/classgridfire_1_1_adaptive_engine_view.html @@ -113,7 +113,7 @@ $(function(){initNavTree('classgridfire_1_1_adaptive_engine_view.html',''); init

An engine view that dynamically adapts the reaction network based on runtime conditions. More...

-

#include <engine_adaptive.h>

+

#include <engine_adaptive.h>

Inheritance diagram for gridfire::AdaptiveEngineView:
@@ -295,8 +295,6 @@ Private Attributes engine_view_abstract.h
AdaptiveEngineView::update()
- -

Definition at line 50 of file engine_adaptive.h.

Member Typedef Documentation

◆ Config

@@ -318,8 +316,6 @@ Private Attributes
-

Definition at line 279 of file engine_adaptive.h.

-
@@ -342,8 +338,6 @@ Private Attributes
-

Definition at line 280 of file engine_adaptive.h.

-
@@ -366,8 +360,6 @@ Private Attributes
-

Definition at line 452 of file engine_adaptive.h.

-

Constructor & Destructor Documentation

@@ -403,8 +395,6 @@ Private Attributes

Initializes the active species and reactions to the full network, and constructs the initial index maps.

-

Definition at line 16 of file engine_adaptive.cpp.

-

Member Function Documentation

@@ -456,8 +446,6 @@ Private Attributes -

Definition at line 368 of file engine_adaptive.cpp.

- @@ -519,8 +507,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 212 of file engine_adaptive.cpp.

- @@ -576,8 +562,6 @@ Private Attributes

Implements gridfire::Engine.

-

Definition at line 152 of file engine_adaptive.cpp.

- @@ -608,8 +592,6 @@ Private Attributes

This method creates a map from the indices of the active reactions to the indices of the corresponding reactions in the full network.

See also
AdaptiveEngineView::update()
-

Definition at line 56 of file engine_adaptive.cpp.

- @@ -640,8 +622,6 @@ Private Attributes

This method creates a map from the indices of the active species to the indices of the corresponding species in the full network.

See also
AdaptiveEngineView::update()
-

Definition at line 27 of file engine_adaptive.cpp.

- @@ -702,8 +682,6 @@ Private Attributes -

Definition at line 442 of file engine_adaptive.cpp.

- @@ -744,8 +722,6 @@ Private Attributes -

Definition at line 641 of file engine_adaptive.cpp.

- @@ -789,8 +765,6 @@ Private Attributes -

Definition at line 399 of file engine_adaptive.cpp.

- @@ -845,8 +819,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 175 of file engine_adaptive.cpp.

- @@ -884,8 +856,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 197 of file engine_adaptive.cpp.

- @@ -916,8 +886,6 @@ Private Attributes

Implements gridfire::EngineView< DynamicEngine >.

-

Definition at line 239 of file engine_adaptive.h.

- @@ -968,8 +936,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 186 of file engine_adaptive.cpp.

- @@ -1000,8 +966,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 229 of file engine_adaptive.cpp.

- @@ -1032,8 +996,6 @@ Private Attributes

Implements gridfire::Engine.

-

Definition at line 148 of file engine_adaptive.cpp.

- @@ -1064,14 +1026,12 @@ Private Attributes
Returns
The current screening model type.
Usage Example:
AdaptiveEngineView engineView(...);
screening::ScreeningType model = engineView.getScreeningModel();
-
gridfire::AdaptiveEngineView::AdaptiveEngineView
AdaptiveEngineView(DynamicEngine &baseEngine)
Constructs an AdaptiveEngineView.
Definition engine_adaptive.cpp:16
-
gridfire::screening::ScreeningType
ScreeningType
Enumerates the available plasma screening models.
Definition screening_types.h:15
+
gridfire::AdaptiveEngineView::AdaptiveEngineView
AdaptiveEngineView(DynamicEngine &baseEngine)
Constructs an AdaptiveEngineView.
Definition engine_adaptive.cpp:16
+
gridfire::screening::ScreeningType
ScreeningType
Enumerates the available plasma screening models.
Definition screening_types.h:15

Implements gridfire::DynamicEngine.

-

Definition at line 296 of file engine_adaptive.cpp.

- @@ -1108,8 +1068,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 266 of file engine_adaptive.cpp.

- @@ -1137,8 +1095,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 312 of file engine_adaptive.cpp.

- @@ -1193,8 +1149,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 238 of file engine_adaptive.cpp.

- @@ -1245,8 +1199,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 202 of file engine_adaptive.cpp.

- @@ -1274,8 +1226,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 144 of file engine_adaptive.cpp.

- @@ -1310,8 +1260,6 @@ Private Attributes
Returns
A vector of abundances for the full network, with the abundances of the active species copied from the culled vector.
-

Definition at line 323 of file engine_adaptive.cpp.

- @@ -1352,8 +1300,6 @@ Private Attributes -

Definition at line 350 of file engine_adaptive.cpp.

- @@ -1394,8 +1340,6 @@ Private Attributes -

Definition at line 341 of file engine_adaptive.cpp.

- @@ -1430,8 +1374,6 @@ Private Attributes
Returns
A vector of abundances for the active species, with the abundances of the active species copied from the full vector.
-

Definition at line 332 of file engine_adaptive.cpp.

- @@ -1459,8 +1401,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 300 of file engine_adaptive.cpp.

- @@ -1488,8 +1428,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 308 of file engine_adaptive.cpp.

- @@ -1534,8 +1472,6 @@ Private Attributes
-

Definition at line 485 of file engine_adaptive.cpp.

-
@@ -1563,8 +1499,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 233 of file engine_adaptive.cpp.

- @@ -1600,14 +1534,12 @@ Private Attributes
Usage Example:
AdaptiveEngineView engineView(...);
engineView.setScreeningModel(screening::ScreeningType::WEAK);
-
gridfire::screening::ScreeningType::WEAK
@ WEAK
Weak screening model (Salpeter, 1954).
Definition screening_types.h:35
+
gridfire::screening::ScreeningType::WEAK
@ WEAK
Weak screening model (Salpeter, 1954).
Definition screening_types.h:35
Postcondition
The screening model of the base engine is updated.

Implements gridfire::DynamicEngine.

-

Definition at line 292 of file engine_adaptive.cpp.

- @@ -1659,8 +1591,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 88 of file engine_adaptive.cpp.

- @@ -1694,8 +1624,6 @@ Private Attributes -

Definition at line 359 of file engine_adaptive.cpp.

-

Member Data Documentation

@@ -1721,8 +1649,6 @@ Private Attributes

The set of reactions that are currently active in the network.

-

Definition at line 292 of file engine_adaptive.h.

- @@ -1747,8 +1673,6 @@ Private Attributes

The set of species that are currently active in the network.

-

Definition at line 290 of file engine_adaptive.h.

- @@ -1773,8 +1697,6 @@ Private Attributes

The underlying engine to which this view delegates calculations.

-

Definition at line 287 of file engine_adaptive.h.

- @@ -1799,8 +1721,6 @@ Private Attributes

A reference to the singleton Config instance, used for retrieving configuration parameters.

-

Definition at line 282 of file engine_adaptive.h.

- @@ -1825,8 +1745,6 @@ Private Attributes

A flag indicating whether the view is stale and needs to be updated.

-

Definition at line 300 of file engine_adaptive.h.

- @@ -1851,8 +1769,6 @@ Private Attributes

A pointer to the logger instance, used for logging messages.

-

Definition at line 284 of file engine_adaptive.h.

- @@ -1877,8 +1793,6 @@ Private Attributes

A map from the indices of the active reactions to the indices of the corresponding reactions in the full network.

-

Definition at line 297 of file engine_adaptive.h.

- @@ -1903,13 +1817,11 @@ Private Attributes

A map from the indices of the active species to the indices of the corresponding species in the full network.

-

Definition at line 295 of file engine_adaptive.h.

-
The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1_defined_engine_view.html b/docs/html/classgridfire_1_1_defined_engine_view.html index aa78d0b8..2e19c656 100644 --- a/docs/html/classgridfire_1_1_defined_engine_view.html +++ b/docs/html/classgridfire_1_1_defined_engine_view.html @@ -109,7 +109,7 @@ $(function(){initNavTree('classgridfire_1_1_defined_engine_view.html',''); initR
-

#include <engine_defined.h>

+

#include <engine_defined.h>

Inheritance diagram for gridfire::DefinedEngineView:
@@ -244,10 +244,7 @@ Private Attributes std::vector< size_t > m_reactionIndexMap   -

Detailed Description

-
-

Definition at line 16 of file engine_defined.h.

-

Constructor & Destructor Documentation

+

Constructor & Destructor Documentation

◆ DefinedEngineView()

@@ -267,8 +264,6 @@ Private Attributes
-

Definition at line 17 of file engine_defined.cpp.

-

Member Function Documentation

@@ -329,8 +324,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 91 of file engine_defined.cpp.

- @@ -384,8 +377,6 @@ Private Attributes

Implements gridfire::Engine.

-

Definition at line 30 of file engine_defined.cpp.

- @@ -411,8 +402,6 @@ Private Attributes
-

Definition at line 321 of file engine_defined.cpp.

-
@@ -448,8 +437,6 @@ Private Attributes -

Definition at line 245 of file engine_defined.cpp.

- @@ -485,8 +472,6 @@ Private Attributes -

Definition at line 216 of file engine_defined.cpp.

- @@ -539,8 +524,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 51 of file engine_defined.cpp.

- @@ -576,8 +559,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 74 of file engine_defined.cpp.

- @@ -607,12 +588,10 @@ Private Attributes
Returns
Const reference to the underlying engine.

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.

Example:

const DynamicEngine& engine = myView.getBaseEngine();
-
gridfire::DynamicEngine
Abstract class for engines supporting Jacobian and stoichiometry operations.
Definition engine_abstract.h:130
+
gridfire::DynamicEngine
Abstract class for engines supporting Jacobian and stoichiometry operations.
Definition engine_abstract.h:130

Implements gridfire::EngineView< DynamicEngine >.

-

Definition at line 22 of file engine_defined.cpp.

- @@ -661,8 +640,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 62 of file engine_defined.cpp.

- @@ -699,8 +676,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 108 of file engine_defined.cpp.

- @@ -731,8 +706,6 @@ Private Attributes

Implements gridfire::Engine.

-

Definition at line 26 of file engine_defined.cpp.

- @@ -763,8 +736,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 184 of file engine_defined.cpp.

- @@ -801,8 +772,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 146 of file engine_defined.cpp.

- @@ -830,8 +799,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 188 of file engine_defined.cpp.

- @@ -885,8 +852,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 122 of file engine_defined.cpp.

- @@ -935,8 +900,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 80 of file engine_defined.cpp.

- @@ -964,8 +927,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 175 of file engine_defined.cpp.

- @@ -1000,8 +961,6 @@ Private Attributes
Returns
A vector of abundances for the active species, with the abundances of the active species copied from the full vector.
-

Definition at line 286 of file engine_defined.cpp.

- @@ -1029,8 +988,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 201 of file engine_defined.cpp.

- @@ -1065,8 +1022,6 @@ Private Attributes
Returns
A vector of abundances for the full network, with the abundances of the active species copied from the defined vector.
-

Definition at line 277 of file engine_defined.cpp.

- @@ -1107,8 +1062,6 @@ Private Attributes -

Definition at line 304 of file engine_defined.cpp.

- @@ -1149,8 +1102,6 @@ Private Attributes -

Definition at line 295 of file engine_defined.cpp.

- @@ -1178,8 +1129,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 212 of file engine_defined.cpp.

- @@ -1207,8 +1156,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 114 of file engine_defined.cpp.

- @@ -1244,8 +1191,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 180 of file engine_defined.cpp.

- @@ -1283,8 +1228,6 @@ Private Attributes

Implements gridfire::DynamicEngine.

-

Definition at line 171 of file engine_defined.cpp.

- @@ -1310,8 +1253,6 @@ Private Attributes
-

Definition at line 313 of file engine_defined.cpp.

-

Member Data Documentation

@@ -1337,8 +1278,6 @@ Private Attributes

Maps indices of active species to indices in the full network.

-

Definition at line 184 of file engine_defined.h.

- @@ -1363,8 +1302,6 @@ Private Attributes

Active reactions in the defined engine.

-

Definition at line 182 of file engine_defined.h.

- @@ -1387,8 +1324,6 @@ Private Attributes
-

Definition at line 178 of file engine_defined.h.

-
@@ -1411,8 +1346,6 @@ Private Attributes
-

Definition at line 177 of file engine_defined.h.

-
@@ -1438,8 +1371,6 @@ Private Attributes

Active species in the defined engine.

Logger instance for trace and debug information.

-

Definition at line 180 of file engine_defined.h.

- @@ -1462,8 +1393,6 @@ Private Attributes
-

Definition at line 189 of file engine_defined.h.

-
@@ -1488,13 +1417,11 @@ Private Attributes

Maps indices of active reactions to indices in the full network.

-

Definition at line 187 of file engine_defined.h.

-
The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1_dynamic_engine.html b/docs/html/classgridfire_1_1_dynamic_engine.html index 39b68d0c..5e0fc303 100644 --- a/docs/html/classgridfire_1_1_dynamic_engine.html +++ b/docs/html/classgridfire_1_1_dynamic_engine.html @@ -109,7 +109,7 @@ $(function(){initNavTree('classgridfire_1_1_dynamic_engine.html',''); initResiza

Abstract class for engines supporting Jacobian and stoichiometry operations. More...

-

#include <engine_abstract.h>

+

#include <engine_abstract.h>

Inheritance diagram for gridfire::DynamicEngine:
@@ -198,8 +198,6 @@ Public Member Functions
  • Computing timescales for each species.

    • 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.

    - -

    Definition at line 130 of file engine_abstract.h.

    Member Function Documentation

    ◆ calculateMolarReactionFlow()

    @@ -341,8 +339,6 @@ Public Member Functions

    Reimplemented in gridfire::GraphEngine, and PyDynamicEngine.

    -

    Definition at line 148 of file engine_abstract.h.

    - @@ -400,8 +396,6 @@ Public Member Functions

    Reimplemented in gridfire::GraphEngine, and PyDynamicEngine.

    -

    Definition at line 305 of file engine_abstract.h.

    - @@ -502,7 +496,7 @@ Public Member Functions

    Get the current electron screening model.

    Returns
    The currently active screening model type.
    Usage Example:
    screening::ScreeningType currentModel = myEngine.getScreeningModel();
    -
    gridfire::screening::ScreeningType
    ScreeningType
    Enumerates the available plasma screening models.
    Definition screening_types.h:15
    +
    gridfire::screening::ScreeningType
    ScreeningType
    Enumerates the available plasma screening models.
    Definition screening_types.h:15

    Implemented in gridfire::AdaptiveEngineView, gridfire::DefinedEngineView, gridfire::GraphEngine, gridfire::MultiscalePartitioningEngineView, and PyDynamicEngine.

    @@ -772,8 +766,6 @@ Public Member Functions

    Reimplemented in gridfire::GraphEngine, and PyDynamicEngine.

    -

    Definition at line 309 of file engine_abstract.h.

    - @@ -835,7 +827,7 @@ Public Member Functions

    This method allows changing the screening model at runtime. Screening corrections account for the electrostatic shielding of nuclei by electrons, which affects reaction rates in dense stellar plasmas.

    Usage Example:
    myEngine.setScreeningModel(screening::ScreeningType::WEAK);
    -
    gridfire::screening::ScreeningType::WEAK
    @ WEAK
    Weak screening model (Salpeter, 1954).
    Definition screening_types.h:35
    +
    gridfire::screening::ScreeningType::WEAK
    @ WEAK
    Weak screening model (Salpeter, 1954).
    Definition screening_types.h:35
    Postcondition
    The engine will use the specified screening model for subsequent rate calculations.
    @@ -876,7 +868,7 @@ Public Member Functions

    This method is intended to be implemented by derived classes to update their internal state based on the provided network conditions. For example, an adaptive engine might use this to re-evaluate which reactions and species are active. For other engines that do not support manually updating, this method might do nothing.

    Usage Example:
    NetIn input = { ... };
    myEngine.update(input);
    - +
    gridfire::NetIn
    Definition network.h:53
    Postcondition
    The internal state of the engine is updated to reflect the new conditions.
    @@ -885,7 +877,7 @@ Public Member Functions
    The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1_engine.html b/docs/html/classgridfire_1_1_engine.html index e6135870..fd105ee2 100644 --- a/docs/html/classgridfire_1_1_engine.html +++ b/docs/html/classgridfire_1_1_engine.html @@ -109,7 +109,7 @@ $(function(){initNavTree('classgridfire_1_1_engine.html',''); initResizable(true

    Abstract base class for a reaction network engine. More...

    -

    #include <engine_abstract.h>

    +

    #include <engine_abstract.h>

    Inheritance diagram for gridfire::Engine:
    @@ -147,10 +147,8 @@ Public Member Functions

    Example:

    class MyEngine : public gridfire::Engine {
    // Implement required methods...
    };
    -
    gridfire::Engine
    Abstract base class for a reaction network engine.
    Definition engine_abstract.h:84
    -
    -

    Definition at line 84 of file engine_abstract.h.

    -

    Constructor & Destructor Documentation

    +
    gridfire::Engine
    Abstract base class for a reaction network engine.
    Definition engine_abstract.h:84
    +

    Constructor & Destructor Documentation

    ◆ ~Engine()

    @@ -258,7 +256,7 @@ Public Member Functions
    The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1_engine_view.html b/docs/html/classgridfire_1_1_engine_view.html index 9a8c6460..c0c10823 100644 --- a/docs/html/classgridfire_1_1_engine_view.html +++ b/docs/html/classgridfire_1_1_engine_view.html @@ -109,7 +109,7 @@ $(function(){initNavTree('classgridfire_1_1_engine_view.html',''); initResizable

    Abstract base class for a "view" of a reaction network engine. More...

    -

    #include <engine_view_abstract.h>

    +

    #include <engine_view_abstract.h>

    @@ -139,12 +139,10 @@ class gridfire::EngineView< EngineT >

    Abstract base class for a "v

    private:
    DynamicEngine& engine_;
    };
    -
    gridfire::DynamicEngine
    Abstract class for engines supporting Jacobian and stoichiometry operations.
    Definition engine_abstract.h:130
    -
    gridfire::EngineView
    Abstract base class for a "view" of a reaction network engine.
    Definition engine_view_abstract.h:74
    +
    gridfire::DynamicEngine
    Abstract class for engines supporting Jacobian and stoichiometry operations.
    Definition engine_abstract.h:130
    +
    gridfire::EngineView
    Abstract base class for a "view" of a reaction network engine.
    Definition engine_view_abstract.h:74
    gridfire::EngineView::getBaseEngine
    virtual const EngineT & getBaseEngine() const =0
    Access the underlying engine instance.
    See also
    gridfire::AdaptiveEngineView for a concrete example of dynamic culling.
    - -

    Definition at line 74 of file engine_view_abstract.h.

    Constructor & Destructor Documentation

    ◆ ~EngineView()

    @@ -211,7 +209,7 @@ template<EngineType EngineT>
    The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1_file_defined_engine_view.html b/docs/html/classgridfire_1_1_file_defined_engine_view.html index 27ea0506..7dc5ff36 100644 --- a/docs/html/classgridfire_1_1_file_defined_engine_view.html +++ b/docs/html/classgridfire_1_1_file_defined_engine_view.html @@ -108,7 +108,7 @@ $(function(){initNavTree('classgridfire_1_1_file_defined_engine_view.html','');
    -

    #include <engine_defined.h>

    +

    #include <engine_defined.h>

    Inheritance diagram for gridfire::FileDefinedEngineView:
    @@ -228,10 +228,7 @@ Additional Inherited Members

    Public Member Functions

    DynamicEngine & m_baseEngine
     
    -

    Detailed Description

    -
    -

    Definition at line 259 of file engine_defined.h.

    -

    Member Typedef Documentation

    +

    Member Typedef Documentation

    ◆ Config

    @@ -252,8 +249,6 @@ Additional Inherited Members
    -

    Definition at line 269 of file engine_defined.h.

    -
    @@ -276,8 +271,6 @@ Additional Inherited Members
    -

    Definition at line 270 of file engine_defined.h.

    -

    Constructor & Destructor Documentation

    @@ -315,8 +308,6 @@ Additional Inherited Members

    FileDefinedEngineView Implementation ///.

    -

    Definition at line 379 of file engine_defined.cpp.

    -

    Member Function Documentation

    @@ -343,8 +334,6 @@ Additional Inherited Members
    -

    Definition at line 266 of file engine_defined.h.

    -
    @@ -370,8 +359,6 @@ Additional Inherited Members
    -

    Definition at line 267 of file engine_defined.h.

    -

    Member Data Documentation

    @@ -395,8 +382,6 @@ Additional Inherited Members
    -

    Definition at line 271 of file engine_defined.h.

    -
    @@ -421,8 +406,6 @@ Additional Inherited Members

    Parser for the network file.

    -

    Definition at line 273 of file engine_defined.h.

    - @@ -445,8 +428,6 @@ Additional Inherited Members
    -

    Definition at line 272 of file engine_defined.h.

    -
    @@ -469,13 +450,11 @@ Additional Inherited Members
    -

    Definition at line 275 of file engine_defined.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1_graph_engine.html b/docs/html/classgridfire_1_1_graph_engine.html index b2cfe5c0..6d3a6de7 100644 --- a/docs/html/classgridfire_1_1_graph_engine.html +++ b/docs/html/classgridfire_1_1_graph_engine.html @@ -113,7 +113,7 @@ $(function(){initNavTree('classgridfire_1_1_graph_engine.html',''); initResizabl

    A reaction network engine that uses a graph-based representation. More...

    -

    #include <engine_graph.h>

    +

    #include <engine_graph.h>

    Inheritance diagram for gridfire::GraphEngine:
    @@ -354,8 +354,6 @@ Private Attributes
  • Exporting the network to DOT and CSV formats for visualization and analysis.
    • See also
    engine_abstract.h
    - -

    Definition at line 100 of file engine_graph.h.

    Constructor & Destructor Documentation

    ◆ GraphEngine() [1/3]

    @@ -394,8 +392,6 @@ Private Attributes

    This constructor builds the reaction network from the given composition using the build_reaclib_nuclear_network function.

    See also
    build_reaclib_nuclear_network
    -

    Definition at line 34 of file engine_graph.cpp.

    - @@ -430,8 +426,6 @@ Private Attributes
    -

    Definition at line 39 of file engine_graph.cpp.

    -
    @@ -466,8 +460,6 @@ Private Attributes

    This constructor uses the given set of reactions to construct the reaction network.

    -

    Definition at line 50 of file engine_graph.cpp.

    -

    Member Function Documentation

    @@ -515,8 +507,6 @@ Private Attributes
    Returns
    StepDerivatives<ADDouble> containing dY/dt and energy generation rate.

    This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state using automatic differentiation.

    -

    Definition at line 594 of file engine_graph.cpp.

    - @@ -563,8 +553,6 @@ Private Attributes
    Returns
    StepDerivatives<double> containing dY/dt and energy generation rate.

    This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state using double precision arithmetic.

    -

    Definition at line 586 of file engine_graph.cpp.

    - @@ -619,8 +607,6 @@ template<IsArithmeticOrAD T>
    Returns
    StepDerivatives<T> containing dY/dt and energy generation rate.

    This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state.

    -

    Definition at line 715 of file engine_graph.h.

    - @@ -665,8 +651,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 448 of file engine_graph.cpp.

    -
    @@ -721,8 +705,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 623 of file engine_graph.cpp.

    - @@ -783,8 +765,6 @@ template<IsArithmeticOrAD T>
    Returns
    Molar flow rate for the reaction (e.g., mol/g/s).

    This method computes the net rate at which the given reaction proceeds under the current state.

    -

    Definition at line 796 of file engine_graph.h.

    - @@ -836,8 +816,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 648 of file engine_graph.h.

    -
    @@ -867,8 +845,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 242 of file engine_graph.cpp.

    -
    @@ -908,8 +884,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 269 of file engine_graph.cpp.

    -
    @@ -944,8 +918,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 346 of file engine_graph.cpp.

    -
    @@ -995,8 +967,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::Engine.

    -

    Definition at line 57 of file engine_graph.cpp.

    - @@ -1022,8 +992,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 947 of file engine_graph.cpp.

    -
    @@ -1052,8 +1020,6 @@ template<IsArithmeticOrAD T>

    Collects the unique species in the network.

    This method collects the unique species in the network from the reactants and products of all reactions.

    -

    Definition at line 106 of file engine_graph.cpp.

    - @@ -1087,8 +1053,6 @@ template<IsArithmeticOrAD T>

    Example usage:

    engine.exportToCSV("network.csv");
    -

    Definition at line 788 of file engine_graph.cpp.

    - @@ -1122,8 +1086,6 @@ template<IsArithmeticOrAD T>

    Example usage:

    engine.exportToDot("network.dot");
    -

    Definition at line 740 of file engine_graph.cpp.

    - @@ -1172,8 +1134,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 632 of file engine_graph.cpp.

    - @@ -1215,8 +1175,6 @@ template<IsArithmeticOrAD T>

    Reimplemented from gridfire::DynamicEngine.

    -

    Definition at line 665 of file engine_graph.cpp.

    - @@ -1247,8 +1205,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 545 of file engine_graph.cpp.

    - @@ -1276,8 +1232,6 @@ template<IsArithmeticOrAD T>

    Reimplemented from gridfire::DynamicEngine.

    -

    Definition at line 434 of file engine_graph.cpp.

    - @@ -1321,8 +1275,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 722 of file engine_graph.cpp.

    - @@ -1357,8 +1309,6 @@ template<IsArithmeticOrAD T>
    Returns
    Map of species to their stoichiometric coefficients.
    -

    Definition at line 727 of file engine_graph.cpp.

    - @@ -1389,8 +1339,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 168 of file engine_graph.cpp.

    - @@ -1421,8 +1369,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::Engine.

    -

    Definition at line 162 of file engine_graph.cpp.

    - @@ -1448,8 +1394,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 619 of file engine_graph.cpp.

    -
    @@ -1478,13 +1422,11 @@ template<IsArithmeticOrAD T>

    Get the current electron screening model.

    Returns
    The currently active screening model type.
    Usage Example:
    screening::ScreeningType currentModel = myEngine.getScreeningModel();
    -
    gridfire::screening::ScreeningType
    ScreeningType
    Enumerates the available plasma screening models.
    Definition screening_types.h:15
    +
    gridfire::screening::ScreeningType
    ScreeningType
    Enumerates the available plasma screening models.
    Definition screening_types.h:15

    Implements gridfire::DynamicEngine.

    -

    Definition at line 607 of file engine_graph.cpp.

    - @@ -1521,8 +1463,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 861 of file engine_graph.cpp.

    - @@ -1550,8 +1490,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 395 of file engine_graph.cpp.

    - @@ -1600,8 +1538,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 842 of file engine_graph.cpp.

    - @@ -1645,8 +1581,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 733 of file engine_graph.cpp.

    - @@ -1681,8 +1615,6 @@ template<IsArithmeticOrAD T>
    Returns
    True if the species is involved in the network, false otherwise.
    -

    Definition at line 179 of file engine_graph.cpp.

    - @@ -1708,8 +1640,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 615 of file engine_graph.cpp.

    -
    @@ -1737,8 +1667,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 898 of file engine_graph.cpp.

    - @@ -1764,8 +1692,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 387 of file engine_graph.cpp.

    -
    @@ -1793,8 +1719,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 399 of file engine_graph.cpp.

    - @@ -1823,8 +1747,6 @@ template<IsArithmeticOrAD T>

    Populates the reaction ID map.

    This method populates the reaction ID map, which maps reaction IDs to REACLIBReaction objects.

    -

    Definition at line 135 of file engine_graph.cpp.

    - @@ -1853,8 +1775,6 @@ template<IsArithmeticOrAD T>

    Populates the species-to-index map.

    This method populates the species-to-index map, which maps species to their index in the stoichiometry matrix.

    -

    Definition at line 144 of file engine_graph.cpp.

    - @@ -1880,8 +1800,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 960 of file engine_graph.cpp.

    -
    @@ -1909,8 +1827,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 407 of file engine_graph.cpp.

    - @@ -1942,8 +1858,6 @@ template<IsArithmeticOrAD T>

    Reimplemented from gridfire::DynamicEngine.

    -

    Definition at line 438 of file engine_graph.cpp.

    - @@ -1978,8 +1892,6 @@ template<IsArithmeticOrAD T> -

    Definition at line 902 of file engine_graph.cpp.

    - @@ -2008,8 +1920,6 @@ template<IsArithmeticOrAD T>

    Reserves space for the Jacobian matrix.

    This method reserves space for the Jacobian matrix, which is used to store the partial derivatives of the right-hand side of the ODE with respect to the species abundances.

    -

    Definition at line 151 of file engine_graph.cpp.

    - @@ -2037,8 +1947,6 @@ template<IsArithmeticOrAD T>

    Implements gridfire::DynamicEngine.

    -

    Definition at line 174 of file engine_graph.cpp.

    - @@ -2056,8 +1964,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 611 of file engine_graph.cpp.

    -
    @@ -2092,14 +1998,12 @@ template<IsArithmeticOrAD T>

    This method allows changing the screening model at runtime. Screening corrections account for the electrostatic shielding of nuclei by electrons, which affects reaction rates in dense stellar plasmas.

    Usage Example:
    myEngine.setScreeningModel(screening::ScreeningType::WEAK);
    -
    gridfire::screening::ScreeningType::WEAK
    @ WEAK
    Weak screening model (Salpeter, 1954).
    Definition screening_types.h:35
    +
    gridfire::screening::ScreeningType::WEAK
    @ WEAK
    Weak screening model (Salpeter, 1954).
    Definition screening_types.h:35
    Postcondition
    The engine will use the specified screening model for subsequent rate calculations.

    Implements gridfire::DynamicEngine.

    -

    Definition at line 602 of file engine_graph.cpp.

    - @@ -2117,8 +2021,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 391 of file engine_graph.cpp.

    -
    @@ -2147,8 +2049,6 @@ template<IsArithmeticOrAD T>

    Synchronizes the internal maps.

    This method synchronizes the internal maps used by the engine, including the species map, reaction ID map, and species-to-index map. It also generates the stoichiometry matrix and records the AD tape.

    -

    Definition at line 81 of file engine_graph.cpp.

    - @@ -2184,14 +2084,12 @@ template<IsArithmeticOrAD T>

    This method is intended to be implemented by derived classes to update their internal state based on the provided network conditions. For example, an adaptive engine might use this to re-evaluate which reactions and species are active. For other engines that do not support manually updating, this method might do nothing.

    Usage Example:
    NetIn input = { ... };
    myEngine.update(input);
    - +
    gridfire::NetIn
    Definition network.h:53
    Postcondition
    The internal state of the engine is updated to reflect the new conditions.

    Implements gridfire::DynamicEngine.

    -

    Definition at line 886 of file engine_graph.cpp.

    - @@ -2221,8 +2119,6 @@ template<IsArithmeticOrAD T>
    Returns
    True if all reactions conserve mass and charge, false otherwise.

    This method checks that all reactions in the network conserve mass and charge. If any reaction does not conserve mass or charge, an error message is logged and false is returned.

    -

    Definition at line 187 of file engine_graph.cpp.

    -

    Member Data Documentation

    @@ -2246,8 +2142,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 466 of file engine_graph.h.

    -
    @@ -2270,8 +2164,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 447 of file engine_graph.h.

    -
    @@ -2294,8 +2186,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 450 of file engine_graph.h.

    -
    @@ -2318,8 +2208,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 475 of file engine_graph.h.

    -
    @@ -2344,8 +2232,6 @@ template<IsArithmeticOrAD T>

    Full sparsity pattern for the Jacobian matrix.

    -

    Definition at line 464 of file engine_graph.h.

    - @@ -2370,8 +2256,6 @@ template<IsArithmeticOrAD T>

    Work object for sparse Jacobian calculations.

    -

    Definition at line 463 of file engine_graph.h.

    - @@ -2396,8 +2280,6 @@ template<IsArithmeticOrAD T>

    Jacobian matrix (species x species).

    -

    Definition at line 461 of file engine_graph.h.

    - @@ -2420,8 +2302,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 448 of file engine_graph.h.

    -
    @@ -2446,8 +2326,6 @@ template<IsArithmeticOrAD T>

    Vector of unique species in the network.

    -

    Definition at line 455 of file engine_graph.h.

    - @@ -2472,8 +2350,6 @@ template<IsArithmeticOrAD T>

    Map from species name to Species object.

    -

    Definition at line 456 of file engine_graph.h.

    - @@ -2498,8 +2374,6 @@ template<IsArithmeticOrAD T>

    Partition function for the network.

    -

    Definition at line 478 of file engine_graph.h.

    - @@ -2524,8 +2398,6 @@ template<IsArithmeticOrAD T>

    Precomputed reactions for efficiency.

    -

    Definition at line 477 of file engine_graph.h.

    - @@ -2550,8 +2422,6 @@ template<IsArithmeticOrAD T>

    Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a performance bottleneck.

    -

    Definition at line 453 of file engine_graph.h.

    - @@ -2576,8 +2446,6 @@ template<IsArithmeticOrAD T>

    Set of REACLIB reactions in the network.

    -

    Definition at line 452 of file engine_graph.h.

    - @@ -2602,8 +2470,6 @@ template<IsArithmeticOrAD T>

    CppAD function for the right-hand side of the ODE.

    -

    Definition at line 462 of file engine_graph.h.

    - @@ -2626,8 +2492,6 @@ template<IsArithmeticOrAD T>
    -

    Definition at line 469 of file engine_graph.h.

    -
    @@ -2652,8 +2516,6 @@ template<IsArithmeticOrAD T>

    Screening type for the reaction network. Default to no screening.

    -

    Definition at line 468 of file engine_graph.h.

    - @@ -2678,8 +2540,6 @@ template<IsArithmeticOrAD T>

    Map from species to their index in the stoichiometry matrix.

    -

    Definition at line 457 of file engine_graph.h.

    - @@ -2704,8 +2564,6 @@ template<IsArithmeticOrAD T>

    Stoichiometry matrix (species x reactions).

    -

    Definition at line 459 of file engine_graph.h.

    - @@ -2730,8 +2588,6 @@ template<IsArithmeticOrAD T>

    Flag to enable or disable using precomputed reactions for efficiency. Mathematically, this should not change the results. Generally end users should not need to change this.

    -

    Definition at line 471 of file engine_graph.h.

    - @@ -2756,13 +2612,11 @@ template<IsArithmeticOrAD T>

    Flag to enable or disable reverse reactions. If false, only forward reactions are considered.

    -

    Definition at line 473 of file engine_graph.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html b/docs/html/classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html index 2f8f7ca8..7a4c54ed 100644 --- a/docs/html/classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html +++ b/docs/html/classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html @@ -133,10 +133,7 @@ Private Attributes const GraphEngine & m_engine   -

    Detailed Description

    -
    -

    Definition at line 406 of file engine_graph.h.

    -

    Constructor & Destructor Documentation

    +

    Constructor & Destructor Documentation

    ◆ AtomicReverseRate()

    @@ -164,8 +161,6 @@ Private Attributes
    -

    Definition at line 408 of file engine_graph.h.

    -

    Member Function Documentation

    @@ -201,8 +196,6 @@ Private Attributes
    -

    Definition at line 1069 of file engine_graph.cpp.

    -
    @@ -252,8 +245,6 @@ Private Attributes
    -

    Definition at line 1029 of file engine_graph.cpp.

    -
    @@ -288,8 +279,6 @@ Private Attributes
    -

    Definition at line 1078 of file engine_graph.cpp.

    -
    @@ -334,8 +323,6 @@ Private Attributes
    -

    Definition at line 1051 of file engine_graph.cpp.

    -

    Member Data Documentation

    @@ -359,8 +346,6 @@ Private Attributes
    -

    Definition at line 444 of file engine_graph.h.

    -
    @@ -383,13 +368,11 @@ Private Attributes
    -

    Definition at line 443 of file engine_graph.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1_multiscale_partitioning_engine_view.html b/docs/html/classgridfire_1_1_multiscale_partitioning_engine_view.html index 19f3ea2c..36f5161e 100644 --- a/docs/html/classgridfire_1_1_multiscale_partitioning_engine_view.html +++ b/docs/html/classgridfire_1_1_multiscale_partitioning_engine_view.html @@ -113,7 +113,7 @@ $(function(){initNavTree('classgridfire_1_1_multiscale_partitioning_engine_view.

    An engine view that partitions the reaction network into multiple groups based on timescales. More...

    -

    #include <engine_multiscale.h>

    +

    #include <engine_multiscale.h>

    Inheritance diagram for gridfire::MultiscalePartitioningEngineView:
    @@ -332,13 +332,11 @@ Private Attributes
    // The integrator will call calculateRHSAndEnergy, etc. on the multiscaleEngine.
    auto Y_initial = multiscaleEngine.mapNetInToMolarAbundanceVector({equilibratedComp, ...});
    auto derivatives = multiscaleEngine.calculateRHSAndEnergy(Y_initial, T9, rho);
    -
    gridfire::GraphEngine
    A reaction network engine that uses a graph-based representation.
    Definition engine_graph.h:100
    -
    gridfire::MultiscalePartitioningEngineView
    An engine view that partitions the reaction network into multiple groups based on timescales.
    Definition engine_multiscale.h:174
    - +
    gridfire::GraphEngine
    A reaction network engine that uses a graph-based representation.
    Definition engine_graph.h:100
    +
    gridfire::MultiscalePartitioningEngineView
    An engine view that partitions the reaction network into multiple groups based on timescales.
    Definition engine_multiscale.h:174
    +
    gridfire::NetIn
    Definition network.h:53

    <DynamicEngine>

    - -

    Definition at line 174 of file engine_multiscale.h.

