perf(precomputation): cleaned up allocations

recovered about 5% execution time
build(.gitignore): .whl added
2025-12-02 13:09:19 -05:00 · 2025-12-02 10:04:42 -05:00 · 2025-12-02 10:04:00 -05:00 · 2025-12-01 13:28:25 -05:00 · 2025-12-01 09:59:43 -05:00 · 2025-12-01 09:59:22 -05:00
3310 changed files with 299237 additions and 101047 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -77,10 +77,11 @@ subprojects/liblogging/
 subprojects/eigen-*/
 subprojects/fourdst/
 subprojects/libplugin/
-subprojects/minizip-ng-4.0.10/
+subprojects/minizip-ng-*/
 subprojects/cvode-*/
 subprojects/kinsol-*/
 subprojects/CLI11-*/
 subprojects/openssl-*/
 *.fbundle
 *.wraplock
@@ -94,7 +95,9 @@ libcomposition.wrap
 libconfig.wrap
 libconstants.wrap
 liblogging.wrap
 libplugin.wrap
 minizip-ng.wrap
 openssl.wrap
 .vscode/
@@ -116,3 +119,7 @@ meson-boost-test/
 *.json
 *.xml
 *_pynucastro_network.py
 cross/python_includes
 *.whl
--- a/2
+++ b/2
@@ -48,7 +48,7 @@ PROJECT_NAME           = GridFire
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
-PROJECT_NUMBER         = v0.7.0_rc2
+PROJECT_NUMBER         = v0.7.4_rc2
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewers a
--- a/README.md
+++ b/README.md
@@ -15,53 +15,6 @@
 ---
 # Table of Contents
 - [Introduction](#introduction)
  - [Design Philosophy and Workflow](#design-philosophy-and-workflow)
  - [Funding](#funding)
 - [Usage](#usage)
  - [Python installation](#python-installation)
    - [pypi](#pypi)
    - [source](#source)
    - [source for developers](#source-for-developers)
    - [patching shared object files](#patching-shared-object-files)
  - [Automatic Build and Installation](#automatic-build-and-installation)
    - [Script Build and Installation Instructions](#script-build-and-installation-instructions)
    - [Currently, known good platforms](#currently-known-good-platforms)
  - [Manual Build Instructions](#manual-build-instructions)
    - [Prerequisites](#prerequisites)
    - [Install Scripts](#install-scripts)
    - [Dependency Installation on Common Platforms](#dependency-installation-on-common-platforms)
    - [Building the C++ Library](#building-the-c-library)
    - [Installing the Library](#installing-the-library)
    - [Minimum compiler versions](#minimum-compiler-versions)
 - [Code Architecture and Logical Flow](#code-architecture-and-logical-flow)
 - [Engines](#engines)
  - [GraphEngine](#graphengine)
  - [GraphEngine Configuration Options](#graphengine-configuration-options)
  - [Available Partition Functions](#available-partition-functions)
  - [AutoDiff](#autodiff)
 - [Reaclib in GridFire](#reaclib-in-gridfire)
 - [Engine Views](#engine-views)
  - [A Note about composability](#a-note-about-composability)
 - [Numerical Solver Strategies](#numerical-solver-strategies)
  - [NetworkSolverStrategy&lt;EngineT&gt;](#networksolverstrategyenginet)
  - [NetIn and NetOut](#netin-and-netout)
  - [DirectNetworkSolver (Implicit Rosenbrock Method)](#directnetworksolver-implicit-rosenbrock-method)
  - [Algorithmic Workflow in DirectNetworkSolver](#algorithmic-workflow-in-directnetworksolver)
  - [Future Solver Implementations](#future-solver-implementations)
 - [Python Extensibility](#python-extensibility)
 - [Usage Examples](#usage-examples)
  - [C++](#c)
    - [GraphEngine Initialization](#graphengine-initialization)
    - [Adaptive Network View](#adaptive-network-view)
    - [Composition Initialization](#composition-initialization)
    - [Common Workflow Example](#common-workflow-example)
    - [Callback Example](#callback-example)
  - [Python](#python)
    - [Common Workflow Example](#common-workflow-example-1)
    - [Python callbacks](#python-callbacks)
 - [Related Projects](#related-projects)
 # Introduction
 GridFire is a C++ library designed to perform general nuclear network
@@ -119,7 +72,7 @@ These wheels have been compiled on many systems
 | Version   | Platform | Architecture | CPython Versions                                           | PyPy Versions |
 |-----------|----------|--------------|------------------------------------------------------------|---------------|
- | 0.7.0_rc1 | macOS    | arm64        | 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) | 3.10, 3.11    |
+| 0.7.0_rc1 | macOS    | arm64        | 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) | 3.10, 3.11    |
 | 0.7.0_rc1 | Linux    | aarch64      | 3.8, 3.9, 3.10, 3.11, 3.12, 3.13 (std & t), 3.14 (std & t) | 3.10, 3.11    |
 | 0.7.0_rc1 | 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    |
 | 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    |
@@ -387,8 +340,8 @@ include:
 - **io Module:** Defines shared interface for parsing network data from files
 - **trigger Module:** Defines interface for complex trigger logic so that repartitioning can be followed.
 - **Policy Module:** Contains "policies" which are small modular units of code that enforce certain contracts.
-For example the `ProtonProtonReactionChainPolicy` enforces than an engine must include at least all the reactions
+  For example the `ProtonProtonReactionChainPolicy` enforces than an engine must include at least all the reactions
-in the proton-proton chain. This module exposes the primary construction interface for users. I.e. select a policy (such as `MainSequencePolicy`), provide a composition, and get back an engine which satisfies that policy.
+  in the proton-proton chain. This module exposes the primary construction interface for users. I.e. select a policy (such as `MainSequencePolicy`), provide a composition, and get back an engine which satisfies that policy.
 - **Python Interface:** Exposes *almost* all C++ functionality to Python,
  allowing users to define compositions, configure engines, and run simulations
  directly from Python scripts.
@@ -564,11 +517,11 @@ A `NetIn` struct contains
 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`
+- The final specific energy generated by the network while evolving to `tMax` (`NetOut::energy`) [erg/g]
-  (`NetOut::energy`)
+- The derivative of energy with respect to temperature at the end of the evolution (`NetOut::dEps_dT`)
-
+- The derivative of energy with respect to density at the end of the evolution (`NetOut::dEps_dRho`)
->**Note:** Currently `GraphEngine` only considers energy due to nuclear mass
+- The total specific energy lost to neutrinos while evolving to `tMax` (`NetOut::total_neutrino_loss`) [erg/g]
->defect and not neutrino loss.
+- The total flux of neutrinos while evolving to `tMax` (`NetOut::total_neutrino_flux`)
 ### CVODESolverStrategy
@@ -793,8 +746,8 @@ All GridFire C++ types have been bound and can be passed around as one would exp
 The syntax for registration is very similar to C++. There are a few things to note about this more robust example
- 1. Note how I use a callback and a log object to store the state of the simulation at each timestep.
+1. Note how I use a callback and a log object to store the state of the simulation at each timestep.
- 2. If you have tools such as mypy installed you will see that the python bindings are strongly typed. This is
+2. If you have tools such as mypy installed you will see that the python bindings are strongly typed. This is
   intentional to help users avoid mistakes when writing code.
 ```python
 from fourdst.composition import Composition
@@ -962,6 +915,8 @@ int main() {
    double energy_out;
    double dEps_dT;
    double dEps_dRho;
    double neutrino_energy_loss;
    double neutrino_flux;
    double mass_lost;
    ret = gf_evolve(
@@ -975,7 +930,10 @@ int main() {
        Y_out,
        &energy_out,
        &dEps_dT,
-        &dEps_dRho, &mass_lost
+        &dEps_dRho,
        &neutrino_energy_loss,
        &neutrino_flux,
        &mass_lost
    );
    GF_CHECK_RET_CODE(ret, gf_context, "Evolution");
@@ -1058,7 +1016,7 @@ program main
    ! Output buffers
    real(c_double), dimension(8) :: Y_out
-    real(c_double) :: energy_out, dedt, dedrho, dmass
+    real(c_double) :: energy_out, dedt, dedrho, nu_E_loss, nu_flux, dmass
    ! Thermodynamic Conditions (Solar Core-ish)
    real(c_double) :: T = 1.5e7      ! 15 Million K
@@ -1082,7 +1040,7 @@ program main
    ! --- 5. Evolve ---
    print *, "Evolving system (dt =", dt, "s)..."
