Merge pull request #6 from tboudreaux/feature/weakRates

Added Weak Rates, KINSol, CVODE, Policy, and much more

.gitignore

@@ -76,6 +76,13 @@ subprojects/libconstants/
 subprojects/liblogging/
 subprojects/eigen-*/
 subprojects/fourdst/
+subprojects/libplugin/
+subprojects/minizip-ng-4.0.10/
+subprojects/cvode-*/
+subprojects/kinsol-*/
+subprojects/CLI11-*/
+*.fbundle
+*.wraplock
 
 *.csv
 *.dot
@@ -104,3 +111,5 @@ output/
 scratch/
 
 meson-boost-test/
+
+*.json

Doxyfile

@@ -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         = 0.6.0
+PROJECT_NUMBER         = v0.7.0-alpha
 
 # 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
@@ -2570,7 +2570,7 @@ HIDE_UNDOC_RELATIONS   = YES
 # set to NO
 # The default value is: NO.
 
-HAVE_DOT               = NO
+HAVE_DOT               = YES
 
 # The DOT_NUM_THREADS specifies the number of dot invocations Doxygen is allowed
 # to run in parallel. When set to 0 Doxygen will base this on the number of
@@ -2798,7 +2798,7 @@ DIR_GRAPH_MAX_DEPTH    = 1
 # The default value is: png.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_IMAGE_FORMAT       = png
+DOT_IMAGE_FORMAT       = svg
 
 # If DOT_IMAGE_FORMAT is set to svg or svg:svg or svg:svg:core, then this option
 # can be set to YES to enable generation of interactive SVG images that allow
@@ -2812,7 +2812,7 @@ DOT_IMAGE_FORMAT       = png
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-INTERACTIVE_SVG        = NO
+INTERACTIVE_SVG        = YES
 
 # The DOT_PATH tag can be used to specify the path where the dot tool can be
 # found. If left blank, it is assumed the dot tool can be found in the path.

README.md

@@ -24,6 +24,7 @@
     - [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)
@@ -62,6 +63,16 @@
     - [Python callbacks](#python-callbacks)
 - [Related Projects](#related-projects)
 
+# Version and Notes
+This repository is currently tracking GridFire version v0.7.0-alpha. Note that this
+is a development version which has known scientific and build issues:
+
+1. Over long runs (say 10Gyr) repartitioning stages can introduce discontinuities into abundances
+2. We do not currently produce He-4 at a rate consistent with literature values. This is a known issue and is being addressed.
+3. When using Weak Rate Library (WRL) weak reactions the network becomes pathologically stiff. Reaclib includes a limited set of reactions which can be used to close the CNO cycle. Network construction then defaults to using all reaclib reactions while we address pathological stiffness with WRL rates.
+4. WRL reactions do track energy loss due to neutrinos and neutrino flux; however, these are not currently reported to the user. They will be in the final v0.7.0 release.
+5. There is a current bug in meson-python which results in multiple duplicate LC_RPATH entries in any shared object files compiled for python linking. Recent versions of the macos dynamic loader (XCode command line tools versions >= 16) refuse to load shared object files with duplicat rpath entries. Because of this running `pip install`. in the root will result in a broken gridfire python install. Instead we have bundled a helper script `pip_install_mac_patch.sh` which should be used to install python bindings on macos for the time being. 
+
 # Introduction
 GridFire is a C++ library designed to perform general nuclear network
 evolution. It is part of the larger SERiF project within the 4D-STAR
@@ -109,7 +120,8 @@ are just that and should maintain nearly the same speed as the C++ code. End
 users are strongly encouraged to use the python module rather than the C++ code.
 
 ### pypi
-Installing from pip is as simple as
+Installing from pip is as simple as. Note that this will install gridfire v0.5.0, currently the latest version on pip. Once
+v0.7.0 is released this will be pushed to pip.
 ```bash
 pip install gridfire
 ```
@@ -150,6 +162,8 @@ pip install .
 > **Note:** that if you do not have all system dependencies installed this will
 > fail, the steps in further sections address these in more detail.
 
+> **Note:** If you are using macos you should use the included `pip_install_mac_patch.sh` script instead of `pip install .` as this will automatically patch the build shared object libraries such that they can be loaded by the macos dynamic loader.
+
 ### source for developers
 If you are a developer and would like an editable and incremental python
 install `meson-python` makes this very easy
@@ -166,6 +180,29 @@ of these it does still take a few seconds to recompile regardless of how small
 a source code change you have made). It is **strongly** recommended that
 developers use this approach and end users *do not*.
 
+#### Patching Shared Object Files
+If you need to patch shared object files generated by meson-python directly you should first located the shared object file
+these will be in the site-packages and site-packages/fourdst directories for your python enviroment.
+
+Look for files named
+
+- `site-packages/gridfire.cpython-3*-darwin.so`
+- `site-packages/fourdst/_phys.cpython-3*-darwin.so` 
+
+then, for each of these files, run
+
+```bash
+otool -l <Path/to/file> | grep RPATH -A2
+```
+
+count the number of occurences of duplicate RPATH entries (these should look like `@loaderpath/.gridfire.mesonpy.libs` or `@loaderpath/../.fourdst.mesonpy.libs`). Then use `install_name_tool` to remove **all but one of these** from each shared object file.
+
+If for example there are 4 occurrences of the path `@loader_path/../.fourdst.mesonpy.libs` in `_phys.cpython-3*-darwin.so` then you should run the following command 3 times
+```bash
+install_name_tool -delete_rpath @loader_path/../.fourdst.mesonpy.libs site-packages/fourdst/_phys.cpython-314-darwin.so
+```
+
+the same for the other shared object file (make sure to count the duplicate rpath entries for each separately as there may be a different number of duplicates in each shared object file).
 