    Member Typedef Documentation

    ◆ QSEPartition

    @@ -363,8 +361,6 @@ Private Attributes

    Type alias for a QSE partition.

    A QSE partition is a tuple containing the fast species, their indices, the slow species, and their indices.

    -

    Definition at line 181 of file engine_multiscale.h.

    -

    Constructor & Destructor Documentation

    @@ -399,8 +395,6 @@ Private Attributes -

    Definition at line 153 of file engine_multiscale.cpp.

    -

    Member Function Documentation

    @@ -447,8 +441,6 @@ Private Attributes

    @purpose To merge timescale pools that are strongly connected by reactions, forming cohesive groups for QSE analysis.

    @how For each pool, it builds a reaction connectivity graph using buildConnectivityGraph. It then finds the connected components within that graph using a Breadth-First Search (BFS). The resulting components from all pools are collected and returned.

    -

    Definition at line 416 of file engine_multiscale.cpp.

    - @@ -521,8 +513,6 @@ Private Attributes

    @purpose To find reaction connections within a specific group of species.

    @how It iterates through all reactions in the base engine. If a reaction involves at least two distinct species from the input species_pool (one as a reactant and one as a product), it adds edges between all reactants and products from that reaction that are also in the pool.

    -

    Definition at line 1344 of file engine_multiscale.cpp.

    - @@ -585,8 +575,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 253 of file engine_multiscale.cpp.

    - @@ -644,8 +632,6 @@ Private Attributes

    Implements gridfire::Engine.

    -

    Definition at line 161 of file engine_multiscale.cpp.

    - @@ -700,8 +686,6 @@ Private Attributes
    Precondition
    The candidate_pools should be connected components from analyzeTimescalePoolConnectivity.
    Postcondition
    A list of candidate QSEGroup objects is returned.
    -

    Definition at line 1405 of file engine_multiscale.cpp.

    - @@ -730,8 +714,6 @@ Private Attributes

    @purpose A convenience overload for equilibrateNetwork.

    @how It unpacks the netIn struct into Y, T9, and rho and then calls the primary equilibrateNetwork method.

    -

    Definition at line 834 of file engine_multiscale.cpp.

    - @@ -773,8 +755,6 @@ Private Attributes
    Precondition
    The input state (Y, T9, rho) must be a valid physical state.
    Postcondition
    The engine's internal partition is updated. A new composition object is returned.
    -

    Definition at line 797 of file engine_multiscale.cpp.

    - @@ -819,8 +799,6 @@ Private Attributes

    @purpose To visualize the partitioned network graph.

    @how This method delegates the DOT file export to the base engine. It does not currently add any partitioning information to the output graph.

    -

    Definition at line 558 of file engine_multiscale.cpp.

    - @@ -877,8 +855,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 204 of file engine_multiscale.cpp.

    - @@ -910,8 +886,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 242 of file engine_multiscale.cpp.

    - @@ -942,8 +916,6 @@ Private Attributes

    Implements gridfire::EngineView< DynamicEngine >.

    -

    Definition at line 412 of file engine_multiscale.cpp.

    - @@ -975,8 +947,6 @@ Private Attributes

    @how It returns a const reference to the m_dynamic_species member vector.

    Precondition
    partitionNetwork() must have been called.
    -

    Definition at line 789 of file engine_multiscale.cpp.

    - @@ -1008,8 +978,6 @@ Private Attributes

    @how It returns a copy of the m_algebraic_species member vector.

    Precondition
    partitionNetwork() must have been called.
    -

    Definition at line 776 of file engine_multiscale.cpp.

    - @@ -1054,8 +1022,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 228 of file engine_multiscale.cpp.

    - @@ -1086,8 +1052,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 286 of file engine_multiscale.cpp.

    - @@ -1118,8 +1082,6 @@ Private Attributes

    Implements gridfire::Engine.

    -

    Definition at line 157 of file engine_multiscale.cpp.

    - @@ -1151,8 +1113,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 408 of file engine_multiscale.cpp.

    - @@ -1209,8 +1169,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 326 of file engine_multiscale.cpp.

    - @@ -1248,8 +1206,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 846 of file engine_multiscale.cpp.

    - @@ -1306,8 +1262,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 295 of file engine_multiscale.cpp.

    - @@ -1352,8 +1306,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 246 of file engine_multiscale.cpp.

    - @@ -1407,8 +1359,6 @@ Private Attributes

    @purpose To identify the core set of dynamic species that will not be part of any QSE group.

    @how It calculates the geometric mean of the destruction timescales for all species in each pool and returns the index of the pool with the maximum mean timescale.

    -

    Definition at line 1291 of file engine_multiscale.cpp.

    - @@ -1447,8 +1397,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 390 of file engine_multiscale.cpp.

    - @@ -1486,8 +1434,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 768 of file engine_multiscale.cpp.

    - @@ -1535,8 +1481,6 @@ Private Attributes

    @purpose To group species into "pools" based on their destruction timescales.

    @how It retrieves all species destruction timescales from the base engine, sorts them, and then iterates through the sorted list, creating a new pool whenever it detects a gap between consecutive timescales that is larger than a predefined threshold (e.g., a factor of 100).

    -

    Definition at line 850 of file engine_multiscale.cpp.

    - @@ -1564,8 +1508,6 @@ Private Attributes

    @purpose A convenience overload for partitionNetwork.

    @how It unpacks the netIn struct into Y, T9, and rho and then calls the primary partitionNetwork method.

    -

    Definition at line 548 of file engine_multiscale.cpp.

    - @@ -1612,8 +1554,6 @@ Private Attributes
    Precondition
    The input state (Y, T9, rho) must be a valid physical state.
    Postcondition
    The internal member variables m_qse_groups, m_dynamic_species, and m_algebraic_species (and their index maps) are populated with the results of the partitioning.
    -

    Definition at line 438 of file engine_multiscale.cpp.

    - @@ -1652,8 +1592,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 793 of file engine_multiscale.cpp.

    - @@ -1697,8 +1635,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 290 of file engine_multiscale.cpp.

    - @@ -1735,8 +1671,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 402 of file engine_multiscale.cpp.

    - @@ -1786,8 +1720,6 @@ Private Attributes
    Precondition
    The input state (Y_full, T9, rho) must be a valid physical state.
    Postcondition
    The algebraic species in the QSE cache are updated with the new equilibrium abundances.
    -

    Definition at line 1136 of file engine_multiscale.cpp.

    - @@ -1835,8 +1767,6 @@ Private Attributes

    Implements gridfire::DynamicEngine.

    -

    Definition at line 356 of file engine_multiscale.cpp.

    - @@ -1890,8 +1820,6 @@ Private Attributes

    @purpose To ensure that a candidate QSE group is truly in equilibrium by checking that the reaction fluxes within the group are much larger than the fluxes leaving the group.

    @how For each candidate group, it calculates the sum of all internal reaction fluxes and the sum of all external (bridge) reaction fluxes. If the ratio of internal to external flux exceeds a configurable threshold, the group is considered valid and is added to the returned vector.

    -

    Definition at line 1002 of file engine_multiscale.cpp.

    -

    Member Data Documentation

    @@ -1917,8 +1845,6 @@ Private Attributes

    Indices of all reactions involving only active species.

    -

    Definition at line 943 of file engine_multiscale.h.

    - @@ -1943,8 +1869,6 @@ Private Attributes

    Indices of all species considered active in the current partition (dynamic + algebraic).

    -

    Definition at line 939 of file engine_multiscale.h.

    - @@ -1969,8 +1893,6 @@ Private Attributes

    Species that are treated as algebraic (in QSE) in the QSE groups.

    -

    Definition at line 930 of file engine_multiscale.h.

    - @@ -1995,8 +1917,6 @@ Private Attributes

    Indices of algebraic species in the full network.

    -

    Definition at line 934 of file engine_multiscale.h.

    - @@ -2021,8 +1941,6 @@ Private Attributes

    The base engine to which this view delegates calculations.

    -

    Definition at line 914 of file engine_multiscale.h.

    - @@ -2047,8 +1965,6 @@ Private Attributes

    Statistics for the QSE abundance cache.

    -

    Definition at line 957 of file engine_multiscale.h.

    - @@ -2073,8 +1989,6 @@ Private Attributes

    The simplified set of species presented to the solver (the "slow" species).

    -

    Definition at line 922 of file engine_multiscale.h.

    - @@ -2099,8 +2013,6 @@ Private Attributes

    Indices mapping the dynamic species back to the base engine's full species list.

    -

    Definition at line 926 of file engine_multiscale.h.

    - @@ -2125,8 +2037,6 @@ Private Attributes

    Logger instance for logging messages.

    -

    Definition at line 910 of file engine_multiscale.h.

    - @@ -2152,8 +2062,6 @@ Private Attributes

    Cache for QSE abundances based on T9, rho, and Y.

    @purpose This is the core of the caching mechanism. It stores the results of QSE solves to avoid re-computation. The key is a QSECacheKey which hashes the thermodynamic state, and the value is the vector of solved molar abundances for the algebraic species.

    -

    Definition at line 953 of file engine_multiscale.h.

    - @@ -2178,13 +2086,11 @@ Private Attributes

    The list of identified equilibrium groups.

    -

    Definition at line 918 of file engine_multiscale.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1_network.html b/docs/html/classgridfire_1_1_network.html index 25aaf984..84a7140b 100644 --- a/docs/html/classgridfire_1_1_network.html +++ b/docs/html/classgridfire_1_1_network.html @@ -107,7 +107,7 @@ $(function(){initNavTree('classgridfire_1_1_network.html',''); initResizable(tru
    -

    #include <network.h>

    +

    #include <network.h>

    Inheritance diagram for gridfire::Network:
    @@ -156,10 +156,7 @@ Protected Attributes  Flag indicating if the network is stiff.
      -

    Detailed Description

    -
    -

    Definition at line 76 of file network.h.

    -

    Constructor & Destructor Documentation

    +

    Constructor & Destructor Documentation

    ◆ Network()

    @@ -183,8 +180,6 @@ Protected Attributes
    -

    Definition at line 41 of file network.cpp.

    -
    @@ -272,8 +267,6 @@ Protected Attributes
    -

    Definition at line 54 of file network.cpp.

    -
    @@ -301,8 +294,6 @@ Protected Attributes

    Reimplemented in gridfire::approx8::Approx8Network.

    -

    Definition at line 92 of file network.h.

    - @@ -320,8 +311,6 @@ Protected Attributes
    -

    Definition at line 58 of file network.cpp.

    -
    @@ -349,8 +338,6 @@ Protected Attributes

    Reimplemented in gridfire::approx8::Approx8Network.

    -

    Definition at line 93 of file network.h.

    -

    Member Data Documentation

    @@ -376,8 +363,6 @@ Protected Attributes

    Configuration instance.

    -

    Definition at line 96 of file network.h.

    - @@ -400,8 +385,6 @@ Protected Attributes
    -

    Definition at line 101 of file network.h.

    -
    @@ -426,8 +409,6 @@ Protected Attributes

    Format of the network.

    -

    Definition at line 100 of file network.h.

    - @@ -452,8 +433,6 @@ Protected Attributes

    Logger instance.

    -

    Definition at line 98 of file network.h.

    - @@ -478,8 +457,6 @@ Protected Attributes

    Log manager instance.

    -

    Definition at line 97 of file network.h.

    - @@ -504,13 +481,11 @@ Protected Attributes

    Flag indicating if the network is stiff.

    -

    Definition at line 103 of file network.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1_network_priming_engine_view.html b/docs/html/classgridfire_1_1_network_priming_engine_view.html index 79a610ab..4b396534 100644 --- a/docs/html/classgridfire_1_1_network_priming_engine_view.html +++ b/docs/html/classgridfire_1_1_network_priming_engine_view.html @@ -111,7 +111,7 @@ $(function(){initNavTree('classgridfire_1_1_network_priming_engine_view.html',''

    Provides a view of a DynamicEngine filtered to reactions involving a specified priming species. More...

    -

    #include <engine_priming.h>

    +

    #include <engine_priming.h>

    Inheritance diagram for gridfire::NetworkPrimingEngineView:
    @@ -230,8 +230,6 @@ Additional Inherited Members

    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.

    See implementation in engine_priming.cpp for details on reaction set construction.

    Note
    Throws std::runtime_error if no priming reactions are found for the species.
    - -

    Definition at line 30 of file engine_priming.h.

    Constructor & Destructor Documentation

    ◆ NetworkPrimingEngineView() [1/2]

    @@ -270,8 +268,6 @@ Additional Inherited Members -

    Definition at line 23 of file engine_priming.cpp.

    - @@ -310,8 +306,6 @@ Additional Inherited Members -

    Definition at line 36 of file engine_priming.cpp.

    -

    Member Function Documentation

    @@ -360,8 +354,6 @@ Additional Inherited Members -

    Definition at line 51 of file engine_priming.cpp.

    -

    Member Data Documentation

    @@ -385,8 +377,6 @@ Additional Inherited Members
    -

    Definition at line 56 of file engine_priming.h.

    -
    @@ -411,13 +401,11 @@ Additional Inherited Members

    The priming species, if specified.

    -

    Definition at line 57 of file engine_priming.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1_reaction.html b/docs/html/classgridfire_1_1_reaction.html index 49aca039..afebea40 100644 --- a/docs/html/classgridfire_1_1_reaction.html +++ b/docs/html/classgridfire_1_1_reaction.html @@ -112,7 +112,7 @@ $(function(){initNavTree('classgridfire_1_1_reaction.html',''); initResizable(tr

    Represents a single nuclear reaction from a specific data source. More...

    -

    #include <reaction.h>

    +

    #include <reaction.h>

    Inheritance diagram for gridfire::Reaction:
    @@ -258,10 +258,8 @@ Friends
    "H_1_H_1_to_H_2", "p(p,g)d", 1, {H_1, H_1}, {H_2}, 5.493, "st08", rate_coeffs
    );
    double rate = p_gamma_d.calculate_rate(0.1); // T9 = 0.1
    -
    gridfire::Reaction::Reaction
    Reaction(const std::string_view id, const std::string_view peName, const int chapter, const std::vector< fourdst::atomic::Species > &reactants, const std::vector< fourdst::atomic::Species > &products, const double qValue, const std::string_view label, const RateCoefficientSet &sets, const bool reverse=false)
    Constructs a Reaction object.
    Definition reaction.cpp:19
    -
    -

    Definition at line 72 of file reaction.h.

    -

    Constructor & Destructor Documentation

    +
    gridfire::Reaction::Reaction
    Reaction(const std::string_view id, const std::string_view peName, const int chapter, const std::vector< fourdst::atomic::Species > &reactants, const std::vector< fourdst::atomic::Species > &products, const double qValue, const std::string_view label, const RateCoefficientSet &sets, const bool reverse=false)
    Constructs a Reaction object.
    Definition reaction.cpp:19
    +

    Constructor & Destructor Documentation

    ◆ ~Reaction()

    @@ -359,8 +357,6 @@ Friends -

    Definition at line 19 of file reaction.cpp.

    -

    Member Function Documentation

    @@ -390,8 +386,6 @@ Friends

    Gets a set of all unique species involved in the reaction.

    Returns
    An unordered_set of all reactant and product species.
    -

    Definition at line 91 of file reaction.cpp.

    - @@ -417,8 +411,6 @@ Friends
    -

    Definition at line 47 of file reaction.cpp.

    -
    @@ -453,8 +445,6 @@ Friends
    Returns
    The calculated reaction rate, as a CppAD::AD<double>.
    -

    Definition at line 43 of file reaction.cpp.

    - @@ -489,8 +479,6 @@ Friends
    Returns
    The calculated reaction rate.
    -

    Definition at line 39 of file reaction.cpp.

    - @@ -534,8 +522,6 @@ template<typename T>
    Returns
    The calculated reaction rate.

    The rate is calculated using the standard REACLIB formula: rate = exp(a0 + a1/T9 + a2/T9^(1/3) + a3*T9^(1/3) + a4*T9 + a5*T9^(5/3) + a6*ln(T9))

    -

    Definition at line 283 of file reaction.h.

    - @@ -564,8 +550,6 @@ template<typename T>

    Gets the REACLIB chapter number.

    Returns
    The chapter number.
    -

    Definition at line 128 of file reaction.h.

    - @@ -600,8 +584,6 @@ template<typename T>
    Returns
    True if the species is involved, false otherwise.
    -

    Definition at line 68 of file reaction.cpp.

    - @@ -636,8 +618,6 @@ template<typename T>
    Returns
    True if the species is a product, false otherwise.
    -

    Definition at line 82 of file reaction.cpp.

    - @@ -672,8 +652,6 @@ template<typename T>
    Returns
    True if the species is a reactant, false otherwise.
    -

    Definition at line 73 of file reaction.cpp.

    - @@ -702,8 +680,6 @@ template<typename T>

    Calculates the excess energy from the mass difference of reactants and products.

    Returns
    The excess energy in MeV.
    -

    Definition at line 144 of file reaction.cpp.

    - @@ -739,8 +715,6 @@ template<typename T>
    Returns
    A 64-bit hash value.

    Uses the XXHash64 algorithm on the reaction's ID string.

    -

    Definition at line 157 of file reaction.cpp.

    - @@ -769,8 +743,6 @@ template<typename T>

    Gets the unique identifier of the reaction.

    Returns
    The reaction ID.
    -

    Definition at line 204 of file reaction.h.

    - @@ -799,8 +771,6 @@ template<typename T>

    Checks if this is a reverse reaction rate.

    Returns
    True if it is a reverse rate, false otherwise.
    -

    Definition at line 228 of file reaction.h.

    - @@ -829,8 +799,6 @@ template<typename T>

    Gets the number of unique species involved in the reaction.

    Returns
    The count of unique species.
    -

    Definition at line 129 of file reaction.cpp.

    - @@ -865,8 +833,6 @@ template<typename T>
    Returns
    True if the reactions are not equal.
    -

    Definition at line 248 of file reaction.h.

    - @@ -901,8 +867,6 @@ template<typename T>
    Returns
    True if the reaction IDs are the same.
    -

    Definition at line 241 of file reaction.h.

    - @@ -931,8 +895,6 @@ template<typename T>

    Gets the reaction name in (projectile, ejectile) notation.

    Returns
    The reaction name (e.g., "p(p,g)d").
    -

    Definition at line 122 of file reaction.h.

    - @@ -961,8 +923,6 @@ template<typename T>

    Gets a set of all unique product species.

    Returns
    An unordered_set of product species.
    -

    Definition at line 106 of file reaction.cpp.

    - @@ -991,8 +951,6 @@ template<typename T>

    Gets the vector of product species.

    Returns
    A const reference to the vector of products.
    -

    Definition at line 222 of file reaction.h.

    - @@ -1021,8 +979,6 @@ template<typename T>

    Gets the Q-value of the reaction.

    Returns
    The Q-value in whatever units the reaction was defined in (usually MeV).
    -

    Definition at line 210 of file reaction.h.

    - @@ -1051,8 +1007,6 @@ template<typename T>

    Gets the set of rate coefficients.

    Returns
    A const reference to the RateCoefficientSet.
    -

    Definition at line 140 of file reaction.h.

    - @@ -1081,8 +1035,6 @@ template<typename T>

    Gets a set of all unique reactant species.

    Returns
    An unordered_set of reactant species.
    -

    Definition at line 98 of file reaction.cpp.

    - @@ -1111,8 +1063,6 @@ template<typename T>

    Gets the vector of reactant species.

    Returns
    A const reference to the vector of reactants.
    -

    Definition at line 216 of file reaction.h.

    - @@ -1141,8 +1091,6 @@ template<typename T>

    Gets the source label for the rate data.

    Returns
    The source label (e.g., "wc12w", "st08").
    -

    Definition at line 134 of file reaction.h.

    - @@ -1171,8 +1119,6 @@ template<typename T>

    Gets a map of all species to their stoichiometric coefficients.

    Returns
    An unordered_map from species to their integer coefficients.
    -

    Definition at line 133 of file reaction.cpp.

    - @@ -1237,8 +1183,6 @@ template<typename T>
    -

    Definition at line 258 of file reaction.h.

    -

    Member Data Documentation

    @@ -1264,8 +1208,6 @@ template<typename T>

    Chapter number from the REACLIB database, defining the reaction structure.

    -

    Definition at line 266 of file reaction.h.

    - @@ -1290,8 +1232,6 @@ template<typename T>

    Unique identifier for the reaction (e.g., "h1+h1=>h2+e+nu").

    -

    Definition at line 264 of file reaction.h.

    - @@ -1314,8 +1254,6 @@ template<typename T>
    -

    Definition at line 263 of file reaction.h.

    -
    @@ -1340,8 +1278,6 @@ template<typename T>

    Name of the reaction in (projectile, ejectile) notation (e.g. "p(p,g)d").

    -

    Definition at line 265 of file reaction.h.

    - @@ -1366,8 +1302,6 @@ template<typename T>

    Products of the reaction.

    -

    Definition at line 269 of file reaction.h.

    - @@ -1392,8 +1326,6 @@ template<typename T>

    Q-value of the reaction in MeV.

    -

    Definition at line 267 of file reaction.h.

    - @@ -1418,8 +1350,6 @@ template<typename T>

    The seven rate coefficients.

    -

    Definition at line 271 of file reaction.h.

    - @@ -1444,8 +1374,6 @@ template<typename T>

    Reactants of the reaction.

    -

    Definition at line 268 of file reaction.h.

    - @@ -1470,8 +1398,6 @@ template<typename T>

    Flag indicating if this is a reverse reaction rate.

    -

    Definition at line 272 of file reaction.h.

    - @@ -1496,13 +1422,11 @@ template<typename T>

    Source label for the rate data (e.g., "wc12w", "st08").

    -

    Definition at line 270 of file reaction.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1approx8_1_1_approx8_network.html b/docs/html/classgridfire_1_1approx8_1_1_approx8_network.html index 85799c08..b13645ff 100644 --- a/docs/html/classgridfire_1_1approx8_1_1_approx8_network.html +++ b/docs/html/classgridfire_1_1approx8_1_1_approx8_network.html @@ -111,7 +111,7 @@ $(function(){initNavTree('classgridfire_1_1approx8_1_1_approx8_network.html','')

    Class for the Approx8 nuclear reaction network. More...

    -

    #include <engine_approx8.h>

    +

    #include <engine_approx8.h>

    Inheritance diagram for gridfire::approx8::Approx8Network:
    @@ -187,8 +187,6 @@ Additional Inherited Members

    Class for the Approx8 nuclear reaction network.

    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    - -

    Definition at line 294 of file engine_approx8.h.

    Constructor & Destructor Documentation

    ◆ Approx8Network()

    @@ -207,8 +205,6 @@ Additional Inherited Members
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 443 of file engine_approx8.cpp.

    -

    Member Function Documentation

    @@ -246,8 +242,6 @@ Additional Inherited Members
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 509 of file engine_approx8.cpp.

    - @@ -286,8 +280,6 @@ Additional Inherited Members
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 445 of file engine_approx8.cpp.

    - @@ -320,8 +312,6 @@ Additional Inherited Members
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 315 of file engine_approx8.h.

    - @@ -359,8 +349,6 @@ Additional Inherited Members
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 505 of file engine_approx8.cpp.

    -

    Member Data Documentation

    @@ -386,8 +374,6 @@ Additional Inherited Members
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 319 of file engine_approx8.h.

    - @@ -412,8 +398,6 @@ Additional Inherited Members
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 320 of file engine_approx8.h.

    - @@ -438,8 +422,6 @@ Additional Inherited Members
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 318 of file engine_approx8.h.

    - @@ -464,13 +446,11 @@ Additional Inherited Members
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 317 of file engine_approx8.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1exceptions_1_1_engine_error.html b/docs/html/classgridfire_1_1exceptions_1_1_engine_error.html index 75707653..23ceeae7 100644 --- a/docs/html/classgridfire_1_1exceptions_1_1_engine_error.html +++ b/docs/html/classgridfire_1_1exceptions_1_1_engine_error.html @@ -103,7 +103,7 @@ $(function(){initNavTree('classgridfire_1_1exceptions_1_1_engine_error.html','')
    -

    #include <error_engine.h>

    +

    #include <error_engine.h>

    Inheritance diagram for gridfire::exceptions::EngineError:
    @@ -117,11 +117,8 @@ Inheritance diagram for gridfire::exceptions::EngineError:
    gridfire::exceptions::UnableToSetNetworkReactionsError
    -

    Detailed Description

    -
    -

    Definition at line 8 of file error_engine.h.

    -
    The documentation for this class was generated from the following file:
      -
    • src/include/gridfire/exceptions/error_engine.h
      • +
      The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html b/docs/html/classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html index d8c14498..0ea1c6ed 100644 --- a/docs/html/classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html +++ b/docs/html/classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html @@ -107,7 +107,7 @@ $(function(){initNavTree('classgridfire_1_1exceptions_1_1_failed_to_partition_en
      -

      #include <error_engine.h>

      +

      #include <error_engine.h>

      Inheritance diagram for gridfire::exceptions::FailedToPartitionEngineError:
      @@ -130,10 +130,7 @@ Private Attributes std::string m_message   -

      Detailed Description

      -
      -

      Definition at line 75 of file error_engine.h.

      -

      Constructor & Destructor Documentation

      +

      Constructor & Destructor Documentation

      ◆ FailedToPartitionEngineError()

      @@ -157,8 +154,6 @@ Private Attributes
      -

      Definition at line 77 of file error_engine.h.

      -

      Member Function Documentation

      @@ -185,8 +180,6 @@ Private Attributes
      -

      Definition at line 80 of file error_engine.h.

      -

      Member Data Documentation

      @@ -210,12 +203,10 @@ Private Attributes
      -

      Definition at line 84 of file error_engine.h.

      -
      The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1exceptions_1_1_network_resized_error.html b/docs/html/classgridfire_1_1exceptions_1_1_network_resized_error.html index fc42c045..1f6a6f20 100644 --- a/docs/html/classgridfire_1_1exceptions_1_1_network_resized_error.html +++ b/docs/html/classgridfire_1_1exceptions_1_1_network_resized_error.html @@ -107,7 +107,7 @@ $(function(){initNavTree('classgridfire_1_1exceptions_1_1_network_resized_error.
      -

      #include <error_engine.h>

      +

      #include <error_engine.h>

      Inheritance diagram for gridfire::exceptions::NetworkResizedError:
      @@ -130,10 +130,7 @@ Private Attributes std::string m_message   -

      Detailed Description

      -
      -

      Definition at line 87 of file error_engine.h.

      -

      Constructor & Destructor Documentation

      +

      Constructor & Destructor Documentation

      ◆ NetworkResizedError()

      @@ -157,8 +154,6 @@ Private Attributes
      -

      Definition at line 89 of file error_engine.h.

      -

      Member Function Documentation

      @@ -185,8 +180,6 @@ Private Attributes
      -

      Definition at line 92 of file error_engine.h.

      -

      Member Data Documentation

      @@ -210,12 +203,10 @@ Private Attributes
      -

      Definition at line 96 of file error_engine.h.

      -
      The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1exceptions_1_1_stale_engine_error.html b/docs/html/classgridfire_1_1exceptions_1_1_stale_engine_error.html index 16030696..0fea1d2c 100644 --- a/docs/html/classgridfire_1_1exceptions_1_1_stale_engine_error.html +++ b/docs/html/classgridfire_1_1exceptions_1_1_stale_engine_error.html @@ -107,7 +107,7 @@ $(function(){initNavTree('classgridfire_1_1exceptions_1_1_stale_engine_error.htm
      -

      #include <error_engine.h>

      +

      #include <error_engine.h>

      Inheritance diagram for gridfire::exceptions::StaleEngineError:
      @@ -130,10 +130,7 @@ Private Attributes std::string m_message   -

      Detailed Description

      -
      -

      Definition at line 62 of file error_engine.h.

      -

      Constructor & Destructor Documentation

      +

      Constructor & Destructor Documentation

      ◆ StaleEngineError()

      @@ -157,8 +154,6 @@ Private Attributes
      -

      Definition at line 64 of file error_engine.h.

      -

      Member Function Documentation

      @@ -185,8 +180,6 @@ Private Attributes
      -

      Definition at line 67 of file error_engine.h.

      -

      Member Data Documentation

      @@ -210,12 +203,10 @@ Private Attributes
      -

      Definition at line 72 of file error_engine.h.

      -
      The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1exceptions_1_1_stale_engine_trigger.html b/docs/html/classgridfire_1_1exceptions_1_1_stale_engine_trigger.html index 02492559..96125ff8 100644 --- a/docs/html/classgridfire_1_1exceptions_1_1_stale_engine_trigger.html +++ b/docs/html/classgridfire_1_1exceptions_1_1_stale_engine_trigger.html @@ -108,7 +108,7 @@ $(function(){initNavTree('classgridfire_1_1exceptions_1_1_stale_engine_trigger.h
      -

      #include <error_engine.h>

      +

      #include <error_engine.h>

      Inheritance diagram for gridfire::exceptions::StaleEngineTrigger:
      @@ -150,10 +150,7 @@ Private Attributes state m_state   -

      Detailed Description

      -
      -

      Definition at line 10 of file error_engine.h.

      -

      Constructor & Destructor Documentation

      +

      Constructor & Destructor Documentation

      ◆ StaleEngineTrigger()

      @@ -177,8 +174,6 @@ Private Attributes
      -

      Definition at line 20 of file error_engine.h.

      -

      Member Function Documentation

      @@ -205,8 +200,6 @@ Private Attributes
      -

      Definition at line 54 of file error_engine.h.

      -
      @@ -232,8 +225,6 @@ Private Attributes
      -

      Definition at line 39 of file error_engine.h.

      -
      @@ -259,8 +250,6 @@ Private Attributes
      -

      Definition at line 43 of file error_engine.h.

      -
      @@ -286,8 +275,6 @@ Private Attributes
      -

      Definition at line 27 of file error_engine.h.

      -
      @@ -313,8 +300,6 @@ Private Attributes
      -

      Definition at line 31 of file error_engine.h.

      -
      @@ -340,8 +325,6 @@ Private Attributes
      -

      Definition at line 50 of file error_engine.h.

      -
      @@ -367,8 +350,6 @@ Private Attributes
      -

      Definition at line 35 of file error_engine.h.

      -
      @@ -394,8 +375,6 @@ Private Attributes
      -

      Definition at line 23 of file error_engine.h.

      -

      Member Data Documentation

      @@ -419,12 +398,10 @@ Private Attributes
      -

      Definition at line 58 of file error_engine.h.

      -
      The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1exceptions_1_1_unable_to_set_network_reactions_error.html b/docs/html/classgridfire_1_1exceptions_1_1_unable_to_set_network_reactions_error.html index 944ee69b..65ce24e4 100644 --- a/docs/html/classgridfire_1_1exceptions_1_1_unable_to_set_network_reactions_error.html +++ b/docs/html/classgridfire_1_1exceptions_1_1_unable_to_set_network_reactions_error.html @@ -107,7 +107,7 @@ $(function(){initNavTree('classgridfire_1_1exceptions_1_1_unable_to_set_network_
      -

      #include <error_engine.h>

      +

      #include <error_engine.h>

      Inheritance diagram for gridfire::exceptions::UnableToSetNetworkReactionsError:
      @@ -130,10 +130,7 @@ Private Attributes std::string m_message   -

      Detailed Description

      -
      -

      Definition at line 99 of file error_engine.h.

      -

      Constructor & Destructor Documentation

      +

      Constructor & Destructor Documentation

      ◆ UnableToSetNetworkReactionsError()

      @@ -157,8 +154,6 @@ Private Attributes
      -

      Definition at line 101 of file error_engine.h.

      -

      Member Function Documentation

      @@ -185,8 +180,6 @@ Private Attributes
      -

      Definition at line 104 of file error_engine.h.

      -

      Member Data Documentation

      @@ -210,12 +203,10 @@ Private Attributes
      -

      Definition at line 109 of file error_engine.h.

      -
      The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1io_1_1_m_e_s_a_network_file_parser.html b/docs/html/classgridfire_1_1io_1_1_m_e_s_a_network_file_parser.html index 06f4fb54..a3e2b628 100644 --- a/docs/html/classgridfire_1_1io_1_1_m_e_s_a_network_file_parser.html +++ b/docs/html/classgridfire_1_1io_1_1_m_e_s_a_network_file_parser.html @@ -111,7 +111,7 @@ $(function(){initNavTree('classgridfire_1_1io_1_1_m_e_s_a_network_file_parser.ht

      A parser for MESA-format network files. More...

      -

      #include <network_file.h>

      +

      #include <network_file.h>

      Inheritance diagram for gridfire::io::MESANetworkFileParser:
      @@ -154,8 +154,6 @@ Private Attributes

      Detailed Description

      A parser for MESA-format network files.

      This class is designed to parse reaction network files that follow the format used by the MESA stellar evolution code.

      - -

      Definition at line 119 of file network_file.h.

      Member Typedef Documentation

      ◆ Config

      @@ -177,8 +175,6 @@ Private Attributes
      -

      Definition at line 144 of file network_file.h.

      -
      @@ -201,8 +197,6 @@ Private Attributes
      -

      Definition at line 145 of file network_file.h.

      -

      Constructor & Destructor Documentation

      @@ -305,8 +299,6 @@ Private Attributes
      -

      Definition at line 146 of file network_file.h.

      -
      @@ -329,8 +321,6 @@ Private Attributes
      -

      Definition at line 149 of file network_file.h.

      -
      @@ -353,12 +343,10 @@ Private Attributes
      -

      Definition at line 147 of file network_file.h.

      -
      The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1io_1_1_network_file_parser.html b/docs/html/classgridfire_1_1io_1_1_network_file_parser.html index 7000236b..e51dfabd 100644 --- a/docs/html/classgridfire_1_1io_1_1_network_file_parser.html +++ b/docs/html/classgridfire_1_1io_1_1_network_file_parser.html @@ -109,7 +109,7 @@ $(function(){initNavTree('classgridfire_1_1io_1_1_network_file_parser.html','');

      An abstract base class for network file parsers. More...

      -

      #include <network_file.h>

      +

      #include <network_file.h>

      Inheritance diagram for gridfire::io::NetworkFileParser:
      @@ -134,8 +134,6 @@ Public Member Functions

      Detailed Description

      An abstract base class for network file parsers.

      This class defines the interface for parsing files that contain reaction network definitions. Derived classes must implement the parse method to handle specific file formats.

      - -

      Definition at line 22 of file network_file.h.

      Constructor & Destructor Documentation

      ◆ ~NetworkFileParser()

      @@ -212,14 +210,14 @@ Public Member Functions
      } catch (const std::runtime_error& e) {
      // ... handle error
      }
      -
      gridfire::io::ParsedNetworkData
      std::vector< std::string > ParsedNetworkData
      Definition network_file.h:12
      +
      gridfire::io::ParsedNetworkData
      std::vector< std::string > ParsedNetworkData
      Definition network_file.h:12

      Implemented in gridfire::io::MESANetworkFileParser, gridfire::io::SimpleReactionListFileParser, and PyNetworkFileParser.

      The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html b/docs/html/classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html index b730288d..4175d731 100644 --- a/docs/html/classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html +++ b/docs/html/classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html @@ -111,7 +111,7 @@ $(function(){initNavTree('classgridfire_1_1io_1_1_simple_reaction_list_file_pars

      A parser for simple text files containing a list of reactions. More...

      -

      #include <network_file.h>

      +

      #include <network_file.h>

      Inheritance diagram for gridfire::io::SimpleReactionListFileParser:
      @@ -152,8 +152,6 @@ Private Attributes

      Detailed Description

      A parser for simple text files containing a list of reactions.

      This parser reads a file where each line contains a single reaction name. It supports comments (lines starting with '#') and ignores empty lines.

      - -

      Definition at line 68 of file network_file.h.

      Member Typedef Documentation

      ◆ Config

      @@ -175,8 +173,6 @@ Private Attributes
      -

      Definition at line 104 of file network_file.h.

      -
      @@ -199,8 +195,6 @@ Private Attributes
      -

      Definition at line 105 of file network_file.h.

      -

      Constructor & Destructor Documentation

      @@ -230,8 +224,6 @@ Private Attributes

      Constructs a SimpleReactionListFileParser.

      Postcondition
      The parser is initialized and ready to parse files.
      -

      Definition at line 42 of file network_file.cpp.