-    call net%evolve(Y_in, T, rho, dt, Y_out, energy_out, dedt, dedrho, dmass, ierr)
+    call net%evolve(Y_in, T, rho, dt, Y_out, energy_out, dedt, dedrho, nu_E_loss, nu_flux, dmass, ierr)
    if (ierr /= 0) then
        print *, "Evolution Failed with error code: ", ierr
--- a/build-config/fourdst/meson.build
+++ b/build-config/fourdst/meson.build
@@ -1,13 +1,33 @@
 # bring in all of the fourdst utility repositories
-fourdst_sp = subproject('fourdst')
+fourdst_build_lib_all = true
 if get_option('unity-safe')
    fourdst_build_lib_all=false
 endif
 fourdst_sp = subproject('fourdst',
                        default_options:
                            ['build-tests=' + get_option('build-tests').to_string(),
                             'build-python=' + get_option('build-python').to_string(),
                             'build-lib-all=' + fourdst_build_lib_all.to_string(),
                             'pkg-config=' + get_option('pkg-config').to_string(),
                             'build-lib-log=true'
                            ]
 )
 composition_dep = fourdst_sp.get_variable('composition_dep')
 log_dep = fourdst_sp.get_variable('log_dep')
 const_dep = fourdst_sp.get_variable('const_dep')
 config_dep = fourdst_sp.get_variable('config_dep')
 if not get_option('unity-safe')
    plugin_dep = fourdst_sp.get_variable('plugin_dep')
 endif
 libcomposition = fourdst_sp.get_variable('libcomposition')
 libconst = fourdst_sp.get_variable('libconst')
 libconfig = fourdst_sp.get_variable('libconfig')
 liblogging = fourdst_sp.get_variable('liblogging')
 if not get_option('unity-safe')
    libplugin = fourdst_sp.get_variable('libplugin')
 endif
--- a/build-config/libplugin/meson.build
+++ b/build-config/libplugin/meson.build
@@ -1,5 +0,0 @@
 libplugin_sp = subproject('libplugin')
 plugin_dep = libplugin_sp.get_variable('plugin_dep')
 libplugin = libplugin_sp.get_variable('libplugin')
--- a/build-config/meson.build
+++ b/build-config/meson.build
@@ -1,11 +1,10 @@
 cmake = import('cmake')
 subdir('fourdst')
 subdir('libplugin')
 subdir('python')
 subdir('fourdst')
 subdir('sundials')
 subdir('boost')
 subdir('cppad')
 subdir('xxHash')
 subdir('eigen')
--- a/build-config/python/meson.build
+++ b/build-config/python/meson.build
@@ -0,0 +1,16 @@
 py_installation = import('python').find_installation('python3', pure: false)
 if meson.is_cross_build() and host_machine.system() == 'darwin'
  py_ver = get_option('python-target-version')
  message('Cross build on Darwin, using python version ' + py_ver)
  py_inc_dir = include_directories('../../cross/python_includes/python-' + py_ver + '/include/python' + py_ver)
  py_dep = declare_dependency(include_directories: py_inc_dir)
  py_module_prefix = ''
  py_module_suffic = 'so'
  meson.override_dependency('python3', py_dep)
 else
  py_dep = py_installation.dependency()
  py_module_prefix = ''
  py_module_suffic = 'so'
 endif
--- a/build-config/sundials/cvode/meson.build
+++ b/build-config/sundials/cvode/meson.build
@@ -4,8 +4,10 @@ cvode_cmake_options = cmake.subproject_options()
 cvode_cmake_options.add_cmake_defines({
    'CMAKE_CXX_FLAGS'   : '-Wno-deprecated-declarations',
    'CMAKE_C_FLAGS'     : '-Wno-deprecated-declarations',
-    'BUILD_SHARED_LIBS' : 'ON',
+    'BUILD_SHARED_LIBS' : 'OFF',
-    'BUILD_STATIC_LIBS' : 'OFF',
+    'BUILD_STATIC_LIBS' : 'ON',
    'EXAMPLES_ENABLE_C': 'OFF',
    'CMAKE_POSITION_INDEPENDENT_CODE': true
 })
@@ -19,29 +21,56 @@ cvode_sp = cmake.subproject(
    options: cvode_cmake_options,
 )
-# For the core SUNDIALS library (SUNContext, etc.)
+sundials_core_tgt = cvode_sp.target('sundials_core_static')
-sundials_core_dep = cvode_sp.dependency('sundials_core_shared')
+sundials_cvode_tgt = cvode_sp.target('sundials_cvode_static')
 sundials_nvecserial_tgt = cvode_sp.target('sundials_nvecserial_static')
 sundials_sunmatrixdense_tgt = cvode_sp.target('sundials_sunmatrixdense_static')
 sundials_sunlinsoldense_tgt = cvode_sp.target('sundials_sunlinsoldense_static')
-# For the CVODE integrator library
+cvode_objs = [
-sundials_cvode_dep = cvode_sp.dependency('sundials_cvode_shared')
+  sundials_core_tgt.extract_all_objects(recursive: true),
  sundials_cvode_tgt.extract_all_objects(recursive: true),
  sundials_nvecserial_tgt.extract_all_objects(recursive: true),
  sundials_sunmatrixdense_tgt.extract_all_objects(recursive: true),
  sundials_sunlinsoldense_tgt.extract_all_objects(recursive: true),
 ]
-# For the serial NVector library
+sundials_core_includes = cvode_sp.include_directories('sundials_core_static')
-sundials_nvecserial_dep = cvode_sp.dependency('sundials_nvecserial_shared')
+sundials_cvode_includes = cvode_sp.include_directories('sundials_cvode_static')
 sundials_nvecserial_includes = cvode_sp.include_directories('sundials_nvecserial_static')
 sundials_sunmatrixdense_includes = cvode_sp.include_directories('sundials_sunmatrixdense_static')
 sundials_sunlinsoldense_includes = cvode_sp.include_directories('sundials_sunlinsoldense_static')
-# For the dense matrix library
+cvode_includes = [
-sundials_sunmatrixdense_dep = cvode_sp.dependency('sundials_sunmatrixdense_shared')
+  sundials_core_includes,
  sundials_cvode_includes,
  sundials_nvecserial_includes,
  sundials_sunmatrixdense_includes,
  sundials_sunlinsoldense_includes
 ]
 # For the dense linear solver library
 sundials_sunlinsoldense_dep = cvode_sp.dependency('sundials_sunlinsoldense_shared')
-cvode_dep = declare_dependency(
+empty_cvode_file = configure_file(
-    dependencies: [
+  output: 'cvode_dummy_ar.cpp',
-        sundials_core_dep,
+  command: ['echo'],
-        sundials_cvode_dep,
+  capture: true
-        sundials_nvecserial_dep,
+  )
-        sundials_sunmatrixdense_dep,
+
-        sundials_sunlinsoldense_dep,
+
-    ],
+
 libcvode_static = static_library(
   'cvode-static',
   empty_cvode_file,
   objects: cvode_objs,
   include_directories: cvode_includes,
   pic: true,
   install: false
 )
 cvode_dep = declare_dependency(
  link_with: libcvode_static,
  include_directories: cvode_includes,
 )
--- a/build-config/sundials/kinsol/meson.build
+++ b/build-config/sundials/kinsol/meson.build
@@ -5,8 +5,10 @@ kinsol_cmake_options = cmake.subproject_options()
 kinsol_cmake_options.add_cmake_defines({
    'CMAKE_CXX_FLAGS'   : '-Wno-deprecated-declarations',
    'CMAKE_C_FLAGS'     : '-Wno-deprecated-declarations',
-    'BUILD_SHARED_LIBS' : 'ON',
+    'BUILD_SHARED_LIBS' : 'OFF',
-    'BUILD_STATIC_LIBS' : 'OFF',
+    'BUILD_STATIC_LIBS' : 'ON',
    'EXAMPLES_ENABLE_C' : 'OFF',
    'CMAKE_POSITION_INDEPENDENT_CODE': true
 })
 kinsol_cmake_options.add_cmake_defines({
@@ -19,11 +21,31 @@ kinsol_sp = cmake.subproject(
    options: kinsol_cmake_options,
 )
-sundials_kinsol_shared = kinsol_sp.dependency('sundials_kinsol_shared')
+sundials_kinsol_static_tgt = kinsol_sp.target('sundials_kinsol_obj_static')
 kinsol_includes = kinsol_sp.include_directories('sundials_kinsol_obj_static')
-kinsol_dep = declare_dependency(
+kinsol_objs = [sundials_kinsol_static_tgt.extract_all_objects(recursive: false)]
-    dependencies: [
+
-        sundials_kinsol_shared,
+empty_kinsol_file = configure_file(
-    ]
+  output: 'kinsol_dummy_ar.cpp',
  command: ['echo'],
  capture: true
  )
 libkinsol_static = static_library(
  'kinsol_static',
  empty_kinsol_file,
  objects: kinsol_objs,
  include_directories: kinsol_includes,
  pic: true,
  install: false
 )
 kinsol_dep = declare_dependency(
  link_with: libkinsol_static,
  include_directories: kinsol_includes
 )
--- a/build-python/fix_rpaths.py
+++ b/build-python/fix_rpaths.py
@@ -78,7 +78,7 @@ def fix_rpaths(binary_path):
 def main():
    if len(sys.argv) != 2:
-        print(f"--- Error: Expected one argument (path to .so file), got {sys.argv}", file=sys.stderr)
+        print(f"--- Error: Expected one argument (path to .dylib/.so file), got {sys.argv}", file=sys.stderr)
        sys.exit(1)
    # Get the file path directly from the command line argument
--- a/build-python/meson.build
+++ b/build-python/meson.build
@@ -1,7 +1,6 @@
 # --- Python Extension Setup ---
 py_installation = import('python').find_installation('python3', pure: false)
 gridfire_py_deps = [
    py_dep,
    pybind11_dep,
    const_dep,
    config_dep,
@@ -9,9 +8,7 @@ gridfire_py_deps = [
    gridfire_dep
 ]
-py_mod = py_installation.extension_module(
+py_sources =  [
    '_gridfire', # Name of the generated .so/.pyd file (without extension)
    sources: [
        meson.project_source_root() + '/src/python/bindings.cpp',
        meson.project_source_root() + '/src/python/types/bindings.cpp',
        meson.project_source_root() + '/src/python/partition/bindings.cpp',
@@ -29,11 +26,28 @@ py_mod = py_installation.extension_module(
        meson.project_source_root() + '/src/python/policy/bindings.cpp',
        meson.project_source_root() + '/src/python/policy/trampoline/py_policy.cpp',
        meson.project_source_root() + '/src/python/utils/bindings.cpp',
-    ],
+    ]
 if meson.is_cross_build() and host_machine.system() == 'darwin'
  py_mod = shared_module(
    '_gridfire',
    sources: py_sources,
    dependencies: gridfire_py_deps,
    name_prefix: '',
    name_suffix: 'so',
    install: true,
    install_dir: py_installation.get_install_dir() + '/gridfire'
    )
 else
  py_mod = py_installation.extension_module(
      '_gridfire', # Name of the generated .so/.pyd file (without extension)
      sources: py_sources,
      dependencies : gridfire_py_deps,
      install : true,
      subdir: 'gridfire',
-)
+  )
 endif
 py_installation.install_sources(
--- a/cross/macos_arm64.ini
+++ b/cross/macos_arm64.ini
@@ -0,0 +1,19 @@
 [binaries]
 c = 'arm64-apple-darwin25-clang'
 cpp = 'arm64-apple-darwin25-clang++'
 ar = 'arm64-apple-darwin25-ar'
 strip = 'arm64-apple-darwin25-strip'
 pkg-config = 'pkg-config'