 ## Automatic Build and Installation
 ### Script Build and Installation Instructions
@@ -351,8 +388,10 @@ include:
   2000](https://www.sciencedirect.com/science/article/pii/S0092640X00908349?via%3Dihub]))
   to weight reaction rates based on nuclear properties.
 - **Solver Module:** Defines numerical integration strategies (e.g.,
-  `DirectNetworkSolver`) for solving the stiff ODE systems arising from reaction
+  `CVODESolverStrategy`) for solving the stiff ODE systems arising from reaction
   networks.
+- **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.
 - **Python Interface:** Exposes *almost* all C++ functionality to Python,
   allowing users to define compositions, configure engines, and run simulations
   directly from Python scripts.
@@ -404,6 +443,7 @@ construction and rate evaluations:
       member of the `NetworkBuildDepth` enum or an integer.
     - `partition::PartitionFunction`: Partition function used when evaluating
       detailed balance for inverse rates.
+    - `NetworkConstructionFlags`: A bitwise flag telling the network how to construct itself. That is, what reaction types should be used in construction. For example one might use `NetworkConstructionFlags::STRONG | NetworkConstructionFlags::BETA_PLUS` to use all strong reactions and β+ decay. By Default this is set to use reaclib strong and reaclib weak (no WRL included by default due to current pathological stiffness issues).
 
 - **setPrecomputation(bool precompute):**
     - Enable/disable caching of reaction rates and stoichiometric data at initialization.
@@ -533,48 +573,23 @@ A `NetOut` struct contains
 >**Note:** Currently `GraphEngine` only considers energy due to nuclear mass
 >defect and not neutrino loss.
 
+### CVODESolverStrategy
 
-### DirectNetworkSolver (Implicit Rosenbrock Method)
+We use the CVODE module from [SUNDIALS](https://computing.llnl.gov/projects/sundials/cvode) as our primary numerical
+solver. Specifically we use the BDF linear multistep method from that which includes advanced adaptive timestepping.
 
-- **Integrator:** Implicit Rosenbrock4 scheme (order 4) via `Boost.Odeint`’s
+Further, we use a trigger system to periodically repartition the network as the state of the network changes. This
-  `rosenbrock4<double>`, optimized for stiff reaction networks with adaptive step
+keeps the stiffness of the network tractable. The algorithm we use for that is 
-  size control using configurable absolute and relative tolerances.
-- **Jacobian Assembly:** Asks the base engine for the Jacobian Matrix
-- **RHS Evaluation:** Asks the base engine for RHS of the abundance evolution
-  equations
-- **Linear Algebra:** Utilizes `Boost.uBLAS` for state vectors and dense Jacobian
-  matrices, with sparse access patterns supported via coordinate lists of nonzero
-  entries.
-- **Error Control and Logging:** Absolute and relative tolerance parameters
-  (`absTol`, `relTol`) are read from configuration; Quill loggers, which run in a
-  separate non blocking thread, capture integration diagnostics and step
-  statistics.
 
-### Algorithmic Workflow in DirectNetworkSolver
+1. Trigger every 1000th time that the simulation time exceeds the simulationTimeInterval
-1. **Initialization:** Convert input temperature to T9 units, retrieve
+2. OR if any off-diagonal Jacobian entry exceeds the offDiagonalThreshold
-   tolerances, and initialize state vector `Y` from equilibrated composition.
+3. OR every 10th time that the timestep growth exceeds the timestepGrowthThreshold (relative or absolute)
-2. **Integrator Setup:** Construct the controlled Rosenbrock4 stepper and bind
+4. OR if the number of convergence failures grows more than 100% from one step to the next or exceeds 5 at any given step.
-   `RHSManager` and `JacobianFunctor`.
-3. **Adaptive Integration Loop:**
-    - Perform `integrate_adaptive` advancing until `tMax`, catching any
-      `StaleEngineTrigger` to repartition the network and update composition.
-    - On each substep, observe states and log via `RHSManager::observe`.
-4. **Finalization:** Assemble final mass fractions, compute accumulated energy,
-   and populate `NetOut` with updated composition and diagnostics.
 
-### Future Solver Implementations
+Moreover, callback functions can be registered in either python or C++ which will take a `const CVODESolverStrategy::TimestepContext&` struct 
-- **Operator Splitting Solvers:** Strategies to decouple thermodynamics,
+as argument. This allows for more complex logging logic. Note that callbacks **do not** let you reach inside the 
-  screening, and reaction substeps for performance on stiff, multiscale
+solver and adjust the state of the network. They are only intended for investigation not extension of physics. If you
-  networks.
+wish to extend the physics this must be implemented at the engine or engine view level.
-- **GPU-Accelerated Solvers:** Planned use of CUDA/OpenCL backends for
-  large-scale network integration.
-- **Callback observer support:** Currently we use an observer built into our
-  `RHSManager` (`RHSManager::observe`); however, we intend to include support for
-  custom, user defined, observer method.
-
-These strategies can be developed by inheriting from `NetworkSolverStrategy`
-and registering against the same engine types without modifying existing engine
-code.
 