      -

      Member Function Documentation

      @@ -283,14 +275,12 @@ Private Attributes

      Usage

      SimpleReactionListFileParser parser;
      ParsedNetworkData data = parser.parse("reactions.txt");
      -
      gridfire::io::SimpleReactionListFileParser::parse
      ParsedNetworkData parse(const std::string &filename) const override
      Parses a simple reaction list file.
      Definition network_file.cpp:44
      -
      gridfire::io::SimpleReactionListFileParser::SimpleReactionListFileParser
      SimpleReactionListFileParser()
      Constructs a SimpleReactionListFileParser.
      Definition network_file.cpp:42
      -
      gridfire::io::ParsedNetworkData
      std::vector< std::string > ParsedNetworkData
      Definition network_file.h:12
      +
      gridfire::io::SimpleReactionListFileParser::parse
      ParsedNetworkData parse(const std::string &filename) const override
      Parses a simple reaction list file.
      Definition network_file.cpp:44
      +
      gridfire::io::SimpleReactionListFileParser::SimpleReactionListFileParser
      SimpleReactionListFileParser()
      Constructs a SimpleReactionListFileParser.
      Definition network_file.cpp:42
      +
      gridfire::io::ParsedNetworkData
      std::vector< std::string > ParsedNetworkData
      Definition network_file.h:12

      Implements gridfire::io::NetworkFileParser.

      -

      Definition at line 44 of file network_file.cpp.

      -

      Member Data Documentation

      @@ -314,8 +304,6 @@ Private Attributes
      -

      Definition at line 106 of file network_file.h.

      -
      @@ -338,13 +326,11 @@ Private Attributes
      -

      Definition at line 107 of file network_file.h.

      -
      The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1partition_1_1_composite_partition_function.html b/docs/html/classgridfire_1_1partition_1_1_composite_partition_function.html index 4c47f0fe..fd55ef12 100644 --- a/docs/html/classgridfire_1_1partition_1_1_composite_partition_function.html +++ b/docs/html/classgridfire_1_1partition_1_1_composite_partition_function.html @@ -111,7 +111,7 @@ $(function(){initNavTree('classgridfire_1_1partition_1_1_composite_partition_fun

      Combines multiple PartitionFunction instances into a single composite strategy. More...

      -

      #include <partition_composite.h>

      +

      #include <partition_composite.h>

      Inheritance diagram for gridfire::partition::CompositePartitionFunction:
      @@ -166,8 +166,6 @@ Private Attributes - -

      Definition at line 27 of file partition_composite.h.

      Constructor & Destructor Documentation

      ◆ CompositePartitionFunction() [1/2]

      @@ -201,8 +199,6 @@ Private Attributes
    -

    Definition at line 11 of file partition_composite.cpp.

    - @@ -228,8 +224,6 @@ Private Attributes
  • -

    Definition at line 20 of file partition_composite.cpp.

    -

    Member Function Documentation

    @@ -264,8 +258,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 88 of file partition_composite.h.

    - @@ -313,8 +305,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 27 of file partition_composite.cpp.

    - @@ -362,8 +352,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 48 of file partition_composite.cpp.

    - @@ -397,8 +385,6 @@ Private Attributes
  • -

    Definition at line 92 of file partition_composite.cpp.

    - @@ -438,8 +424,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 66 of file partition_composite.cpp.

    - @@ -474,8 +458,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 76 of file partition_composite.cpp.

    -

    Member Data Documentation

    @@ -499,8 +481,6 @@ Private Attributes
    -

    Definition at line 92 of file partition_composite.h.

    -
    @@ -525,13 +505,11 @@ Private Attributes

    Set of partition functions to use in the composite partition function.

    -

    Definition at line 93 of file partition_composite.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1partition_1_1_ground_state_partition_function.html b/docs/html/classgridfire_1_1partition_1_1_ground_state_partition_function.html index 934cb1aa..358b1a64 100644 --- a/docs/html/classgridfire_1_1partition_1_1_ground_state_partition_function.html +++ b/docs/html/classgridfire_1_1partition_1_1_ground_state_partition_function.html @@ -111,7 +111,7 @@ $(function(){initNavTree('classgridfire_1_1partition_1_1_ground_state_partition_

    Partition function implementation for nuclear ground states. More...

    -

    #include <partition_ground.h>

    +

    #include <partition_ground.h>

    Inheritance diagram for gridfire::partition::GroundStatePartitionFunction:
    @@ -156,8 +156,6 @@ Private Attributes

    Detailed Description

    Partition function implementation for nuclear ground states.

    Computes the partition function as (2J + 1) based on the ground state spin J of each isotope. The temperature derivative is always zero. Ground state spins are loaded from the fourdst::atomic::species registry at construction.

    See also
    partition_ground.cpp for implementation details.
    - -

    Definition at line 22 of file partition_ground.h.

    Constructor & Destructor Documentation

    ◆ GroundStatePartitionFunction()

    @@ -181,8 +179,6 @@ Private Attributes
  • -

    Definition at line 12 of file partition_ground.cpp.

    -

    Member Function Documentation

    @@ -217,8 +213,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 88 of file partition_ground.h.

    - @@ -277,8 +271,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 18 of file partition_ground.cpp.

    - @@ -337,8 +329,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 29 of file partition_ground.cpp.

    - @@ -382,8 +372,6 @@ Private Attributes
  • -

    Definition at line 44 of file partition_ground.cpp.

    - @@ -429,8 +417,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 38 of file partition_ground.cpp.

    - @@ -464,8 +450,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 82 of file partition_ground.h.

    -

    Member Data Documentation

    @@ -489,8 +473,6 @@ Private Attributes
    -

    Definition at line 93 of file partition_ground.h.

    -
    @@ -513,13 +495,11 @@ Private Attributes
    -

    Definition at line 92 of file partition_ground.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1partition_1_1_partition_function.html b/docs/html/classgridfire_1_1partition_1_1_partition_function.html index 26453686..4f6252cc 100644 --- a/docs/html/classgridfire_1_1partition_1_1_partition_function.html +++ b/docs/html/classgridfire_1_1partition_1_1_partition_function.html @@ -109,7 +109,7 @@ $(function(){initNavTree('classgridfire_1_1partition_1_1_partition_function.html

    Abstract interface for evaluating nuclear partition functions. More...

    -

    #include <partition_abstract.h>

    +

    #include <partition_abstract.h>

    Inheritance diagram for gridfire::partition::PartitionFunction:
    @@ -147,8 +147,6 @@ Public Member Functions

    Detailed Description

    Abstract interface for evaluating nuclear partition functions.

    Provides methods to compute the partition function and its temperature derivative for a given isotope, to query if the function supports that isotope, and to clone the function object. Concrete implementations must provide temperature- dependent statistical models.

    - -

    Definition at line 17 of file partition_abstract.h.

    Constructor & Destructor Documentation

    ◆ ~PartitionFunction()

    @@ -383,7 +381,7 @@ Public Member Functions
    The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1partition_1_1_rauscher_thielemann_partition_function.html b/docs/html/classgridfire_1_1partition_1_1_rauscher_thielemann_partition_function.html index 6e7d5439..c8d433be 100644 --- a/docs/html/classgridfire_1_1partition_1_1_rauscher_thielemann_partition_function.html +++ b/docs/html/classgridfire_1_1partition_1_1_rauscher_thielemann_partition_function.html @@ -114,7 +114,7 @@ $(function(){initNavTree('classgridfire_1_1partition_1_1_rauscher_thielemann_par

    Partition function using Rauscher-Thielemann tabulated normalized G-values. More...

    -

    #include <partition_rauscher_thielemann.h>

    +

    #include <partition_rauscher_thielemann.h>

    Inheritance diagram for gridfire::partition::RauscherThielemannPartitionFunction:
    @@ -200,8 +200,6 @@ Private Attributes - -

    Definition at line 26 of file partition_rauscher_thielemann.h.

    Member Enumeration Documentation

    ◆ Bounds

    @@ -233,8 +231,6 @@ Private Attributes -

    Definition at line 89 of file partition_rauscher_thielemann.h.

    -

    Constructor & Destructor Documentation

    @@ -257,8 +253,6 @@ Private Attributes

    Reads embedded RT partition data records and fills m_partitionData.

    Precondition
    Embedded data arrays are available and non-empty.
    Postcondition
    m_partitionData contains entries for all isotopes in data.
    -

    Definition at line 20 of file partition_rauscher_thielemann.cpp.

    -

    Member Function Documentation

    @@ -291,8 +285,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 81 of file partition_rauscher_thielemann.h.

    - @@ -348,8 +340,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 43 of file partition_rauscher_thielemann.cpp.

    - @@ -405,8 +395,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 78 of file partition_rauscher_thielemann.cpp.

    - @@ -458,8 +446,6 @@ Private Attributes -

    Definition at line 117 of file partition_rauscher_thielemann.cpp.

    - @@ -505,8 +491,6 @@ Private Attributes
    Returns
    InterpolationPoints containing bounds and G values.
    -

    Definition at line 105 of file partition_rauscher_thielemann.cpp.

    - @@ -546,8 +530,6 @@ Private Attributes
    Returns
    Key computed as z*1000 + a.
    -

    Definition at line 145 of file partition_rauscher_thielemann.cpp.

    - @@ -590,8 +572,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 98 of file partition_rauscher_thielemann.cpp.

    - @@ -623,8 +603,6 @@ Private Attributes

    Implements gridfire::partition::PartitionFunction.

    -

    Definition at line 75 of file partition_rauscher_thielemann.h.

    -

    Member Data Documentation

    @@ -648,8 +626,6 @@ Private Attributes
    -

    Definition at line 112 of file partition_rauscher_thielemann.h.

    -
    @@ -674,13 +650,11 @@ Private Attributes

    Map of isotope key to data.

    -

    Definition at line 113 of file partition_rauscher_thielemann.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1reaction_1_1_logical_reaction.html b/docs/html/classgridfire_1_1reaction_1_1_logical_reaction.html index b3fff312..8599e41d 100644 --- a/docs/html/classgridfire_1_1reaction_1_1_logical_reaction.html +++ b/docs/html/classgridfire_1_1reaction_1_1_logical_reaction.html @@ -112,7 +112,7 @@ $(function(){initNavTree('classgridfire_1_1reaction_1_1_logical_reaction.html','

    Represents a "logical" reaction that aggregates rates from multiple sources. More...

    -

    #include <reaction.h>

    +

    #include <reaction.h>

    Inheritance diagram for gridfire::reaction::LogicalReaction:
    @@ -287,8 +287,6 @@ Additional Inherited Members

    Detailed Description

    Represents a "logical" reaction that aggregates rates from multiple sources.

    A LogicalReaction shares the same reactants and products but combines rates from different evaluations (e.g., "wc12" and "st08" for the same physical reaction). The total rate is the sum of the individual rates. It inherits from Reaction, using the properties of the first provided reaction as its base properties (reactants, products, Q-value, etc.).

    - -

    Definition at line 310 of file reaction.h.

    Constructor & Destructor Documentation

    ◆ LogicalReaction()

    @@ -327,8 +325,6 @@ Additional Inherited Members -

    Definition at line 163 of file reaction.cpp.

    -

    Member Function Documentation

    @@ -361,8 +357,6 @@ Additional Inherited Members -

    Definition at line 192 of file reaction.cpp.

    - @@ -388,8 +382,6 @@ Additional Inherited Members
    -

    Definition at line 359 of file reaction.h.

    -
    @@ -415,8 +407,6 @@ Additional Inherited Members
    -

    Definition at line 360 of file reaction.h.

    -
    @@ -444,8 +434,6 @@ Additional Inherited Members

    Reimplemented from gridfire::reaction::Reaction.

    -

    Definition at line 218 of file reaction.cpp.

    - @@ -482,8 +470,6 @@ Additional Inherited Members

    Reimplemented from gridfire::reaction::Reaction.

    -

    Definition at line 269 of file reaction.cpp.

    - @@ -520,8 +506,6 @@ Additional Inherited Members

    Reimplemented from gridfire::reaction::Reaction.

    -

    Definition at line 214 of file reaction.cpp.

    - @@ -565,8 +549,6 @@ template<typename T>
    Returns
    The total calculated reaction rate.

    This method iterates through all stored RateCoefficientSets, calculates the rate for each, and returns their sum.

    -

    Definition at line 385 of file reaction.h.

    - @@ -592,8 +574,6 @@ template<typename T>
    -

    Definition at line 361 of file reaction.h.

    -
    @@ -619,8 +599,6 @@ template<typename T>
    -

    Definition at line 362 of file reaction.h.

    -
    @@ -649,8 +627,6 @@ template<typename T>

    Gets the number of source rates contributing to this logical reaction.

    Returns
    The number of aggregated rates.
    -

    Definition at line 331 of file reaction.h.

    - @@ -679,8 +655,6 @@ template<typename T>

    Gets the list of source labels for the aggregated rates.

    Returns
    A vector of source label strings.
    -

    Definition at line 337 of file reaction.h.

    -

    Friends And Related Symbol Documentation

    @@ -711,8 +685,6 @@ template<typename T>
    -

    Definition at line 366 of file reaction.h.

    -

    Member Data Documentation

    @@ -738,8 +710,6 @@ template<typename T>

    List of rate coefficient sets from each source.

    -

    Definition at line 373 of file reaction.h.

    - @@ -764,13 +734,11 @@ template<typename T>

    List of source labels.

    -

    Definition at line 372 of file reaction.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1reaction_1_1_reaction.html b/docs/html/classgridfire_1_1reaction_1_1_reaction.html index 8ede233e..c7585baa 100644 --- a/docs/html/classgridfire_1_1reaction_1_1_reaction.html +++ b/docs/html/classgridfire_1_1reaction_1_1_reaction.html @@ -112,7 +112,7 @@ $(function(){initNavTree('classgridfire_1_1reaction_1_1_reaction.html',''); init

    Represents a single nuclear reaction from a specific data source. More...

    -

    #include <reaction.h>

    +

    #include <reaction.h>

    Inheritance diagram for gridfire::reaction::Reaction:
    @@ -258,10 +258,8 @@ Friends
    "H_1_H_1_to_H_2", "p(p,g)d", 1, {H_1, H_1}, {H_2}, 5.493, "st08", rate_coeffs
    );
    double rate = p_gamma_d.calculate_rate(0.1); // T9 = 0.1
    -
    gridfire::reaction::Reaction::Reaction
    Reaction(const std::string_view id, const std::string_view peName, const int chapter, const std::vector< fourdst::atomic::Species > &reactants, const std::vector< fourdst::atomic::Species > &products, const double qValue, const std::string_view label, const RateCoefficientSet &sets, const bool reverse=false)
    Constructs a Reaction object.
    Definition reaction.cpp:19
    -
    -

    Definition at line 72 of file reaction.h.

    -

    Constructor & Destructor Documentation

    +
    gridfire::reaction::Reaction::Reaction
    Reaction(const std::string_view id, const std::string_view peName, const int chapter, const std::vector< fourdst::atomic::Species > &reactants, const std::vector< fourdst::atomic::Species > &products, const double qValue, const std::string_view label, const RateCoefficientSet &sets, const bool reverse=false)
    Constructs a Reaction object.
    Definition reaction.cpp:19
    +

    Constructor & Destructor Documentation

    ◆ ~Reaction()

    @@ -359,8 +357,6 @@ Friends -

    Definition at line 19 of file reaction.cpp.

    -

    Member Function Documentation

    @@ -390,8 +386,6 @@ Friends

    Gets a set of all unique species involved in the reaction.

    Returns
    An unordered_set of all reactant and product species.
    -

    Definition at line 91 of file reaction.cpp.

    - @@ -419,8 +413,6 @@ Friends

    Reimplemented in gridfire::reaction::LogicalReaction.

    -

    Definition at line 47 of file reaction.cpp.

    - @@ -457,8 +449,6 @@ Friends

    Reimplemented in gridfire::reaction::LogicalReaction.

    -

    Definition at line 43 of file reaction.cpp.

    - @@ -495,8 +485,6 @@ Friends

    Reimplemented in gridfire::reaction::LogicalReaction.

    -

    Definition at line 39 of file reaction.cpp.

    - @@ -540,8 +528,6 @@ template<typename T>
    Returns
    The calculated reaction rate.

    The rate is calculated using the standard REACLIB formula: rate = exp(a0 + a1/T9 + a2/T9^(1/3) + a3*T9^(1/3) + a4*T9 + a5*T9^(5/3) + a6*ln(T9))

    -

    Definition at line 283 of file reaction.h.

    - @@ -570,8 +556,6 @@ template<typename T>

    Gets the REACLIB chapter number.

    Returns
    The chapter number.
    -

    Definition at line 128 of file reaction.h.

    - @@ -606,8 +590,6 @@ template<typename T>
    Returns
    True if the species is involved, false otherwise.
    -

    Definition at line 68 of file reaction.cpp.

    - @@ -642,8 +624,6 @@ template<typename T>
    Returns
    True if the species is a product, false otherwise.
    -

    Definition at line 82 of file reaction.cpp.

    - @@ -678,8 +658,6 @@ template<typename T>
    Returns
    True if the species is a reactant, false otherwise.
    -

    Definition at line 73 of file reaction.cpp.

    - @@ -708,8 +686,6 @@ template<typename T>

    Calculates the excess energy from the mass difference of reactants and products.

    Returns
    The excess energy in MeV.
    -

    Definition at line 144 of file reaction.cpp.

    - @@ -745,8 +721,6 @@ template<typename T>
    Returns
    A 64-bit hash value.

    Uses the XXHash64 algorithm on the reaction's ID string.

    -

    Definition at line 157 of file reaction.cpp.

    - @@ -775,8 +749,6 @@ template<typename T>

    Gets the unique identifier of the reaction.

    Returns
    The reaction ID.
    -

    Definition at line 204 of file reaction.h.

    - @@ -805,8 +777,6 @@ template<typename T>

    Checks if this is a reverse reaction rate.

    Returns
    True if it is a reverse rate, false otherwise.
    -

    Definition at line 228 of file reaction.h.

    - @@ -835,8 +805,6 @@ template<typename T>

    Gets the number of unique species involved in the reaction.

    Returns
    The count of unique species.
    -

    Definition at line 129 of file reaction.cpp.

    - @@ -871,8 +839,6 @@ template<typename T>
    Returns
    True if the reactions are not equal.
    -

    Definition at line 248 of file reaction.h.

    - @@ -907,8 +873,6 @@ template<typename T>
    Returns
    True if the reaction IDs are the same.
    -

    Definition at line 241 of file reaction.h.

    - @@ -937,8 +901,6 @@ template<typename T>

    Gets the reaction name in (projectile, ejectile) notation.

    Returns
    The reaction name (e.g., "p(p,g)d").
    -

    Definition at line 122 of file reaction.h.

    - @@ -967,8 +929,6 @@ template<typename T>

    Gets a set of all unique product species.

    Returns
    An unordered_set of product species.
    -

    Definition at line 106 of file reaction.cpp.

    - @@ -997,8 +957,6 @@ template<typename T>

    Gets the vector of product species.

    Returns
    A const reference to the vector of products.
    -

    Definition at line 222 of file reaction.h.

    - @@ -1027,8 +985,6 @@ template<typename T>

    Gets the Q-value of the reaction.

    Returns
    The Q-value in whatever units the reaction was defined in (usually MeV).
    -

    Definition at line 210 of file reaction.h.

    - @@ -1057,8 +1013,6 @@ template<typename T>

    Gets the set of rate coefficients.

    Returns
    A const reference to the RateCoefficientSet.
    -

    Definition at line 140 of file reaction.h.

    - @@ -1087,8 +1041,6 @@ template<typename T>

    Gets a set of all unique reactant species.

    Returns
    An unordered_set of reactant species.
    -

    Definition at line 98 of file reaction.cpp.

    - @@ -1117,8 +1069,6 @@ template<typename T>

    Gets the vector of reactant species.

    Returns
    A const reference to the vector of reactants.
    -

    Definition at line 216 of file reaction.h.

    - @@ -1147,8 +1097,6 @@ template<typename T>

    Gets the source label for the rate data.

    Returns
    The source label (e.g., "wc12w", "st08").
    -

    Definition at line 134 of file reaction.h.

    - @@ -1177,8 +1125,6 @@ template<typename T>

    Gets a map of all species to their stoichiometric coefficients.

    Returns
    An unordered_map from species to their integer coefficients.
    -

    Definition at line 133 of file reaction.cpp.

    - @@ -1243,8 +1189,6 @@ template<typename T>
    -

    Definition at line 258 of file reaction.h.

    -

    Member Data Documentation

    @@ -1270,8 +1214,6 @@ template<typename T>

    Chapter number from the REACLIB database, defining the reaction structure.

    -

    Definition at line 266 of file reaction.h.

    - @@ -1296,8 +1238,6 @@ template<typename T>

    Unique identifier for the reaction (e.g., "h1+h1=>h2+e+nu").

    -

    Definition at line 264 of file reaction.h.

    - @@ -1320,8 +1260,6 @@ template<typename T>
    -

    Definition at line 263 of file reaction.h.

    -
    @@ -1346,8 +1284,6 @@ template<typename T>

    Name of the reaction in (projectile, ejectile) notation (e.g. "p(p,g)d").

    -

    Definition at line 265 of file reaction.h.

    - @@ -1372,8 +1308,6 @@ template<typename T>

    Products of the reaction.

    -

    Definition at line 269 of file reaction.h.

    - @@ -1398,8 +1332,6 @@ template<typename T>

    Q-value of the reaction in MeV.

    -

    Definition at line 267 of file reaction.h.

    - @@ -1424,8 +1356,6 @@ template<typename T>

    The seven rate coefficients.

    -

    Definition at line 271 of file reaction.h.

    - @@ -1450,8 +1380,6 @@ template<typename T>

    Reactants of the reaction.

    -

    Definition at line 268 of file reaction.h.

    - @@ -1476,8 +1404,6 @@ template<typename T>

    Flag indicating if this is a reverse reaction rate.

    -

    Definition at line 272 of file reaction.h.

    - @@ -1502,13 +1428,11 @@ template<typename T>

    Source label for the rate data (e.g., "wc12w", "st08").

    -

    Definition at line 270 of file reaction.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1reaction_1_1_templated_reaction_set.html b/docs/html/classgridfire_1_1reaction_1_1_templated_reaction_set.html index 5d57c742..ece7c6d8 100644 --- a/docs/html/classgridfire_1_1reaction_1_1_templated_reaction_set.html +++ b/docs/html/classgridfire_1_1reaction_1_1_templated_reaction_set.html @@ -108,7 +108,7 @@ $(function(){initNavTree('classgridfire_1_1reaction_1_1_templated_reaction_set.h
    -

    #include <reaction.h>

    +

    #include <reaction.h>

    @@ -196,11 +196,7 @@ Friends

    Public Member Functions

    std::ostream & operator<< (std::ostream &os, const TemplatedReactionSet< ReactionT > &r)
     
    -

    Detailed Description

    -
    template<typename ReactionT>
    -class gridfire::reaction::TemplatedReactionSet< ReactionT >
    -

    Definition at line 406 of file reaction.h.

    -

    Constructor & Destructor Documentation

    +

    Constructor & Destructor Documentation

    ◆ TemplatedReactionSet() [1/3]

    @@ -234,8 +230,6 @@ template<typename ReactionT>
    -

    Definition at line 568 of file reaction.h.

    - @@ -255,8 +249,6 @@ template<typename ReactionT>
    -

    Definition at line 583 of file reaction.h.

    -
    @@ -284,8 +276,6 @@ template<typename ReactionT> -

    Definition at line 586 of file reaction.h.

    -

    Member Function Documentation

    @@ -314,8 +304,6 @@ template<typename ReactionT> -

    Definition at line 609 of file reaction.h.

    - @@ -343,8 +331,6 @@ template<typename ReactionT>
    -

    Definition at line 531 of file reaction.h.

    -
    @@ -372,8 +358,6 @@ template<typename ReactionT>
    -

    Definition at line 532 of file reaction.h.

    -
    @@ -395,8 +379,6 @@ template<typename ReactionT>

    Removes all reactions from the set.

    -

    Definition at line 649 of file reaction.h.

    - @@ -433,8 +415,6 @@ template<typename ReactionT>
    Returns
    True if the reaction is in the set, false otherwise.
    -

    Definition at line 639 of file reaction.h.

    - @@ -471,8 +451,6 @@ template<typename ReactionT>
    Returns
    True if the reaction is in the set, false otherwise.
    -

    Definition at line 629 of file reaction.h.

    - @@ -509,8 +487,6 @@ template<typename ReactionT>
    Returns
    True if the species is a product in any reaction.
    -

    Definition at line 675 of file reaction.h.

    - @@ -547,8 +523,6 @@ template<typename ReactionT>
    Returns
    True if the species is a reactant in any reaction.
    -

    Definition at line 665 of file reaction.h.

    - @@ -585,8 +559,6 @@ template<typename ReactionT>
    Returns
    True if the species is involved in any reaction.
    -

    Definition at line 655 of file reaction.h.

    - @@ -614,8 +586,6 @@ template<typename ReactionT>
    -

    Definition at line 533 of file reaction.h.

    -
    @@ -643,8 +613,6 @@ template<typename ReactionT>
    -

    Definition at line 534 of file reaction.h.

    -
    @@ -672,8 +640,6 @@ template<typename ReactionT>
    -

    Definition at line 734 of file reaction.h.

    -
    @@ -711,8 +677,6 @@ template<typename ReactionT>
    Returns
    A 64-bit hash value.

    The algorithm computes the hash of each individual reaction, sorts the hashes, and then computes a final hash over the sorted list of hashes. This ensures the hash is order-independent.

    -

    Definition at line 716 of file reaction.h.

    - @@ -741,8 +705,6 @@ template<typename ReactionT>
    Returns
    True if the sets are not equal.
    -

    Definition at line 711 of file reaction.h.

    - @@ -771,8 +733,6 @@ template<typename ReactionT>
    Returns
    A reference to this ReactionSet.
    -

    Definition at line 599 of file reaction.h.

    - @@ -801,8 +761,6 @@ template<typename ReactionT>
    Returns
    True if the sets are equal (same size and hash).
    -

    Definition at line 703 of file reaction.h.

    - @@ -845,8 +803,6 @@ template<typename ReactionT> -

    Definition at line 694 of file reaction.h.

    - @@ -889,8 +845,6 @@ template<typename ReactionT> -

    Definition at line 685 of file reaction.h.

    - @@ -918,8 +872,6 @@ template<typename ReactionT> -

    Definition at line 616 of file reaction.h.

    - @@ -950,8 +902,6 @@ template<typename ReactionT>

    Gets the number of reactions in the set.

    Returns
    The size of the set.
    -

    Definition at line 459 of file reaction.h.

    -

    Friends And Related Symbol Documentation

    @@ -984,8 +934,6 @@ template<typename ReactionT>
    -

    Definition at line 537 of file reaction.h.

    -

    Member Data Documentation

    @@ -1011,8 +959,6 @@ template<typename ReactionT>
    -

    Definition at line 557 of file reaction.h.

    -
    @@ -1037,8 +983,6 @@ template<typename ReactionT>
    -

    Definition at line 555 of file reaction.h.

    -
    @@ -1065,8 +1009,6 @@ template<typename ReactionT>

    Maps reaction IDs to Reaction objects for quick lookup.

    -

    Definition at line 558 of file reaction.h.

    - @@ -1091,12 +1033,10 @@ template<typename ReactionT>
    -

    Definition at line 556 of file reaction.h.

    -
    The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1screening_1_1_bare_screening_model.html b/docs/html/classgridfire_1_1screening_1_1_bare_screening_model.html index 85edaf5a..ba4bf22d 100644 --- a/docs/html/classgridfire_1_1screening_1_1_bare_screening_model.html +++ b/docs/html/classgridfire_1_1screening_1_1_bare_screening_model.html @@ -111,7 +111,7 @@ $(function(){initNavTree('classgridfire_1_1screening_1_1_bare_screening_model.ht

    A screening model that applies no screening effect. More...

    -

    #include <screening_bare.h>

    +

    #include <screening_bare.h>

    Inheritance diagram for gridfire::screening::BareScreeningModel:
    @@ -158,8 +158,6 @@ Additional Inherited Members

    Detailed Description

    A screening model that applies no screening effect.

    This class implements the ScreeningModel interface but returns a screening factor of 1.0 for all reactions, regardless of the plasma conditions. It represents the case of bare, unscreened nuclei and serves as a baseline or can be used when screening effects are negligible or intentionally ignored.

    - -

    Definition at line 21 of file screening_bare.h.

    Member Typedef Documentation

    ◆ ADDouble

    @@ -183,8 +181,6 @@ Additional Inherited Members

    Alias for CppAD Automatic Differentiation type for double precision.

    -

    Definition at line 23 of file screening_bare.h.

    -

    Member Function Documentation

    @@ -271,8 +267,6 @@ template<typename T>
    Returns
    A std::vector<T> of the same size as reactions, with all elements set to 1.0.
    -

    Definition at line 126 of file screening_bare.h.

    - @@ -333,8 +327,6 @@ template<typename T>

    Implements gridfire::screening::ScreeningModel.

    -

    Definition at line 12 of file screening_bare.cpp.

    - @@ -399,18 +391,16 @@ template<typename T>
    reactions, species, Y, T9, rho
    );
    // 'factors' will contain [1.0, 1.0, ...]
    -
    gridfire::screening::BareScreeningModel
    A screening model that applies no screening effect.
    Definition screening_bare.h:21
    -
    gridfire::screening::BareScreeningModel::calculateScreeningFactors
    std::vector< double > calculateScreeningFactors(const reaction::LogicalReactionSet &reactions, const std::vector< fourdst::atomic::Species > &species, const std::vector< double > &Y, const double T9, const double rho) const override
    Calculates screening factors, which are always 1.0.
    Definition screening_bare.cpp:22
    +
    gridfire::screening::BareScreeningModel
    A screening model that applies no screening effect.
    Definition screening_bare.h:21
    +
    gridfire::screening::BareScreeningModel::calculateScreeningFactors
    std::vector< double > calculateScreeningFactors(const reaction::LogicalReactionSet &reactions, const std::vector< fourdst::atomic::Species > &species, const std::vector< double > &Y, const double T9, const double rho) const override
    Calculates screening factors, which are always 1.0.
    Definition screening_bare.cpp:22

    Implements gridfire::screening::ScreeningModel.

    -

    Definition at line 22 of file screening_bare.cpp.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1screening_1_1_screening_model.html b/docs/html/classgridfire_1_1screening_1_1_screening_model.html index 098d1636..7d7296ce 100644 --- a/docs/html/classgridfire_1_1screening_1_1_screening_model.html +++ b/docs/html/classgridfire_1_1screening_1_1_screening_model.html @@ -110,7 +110,7 @@ $(function(){initNavTree('classgridfire_1_1screening_1_1_screening_model.html','

    An abstract base class for plasma screening models. More...

    -

    #include <screening_abstract.h>

    +

    #include <screening_abstract.h>

    Inheritance diagram for gridfire::screening::ScreeningModel:
    @@ -145,8 +145,6 @@ Public Member Functions

    An abstract base class for plasma screening models.

    This class defines the interface for models that calculate the enhancement factor for nuclear reaction rates due to the electrostatic screening of interacting nuclei by the surrounding plasma. Concrete implementations of this class will provide specific screening prescriptions (e.g., WEAK, BARE, STRONG, etc.).

    The interface provides methods for calculating screening factors for both standard double-precision inputs and for CppAD's automatic differentiation types, allowing the screening contributions to be included in Jacobian calculations.

    - -

    Definition at line 27 of file screening_abstract.h.

    Member Typedef Documentation

    ◆ ADDouble

    @@ -162,8 +160,6 @@ Public Member Functions

    Alias for CppAD Automatic Differentiation type for double precision.

    -

    Definition at line 30 of file screening_abstract.h.

    -

    Constructor & Destructor Documentation

    @@ -334,7 +330,7 @@ Public Member Functions
    The documentation for this class was generated from the following file: diff --git a/docs/html/classgridfire_1_1screening_1_1_weak_screening_model.html b/docs/html/classgridfire_1_1screening_1_1_weak_screening_model.html index b02922c8..fd61e404 100644 --- a/docs/html/classgridfire_1_1screening_1_1_weak_screening_model.html +++ b/docs/html/classgridfire_1_1screening_1_1_weak_screening_model.html @@ -111,7 +111,7 @@ $(function(){initNavTree('classgridfire_1_1screening_1_1_weak_screening_model.ht

    Implements the weak screening model based on the Debye-Hückel approximation. More...

    -

    #include <screening_weak.h>

    +

    #include <screening_weak.h>

    Inheritance diagram for gridfire::screening::WeakScreeningModel:
    @@ -158,8 +158,6 @@ Additional Inherited Members

    Detailed Description

    Implements the weak screening model based on the Debye-Hückel approximation.

    This class provides a concrete implementation of the ScreeningModel interface for the weak screening regime, following the formulation of Salpeter (1954). This approach applies the Debye-Hückel theory to model the electrostatic shielding of nuclei in a plasma. It is applicable to non-degenerate, non-relativistic plasmas where thermal energy dominates the electrostatic potential energy.

    - -

    Definition at line 26 of file screening_weak.h.

    Member Function Documentation

    ◆ calculateFactors_impl()

    @@ -257,8 +255,6 @@ template<typename T>
  • Final Factor: The screening factor for the reaction is exp(H_12).
    • -

    Definition at line 141 of file screening_weak.h.

    - @@ -319,8 +315,6 @@ template<typename T>

    Implements gridfire::screening::ScreeningModel.

    -

    Definition at line 12 of file screening_weak.cpp.

    - @@ -383,13 +377,11 @@ template<typename T>
    std::vector<double> factors = weak_model.calculateScreeningFactors(
    reactions, species, Y, T9, rho
    );
    -
    gridfire::screening::WeakScreeningModel
    Implements the weak screening model based on the Debye-Hückel approximation.
    Definition screening_weak.h:26
    -
    gridfire::screening::WeakScreeningModel::calculateScreeningFactors
    std::vector< double > calculateScreeningFactors(const reaction::LogicalReactionSet &reactions, const std::vector< fourdst::atomic::Species > &species, const std::vector< double > &Y, const double T9, const double rho) const override
    Calculates weak screening factors for a set of reactions.
    Definition screening_weak.cpp:22
    +
    gridfire::screening::WeakScreeningModel
    Implements the weak screening model based on the Debye-Hückel approximation.
    Definition screening_weak.h:26
    +
    gridfire::screening::WeakScreeningModel::calculateScreeningFactors
    std::vector< double > calculateScreeningFactors(const reaction::LogicalReactionSet &reactions, const std::vector< fourdst::atomic::Species > &species, const std::vector< double > &Y, const double T9, const double rho) const override
    Calculates weak screening factors for a set of reactions.
    Definition screening_weak.cpp:22

    Implements gridfire::screening::ScreeningModel.

    -

    Definition at line 22 of file screening_weak.cpp.

    -

    Member Data Documentation

    @@ -415,13 +407,11 @@ template<typename T>

    Logger instance for recording trace and debug information.

    -

    Definition at line 81 of file screening_weak.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1solver_1_1_direct_network_solver.html b/docs/html/classgridfire_1_1solver_1_1_direct_network_solver.html index 17f4c720..769543c6 100644 --- a/docs/html/classgridfire_1_1solver_1_1_direct_network_solver.html +++ b/docs/html/classgridfire_1_1solver_1_1_direct_network_solver.html @@ -111,7 +111,7 @@ $(function(){initNavTree('classgridfire_1_1solver_1_1_direct_network_solver.html

    A network solver that directly integrates the reaction network ODEs. More...

    -

    #include <solver.h>

    +

    #include <solver.h>

    Inheritance diagram for gridfire::solver::DirectNetworkSolver:
    @@ -171,8 +171,6 @@ Additional Inherited Members

    Detailed Description

    A network solver that directly integrates the reaction network ODEs.

    This solver uses a Runge-Kutta method to directly integrate the reaction network ODEs. It is simpler than the QSENetworkSolver, but it can be less efficient for stiff networks with disparate timescales.

    - -

    Definition at line 65 of file solver.h.

    Member Function Documentation

    ◆ evaluate()

    @@ -208,8 +206,6 @@ Additional Inherited Members

    Implements gridfire::solver::NetworkSolverStrategy< DynamicEngine >.

    -

    Definition at line 22 of file solver.cpp.

    -

    Member Data Documentation

    @@ -235,8 +231,6 @@ Additional Inherited Members

    Configuration instance.

    -

    Definition at line 181 of file solver.h.

    - @@ -261,13 +255,11 @@ Additional Inherited Members

    Logger instance.

    -

    Definition at line 180 of file solver.h.

    -
    The documentation for this class was generated from the following files: diff --git a/docs/html/classgridfire_1_1solver_1_1_network_solver_strategy.html b/docs/html/classgridfire_1_1solver_1_1_network_solver_strategy.html index 12e9bf26..da5c2337 100644 --- a/docs/html/classgridfire_1_1solver_1_1_network_solver_strategy.html +++ b/docs/html/classgridfire_1_1solver_1_1_network_solver_strategy.html @@ -110,7 +110,7 @@ $(function(){initNavTree('classgridfire_1_1solver_1_1_network_solver_strategy.ht

    Abstract base class for network solver strategies. More...

    -

    #include <solver.h>

    +

    #include <solver.h>

    @@ -140,8 +140,6 @@ class gridfire::solver::NetworkSolverStrategy< EngineT >

    Abstract

    Public Member Functions

    - -

    Definition at line 27 of file solver.h.

    Constructor & Destructor Documentation

    ◆ NetworkSolverStrategy()

    @@ -176,8 +174,6 @@ template<typename EngineT> -

    Definition at line 33 of file solver.h.