 ranlib = '/usr/bin/true'
 [host_machine]
 system = 'darwin'
 cpu_family = 'aarch64'
 cpu = 'arm64'
 endian = 'little'
 [built-in options]
 c_args = ['-mmacosx-version-min=15.0']
 cpp_args = ['-mmacos-version-min=15.0']
 c_link_args = ['-mmacosx-version-min=15.0']
 cpp_link_args = ['-mmacos-version-min=15.0']
--- a/docs/html/CVODEsolverstrategy_8cpp.html
+++ b/docs/html/CVODEsolverstrategy_8cpp.html
@@ -0,0 +1,143 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
 <head>
 <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
 <meta http-equiv="X-UA-Compatible" content="IE=11"/>
 <meta name="generator" content="Doxygen 1.9.8"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
 <title>GridFire: src/lib/solver/strategies/CVODE_solver_strategy.cpp File Reference</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
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 <link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
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 </head>
 <body>
 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
 <div id="titlearea">
 <table cellspacing="0" cellpadding="0">
 <tbody>
 <tr id="projectrow">
  <td id="projectalign">
   <div id="projectname">GridFire<span id="projectnumber">&#160;v0.7.1_rc2</span>
   </div>
   <div id="projectbrief">General Purpose Nuclear Network</div>
  </td>
 </tr>
 </tbody>
 </table>
 </div>
 <!-- end header part -->
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  <div class="headertitle"><div class="title">CVODE_solver_strategy.cpp File Reference</div></div>
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 <div class="textblock"><code>#include &quot;<a class="el" href="CVODE__solver__strategy_8h.html">gridfire/solver/strategies/CVODE_solver_strategy.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="types_8h.html">gridfire/types/types.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="table__format_8h.html">gridfire/utils/table_format.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="dynamic__engine__diagnostics_8h.html">gridfire/engine/diagnostics/dynamic_engine_diagnostics.h</a>&quot;</code><br />
 <code>#include &quot;quill/LogMacros.h&quot;</code><br />
 <code>#include &quot;fourdst/composition/composition.h&quot;</code><br />
 <code>#include &lt;cstdint&gt;</code><br />
 <code>#include &lt;limits&gt;</code><br />
 <code>#include &lt;string&gt;</code><br />
 <code>#include &lt;unordered_map&gt;</code><br />
 <code>#include &lt;stdexcept&gt;</code><br />
 <code>#include &lt;algorithm&gt;</code><br />
 <code>#include &quot;fourdst/atomic/species.h&quot;</code><br />
 <code>#include &quot;fourdst/composition/exceptions/exceptions_composition.h&quot;</code><br />
 <code>#include &quot;<a class="el" href="engine__graph_8h.html">gridfire/engine/engine_graph.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="engine__types_8h.html">gridfire/engine/types/engine_types.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="engine__partitioning__trigger_8h.html">gridfire/solver/strategies/triggers/engine_partitioning_trigger.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="trigger__pprint_8h.html">gridfire/trigger/procedures/trigger_pprint.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="error__solver_8h.html">gridfire/exceptions/error_solver.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="sundials_8h.html">gridfire/utils/sundials.h</a>&quot;</code><br />
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 Include dependency graph for CVODE_solver_strategy.cpp:</div>
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 <tr class="memitem:namespacegridfire" id="r_namespacegridfire"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire.html">gridfire</a></td></tr>
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 <tr class="memitem:namespacegridfire_1_1solver" id="r_namespacegridfire_1_1solver"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire_1_1solver.html">gridfire::solver</a></td></tr>
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    <li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_c85d3e3c5052e9ad9ce18c6863244a25.html">lib</a></li><li class="navelem"><a class="el" href="dir_4fd0dc9a50f7a53e22cb356c650f915e.html">solver</a></li><li class="navelem"><a class="el" href="dir_b0553efdd4ad7f265c0580564941af0c.html">strategies</a></li><li class="navelem"><a class="el" href="CVODE__solver__strategy_8cpp.html">CVODE_solver_strategy.cpp</a></li>
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  <div class="headertitle"><div class="title">CVODE_solver_strategy.h File Reference</div></div>
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 <div class="textblock"><code>#include &quot;<a class="el" href="strategy__abstract_8h.html">gridfire/solver/strategies/strategy_abstract.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="engine__abstract_8h.html">gridfire/engine/engine_abstract.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="types_8h.html">gridfire/types/types.h</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="exceptions_8h.html">gridfire/exceptions/exceptions.h</a>&quot;</code><br />
 <code>#include &quot;fourdst/atomic/atomicSpecies.h&quot;</code><br />
 <code>#include &quot;fourdst/config/config.h&quot;</code><br />
 <code>#include &lt;functional&gt;</code><br />
 <code>#include &lt;any&gt;</code><br />
 <code>#include &lt;string&gt;</code><br />
 <code>#include &lt;vector&gt;</code><br />
 <code>#include &lt;tuple&gt;</code><br />
 <code>#include &lt;cvode/cvode.h&gt;</code><br />
 <code>#include &lt;sundials/sundials_types.h&gt;</code><br />
 <code>#include &lt;sundials/sundials_context.h&gt;</code><br />
 <code>#include &lt;sunmatrix/sunmatrix_dense.h&gt;</code><br />
 <code>#include &lt;sunlinsol/sunlinsol_dense.h&gt;</code><br />
 <code>#include &lt;nvector/nvector_serial.h&gt;</code><br />
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-<tr id="row_0_0_6_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1_file_defined_engine_view.html" target="_self">FileDefinedEngineView</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_6_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1FileDefinedEngineView.html" target="_self">FileDefinedEngineView</a></td><td class="desc"></td></tr>
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+<tr id="row_0_0_7_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_0_7_" class="arrow" onclick="toggleFolder('0_0_7_')">&#9658;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1GraphEngine.html" target="_self">GraphEngine</a></td><td class="desc">A reaction network engine that uses a graph-based representation </td></tr>
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+<tr id="row_0_0_7_1_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1engine_1_1GraphEngine_1_1constants.html" target="_self">constants</a></td><td class="desc"></td></tr>
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+<tr id="row_0_0_7_2_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1engine_1_1GraphEngine_1_1PrecomputedReaction.html" target="_self">PrecomputedReaction</a></td><td class="desc"></td></tr>
-<tr id="row_0_0_8_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_0_8_" class="arrow" onclick="dynsection.toggleFolder('0_0_8_')">&#9658;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1_multiscale_partitioning_engine_view.html" target="_self">MultiscalePartitioningEngineView</a></td><td class="desc">An engine view that partitions the reaction network into multiple groups based on timescales </td></tr>
+<tr id="row_0_0_8_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_0_8_" class="arrow" onclick="toggleFolder('0_0_8_')">&#9658;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1MultiscalePartitioningEngineView.html" target="_self">MultiscalePartitioningEngineView</a></td><td class="desc">An engine view that partitions the reaction network into multiple groups based on timescales </td></tr>
-<tr id="row_0_0_8_0_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1engine_1_1_multiscale_partitioning_engine_view_1_1_flux_validation_result.html" target="_self">FluxValidationResult</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_8_0_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1engine_1_1MultiscalePartitioningEngineView_1_1FluxValidationResult.html" target="_self">FluxValidationResult</a></td><td class="desc"></td></tr>
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+<tr id="row_0_0_8_1_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1engine_1_1MultiscalePartitioningEngineView_1_1QSEGroup.html" target="_self">QSEGroup</a></td><td class="desc">Struct representing a QSE group </td></tr>
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+<tr id="row_0_0_8_2_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span id="arr_0_0_8_2_" class="arrow" onclick="toggleFolder('0_0_8_2_')">&#9658;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1MultiscalePartitioningEngineView_1_1QSESolver.html" target="_self">QSESolver</a></td><td class="desc"></td></tr>
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+<tr id="row_0_0_8_2_0_" class="even" style="display:none;"><td class="entry"><span style="width:80px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1engine_1_1MultiscalePartitioningEngineView_1_1QSESolver_1_1UserData.html" target="_self">UserData</a></td><td class="desc"></td></tr>
-<tr id="row_0_0_9_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1_network_jacobian.html" target="_self">NetworkJacobian</a></td><td class="desc">A wrapper class for handling the network Jacobian matrix </td></tr>
+<tr id="row_0_0_9_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1NetworkJacobian.html" target="_self">NetworkJacobian</a></td><td class="desc">A wrapper class for handling the network Jacobian matrix </td></tr>