 ## Python Extensibility
 Through the Python bindings, users can subclass engine view classes directly in
@@ -667,7 +682,7 @@ int main(){
     gridfire::AdaptiveEngineView adaptView(msView);
 
     // 5. Construct implicit solver (handles remaining stiffness)
-    gridfire::DirectNetworkSolver solver(adaptView);
+    gridfire::CVODESolverStrategey solver(adaptView);
 
     // 6. Prepare input conditions
     NetIn input{
@@ -684,20 +699,6 @@ int main(){
 }
 ```
 
-#### Workflow Components and Effects
-- **GraphEngine** constructs the full reaction network, capturing all species
-  and reactions.
-- **MultiscalePartitioningEngineView** segregates reactions by characteristic
-  timescales (Hix & Thielemann), reducing the effective stiffness by treating
-  fast processes separately.
-- **AdaptiveEngineView** prunes low-flux species/reactions at runtime,
-  decreasing dimensionality and improving computational efficiency.
-- **DirectNetworkSolver** employs an implicit Rosenbrock method to stably
-  integrate the remaining stiff system with adaptive step control.
-
-This layered approach enhances stability for stiff networks while maintaining
-accuracy and performance.
-
 ### Callback Example
 Custom callback functions can be registered with any solver. Because it might make sense for each solver to provide
 different context to the callback function, you should use the struct `gridfire::solver::<SolverName>::TimestepContext`
@@ -712,7 +713,7 @@ the callback function.
 
 #include <iostream>
 
-void callback(const gridfire::solver::DirectNetworkSolver::TimestepContext& context) {
+void callback(const gridfire::solver::CVODESolverStrategy::TimestepContext& context) {
     int H1Index = context.engine.getSpeciesIndex(fourdst::atomic::H_1);
     int He4Index = context.engine.getSpeciesIndex(fourdst::atomic::He_4);
 
@@ -741,7 +742,7 @@ int main(){
     gridfire::AdaptiveEngineView adaptView(msView);
 
     // 5. Construct implicit solver (handles remaining stiffness)
-    gridfire::DirectNetworkSolver solver(adaptView);
+    gridfire::CVODESolverStrategy solver(adaptView);
     solver.set_callback(callback);
 
     // 6. Prepare input conditions
@@ -758,12 +759,29 @@ int main(){
     std::cout << "Final results are: " << output << std::endl;
 }
 ```
+>**Note:** If you want to see exactly why each repartitioning stage was triggered in a human readable manner add the flag True to `solver.evaluate` (`solver.evaluate(input, true)`).
 
 >**Note:** A fully detailed list of all available information in the TimestepContext struct is available in the API documentation.
 
 >**Note:** The order of species in the boost state vector (`ctx.state`) is **not guaranteed** to be any particular order run over run. Therefore, in order to reliably extract
 > values from it, you **must** use the `getSpeciesIndex` method of the engine to get the index of the species you are interested in (these will always be in the same order).
 
+If you wish to know what is provided by a solver context without investigating the code you can simply do
+
+```c++
+void callback(const gridfire::solver::SolverContextBase& context) {
+    for (const auto& [parameterName, description] : context.describe()) {
+        std::cout << parameterName << ": " << description << "\n";
+    }
+    std::cout << std::flush();
+    exit(0);
+}
+```
+
+If you set this as the callback (to any solver strategy) it will print out the available parameters and what they
+are and then close the code. This is useful when writing new callbacks.
+
+
 #### Callback Context
 