    - @@ -273,12 +269,10 @@ template<typename EngineT>

    The engine used by this solver strategy.

    -

    Definition at line 47 of file solver.h.

    -
    The documentation for this class was generated from the following file: diff --git a/docs/html/concept_0d012022023301355052304263320136165002200160012126_1_1_is_dynamic_engine.html b/docs/html/concept_0d012022023301355052304263320136165002200160012126_1_1_is_dynamic_engine.html index dbfcefef..e26aa1fe 100644 --- a/docs/html/concept_0d012022023301355052304263320136165002200160012126_1_1_is_dynamic_engine.html +++ b/docs/html/concept_0d012022023301355052304263320136165002200160012126_1_1_is_dynamic_engine.html @@ -105,11 +105,8 @@ $(function(){initNavTree('concept_0d01202202330135505230426332013616500220016001

    Concept definition

    template<typename T>
    concept @012022023301355052304263320136165002200160012126::IsDynamicEngine = std::is_base_of_v<gridfire::DynamicEngine, T>
    - -

    Detailed Description

    -
    -

    Definition at line 18 of file bindings.cpp.

    -
    + + + diff --git a/docs/html/construction_8cpp.html b/docs/html/construction_8cpp.html index 819066f2..5988ff84 100644 --- a/docs/html/construction_8cpp.html +++ b/docs/html/construction_8cpp.html @@ -107,18 +107,16 @@ $(function(){initNavTree('construction_8cpp.html',''); initResizable(true); });
    construction.cpp File Reference
    -
    #include "gridfire/engine/procedures/construction.h"
    +
    #include "gridfire/engine/procedures/construction.h"
    #include <ranges>
    #include <stdexcept>
    -#include "gridfire/reaction/reaction.h"
    -#include "gridfire/reaction/reaclib.h"
    +#include "gridfire/reaction/reaction.h"
    +#include "gridfire/reaction/reaclib.h"
    #include "fourdst/composition/composition.h"
    #include "fourdst/logging/logging.h"
    #include "quill/Logger.h"
    #include "quill/LogMacros.h"
    -
    -

    Go to the source code of this file.

    - +
    diff --git a/docs/html/construction_8h.html b/docs/html/construction_8h.html index 6081081c..13eda590 100644 --- a/docs/html/construction_8h.html +++ b/docs/html/construction_8h.html @@ -105,13 +105,11 @@ $(function(){initNavTree('construction_8h.html',''); initResizable(true); });
    construction.h File Reference
    -
    #include "gridfire/reaction/reaction.h"
    -#include "gridfire/engine/types/building.h"
    +
    #include "gridfire/reaction/reaction.h"
    +#include "gridfire/engine/types/building.h"
    #include "fourdst/composition/composition.h"
    #include <variant>
    -
    -

    Go to the source code of this file.

    -

    Classes

    class  gridfire::Reaction
    +
    diff --git a/docs/html/dir_048d8e0a5613c02d1dd32a8c2b4fae8e.html b/docs/html/dir_048d8e0a5613c02d1dd32a8c2b4fae8e.html index 2134ab4d..f6f470f5 100644 --- a/docs/html/dir_048d8e0a5613c02d1dd32a8c2b4fae8e.html +++ b/docs/html/dir_048d8e0a5613c02d1dd32a8c2b4fae8e.html @@ -110,9 +110,9 @@ Directories

    Namespaces

    namespace  gridfire
    - + - +

    Files

     bindings.cpp
     bindings.cpp
     
     bindings.h
     bindings.h
     
    diff --git a/docs/html/dir_1ae9febcce3c81c54e014e2202672ae2.html b/docs/html/dir_1ae9febcce3c81c54e014e2202672ae2.html index 23674d07..54daf032 100644 --- a/docs/html/dir_1ae9febcce3c81c54e014e2202672ae2.html +++ b/docs/html/dir_1ae9febcce3c81c54e014e2202672ae2.html @@ -105,9 +105,9 @@ $(function(){initNavTree('dir_1ae9febcce3c81c54e014e2202672ae2.html',''); initRe - + - +

    Files

     bindings.cpp
     bindings.cpp
     
     bindings.h
     bindings.h
     
    diff --git a/docs/html/dir_1c671bae89ad45c4f6571bd7c3fca7f2.html b/docs/html/dir_1c671bae89ad45c4f6571bd7c3fca7f2.html index fc44add0..99d2639a 100644 --- a/docs/html/dir_1c671bae89ad45c4f6571bd7c3fca7f2.html +++ b/docs/html/dir_1c671bae89ad45c4f6571bd7c3fca7f2.html @@ -105,9 +105,9 @@ $(function(){initNavTree('dir_1c671bae89ad45c4f6571bd7c3fca7f2.html',''); initRe - + - +

    Files

     io.h
     io.h
     
     network_file.h
     network_file.h
     
    diff --git a/docs/html/dir_1d1d50ce0d70b163d7d102a960190628.html b/docs/html/dir_1d1d50ce0d70b163d7d102a960190628.html index 5d1513e9..8a8466f6 100644 --- a/docs/html/dir_1d1d50ce0d70b163d7d102a960190628.html +++ b/docs/html/dir_1d1d50ce0d70b163d7d102a960190628.html @@ -110,19 +110,19 @@ Directories - + - + - + - + - + - + - +

    Files

     partition.h
     partition.h
     
     partition_abstract.h
     partition_abstract.h
     
     partition_ground.h
     partition_ground.h
     
     partition_rauscher_thielemann.h
     partition_rauscher_thielemann.h
     
     partition_types.h
     partition_types.h
     
     rauscher_thielemann_partition_data.h
     rauscher_thielemann_partition_data.h
     
     rauscher_thielemann_partition_data_record.h
     rauscher_thielemann_partition_data_record.h
     
    diff --git a/docs/html/dir_3626e0c0e3c5d7812d6b277dfa4ec364.html b/docs/html/dir_3626e0c0e3c5d7812d6b277dfa4ec364.html index 346d08c3..5d6c7a85 100644 --- a/docs/html/dir_3626e0c0e3c5d7812d6b277dfa4ec364.html +++ b/docs/html/dir_3626e0c0e3c5d7812d6b277dfa4ec364.html @@ -126,7 +126,7 @@ Directories - +

    Files

     network.h
     network.h
     
    diff --git a/docs/html/dir_3cc0b3e3c66436f74054a789a4a47fbc.html b/docs/html/dir_3cc0b3e3c66436f74054a789a4a47fbc.html index 48834454..77c07f1c 100644 --- a/docs/html/dir_3cc0b3e3c66436f74054a789a4a47fbc.html +++ b/docs/html/dir_3cc0b3e3c66436f74054a789a4a47fbc.html @@ -112,9 +112,9 @@ Directories - + - +

    Files

     engine_approx8.cpp
     engine_approx8.cpp
     
     engine_graph.cpp
     engine_graph.cpp
     
    diff --git a/docs/html/dir_43d540904cac5d711ae55af9d63e6471.html b/docs/html/dir_43d540904cac5d711ae55af9d63e6471.html index eca34a49..d5dcb6e5 100644 --- a/docs/html/dir_43d540904cac5d711ae55af9d63e6471.html +++ b/docs/html/dir_43d540904cac5d711ae55af9d63e6471.html @@ -105,9 +105,9 @@ $(function(){initNavTree('dir_43d540904cac5d711ae55af9d63e6471.html',''); initRe - + - +

    Files

     construction.cpp
     construction.cpp
     
     priming.cpp
     priming.cpp
     
    diff --git a/docs/html/dir_4eba3bf96e8b886928c6be1f4154164d.html b/docs/html/dir_4eba3bf96e8b886928c6be1f4154164d.html index a3171a41..123661b1 100644 --- a/docs/html/dir_4eba3bf96e8b886928c6be1f4154164d.html +++ b/docs/html/dir_4eba3bf96e8b886928c6be1f4154164d.html @@ -110,9 +110,9 @@ Directories - + - +

    Files

     bindings.cpp
     bindings.cpp
     
     bindings.h
     bindings.h
     
    diff --git a/docs/html/dir_4fd0dc9a50f7a53e22cb356c650f915e.html b/docs/html/dir_4fd0dc9a50f7a53e22cb356c650f915e.html index bdc0bfdd..154e2e6f 100644 --- a/docs/html/dir_4fd0dc9a50f7a53e22cb356c650f915e.html +++ b/docs/html/dir_4fd0dc9a50f7a53e22cb356c650f915e.html @@ -105,7 +105,7 @@ $(function(){initNavTree('dir_4fd0dc9a50f7a53e22cb356c650f915e.html',''); initRe - +

    Files

     solver.cpp
     solver.cpp
     
    diff --git a/docs/html/dir_5c0d64f70903e893b1efe571a4b8de29.html b/docs/html/dir_5c0d64f70903e893b1efe571a4b8de29.html index 2fac23de..5d75b480 100644 --- a/docs/html/dir_5c0d64f70903e893b1efe571a4b8de29.html +++ b/docs/html/dir_5c0d64f70903e893b1efe571a4b8de29.html @@ -128,7 +128,7 @@ Directories - +

    Files

     bindings.cpp
     bindings.cpp
     
    diff --git a/docs/html/dir_64012712bac8d4927da7703e58c6c3c3.html b/docs/html/dir_64012712bac8d4927da7703e58c6c3c3.html index 3c6e9a21..63dd42cc 100644 --- a/docs/html/dir_64012712bac8d4927da7703e58c6c3c3.html +++ b/docs/html/dir_64012712bac8d4927da7703e58c6c3c3.html @@ -110,9 +110,9 @@ Directories - + - +

    Files

     bindings.cpp
     bindings.cpp
     
     bindings.h
     bindings.h
     
    diff --git a/docs/html/dir_65bc51589f8002bfcb72faf47ab41180.html b/docs/html/dir_65bc51589f8002bfcb72faf47ab41180.html index c50d01d4..0cdbee1e 100644 --- a/docs/html/dir_65bc51589f8002bfcb72faf47ab41180.html +++ b/docs/html/dir_65bc51589f8002bfcb72faf47ab41180.html @@ -105,7 +105,7 @@ $(function(){initNavTree('dir_65bc51589f8002bfcb72faf47ab41180.html',''); initRe - +

    Files

     network_file.cpp
     network_file.cpp
     
    diff --git a/docs/html/dir_6f67cad5a3dd5daef2b4bab22419acbf.html b/docs/html/dir_6f67cad5a3dd5daef2b4bab22419acbf.html index 6da01371..884a1f07 100644 --- a/docs/html/dir_6f67cad5a3dd5daef2b4bab22419acbf.html +++ b/docs/html/dir_6f67cad5a3dd5daef2b4bab22419acbf.html @@ -105,9 +105,9 @@ $(function(){initNavTree('dir_6f67cad5a3dd5daef2b4bab22419acbf.html',''); initRe - + - +

    Files

     bindings.cpp
     bindings.cpp
     
     bindings.h
     bindings.h
     
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    Files

     py_engine.cpp
     py_engine.cpp
     
     py_engine.h
     py_engine.h
     
    diff --git a/docs/html/dir_7eae81c2ec58ffa76af06bb25bb86137.html b/docs/html/dir_7eae81c2ec58ffa76af06bb25bb86137.html index b61554ec..7d17b0b9 100644 --- a/docs/html/dir_7eae81c2ec58ffa76af06bb25bb86137.html +++ b/docs/html/dir_7eae81c2ec58ffa76af06bb25bb86137.html @@ -110,9 +110,9 @@ Directories - + - +

    Files

     bindings.cpp
     bindings.cpp
     
     bindings.h
     bindings.h
     
    diff --git a/docs/html/dir_80d0745b866022f2047f807b3376dff7.html b/docs/html/dir_80d0745b866022f2047f807b3376dff7.html index 2b65dc94..0bba839c 100644 --- a/docs/html/dir_80d0745b866022f2047f807b3376dff7.html +++ b/docs/html/dir_80d0745b866022f2047f807b3376dff7.html @@ -105,11 +105,11 @@ $(function(){initNavTree('dir_80d0745b866022f2047f807b3376dff7.html',''); initRe - + - + - +

    Files

     building.h
     building.h
     
     engine_types.h
     engine_types.h
     
     reporting.h
     reporting.h
     
    diff --git a/docs/html/dir_87d18a4dc5174905bfd7d2dc734defe6.html b/docs/html/dir_87d18a4dc5174905bfd7d2dc734defe6.html index 04369810..e6306f4f 100644 --- a/docs/html/dir_87d18a4dc5174905bfd7d2dc734defe6.html +++ b/docs/html/dir_87d18a4dc5174905bfd7d2dc734defe6.html @@ -105,7 +105,7 @@ $(function(){initNavTree('dir_87d18a4dc5174905bfd7d2dc734defe6.html',''); initRe - +

    Files

     logging.cpp
     logging.cpp
     
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    Files

     logging.h
     logging.h
     
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    Files

     reaclib.cpp
     reaclib.cpp
     
     reaction.cpp
     reaction.cpp
     
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    Files

     py_partition.cpp
     py_partition.cpp
     
     py_partition.h
     py_partition.h
     
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    Files

     expectations.h
     expectations.h
     
     expected_engine.h
     expected_engine.h
     
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    Files

     partition_composite.cpp
     partition_composite.cpp
     
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    Files

     screening.h
     screening.h
     
     screening_abstract.h
     screening_abstract.h
     
     screening_bare.h
     screening_bare.h
     
     screening_types.h
     screening_types.h
     
     screening_weak.h
     screening_weak.h
     
    diff --git a/docs/html/dir_aff155d61c3b73b9ab7dcdc908c4d49e.html b/docs/html/dir_aff155d61c3b73b9ab7dcdc908c4d49e.html index 9231ee73..3ea1ee04 100644 --- a/docs/html/dir_aff155d61c3b73b9ab7dcdc908c4d49e.html +++ b/docs/html/dir_aff155d61c3b73b9ab7dcdc908c4d49e.html @@ -114,15 +114,15 @@ Directories - + - + - + - +

    Files

     engine.h
     engine.h
     Core header for the GridFire reaction network engine module.
     
     engine_abstract.h
     engine_abstract.h
     Abstract interfaces for reaction network engines in GridFire.
     
     engine_approx8.h
     engine_approx8.h
     
     engine_graph.h
     engine_graph.h
     
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    Files

     bindings.cpp
     bindings.cpp
     
     bindings.h
     bindings.h
     
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    Files

     bindings.cpp
     bindings.cpp
     
     bindings.h
     bindings.h
     
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    Files

     py_solver.cpp
     py_solver.cpp
     
     py_solver.h
     py_solver.h
     
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    Files

     screening_bare.cpp
     screening_bare.cpp
     
     screening_types.cpp
     screening_types.cpp
     
     screening_weak.cpp
     screening_weak.cpp
     
    diff --git a/docs/html/dir_c85d3e3c5052e9ad9ce18c6863244a25.html b/docs/html/dir_c85d3e3c5052e9ad9ce18c6863244a25.html index 3ec545d5..6fd289d7 100644 --- a/docs/html/dir_c85d3e3c5052e9ad9ce18c6863244a25.html +++ b/docs/html/dir_c85d3e3c5052e9ad9ce18c6863244a25.html @@ -122,7 +122,7 @@ Directories - +

    Files

     network.cpp
     network.cpp
     
    diff --git a/docs/html/dir_cd87a60aa1dbf4ee960e0533fd7a9743.html b/docs/html/dir_cd87a60aa1dbf4ee960e0533fd7a9743.html index be8fcc29..585daddf 100644 --- a/docs/html/dir_cd87a60aa1dbf4ee960e0533fd7a9743.html +++ b/docs/html/dir_cd87a60aa1dbf4ee960e0533fd7a9743.html @@ -105,9 +105,9 @@ $(function(){initNavTree('dir_cd87a60aa1dbf4ee960e0533fd7a9743.html',''); initRe - + - +

    Files

     error_engine.h
     error_engine.h
     
     exceptions.h
     exceptions.h
     
    diff --git a/docs/html/dir_d0a49494bbb6e91de214e6669adf5efa.html b/docs/html/dir_d0a49494bbb6e91de214e6669adf5efa.html index f7713659..f97b160d 100644 --- a/docs/html/dir_d0a49494bbb6e91de214e6669adf5efa.html +++ b/docs/html/dir_d0a49494bbb6e91de214e6669adf5efa.html @@ -110,9 +110,9 @@ Directories - + - +

    Files

     bindings.cpp
     bindings.cpp
     
     bindings.h
     bindings.h
     
    diff --git a/docs/html/dir_d5492b42d970deba31f48df1b35a6c47.html b/docs/html/dir_d5492b42d970deba31f48df1b35a6c47.html index c4ee1ac8..5d0314d1 100644 --- a/docs/html/dir_d5492b42d970deba31f48df1b35a6c47.html +++ b/docs/html/dir_d5492b42d970deba31f48df1b35a6c47.html @@ -105,18 +105,18 @@ $(function(){initNavTree('dir_d5492b42d970deba31f48df1b35a6c47.html',''); initRe - + - + - + - + - + - +

    Files

     engine_adaptive.h
     engine_adaptive.h
     
     engine_defined.h
     engine_defined.h
     
     engine_multiscale.h
     engine_multiscale.h
     
     engine_priming.h
     engine_priming.h
     
     engine_view_abstract.h
     engine_view_abstract.h
     Abstract interfaces for engine "views" in GridFire.
     
     engine_views.h
     engine_views.h
     
    diff --git a/docs/html/dir_d70391a28a381da2f0629437a1b6db28.html b/docs/html/dir_d70391a28a381da2f0629437a1b6db28.html index 9c331b2d..62743ab7 100644 --- a/docs/html/dir_d70391a28a381da2f0629437a1b6db28.html +++ b/docs/html/dir_d70391a28a381da2f0629437a1b6db28.html @@ -105,9 +105,9 @@ $(function(){initNavTree('dir_d70391a28a381da2f0629437a1b6db28.html',''); initRe - + - +

    Files

     bindings.cpp
     bindings.cpp
     
     bindings.h
     bindings.h
     
    diff --git a/docs/html/dir_dd8201c056cb17022d2864e6e5aa368d.html b/docs/html/dir_dd8201c056cb17022d2864e6e5aa368d.html index ff153c38..1b8fa0f6 100644 --- a/docs/html/dir_dd8201c056cb17022d2864e6e5aa368d.html +++ b/docs/html/dir_dd8201c056cb17022d2864e6e5aa368d.html @@ -105,9 +105,9 @@ $(function(){initNavTree('dir_dd8201c056cb17022d2864e6e5aa368d.html',''); initRe - + - +

    Files

     py_io.cpp
     py_io.cpp
     
     py_io.h
     py_io.h
     
    diff --git a/docs/html/dir_e2a8863ee8e7cd9122c04bdba1c35a3b.html b/docs/html/dir_e2a8863ee8e7cd9122c04bdba1c35a3b.html index dcd7dcc9..58f732a5 100644 --- a/docs/html/dir_e2a8863ee8e7cd9122c04bdba1c35a3b.html +++ b/docs/html/dir_e2a8863ee8e7cd9122c04bdba1c35a3b.html @@ -105,7 +105,7 @@ $(function(){initNavTree('dir_e2a8863ee8e7cd9122c04bdba1c35a3b.html',''); initRe - +

    Files

     solver.h
     solver.h
     
    diff --git a/docs/html/dir_e87948a39c0c6c3f66d9f5f967ab86bd.html b/docs/html/dir_e87948a39c0c6c3f66d9f5f967ab86bd.html index c1b7fc3c..917592d5 100644 --- a/docs/html/dir_e87948a39c0c6c3f66d9f5f967ab86bd.html +++ b/docs/html/dir_e87948a39c0c6c3f66d9f5f967ab86bd.html @@ -105,13 +105,13 @@ $(function(){initNavTree('dir_e87948a39c0c6c3f66d9f5f967ab86bd.html',''); initRe - + - + - + - +

    Files

     engine_adaptive.cpp
     engine_adaptive.cpp
     
     engine_defined.cpp
     engine_defined.cpp
     
     engine_multiscale.cpp
     engine_multiscale.cpp
     
     engine_priming.cpp
     engine_priming.cpp
     
    diff --git a/docs/html/dir_f2d7b0c77cb2532170ac94ead6e4ba70.html b/docs/html/dir_f2d7b0c77cb2532170ac94ead6e4ba70.html index 886dcaed..3890f35c 100644 --- a/docs/html/dir_f2d7b0c77cb2532170ac94ead6e4ba70.html +++ b/docs/html/dir_f2d7b0c77cb2532170ac94ead6e4ba70.html @@ -105,12 +105,12 @@ $(function(){initNavTree('dir_f2d7b0c77cb2532170ac94ead6e4ba70.html',''); initRe - + - + - +

    Files

     reaclib.h
     reaclib.h
     
     reaction.h
     reaction.h
     Defines classes for representing and managing nuclear reactions.
     
     reactions_data.h
     reactions_data.h
     
    diff --git a/docs/html/dir_f575fd282ecf3769a887e0c3d3cafd55.html b/docs/html/dir_f575fd282ecf3769a887e0c3d3cafd55.html index f0d84aa4..2dd06b20 100644 --- a/docs/html/dir_f575fd282ecf3769a887e0c3d3cafd55.html +++ b/docs/html/dir_f575fd282ecf3769a887e0c3d3cafd55.html @@ -105,7 +105,7 @@ $(function(){initNavTree('dir_f575fd282ecf3769a887e0c3d3cafd55.html',''); initRe - +

    Files

     partition_composite.h
     partition_composite.h
     
    diff --git a/docs/html/dir_fe5109f07276e0a4a472af6b22fd99c7.html b/docs/html/dir_fe5109f07276e0a4a472af6b22fd99c7.html index 99a5be94..e2098965 100644 --- a/docs/html/dir_fe5109f07276e0a4a472af6b22fd99c7.html +++ b/docs/html/dir_fe5109f07276e0a4a472af6b22fd99c7.html @@ -110,9 +110,9 @@ Directories - + - +

    Files

     partition_ground.cpp
     partition_ground.cpp
     
     partition_rauscher_thielemann.cpp
     partition_rauscher_thielemann.cpp
     
    diff --git a/docs/html/dir_fe7d6b610561b6ccbae8c0cd892464cf.html b/docs/html/dir_fe7d6b610561b6ccbae8c0cd892464cf.html index 63544d7f..3937bee3 100644 --- a/docs/html/dir_fe7d6b610561b6ccbae8c0cd892464cf.html +++ b/docs/html/dir_fe7d6b610561b6ccbae8c0cd892464cf.html @@ -105,9 +105,9 @@ $(function(){initNavTree('dir_fe7d6b610561b6ccbae8c0cd892464cf.html',''); initRe - + - +

    Files

     py_screening.cpp
     py_screening.cpp
     
     py_screening.h
     py_screening.h
     
    diff --git a/docs/html/dir_fedd162cb41c94f7e299c266e75251fd.html b/docs/html/dir_fedd162cb41c94f7e299c266e75251fd.html index db23b2fb..561ddb81 100644 --- a/docs/html/dir_fedd162cb41c94f7e299c266e75251fd.html +++ b/docs/html/dir_fedd162cb41c94f7e299c266e75251fd.html @@ -105,11 +105,11 @@ $(function(){initNavTree('dir_fedd162cb41c94f7e299c266e75251fd.html',''); initRe - + - + - +

    Files

     construction.h
     construction.h
     
     engine_procedures.h
     engine_procedures.h
     
     priming.h
     priming.h
     
    diff --git a/docs/html/doxygen_crawl.html b/docs/html/doxygen_crawl.html index 1743ce56..79f86151 100644 --- a/docs/html/doxygen_crawl.html +++ b/docs/html/doxygen_crawl.html @@ -12,9 +12,7 @@ - - @@ -622,9 +620,7 @@ - - @@ -678,7 +674,6 @@ - @@ -686,64 +681,37 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -825,6 +793,7 @@ + @@ -840,34 +809,61 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - + + + + + + + @@ -978,13 +974,9 @@ - - - - @@ -993,7 +985,6 @@ - @@ -1001,109 +992,63 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1343,16 +1288,12 @@ - - - - diff --git a/docs/html/dynsections.js b/docs/html/dynsections.js index 0c356052..3cc426a6 100644 --- a/docs/html/dynsections.js +++ b/docs/html/dynsections.js @@ -196,10 +196,3 @@ let codefold = { }, }; /* @license-end */ -$(function() { - $('.code,.codeRef').each(function() { - $(this).data('powertip',$('#a'+$(this).attr('href').replace(/.*\//,'').replace(/[^a-z_A-Z0-9]/g,'_')).html()); - $.fn.powerTip.smartPlacementLists.s = [ 's', 'n', 'ne', 'se' ]; - $(this).powerTip({ placement: 's', smartPlacement: true, mouseOnToPopup: true }); - }); -}); diff --git a/docs/html/engine_2bindings_8cpp.html b/docs/html/engine_2bindings_8cpp.html index c4f39ef4..1e833214 100644 --- a/docs/html/engine_2bindings_8cpp.html +++ b/docs/html/engine_2bindings_8cpp.html @@ -109,12 +109,10 @@ $(function(){initNavTree('engine_2bindings_8cpp.html',''); initResizable(true); #include <pybind11/stl.h>
    #include <pybind11/stl_bind.h>
    #include <iostream>
    -#include "    bindings.h"
    -#include "gridfire/engine/engine.h"
    -#include "trampoline/py_engine.h"
    - -

    Go to the source code of this file.

    - +#include "bindings.h"
    +#include "gridfire/engine/engine.h"
    +#include "trampoline/py_engine.h"
    +
    @@ -151,8 +149,6 @@ Functions

    Concepts

    concept  @012022023301355052304263320136165002200160012126::IsDynamicEngine
    -

    Definition at line 172 of file bindings.cpp.

    -
    @@ -170,8 +166,6 @@ Functions
    -

    Definition at line 168 of file bindings.cpp.

    -
    @@ -189,8 +183,6 @@ Functions
    -

    Definition at line 176 of file bindings.cpp.

    -
    @@ -208,8 +200,6 @@ Functions
    -

    Definition at line 155 of file bindings.cpp.

    -
    @@ -227,8 +217,6 @@ Functions
    -

    Definition at line 114 of file bindings.cpp.

    -
    @@ -246,8 +234,6 @@ Functions
    -

    Definition at line 270 of file bindings.cpp.

    -
    diff --git a/docs/html/engine_2bindings_8h.html b/docs/html/engine_2bindings_8h.html index 0d576583..2dcabe5e 100644 --- a/docs/html/engine_2bindings_8h.html +++ b/docs/html/engine_2bindings_8h.html @@ -105,9 +105,7 @@ $(function(){initNavTree('engine_2bindings_8h.html',''); initResizable(true); })
    #include <pybind11/pybind11.h>
    -
    -

    Go to the source code of this file.

    - +
    @@ -139,8 +137,6 @@ Functions

    Functions

    void register_engine_bindings (pybind11::module &m)
    -

    Definition at line 172 of file bindings.cpp.

    -
    @@ -158,8 +154,6 @@ Functions
    -

    Definition at line 168 of file bindings.cpp.

    -
    @@ -177,8 +171,6 @@ Functions
    -

    Definition at line 176 of file bindings.cpp.

    -
    @@ -196,8 +188,6 @@ Functions
    -

    Definition at line 155 of file bindings.cpp.

    -
    @@ -232,8 +222,6 @@ Functions
    -

    Definition at line 270 of file bindings.cpp.

    -
    diff --git a/docs/html/engine_8h.html b/docs/html/engine_8h.html index 615f74dd..1ac123a5 100644 --- a/docs/html/engine_8h.html +++ b/docs/html/engine_8h.html @@ -105,14 +105,12 @@ $(function(){initNavTree('engine_8h.html',''); initResizable(true); });

    Core header for the GridFire reaction network engine module. More...

    -
    #include "gridfire/engine/engine_abstract.h"
    -#include "gridfire/engine/engine_graph.h"
    -#include "gridfire/engine/views/engine_views.h"
    -#include "gridfire/engine/procedures/engine_procedures.h"
    -#include "gridfire/engine/types/engine_types.h"
    -
    -

    Go to the source code of this file.

    -

    Detailed Description

    +
    #include "gridfire/engine/engine_abstract.h"
    +#include "gridfire/engine/engine_graph.h"
    +#include "gridfire/engine/views/engine_views.h"
    +#include "gridfire/engine/procedures/engine_procedures.h"
    +#include "gridfire/engine/types/engine_types.h"
    +

    Detailed Description

    Core header for the GridFire reaction network engine module.

    This module defines the core interfaces and classes for reaction network engines in GridFire. It provides abstract base classes for engines, dynamic engines, and engine views, as well as concrete engine implementations and view implementations.

    The engine module is designed to support a wide range of reaction network simulations, from simple single-zone calculations to complex multi-zone simulations with adaptive network topologies.

    @@ -156,7 +154,7 @@ GraphEngine Example
    // Create a GraphEngine
    gridfire::GraphEngine engine(composition);
    -
    gridfire::GraphEngine
    A reaction network engine that uses a graph-based representation.
    Definition engine_graph.h:100
    +
    gridfire::GraphEngine
    A reaction network engine that uses a graph-based representation.
    Definition engine_graph.h:100
    engine_graph.h

    AdaptiveEngineView Example

    @@ -173,7 +171,7 @@ AdaptiveEngineView Example
    // Create an AdaptiveEngineView
    gridfire::AdaptiveEngineView engine(baseEngine);
    -
    gridfire::AdaptiveEngineView
    An engine view that dynamically adapts the reaction network based on runtime conditions.
    Definition engine_adaptive.h:50
    +
    gridfire::AdaptiveEngineView
    An engine view that dynamically adapts the reaction network based on runtime conditions.
    Definition engine_adaptive.h:50
    engine_adaptive.h

    DefinedEngineView Example

    @@ -191,7 +189,7 @@ DefinedEngineView Example
    // Create a DefinedEngineView
    std::vector<std::string> peNames = {"p(p,e+)d", "he4(a,g)be8"};
    gridfire::DefinedEngineView engine(peNames, baseEngine);
    - +
    gridfire::DefinedEngineView
    Definition engine_defined.h:16
    engine_defined.h

    MultiscalePartitioningEngineView Example

    @@ -208,7 +206,7 @@ MultiscalePartitioningEngineView Example
    // Create a MultiscalePartitioningEngineView
    gridfire::MultiscalePartitioningEngineView engine(baseEngine);
    -
    gridfire::MultiscalePartitioningEngineView
    An engine view that partitions the reaction network into multiple groups based on timescales.
    Definition engine_multiscale.h:174
    +
    gridfire::MultiscalePartitioningEngineView
    An engine view that partitions the reaction network into multiple groups based on timescales.
    Definition engine_multiscale.h:174
    engine_multiscale.h

    NetworkPrimingEngineView Example

    @@ -226,11 +224,9 @@ NetworkPrimingEngineView Example
    // Create a NetworkPrimingEngineView
    std::string primingSymbol = "p";
    gridfire::NetworkPrimingEngineView engine(primingSymbol, baseEngine);
    -
    gridfire::NetworkPrimingEngineView
    Provides a view of a DynamicEngine filtered to reactions involving a specified priming species.
    Definition engine_priming.h:30
    +
    gridfire::NetworkPrimingEngineView
    Provides a view of a DynamicEngine filtered to reactions involving a specified priming species.
    Definition engine_priming.h:30
    engine_priming.h
    - -

    Definition in file engine.h.

    - + diff --git a/docs/html/exceptions_2bindings_8h.html b/docs/html/exceptions_2bindings_8h.html index 1cb7755e..5f311196 100644 --- a/docs/html/exceptions_2bindings_8h.html +++ b/docs/html/exceptions_2bindings_8h.html @@ -105,9 +105,7 @@ $(function(){initNavTree('exceptions_2bindings_8h.html',''); initResizable(true)
    #include <pybind11/pybind11.h>
    -
    -

    Go to the source code of this file.

    - +
    diff --git a/docs/html/exceptions_8h.html b/docs/html/exceptions_8h.html index c60bd8e5..40d3db8b 100644 --- a/docs/html/exceptions_8h.html +++ b/docs/html/exceptions_8h.html @@ -102,10 +102,8 @@ $(function(){initNavTree('exceptions_8h.html',''); initResizable(true); });
    exceptions.h File Reference
    -
    #include "gridfire/exceptions/error_engine.h"
    -
    -

    Go to the source code of this file.

    -
    +
    #include "gridfire/exceptions/error_engine.h"
    +

    Functions

    void register_exception_bindings (pybind11::module &m)
    +#include "bindings.h"
    +#include "gridfire/expectations/expectations.h"
    +
    @@ -133,8 +131,6 @@ Functions

    Functions

    void register_expectation_bindings (py::module &m)
    -

    Definition at line 11 of file bindings.cpp.

    -
    diff --git a/docs/html/expectations_2bindings_8h.html b/docs/html/expectations_2bindings_8h.html index b6a12d7a..f5de19ae 100644 --- a/docs/html/expectations_2bindings_8h.html +++ b/docs/html/expectations_2bindings_8h.html @@ -105,9 +105,7 @@ $(function(){initNavTree('expectations_2bindings_8h.html',''); initResizable(tru
    #include <pybind11/pybind11.h>
    -
    -

    Go to the source code of this file.

    - +
    diff --git a/docs/html/expectations_8h.html b/docs/html/expectations_8h.html index ac81b3c1..fc44c550 100644 --- a/docs/html/expectations_8h.html +++ b/docs/html/expectations_8h.html @@ -102,10 +102,8 @@ $(function(){initNavTree('expectations_8h.html',''); initResizable(true); });
    expectations.h File Reference
    -
    #include "gridfire/expectations/expected_engine.h"
    -
    -

    Go to the source code of this file.

    -
    +
    #include "gridfire/expectations/expected_engine.h"
    +

    Functions

    void register_expectation_bindings (pybind11::module &m)
    +
    diff --git a/docs/html/files.html b/docs/html/files.html index 1926aa38..98fe5df5 100644 --- a/docs/html/files.html +++ b/docs/html/files.html @@ -111,136 +111,136 @@ $(function(){initNavTree('files.html',''); initResizable(true); }); - - - + + + - - - + + + - - - - - - - - - - + + + + + + + + + + - - + + - - + + - - + + - - - - - - - - + + + + + + + + - - - + + + - - - - - + + + + + - + - - + + - - + + - - - - - - + + + + + + - + - - - + + + - - + + - - - + + + - + - - + + - - - - + + + + - - + + - - + + - - - - + + + + - - - - + + + + - - + + - - - - + + + + - - - - + + + + - - + + - - - + + +

    Classes

    struct  gridfire::expectations::EngineError
     ▼ gridfire
     ► engine
     ► exceptions
     ► expectations
     ► io
     ► partition
     ► reaction
     ► screening
     ► solver
     ► utils
     network.h
     network.h
     ▼ lib
     ▼ engine
     ► procedures
     ► views
     engine_approx8.cpp
     engine_graph.cpp
     engine_approx8.cpp
     engine_graph.cpp
     ▼ io
     network_file.cpp
     network_file.cpp
     ▼ partition
     ► composite
     partition_ground.cpp
     partition_rauscher_thielemann.cpp
     partition_ground.cpp
     partition_rauscher_thielemann.cpp
     ▼ reaction
     reaclib.cpp
     reaction.cpp
     reaclib.cpp
     reaction.cpp
     ▼ screening
     screening_bare.cpp
     screening_types.cpp
     screening_weak.cpp
     screening_bare.cpp
     screening_types.cpp
     screening_weak.cpp
     ▼ solver
     solver.cpp
     solver.cpp
     ▼ utils
     logging.cpp
     network.cpp
     logging.cpp
     network.cpp
     ▼ python
     ▼ engine
     ► trampoline
     bindings.cpp
     bindings.h
     bindings.cpp
     bindings.h
     ▼ exceptions
     bindings.cpp
     bindings.h
     bindings.cpp
     bindings.h
     ▼ expectations
     bindings.cpp
     bindings.h
     bindings.cpp
     bindings.h
     ▼ io
     ► trampoline
     bindings.cpp
     bindings.h
     bindings.cpp
     bindings.h
     ▼ partition
     ► trampoline
     bindings.cpp
     bindings.h
     bindings.cpp
     bindings.h
     ▼ reaction
     bindings.cpp
     bindings.h
     bindings.cpp
     bindings.h
     ▼ screening
     ► trampoline
     bindings.cpp
     bindings.h
     bindings.cpp
     bindings.h
     ▼ solver
     ► trampoline
     bindings.cpp
     bindings.h
     bindings.cpp
     bindings.h
     ▼ types
     bindings.cpp
     bindings.h
     bindings.cpp
     bindings.h
     ▼ utils
     bindings.cpp
     bindings.h
     bindings.cpp
     bindings.cpp
     bindings.h
     bindings.cpp
    diff --git a/docs/html/index.html b/docs/html/index.html index 1be05803..d128a47d 100644 --- a/docs/html/index.html +++ b/docs/html/index.html @@ -104,82 +104,209 @@ $(function(){initNavTree('index.html',''); initResizable(true); });

    GridFire Logo

    -
    -

    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. GridFire is primarily focused on modeling the most relevant burning stages for stellar evolution modeling. Currently, there is limited support for inverse reactions. Therefore, GridFire has a limited set of tools to evolves a fusing plasma in NSE; however, this is not the primary focus of the library and has therefor not had significant development. For those interested in modeling super nova, neutron star mergers, or other high-energy astrophysical phenomena, we strongly recomment using SkyNet.