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+<tr id="row_0_0_10_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1NetworkPrimingEngineView.html" target="_self">NetworkPrimingEngineView</a></td><td class="desc">Provides a view of a <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> filtered to reactions involving a specified priming species </td></tr>
-<tr id="row_0_0_11_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1engine_1_1_priming_report.html" target="_self">PrimingReport</a></td><td class="desc">Captures the result of a network priming operation </td></tr>
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+<tr id="row_0_0_12_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1engine_1_1StepDerivatives.html" target="_self">StepDerivatives</a></td><td class="desc">Structure holding derivatives and energy generation for a network step </td></tr>
-<tr id="row_0_0_13_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1_reaction_set.html" target="_self">ReactionSet</a></td><td class="desc"></td></tr>
+<tr id="row_0_1_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_1_" class="arrow" onclick="toggleFolder('0_1_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1exceptions.html" target="_self">exceptions</a></td><td class="desc">Namespace for GridFire exception classes. All custom exceptions defined in GridFire inherit from std::exception and are organized within this namespace for clarity and modularity </td></tr>
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+<tr id="row_0_1_0_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1BadCollectionError.html" target="_self">BadCollectionError</a></td><td class="desc">Exception for invalid composition collection in the engine </td></tr>
-<tr id="row_0_1_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_1_" class="arrow" onclick="dynsection.toggleFolder('0_1_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1exceptions.html" target="_self">exceptions</a></td><td class="desc">Namespace for GridFire exception classes. All custom exceptions defined in GridFire inherit from std::exception and are organized within this namespace for clarity and modularity </td></tr>
+<tr id="row_0_1_1_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1BadRHSEngineError.html" target="_self">BadRHSEngineError</a></td><td class="desc">Exception for errors in calculating the right-hand side (RHS) </td></tr>
-<tr id="row_0_1_0_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_bad_collection_error.html" target="_self">BadCollectionError</a></td><td class="desc">Exception for invalid composition collection in the engine </td></tr>
+<tr id="row_0_1_2_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1CVODESolverFailureError.html" target="_self">CVODESolverFailureError</a></td><td class="desc">Exception for failures in the CVODE solver </td></tr>
-<tr id="row_0_1_1_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_bad_r_h_s_engine_error.html" target="_self">BadRHSEngineError</a></td><td class="desc">Exception for errors in calculating the right-hand side (RHS) </td></tr>
+<tr id="row_0_1_3_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1DebugException.html" target="_self">DebugException</a></td><td class="desc">Exception class for debug-only errors </td></tr>
-<tr id="row_0_1_2_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_c_v_o_d_e_solver_failure_error.html" target="_self">CVODESolverFailureError</a></td><td class="desc">Exception for failures in the CVODE solver </td></tr>
+<tr id="row_0_1_4_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1EngineError.html" target="_self">EngineError</a></td><td class="desc">Base class for engine-related exceptions </td></tr>
-<tr id="row_0_1_3_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_debug_exception.html" target="_self">DebugException</a></td><td class="desc">Exception class for debug-only errors </td></tr>
+<tr id="row_0_1_5_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1FailedToPartitionEngineError.html" target="_self">FailedToPartitionEngineError</a></td><td class="desc">Exception for failures in partitioning the engine </td></tr>
-<tr id="row_0_1_4_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_engine_error.html" target="_self">EngineError</a></td><td class="desc">Base class for engine-related exceptions </td></tr>
+<tr id="row_0_1_6_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1GridFireError.html" target="_self">GridFireError</a></td><td class="desc">Base class for GridFire exceptions </td></tr>
-<tr id="row_0_1_5_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html" target="_self">FailedToPartitionEngineError</a></td><td class="desc">Exception for failures in partitioning the engine </td></tr>
+<tr id="row_0_1_7_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1HashingError.html" target="_self">HashingError</a></td><td class="desc">Exception class for hashing-related errors in GridFire </td></tr>
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+<tr id="row_0_1_8_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1IllConditionedJacobianError.html" target="_self">IllConditionedJacobianError</a></td><td class="desc">Exception thrown when the Jacobian matrix is ill-conditioned </td></tr>
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-<tr id="row_0_1_8_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_ill_conditioned_jacobian_error.html" target="_self">IllConditionedJacobianError</a></td><td class="desc">Exception thrown when the Jacobian matrix is ill-conditioned </td></tr>
+<tr id="row_0_1_10_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1JacobianError.html" target="_self">JacobianError</a></td><td class="desc">Base class for Jacobian-related exceptions </td></tr>
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+<tr id="row_0_1_11_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1KINSolSolverFailureError.html" target="_self">KINSolSolverFailureError</a></td><td class="desc">Exception for failures in the KINSOL solver </td></tr>
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+<tr id="row_0_1_13_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1MissingKeyReactionError.html" target="_self">MissingKeyReactionError</a></td><td class="desc">Exception thrown when a constructed network fails to include a key reaction required by the policy </td></tr>
-<tr id="row_0_1_12_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_missing_base_reaction_error.html" target="_self">MissingBaseReactionError</a></td><td class="desc">Exception thrown when a required reaction is missing from the underlying database (e.g., REACLIB) </td></tr>
+<tr id="row_0_1_14_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1MissingSeedSpeciesError.html" target="_self">MissingSeedSpeciesError</a></td><td class="desc">Exception thrown when a required seed species is not found in the initial composition </td></tr>
-<tr id="row_0_1_13_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_missing_key_reaction_error.html" target="_self">MissingKeyReactionError</a></td><td class="desc">Exception thrown when a constructed network fails to include a key reaction required by the policy </td></tr>
+<tr id="row_0_1_15_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1NetworkResizedError.html" target="_self">NetworkResizedError</a></td><td class="desc">Exception for errors during network resizing </td></tr>
-<tr id="row_0_1_14_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_missing_seed_species_error.html" target="_self">MissingSeedSpeciesError</a></td><td class="desc">Exception thrown when a required seed species is not found in the initial composition </td></tr>
+<tr id="row_0_1_16_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1PolicyError.html" target="_self">PolicyError</a></td><td class="desc">Base class for all exceptions related to network policy operations </td></tr>
-<tr id="row_0_1_15_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_network_resized_error.html" target="_self">NetworkResizedError</a></td><td class="desc">Exception for errors during network resizing </td></tr>
+<tr id="row_0_1_17_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1ReactionError.html" target="_self">ReactionError</a></td><td class="desc">Base class for all exceptions related to reaction operations </td></tr>
-<tr id="row_0_1_16_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_policy_error.html" target="_self">PolicyError</a></td><td class="desc">Base class for all exceptions related to network policy operations </td></tr>
+<tr id="row_0_1_18_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1ReactionParsingError.html" target="_self">ReactionParsingError</a></td><td class="desc"></td></tr>
-<tr id="row_0_1_17_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_reaction_error.html" target="_self">ReactionError</a></td><td class="desc">Base class for all exceptions related to reaction operations </td></tr>
+<tr id="row_0_1_19_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1SingularJacobianError.html" target="_self">SingularJacobianError</a></td><td class="desc">Exception thrown when the Jacobian matrix is singular </td></tr>
-<tr id="row_0_1_18_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_reaction_parsing_error.html" target="_self">ReactionParsingError</a></td><td class="desc"></td></tr>
+<tr id="row_0_1_20_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1SolverError.html" target="_self">SolverError</a></td><td class="desc">Base class for all exceptions related to solver operations </td></tr>
-<tr id="row_0_1_19_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_singular_jacobian_error.html" target="_self">SingularJacobianError</a></td><td class="desc">Exception thrown when the Jacobian matrix is singular </td></tr>