 Since each solver may provide different context to the callback function, and it may be frustrating to refer to the
@@ -789,7 +807,7 @@ All GridFire C++ types have been bound and can be passed around as one would exp
 This example implements the same logic as the above C++ example
 ```python
 from gridfire.engine import GraphEngine, MultiscalePartitioningEngineView, AdaptiveEngineView
-from gridfire.solver import DirectNetworkSolver
+from gridfire.solver import CVODESolverStrategey
 from gridfire.type import NetIn
 
 from fourdst.composition import Composition
@@ -819,7 +837,7 @@ qseEngine = MultiscalePartitioningEngineView(baseEngine)
 
 adaptiveEngine = AdaptiveEngineView(qseEngine)
 
-solver = DirectNetworkSolver(adaptiveEngine)
+solver = CVODESolverStrategey(adaptiveEngine)
 
 results = solver.evaluate(netIn)
 
@@ -869,12 +887,14 @@ adaptiveEngine = AdaptiveEngineView(qseEngine)
 solver = DirectNetworkSolver(adaptiveEngine)
 
 
+data: List[Tuple[float, Dict[str, Tuple[float, float]]]] = []
 def callback(context):
-    H1Index = context.engine.getSpeciesIndex(species["H-1"])
+    engine = context.engine
-    He4Index = context.engine.getSpeciesIndex(species["He-4"])
+    abundances: Dict[str, Tuple[float, float]] = {}
-    C12ndex = context.engine.getSpeciesIndex(species["C-12"])
+    for species in engine.getNetworkSpecies():
-    Mgh24ndex = context.engine.getSpeciesIndex(species["Mg-24"])
+        sid = engine.getSpeciesIndex(species)
-    print(f"Time: {context.t}, H-1: {context.state[H1Index]}, He-4: {context.state[He4Index]}, C-12: {context.state[C12ndex]}, Mg-24: {context.state[Mgh24ndex]}")
+        abundances[species.name()] = (species.mass(), context.state[sid])
+    data.append((context.t,abundances))
 
 solver.set_callback(callback)
 results = solver.evaluate(netIn)

assets/static/meson.build

@@ -1 +0,0 @@
-subdir('reaclib')

assets/static/reaclib/readme.md

@@ -1 +0,0 @@
-Use the utility `utils/reaclib/format.py` to generate reacitons.bin

build-config/CLI11/meson.build

@@ -0,0 +1,2 @@
+cli11_proj = subproject('cli11')
+cli11_dep = cli11_proj.get_variable('CLI11_dep')

build-config/json/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2013-2025 Niels Lohmann
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

build-config/json/meson.build

@@ -0,0 +1,3 @@
+json_dep = declare_dependency(
+    include_directories: include_directories('include')
+)

build-config/libplugin/meson.build

@@ -0,0 +1,5 @@
+libplugin_sp = subproject('libplugin')
+
+plugin_dep = libplugin_sp.get_variable('plugin_dep')
+libplugin = libplugin_sp.get_variable('libplugin')
+

build-config/meson.build

@@ -1,11 +1,17 @@
 cmake = import('cmake')
 
 subdir('fourdst')
+subdir('libplugin')
+
+subdir('sundials')
+
 subdir('boost')
 subdir('cppad')
 subdir('xxHash')
 subdir('eigen')
 
+subdir('json')
+
 subdir('pybind')
 
-
+subdir('CLI11')

build-config/sundials/cvode/meson.build

@@ -0,0 +1,47 @@
+cmake = import('cmake')
+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_STATIC_LIBS' : 'OFF',
+
+})
+
+cvode_cmake_options.add_cmake_defines({
+    'CMAKE_INSTALL_LIBDIR': get_option('libdir'),
+    'CMAKE_INSTALL_INCLUDEDIR': get_option('includedir')
+})
+
+cvode_sp = cmake.subproject(
+    'cvode',
+    options: cvode_cmake_options,
+)
+
+# For the core SUNDIALS library (SUNContext, etc.)
+sundials_core_dep = cvode_sp.dependency('sundials_core_shared')
+
+# For the CVODE integrator library
+sundials_cvode_dep = cvode_sp.dependency('sundials_cvode_shared')
+
+# For the serial NVector library
+sundials_nvecserial_dep = cvode_sp.dependency('sundials_nvecserial_shared')
+
+# For the dense matrix library
+sundials_sunmatrixdense_dep = cvode_sp.dependency('sundials_sunmatrixdense_shared')
+
+# For the dense linear solver library
+sundials_sunlinsoldense_dep = cvode_sp.dependency('sundials_sunlinsoldense_shared')
+
+cvode_dep = declare_dependency(
+    dependencies: [
+        sundials_core_dep,
+        sundials_cvode_dep,
+        sundials_nvecserial_dep,
+        sundials_sunmatrixdense_dep,
+        sundials_sunlinsoldense_dep,
+    ],
+)
+
+

build-config/sundials/kinsol/meson.build

@@ -0,0 +1,29 @@
+cmake = import('cmake')
+
+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_STATIC_LIBS' : 'OFF',
+})
+
+kinsol_cmake_options.add_cmake_defines({
+    'CMAKE_INSTALL_LIBDIR': get_option('libdir'),
+    'CMAKE_INSTALL_INCLUDEDIR': get_option('includedir')
+})
+
+kinsol_sp = cmake.subproject(
+    'kinsol',
+    options: kinsol_cmake_options,
+)
+
+sundials_kinsol_shared = kinsol_sp.dependency('sundials_kinsol_shared')
+
+kinsol_dep = declare_dependency(
+    dependencies: [
+        sundials_kinsol_shared,
+    ]
+)
+

build-config/sundials/meson.build

@@ -0,0 +1,9 @@
+subdir('cvode')
+subdir('kinsol')
+
+sundials_dep = declare_dependency(
+    dependencies: [
+        cvode_dep,
+        kinsol_dep,
+    ],
+)

build-python/fix_rpaths.py

@@ -0,0 +1,95 @@
+#!/usr/bin/env python3
+
+import os
+import sys
+import glob
+import subprocess
+from collections import OrderedDict
+
+def get_rpaths(binary_path):
+    """Uses otool to extract a list of all LC_RPATH entries."""
+    print(f"--- Checking rpaths for: {binary_path}")
+    rpaths = []
+    try:
+        proc = subprocess.run(
+            ['otool', '-l', binary_path],
+            capture_output=True,
+            text=True,
+            check=True
+        )
+
+        lines = proc.stdout.splitlines()
+        for i, line in enumerate(lines):
+            if "cmd LC_RPATH" in line.strip():
+                if i + 2 < len(lines):
+                    path_line = lines[i + 2].strip()
+                    if path_line.startswith("path "):
+                        # Extract the path, e.g., "path /foo/bar (offset 12)"
+                        rpath = path_line.split(" ")[1]
+                        rpaths.append(rpath)
+
+    except (subprocess.CalledProcessError, FileNotFoundError) as e:
+        print(f"Error running otool: {e}")
+        return []
+
+    return rpaths
+
+def fix_rpaths(binary_path):