    -

    Design Philosophy and Workflow: 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 multiscale 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.

    +

    +Introduction

    +

    GridFire is a C++ library designed to perform general nuclear network evolution. It is part of the larger SERiF project within the 4D-STAR collaboration. GridFire is primarily focused on modeling the most relevant burning stages for stellar evolution modeling. Currently, there is limited support for inverse reactions. Therefore, GridFire has a limited set of tools to evolves a fusing plasma in NSE; however, this is not the primary focus of the library and has therefor not had significant development. For those interested in modeling super nova, neutron star mergers, or other high-energy astrophysical phenomena, we strongly recomment using SkyNet.

    +Design Philosophy and Workflow

    +

    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. A GraphNetwork uses JINA Reaclib reaction rates (Cyburt et al., ApJS 189 (2010) 240.) along with a dynamically constructed network topology. To manage the inherent stiffness and multiscale 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.

    +

    Funding

    GridFire is a part of the 4D-STAR collaboration.

    4D-STAR is funded by European Research Council (ERC) under the Horizon Europe programme (Synergy Grant agreement No. 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 Council.

    -

    -Build and Installation Instructions

    -

    +

    +Usage

    +

    +Python installation

    +

    By far the easiest way to install is with pip. This will install either pre-compiled wheels or, if your system has not had a wheel compiled for it, it will try to build locally (this may take a long time). The python bindings are just that and should maintain nearly the same speed as the C++ code. End users are strongly encorages to use the python module rather than the C++ code.

    +

    +pypi

    +

    Installing from pip is as simple as

    pip install gridfire
    +

    These wheels have been compiled on many systems

    + + + + + + + + + +
    Version Platform Architecture CPython Versions PyPy Versions
    0.5.0 macOS arm64 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) 3.10, 3.11
    0.5.0 Linux aarch64 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) 3.10, 3.11
    0.5.0 Linux x86_64 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) 3.10, 3.11
    +
    +

    Note: Currently macOS x86_64 does not have a precompiled wheel. Due to that platform being phased out it is likely that there will never be precompiled wheels or releases for it.

    +
    +
    +

    Note: macOS wheels were targeted to MacOS 12 Monterey and should work on any version more recent than that (at least as of August 2025).

    +
    +
    +

    Note: Linux wheels were compiled using manylinux_2_28 and are expected to work on Debian 10+, Ubuntu 18.10+, Fedora 29+, or CentOS/RHEL 8+

    +
    +
    +

    Note: If your system does not have a prebuilt wheel the source distribution will download from pypi and try to build. This may simply not work if you do not have the correct system dependencies installed. If it fails the best bet is to try to build boost >= 1.83.0 from source and install (https://www.boost.org/) as that is the most common broken dependency.

    +
    +

    +source

    +

    The user may also build the python bindings directly from source

    +
    git clone https://github.com/4D-STAR/GridFire
    +
    cd GridFire
    +
    pip install .
    +
    +

    Note: that if you do not have all system dependencies installed this will fail, the steps in further sections address these in more detail.

    +
    +

    +source for developers

    +

    If you are a developer and would like an editable and incrimental python install meson-python makes this very easy

    +
    git clone https://github.com/4D-STAR/GridFire
    +
    cd GridFire
    +
    pip install -e . --no-build-isolation -vv
    +

    This will generate incrimental builds whenever source code changes and you run a python script automartically (note that since meson setup must run for each of these it does still take a few seconds to recompile regardless of how small a source code change you have made). It is strongly reccomended that developers use this approach and end users do not.

    +

    +Automatic Build and Installation

    +

    +Script Build and Installation Instructions

    +

    The easiest way to build GridFire is using the install.sh or install-tui.sh scripts in the root directory. To use these scripts, simply run:

    +
    ./install.sh
    +
    # or
    +
    ./install-tui.sh
    +

    The regular installation script will select a standard "ideal" set of build options for you. If you want more control over the build options, you can use the install-tui.sh script, which will provide a text-based user interface to select the build options you want.

    +

    Generally, both are intended to be easy to use and will prompt you automatically to install any missing dependencies.

    +

    +Currently known good platforms

    +

    The installation script has been tested and found to work on clean installations of the following platforms:

      +
    • MacOS 15.3.2 (Apple Silicon + brew installed)
      • +
    • Fedora 42.0 (aarch64)
      • +
    • Ubuntu 25.04 (aarch64)
      • +
    • Ubuntu 22.04 (X86_64)
      • +
    +
    +

    Note: On Ubuntu 22.04 the user needs to install boost libraries manually as the versions in the Ubuntu repositories are too old. The installer automatically detects this and will instruct the user in how to do this.

    +
    +

    +Manual Build Instructions

    +

    Prerequisites

    +

    These only need to be manually installed if the user is not making use of the install.sh or install-tui.sh

    +

    +Required

    • C++ compiler supporting C++23 standard
    • Meson build system (>= 1.5.0)
      • -
    • Python 3.10 or newer
      • +
    • Python 3.8 or newer
      • +
    • CMake 3.20 or newer
      • +
    • ninja 1.10.0 or newer
    • Python packages: meson-python>=0.15.0
      • -
    • Boost libraries (>= 1.75.0) installed system-wide
      • +
    • Boost libraries (>= 1.83.0) installed system-wide (or at least findable by meson with pkg-config)
      • +
    +

    +Optional

    +
      +
    • dialog (used by the install.sh script, not needed if using pip or meson directly)
      • +
    • pip (used by the install.sh script or by calling pip directly, not needed if using meson directly)
    -

    Note: Boost is the only external library dependency; no additional libraries are required beyond a C++ compiler, Meson, Python, and Boost.

    +

    Note: Boost is the only external library dependency used by GridFire directly.

    Note: Windows is not supported at this time and there are no plans to support it in the future. Windows users are encouraged to use WSL2 or a Linux VM.

    -

    +
    +

    Note: If install-tui.sh is not able to find a usable version of boost it will provide directions to fetch, compile, and install a usable version.

    +
    +

    +Install Scripts

    +

    GridFire ships with an installer (install.sh) which is intended to make the process of installation both easier and more repetable.

    +

    +Ease of Installation

    +

    Both scripts are intended to automate installation more or less completly. This includes dependency checking. In the event that a dependency cannot be found they try to install (after explicitly asking for user permission). If that does not work they will provide a clear message as to what went wrong.

    +

    +Reproducibility

    +

    The TUI mode provides easy modification of meson build system and compiler settings which can then be saved to a config file. This config file can then be loaded by either tui mode or cli mode (with the --config) flag meaning that build configurations can be made and reused. Note that this is not a deterministicly reproducible build system as it does not interact with any system dependencies or settings, only meson and compiler settings.

    +

    +Examples

    +
    +TUI config and saving
    +

    asciicast

    +
    +TUI config loading and meson setup
    +

    asciicast

    +
    +CLI config loading, setup, and build
    +

    asciicast

    +
    +

    Note: install-tui.sh is simply a script which calles install.sh with the --tui flag. You can get the exact same results by running install.sh --tui.

    +
    +
    +

    Note: Call install.sh with the --help or --h flag to see command line options

    +
    +
    +

    Note: clang tends to compile GridFire much faster than gcc thus why I select it in the above asciinema recording.

    +
    +

    Dependency Installation on Common Platforms

      -
    • Ubuntu/Debian:
      sudo apt-get update && \
      -
      sudo apt-get install -y build-essential meson python3 python3-pip libboost-all-dev
      -
      • -
    • Fedora/CentOS/RHEL:
      sudo dnf install -y gcc-c++ meson python3 python3-pip boost-devel
      -
      • -
    • macOS (Homebrew):
      brew update && \
      -
      brew install boost meson python
      +
    • Ubuntu/Debian:
      sudo apt-get update
      +
      sudo apt-get install -y build-essential meson python3 python3-pip libboost-all-dev
    -

    +
    +

    Note: Depending on the ubuntu version you have the libboost-all-dev libraries may be too old. If this is the case refer to the boost documentation for how to download and install a version >=1.83.0

    +
    +
    +

    Note: On recent versions of ubuntu python has switched to being externally managed by the system. We strongly recomend that if you install manaully all python pacakges are installed inside some kind of virtual enviroment (e.g. pyenv, conda, python-venv, etc...). When using the installer script this is handled automatically using python-venv.

    +
    +
      +
    • Fedora/CentOS/RHEL:
      sudo dnf install -y gcc-c++ meson python3 python3-pip boost-devel
      +
      • +
    • macOS (Homebrew):
      brew update
      +
      brew install boost meson python
      +
      • +
    +

    Building the C++ Library

    meson setup build
    meson compile -C build
    -

    +

    +Clang vs. GCC

    +

    As noted above clang tends to compile GridFire much faster than gcc. If your system has both clang and gcc installed you may force meson to use clang via enviromental variables

    +
    CC=clang CXX=clang++ meson setup build_clang
    +
    meson compile -C build_clang
    +

    Installing the Library

    meson install -C build
    -

    -Python Bindings and Installation

    -

    The Python interface is provided via meson-python and pybind11. To install the Python package:

    pip install .
    -

    -Developer Workflow

    -
      -
    1. Clone the repository and install dependencies listed in pyproject.toml.
      2. -
    2. Configure and build with Meson:
      meson setup build
      -
      meson compile -C build
      -
      3. -
    3. Run the unit tests:
      meson test -C build
      -
      4. -
    4. Iterate on code, rebuild, and rerun tests.
      5. -
    -

    +

    +Minimum compiler versions

    +

    GridFire uses C++23 features and therefore only compilers and standard library implimentations which support C++23 are supported. Generally we have found that gcc >= 13.0.0 or clang >= 16.0.0 work well.

    +

    Code Architecture and Logical Flow

    GridFire is organized into a series of composable modules, each responsible for a specific aspect of nuclear reaction network modeling. The core components include:

      -
    • 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.
      • +
    • Engine Module: Core interfaces and implementations (e.g., GraphEngine) that evaluate reaction network rate equations and energy generation. Also implimented Views submodule.
      • +
    • Engine::Views Module: Composable engine optimization and modification (e.g. MultiscalePartitioningEngineView) which can be used to make a problem more tractable or applicable.
      • +
    • Screening Module: Implements nuclear reaction screening corrections (e.g. WeakScreening (Salpeter, 1954), BareScreening) affecting reaction rates.
    • Reaction Module: Parses and manages Reaclib reaction rate data, providing temperature- and density-dependent rate evaluations.
      • -
    • Partition Module: Implements partition functions (e.g., GroundStatePartitionFunction, RauscherThielemannPartitionFunction) to weight reaction rates based on nuclear properties.
      • +
    • Partition Module: Implements partition functions (e.g., GroundStatePartitionFunction, RauscherThielemannPartitionFunction (Rauscher & Thielemann, 2000) to weight reaction rates based on nuclear properties.
    • Solver Module: Defines numerical integration strategies (e.g., DirectNetworkSolver) for solving the stiff ODE systems arising from reaction networks.
    • Python Interface: Exposes almost all C++ functionality to Python, allowing users to define compositions, configure engines, and run simulations directly from Python scripts.

    Generally a user will start by selecting a base engine (currently we only offer GraphEngine), which constructs the full reaction network graph from a given composition. The user can then apply various engine views to adapt the network topology, such as partitioning fast and slow reactions, adaptively culling low-flow pathways, or priming the network with specific species. Finally, a numerical solver is selected to integrate the network over time, producing updated abundances and diagnostics.

    -

    +

    +Engines

    +

    GridFire is, at its core, based on a series of Engines. These are constructs which know how to report information on series of ODEs which need to be solved to evolver abundnances. The important thing to understand about Engines is that they contain all of the detailed physics GridFire uses. For example a Solver takes an Engine but does not compute physics itself. Rather, it asks the Engine for stuff like the jacobian matrix, stoichiometry, nuclear energy generation rate, and change in abundance with time.

    +

    Refer to the API documentation for the exact interface which an Engine must impliment to be compatible with GridFire solvers.

    +

    Currently we only impliment GraphEngine which is intended to be a very general and adaptable Engine.

    +

    +GraphEngine

    +

    In GridFire the GraphEngine will generally be the most fundamental building block of a nuclear network. A GraphEngine represents a directional hypergraph connecting some set of atomic species through reactions listed in the JINA Reaclib database.

    +

    GraphEngines are constructed from a seed composition of species from which they recursivley expand their topology outward, following known reaction pathways and adding new species to the tracked list as they expand.

    +

    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.
        • +
      • composition: The initial seed composition to start network construction from.
        • +
      • BuildDepthType (Full, Shallow, SecondOrder, etc...): controls number of recursions used to construct the network topology. Can either be an member of the NetworkBuildDepth enum or an integerl.
        • +
      • partition::PartitionFunction: Partition function used when evlauating detailed balance for inverse rates.
    • setPrecomputation(bool precompute):
        @@ -198,23 +325,29 @@ GraphEngine Configuration Options
    -

    +

    Available Partition Functions

    - + - + + +
    Function Name Identifier Description
    Function Name Identifier / Enum Description
    GroundStatePartitionFunction "GroundState" Weights using nuclear ground-state spin factors.
    RauscherThielemannPartitionFunction "RauscherThielemann" Interpolates normalized g-factors per Rauscher & Thielemann.
    RauscherThielemannPartitionFunction "RauscherThielemann" Interpolates normalized g-factors per Rauscher & Thielemann.
    CompositePartitionFunction "Composite" Combines multiple partition functions for situations where different partitions functions are used for different domains
    -

    These functions implement:

    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;
    -

    +

    +AutoDiff

    +

    One of the primary tasks any engine must accomplish is to report the jacobian matrix of the system to the solver. GraphEngine uses CppAD, a C++ auto differentiation library, to generate analytic jacobian matricies very efficiently.

    +

    +Reaclib in GridFire

    +

    All reactions in JINA Reaclib which only include reactants iron and lighter were downloaded on June 17th, 2025 where the most recent documented change on the JINA Reaclib site was on June 24th, 2021.

    +

    All of thes reactions have been compiled into a header file which is then statically compiled into the gridfire binaries (specifically into lib_reaction_reaclib.cpp.o). This does increase the binary size by a few MB; however, the benafit is faster load times and more importantly no need for end users to manage resource files.

    +

    If a developer wants to add new reaclib reactions we include a script at utils/reaclib/format.py which can injest a reaclib data file and produce the needed header file. More details on this process are included in utils/reaclib/readme.md

    +

    Engine Views

    -

    The GridFire engine supports multiple engine view strategies to adapt or restrict network topology. Each view implements a specific algorithm:

    +

    The GridFire engine supports multiple engine view strategies to adapt or restrict network topology. Generally when extending GridFire the approach is likely to be one of adding new EngineViews.

    @@ -223,29 +356,58 @@ Engine Views - + - + + +
    View Name Purpose Algorithm / Reference When to Use
    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
    FileDefinedEngineView Load a defined engine view from a file using some parser Same as DefinedEngineView but loads from a file Same as DefinedEngineView
    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
    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 ignition and network priming 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.

    -

    +

    +A Note about composability

    +

    There are certain functions for which it is expected that a call to an engine view will propegate the result down the chain of engine views, eventually reaching the base engine (e.g. DynamicEngine::update). We do not strongly enforce this as it is not hard to contrive a situation where that is not the mose useful behavior; however, we do strongly encorage developers to think carefully about passing along calls to base engine methods when implimenting new views.

    +

    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<EngineT>: Abstract strategy templated on an engine type. Requires implementation of:
      NetOut evaluate(const NetIn& netIn);
      -
      which integrates the network over one timestep and returns updated abundances, temperature, density, and diagnostics.
      • +

      +NetworkSolverStrategy<EngineT>:

      +

      All GridFire solvers impliment the abstract strategy templated by NetworkSolverStrategy which enforces only that there is some evaluate method with the following signature

      +
      NetOut evaluate(const NetIn& netIn);
      +

      Which is intended to integrate some network over some time and returns updated abundances, temperature, density, and diagnostics.

      +

      +NetIn and NetOut

      +

      GridFire solvers use a unified input and output type for their public interface (though as developers will quickly learn, internally these are immediatly broken down into simpler data structures). All solvers expect a NetIn struct for the input type to the evaluate method and return a NetOut struct.

      +

      +NetIn

      +

      A NetIn struct contains

        +
      • The composition to start the timestep at. (NetIn::composition)
        • +
      • The temperature in Kelvin (NetIn::temperature)
        • +
      • The density in g/cm^3 (NetIn::density)
        • +
      • The max time to evolve the network too in seconds (NetIn::tMax)
        • +
      • The initial timestep to use in seconds (NetIn::dt0)
        • +
      • The initial energy in the system in ergs (NetIn::energy)
      -

      +

      >Note: It is often useful to set NetIn::dt0 to something very small and >let an iterative timestepper push the timestep up. Often for main sequence >burning I use ~1e-12 for dt0

      +

      >Note: The composition must be a fourdst::composition::Composition >object. This is made avalible through the foursdt library and the >fourdst/composition/Composition.h header. fourdst is installed >automatically with GridFire

      +

      >Note: In Python composition comes from fourdst.composition.Composition >and similarly is installed automatically when building GridFire python >bindings.

      +

      +NetOut

      +

      A NetOut struct contains

        +
      • The final composition after evolving to tMax (NetOut::composition)
        • +
      • The number of steps the solver took to evolve to tmax (NetOut::num_steps)
        • +
      • The final energy generated by the network while evolving to tMax (NetOut::energy)
        • +
      +

      >Note: Currently GraphEngine only considers energy due to nuclear mass >defect and not neutrino loss.

      +

      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.
        • +
      • 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: Asks the base engine for the Jacobian Matrix
        • +
      • RHS Evaluation: Assk the base engine for RHS of the abundance evolution equations
        • +
      • 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 loggers, which run in a seperate non blocking thread, capture 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. @@ -257,27 +419,33 @@ Algorithmic Workflow in DirectNetworkSolver
      2. 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.
        • +
      • Callback observer support: Currently we use an observer built into our RHSManager (RHSManager::observe); however, we intend to inlucde support for custom, user defined, observer method.

      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

      +

      +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.

      +

      +Usage Examples

      +

      +C++

      +

      +GraphEngine Initialization

      #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);
      -
      gridfire::GraphEngine
      A reaction network engine that uses a graph-based representation.
      Definition engine_graph.h:100
      +
      gridfire::GraphEngine
      A reaction network engine that uses a graph-based representation.
      Definition engine_graph.h:100
      engine_graph.h
      -

      -C++ Example: Adaptive Network View

      +

      +Adaptive Network View

      #include "gridfire/engine/views/engine_adaptive.h"
      #include "gridfire/engine/engine_graph.h"
      @@ -285,48 +453,46 @@ C++ Example: Adaptive Network View
      gridfire::GraphEngine baseEngine(comp);
      // Dynamically adapt network topology based on reaction flows
      gridfire::AdaptiveEngineView adaptiveView(baseEngine);
      -
      gridfire::AdaptiveEngineView
      An engine view that dynamically adapts the reaction network based on runtime conditions.
      Definition engine_adaptive.h:50
      +
      gridfire::AdaptiveEngineView
      An engine view that dynamically adapts the reaction network based on runtime conditions.
      Definition engine_adaptive.h:50
      engine_adaptive.h
      -

      -Python Example

      -
      import gridfire
      +

      +Composition Initialization

      +
      #include "fourdst/composition/composition.h"
      +
      #include <vector>
      +
      #include <string>
      +
      #include <iostream>
      -
      from fourdst.composition import Composition
      +
      fourdst::composition::Composition comp;
      -
      symbols = ["H-1", ...]
      -
      X = [0.708, ...]
      +
      std::vector<std::string> symbols = {"H-1", "He-4", "C-12"};
      +
      std::vector<double> massFractions = {0.7, 0.29, 0.01};
      -
      comp = Composition()
      -
      comp.registerSymbols(symbols)
      -
      comp.setMassFraction(X)
      -
      comp.finalize(true)
      -
      # Initialize GraphEngine with predefined composition
      -
      engine = gridfire.GraphEngine(comp)
      -
      netIn = gridfire.types.NetIn
      -
      netIn.composition = comp
      -
      netIn.tMax = 1e-3
      -
      netIn.temperature = 1.5e7
      -
      netIn.density = 1.6e2
      -
      netIn.dt0 = 1e-12
      +
      comp.registerSymbols(symbols);
      +
      comp.setMassFraction(symbols, massFractions);
      -
      # Perform one integration step
      -
      netOut = engine.evaluate(netIn)
      -
      print(netOut)
      -

      More detailed python usage can be found here

      -

      -Common Workflow Example

      +
      comp.finalize(true);
      +
      +
      std::cout << comp << std::endl;
      +

      +Common Workflow Example

      A representative workflow often composes multiple engine views to balance accuracy, stability, and performance when integrating stiff nuclear networks:

      -
      #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 "gridfire/engine/engine.h" // Unified header for real usage
      #include "fourdst/composition/composition.h"
      // 1. Define initial composition
      fourdst::composition::Composition comp;
      +
      +
      std::vector<std::string> symbols = {"H-1", "He-4", "C-12"};
      +
      std::vector<double> massFractions = {0.7, 0.29, 0.01};
      +
      +
      comp.registerSymbols(symbols);
      +
      comp.setMassFraction(symbols, massFractions);
      +
      +
      comp.finalize(true);
      +
      // 2. Create base network engine (full reaction graph)
      -
      gridfire::GraphEngine baseEngine(comp);
      +
      gridfire::GraphEngine baseEngine(comp, NetworkBuildDepth::SecondOrder)
      // 3. Partition network into fast/slow subsets (reduces stiffness)
      gridfire::MultiscalePartitioningEngineView msView(baseEngine);
      @@ -348,26 +514,69 @@ Common Workflow Example
      // 7. Execute integration
      NetOut output = solver.evaluate(input);
      -
      gridfire::MultiscalePartitioningEngineView
      An engine view that partitions the reaction network into multiple groups based on timescales.
      Definition engine_multiscale.h:174
      -
      engine_multiscale.h
      - -

      Workflow Components and Effects:

        +
        std::cout << "Final results are: " << output << std::endl;
        +
        gridfire::MultiscalePartitioningEngineView
        An engine view that partitions the reaction network into multiple groups based on timescales.
        Definition engine_multiscale.h:174
        +
        engine.h
        Core header for the GridFire reaction network engine module.
        +

      +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: hub module managing versioning of libcomposition, libconfig, liblogging, and libconstants
        • -
      • libcomposition (docs): Composition management toolkit.
        • -
      • libconfig: Configuration file parsing utilities.
        • -
      • liblogging: Flexible logging framework.
        • -
      • libconstants: Physical constants
        • -
      +

      +Python

      +

      The python bindings intentionally look very similar to the C++ code. Generally all examples can be adapted to python by replacing includes of paths with imports of modules such that

      +

      #include "gridfire/engine/GraphEngine.h</tt> becomes <tt>import gridfire.engine.GraphEngine</tt> + +All GridFire C++ types have been bound and can be passed around as one would expect. + +@subsubsection autotoc_md53 Common Workflow Examople +This example impliments the same logic as the above C++ example +@icode{python} +import gridfire + + +from fourdst.composition import Composition + +symbols = ["H-1", ...] +X = [0.7, ...] + +comp = Composition() +comp.registerSymbols(symbols) +comp.setMassFraction(X) +comp.finalize(true) +# Initialize GraphEngine with predefined composition +engine = gridfire.GraphEngine(comp) +netIn = gridfire.types.NetIn +netIn.composition = comp +netIn.tMax = 1e-3 +netIn.temperature = 1.5e7 +netIn.density = 1.6e2 +netIn.dt0 = 1e-12 + +# Perform one integration step +netOut = engine.evaluate(netIn) +print(netOut) +@endicode + + + +@section autotoc_md54 Related Projects + +GridFire integrates with and builds upon several key 4D-STAR libraries: + +- <a href="https://github.com/4D-STAR/fourdst" >fourdst</a>: hub module managing versioning + of <tt>libcomposition</tt>, <tt>libconfig</tt>, <tt>liblogging</tt>, and <tt>libconstants</tt> +- <a href="https://github.com/4D-STAR/libcomposition" >libcomposition</a> + (<a href="https://4d-star.github.io/libcomposition/" >docs</a>): Composition management + toolkit. +- <a href="https://github.com/4D-STAR/libconfig" >libconfig</a>: Configuration file parsing + utilities. +- <a href="https://github.com/4D-STAR/liblogging" >liblogging</a>: Flexible logging framework. +- <a href="https://github.com/4D-STAR/libconstants" >libconstants: Physical constants

      diff --git a/docs/html/io_2bindings_8cpp.html b/docs/html/io_2bindings_8cpp.html index 004fd550..fc0f97b3 100644 --- a/docs/html/io_2bindings_8cpp.html +++ b/docs/html/io_2bindings_8cpp.html @@ -109,12 +109,10 @@ $(function(){initNavTree('io_2bindings_8cpp.html',''); initResizable(true); }); #include <pybind11/stl_bind.h>
      #include <string_view>
      #include <vector>
      -#include "bindings.h"
      -#include "gridfire/io/io.h"
      -#include "trampoline/py_io.h"
      - -

      Go to the source code of this file.

      - +#include "bindings.h"
      +#include "gridfire/io/io.h"
      +#include "trampoline/py_io.h"
      +
      @@ -136,8 +134,6 @@ Functions

      Functions

      void register_io_bindings (py::module &m)
      -

      Definition at line 15 of file bindings.cpp.

      -
      diff --git a/docs/html/io_2bindings_8h.html b/docs/html/io_2bindings_8h.html index c00d6886..5297f0c3 100644 --- a/docs/html/io_2bindings_8h.html +++ b/docs/html/io_2bindings_8h.html @@ -105,9 +105,7 @@ $(function(){initNavTree('io_2bindings_8h.html',''); initResizable(true); });
      #include <pybind11/pybind11.h>
      -
      -

      Go to the source code of this file.

      - +
      diff --git a/docs/html/io_8h.html b/docs/html/io_8h.html index 6c9fabea..a9c3ea3a 100644 --- a/docs/html/io_8h.html +++ b/docs/html/io_8h.html @@ -102,10 +102,8 @@ $(function(){initNavTree('io_8h.html',''); initResizable(true); });
      io.h File Reference
      -
      #include "gridfire/io/network_file.h"
      -
      -

      Go to the source code of this file.

      -
      +
      #include "gridfire/io/network_file.h"
      +
      -
      #include "gridfire/utils/logging.h"
      -#include "gridfire/engine/engine_abstract.h"
      +
      #include "gridfire/utils/logging.h"
      +#include "gridfire/engine/engine_abstract.h"
      #include <sstream>
      #include <iomanip>
      #include <algorithm>
      @@ -112,9 +112,7 @@ $(function(){initNavTree('logging_8cpp.html',''); initResizable(true); }); #include <string>
      #include <iostream>
      #include <vector>
      -
      -

      Go to the source code of this file.

      -
      +
      -
      #include "gridfire/engine/engine_abstract.h"
      +
      #include "gridfire/engine/engine_abstract.h"
      #include <string>
      #include <vector>
      -
      -

      Go to the source code of this file.

      -

      Functions

      void register_io_bindings (pybind11::module &m)
      +
      diff --git a/docs/html/md_docs_2static_2usage.html b/docs/html/md_docs_2static_2usage.html index 6a320b04..4f54cc51 100644 --- a/docs/html/md_docs_2static_2usage.html +++ b/docs/html/md_docs_2static_2usage.html @@ -102,15 +102,15 @@ $(function(){initNavTree('md_docs_2static_2usage.html',''); initResizable(true);
      GridFire Python Usage Guide
      -

      +

      This tutorial walks you through installing GridFire’s Python bindings, choosing engines and views thoughtfully, running a simulation, and visualizing your results.

      -

      +

      1. Installation

      -

      +

      1.1 PyPI Release

      The quickest way to get started is:

      pip install gridfire
      -

      +

      1.2 Development from Source

      If you want the cutting-edge features or need to hack the C++ backend:

      git clone https://github.com/4DSTAR/GridFire.git
      cd GridFire
      @@ -122,7 +122,7 @@ $(function(){initNavTree('md_docs_2static_2usage.html',''); initResizable(true);

      You can also build manually with Meson (generally end users will not need to do this):

      meson setup build-python
      meson compile -C build_gridfire
      -

      +

      2. Why These Engines and Views?

      GridFire’s design balances physical fidelity and performance. Here’s why we pick each component:

        @@ -162,7 +162,7 @@ $(function(){initNavTree('md_docs_2static_2usage.html',''); initResizable(true);

      By composing these views in sequence, you can tailor accuracy vs performance for your scientific question. Commonly one might use a flow like GraphEngine → Partitioning → Adaptive to capture both full-network physics and manageable stiffness.

      -

      +

      3. Step-by-Step Example

      Adapted from tests/python/test.py. Comments explain each choice.

      import matplotlib.pyplot as plt
      @@ -207,7 +207,7 @@ $(function(){initNavTree('md_docs_2static_2usage.html',''); initResizable(true);
      # 8. Final result:
      print(f"Final H-1 fraction: {netOut.composition.getMassFraction('H-1')}")
      - +
      gridfire::solver
      Definition solver.h:15

      Why these choices?

      • buildDepth=2: In Emily’s preliminary tests, depth=2 captures key reaction loops without the overhead of a full network.
        @@ -217,7 +217,7 @@ $(function(){initNavTree('md_docs_2static_2usage.html',''); initResizable(true);
      • Implicit solver: Rosenbrock4 handles stiff systems robustly, letting you push to longer tMax.
      -

      +

      4. Visualizing Reaction Networks

      GridFire engines and views provide built-in export methods for Graphviz DOT and CSV formats:

      # Export the base network to DOT for Graphviz
      @@ -244,7 +244,7 @@ $(function(){initNavTree('md_docs_2static_2usage.html',''); initResizable(true);
      df.to_csv('H1_evolution.csv', index=False)

      Then plot in pandas or Excel for custom figures.

      -

      +

      5. Beyond the Basics

      • Custom Partition Functions: In Python, subclass gridfire.partition.PartitionFunction, override evaluate, supports, and clone to implement new weighting schemes.
        diff --git a/docs/html/namespacegridfire.html b/docs/html/namespacegridfire.html index 5e084d1c..f9c08f9b 100644 --- a/docs/html/namespacegridfire.html +++ b/docs/html/namespacegridfire.html @@ -298,8 +298,6 @@ Variables

        Alias for CppAD AD type for double precision.

        This alias simplifies the use of the CppAD automatic differentiation type.

        -

        Definition at line 44 of file engine_graph.h.

        -
      @@ -318,8 +316,6 @@ Variables
      Precondition
      If using the integer alternative, the value must be >= 0 or -1 to indicate a full build.
      Postcondition
      The network builder will interpret and apply the specified depth to control reaction expansion.
      -

      Definition at line 37 of file building.h.

      - @@ -336,8 +332,6 @@ Variables

      A set of logical reactions.

      -

      Definition at line 563 of file reaction.h.

      - @@ -354,8 +348,6 @@ Variables

      A set of reactions, typically from a single source like REACLIB.

      -

      Definition at line 562 of file reaction.h.

      - @@ -370,8 +362,6 @@ Variables

      Namespaces

      namespace  gridfire
      -

      Definition at line 65 of file engine_abstract.h.

      -

      Enumeration Type Documentation

      @@ -414,8 +404,6 @@ Variables FifthOrder  -

      Definition at line 21 of file building.h.

      - @@ -437,8 +425,6 @@ Variables UNKNOWN  -

      Definition at line 41 of file network.h.

      - @@ -482,8 +468,6 @@ Variables BASE_NETWORK_TOO_SHALLOW  -

      Definition at line 31 of file reporting.h.

      -

      Function Documentation

      @@ -511,8 +495,6 @@ Variables
      -

      Definition at line 24 of file construction.cpp.

      -
      @@ -614,8 +596,6 @@ Resolved integer depth from maxLayers must not be zero.
      Postcondition
      Returned creation rate is non-negative.
      Returns
      Sum of stoichiometry-weighted creation flows for the species.
      -

      Definition at line 213 of file priming.cpp.

      - @@ -668,8 +648,6 @@ Resolved integer depth from maxLayers must not be zero.
      Postcondition
      Returned rate constant is non-negative.
      Returns
      Sum of absolute stoichiometry-weighted destruction flows for the species.
      -

      Definition at line 193 of file priming.cpp.

      - @@ -706,8 +684,6 @@ Resolved integer depth from maxLayers must not be zero.
      -

      Definition at line 17 of file priming.cpp.

      -
      @@ -743,8 +719,6 @@ Resolved integer depth from maxLayers must not be zero.
      Postcondition
      engine.networkReactions restored to its initial state; returned report contains primedComposition, massFractionChanges for each species, success flag, and status code.
      Returns
      PrimingReport encapsulating the results of the priming operation.
      -

      Definition at line 39 of file priming.cpp.

      - @@ -762,8 +736,6 @@ Resolved integer depth from maxLayers must not be zero.
      -

      Definition at line 65 of file network.cpp.

      -

      Variable Documentation

      @@ -791,12 +763,10 @@ Resolved integer depth from maxLayers must not be zero.
      {REACLIB, "REACLIB"},
      {UNKNOWN, "Unknown"}
      }
      -
      gridfire::APPROX8
      @ APPROX8
      Approx8 nuclear reaction network format.
      Definition network.h:42
      -
      gridfire::REACLIB
      @ REACLIB
      General REACLIB nuclear reaction network format.
      Definition network.h:43
      -
      gridfire::UNKNOWN
      @ UNKNOWN
      Definition network.h:44
      +
      gridfire::APPROX8
      @ APPROX8
      Approx8 nuclear reaction network format.
      Definition network.h:42
      +
      gridfire::REACLIB
      @ REACLIB
      General REACLIB nuclear reaction network format.
      Definition network.h:43
      +
      gridfire::UNKNOWN
      @ UNKNOWN
      Definition network.h:44
      -

      Definition at line 47 of file network.h.

      - @@ -822,8 +792,6 @@ Resolved integer depth from maxLayers must not be zero.

      Minimum abundance threshold below which species are ignored.

      Species with abundances below this threshold are treated as zero in reaction rate calculations. This helps to improve performance by avoiding unnecessary calculations for trace species.

      -

      Definition at line 66 of file engine_graph.h.

      - @@ -849,8 +817,6 @@ Resolved integer depth from maxLayers must not be zero.

      Minimum density threshold below which reactions are ignored.

      Reactions are not calculated if the density falls below this threshold. This helps to improve performance by avoiding unnecessary calculations in very low-density regimes.

      -

      Definition at line 57 of file engine_graph.h.

      - @@ -876,8 +842,6 @@ Resolved integer depth from maxLayers must not be zero.

      Minimum value for Jacobian matrix entries.

      Jacobian matrix entries with absolute values below this threshold are treated as zero to maintain sparsity and improve performance.

      -

      Definition at line 74 of file engine_graph.h.

      - @@ -908,19 +872,17 @@ Resolved integer depth from maxLayers must not be zero.
      {PrimingReportStatus::FAILED_TO_FIND_PRIMING_REACTIONS, "Failed to Find Priming Reactions"},
      {PrimingReportStatus::BASE_NETWORK_TOO_SHALLOW, "Base Network Too Shallow"}
      }
      - - - - - - - +
      gridfire::PrimingReportStatus::FAILED_TO_FIND_PRIMING_REACTIONS
      @ FAILED_TO_FIND_PRIMING_REACTIONS
      Definition reporting.h:37
      +
      gridfire::PrimingReportStatus::MAX_ITERATIONS_REACHED
      @ MAX_ITERATIONS_REACHED
      Definition reporting.h:34
      +
      gridfire::PrimingReportStatus::FULL_SUCCESS
      @ FULL_SUCCESS
      Definition reporting.h:32
      +
      gridfire::PrimingReportStatus::NO_SPECIES_TO_PRIME
      @ NO_SPECIES_TO_PRIME
      Definition reporting.h:33
      +
      gridfire::PrimingReportStatus::FAILED_TO_FIND_CREATION_CHANNEL
      @ FAILED_TO_FIND_CREATION_CHANNEL
      Definition reporting.h:36
      +
      gridfire::PrimingReportStatus::BASE_NETWORK_TOO_SHALLOW
      @ BASE_NETWORK_TOO_SHALLOW
      Definition reporting.h:38
      +
      gridfire::PrimingReportStatus::FAILED_TO_FINALIZE_COMPOSITION
      @ FAILED_TO_FINALIZE_COMPOSITION
      Definition reporting.h:35

      Mapping from PrimingReportStatus codes to human-readable strings.

      Used when formatting or logging the priming status. No preconditions. The map contains entries for all PrimingReportStatus values.

      -

      Definition at line 47 of file reporting.h.

      - @@ -943,8 +905,6 @@ Resolved integer depth from maxLayers must not be zero.
      -

      Definition at line 150 of file engine_multiscale.cpp.

      -
      diff --git a/docs/html/namespacegridfire_1_1approx8.html b/docs/html/namespacegridfire_1_1approx8.html index 51bbe1e2..f1a6366e 100644 --- a/docs/html/namespacegridfire_1_1approx8.html +++ b/docs/html/namespacegridfire_1_1approx8.html @@ -211,8 +211,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 51 of file engine_approx8.h.