+<tr id="row_0_1_21_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1StaleJacobianError.html" target="_self">StaleJacobianError</a></td><td class="desc">Exception for stale Jacobian matrix access </td></tr>
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+<tr id="row_0_1_22_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1SUNDIALSError.html" target="_self">SUNDIALSError</a></td><td class="desc">Base class for exceptions related to SUNDIALS solver operations </td></tr>
-<tr id="row_0_1_21_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_stale_jacobian_error.html" target="_self">StaleJacobianError</a></td><td class="desc">Exception for stale Jacobian matrix access </td></tr>
+<tr id="row_0_1_23_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1UnableToSetNetworkReactionsError.html" target="_self">UnableToSetNetworkReactionsError</a></td><td class="desc">Exception for failures in setting network reactions </td></tr>
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+<tr id="row_0_1_24_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1UninitializedJacobianError.html" target="_self">UninitializedJacobianError</a></td><td class="desc">Exception for uninitialized Jacobian matrix access </td></tr>
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+<tr id="row_0_1_25_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1UnknownJacobianError.html" target="_self">UnknownJacobianError</a></td><td class="desc">Exception for unknown Jacobian matrix access </td></tr>
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+<tr id="row_0_1_26_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1UtilityError.html" target="_self">UtilityError</a></td><td class="desc">Base class for utility-related errors in GridFire </td></tr>
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+<tr id="row_0_2_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_2_" class="arrow" onclick="toggleFolder('0_2_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1io.html" target="_self">io</a></td><td class="desc"></td></tr>
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+<tr id="row_0_2_0_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_2_0_" class="arrow" onclick="toggleFolder('0_2_0_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1io_1_1gen.html" target="_self">gen</a></td><td class="desc">Namespace for generative input/output functionalities </td></tr>
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+<tr id="row_0_2_0_0_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1io_1_1gen_1_1PyFunctionDef.html" target="_self">PyFunctionDef</a></td><td class="desc">Structure representing a Python function definition </td></tr>
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+<tr id="row_0_2_1_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1io_1_1MESANetworkFileParser.html" target="_self">MESANetworkFileParser</a></td><td class="desc">A parser for MESA-format network files </td></tr>
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+<tr id="row_0_3_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_3_" class="arrow" onclick="toggleFolder('0_3_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1partition.html" target="_self">partition</a></td><td class="desc"></td></tr>
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+<tr id="row_0_3_0_" class="odd" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_3_0_" class="arrow" onclick="toggleFolder('0_3_0_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1partition_1_1record.html" target="_self">record</a></td><td class="desc"></td></tr>
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+<tr id="row_0_3_4_2_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1partition_1_1RauscherThielemannPartitionFunction_1_1IsotopeData.html" target="_self">IsotopeData</a></td><td class="desc"></td></tr>
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+<tr id="row_0_4_5_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1policy_1_1HotCNOChainPolicy.html" target="_self">HotCNOChainPolicy</a></td><td class="desc">Hot CNO Chain Policy </td></tr>
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+<tr id="row_0_4_6_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1policy_1_1HotCNOIChainPolicy.html" target="_self">HotCNOIChainPolicy</a></td><td class="desc">Hot CNO I Chain Policy </td></tr>
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+<tr id="row_0_4_8_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1policy_1_1HotCNOIIIChainPolicy.html" target="_self">HotCNOIIIChainPolicy</a></td><td class="desc">Hot CNO III Chain Policy </td></tr>
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+<tr id="row_0_5_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_5_" class="arrow" onclick="toggleFolder('0_5_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1rates.html" target="_self">rates</a></td><td class="desc"></td></tr>
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+<tr id="row_0_5_0_2_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1rates_1_1weak_1_1IsotopeGrid.html" target="_self">IsotopeGrid</a></td><td class="desc">Regular 2D grid and payloads for a single isotope (A,Z) </td></tr>
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+<tr id="row_0_5_0_6_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1rates_1_1weak_1_1WeakRatePayload.html" target="_self">WeakRatePayload</a></td><td class="desc">Interpolated weak-rate payload at a single state </td></tr>
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+<tr id="row_0_5_0_7_0_" class="odd" style="display:none;"><td class="entry"><span style="width:80px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1rates_1_1weak_1_1WeakReaction_1_1AtomicWeakRate.html" target="_self">AtomicWeakRate</a></td><td class="desc">CppAD atomic that wraps weak-rate interpolation for AD evaluation </td></tr>
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+<tr id="row_0_5_0_7_1_" class="odd" style="display:none;"><td class="entry"><span style="width:80px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1rates_1_1weak_1_1WeakReaction_1_1constants.html" target="_self">constants</a></td><td class="desc"></td></tr>
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+<tr id="row_0_5_0_8_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1rates_1_1weak_1_1WeakReactionEntry.html" target="_self">WeakReactionEntry</a></td><td class="desc">A single weak-reaction data point (type, state, and log values) </td></tr>
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+<tr id="row_0_5_0_9_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1rates_1_1weak_1_1WeakReactionMap.html" target="_self">WeakReactionMap</a></td><td class="desc">Index of available weak reactions keyed by species </td></tr>
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+<tr id="row_0_6_0_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1reaclib_1_1ReactionRecord.html" target="_self">ReactionRecord</a></td><td class="desc"></td></tr>
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+<tr id="row_0_7_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_7_" class="arrow" onclick="toggleFolder('0_7_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1reaction.html" target="_self">reaction</a></td><td class="desc"></td></tr>
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-<tr id="row_0_7_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_7_" class="arrow" onclick="dynsection.toggleFolder('0_7_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1reaction.html" target="_self">reaction</a></td><td class="desc"></td></tr>
+<tr id="row_0_7_1_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1reaction_1_1RateCoefficientSet.html" target="_self">RateCoefficientSet</a></td><td class="desc">Holds the seven coefficients for the REACLIB rate equation </td></tr>
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+<tr id="row_0_7_2_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1reaction_1_1ReaclibReaction.html" target="_self">ReaclibReaction</a></td><td class="desc"></td></tr>
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+<tr id="row_0_7_3_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1reaction_1_1Reaction.html" target="_self">Reaction</a></td><td class="desc">Represents a single nuclear reaction from a specific data source </td></tr>
-<tr id="row_0_7_2_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1reaction_1_1_reaclib_reaction.html" target="_self">ReaclibReaction</a></td><td class="desc"></td></tr>
+<tr id="row_0_7_4_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1reaction_1_1ReactionSet.html" target="_self">ReactionSet</a></td><td class="desc"></td></tr>
-<tr id="row_0_7_3_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1reaction_1_1_reaction.html" target="_self">Reaction</a></td><td class="desc">Represents a single nuclear reaction from a specific data source </td></tr>
+<tr id="row_0_7_5_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1reaction_1_1WeakReaclibReaction.html" target="_self">WeakReaclibReaction</a></td><td class="desc"></td></tr>
-<tr id="row_0_7_4_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html" target="_self">ReactionSet</a></td><td class="desc"></td></tr>
+<tr id="row_0_8_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_8_" class="arrow" onclick="toggleFolder('0_8_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1screening.html" target="_self">screening</a></td><td class="desc"></td></tr>
-<tr id="row_0_8_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_8_" class="arrow" onclick="dynsection.toggleFolder('0_8_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1screening.html" target="_self">screening</a></td><td class="desc"></td></tr>