+    all_rpaths = get_rpaths(binary_path)
+    if not all_rpaths:
+        print("--- No rpaths found or otool failed.")
+        return
+
+    unique_rpaths = list(OrderedDict.fromkeys(all_rpaths))
+    for rpath in unique_rpaths:
+        print(f" - RPATH: {rpath}")
+
+    if len(all_rpaths) == len(unique_rpaths):
+        print("--- No duplicate rpaths found. Nothing to do.")
+        return
+
+    print(f"--- Found {len(all_rpaths)} rpaths; {len(unique_rpaths)} are unique.")
+    print(f"--- Fixing duplicates in: {binary_path}")
+
+    try:
+        for rpath in all_rpaths:
+            subprocess.run(
+                ['install_name_tool', '-delete_rpath', rpath, binary_path],
+                check=True,
+                capture_output=True
+            )
+
+        for rpath in unique_rpaths:
+            subprocess.run(
+                ['install_name_tool', '-add_rpath', rpath, binary_path],
+                check=True,
+                capture_output=True
+            )
+
+        print("--- Successfully fixed rpaths.")
+
+    except (subprocess.CalledProcessError, FileNotFoundError) as e:
+        print(f"--- Error running install_name_tool: {e}")
+        if e.stderr:
+            print(f"STDERR: {e.stderr.decode()}")
+        if e.stdout:
+            print(f"STDOUT: {e.stdout.decode()}")
+        sys.exit(1) # Fail the install if we can't fix it
+
+def main():
+    if len(sys.argv) != 2:
+        print(f"--- Error: Expected one argument (path to .so file), got {sys.argv}", file=sys.stderr)
+        sys.exit(1)
+
+    # Get the file path directly from the command line argument
+    so_file_path = sys.argv[1]
+
+    if not os.path.exists(so_file_path):
+        print(f"--- Error: File not found at {so_file_path}", file=sys.stderr)
+        sys.exit(1)
+
+    print(f"--- Fixing rpaths for built file: {so_file_path}")
+    fix_rpaths(so_file_path)
+
+if __name__ == "__main__":
+    main()

build-python/meson.build

@@ -1,6 +1,14 @@
 # --- Python Extension Setup ---
 py_installation = import('python').find_installation('python3')
 
+gridfire_py_deps = [
+    pybind11_dep,
+    const_dep,
+    config_dep,
+    composition_dep,
+    gridfire_dep
+]
+
 py_mod = py_installation.extension_module(
     'gridfire', # Name of the generated .so/.pyd file (without extension)
     sources: [
@@ -21,13 +29,7 @@ py_mod = py_installation.extension_module(
         meson.project_source_root() + '/src/python/solver/trampoline/py_solver.cpp',
         meson.project_source_root() + '/src/python/utils/bindings.cpp',
     ],
-    dependencies : [
+    dependencies : gridfire_py_deps,
-        pybind11_dep,
-        const_dep,
-        config_dep,
-        composition_dep,
-        gridfire_dep,
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+<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 />
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+<code>#include &lt;sunlinsol/sunlinsol_dense.h&gt;</code><br />
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+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structgridfire_1_1solver_1_1_c_v_o_d_e_solver_strategy_1_1_timestep_context.html">gridfire::solver::CVODESolverStrategy::TimestepContext</a></td></tr>
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+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structgridfire_1_1solver_1_1_c_v_o_d_e_solver_strategy_1_1_c_v_o_d_e_user_data.html">gridfire::solver::CVODESolverStrategy::CVODEUserData</a></td></tr>
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-<tr id="row_0_1_0_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1_engine_error.html" target="_self">EngineError</a></td><td class="desc"></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_1_graph_engine_1_1constants.html" target="_self">constants</a></td><td class="desc"></td></tr>
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+<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>
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-<tr id="row_0_4_4_1_" class="even"><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_1_rauscher_thielemann_partition_function_1_1_interpolation_points.html" target="_self">InterpolationPoints</a></td><td class="desc"></td></tr>
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-<tr id="row_0_4_4_2_" class="odd"><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_1_rauscher_thielemann_partition_function_1_1_isotope_data.html" target="_self">IsotopeData</a></td><td class="desc"></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_5_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_5_" class="arrow" onclick="dynsection.toggleFolder('0_5_')">&#9660;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1reaclib.html" target="_self">reaclib</a></td><td class="desc"></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_1_grid_fire_error.html" target="_self">GridFireError</a></td><td class="desc">Base class for GridFire exceptions </td></tr>
-<tr id="row_0_5_0_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1reaclib_1_1_reaction_record.html" target="_self">ReactionRecord</a></td><td class="desc"></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_1_hashing_error.html" target="_self">HashingError</a></td><td class="desc">Exception class for hashing-related errors in GridFire </td></tr>
-<tr id="row_0_6_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_6_" class="arrow" onclick="dynsection.toggleFolder('0_6_')">&#9660;</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_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_6_0_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html" target="_self">LogicalReaction</a></td><td class="desc">Represents a "logical" reaction that aggregates rates from multiple sources </td></tr>
+<tr id="row_0_1_9_" 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_invalid_q_s_e_solution_error.html" target="_self">InvalidQSESolutionError</a></td><td class="desc">Exception for invalid QSE solution in the engine </td></tr>