      - @@ -231,8 +229,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 57 of file engine_approx8.h.

      - @@ -251,8 +247,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 45 of file engine_approx8.h.

      -

      Function Documentation

      @@ -282,8 +276,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 157 of file engine_approx8.cpp.

      - @@ -312,8 +304,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 227 of file engine_approx8.cpp.

      - @@ -342,8 +332,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 233 of file engine_approx8.cpp.

      - @@ -372,8 +360,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 150 of file engine_approx8.cpp.

      - @@ -402,8 +388,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 122 of file engine_approx8.cpp.

      - @@ -423,8 +407,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 93 of file engine_approx8.cpp.

      - @@ -453,8 +435,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 129 of file engine_approx8.cpp.

      - @@ -483,8 +463,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 135 of file engine_approx8.cpp.

      - @@ -513,8 +491,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 173 of file engine_approx8.cpp.

      - @@ -543,8 +519,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 164 of file engine_approx8.cpp.

      - @@ -573,8 +547,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 181 of file engine_approx8.cpp.

      - @@ -603,8 +575,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 197 of file engine_approx8.cpp.

      - @@ -633,8 +603,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 190 of file engine_approx8.cpp.

      - @@ -663,8 +631,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 218 of file engine_approx8.cpp.

      - @@ -693,8 +659,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 210 of file engine_approx8.cpp.

      - @@ -723,8 +687,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 204 of file engine_approx8.cpp.

      - @@ -753,8 +715,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 115 of file engine_approx8.cpp.

      - @@ -778,8 +738,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 110 of file engine_approx8.cpp.

      - @@ -803,8 +761,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 82 of file engine_approx8.cpp.

      - @@ -833,8 +789,6 @@ Functions
      Examples
      /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
      -

      Definition at line 142 of file engine_approx8.cpp.

      - diff --git a/docs/html/namespacegridfire_1_1expectations.html b/docs/html/namespacegridfire_1_1expectations.html index 7f22c28e..23100460 100644 --- a/docs/html/namespacegridfire_1_1expectations.html +++ b/docs/html/namespacegridfire_1_1expectations.html @@ -152,8 +152,6 @@ Enumerations STALE  -

      Definition at line 7 of file expected_engine.h.

      - @@ -179,8 +177,6 @@ Enumerations EnumeratorSYSTEM_RESIZED  -

      Definition at line 13 of file expected_engine.h.

      - diff --git a/docs/html/namespacegridfire_1_1io.html b/docs/html/namespacegridfire_1_1io.html index ab872584..e4eefb7d 100644 --- a/docs/html/namespacegridfire_1_1io.html +++ b/docs/html/namespacegridfire_1_1io.html @@ -136,8 +136,6 @@ Typedefs
      -

      Definition at line 12 of file network_file.h.

      -
      diff --git a/docs/html/namespacegridfire_1_1partition.html b/docs/html/namespacegridfire_1_1partition.html index a14c6f53..4aa0f6c9 100644 --- a/docs/html/namespacegridfire_1_1partition.html +++ b/docs/html/namespacegridfire_1_1partition.html @@ -169,8 +169,6 @@ Variables -

      Definition at line 15 of file partition_types.h.

      -

      Variable Documentation

      @@ -197,15 +195,13 @@ Variables
      {RauscherThielemann, "RauscherThielemann"},
      {GroundState, "GroundState"}
      }
      -
      gridfire::partition::RauscherThielemann
      @ RauscherThielemann
      Rauscher-Thielemann partition function.
      Definition partition_types.h:16
      -
      gridfire::partition::GroundState
      @ GroundState
      Ground state partition function.
      Definition partition_types.h:17
      +
      gridfire::partition::RauscherThielemann
      @ RauscherThielemann
      Rauscher-Thielemann partition function.
      Definition partition_types.h:16
      +
      gridfire::partition::GroundState
      @ GroundState
      Ground state partition function.
      Definition partition_types.h:17

      Mapping from BasePartitionType enum to human-readable string.

      Used for logging, reporting, or serialization. Ensure that all enum values are represented in this map.

      Precondition
      Contains entries for all values of BasePartitionType.
      Postcondition
      Can convert BasePartitionType to corresponding string.
      -

      Definition at line 28 of file partition_types.h.

      - @@ -232,8 +228,6 @@ Variables
      2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0
      }
      -

      Definition at line 15 of file partition_rauscher_thielemann.cpp.

      - @@ -270,8 +264,6 @@ Variables -

      Definition at line 42 of file partition_types.h.

      - diff --git a/docs/html/namespacegridfire_1_1reaclib.html b/docs/html/namespacegridfire_1_1reaclib.html index 5c30a512..cd2546bb 100644 --- a/docs/html/namespacegridfire_1_1reaclib.html +++ b/docs/html/namespacegridfire_1_1reaclib.html @@ -151,8 +151,6 @@ Variables

      This function uses a singleton pattern to ensure the reaction data is loaded from the embedded binary only once, the very first time it is requested.

      Returns
      A constant reference to the application-wide reaction set.
      -

      Definition at line 138 of file reaclib.cpp.

      - @@ -178,8 +176,6 @@ Variables
      -

      Definition at line 79 of file reaclib.cpp.

      -
      @@ -201,8 +197,6 @@ Variables
      -

      Definition at line 44 of file reaclib.cpp.

      -
      @@ -228,8 +222,6 @@ Variables
      -

      Definition at line 58 of file reaclib.cpp.

      -

      Variable Documentation

      @@ -253,8 +245,6 @@ Variables
      -

      Definition at line 29 of file reaclib.cpp.

      -
      @@ -277,8 +267,6 @@ Variables
      -

      Definition at line 7 of file reaclib.h.

      -
      diff --git a/docs/html/namespacegridfire_1_1reaction.html b/docs/html/namespacegridfire_1_1reaction.html index 289314e6..ab658929 100644 --- a/docs/html/namespacegridfire_1_1reaction.html +++ b/docs/html/namespacegridfire_1_1reaction.html @@ -150,8 +150,6 @@ Functions

      A set of logical reactions.

      -

      Definition at line 563 of file reaction.h.

      - @@ -168,8 +166,6 @@ Functions

      A set of reactions, typically from a single source like REACLIB.

      -

      Definition at line 562 of file reaction.h.

      -

      Function Documentation

      @@ -188,8 +184,6 @@ Functions
      -

      Definition at line 273 of file reaction.cpp.

      -
      diff --git a/docs/html/namespacegridfire_1_1screening.html b/docs/html/namespacegridfire_1_1screening.html index 4f1ec6c0..3cb19b02 100644 --- a/docs/html/namespacegridfire_1_1screening.html +++ b/docs/html/namespacegridfire_1_1screening.html @@ -152,8 +152,6 @@ Functions
      -

      Definition at line 11 of file screening_bare.cpp.

      -

      Enumeration Type Documentation

      @@ -193,8 +191,6 @@ Functions -

      Definition at line 15 of file screening_types.h.

      -

      Function Documentation

      @@ -234,11 +230,9 @@ Functions
      std::vector<double> factors = screening_model->calculateScreeningFactors(
      reactions, species, Y, T9, rho
      );
      -
      gridfire::screening::selectScreeningModel
      std::unique_ptr< ScreeningModel > selectScreeningModel(ScreeningType type)
      A factory function to select and create a screening model.
      Definition screening_types.cpp:9
      -
      gridfire::screening::ScreeningType::WEAK
      @ WEAK
      Weak screening model (Salpeter, 1954).
      Definition screening_types.h:35
      +
      gridfire::screening::selectScreeningModel
      std::unique_ptr< ScreeningModel > selectScreeningModel(ScreeningType type)
      A factory function to select and create a screening model.
      Definition screening_types.cpp:9
      +
      gridfire::screening::ScreeningType::WEAK
      @ WEAK
      Weak screening model (Salpeter, 1954).
      Definition screening_types.h:35
      -

      Definition at line 9 of file screening_types.cpp.

      - diff --git a/docs/html/namespacegridfire_1_1solver.html b/docs/html/namespacegridfire_1_1solver.html index 0fe8d8c4..c471bf68 100644 --- a/docs/html/namespacegridfire_1_1solver.html +++ b/docs/html/namespacegridfire_1_1solver.html @@ -136,8 +136,6 @@ Typedefs

      Type alias for a network solver strategy that uses a DynamicEngine.

      -

      Definition at line 53 of file solver.h.

      - diff --git a/docs/html/namespacegridfire_1_1utils.html b/docs/html/namespacegridfire_1_1utils.html index 469a25be..c75f0935 100644 --- a/docs/html/namespacegridfire_1_1utils.html +++ b/docs/html/namespacegridfire_1_1utils.html @@ -179,10 +179,8 @@ Functions
      // he4 inf
      // c12 8.765e-02
      // ==========================
      -
      gridfire::utils::formatNuclearTimescaleLogString
      std::string formatNuclearTimescaleLogString(const DynamicEngine &engine, const std::vector< double > &Y, const double T9, const double rho)
      Formats a map of nuclear species timescales into a human-readable string.
      Definition logging.cpp:13
      +
      gridfire::utils::formatNuclearTimescaleLogString
      std::string formatNuclearTimescaleLogString(const DynamicEngine &engine, const std::vector< double > &Y, const double T9, const double rho)
      Formats a map of nuclear species timescales into a human-readable string.
      Definition logging.cpp:13
      -

      Definition at line 13 of file logging.cpp.

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+"utils_2bindings_8cpp.html#a7af842f50ca4a721518e716d0229697c":[8,0,1,2,9,0,0], +"utils_2bindings_8h.html":[8,0,1,2,9,1], +"utils_2bindings_8h.html#a9eefca377142320755a869fafc6311c7":[8,0,1,2,9,1,0] }; diff --git a/docs/html/network_8cpp.html b/docs/html/network_8cpp.html index 59049c27..385ef264 100644 --- a/docs/html/network_8cpp.html +++ b/docs/html/network_8cpp.html @@ -105,14 +105,12 @@ $(function(){initNavTree('network_8cpp.html',''); initResizable(true); });
      network.cpp File Reference
      -
      #include "gridfire/network.h"
      -#include "gridfire/reaction/reaclib.h"
      -#include "gridfire/reaction/reaction.h"
      +
      #include "gridfire/network.h"
      +#include "gridfire/reaction/reaclib.h"
      +#include "gridfire/reaction/reaction.h"
      #include <ranges>
      #include "quill/LogMacros.h"
      -
      -

      Go to the source code of this file.

      - +
      diff --git a/docs/html/network_8h.html b/docs/html/network_8h.html index 08fce15b..d966e281 100644 --- a/docs/html/network_8h.html +++ b/docs/html/network_8h.html @@ -113,12 +113,10 @@ $(function(){initNavTree('network_8h.html',''); initResizable(true); }); #include "fourdst/composition/species.h"
      #include "fourdst/composition/composition.h"
      #include "fourdst/constants/const.h"
      -#include "gridfire/reaction/reaction.h"
      +#include "gridfire/reaction/reaction.h"
      #include "quill/Logger.h"
      #include <unordered_map>
      - -

      Go to the source code of this file.

      -

      Namespaces

      namespace  gridfire
      +
      diff --git a/docs/html/network__file_8cpp.html b/docs/html/network__file_8cpp.html index b7d9e114..13f770e4 100644 --- a/docs/html/network__file_8cpp.html +++ b/docs/html/network__file_8cpp.html @@ -104,16 +104,14 @@ $(function(){initNavTree('network__file_8cpp.html',''); initResizable(true); });
      network_file.cpp File Reference
      -
      #include "gridfire/io/network_file.h"
      +
      #include "gridfire/io/network_file.h"
      #include <string>
      #include <vector>
      #include <algorithm>
      #include <fstream>
      #include <stdexcept>
      #include "quill/LogMacros.h"
      -
      -

      Go to the source code of this file.

      -

      Classes

      struct  gridfire::NetIn
      +
      diff --git a/docs/html/network__file_8h.html b/docs/html/network__file_8h.html index ce07b7d5..cf70dd8a 100644 --- a/docs/html/network__file_8h.html +++ b/docs/html/network__file_8h.html @@ -111,9 +111,7 @@ $(function(){initNavTree('network__file_8h.html',''); initResizable(true); }); #include "quill/Logger.h"
      #include <string>
      #include <vector>
      - -

      Go to the source code of this file.

      -

      Namespaces

      namespace  gridfire
      +
      diff --git a/docs/html/partition_2bindings_8cpp.html b/docs/html/partition_2bindings_8cpp.html index fea17853..199feb69 100644 --- a/docs/html/partition_2bindings_8cpp.html +++ b/docs/html/partition_2bindings_8cpp.html @@ -109,12 +109,10 @@ $(function(){initNavTree('partition_2bindings_8cpp.html',''); initResizable(true #include <pybind11/stl_bind.h>
      #include <iostream>
      #include <memory>
      -#include "bindings.h"
      -#include "gridfire/partition/partition.h"
      -#include "trampoline/py_partition.h"
      - -

      Go to the source code of this file.

      -

      Classes

      class  gridfire::io::NetworkFileParser
      +#include "bindings.h"
      +#include "gridfire/partition/partition.h"
      +#include "trampoline/py_partition.h"
      +
      @@ -146,8 +144,6 @@ Functions

      Functions

      void register_partition_bindings (pybind11::module &m)
      -

      Definition at line 92 of file bindings.cpp.

      -
      @@ -165,8 +161,6 @@ Functions
      -

      Definition at line 47 of file bindings.cpp.

      -
      @@ -184,8 +178,6 @@ Functions
      -

      Definition at line 20 of file bindings.cpp.

      -
      @@ -203,8 +195,6 @@ Functions
      -

      Definition at line 32 of file bindings.cpp.

      -
      @@ -222,8 +212,6 @@ Functions
      -

      Definition at line 74 of file bindings.cpp.

      -
      @@ -241,8 +229,6 @@ Functions
      -

      Definition at line 65 of file bindings.cpp.

      -
      diff --git a/docs/html/partition_2bindings_8h.html b/docs/html/partition_2bindings_8h.html index 187e9640..84e9a572 100644 --- a/docs/html/partition_2bindings_8h.html +++ b/docs/html/partition_2bindings_8h.html @@ -105,9 +105,7 @@ $(function(){initNavTree('partition_2bindings_8h.html',''); initResizable(true);
      #include <pybind11/pybind11.h>
      -
      -

      Go to the source code of this file.

      - +
      @@ -139,8 +137,6 @@ Functions

      Functions

      void register_partition_bindings (pybind11::module &m)
      -

      Definition at line 92 of file bindings.cpp.

      -
      @@ -158,8 +154,6 @@ Functions
      -

      Definition at line 47 of file bindings.cpp.

      -
      @@ -177,8 +171,6 @@ Functions
      -

      Definition at line 20 of file bindings.cpp.

      -
      @@ -196,8 +188,6 @@ Functions
      -

      Definition at line 32 of file bindings.cpp.

      -
      @@ -215,8 +205,6 @@ Functions
      -

      Definition at line 74 of file bindings.cpp.

      -
      @@ -234,8 +222,6 @@ Functions
      -

      Definition at line 65 of file bindings.cpp.

      -
      diff --git a/docs/html/partition_8h.html b/docs/html/partition_8h.html index ee39e55b..59066171 100644 --- a/docs/html/partition_8h.html +++ b/docs/html/partition_8h.html @@ -102,15 +102,13 @@ $(function(){initNavTree('partition_8h.html',''); initResizable(true); });
      partition.h File Reference
      -
      #include "gridfire/partition/partition_types.h"
      -#include "gridfire/partition/partition_abstract.h"
      -#include "gridfire/partition/partition_ground.h"
      -#include "gridfire/partition/partition_rauscher_thielemann.h"
      -#include "gridfire/partition/rauscher_thielemann_partition_data_record.h"
      -#include "gridfire/partition/composite/partition_composite.h"
      -
      -

      Go to the source code of this file.

      -
      +
      #include "gridfire/partition/partition_types.h"
      +#include "gridfire/partition/partition_abstract.h"
      +#include "gridfire/partition/partition_ground.h"
      +#include "gridfire/partition/partition_rauscher_thielemann.h"
      +#include "gridfire/partition/rauscher_thielemann_partition_data_record.h"
      +#include "gridfire/partition/composite/partition_composite.h"
      +
      diff --git a/docs/html/py__screening_8h.html b/docs/html/py__screening_8h.html index 2109def8..d630c775 100644 --- a/docs/html/py__screening_8h.html +++ b/docs/html/py__screening_8h.html @@ -104,15 +104,13 @@ $(function(){initNavTree('py__screening_8h.html',''); initResizable(true); });
      py_screening.h File Reference
      -
      #include "gridfire/screening/screening.h"
      +
      #include "gridfire/screening/screening.h"
      #include <pybind11/pybind11.h>
      #include <pybind11/stl.h>
      #include <pybind11/functional.h>
      #include <vector>
      #include "cppad/cppad.hpp"
      -
      -

      Go to the source code of this file.

      - +
      diff --git a/docs/html/py__solver_8cpp.html b/docs/html/py__solver_8cpp.html index 5ba0a501..9e239812 100644 --- a/docs/html/py__solver_8cpp.html +++ b/docs/html/py__solver_8cpp.html @@ -102,15 +102,13 @@ $(function(){initNavTree('py__solver_8cpp.html',''); initResizable(true); });
      py_solver.cpp File Reference
      -
      #include "gridfire/solver/solver.h"
      +
      #include "gridfire/solver/solver.h"
      #include <pybind11/pybind11.h>
      #include <pybind11/stl.h>
      #include <pybind11/functional.h>
      #include <vector>
      -#include "py_solver.h"
      -
      -

      Go to the source code of this file.

      -
      +#include "py_solver.h"
      +
      -
      #include "gridfire/solver/solver.h"
      +
      #include "gridfire/solver/solver.h"
      #include <vector>
      -
      -

      Go to the source code of this file.

      -

      Classes

      class  PyScreening
      +
      diff --git a/docs/html/rauscher__thielemann__partition__data_8h.html b/docs/html/rauscher__thielemann__partition__data_8h.html index b02b7fac..759f7230 100644 --- a/docs/html/rauscher__thielemann__partition__data_8h.html +++ b/docs/html/rauscher__thielemann__partition__data_8h.html @@ -105,9 +105,7 @@ $(function(){initNavTree('rauscher__thielemann__partition__data_8h.html',''); in
      #include <cstddef>
      -
      -

      Go to the source code of this file.

      -

      Classes

      class  PyDynamicNetworkSolverStrategy
      +
      @@ -128,8 +126,6 @@ Variables

      Variables

      const unsigned char rauscher_thielemann_partition_data []
      -

      Definition at line 5 of file rauscher_thielemann_partition_data.h.

      -
      @@ -144,8 +140,6 @@ Variables
      -

      Definition at line 69897 of file rauscher_thielemann_partition_data.h.

      -
      diff --git a/docs/html/rauscher__thielemann__partition__data__record_8h.html b/docs/html/rauscher__thielemann__partition__data__record_8h.html index aef63203..8b44a974 100644 --- a/docs/html/rauscher__thielemann__partition__data__record_8h.html +++ b/docs/html/rauscher__thielemann__partition__data__record_8h.html @@ -106,9 +106,7 @@ $(function(){initNavTree('rauscher__thielemann__partition__data__record_8h.html'
      #include <cstdint>
      -
      -

      Go to the source code of this file.

      - +
      diff --git a/docs/html/reaclib_8cpp.html b/docs/html/reaclib_8cpp.html index 58c7bf6a..78befa3b 100644 --- a/docs/html/reaclib_8cpp.html +++ b/docs/html/reaclib_8cpp.html @@ -109,16 +109,14 @@ $(function(){initNavTree('reaclib_8cpp.html',''); initResizable(true); });
      #include "fourdst/composition/atomicSpecies.h"
      #include "fourdst/composition/species.h"
      -#include "gridfire/reaction/reaclib.h"
      -#include "gridfire/reaction/reactions_data.h"
      -#include "gridfire/network.h"
      +#include "gridfire/reaction/reaclib.h"
      +#include "gridfire/reaction/reactions_data.h"
      +#include "gridfire/network.h"
      #include <stdexcept>
      #include <sstream>
      #include <vector>
      #include <string>
      -
      -

      Go to the source code of this file.

      -

      Classes

      struct  gridfire::partition::record::RauscherThielemannPartitionDataRecord
      +
      @@ -166,8 +164,6 @@ Variables

      Classes

      struct  gridfire::reaclib::ReactionRecord
      -

      Definition at line 13 of file reaclib.cpp.

      -
      diff --git a/docs/html/reaclib_8h.html b/docs/html/reaclib_8h.html index 97ca09fa..41e03f41 100644 --- a/docs/html/reaclib_8h.html +++ b/docs/html/reaclib_8h.html @@ -106,10 +106,8 @@ $(function(){initNavTree('reaclib_8h.html',''); initResizable(true); });
      reaclib.h File Reference
      -
      #include "gridfire/reaction/reaction.h"
      -
      -

      Go to the source code of this file.

      - +
      #include "gridfire/reaction/reaction.h"
      +
      diff --git a/docs/html/reaction_2bindings_8cpp.html b/docs/html/reaction_2bindings_8cpp.html index 96f84785..d7eb4062 100644 --- a/docs/html/reaction_2bindings_8cpp.html +++ b/docs/html/reaction_2bindings_8cpp.html @@ -109,12 +109,10 @@ $(function(){initNavTree('reaction_2bindings_8cpp.html',''); initResizable(true) #include <pybind11/stl_bind.h>
      #include <string_view>
      #include <vector>
      -#include "bindings.h"
      -#include "gridfire/reaction/reaction.h"
      -#include "gridfire/reaction/reaclib.h"
      - -

      Go to the source code of this file.

      -

      Namespaces

      namespace  gridfire
      +#include "bindings.h"
      +#include "gridfire/reaction/reaction.h"
      +#include "gridfire/reaction/reaclib.h"
      +
      @@ -136,8 +134,6 @@ Functions

      Functions

      void register_reaction_bindings (py::module &m)
      -

      Definition at line 16 of file bindings.cpp.

      -
      diff --git a/docs/html/reaction_2bindings_8h.html b/docs/html/reaction_2bindings_8h.html index aedfcea6..437ab374 100644 --- a/docs/html/reaction_2bindings_8h.html +++ b/docs/html/reaction_2bindings_8h.html @@ -105,9 +105,7 @@ $(function(){initNavTree('reaction_2bindings_8h.html',''); initResizable(true);
      #include <pybind11/pybind11.h>
      -
      -

      Go to the source code of this file.

      - +
      diff --git a/docs/html/reaction_8cpp.html b/docs/html/reaction_8cpp.html index 052a669f..a4a68302 100644 --- a/docs/html/reaction_8cpp.html +++ b/docs/html/reaction_8cpp.html @@ -106,7 +106,7 @@ $(function(){initNavTree('reaction_8cpp.html',''); initResizable(true); });
      reaction.cpp File Reference
      -
      #include "gridfire/reaction/reaction.h"
      +
      #include "gridfire/reaction/reaction.h"
      #include <string_view>
      #include <string>
      #include <vector>
      @@ -116,9 +116,7 @@ $(function(){initNavTree('reaction_8cpp.html',''); initResizable(true); }); #include "quill/LogMacros.h"
      #include "fourdst/composition/atomicSpecies.h"
      #include "xxhash64.h"
      -
      -

      Go to the source code of this file.

      -

      Functions

      void register_reaction_bindings (pybind11::module &m)
      +
      diff --git a/docs/html/reaction_8h.html b/docs/html/reaction_8h.html index 01f3eabf..d4280905 100644 --- a/docs/html/reaction_8h.html +++ b/docs/html/reaction_8h.html @@ -119,9 +119,7 @@ $(function(){initNavTree('reaction_8h.html',''); initResizable(true); }); #include <unordered_set>
      #include "cppad/cppad.hpp"
      #include "xxhash64.h"
      - -

      Go to the source code of this file.

      -

      Classes

      struct  std::hash< gridfire::reaction::Reaction >
      +
      @@ -160,8 +158,6 @@ Functions

      Detailed Description

      Defines classes for representing and managing nuclear reactions.

      This file contains the core data structures for handling nuclear reactions, including individual reactions from specific sources (Reaction), collections of reactions (ReactionSet), and logical reactions that aggregate rates from multiple sources (LogicalReaction, LogicalReactionSet).

      - -

      Definition in file reaction.h.

      diff --git a/docs/html/reactions__data_8h.html b/docs/html/reactions__data_8h.html index 51a0a757..ce814d18 100644 --- a/docs/html/reactions__data_8h.html +++ b/docs/html/reactions__data_8h.html @@ -105,9 +105,7 @@ $(function(){initNavTree('reactions__data_8h.html',''); initResizable(true); });
      #include <cstddef>
      -
      -

      Go to the source code of this file.

      -

      Classes

      struct  gridfire::reaction::RateCoefficientSet
      +
      @@ -128,8 +126,6 @@ Variables

      Variables

      const unsigned char raw_reactions_data []
      -

      Definition at line 5 of file reactions_data.h.

      -
      @@ -144,8 +140,6 @@ Variables
      -

      Definition at line 181934 of file reactions_data.h.

      -
      diff --git a/docs/html/reporting_8h.html b/docs/html/reporting_8h.html index 7e684d2b..b3f139ac 100644 --- a/docs/html/reporting_8h.html +++ b/docs/html/reporting_8h.html @@ -116,9 +116,7 @@ $(function(){initNavTree('reporting_8h.html',''); initResizable(true); }); #include <sstream>
      #include "fourdst/composition/composition.h"
      #include "fourdst/composition/atomicSpecies.h"
      - -

      Go to the source code of this file.

      - +
      diff --git a/docs/html/screening_2bindings_8cpp.html b/docs/html/screening_2bindings_8cpp.html index e75917c9..ff97db52 100644 --- a/docs/html/screening_2bindings_8cpp.html +++ b/docs/html/screening_2bindings_8cpp.html @@ -109,12 +109,10 @@ $(function(){initNavTree('screening_2bindings_8cpp.html',''); initResizable(true #include <pybind11/stl_bind.h>
      #include <string_view>
      #include <vector>
      -#include "bindings.h"
      -#include "gridfire/screening/screening.h"
      -#include "trampoline/py_screening.h"
      - -

      Go to the source code of this file.

      -

      Classes

      struct  gridfire::PrimingReport
      +#include "bindings.h"
      +#include "gridfire/screening/screening.h"
      +#include "trampoline/py_screening.h"
      +
      @@ -136,8 +134,6 @@ Functions

      Functions

      void register_screening_bindings (py::module &m)
      -

      Definition at line 15 of file bindings.cpp.

      -
      diff --git a/docs/html/screening_2bindings_8h.html b/docs/html/screening_2bindings_8h.html index e3c837af..50d96b37 100644 --- a/docs/html/screening_2bindings_8h.html +++ b/docs/html/screening_2bindings_8h.html @@ -105,9 +105,7 @@ $(function(){initNavTree('screening_2bindings_8h.html',''); initResizable(true);
      #include <pybind11/pybind11.h>
      -
      -

      Go to the source code of this file.

      - +
      diff --git a/docs/html/screening_8h.html b/docs/html/screening_8h.html index 960ec000..501cb9c8 100644 --- a/docs/html/screening_8h.html +++ b/docs/html/screening_8h.html @@ -102,13 +102,11 @@ $(function(){initNavTree('screening_8h.html',''); initResizable(true); });
      screening.h File Reference
      -
      #include "gridfire/screening/screening_types.h"
      -#include "gridfire/screening/screening_abstract.h"
      -#include "gridfire/screening/screening_bare.h"
      -#include "gridfire/screening/screening_weak.h"
      -
      -

      Go to the source code of this file.

      -
      +
      #include "gridfire/screening/screening_types.h"
      +#include "gridfire/screening/screening_abstract.h"
      +#include "gridfire/screening/screening_bare.h"
      +#include "gridfire/screening/screening_weak.h"
      +
      -
      #include "gridfire/reaction/reaction.h"
      +
      #include "gridfire/reaction/reaction.h"
      #include "fourdst/composition/atomicSpecies.h"
      #include "cppad/cppad.hpp"
      #include <vector>
      -
      -

      Go to the source code of this file.

      -

      Functions

      void register_screening_bindings (pybind11::module &m)
      +
      diff --git a/docs/html/screening__bare_8cpp.html b/docs/html/screening__bare_8cpp.html index 414ebc47..26568a62 100644 --- a/docs/html/screening__bare_8cpp.html +++ b/docs/html/screening__bare_8cpp.html @@ -105,13 +105,11 @@ $(function(){initNavTree('screening__bare_8cpp.html',''); initResizable(true); }
      screening_bare.cpp File Reference
      -
      #include "gridfire/screening/screening_bare.h"
      +
      #include "gridfire/screening/screening_bare.h"
      #include "fourdst/composition/atomicSpecies.h"
      #include "cppad/cppad.hpp"
      #include <vector>
      -
      -

      Go to the source code of this file.

      -

      Classes

      class  gridfire::screening::ScreeningModel
      +
      diff --git a/docs/html/screening__bare_8h.html b/docs/html/screening__bare_8h.html index 6fab6c5e..f877531f 100644 --- a/docs/html/screening__bare_8h.html +++ b/docs/html/screening__bare_8h.html @@ -105,12 +105,10 @@ $(function(){initNavTree('screening__bare_8h.html',''); initResizable(true); });
      screening_bare.h File Reference
      -
      #include "gridfire/screening/screening_abstract.h"
      -#include "gridfire/reaction/reaction.h"
      +
      #include "gridfire/screening/screening_abstract.h"
      +#include "gridfire/reaction/reaction.h"
      #include "cppad/cppad.hpp"
      -
      -

      Go to the source code of this file.

      -

      Namespaces

      namespace  gridfire
      +
      diff --git a/docs/html/screening__types_8cpp.html b/docs/html/screening__types_8cpp.html index 2711abd7..21dfd42c 100644 --- a/docs/html/screening__types_8cpp.html +++ b/docs/html/screening__types_8cpp.html @@ -105,14 +105,12 @@ $(function(){initNavTree('screening__types_8cpp.html',''); initResizable(true);
      screening_types.cpp File Reference
      -
      #include "gridfire/screening/screening_abstract.h"
      -#include "gridfire/screening/screening_types.h"
      -#include "gridfire/screening/screening_weak.h"
      -#include "gridfire/screening/screening_bare.h"
      +
      #include "gridfire/screening/screening_abstract.h"
      +#include "gridfire/screening/screening_types.h"
      +#include "gridfire/screening/screening_weak.h"
      +#include "gridfire/screening/screening_bare.h"
      #include <memory>
      -
      -

      Go to the source code of this file.

      -

      Classes

      class  gridfire::screening::BareScreeningModel
      +
      diff --git a/docs/html/screening__types_8h.html b/docs/html/screening__types_8h.html index aa13cf91..f663f9d9 100644 --- a/docs/html/screening__types_8h.html +++ b/docs/html/screening__types_8h.html @@ -106,11 +106,9 @@ $(function(){initNavTree('screening__types_8h.html',''); initResizable(true); })
      screening_types.h File Reference
      -
      #include "gridfire/screening/screening_abstract.h"
      +
      #include "gridfire/screening/screening_abstract.h"
      #include <memory>
      -
      -

      Go to the source code of this file.

      -

      Namespaces

      namespace  gridfire
      +
      diff --git a/docs/html/screening__weak_8cpp.html b/docs/html/screening__weak_8cpp.html index e84fd671..d5d4fa77 100644 --- a/docs/html/screening__weak_8cpp.html +++ b/docs/html/screening__weak_8cpp.html @@ -104,13 +104,11 @@ $(function(){initNavTree('screening__weak_8cpp.html',''); initResizable(true); }
      screening_weak.cpp File Reference
      -
      #include "gridfire/screening/screening_weak.h"
      +
      #include "gridfire/screening/screening_weak.h"
      #include "fourdst/composition/atomicSpecies.h"
      #include "cppad/cppad.hpp"
      #include <vector>
      -
      -

      Go to the source code of this file.

      -

      Namespaces

      namespace  gridfire
      +
      diff --git a/docs/html/screening__weak_8h.html b/docs/html/screening__weak_8h.html index 563e0e18..559772b8 100644 --- a/docs/html/screening__weak_8h.html +++ b/docs/html/screening__weak_8h.html @@ -105,15 +105,13 @@ $(function(){initNavTree('screening__weak_8h.html',''); initResizable(true); });
      screening_weak.h File Reference
      -
      #include "gridfire/screening/screening_abstract.h"
      -#include "gridfire/reaction/reaction.h"
      +
      #include "gridfire/screening/screening_abstract.h"
      +#include "gridfire/reaction/reaction.h"
      #include "fourdst/logging/logging.h"
      #include "quill/Logger.h"
      #include "quill/LogMacros.h"
      #include "cppad/cppad.hpp"
      -
      -

      Go to the source code of this file.

      -

      Namespaces

      namespace  gridfire
      +
      diff --git a/docs/html/search/all_0.js b/docs/html/search/all_0.js index 48214497..12b474d5 100644 --- a/docs/html/search/all_0.js +++ b/docs/html/search/all_0.js @@ -1,7 +1,7 @@ var searchData= [ - ['1_201_20pypi_20release_0',['1.1 PyPI Release',['../md_docs_2static_2usage.html#autotoc_md26',1,'']]], - ['1_202_20development_20from_20source_1',['1.2 Development from Source',['../md_docs_2static_2usage.html#autotoc_md27',1,'']]], - ['1_20installation_2',['1. Installation',['../md_docs_2static_2usage.html#autotoc_md25',1,'']]], - ['1_20pypi_20release_3',['1.1 PyPI Release',['../md_docs_2static_2usage.html#autotoc_md26',1,'']]] + ['1_201_20pypi_20release_0',['1.1 PyPI Release',['../md_docs_2static_2usage.html#autotoc_md58',1,'']]], + ['1_202_20development_20from_20source_1',['1.2 Development from Source',['../md_docs_2static_2usage.html#autotoc_md59',1,'']]], + ['1_20installation_2',['1. 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diff --git a/docs/html/search/searchdata.js b/docs/html/search/searchdata.js index 698ee1b3..1a3fd50c 100644 --- a/docs/html/search/searchdata.js +++ b/docs/html/search/searchdata.js @@ -1,6 +1,6 @@ var indexSectionsWithContent = { - 0: "12345abcdefghijklmnopqrstuvwyz~", + 0: "12345:abcdefghijklmnopqrstuvwyz~", 1: "abcdefghijlmnopqrstuw", 2: "gs", 3: "bceilmnprsu", diff --git a/docs/html/solver_2bindings_8cpp.html b/docs/html/solver_2bindings_8cpp.html index 413b900f..d59dfd8b 100644 --- a/docs/html/solver_2bindings_8cpp.html +++ b/docs/html/solver_2bindings_8cpp.html @@ -107,12 +107,10 @@ $(function(){initNavTree('solver_2bindings_8cpp.html',''); initResizable(true);
      #include <pybind11/pybind11.h>
      #include <pybind11/stl.h>
      #include <pybind11/stl_bind.h>
      -#include "bindings.h"
      -#include "gridfire/solver/solver.h"
      -#include "trampoline/py_solver.h"
      -
      -

      Go to the source code of this file.

      -

      Classes

      class  gridfire::screening::WeakScreeningModel
      +#include "bindings.h"
      +#include "gridfire/solver/solver.h"
      +#include "trampoline/py_solver.h"
      +
      @@ -134,8 +132,6 @@ Functions

      Functions

      void register_solver_bindings (py::module &m)
      -

      Definition at line 13 of file bindings.cpp.

      -
      diff --git a/docs/html/solver_2bindings_8h.html b/docs/html/solver_2bindings_8h.html index 8313a9b7..23ed6d18 100644 --- a/docs/html/solver_2bindings_8h.html +++ b/docs/html/solver_2bindings_8h.html @@ -105,9 +105,7 @@ $(function(){initNavTree('solver_2bindings_8h.html',''); initResizable(true); })
      #include <pybind11/pybind11.h>
      -
      -

      Go to the source code of this file.

      - +
      diff --git a/docs/html/solver_8cpp.html b/docs/html/solver_8cpp.html index 3f3ddfc7..73564461 100644 --- a/docs/html/solver_8cpp.html +++ b/docs/html/solver_8cpp.html @@ -104,10 +104,10 @@ $(function(){initNavTree('solver_8cpp.html',''); initResizable(true); });
      solver.cpp File Reference
      -
      #include "gridfire/solver/solver.h"
      -#include "gridfire/engine/engine_graph.h"
      -#include "gridfire/network.h"
      -#include "gridfire/exceptions/error_engine.h"
      +
      #include "gridfire/solver/solver.h"
      +#include "gridfire/engine/engine_graph.h"
      +#include "gridfire/network.h"
      +#include "gridfire/exceptions/error_engine.h"
      #include "fourdst/composition/atomicSpecies.h"
      #include "fourdst/composition/composition.h"
      #include "fourdst/config/config.h"
      @@ -118,9 +118,7 @@ $(function(){initNavTree('solver_8cpp.html',''); initResizable(true); }); #include <stdexcept>
      #include <iomanip>
      #include "quill/LogMacros.h"
      -
      -

      Go to the source code of this file.