+<tr id="row_0_8_0_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1screening_1_1BareScreeningModel.html" target="_self">BareScreeningModel</a></td><td class="desc">A screening model that applies no screening effect </td></tr>
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+<tr id="row_0_8_1_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1screening_1_1IntermediateScreeningModel.html" target="_self">IntermediateScreeningModel</a></td><td class="desc"></td></tr>
-<tr id="row_0_8_1_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1screening_1_1_intermediate_screening_model.html" target="_self">IntermediateScreeningModel</a></td><td class="desc"></td></tr>
+<tr id="row_0_8_2_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1screening_1_1ScreeningModel.html" target="_self">ScreeningModel</a></td><td class="desc">An abstract base class for plasma screening models </td></tr>
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+<tr id="row_0_8_3_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1screening_1_1WeakScreeningModel.html" target="_self">WeakScreeningModel</a></td><td class="desc">Implements the weak screening model based on the Debye-Hückel approximation </td></tr>
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+<tr id="row_0_9_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_9_" class="arrow" onclick="toggleFolder('0_9_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1solver.html" target="_self">solver</a></td><td class="desc"></td></tr>
-<tr id="row_0_9_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_9_" class="arrow" onclick="dynsection.toggleFolder('0_9_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1solver.html" target="_self">solver</a></td><td class="desc"></td></tr>
+<tr id="row_0_9_0_" class="odd" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_9_0_" class="arrow" onclick="toggleFolder('0_9_0_')">&#9658;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1solver_1_1CVODESolverStrategy.html" target="_self">CVODESolverStrategy</a></td><td class="desc">Stiff ODE integrator backed by SUNDIALS CVODE (BDF) for network + energy </td></tr>
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+<tr id="row_0_9_0_0_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1solver_1_1CVODESolverStrategy_1_1CVODERHSOutputData.html" target="_self">CVODERHSOutputData</a></td><td class="desc"></td></tr>
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+<tr id="row_0_9_0_2_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1solver_1_1CVODESolverStrategy_1_1TimestepContext.html" target="_self">TimestepContext</a></td><td class="desc">Immutable view of the current integration state passed to callbacks </td></tr>
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+<tr id="row_0_9_1_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html" target="_self">NetworkSolverStrategy</a></td><td class="desc">Abstract base class for network solver strategies </td></tr>
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+<tr id="row_0_9_2_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1solver_1_1SolverContextBase.html" target="_self">SolverContextBase</a></td><td class="desc">Base class for solver callback contexts </td></tr>
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+<tr id="row_0_10_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_10_" class="arrow" onclick="toggleFolder('0_10_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1trigger.html" target="_self">trigger</a></td><td class="desc"></td></tr>
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 <tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structgridfire_1_1policy_1_1_temperature_dependent_chain_policy_1_1_active_temp_range.html">gridfire::policy::TemperatureDependentChainPolicy::ActiveTempRange</a></td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structgridfire_1_1policy_1_1TemperatureDependentChainPolicy_1_1ActiveTempRange.html">gridfire::policy::TemperatureDependentChainPolicy::ActiveTempRange</a></td></tr>
-<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Struct to hold the active temperature range for the reaction chain.  <a href="structgridfire_1_1policy_1_1_temperature_dependent_chain_policy_1_1_active_temp_range.html#details">More...</a><br /></td></tr>
+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Struct to hold the active temperature range for the reaction chain.  <a href="structgridfire_1_1policy_1_1TemperatureDependentChainPolicy_1_1ActiveTempRange.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Proton-Proton I Chain Policy.  <a href="classgridfire_1_1policy_1_1ProtonProtonIChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Proton-Proton II Chain Policy.  <a href="classgridfire_1_1policy_1_1ProtonProtonIIChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Proton-Proton III Chain Policy.  <a href="classgridfire_1_1policy_1_1ProtonProtonIIIChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Proton-Proton Chain Policy.  <a href="classgridfire_1_1policy_1_1ProtonProtonChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">CNO I Chain Policy.  <a href="classgridfire_1_1policy_1_1CNOIChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">CNO II Chain Policy.  <a href="classgridfire_1_1policy_1_1CNOIIChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">CNO III Chain Policy.  <a href="classgridfire_1_1policy_1_1CNOIIIChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">CNO IV Chain Policy.  <a href="classgridfire_1_1policy_1_1CNOIVChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">CNO Chain Policy.  <a href="classgridfire_1_1policy_1_1CNOChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Hot CNO I Chain Policy.  <a href="classgridfire_1_1policy_1_1HotCNOIChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Hot CNO II Chain Policy.  <a href="classgridfire_1_1policy_1_1HotCNOIIChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Hot CNO III Chain Policy.  <a href="classgridfire_1_1policy_1_1HotCNOIIIChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Hot CNO Chain Policy.  <a href="classgridfire_1_1policy_1_1HotCNOChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Triple-Alpha Chain Policy.  <a href="classgridfire_1_1policy_1_1TripleAlphaChainPolicy.html#details">More...</a><br /></td></tr>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Main Sequence Reaction Chain Policy.  <a href="classgridfire_1_1policy_1_1MainSequenceReactionChainPolicy.html#details">More...</a><br /></td></tr>
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 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="namespaces" name="namespaces"></a>
 Namespaces</h2></td></tr>
-<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire.html">gridfire</a></td></tr>
+<tr class="memitem:namespacegridfire" id="r_namespacegridfire"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire.html">gridfire</a></td></tr>
 <tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire_1_1policy.html">gridfire::policy</a></td></tr>
+<tr class="memitem:namespacegridfire_1_1policy" id="r_namespacegridfire_1_1policy"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire_1_1policy.html">gridfire::policy</a></td></tr>
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 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Concrete implementations of ReactionChainPolicy for key stellar reaction chains. </p>
 <p>This file provides concrete policies for fundamental nuclear reaction chains, such as the Proton-Proton chain and the CNO cycle. These policies inherit from ReactionChainPolicy (see <code><a class="el" href="policy__abstract_8h.html" title="Abstract policy interfaces used to construct reaction networks (DynamicEngine) from seed compositions...">policy_abstract.h</a></code>) and provide a pre-defined set of reactions.</p>
 <p>They are typically used by higher-level NetworkPolicy implementations (e.g., <code>MainSequencePolicy</code> in <code><a class="el" href="stellar__policy_8h.html" title="High-level concrete NetworkPolicy for specific stellar environments.">stellar_policy.h</a></code>) to compose a complete set of required reactions for a particular stellar environment.</p>
-<dl class="section note"><dt>Note</dt><dd>Constructors for these policies may throw <code><a class="el" href="classgridfire_1_1exceptions_1_1_missing_base_reaction_error.html" title="Exception thrown when a required reaction is missing from the underlying database (e....">gridfire::exceptions::MissingBaseReactionError</a></code> if a required reaction is not found in the underlying REACLIB database. This usually indicates an issue with the GridFire installation or the bundled reaction data. </dd></dl>
+<dl class="section note"><dt>Note</dt><dd>Constructors for these policies may throw <code><a class="el" href="classgridfire_1_1exceptions_1_1MissingBaseReactionError.html" title="Exception thrown when a required reaction is missing from the underlying database (e....">gridfire::exceptions::MissingBaseReactionError</a></code> if a required reaction is not found in the underlying REACLIB database. This usually indicates an issue with the GridFire installation or the bundled reaction data. </dd></dl>
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  <div class="headertitle"><div class="title">PyDynamicEngine Member List</div></div>
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 <p>This is the complete list of members for <a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a>, including all inherited members.</p>
 <table class="directory">