-<tr id="row_0_6_1_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1reaction_1_1_rate_coefficient_set.html" target="_self">RateCoefficientSet</a></td><td class="desc">Holds the seven coefficients for the REACLIB rate equation </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_1_jacobian_error.html" target="_self">JacobianError</a></td><td class="desc">Base class for Jacobian-related exceptions </td></tr>
-<tr id="row_0_6_2_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="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_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_1_k_i_n_sol_solver_failure_error.html" target="_self">KINSolSolverFailureError</a></td><td class="desc">Exception for failures in the KINSOL solver </td></tr>
-<tr id="row_0_6_3_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1reaction_1_1_templated_reaction_set.html" target="_self">TemplatedReactionSet</a></td><td class="desc"></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_7_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_7_" class="arrow" onclick="dynsection.toggleFolder('0_7_')">&#9660;</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_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_7_0_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1screening_1_1_bare_screening_model.html" target="_self">BareScreeningModel</a></td><td class="desc">A screening model that applies no screening effect </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_7_1_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1screening_1_1_screening_model.html" target="_self">ScreeningModel</a></td><td class="desc">An abstract base class for plasma screening models </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_7_2_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1screening_1_1_weak_screening_model.html" target="_self">WeakScreeningModel</a></td><td class="desc">Implements the weak screening model based on the Debye-Hückel approximation </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_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_')">&#9660;</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_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_8_0_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_8_0_" class="arrow" onclick="dynsection.toggleFolder('0_8_0_')">&#9660;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1solver_1_1_direct_network_solver.html" target="_self">DirectNetworkSolver</a></td><td class="desc">A network solver that directly integrates the reaction network ODEs </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_8_0_0_" class="odd"><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_1_direct_network_solver_1_1_jacobian_functor.html" target="_self">JacobianFunctor</a></td><td class="desc">Functor for calculating the Jacobian matrix </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_8_0_1_" class="even"><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_1_direct_network_solver_1_1_r_h_s_manager.html" target="_self">RHSManager</a></td><td class="desc">Functor for calculating the right-hand side of the ODEs </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_1_solver_error.html" target="_self">SolverError</a></td><td class="desc">Base class for all exceptions related to solver operations </td></tr>
-<tr id="row_0_8_0_2_" class="odd"><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_1_direct_network_solver_1_1_timestep_context.html" target="_self">TimestepContext</a></td><td class="desc">Context for the timestep callback function for the <a class="el" href="classgridfire_1_1solver_1_1_direct_network_solver.html" title="A network solver that directly integrates the reaction network ODEs.">DirectNetworkSolver</a> </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_8_1_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1solver_1_1_network_solver_strategy.html" target="_self">NetworkSolverStrategy</a></td><td class="desc">Abstract base class for network solver strategies </td></tr>
+<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_1_s_u_n_d_i_a_l_s_error.html" target="_self">SUNDIALSError</a></td><td class="desc">Base class for exceptions related to SUNDIALS solver operations </td></tr>
-<tr id="row_0_8_2_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1solver_1_1_solver_context_base.html" target="_self">SolverContextBase</a></td><td class="desc">Base class for solver callback contexts </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_1_unable_to_set_network_reactions_error.html" target="_self">UnableToSetNetworkReactionsError</a></td><td class="desc">Exception for failures in setting network reactions </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_')">&#9660;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_adaptive_engine_view.html" target="_self">AdaptiveEngineView</a></td><td class="desc">An engine view that dynamically adapts the reaction network based on runtime conditions </td></tr>
+<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_1_uninitialized_jacobian_error.html" target="_self">UninitializedJacobianError</a></td><td class="desc">Exception for uninitialized Jacobian matrix access </td></tr>
-<tr id="row_0_9_0_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html" target="_self">ReactionFlow</a></td><td class="desc">A struct to hold a reaction and its flow rate </td></tr>
+<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_1_unknown_jacobian_error.html" target="_self">UnknownJacobianError</a></td><td class="desc">Exception for unknown Jacobian matrix access </td></tr>
-<tr id="row_0_10_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_defined_engine_view.html" target="_self">DefinedEngineView</a></td><td class="desc"></td></tr>
+<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_1_utility_error.html" target="_self">UtilityError</a></td><td class="desc">Base class for utility-related errors in GridFire </td></tr>
-<tr id="row_0_11_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_dynamic_engine.html" target="_self">DynamicEngine</a></td><td class="desc">Abstract class for engines supporting Jacobian and stoichiometry operations </td></tr>