      -

      Functions

      void register_solver_bindings (pybind11::module &m)
      +
      diff --git a/docs/html/solver_8h.html b/docs/html/solver_8h.html index ec0481f0..f8607dd4 100644 --- a/docs/html/solver_8h.html +++ b/docs/html/solver_8h.html @@ -106,17 +106,15 @@ $(function(){initNavTree('solver_8h.html',''); initResizable(true); });
      solver.h File Reference
      -
      #include "gridfire/engine/engine_graph.h"
      -#include "gridfire/engine/engine_abstract.h"
      -#include "../engine/views/engine_adaptive.h"
      -#include "gridfire/network.h"
      +
      #include "gridfire/engine/engine_graph.h"
      +#include "gridfire/engine/engine_abstract.h"
      +#include "../engine/views/engine_adaptive.h"
      +#include "gridfire/network.h"
      #include "fourdst/logging/logging.h"
      #include "fourdst/config/config.h"
      #include "quill/Logger.h"
      #include <vector>
      -
      -

      Go to the source code of this file.

      -

      Namespaces

      namespace  gridfire
      +
      diff --git a/docs/html/struct_r_h_s_functor.html b/docs/html/struct_r_h_s_functor.html index 669595df..9228aae9 100644 --- a/docs/html/struct_r_h_s_functor.html +++ b/docs/html/struct_r_h_s_functor.html @@ -109,7 +109,7 @@ $(function(){initNavTree('struct_r_h_s_functor.html',''); initResizable(true); }

      Functor for calculating the right-hand side of the ODEs.

      This functor is used by the ODE solver to calculate the time derivatives of the species abundances. It takes the current abundances as input and returns the time derivatives.

      The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html b/docs/html/structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html index 03bdf396..e26da14b 100644 --- a/docs/html/structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html +++ b/docs/html/structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html @@ -118,8 +118,6 @@ Public Attributes

      Classes

      class  gridfire::solver::NetworkSolverStrategy< EngineT >

      Detailed Description

      A struct to hold a reaction and its flow rate.

      - -

      Definition at line 306 of file engine_adaptive.h.

      Member Data Documentation

      ◆ flowRate

      @@ -133,8 +131,6 @@ Public Attributes
      -

      Definition at line 308 of file engine_adaptive.h.

      -
      @@ -149,12 +145,10 @@ Public Attributes
      -

      Definition at line 307 of file engine_adaptive.h.

      -
      The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html b/docs/html/structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html index 10eba120..f76af830 100644 --- a/docs/html/structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html +++ b/docs/html/structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html @@ -130,10 +130,7 @@ Public Attributes  Symmetry factor for reverse reactions.
        -

      Detailed Description

      -
      -

      Definition at line 384 of file engine_graph.h.

      -

      Member Data Documentation

      +

      Member Data Documentation

      ◆ affected_species_indices

      @@ -146,8 +143,6 @@ Public Attributes
      -

      Definition at line 390 of file engine_graph.h.

      -
      @@ -164,8 +159,6 @@ Public Attributes

      Powers of each unique product in the reverse reaction.

      -

      Definition at line 395 of file engine_graph.h.

      - @@ -180,8 +173,6 @@ Public Attributes
      -

      Definition at line 388 of file engine_graph.h.

      -
      @@ -196,8 +187,6 @@ Public Attributes
      -

      Definition at line 386 of file engine_graph.h.

      -
      @@ -214,8 +203,6 @@ Public Attributes

      Symmetry factor for reverse reactions.

      -

      Definition at line 396 of file engine_graph.h.

      - @@ -230,8 +217,6 @@ Public Attributes
      -

      Definition at line 391 of file engine_graph.h.

      -
      @@ -246,8 +231,6 @@ Public Attributes
      -

      Definition at line 389 of file engine_graph.h.

      -
      @@ -264,8 +247,6 @@ Public Attributes

      Unique product indices for reverse reactions.

      -

      Definition at line 394 of file engine_graph.h.

      - @@ -280,12 +261,10 @@ Public Attributes
      -

      Definition at line 387 of file engine_graph.h.

      -
      The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1_graph_engine_1_1constants.html b/docs/html/structgridfire_1_1_graph_engine_1_1constants.html index d032d9a9..2d7c534a 100644 --- a/docs/html/structgridfire_1_1_graph_engine_1_1constants.html +++ b/docs/html/structgridfire_1_1_graph_engine_1_1constants.html @@ -121,10 +121,7 @@ Public Attributes  Boltzmann constant in erg/K.
        -

      Detailed Description

      -
      -

      Definition at line 399 of file engine_graph.h.

      -

      Member Data Documentation

      +

      Member Data Documentation

      ◆ c

      @@ -139,8 +136,6 @@ Public Attributes

      Speed of light in cm/s.

      -

      Definition at line 402 of file engine_graph.h.

      - @@ -157,8 +152,6 @@ Public Attributes

      Boltzmann constant in erg/K.

      -

      Definition at line 403 of file engine_graph.h.

      - @@ -175,8 +168,6 @@ Public Attributes

      Avogadro's number.

      -

      Definition at line 401 of file engine_graph.h.

      - @@ -193,12 +184,10 @@ Public Attributes

      Atomic mass unit in g.

      -

      Definition at line 400 of file engine_graph.h.

      -
      The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html b/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html index 75f2622c..5b883b8c 100644 --- a/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html +++ b/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html @@ -162,8 +162,6 @@ Public Attributes

      Detailed Description

      Struct for tracking cache statistics.

      @purpose A simple utility to monitor the performance of the QSE cache by counting hits and misses for various engine operations.

      - -

      Definition at line 822 of file engine_multiscale.h.

      Member Enumeration Documentation

      ◆ operators

      @@ -194,8 +192,6 @@ Public Attributes All  -

      Definition at line 823 of file engine_multiscale.h.

      -

      Member Function Documentation

      @@ -228,8 +224,6 @@ Public Attributes -

      Definition at line 1612 of file engine_multiscale.cpp.

      - @@ -264,8 +258,6 @@ Public Attributes
      Returns
      The number of hits.
      -

      Definition at line 1629 of file engine_multiscale.cpp.

      - @@ -297,8 +289,6 @@ Public Attributes -

      Definition at line 1620 of file engine_multiscale.cpp.

      - @@ -333,8 +323,6 @@ Public Attributes
      Returns
      The number of misses.
      -

      Definition at line 1636 of file engine_multiscale.cpp.

      -

      Member Data Documentation

      @@ -352,8 +340,6 @@ Public Attributes

      Total number of cache hits.

      -

      Definition at line 848 of file engine_multiscale.h.

      - @@ -370,8 +356,6 @@ Public Attributes

      Total number of cache misses.

      -

      Definition at line 852 of file engine_multiscale.h.

      - @@ -393,17 +377,15 @@ Public Attributes
      {operators::GetSpeciesDestructionTimescales, 0},
      {operators::Other, 0}
      }
      - - - - - - +
      gridfire::MultiscalePartitioningEngineView::CacheStats::operators::CalculateMolarReactionFlow
      @ CalculateMolarReactionFlow
      Definition engine_multiscale.h:826
      + + + +
      gridfire::MultiscalePartitioningEngineView::CacheStats::operators::GetSpeciesDestructionTimescales
      @ GetSpeciesDestructionTimescales
      Definition engine_multiscale.h:828
      +

      Map from operators to the number of cache hits for that operator.

      -

      Definition at line 857 of file engine_multiscale.h.

      - @@ -428,8 +410,6 @@ Public Attributes

      Map from operators to the number of cache misses for that operator.

      -

      Definition at line 869 of file engine_multiscale.h.

      - @@ -454,13 +434,11 @@ Public Attributes

      Map from operators to their string names for logging.

      -

      Definition at line 836 of file engine_multiscale.h.

      -
      The documentation for this struct was generated from the following files: diff --git a/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html b/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html index f543429a..eb6e570b 100644 --- a/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html +++ b/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html @@ -171,8 +171,6 @@ Public Attributes
    • df: Computes the Jacobian of the objective function. It calls the base engine's generateJacobianMatrix and extracts the sub-matrix corresponding to the algebraic species. It applies the chain rule to account for the asinh scaling used on the abundances.

    The abundances are scaled using asinh to handle the large dynamic range and ensure positivity.

    - -

    Definition at line 729 of file engine_multiscale.h.

    Member Typedef Documentation

    ◆ InputType

    @@ -186,8 +184,6 @@ Public Attributes
    -

    Definition at line 730 of file engine_multiscale.h.

    -
    @@ -202,8 +198,6 @@ Public Attributes
    -

    Definition at line 732 of file engine_multiscale.h.

    -
    @@ -218,8 +212,6 @@ Public Attributes
    -

    Definition at line 731 of file engine_multiscale.h.

    -

    Member Enumeration Documentation

    @@ -239,8 +231,6 @@ Public Attributes ValuesAtCompileTime  -

    Definition at line 733 of file engine_multiscale.h.

    -

    Constructor & Destructor Documentation

    @@ -304,8 +294,6 @@ Public Attributes -

    Definition at line 773 of file engine_multiscale.h.

    -

    Member Function Documentation

    @@ -338,8 +326,6 @@ Public Attributes
    Returns
    0 on success.
    -

    Definition at line 1525 of file engine_multiscale.cpp.

    - @@ -368,8 +354,6 @@ Public Attributes

    Gets the number of input values to the functor (size of the variable vector).

    Returns
    The number of algebraic species being solved.
    -

    Definition at line 797 of file engine_multiscale.h.

    - @@ -401,8 +385,6 @@ Public Attributes
    Returns
    0 on success.
    -

    Definition at line 1503 of file engine_multiscale.cpp.

    - @@ -431,8 +413,6 @@ Public Attributes

    Gets the number of output values from the functor (size of the residual vector).

    Returns
    The number of algebraic species being solved.
    -

    Definition at line 792 of file engine_multiscale.h.

    -

    Member Data Documentation

    @@ -450,8 +430,6 @@ Public Attributes

    Indices of the species to solve for in the QSE group.

    -

    Definition at line 745 of file engine_multiscale.h.

    - @@ -468,8 +446,6 @@ Public Attributes

    Density in g/cm^3.

    -

    Definition at line 757 of file engine_multiscale.h.

    - @@ -486,8 +462,6 @@ Public Attributes

    Temperature in units of 10^9 K.

    -

    Definition at line 753 of file engine_multiscale.h.

    - @@ -504,8 +478,6 @@ Public Attributes

    Pointer to the MultiscalePartitioningEngineView instance.

    -

    Definition at line 741 of file engine_multiscale.h.

    - @@ -522,8 +494,6 @@ Public Attributes

    Initial abundances of all species in the full network.

    -

    Definition at line 749 of file engine_multiscale.h.

    - @@ -540,13 +510,11 @@ Public Attributes

    Scaling factors for the species abundances, used to improve solver stability.

    -

    Definition at line 761 of file engine_multiscale.h.

    -
    The documentation for this struct was generated from the following files: diff --git a/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html b/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html index 8f459670..e416d288 100644 --- a/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html +++ b/docs/html/structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html @@ -146,8 +146,6 @@ Public Attributes

    Detailed Description

    Struct representing a QSE group.

    @purpose A container to hold all information about a set of species that are potentially in quasi-steady-state equilibrium with each other.

    - -

    Definition at line 677 of file engine_multiscale.h.

    Member Function Documentation

    ◆ operator!=()

    @@ -173,8 +171,6 @@ Public Attributes
    Returns
    True if the sets of species indices are not identical.
    -

    Definition at line 1608 of file engine_multiscale.cpp.

    - @@ -201,8 +197,6 @@ Public Attributes
    Returns
    True if this group's mean timescale is less than the other's.
    -

    Definition at line 1600 of file engine_multiscale.cpp.

    - @@ -229,8 +223,6 @@ Public Attributes
    Returns
    True if the sets of species indices are identical.
    -

    Definition at line 1596 of file engine_multiscale.cpp.

    - @@ -257,8 +249,6 @@ Public Attributes
    Returns
    True if this group's mean timescale is greater than the other's.
    -

    Definition at line 1604 of file engine_multiscale.cpp.

    -

    Member Data Documentation

    @@ -276,8 +266,6 @@ Public Attributes

    Indices of algebraic species in this group.

    -

    Definition at line 680 of file engine_multiscale.h.

    - @@ -294,8 +282,6 @@ Public Attributes

    Flag set by flux analysis.

    -

    Definition at line 679 of file engine_multiscale.h.

    - @@ -312,8 +298,6 @@ Public Attributes

    Mean timescale of the group.

    -

    Definition at line 682 of file engine_multiscale.h.

    - @@ -330,8 +314,6 @@ Public Attributes

    Indices of dynamic species in this group.

    -

    Definition at line 681 of file engine_multiscale.h.

    - @@ -348,13 +330,11 @@ Public Attributes

    Indices of all species in this group.

    -

    Definition at line 678 of file engine_multiscale.h.

    -
    The documentation for this struct was generated from the following files: diff --git a/docs/html/structgridfire_1_1_net_in.html b/docs/html/structgridfire_1_1_net_in.html index 3c140993..d41b2db2 100644 --- a/docs/html/structgridfire_1_1_net_in.html +++ b/docs/html/structgridfire_1_1_net_in.html @@ -107,7 +107,7 @@ $(function(){initNavTree('structgridfire_1_1_net_in.html',''); initResizable(tru
    -

    #include <network.h>

    +

    #include <network.h>

    @@ -138,10 +138,7 @@ Public Attributes

    Public Member Functions

     Culling threshold for reactions (default is 0.0, meaning no culling)
     
    -

    Detailed Description

    -
    -

    Definition at line 53 of file network.h.

    -

    Member Function Documentation

    +

    Member Function Documentation

    ◆ MolarAbundance()

    @@ -157,8 +154,6 @@ Public Attributes
    -

    Definition at line 30 of file network.cpp.

    -

    Member Data Documentation

    @@ -176,8 +171,6 @@ Public Attributes

    Composition of the network.

    -

    Definition at line 54 of file network.h.

    - @@ -194,8 +187,6 @@ Public Attributes

    Culling threshold for reactions (default is 0.0, meaning no culling)

    -

    Definition at line 60 of file network.h.

    - @@ -212,8 +203,6 @@ Public Attributes

    Density in g/cm^3.

    -

    Definition at line 58 of file network.h.

    - @@ -230,8 +219,6 @@ Public Attributes

    Initial time step.

    -

    Definition at line 56 of file network.h.

    - @@ -248,8 +235,6 @@ Public Attributes

    Energy in ergs.

    -

    Definition at line 59 of file network.h.

    - @@ -266,8 +251,6 @@ Public Attributes

    Temperature in Kelvin.

    -

    Definition at line 57 of file network.h.

    - @@ -284,13 +267,11 @@ Public Attributes

    Maximum time.

    -

    Definition at line 55 of file network.h.

    -
    The documentation for this struct was generated from the following files: diff --git a/docs/html/structgridfire_1_1_net_out.html b/docs/html/structgridfire_1_1_net_out.html index 4834ad19..2e8e5930 100644 --- a/docs/html/structgridfire_1_1_net_out.html +++ b/docs/html/structgridfire_1_1_net_out.html @@ -107,7 +107,7 @@ $(function(){initNavTree('structgridfire_1_1_net_out.html',''); initResizable(tr
    -

    #include <network.h>

    +

    #include <network.h>

    @@ -126,10 +126,7 @@ Friends

    Public Attributes

    std::ostream & operator<< (std::ostream &os, const NetOut &netOut)
     
    -

    Detailed Description

    -
    -

    Definition at line 65 of file network.h.

    -

    Friends And Related Symbol Documentation

    +

    Friends And Related Symbol Documentation

    ◆ operator<<

    @@ -157,8 +154,6 @@ Friends
    -

    Definition at line 70 of file network.h.

    -

    Member Data Documentation

    @@ -176,8 +171,6 @@ Friends

    Composition of the network after evaluation.

    -

    Definition at line 66 of file network.h.

    - @@ -194,8 +187,6 @@ Friends

    Energy in ergs after evaluation.

    -

    Definition at line 68 of file network.h.

    - @@ -212,12 +203,10 @@ Friends

    Number of steps taken in the evaluation.

    -

    Definition at line 67 of file network.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1_priming_report.html b/docs/html/structgridfire_1_1_priming_report.html index 1a72da2a..17ce6d93 100644 --- a/docs/html/structgridfire_1_1_priming_report.html +++ b/docs/html/structgridfire_1_1_priming_report.html @@ -110,7 +110,7 @@ $(function(){initNavTree('structgridfire_1_1_priming_report.html',''); initResiz

    Captures the result of a network priming operation. More...

    -

    #include <reporting.h>

    +

    #include <reporting.h>

    @@ -134,8 +134,6 @@ Friends

    Contains the finalized composition, the changes in mass fractions for species, a success flag, and a detailed status code.

    Precondition
    A priming algorithm must be executed before constructing a valid report.
    Postcondition
    All fields reflect the outcome of the priming run.
    - -

    Definition at line 67 of file reporting.h.

    Friends And Related Symbol Documentation

    ◆ operator<<

    @@ -175,8 +173,6 @@ Friends
    Returns
    Reference to the modified output stream.
    Postcondition
    The stream contains a textual representation of the report.
    -

    Definition at line 89 of file reporting.h.

    -

    Member Data Documentation

    @@ -193,8 +189,6 @@ Friends

    List of pairs (species, rate change) representing destruction (<0) or creation (>0) rates of species during priming.

    -

    Definition at line 74 of file reporting.h.

    -
    @@ -210,8 +204,6 @@ Friends

    Finalized composition after priming.

    -

    Definition at line 69 of file reporting.h.

    -
    @@ -227,8 +219,6 @@ Friends

    Detailed status code indicating the result.

    -

    Definition at line 78 of file reporting.h.

    -
    @@ -244,12 +234,10 @@ Friends

    True if priming completed without error.

    -

    Definition at line 76 of file reporting.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1_q_s_e_cache_config.html b/docs/html/structgridfire_1_1_q_s_e_cache_config.html index 291cb1d2..3f7973c1 100644 --- a/docs/html/structgridfire_1_1_q_s_e_cache_config.html +++ b/docs/html/structgridfire_1_1_q_s_e_cache_config.html @@ -109,7 +109,7 @@ $(function(){initNavTree('structgridfire_1_1_q_s_e_cache_config.html',''); initR

    Configuration struct for the QSE cache. More...

    -

    #include <engine_multiscale.h>

    +

    #include <engine_multiscale.h>

    Public Attributes

    @@ -128,8 +128,6 @@ Public Attributes

    @purpose This struct defines the tolerances used to determine if a QSE cache key is considered a hit. It allows for tuning the sensitivity of the cache.

    @how It works by providing binning widths for temperature, density, and abundances. When a QSECacheKey is created, it uses these tolerances to discretize the continuous physical values into bins. If two sets of conditions fall into the same bins, they will produce the same hash and be considered a cache hit.

    Usage Example:
    Although not typically set by the user directly, the QSECacheKey uses this internally. A smaller tolerance (e.g., T9_tol = 1e-4) makes the cache more sensitive, leading to more frequent re-partitions, while a larger tolerance (T9_tol = 1e-2) makes it less sensitive.
    - -

    Definition at line 27 of file engine_multiscale.h.

    Member Data Documentation

    ◆ rho_tol

    @@ -145,8 +143,6 @@ Public Attributes

    Absolute tolerance to produce the same hash for rho.

    -

    Definition at line 29 of file engine_multiscale.h.

    - @@ -163,8 +159,6 @@ Public Attributes

    Absolute tolerance to produce the same hash for T9.

    -

    Definition at line 28 of file engine_multiscale.h.

    - @@ -181,12 +175,10 @@ Public Attributes

    Absolute tolerance to produce the same hash for species abundances.

    -

    Definition at line 30 of file engine_multiscale.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1_q_s_e_cache_key.html b/docs/html/structgridfire_1_1_q_s_e_cache_key.html index f9f168a1..b5a7f68c 100644 --- a/docs/html/structgridfire_1_1_q_s_e_cache_key.html +++ b/docs/html/structgridfire_1_1_q_s_e_cache_key.html @@ -111,7 +111,7 @@ $(function(){initNavTree('structgridfire_1_1_q_s_e_cache_key.html',''); initResi

    Key struct for the QSE abundance cache. More...

    -

    #include <engine_multiscale.h>

    +

    #include <engine_multiscale.h>

    Public Attributes

    @@ -150,8 +150,6 @@ Public Attributes

    Key struct for the QSE abundance cache.

    @purpose This struct is used as the key for the QSE abundance cache (m_qse_abundance_cache) within the MultiscalePartitioningEngineView. Its primary goal is to avoid expensive re-partitioning and QSE solves for thermodynamic conditions that are "close enough" to previously computed ones.

    @how It works by storing the temperature (m_T9), density (m_rho), and species abundances (m_Y). A pre-computed hash is generated in the constructor by calling the hash() method. This method discretizes the continuous physical values into bins using the tolerances defined in QSECacheConfig. The operator== simply compares the pre-computed hash values for fast lookups in the std::unordered_map.

    - -

    Definition at line 47 of file engine_multiscale.h.

    Constructor & Destructor Documentation

    ◆ QSECacheKey()

    @@ -188,8 +186,6 @@ Public Attributes
    Postcondition
    The m_hash member is computed and stored.
    -

    Definition at line 1556 of file engine_multiscale.cpp.

    -

    Member Function Documentation

    @@ -231,8 +227,6 @@ Public Attributes
    Returns
    The bin number as a long integer.

    @how The algorithm is floor(value / tol).

    -

    Definition at line 1588 of file engine_multiscale.cpp.

    - @@ -254,8 +248,6 @@ Public Attributes
    Returns
    The computed hash value.

    @how This method combines the hashes of the binned temperature, density, and each species abundance. The bin() static method is used for discretization.

    -

    Definition at line 1567 of file engine_multiscale.cpp.

    - @@ -282,8 +274,6 @@ Public Attributes
    Returns
    True if the pre-computed hashes are equal, false otherwise.
    -

    Definition at line 1592 of file engine_multiscale.cpp.

    -

    Member Data Documentation

    @@ -304,8 +294,6 @@ Public Attributes
    1e-3
    }
    -

    Definition at line 55 of file engine_multiscale.h.

    - @@ -322,8 +310,6 @@ Public Attributes

    Precomputed hash value for this key.

    -

    Definition at line 52 of file engine_multiscale.h.

    - @@ -338,8 +324,6 @@ Public Attributes

    Public Member Functions

    -

    Definition at line 49 of file engine_multiscale.h.

    -
    @@ -354,8 +338,6 @@ Public Attributes
    -

    Definition at line 48 of file engine_multiscale.h.

    -
    @@ -372,13 +354,11 @@ Public Attributes

    Note that the ordering of Y must match the dynamic species indices in the view.

    -

    Definition at line 50 of file engine_multiscale.h.

    -
    The documentation for this struct was generated from the following files: diff --git a/docs/html/structgridfire_1_1_step_derivatives.html b/docs/html/structgridfire_1_1_step_derivatives.html index 697a25da..a7eb4397 100644 --- a/docs/html/structgridfire_1_1_step_derivatives.html +++ b/docs/html/structgridfire_1_1_step_derivatives.html @@ -109,7 +109,7 @@ $(function(){initNavTree('structgridfire_1_1_step_derivatives.html',''); initRes

    Structure holding derivatives and energy generation for a network step. More...

    -

    #include <engine_abstract.h>

    +

    #include <engine_abstract.h>

    @@ -135,12 +135,10 @@ struct gridfire::StepDerivatives< T >

    Structure holding derivative

    // Use derivative
    }
    double energyRate = result.nuclearEnergyGenerationRate;
    -
    gridfire::StepDerivatives
    Structure holding derivatives and energy generation for a network step.
    Definition engine_abstract.h:60
    -
    gridfire::StepDerivatives::nuclearEnergyGenerationRate
    T nuclearEnergyGenerationRate
    Specific energy generation rate (e.g., erg/g/s).
    Definition engine_abstract.h:62
    -
    gridfire::StepDerivatives::dydt
    std::vector< T > dydt
    Derivatives of abundances (dY/dt for each species).
    Definition engine_abstract.h:61
    - -

    Definition at line 60 of file engine_abstract.h.

    -

    Member Data Documentation

    +
    gridfire::StepDerivatives
    Structure holding derivatives and energy generation for a network step.
    Definition engine_abstract.h:60
    +
    gridfire::StepDerivatives::nuclearEnergyGenerationRate
    T nuclearEnergyGenerationRate
    Specific energy generation rate (e.g., erg/g/s).
    Definition engine_abstract.h:62
    +
    gridfire::StepDerivatives::dydt
    std::vector< T > dydt
    Derivatives of abundances (dY/dt for each species).
    Definition engine_abstract.h:61
    +

    Member Data Documentation

    ◆ dydt

    @@ -157,8 +155,6 @@ template<IsArithmeticOrAD T>

    Derivatives of abundances (dY/dt for each species).

    -

    Definition at line 61 of file engine_abstract.h.

    - @@ -177,12 +173,10 @@ template<IsArithmeticOrAD T>

    Specific energy generation rate (e.g., erg/g/s).

    -

    Definition at line 62 of file engine_abstract.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1approx8_1_1_approx8_net.html b/docs/html/structgridfire_1_1approx8_1_1_approx8_net.html index f0021614..9ad55d86 100644 --- a/docs/html/structgridfire_1_1approx8_1_1_approx8_net.html +++ b/docs/html/structgridfire_1_1approx8_1_1_approx8_net.html @@ -109,7 +109,7 @@ $(function(){initNavTree('structgridfire_1_1approx8_1_1_approx8_net.html',''); i

    Contains constants and arrays related to the nuclear network. More...

    -

    #include <engine_approx8.h>

    +

    #include <engine_approx8.h>

    Public Attributes

    @@ -148,8 +148,6 @@ Static Public Attributes

    Contains constants and arrays related to the nuclear network.

    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    - -

    Definition at line 63 of file engine_approx8.h.

    Member Data Documentation

    ◆ aIon

    @@ -183,8 +181,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 80 of file engine_approx8.h.

    - @@ -209,8 +205,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 67 of file engine_approx8.h.

    - @@ -235,8 +229,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 74 of file engine_approx8.h.

    - @@ -261,8 +253,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 75 of file engine_approx8.h.

    - @@ -287,8 +277,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 64 of file engine_approx8.h.

    - @@ -313,8 +301,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 65 of file engine_approx8.h.

    - @@ -339,8 +325,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 66 of file engine_approx8.h.

    - @@ -365,8 +349,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 71 of file engine_approx8.h.

    - @@ -391,8 +373,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 68 of file engine_approx8.h.

    - @@ -417,8 +397,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 70 of file engine_approx8.h.

    - @@ -443,8 +421,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 69 of file engine_approx8.h.

    - @@ -469,8 +445,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 73 of file engine_approx8.h.

    - @@ -505,8 +479,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 91 of file engine_approx8.h.

    - @@ -531,8 +503,6 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 77 of file engine_approx8.h.

    - @@ -557,12 +527,10 @@ Static Public Attributes
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 78 of file engine_approx8.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1approx8_1_1_jacobian.html b/docs/html/structgridfire_1_1approx8_1_1_jacobian.html index ed2e3bda..027adc61 100644 --- a/docs/html/structgridfire_1_1approx8_1_1_jacobian.html +++ b/docs/html/structgridfire_1_1approx8_1_1_jacobian.html @@ -109,7 +109,7 @@ $(function(){initNavTree('structgridfire_1_1approx8_1_1_jacobian.html',''); init

    Functor to calculate the Jacobian matrix for implicit solvers. More...

    -

    #include <engine_approx8.h>

    +

    #include <engine_approx8.h>

    Static Public Attributes

    @@ -121,8 +121,6 @@ Public Member Functions

    Functor to calculate the Jacobian matrix for implicit solvers.

    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    - -

    Definition at line 267 of file engine_approx8.h.

    Member Function Documentation

    ◆ operator()()

    @@ -165,13 +163,11 @@ Public Member Functions
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 243 of file engine_approx8.cpp.

    -
    The documentation for this struct was generated from the following files: diff --git a/docs/html/structgridfire_1_1approx8_1_1_o_d_e.html b/docs/html/structgridfire_1_1approx8_1_1_o_d_e.html index c46d76c2..24251b23 100644 --- a/docs/html/structgridfire_1_1approx8_1_1_o_d_e.html +++ b/docs/html/structgridfire_1_1approx8_1_1_o_d_e.html @@ -109,7 +109,7 @@ $(function(){initNavTree('structgridfire_1_1approx8_1_1_o_d_e.html',''); initRes

    Functor to calculate the derivatives for the ODE solver. More...

    -

    #include <engine_approx8.h>

    +

    #include <engine_approx8.h>

    Public Member Functions

    @@ -121,8 +121,6 @@ Public Member Functions

    Functor to calculate the derivatives for the ODE solver.

    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    - -

    Definition at line 281 of file engine_approx8.h.

    Member Function Documentation

    ◆ operator()()

    @@ -159,13 +157,11 @@ Public Member Functions
    Examples
    /Users/tboudreaux/Programming/4DSTAR/GridFire/src/include/gridfire/engine/engine_approx8.h.
    -

    Definition at line 348 of file engine_approx8.cpp.

    -
    The documentation for this struct was generated from the following files: diff --git a/docs/html/structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html b/docs/html/structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html index bcc3cce9..4e34336d 100644 --- a/docs/html/structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html +++ b/docs/html/structgridfire_1_1exceptions_1_1_stale_engine_trigger_1_1state.html @@ -106,7 +106,7 @@ $(function(){initNavTree('structgridfire_1_1exceptions_1_1_stale_engine_trigger_
    -

    #include <error_engine.h>

    +

    #include <error_engine.h>

    Public Member Functions

    @@ -123,10 +123,7 @@ Public Attributes

    Public Attributes

    double m_eps_nuc
     
    -

    Detailed Description

    -
    -

    Definition at line 12 of file error_engine.h.

    -

    Member Data Documentation

    +

    Member Data Documentation

    ◆ m_eps_nuc

    @@ -139,8 +136,6 @@ Public Attributes
    -

    Definition at line 18 of file error_engine.h.

    -
    @@ -155,8 +150,6 @@ Public Attributes
    -

    Definition at line 14 of file error_engine.h.

    -
    @@ -171,8 +164,6 @@ Public Attributes
    -

    Definition at line 16 of file error_engine.h.

    -
    @@ -187,8 +178,6 @@ Public Attributes
    -

    Definition at line 13 of file error_engine.h.

    -
    @@ -203,8 +192,6 @@ Public Attributes
    -

    Definition at line 17 of file error_engine.h.

    -
    @@ -219,12 +206,10 @@ Public Attributes
    -

    Definition at line 15 of file error_engine.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1expectations_1_1_engine_error.html b/docs/html/structgridfire_1_1expectations_1_1_engine_error.html index cbf312e7..35351ca3 100644 --- a/docs/html/structgridfire_1_1expectations_1_1_engine_error.html +++ b/docs/html/structgridfire_1_1expectations_1_1_engine_error.html @@ -108,7 +108,7 @@ $(function(){initNavTree('structgridfire_1_1expectations_1_1_engine_error.html',
    -

    #include <expected_engine.h>

    +

    #include <expected_engine.h>

    Inheritance diagram for gridfire::expectations::EngineError:
    @@ -139,10 +139,7 @@ Friends std::ostream & operator<< (std::ostream &os, const EngineError &e)   -

    Detailed Description

    -
    -

    Definition at line 18 of file expected_engine.h.

    -

    Constructor & Destructor Documentation

    +

    Constructor & Destructor Documentation

    ◆ EngineError()

    @@ -170,8 +167,6 @@ Friends
    -

    Definition at line 22 of file expected_engine.h.

    -
    @@ -227,8 +222,6 @@ Friends
    -

    Definition at line 27 of file expected_engine.h.

    -

    Member Data Documentation

    @@ -244,8 +237,6 @@ Friends
    -

    Definition at line 19 of file expected_engine.h.

    -
    @@ -260,12 +251,10 @@ Friends
    -

    Definition at line 20 of file expected_engine.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1expectations_1_1_engine_index_error.html b/docs/html/structgridfire_1_1expectations_1_1_engine_index_error.html index ed66eb43..d153b72b 100644 --- a/docs/html/structgridfire_1_1expectations_1_1_engine_index_error.html +++ b/docs/html/structgridfire_1_1expectations_1_1_engine_index_error.html @@ -108,7 +108,7 @@ $(function(){initNavTree('structgridfire_1_1expectations_1_1_engine_index_error.
    -

    #include <expected_engine.h>

    +

    #include <expected_engine.h>

    Inheritance diagram for gridfire::expectations::EngineIndexError:
    @@ -144,10 +144,7 @@ Friends std::ostream & operator<< (std::ostream &os, const EngineIndexError &e)   -

    Detailed Description

    -
    -

    Definition at line 33 of file expected_engine.h.

    -

    Constructor & Destructor Documentation

    +

    Constructor & Destructor Documentation

    ◆ EngineIndexError()

    @@ -171,8 +168,6 @@ Friends
    -

    Definition at line 36 of file expected_engine.h.

    -

    Friends And Related Symbol Documentation

    @@ -203,8 +198,6 @@ Friends
    -

    Definition at line 38 of file expected_engine.h.

    -

    Member Data Documentation

    @@ -220,12 +213,10 @@ Friends
    -

    Definition at line 34 of file expected_engine.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1expectations_1_1_stale_engine_error.html b/docs/html/structgridfire_1_1expectations_1_1_stale_engine_error.html index a1a5ca94..da40c5ed 100644 --- a/docs/html/structgridfire_1_1expectations_1_1_stale_engine_error.html +++ b/docs/html/structgridfire_1_1expectations_1_1_stale_engine_error.html @@ -107,7 +107,7 @@ $(function(){initNavTree('structgridfire_1_1expectations_1_1_stale_engine_error.
    -

    #include <expected_engine.h>

    +

    #include <expected_engine.h>

    Inheritance diagram for gridfire::expectations::StaleEngineError:
    @@ -140,10 +140,7 @@ Public Attributes const EngineErrorTypes type = EngineErrorTypes::FAILURE   -

    Detailed Description

    -
    -

    Definition at line 44 of file expected_engine.h.

    -

    Constructor & Destructor Documentation

    +

    Constructor & Destructor Documentation

    ◆ StaleEngineError()

    @@ -167,8 +164,6 @@ Public Attributes
    -

    Definition at line 47 of file expected_engine.h.

    -

    Member Function Documentation

    @@ -195,8 +190,6 @@ Public Attributes
    -

    Definition at line 50 of file expected_engine.h.

    -

    Member Data Documentation

    @@ -212,12 +205,10 @@ Public Attributes
    -

    Definition at line 45 of file expected_engine.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_identified_isotope.html b/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_identified_isotope.html index ba5d2bc6..42bf4fbe 100644 --- a/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_identified_isotope.html +++ b/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_identified_isotope.html @@ -117,10 +117,7 @@ Public Attributes size_t lowerIndex   -

    Detailed Description

    -
    -

    Definition at line 105 of file partition_rauscher_thielemann.h.

    -

    Member Data Documentation

    +

    Member Data Documentation

    ◆ bound

    @@ -133,8 +130,6 @@ Public Attributes
    -

    Definition at line 106 of file partition_rauscher_thielemann.h.

    -
    @@ -149,8 +144,6 @@ Public Attributes
    -

    Definition at line 107 of file partition_rauscher_thielemann.h.

    -
    @@ -165,8 +158,6 @@ Public Attributes
    -

    Definition at line 109 of file partition_rauscher_thielemann.h.

    -
    @@ -181,12 +172,10 @@ Public Attributes
    -

    Definition at line 108 of file partition_rauscher_thielemann.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_interpolation_points.html b/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_interpolation_points.html index 548cb04f..f7a34612 100644 --- a/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_interpolation_points.html +++ b/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_interpolation_points.html @@ -121,10 +121,7 @@ Public Attributes  Normalized G at lower bound.
      -

    Detailed Description

    -
    -

    Definition at line 99 of file partition_rauscher_thielemann.h.

    -

    Member Data Documentation

    +

    Member Data Documentation

    ◆ G_norm_high

    @@ -139,8 +136,6 @@ Public Attributes

    Normalized G at upper bound.

    -

    Definition at line 101 of file partition_rauscher_thielemann.h.

    - @@ -157,8 +152,6 @@ Public Attributes

    Normalized G at lower bound.

    -

    Definition at line 103 of file partition_rauscher_thielemann.h.

    - @@ -175,8 +168,6 @@ Public Attributes

    Upper temperature bound.

    -

    Definition at line 100 of file partition_rauscher_thielemann.h.

    - @@ -193,12 +184,10 @@ Public Attributes

    Lower temperature bound.

    -

    Definition at line 102 of file partition_rauscher_thielemann.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_isotope_data.html b/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_isotope_data.html index 9d07b6f1..113a42a2 100644 --- a/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_isotope_data.html +++ b/docs/html/structgridfire_1_1partition_1_1_rauscher_thielemann_partition_function_1_1_isotope_data.html @@ -115,10 +115,7 @@ Public Attributes  Normalized G values on RT grid.
      -

    Detailed Description

    -
    -

    Definition at line 95 of file partition_rauscher_thielemann.h.