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a6832a7898da51017a20f578e33cba729">calculateEpsDerivatives</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a8facba88b6df6e016ce53a0ff3cff125">calculateMolarReactionFlow</a>(const gridfire::reaction::Reaction &amp;reaction, const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#aac1f2005c0a58befc4e01627c9357924">calculateRHSAndEnergy</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a239826d90cb5db236e68230f7ac84bcb">collectComposition</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a298f700c647d2c3973d2a35d370c823e">generateJacobianMatrix</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a2b1c054b250abccc2af9a7275c68df4a">generateJacobianMatrix</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho, const std::vector&lt; fourdst::atomic::Species &gt; &amp;activeSpecies) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a204643754cac3cf37c550ecd32f659fe">generateJacobianMatrix</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho, const gridfire::engine::SparsityPattern &amp;sparsityPattern) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a2066649ca11a869c054079ea12d8d0e9">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a541cf022fe3253279f8f1309c10556d7">getDepth</a>() const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a1d5143640666631501cf229bc491516e">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#afc745e7ab5da5d8b3cf916044515cd7d">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#ab4cfdca5e15957c5cef75ffa6dedeee5">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a8d34faa3d6ea804a3467979858d33535">getSpeciesDestructionTimescales</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a95d10a7b240d543a1bc6c67ddf2dc8e0">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a2947824dca9662e113153de5c6516609">getSpeciesStatus</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a71678a567bb0cedd8a97aff9ceddd814">getSpeciesTimescales</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a3dd5cf419f25e76e144af35df15a2067">getStoichiometryMatrixEntry</a>(const fourdst::atomic::Species &amp;species, const gridfire::reaction::Reaction &amp;reaction) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a55bf19ed7534a312a36faf74753f7b14">isStale</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a2246382b1c98ba69cdb419bba63a6d03">m_species_cache</a></td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a61bb4b430fe740cfb2c24e5cc673e4ac">mapNetInToMolarAbundanceVector</a>(const gridfire::NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a6118af81e45d2850f7a2517891147274">primeEngine</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#a25e52496b36d731127603c31e9dcaa97">rebuild</a>(const fourdst::composition::CompositionAbstract &amp;comp, gridfire::engine::BuildDepthType depth) override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#af469cba3be850d53f659ec173f0eb4e4">setNetworkReactions</a>(const gridfire::reaction::ReactionSet &amp;reactions) override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicEngine.html#afa3abfd612033336a656f092721c14ac">setScreeningModel</a>(gridfire::screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicEngine.html#af8e6a8cd44f278535d7bcc9a896d6da8">update</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classPyDynamicEngine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1engine_1_1Engine.html#af0ea99416c28933d364a872fc6aff556">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1engine_1_1Engine.html">gridfire::engine::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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 <p>Access the underlying engine instance. </p>
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 <p>Implements <a class="el" href="classgridfire_1_1engine_1_1EngineView.html#a7884ea8e5618e295e64150f3ecf2c6b5">gridfire::engine::EngineView&lt; gridfire::engine::DynamicEngine &gt;</a>.</p>
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 <li>src/python/engine/trampoline/<a class="el" href="py__engine_8h.html">py_engine.h</a></li>
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  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicNetworkSolverStrategy.html#a147a0a543268427a5930143902217ac3">describe_callback_context</a>() const override</td><td class="entry"><a class="el" href="classPyDynamicNetworkSolverStrategy.html">PyDynamicNetworkSolverStrategy</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
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  <tr class="even"><td class="entry"><a class="el" href="classPyDynamicNetworkSolverStrategy.html#a5adc2c51958c6114b4c46264e4d68917">PyDynamicNetworkSolverStrategy</a>(gridfire::engine::DynamicEngine &amp;engine)</td><td class="entry"><a class="el" href="classPyDynamicNetworkSolverStrategy.html">PyDynamicNetworkSolverStrategy</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">explicit</span><span class="mlabel">private</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="classPyDynamicNetworkSolverStrategy.html#a112a7babc03858a69d6994a7155370d3">set_callback</a>(const std::any &amp;callback) override</td><td class="entry"><a class="el" href="classPyDynamicNetworkSolverStrategy.html">PyDynamicNetworkSolverStrategy</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html#a1693dc93f63599c89587d729aca8e318">~NetworkSolverStrategy</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html">gridfire::solver::NetworkSolverStrategy&lt; EngineT &gt;</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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 <p><code>#include &lt;py_solver.h&gt;</code></p>
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 <table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
 Private Member Functions</h2></td></tr>
 <tr class="memitem:a5adc2c51958c6114b4c46264e4d68917" id="r_a5adc2c51958c6114b4c46264e4d68917"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPyDynamicNetworkSolverStrategy.html#a5adc2c51958c6114b4c46264e4d68917">PyDynamicNetworkSolverStrategy</a> (<a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html">gridfire::engine::DynamicEngine</a> &amp;engine)</td></tr>
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 <tr class="memdesc:a2095abb83ed6229ebb27b4883cec51c4"><td class="mdescLeft">&#160;</td><td class="mdescRight">Evaluates the network for a given timestep.  <br /></td></tr>
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 <tr class="memitem:a147a0a543268427a5930143902217ac3" id="r_a147a0a543268427a5930143902217ac3"><td class="memItemLeft" align="right" valign="top">std::vector&lt; std::tuple&lt; std::string, std::string &gt; &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPyDynamicNetworkSolverStrategy.html#a147a0a543268427a5930143902217ac3">describe_callback_context</a> () const override</td></tr>
 <tr class="memdesc:a147a0a543268427a5930143902217ac3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Describe the context that will be passed to the callback function.  <br /></td></tr>
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 Additional Inherited Members</h2></td></tr>
 <tr class="inherit_header pub_methods_classgridfire_1_1solver_1_1NetworkSolverStrategy"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classgridfire_1_1solver_1_1NetworkSolverStrategy')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html">gridfire::solver::NetworkSolverStrategy&lt; EngineT &gt;</a></td></tr>
 <tr class="memitem:a01cbbec0eb5c3a60f50da38cdaf66505 inherit pub_methods_classgridfire_1_1solver_1_1NetworkSolverStrategy" id="r_a01cbbec0eb5c3a60f50da38cdaf66505"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html#a01cbbec0eb5c3a60f50da38cdaf66505">NetworkSolverStrategy</a> (EngineT &amp;engine)</td></tr>
 <tr class="memdesc:a01cbbec0eb5c3a60f50da38cdaf66505 inherit pub_methods_classgridfire_1_1solver_1_1NetworkSolverStrategy"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructor for the <a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html" title="Abstract base class for network solver strategies.">NetworkSolverStrategy</a>.  <br /></td></tr>
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 <tr class="memitem:a1693dc93f63599c89587d729aca8e318 inherit pub_methods_classgridfire_1_1solver_1_1NetworkSolverStrategy" id="r_a1693dc93f63599c89587d729aca8e318"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html#a1693dc93f63599c89587d729aca8e318">~NetworkSolverStrategy</a> ()=default</td></tr>
 <tr class="memdesc:a1693dc93f63599c89587d729aca8e318 inherit pub_methods_classgridfire_1_1solver_1_1NetworkSolverStrategy"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor.  <br /></td></tr>
 <tr class="separator:a1693dc93f63599c89587d729aca8e318 inherit pub_methods_classgridfire_1_1solver_1_1NetworkSolverStrategy"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="inherit_header pro_attribs_classgridfire_1_1solver_1_1NetworkSolverStrategy"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classgridfire_1_1solver_1_1NetworkSolverStrategy')"><img src="closed.png" alt="-"/>&#160;Protected Attributes inherited from <a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html">gridfire::solver::NetworkSolverStrategy&lt; EngineT &gt;</a></td></tr>
 <tr class="memitem:a724924d94eaf82b67d9988a55c3261e8 inherit pro_attribs_classgridfire_1_1solver_1_1NetworkSolverStrategy" id="r_a724924d94eaf82b67d9988a55c3261e8"><td class="memItemLeft" align="right" valign="top">EngineT &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html#a724924d94eaf82b67d9988a55c3261e8">m_engine</a></td></tr>
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 <p>Describe the context that will be passed to the callback function. </p>
 <dl class="section return"><dt>Returns</dt><dd>A vector of tuples, each containing a string for the parameter's name and a string for its type.</dd></dl>
 <p>This method should be overridden by derived classes to provide a description of the context that will be passed to the callback function. The intent of this method is that an end user can investigate the context that will be passed to the callback function, and use this information to craft their own callback function. </p>