+<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="dynsection.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>
-<tr id="row_0_12_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_engine.html" target="_self">Engine</a></td><td class="desc">Abstract base class for a reaction network engine </td></tr>
+<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="dynsection.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>
-<tr id="row_0_13_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_engine_view.html" target="_self">EngineView</a></td><td class="desc">Abstract base class for a "view" of a reaction network engine </td></tr>
+<tr id="row_0_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_1_py_function_def.html" target="_self">PyFunctionDef</a></td><td class="desc">Structure representing a Python function definition </td></tr>
-<tr id="row_0_14_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1_file_defined_engine_view.html" target="_self">FileDefinedEngineView</a></td><td class="desc"></td></tr>
+<tr id="row_0_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_1_m_e_s_a_network_file_parser.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_2_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_1io_1_1_network_file_parser.html" target="_self">NetworkFileParser</a></td><td class="desc">An abstract base class for network file parsers </td></tr>
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+<tr id="row_0_2_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_1io_1_1_simple_reaction_list_file_parser.html" target="_self">SimpleReactionListFileParser</a></td><td class="desc">A parser for simple text files containing a list of reactions </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="dynsection.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>
-<tr id="row_0_15_2_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html" target="_self">PrecomputedReaction</a></td><td class="desc"></td></tr>
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+<tr id="row_0_3_4_1_" 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_1_rauscher_thielemann_partition_function_1_1_interpolation_points.html" target="_self">InterpolationPoints</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_1_rauscher_thielemann_partition_function_1_1_isotope_data.html" target="_self">IsotopeData</a></td><td class="desc"></td></tr>
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+<tr id="row_0_4_7_" 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_1_hot_c_n_o_i_i_chain_policy.html" target="_self">HotCNOIIChainPolicy</a></td><td class="desc">Hot CNO II 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_1_hot_c_n_o_i_i_i_chain_policy.html" target="_self">HotCNOIIIChainPolicy</a></td><td class="desc">Hot CNO III Chain Policy </td></tr>
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+<tr id="row_0_13_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1_net_out.html" target="_self">NetOut</a></td><td class="desc"></td></tr>
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+<tr id="row_7_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_network_file_parser.html" target="_self">PyNetworkFileParser</a></td><td class="desc"></td></tr>
+<tr id="row_8_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_partition_function.html" target="_self">PyPartitionFunction</a></td><td class="desc"></td></tr>
+<tr id="row_9_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_screening.html" target="_self">PyScreening</a></td><td class="desc"></td></tr>
+<tr id="row_10_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_py_solver_context_base.html" target="_self">PySolverContextBase</a></td><td class="desc"></td></tr>
+<tr id="row_11_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_solver_plugin_interface.html" target="_self">SolverPluginInterface</a></td><td class="desc"></td></tr>
 </table>
 </div><!-- directory -->
 </div><!-- contents -->

docs/html/annotated_dup.js

@@ -1,26 +1,56 @@
 var annotated_dup =
 [
     [ "gridfire", "namespacegridfire.html", [
-      [ "approx8", "namespacegridfire_1_1approx8.html", [
+      [ "engine", "namespacegridfire_1_1engine.html", [
-        [ "Approx8Net", "structgridfire_1_1approx8_1_1_approx8_net.html", "structgridfire_1_1approx8_1_1_approx8_net" ],
+        [ "AdaptiveEngineView", "classgridfire_1_1engine_1_1_adaptive_engine_view.html", "classgridfire_1_1engine_1_1_adaptive_engine_view" ],
-        [ "Approx8Network", "classgridfire_1_1approx8_1_1_approx8_network.html", "classgridfire_1_1approx8_1_1_approx8_network" ],
+        [ "DefinedEngineView", "classgridfire_1_1engine_1_1_defined_engine_view.html", "classgridfire_1_1engine_1_1_defined_engine_view" ],
-        [ "Jacobian", "structgridfire_1_1approx8_1_1_jacobian.html", "structgridfire_1_1approx8_1_1_jacobian" ],
+        [ "DynamicEngine", "classgridfire_1_1engine_1_1_dynamic_engine.html", "classgridfire_1_1engine_1_1_dynamic_engine" ],
-        [ "ODE", "structgridfire_1_1approx8_1_1_o_d_e.html", "structgridfire_1_1approx8_1_1_o_d_e" ]
+        [ "EnergyDerivatives", "structgridfire_1_1engine_1_1_energy_derivatives.html", "structgridfire_1_1engine_1_1_energy_derivatives" ],
+        [ "Engine", "classgridfire_1_1engine_1_1_engine.html", "classgridfire_1_1engine_1_1_engine" ],
+        [ "EngineView", "classgridfire_1_1engine_1_1_engine_view.html", "classgridfire_1_1engine_1_1_engine_view" ],
+        [ "FileDefinedEngineView", "classgridfire_1_1engine_1_1_file_defined_engine_view.html", "classgridfire_1_1engine_1_1_file_defined_engine_view" ],
+        [ "GraphEngine", "classgridfire_1_1engine_1_1_graph_engine.html", "classgridfire_1_1engine_1_1_graph_engine" ],
+        [ "MultiscalePartitioningEngineView", "classgridfire_1_1engine_1_1_multiscale_partitioning_engine_view.html", "classgridfire_1_1engine_1_1_multiscale_partitioning_engine_view" ],
+        [ "NetworkJacobian", "classgridfire_1_1engine_1_1_network_jacobian.html", "classgridfire_1_1engine_1_1_network_jacobian" ],