    -

    Member Data Documentation

    +

    Member Data Documentation

    ◆ ground_state_spin

    @@ -133,8 +130,6 @@ Public Attributes

    Spin of the isotope ground state.

    -

    Definition at line 96 of file partition_rauscher_thielemann.h.

    - @@ -151,12 +146,10 @@ Public Attributes

    Normalized G values on RT grid.

    -

    Definition at line 97 of file partition_rauscher_thielemann.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1partition_1_1record_1_1_rauscher_thielemann_partition_data_record.html b/docs/html/structgridfire_1_1partition_1_1record_1_1_rauscher_thielemann_partition_data_record.html index d671e56a..c1caddbb 100644 --- a/docs/html/structgridfire_1_1partition_1_1record_1_1_rauscher_thielemann_partition_data_record.html +++ b/docs/html/structgridfire_1_1partition_1_1record_1_1_rauscher_thielemann_partition_data_record.html @@ -109,7 +109,7 @@ $(function(){initNavTree('structgridfire_1_1partition_1_1record_1_1_rauscher_thi

    Packed binary record of Rauscher-Thielemann partition function data for an isotope. More...

    -

    #include <rauscher_thielemann_partition_data_record.h>

    +

    #include <rauscher_thielemann_partition_data_record.h>

    @@ -130,8 +130,6 @@ Public Attributes

    Packed binary record of Rauscher-Thielemann partition function data for an isotope.

    Each record stores the atomic number (Z), mass number (A), ground state spin J, and an array of 24 normalized G-values corresponding to fixed temperature grid points. This struct is read directly from embedded binary data and must remain tightly packed.

    Note
    Alignment is set to 1 byte to match the binary layout.
    - -

    Definition at line 17 of file rauscher_thielemann_partition_data_record.h.

    Member Data Documentation

    ◆ a

    @@ -147,8 +145,6 @@ Public Attributes

    Mass number.

    -

    Definition at line 19 of file rauscher_thielemann_partition_data_record.h.

    - @@ -165,8 +161,6 @@ Public Attributes

    Ground state spin.

    -

    Definition at line 20 of file rauscher_thielemann_partition_data_record.h.

    - @@ -183,8 +177,6 @@ Public Attributes

    Normalized g-values for the first 24 energy levels.

    -

    Definition at line 21 of file rauscher_thielemann_partition_data_record.h.

    - @@ -201,12 +193,10 @@ Public Attributes

    Atomic number.

    -

    Definition at line 18 of file rauscher_thielemann_partition_data_record.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1reaclib_1_1_reaction_record.html b/docs/html/structgridfire_1_1reaclib_1_1_reaction_record.html index eed87942..4e8d09c0 100644 --- a/docs/html/structgridfire_1_1reaclib_1_1_reaction_record.html +++ b/docs/html/structgridfire_1_1reaclib_1_1_reaction_record.html @@ -125,10 +125,7 @@ Public Attributes

    Public Attributes

    char products_str [128]
     
    -

    Detailed Description

    -
    -

    Definition at line 32 of file reaclib.cpp.

    -

    Member Data Documentation

    +

    Member Data Documentation

    ◆ chapter

    @@ -141,8 +138,6 @@ Public Attributes
    -

    Definition at line 33 of file reaclib.cpp.

    -
    @@ -157,8 +152,6 @@ Public Attributes
    -

    Definition at line 35 of file reaclib.cpp.

    -
    @@ -173,8 +166,6 @@ Public Attributes
    -

    Definition at line 37 of file reaclib.cpp.

    -
    @@ -189,8 +180,6 @@ Public Attributes
    -

    Definition at line 40 of file reaclib.cpp.

    -
    @@ -205,8 +194,6 @@ Public Attributes
    -

    Definition at line 34 of file reaclib.cpp.

    -
    @@ -221,8 +208,6 @@ Public Attributes
    -

    Definition at line 39 of file reaclib.cpp.

    -
    @@ -237,8 +222,6 @@ Public Attributes
    -

    Definition at line 36 of file reaclib.cpp.

    -
    @@ -253,12 +236,10 @@ Public Attributes
    -

    Definition at line 38 of file reaclib.cpp.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1reaction_1_1_rate_coefficient_set.html b/docs/html/structgridfire_1_1reaction_1_1_rate_coefficient_set.html index 417a9150..c20b0a6e 100644 --- a/docs/html/structgridfire_1_1reaction_1_1_rate_coefficient_set.html +++ b/docs/html/structgridfire_1_1reaction_1_1_rate_coefficient_set.html @@ -110,7 +110,7 @@ $(function(){initNavTree('structgridfire_1_1reaction_1_1_rate_coefficient_set.ht

    Holds the seven coefficients for the REACLIB rate equation. More...

    -

    #include <reaction.h>

    +

    #include <reaction.h>

    @@ -145,8 +145,6 @@ Friends

    Detailed Description

    Holds the seven coefficients for the REACLIB rate equation.

    This struct stores the parameters (a0-a6) used to calculate reaction rates as a function of temperature.

    - -

    Definition at line 33 of file reaction.h.

    Friends And Related Symbol Documentation

    ◆ operator<<

    @@ -185,8 +183,6 @@ Friends
    Returns
    The output stream.
    -

    Definition at line 48 of file reaction.h.

    -

    Member Data Documentation

    @@ -204,8 +200,6 @@ Friends

    Coefficient a0.

    -

    Definition at line 34 of file reaction.h.

    - @@ -222,8 +216,6 @@ Friends

    Coefficient a1.

    -

    Definition at line 35 of file reaction.h.

    - @@ -240,8 +232,6 @@ Friends

    Coefficient a2.

    -

    Definition at line 36 of file reaction.h.

    - @@ -258,8 +248,6 @@ Friends

    Coefficient a3.

    -

    Definition at line 37 of file reaction.h.

    - @@ -276,8 +264,6 @@ Friends

    Coefficient a4.

    -

    Definition at line 38 of file reaction.h.

    - @@ -294,8 +280,6 @@ Friends

    Coefficient a5.

    -

    Definition at line 39 of file reaction.h.

    - @@ -312,12 +296,10 @@ Friends

    Coefficient a6.

    -

    Definition at line 40 of file reaction.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html b/docs/html/structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html index ebe4fe34..470438bd 100644 --- a/docs/html/structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html +++ b/docs/html/structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html @@ -134,8 +134,6 @@ Public Attributes

    Detailed Description

    Functor for calculating the Jacobian matrix.

    This functor is used by the ODE solver to calculate the Jacobian matrix of the ODEs. It takes the current abundances as input and returns the Jacobian matrix.

    - -

    Definition at line 143 of file solver.h.

    Constructor & Destructor Documentation

    ◆ JacobianFunctor()

    @@ -179,8 +177,6 @@ Public Attributes -

    Definition at line 154 of file solver.h.

    -

    Member Function Documentation

    @@ -224,8 +220,6 @@ Public Attributes -

    Definition at line 215 of file solver.cpp.

    -

    Member Data Documentation

    @@ -243,8 +237,6 @@ Public Attributes

    The engine used to evaluate the network.

    -

    Definition at line 144 of file solver.h.

    - @@ -261,8 +253,6 @@ Public Attributes

    Density in g/cm^3.

    -

    Definition at line 146 of file solver.h.

    - @@ -279,13 +269,11 @@ Public Attributes

    Temperature in units of 10^9 K.

    -

    Definition at line 145 of file solver.h.

    -
    The documentation for this struct was generated from the following files: diff --git a/docs/html/structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_manager.html b/docs/html/structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_manager.html index f04fe281..6096c2da 100644 --- a/docs/html/structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_manager.html +++ b/docs/html/structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_manager.html @@ -146,10 +146,7 @@ Public Attributes

    Public Attributes

    double m_last_step_time = 1e-20
     
    -

    Detailed Description

    -
    -

    Definition at line 88 of file solver.h.

    -

    Constructor & Destructor Documentation

    +

    Constructor & Destructor Documentation

    ◆ RHSManager()

    @@ -192,8 +189,6 @@ Public Attributes -

    Definition at line 109 of file solver.h.

    -

    Member Function Documentation

    @@ -216,8 +211,6 @@ Public Attributes
    -

    Definition at line 189 of file solver.cpp.

    -
    @@ -239,8 +232,6 @@ Public Attributes
    -

    Definition at line 167 of file solver.cpp.

    -
    @@ -277,8 +268,6 @@ Public Attributes -

    Definition at line 152 of file solver.cpp.

    -

    Member Data Documentation

    @@ -302,8 +291,6 @@ Public Attributes
    -

    Definition at line 94 of file solver.h.

    -
    @@ -326,8 +313,6 @@ Public Attributes
    -

    Definition at line 93 of file solver.h.

    -
    @@ -344,8 +329,6 @@ Public Attributes

    The engine used to evaluate the network.

    -

    Definition at line 89 of file solver.h.

    - @@ -370,8 +353,6 @@ Public Attributes

    Last time the state was observed.

    -

    Definition at line 96 of file solver.h.

    - @@ -394,8 +375,6 @@ Public Attributes
    -

    Definition at line 101 of file solver.h.

    -
    @@ -412,8 +391,6 @@ Public Attributes

    Logger instance.

    -

    Definition at line 99 of file solver.h.

    - @@ -436,8 +413,6 @@ Public Attributes
    -

    Definition at line 100 of file solver.h.

    -
    @@ -454,8 +429,6 @@ Public Attributes

    Density in g/cm^3.

    -

    Definition at line 91 of file solver.h.

    - @@ -472,13 +445,11 @@ Public Attributes

    Temperature in units of 10^9 K.

    -

    Definition at line 90 of file solver.h.

    -
    The documentation for this struct was generated from the following files: diff --git a/docs/html/structstd_1_1hash_3_01gridfire_1_1_q_s_e_cache_key_01_4.html b/docs/html/structstd_1_1hash_3_01gridfire_1_1_q_s_e_cache_key_01_4.html index 207739ab..db738b4e 100644 --- a/docs/html/structstd_1_1hash_3_01gridfire_1_1_q_s_e_cache_key_01_4.html +++ b/docs/html/structstd_1_1hash_3_01gridfire_1_1_q_s_e_cache_key_01_4.html @@ -106,7 +106,7 @@ $(function(){initNavTree('structstd_1_1hash_3_01gridfire_1_1_q_s_e_cache_key_01_
    -

    #include <engine_multiscale.h>

    +

    #include <engine_multiscale.h>

    @@ -114,10 +114,7 @@ Public Member Functions

    Public Member Functions

     Computes the hash of a QSECacheKey for use in std::unordered_map.
     
    -

    Detailed Description

    -
    -

    Definition at line 109 of file engine_multiscale.h.

    -

    Member Function Documentation

    +

    Member Function Documentation

    ◆ operator()()

    @@ -150,12 +147,10 @@ Public Member Functions
    Returns
    The pre-computed hash value of the key.
    -

    Definition at line 115 of file engine_multiscale.h.

    -
    The documentation for this struct was generated from the following file: diff --git a/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_logical_reaction_set_01_4.html b/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_logical_reaction_set_01_4.html index 622e8d9c..e79c698c 100644 --- a/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_logical_reaction_set_01_4.html +++ b/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_logical_reaction_set_01_4.html @@ -111,10 +111,7 @@ Public Member Functions size_t operator() (const gridfire::reaction::LogicalReactionSet &s) const noexcept   -

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    The documentation for this struct was generated from the following file: diff --git a/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_01_4.html b/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_01_4.html index 3408c988..b02a6d37 100644 --- a/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_01_4.html +++ b/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_01_4.html @@ -111,10 +111,7 @@ Public Member Functions size_t operator() (const gridfire::reaction::Reaction &r) const noexcept   -

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    The documentation for this struct was generated from the following file: diff --git a/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_set_01_4.html b/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_set_01_4.html index 36301097..ee979f63 100644 --- a/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_set_01_4.html +++ b/docs/html/structstd_1_1hash_3_01gridfire_1_1reaction_1_1_reaction_set_01_4.html @@ -111,10 +111,7 @@ Public Member Functions size_t operator() (const gridfire::reaction::ReactionSet &s) const noexcept   -

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    The documentation for this struct was generated from the following file: diff --git a/docs/html/types_2bindings_8cpp.html b/docs/html/types_2bindings_8cpp.html index e8254db5..7dfbe325 100644 --- a/docs/html/types_2bindings_8cpp.html +++ b/docs/html/types_2bindings_8cpp.html @@ -107,11 +107,9 @@ $(function(){initNavTree('types_2bindings_8cpp.html',''); initResizable(true); }
    #include <pybind11/pybind11.h>
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    #include <pybind11/pybind11.h>
    #include <pybind11/stl.h>
    #include <pybind11/stl_bind.h>
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    diff --git a/docs/html/utils_2bindings_8h.html b/docs/html/utils_2bindings_8h.html index b7a63188..2e0c6bf8 100644 --- a/docs/html/utils_2bindings_8h.html +++ b/docs/html/utils_2bindings_8h.html @@ -105,9 +105,7 @@ $(function(){initNavTree('utils_2bindings_8h.html',''); initResizable(true); });
    #include <pybind11/pybind11.h>
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    diff --git a/docs/static/mainpage.md b/docs/static/mainpage.md index 4fc59d7d..9dd28db2 100644 --- a/docs/static/mainpage.md +++ b/docs/static/mainpage.md @@ -1,64 +1,243 @@ ![GridFire Logo](../../assets/logo/GridFire.png) ---- -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. GridFire is primarily focused on modeling the most -relevant burning stages for stellar evolution modeling. Currently, there is limited support for inverse reactions. -Therefore, GridFire has a limited set of tools to evolves a fusing plasma in NSE; however, -this is not the primary focus of the library and has therefor not had significant development. For those interested in -modeling super nova, neutron star mergers, or other -high-energy astrophysical phenomena, we **strongly** recomment -using [SkyNet](https://bitbucket.org/jlippuner/skynet/src/master/). +# Introduction +GridFire is a C++ library designed to perform general nuclear network +evolution. It is part of the larger SERiF project within the 4D-STAR +collaboration. GridFire is primarily focused on modeling the most relevant +burning stages for stellar evolution modeling. Currently, there is limited +support for inverse reactions. Therefore, GridFire has a limited set of tools +to evolves a fusing plasma in NSE; however, this is not the primary focus of +the library and has therefor not had significant development. For those +interested in modeling super nova, neutron star mergers, or other high-energy +astrophysical phenomena, we **strongly** recomment using +[SkyNet](https://bitbucket.org/jlippuner/skynet/src/master/). -**Design Philosophy and Workflow:** -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 multiscale 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. +## Design Philosophy and Workflow +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. A GraphNetwork uses [JINA +Reaclib](https://reaclib.jinaweb.org/index.php) reaction rates ([Cyburt et al., ApJS 189 +(2010) 240.](https://iopscience.iop.org/article/10.1088/0067-0049/189/1/240)) along +with a dynamically constructed network topology. To manage the inherent +stiffness and multiscale 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. ## Funding GridFire is a part of the 4D-STAR collaboration. -4D-STAR is funded by European Research Council (ERC) under the Horizon Europe programme (Synergy Grant agreement No. -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 Council. +4D-STAR is funded by European Research Council (ERC) under the Horizon Europe +programme (Synergy Grant agreement No. 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 Council. -## Build and Installation Instructions +# Usage + +## Python installation +By far the easiest way to install is with pip. This will install either +pre-compiled wheels or, if your system has not had a wheel compiled for it, it +will try to build locally (this may take **a long time**). The python bindings +are just that and should maintain nearly the same speed as the C++ code. End +users are strongly encorages to use the python module rather than the C++ code. + +### pypi +Installing from pip is as simple as +```bash +pip install gridfire +``` + +These wheels have been compiled on many systems + +| Version | Platform | Architecture | CPython Versions | PyPy Versions | +| ------- | -------- | ------------ | ---------------------------------------------------------- | ------------- | +| 0.5.0 | macOS | arm64 | 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) | 3.10, 3.11 | +| 0.5.0 | Linux | aarch64 | 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) | 3.10, 3.11 | +| 0.5.0 | Linux | x86\_64 | 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) | 3.10, 3.11 | + +> **Note**: Currently macOS x86\_64 does **not** have a precompiled wheel. Due +> to that platform being phased out it is likely that there will never be +> precompiled wheels or releases for it. + +> **Note:** macOS wheels were targeted to MacOS 12 Monterey and should work on +> any version more recent than that (at least as of August 2025). + +> **Note:** Linux wheels were compiled using manylinux_2_28 and are expected to +> work on Debian 10+, Ubuntu 18.10+, Fedora 29+, or CentOS/RHEL 8+ + +> **Note:** If your system does not have a prebuilt wheel the source +> distribution will download from pypi and try to build. This may simply not +> work if you do not have the correct system dependencies installed. If it +> fails the best bet is to try to build boost >= 1.83.0 from source and install +> (https://www.boost.org/) as that is the most common broken dependency. + +### source +The user may also build the python bindings directly from source + +```bash +git clone https://github.com/4D-STAR/GridFire +cd GridFire +pip install . +``` + +> **Note:** that if you do not have all system dependencies installed this will +> fail, the steps in further sections address these in more detail. + +### source for developers +If you are a developer and would like an editable and incrimental python +install `meson-python` makes this very easy + +```bash +git clone https://github.com/4D-STAR/GridFire +cd GridFire +pip install -e . --no-build-isolation -vv +``` + +This will generate incrimental builds whenever source code changes and you run +a python script automartically (note that since `meson setup` must run for each +of these it does still take a few seconds to recompile regardless of how small +a source code change you have made). It is **strongly** reccomended that +developers use this approach and end users *do not*. + + +## Automatic Build and Installation +### Script Build and Installation Instructions + +The easiest way to build GridFire is using the `install.sh` or `install-tui.sh` +scripts in the root directory. To use these scripts, simply run: + +```bash +./install.sh +# or +./install-tui.sh +``` +The regular installation script will select a standard "ideal" set of build +options for you. If you want more control over the build options, you can use +the `install-tui.sh` script, which will provide a text-based user interface to +select the build options you want. + +Generally, both are intended to be easy to use and will prompt you +automatically to install any missing dependencies. + + +### Currently known good platforms +The installation script has been tested and found to work on clean +installations of the following platforms: +- MacOS 15.3.2 (Apple Silicon + brew installed) +- Fedora 42.0 (aarch64) +- Ubuntu 25.04 (aarch64) +- Ubuntu 22.04 (X86_64) + +> **Note:** On Ubuntu 22.04 the user needs to install boost libraries manually +> as the versions in the Ubuntu repositories +> are too old. The installer automatically detects this and will instruct the +> user in how to do this. + +## Manual Build Instructions ### Prerequisites +These only need to be manually installed if the user is not making use of the +`install.sh` or `install-tui.sh` + +#### Required - C++ compiler supporting C++23 standard - Meson build system (>= 1.5.0) -- Python 3.10 or newer +- Python 3.8 or newer +- CMake 3.20 or newer +- ninja 1.10.0 or newer - Python packages: `meson-python>=0.15.0` -- Boost libraries (>= 1.75.0) installed system-wide +- Boost libraries (>= 1.83.0) installed system-wide (or at least findable by + meson with pkg-config) -> **Note:** Boost is the only external library dependency; no additional libraries are required beyond a C++ compiler, Meson, Python, and Boost. +#### Optional +- dialog (used by the `install.sh` script, not needed if using pip or meson + directly) +- pip (used by the `install.sh` script or by calling pip directly, not needed + if using meson directly) -> **Note:** Windows is not supported at this time and *there are no plans to support it in the future*. Windows users are encouraged to use WSL2 or a Linux VM. +> **Note:** Boost is the only external library dependency used by GridFire directly. + +> **Note:** Windows is not supported at this time and *there are no plans to +> support it in the future*. Windows users are encouraged to use WSL2 or a +> Linux VM. + +> **Note:** If `install-tui.sh` is not able to find a usable version of boost +> it will provide directions to fetch, compile, and install a usable version. + +### Install Scripts +GridFire ships with an installer (`install.sh`) which is intended to make the +process of installation both easier and more repetable. + +#### Ease of Installation +Both scripts are intended to automate installation more or less completly. This +includes dependency checking. In the event that a dependency cannot be found +they try to install (after explicitly asking for user permission). If that does +not work they will provide a clear message as to what went wrong. + +#### Reproducibility +The TUI mode provides easy modification of meson build system and compiler +settings which can then be saved to a config file. This config file can then be +loaded by either tui mode or cli mode (with the `--config`) flag meaning that +build configurations can be made and reused. Note that this is **not** a +deterministicly reproducible build system as it does not interact with any +system dependencies or settings, only meson and compiler settings. + +#### Examples + +##### TUI config and saving +[![asciicast](https://asciinema.org/a/ahIrQPL71ErZv5EKKujfO1ZEW.svg)](https://asciinema.org/a/ahIrQPL71ErZv5EKKujfO1ZEW) + +##### TUI config loading and meson setup +[![asciicast](https://asciinema.org/a/zGdzt9kYsETltG0TJKC50g3BK.svg)](https://asciinema.org/a/zGdzt9kYsETltG0TJKC50g3BK) + +##### CLI config loading, setup, and build +[![asciicast](https://asciinema.org/a/GYaWTXZbDJRD4ohde0s3DkFMC.svg)](https://asciinema.org/a/GYaWTXZbDJRD4ohde0s3DkFMC) + + +> **Note:** `install-tui.sh` is simply a script which calles `install.sh` with +> the `--tui` flag. You can get the exact same results by running `install.sh +> --tui`. + +> **Note:** Call `install.sh` with the `--help` or `--h` flag to see command +> line options + +> **Note:** `clang` tends to compile GridFire much faster than `gcc` thus why I +> select it in the above asciinema recording. ### 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 - ``` +```bash +sudo apt-get update +sudo apt-get install -y build-essential meson python3 python3-pip libboost-all-dev +``` + +> **Note:** Depending on the ubuntu version you have the libboost-all-dev +> libraries may be too old. If this is the case refer to the boost +> documentation for how to download and install a version `>=1.83.0` + +> **Note:** On recent versions of ubuntu python has switched to being +> externally managed by the system. We **strongly** recomend that if you +> install manaully all python pacakges are installed inside some kind of +> virtual enviroment (e.g. `pyenv`, `conda`, `python-venv`, etc...). When using +> the installer script this is handled automatically using `python-venv`. - **Fedora/CentOS/RHEL:** - ```bash - sudo dnf install -y gcc-c++ meson python3 python3-pip boost-devel - ``` +```bash +sudo dnf install -y gcc-c++ meson python3 python3-pip boost-devel +``` - **macOS (Homebrew):** - ```bash - brew update && \ - brew install boost meson python - ``` +```bash +brew update +brew install boost meson python +``` ### Building the C++ Library ```bash @@ -66,54 +245,104 @@ meson setup build meson compile -C build ``` +#### Clang vs. GCC +As noted above `clang` tends to compile GridFire much faster than `gcc`. If +your system has both `clang` and `gcc` installed you may force meson to use +clang via enviromental variables + +```bash +CC=clang CXX=clang++ meson setup build_clang +meson compile -C build_clang +``` + ### 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 . -``` +### Minimum compiler versions +GridFire uses C++23 features and therefore only compilers and standard library +implimentations which support C++23 are supported. Generally we have found that +`gcc >= 13.0.0` or `clang >= 16.0.0` work well. -### 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 a series of composable modules, each responsible for a specific aspect of nuclear reaction network modeling. The core components include: +GridFire is organized into a series of composable modules, each responsible for +a specific aspect of nuclear reaction network modeling. The core components +include: -- **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. -- **Reaction Module:** Parses and manages Reaclib reaction rate data, providing temperature- and density-dependent rate evaluations. -- **Partition Module:** Implements partition functions (e.g., `GroundStatePartitionFunction`, `RauscherThielemannPartitionFunction`) to weight reaction rates based on nuclear properties. -- **Solver Module:** Defines numerical integration strategies (e.g., `DirectNetworkSolver`) for solving the stiff ODE systems arising from reaction networks. -- **Python Interface:** Exposes *almost* all C++ functionality to Python, allowing users to define compositions, configure engines, and run simulations directly from Python scripts. +- **Engine Module:** Core interfaces and implementations (e.g., `GraphEngine`) + that evaluate reaction network rate equations and energy generation. Also + implimented `Views` submodule. +- **Engine::Views Module:** Composable engine optimization and modification + (e.g. `MultiscalePartitioningEngineView`) which can be used to make a problem + more tractable or applicable. +- **Screening Module:** Implements nuclear reaction screening corrections (e.g. + `WeakScreening` ([Salpeter, + 1954](https://adsabs.harvard.edu/full/1954AuJPh...7..373S)), `BareScreening`) + affecting reaction rates. +- **Reaction Module:** Parses and manages Reaclib reaction rate data, providing + temperature- and density-dependent rate evaluations. +- **Partition Module:** Implements partition functions (e.g., + `GroundStatePartitionFunction`, `RauscherThielemannPartitionFunction` + ([Rauscher & Thielemann, + 2000](https://www.sciencedirect.com/science/article/pii/S0092640X00908349?via%3Dihub])) + to weight reaction rates based on nuclear properties. +- **Solver Module:** Defines numerical integration strategies (e.g., + `DirectNetworkSolver`) for solving the stiff ODE systems arising from reaction + networks. +- **Python Interface:** Exposes *almost* all C++ functionality to Python, + allowing users to define compositions, configure engines, and run simulations + directly from Python scripts. -Generally a user will start by selecting a base engine (currently we only offer `GraphEngine`), which constructs the -full reaction network graph from a given composition. The user can then apply various engine views to adapt the network -topology, such as partitioning fast and slow reactions, adaptively culling low-flow pathways, or priming the network -with specific species. Finally, a numerical solver is selected to integrate the network over time, producing updated +Generally a user will start by selecting a base engine (currently we only offer +`GraphEngine`), which constructs the full reaction network graph from a given +composition. The user can then apply various engine views to adapt the network +topology, such as partitioning fast and slow reactions, adaptively culling +low-flow pathways, or priming the network with specific species. Finally, a +numerical solver is selected to integrate the network over time, producing +updated abundances and diagnostics. +## Engines +GridFire is, at its core, based on a series of `Engines`. These are constructs +which know how to report information on series of ODEs which need to be solved +to evolver abundnances. The important thing to understand about `Engines` is +that they contain all of the detailed physics GridFire uses. For example a +`Solver` takes an `Engine` but does not compute physics itself. Rather, it asks +the `Engine` for stuff like the jacobian matrix, stoichiometry, nuclear energy +generation rate, and change in abundance with time. + +Refer to the API documentation for the exact interface which an `Engine` must +impliment to be compatible with GridFire solvers. + +Currently we only impliment `GraphEngine` which is intended to be a very general and +adaptable `Engine`. + +### GraphEngine +In GridFire the `GraphEngine` will generally be the most fundamental building +block of a nuclear network. A `GraphEngine` represents a directional hypergraph +connecting some set of atomic species through reactions listed in the [JINA +Reaclib database](https://reaclib.jinaweb.org/index.php). + +`GraphEngine`s are constructed from a seed composition of species from which +they recursivley expand their topology outward, following known reaction +pathways and adding new species to the tracked list as they expand. + + ### GraphEngine Configuration Options -GraphEngine exposes runtime configuration methods to tailor network construction and rate evaluations: +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`. + - `composition`: The initial seed composition to start network construction from. + - `BuildDepthType` (`Full`, `Shallow`, `SecondOrder`, etc...): controls + number of recursions used to construct the network topology. Can either be an + member of the `NetworkBuildDepth` enum or an integerl. + - `partition::PartitionFunction`: Partition function used when evlauating + detailed balance for inverse rates. - **setPrecomputation(bool precompute):** - Enable/disable caching of reaction rates and stoichiometric data at initialization. @@ -129,70 +358,175 @@ GraphEngine exposes runtime configuration methods to tailor network construction ### Available Partition Functions -| Function Name | Identifier | Description | +| Function Name | Identifier / Enum | Description | |---------------------------------------|--------------------------|-----------------------------------------------------------------| -| `GroundStatePartitionFunction` | "GroundState" | Weights using nuclear ground-state spin factors. | -| `RauscherThielemannPartitionFunction` | "RauscherThielemann" | Interpolates normalized g-factors per Rauscher & Thielemann. | +| `GroundStatePartitionFunction` | "GroundState" | Weights using nuclear ground-state spin factors. | +| `RauscherThielemannPartitionFunction` | "RauscherThielemann" | Interpolates normalized g-factors per Rauscher & Thielemann. | +| `CompositePartitionFunction` | "Composite" | Combines multiple partition functions for situations where different partitions functions are used for different domains | + +### AutoDiff +One of the primary tasks any engine must accomplish is to report the jacobian +matrix of the system to the solver. `GraphEngine` uses `CppAD`, a C++ auto +differentiation library, to generate analytic jacobian matricies very +efficiently. + + +## Reaclib in GridFire +All reactions in JINA Reaclib which only include reactants iron and lighter +were downloaded on June 17th, 2025 where the most recent documented change on +the JINA Reaclib site was on June 24th, 2021. + +All of thes reactions have been compiled into a header file which is then +statically compiled into the gridfire binaries (specifically into +lib_reaction_reaclib.cpp.o). This does increase the binary size by a few MB; +however, the benafit is faster load times and more importantly no need for end +users to manage resource files. + +If a developer wants to add new reaclib reactions we include a script at +`utils/reaclib/format.py` which can injest a reaclib data file and produce the +needed header file. More details on this process are included in +`utils/reaclib/readme.md` -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: +The GridFire engine supports multiple engine view strategies to adapt or +restrict network topology. Generally when extending GridFire the approach is +likely to be one of adding new `EngineViews`. | 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 | +| FileDefinedEngineView | Load a defined engine view from a file using some parser | Same as DefinedEngineView but loads from a file | Same as DefinedEngineView | 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| +| NetworkPrimingEngineView | Primes the network with an initial species or set of species for ignition studies| Single-species ignition and network priming | 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. +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. +### A Note about composability +There are certain functions for which it is expected that a call to an engine +view will propegate the result down the chain of engine views, eventually +reaching the base engine (e.g. `DynamicEngine::update`). We do not strongly +enforce this as it is not hard to contrive a situation where that is not the +mose useful behavior; however, we do strongly encorage developers to think +carefully about passing along calls to base engine methods when implimenting +new views. ## 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. +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<EngineT>: +All GridFire solvers impliment the abstract strategy templated by +`NetworkSolverStrategy` which enforces only that there is some `evaluate` +method with the following signature + +```cpp +NetOut evaluate(const NetIn& netIn); +``` +Which is intended to integrate some network over some time and returns updated +abundances, temperature, density, and diagnostics. + +### NetIn and NetOut +GridFire solvers use a unified input and output type for their public interface +(though as developers will quickly learn, internally these are immediatly +broken down into simpler data structures). All solvers expect a `NetIn` struct +for the input type to the `evaluate` method and return a `NetOut` struct. + +#### NetIn +A `NetIn` struct contains +- The composition to start the timestep at. (`NetIn::composition`) +- The temperature in Kelvin (`NetIn::temperature`) +- The density in g/cm^3 (`NetIn::density`) +- The max time to evolve the network too in seconds (`NetIn::tMax`) +- The initial timestep to use in seconds (`NetIn::dt0`) +- The initial energy in the system in ergs (`NetIn::energy`) + +>**Note:** It is often useful to set `NetIn::dt0` to something *very* small and +>let an iterative timestepper push the timestep up. Often for main sequence +>burning I use ~1e-12 for dt0 + +>**Note:** The composition must be a `fourdst::composition::Composition` +>object. This is made avalible through the `foursdt` library and the +>`fourdst/composition/Composition.h` header. `fourdst` is installed +>automatically with GridFire + +>**Note:** In Python composition comes from `fourdst.composition.Composition` +>and similarly is installed automatically when building GridFire python +>bindings. + +#### NetOut +A `NetOut` struct contains +- The final composition after evolving to `tMax` (`NetOut::composition`) +- The number of steps the solver took to evolve to `tmax` (`NetOut::num_steps`) +- The final energy generated by the network while evolving to `tMax` + (`NetOut::energy`) + +>**Note:** Currently `GraphEngine` only considers energy due to nuclear mass +>defect and not neutrino loss. -- **NetworkSolverStrategy<EngineT>**: 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`, 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. +- **Integrator:** Implicit Rosenbrock4 scheme (order 4) via `Boost.Odeint`’s + `rosenbrock4`, optimized for stiff reaction networks with adaptive step + size control using configurable absolute and relative tolerances. +- **Jacobian Assembly:** Asks the base engine for the Jacobian Matrix +- **RHS Evaluation:** Assk the base engine for RHS of the abundance evolution + equations +- **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 loggers, which run in a + seperate non blocking thread, capture 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`. +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. + - 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. +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. +- **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. +- **Callback observer support:** Currently we use an observer built into our + `RHSManager` (`RHSManager::observe`); however, we intend to inlucde support for + custom, user defined, observer method. -These strategies can be developed by inheriting from `NetworkSolverStrategy` and registering against the same engine types without modifying existing engine code. +These strategies can be developed by inheriting from `NetworkSolverStrategy` +and registering against the same engine types without modifying existing engine +code. -## Usage Examples +## 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. -### C++ Example: GraphEngine Initialization + +# Usage Examples + +## C++ + +### GraphEngine Initialization ```cpp #include "gridfire/engine/engine_graph.h" #include "fourdst/composition/composition.h" @@ -202,7 +536,7 @@ fourdst::composition::Composition comp; gridfire::GraphEngine engine(comp); ``` -### C++ Example: Adaptive Network View +### Adaptive Network View ```cpp #include "gridfire/engine/views/engine_adaptive.h" #include "gridfire/engine/engine_graph.h" @@ -213,51 +547,49 @@ gridfire::GraphEngine baseEngine(comp); gridfire::AdaptiveEngineView adaptiveView(baseEngine); ``` -### Python Example -```python -import gridfire +### Composition Initialization +```cpp +#include "fourdst/composition/composition.h" +#include +#include +#include -from fourdst.composition import Composition +fourdst::composition::Composition comp; -symbols = ["H-1", ...] -X = [0.708, ...] +std::vector symbols = {"H-1", "He-4", "C-12"}; +std::vector massFractions = {0.7, 0.29, 0.01}; -comp = Composition() -comp.registerSymbols(symbols) -comp.setMassFraction(X) -comp.finalize(true) -# Initialize GraphEngine with predefined composition -engine = gridfire.GraphEngine(comp) -netIn = gridfire.types.NetIn -netIn.composition = comp -netIn.tMax = 1e-3 -netIn.temperature = 1.5e7 -netIn.density = 1.6e2 -netIn.dt0 = 1e-12 +comp.registerSymbols(symbols); +comp.setMassFraction(symbols, massFractions); -# Perform one integration step -netOut = engine.evaluate(netIn) -print(netOut) +comp.finalize(true); + +std::cout << comp << std::endl; ``` -More detailed python usage can be found [here](usage.md) +### Common Workflow Example -## Common Workflow Example - -A representative workflow often composes multiple engine views to balance accuracy, stability, and performance when integrating stiff nuclear networks: +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 "gridfire/engine/engine.h" // Unified header for real usage #include "fourdst/composition/composition.h" // 1. Define initial composition fourdst::composition::Composition comp; + +std::vector symbols = {"H-1", "He-4", "C-12"}; +std::vector massFractions = {0.7, 0.29, 0.01}; + +comp.registerSymbols(symbols); +comp.setMassFraction(symbols, massFractions); + +comp.finalize(true); + // 2. Create base network engine (full reaction graph) -gridfire::GraphEngine baseEngine(comp); +gridfire::GraphEngine baseEngine(comp, NetworkBuildDepth::SecondOrder) // 3. Partition network into fast/slow subsets (reduces stiffness) gridfire::MultiscalePartitioningEngineView msView(baseEngine); @@ -279,22 +611,73 @@ NetIn input{ // 7. Execute integration NetOut output = solver.evaluate(input); +std::cout << "Final results are: " << output << std::endl; ``` -**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. +#### 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. +This layered approach enhances stability for stiff networks while maintaining +accuracy and performance. -## Related Projects +## Python +The python bindings intentionally look **very** similar to the C++ code. +Generally all examples can be adapted to python by replacing includes of paths +with imports of modules such that + +`#include "gridfire/engine/GraphEngine.h` becomes `import gridfire.engine.GraphEngine` + +All GridFire C++ types have been bound and can be passed around as one would expect. + +### Common Workflow Examople +This example impliments the same logic as the above C++ example +```python +import gridfire + + +from fourdst.composition import Composition + +symbols = ["H-1", ...] +X = [0.7, ...] + +comp = Composition() +comp.registerSymbols(symbols) +comp.setMassFraction(X) +comp.finalize(true) +# Initialize GraphEngine with predefined composition +engine = gridfire.GraphEngine(comp) +netIn = gridfire.types.NetIn +netIn.composition = comp +netIn.tMax = 1e-3 +netIn.temperature = 1.5e7 +netIn.density = 1.6e2 +netIn.dt0 = 1e-12 + +# Perform one integration step +netOut = engine.evaluate(netIn) +print(netOut) +``` + + + +# 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. +- [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

    Functions

    void register_utils_bindings (pybind11::module &m)