 <p>Implements <a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html#ae09169769774f17df8701c42a64ed656">gridfire::solver::NetworkSolverStrategy&lt; EngineT &gt;</a>.</p>
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 <p>Evaluates the network for a given timestep. </p>
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 <p>Implements <a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html#ace539b0482db171845ff1bd38d76b70f">gridfire::solver::NetworkSolverStrategy&lt; EngineT &gt;</a>.</p>
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 <p>set the callback function to be called at the end of each timestep. </p>
 <p>This function allows the user to set a callback function that will be called at the end of each timestep. The callback function will receive a <a class="el" href="namespacegridfire_1_1solver.html">gridfire::solver</a>::&lt;SOMESOLVER&gt;::TimestepContext object. Note that depending on the solver, this context may contain different information. Further, the exact signature of the callback function is left up to each solver. Every solver should provide a type or type alias TimestepCallback that defines the signature of the callback function so that the user can easily get that type information.</p>
 <dl class="params"><dt>Parameters</dt><dd>
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 <p>Implements <a class="el" href="classgridfire_1_1solver_1_1NetworkSolverStrategy.html#a4d97ee85933d5e5f90d4194bb021a1dc">gridfire::solver::NetworkSolverStrategy&lt; EngineT &gt;</a>.</p>
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 <li>src/python/solver/trampoline/<a class="el" href="py__solver_8h.html">py_solver.h</a></li>
 <li>src/python/solver/trampoline/<a class="el" href="py__solver_8cpp.html">py_solver.cpp</a></li>
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  <tr class="even"><td class="entry"><a class="el" href="classPyEngine.html#abc26a86d4f93b37564d32814edbbac4d">calculateRHSAndEnergy</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classPyEngine.html">PyEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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 <p><code>#include &lt;py_engine.h&gt;</code></p>
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 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
 Public Member Functions</h2></td></tr>
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 <tr class="memdesc:a2d240423899e039c2ca688e96f8af1f2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the list of species in the network.  <br /></td></tr>
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 <tr class="memdesc:abc26a86d4f93b37564d32814edbbac4d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation.  <br /></td></tr>
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 <tr class="memitem:af0ea99416c28933d364a872fc6aff556 inherit pub_methods_classgridfire_1_1engine_1_1Engine" id="r_af0ea99416c28933d364a872fc6aff556"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1Engine.html#af0ea99416c28933d364a872fc6aff556">~Engine</a> ()=default</td></tr>
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 <h2 class="memtitle"><span class="permalink"><a href="#abc26a86d4f93b37564d32814edbbac4d">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
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 <p>Calculate the right-hand side (dY/dt) and energy generation. </p>
 <dl class="params"><dt>Parameters</dt><dd>
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 <p>This function must be implemented by derived classes to compute the time derivatives of all species and the specific nuclear energy generation rate for the current state. </p>
 <p>Implements <a class="el" href="classgridfire_1_1engine_1_1Engine.html#a764fc091c72c12c8529105d7c96badb2">gridfire::engine::Engine</a>.</p>
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 <p>Get the list of species in the network. </p>
 <dl class="section return"><dt>Returns</dt><dd>Vector of Species objects representing all network species. </dd></dl>
 <p>Implements <a class="el" href="classgridfire_1_1engine_1_1Engine.html#a3263c3fde2509d5d8ec4da3b6e946c48">gridfire::engine::Engine</a>.</p>
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 <hr/>The documentation for this class was generated from the following files:<ul>
 <li>src/python/engine/trampoline/<a class="el" href="py__engine_8h.html">py_engine.h</a></li>
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 <tr class="memitem:a17d63e853d6efca31064e9147c80d497 inherit pub_methods_classgridfire_1_1engine_1_1EngineView" id="r_a17d63e853d6efca31064e9147c80d497"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1EngineView.html#a17d63e853d6efca31064e9147c80d497">~EngineView</a> ()=default</td></tr>
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 <p>Access the underlying engine instance. </p>
 <dl class="section return"><dt>Returns</dt><dd>Const reference to the underlying engine.</dd></dl>
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 <p>Implements <a class="el" href="classgridfire_1_1engine_1_1EngineView.html#a7884ea8e5618e295e64150f3ecf2c6b5">gridfire::engine::EngineView&lt; gridfire::engine::Engine &gt;</a>.</p>
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 <li>src/python/engine/trampoline/<a class="el" href="py__engine_8h.html">py_engine.h</a></li>
 <li>src/python/engine/trampoline/<a class="el" href="py__engine_8cpp.html">py_engine.cpp</a></li>
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--- a/Show More
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Author	SHA1	Message	Date
Emily Boudreaux	d852ee43fe	perf(precomputation): cleaned up allocations recovered about 5% execution time	2025-12-02 13:09:19 -05:00
Emily Boudreaux	ed2c1d5816	build(.gitignore): .whl added .whl files added to gitignore so large precompiled wheel folders are not accidently commited	2025-12-02 10:04:42 -05:00
Emily Boudreaux	8a22496398	fix(wheels): Repair wheel macos Script to repair RPATH issues in wheels on macos	2025-12-02 10:04:00 -05:00
Emily Boudreaux	e0a05bbd1a	build(cross): macOS cross compilation macos cross compilation now works. macos binaries can be compiled on linux with osxcross installed and built	2025-12-01 13:28:25 -05:00
Emily Boudreaux	e260c7b02c	fix(build): fortran Fortran language only added if build-fortran enabled	2025-12-01 09:59:43 -05:00
Emily Boudreaux	b06b622c06	build(cross): working on cross compilation We want to be able to build all targets on one machine, began implimenting cross compilation	2025-12-01 09:59:22 -05:00
Emily Boudreaux	dac09ae24c	build(fortran): added check for fortran fortran tests only build when fortran build option is enabled	2025-11-30 10:19:56 -05:00
Emily Boudreaux	4fe242a5ef	build(meson): added checks for header compatibility	2025-11-30 10:16:44 -05:00
Emily Boudreaux	a0dcfe4332	build(python): added fvisibility=hidden for python builds In order to avoid massive binaries uploaded to pypi we have worked to reduce the number of symbols included in binaries	2025-11-29 07:15:06 -05:00
Emily Boudreaux	75a88b9720	fix(unity): GridFire supports unity builds GridFire can now support unity builds. This is useful for python bindings. The main limitation is that openssl (a dependency of libplugin) does not support unity builds. Therefore when building in a unity build libplugin must be disabled. This is done with the -Dunity-safe=ture flag at setup time	2025-11-28 11:56:41 -05:00
Emily Boudreaux	bb558811c6	docs(version): v0.7.2_rc2 -> v0.7.3_rc2	2025-11-28 11:30:14 -05:00
Emily Boudreaux	21829c64eb	docs(.gitignore): added libplugin.wrap to gitignore	2025-11-28 11:29:23 -05:00
Emily Boudreaux	7c33b89c77	build(options): Options propegate much more reliably Build options such as build-python and build-fortran have much more predicatable and sensible behavior	2025-11-28 11:28:49 -05:00
Emily Boudreaux	7a4ccff021	fix(clang): fixed a few compiler warnings in clang	2025-11-28 09:53:54 -05:00
Emily M. Boudreaux	21cabfdb66	docs(version): version bump v0.7.0_rc2 -> v0.7.1_rc2 This version brings repairs to gcc builds	2025-11-28 09:46:31 -05:00
Emily M. Boudreaux	a472dc5214	docs(docs): rebuilt for version v0.7.1_rc2	2025-11-28 09:46:00 -05:00
Emily M. Boudreaux	033c5a083d	fix(gcc): Fixed Gridfire on gcc GridFire failed to compile on gcc and gnu stdlibc++ this has been resolved. Further, the boost dependency has been removed since we no longer use boost at all. This should dramatically simplify installation. Finally we have added some build system checks to ensure that the correct version of a C++ and fortran compiler are present on the system	2025-11-28 09:42:54 -05:00
Emily Boudreaux	08a031f30c	Merge pull request #9 from tboudreaux/feature/neutrionoLoss Neutrino Output from GridFire Solvers	2025-11-27 15:10:26 -05:00
Emily Boudreaux	07b2cfd055	docs(docs): rebuilt	2025-11-27 15:06:27 -05:00
Emily Boudreaux	30a5a4d803	docs(readme): Updated Updated readme and docs to reflect new output (neutrino)	2025-11-27 15:06:02 -05:00
Emily Boudreaux	39a689ee5d	feat(neutrino): Updated neutrino output GridFire now reports neutrino loss for reaclib reactions. Note this currently is only computed if precomputation is enabled.	2025-11-27 15:00:51 -05:00
Emily Boudreaux	05175ae87c	feat(neutrino): Started framework for neutrino loss Neutrino loss is essential for neutrino cooling. Started adding framework to track this. Reaclib reactions use a simple heuristic where electron capture reactions loss 100% of their energy to neutrinos whereas beta decay reactions loose 50% of their energy to neutrinos	2025-11-27 14:34:20 -05:00
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