+        [ "NetworkPrimingEngineView", "classgridfire_1_1engine_1_1_network_priming_engine_view.html", "classgridfire_1_1engine_1_1_network_priming_engine_view" ],
+        [ "PrimingReport", "structgridfire_1_1engine_1_1_priming_report.html", "structgridfire_1_1engine_1_1_priming_report" ],
+        [ "Reaction", "classgridfire_1_1engine_1_1_reaction.html", "classgridfire_1_1engine_1_1_reaction" ],
+        [ "ReactionSet", "classgridfire_1_1engine_1_1_reaction_set.html", "classgridfire_1_1engine_1_1_reaction_set" ],
+        [ "StepDerivatives", "structgridfire_1_1engine_1_1_step_derivatives.html", "structgridfire_1_1engine_1_1_step_derivatives" ]
       ] ],
       [ "exceptions", "namespacegridfire_1_1exceptions.html", [
-        [ "EngineError", "classgridfire_1_1exceptions_1_1_engine_error.html", null ],
+        [ "BadCollectionError", "classgridfire_1_1exceptions_1_1_bad_collection_error.html", null ],
-        [ "FailedToPartitionEngineError", "classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html", "classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error" ],
+        [ "BadRHSEngineError", "classgridfire_1_1exceptions_1_1_bad_r_h_s_engine_error.html", null ],
-        [ "NetworkResizedError", "classgridfire_1_1exceptions_1_1_network_resized_error.html", "classgridfire_1_1exceptions_1_1_network_resized_error" ],
+        [ "CVODESolverFailureError", "classgridfire_1_1exceptions_1_1_c_v_o_d_e_solver_failure_error.html", null ],
-        [ "StaleEngineError", "classgridfire_1_1exceptions_1_1_stale_engine_error.html", "classgridfire_1_1exceptions_1_1_stale_engine_error" ],
+        [ "DebugException", "classgridfire_1_1exceptions_1_1_debug_exception.html", "classgridfire_1_1exceptions_1_1_debug_exception" ],
-        [ "StaleEngineTrigger", "classgridfire_1_1exceptions_1_1_stale_engine_trigger.html", "classgridfire_1_1exceptions_1_1_stale_engine_trigger" ],
+        [ "EngineError", "classgridfire_1_1exceptions_1_1_engine_error.html", "classgridfire_1_1exceptions_1_1_engine_error" ],
-        [ "UnableToSetNetworkReactionsError", "classgridfire_1_1exceptions_1_1_unable_to_set_network_reactions_error.html", "classgridfire_1_1exceptions_1_1_unable_to_set_network_reactions_error" ]
+        [ "FailedToPartitionEngineError", "classgridfire_1_1exceptions_1_1_failed_to_partition_engine_error.html", null ],
-      ] ],
+        [ "GridFireError", "classgridfire_1_1exceptions_1_1_grid_fire_error.html", "classgridfire_1_1exceptions_1_1_grid_fire_error" ],
-      [ "expectations", "namespacegridfire_1_1expectations.html", [
+        [ "HashingError", "classgridfire_1_1exceptions_1_1_hashing_error.html", null ],
-        [ "EngineError", "structgridfire_1_1expectations_1_1_engine_error.html", "structgridfire_1_1expectations_1_1_engine_error" ],
+        [ "IllConditionedJacobianError", "classgridfire_1_1exceptions_1_1_ill_conditioned_jacobian_error.html", null ],
-        [ "EngineIndexError", "structgridfire_1_1expectations_1_1_engine_index_error.html", "structgridfire_1_1expectations_1_1_engine_index_error" ],
+        [ "InvalidQSESolutionError", "classgridfire_1_1exceptions_1_1_invalid_q_s_e_solution_error.html", null ],
-        [ "StaleEngineError", "structgridfire_1_1expectations_1_1_stale_engine_error.html", "structgridfire_1_1expectations_1_1_stale_engine_error" ]
+        [ "JacobianError", "classgridfire_1_1exceptions_1_1_jacobian_error.html", null ],
+        [ "KINSolSolverFailureError", "classgridfire_1_1exceptions_1_1_k_i_n_sol_solver_failure_error.html", null ],
+        [ "MissingBaseReactionError", "classgridfire_1_1exceptions_1_1_missing_base_reaction_error.html", null ],
+        [ "MissingKeyReactionError", "classgridfire_1_1exceptions_1_1_missing_key_reaction_error.html", null ],
+        [ "MissingSeedSpeciesError", "classgridfire_1_1exceptions_1_1_missing_seed_species_error.html", null ],
+        [ "NetworkResizedError", "classgridfire_1_1exceptions_1_1_network_resized_error.html", null ],
+        [ "PolicyError", "classgridfire_1_1exceptions_1_1_policy_error.html", "classgridfire_1_1exceptions_1_1_policy_error" ],
+        [ "ReactionError", "classgridfire_1_1exceptions_1_1_reaction_error.html", "classgridfire_1_1exceptions_1_1_reaction_error" ],
+        [ "ReactionParsingError", "classgridfire_1_1exceptions_1_1_reaction_parsing_error.html", "classgridfire_1_1exceptions_1_1_reaction_parsing_error" ],
+        [ "SingularJacobianError", "classgridfire_1_1exceptions_1_1_singular_jacobian_error.html", null ],
+        [ "SolverError", "classgridfire_1_1exceptions_1_1_solver_error.html", "classgridfire_1_1exceptions_1_1_solver_error" ],
+        [ "StaleJacobianError", "classgridfire_1_1exceptions_1_1_stale_jacobian_error.html", null ],
+        [ "SUNDIALSError", "classgridfire_1_1exceptions_1_1_s_u_n_d_i_a_l_s_error.html", null ],
+        [ "UnableToSetNetworkReactionsError", "classgridfire_1_1exceptions_1_1_unable_to_set_network_reactions_error.html", null ],
+        [ "UninitializedJacobianError", "classgridfire_1_1exceptions_1_1_uninitialized_jacobian_error.html", null ],
+        [ "UnknownJacobianError", "classgridfire_1_1exceptions_1_1_unknown_jacobian_error.html", null ],
+        [ "UtilityError", "classgridfire_1_1exceptions_1_1_utility_error.html", "classgridfire_1_1exceptions_1_1_utility_error" ]
       ] ],
       [ "io", "namespacegridfire_1_1io.html", [
+        [ "gen", "namespacegridfire_1_1io_1_1gen.html", [
+          [ "PyFunctionDef", "structgridfire_1_1io_1_1gen_1_1_py_function_def.html", "structgridfire_1_1io_1_1gen_1_1_py_function_def" ]
+        ] ],
         [ "MESANetworkFileParser", "classgridfire_1_1io_1_1_m_e_s_a_network_file_parser.html", "classgridfire_1_1io_1_1_m_e_s_a_network_file_parser" ],
         [ "NetworkFileParser", "classgridfire_1_1io_1_1_network_file_parser.html", "classgridfire_1_1io_1_1_network_file_parser" ],
         [ "SimpleReactionListFileParser", "classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html", "classgridfire_1_1io_1_1_simple_reaction_list_file_parser" ]
@@ -34,46 +64,92 @@ var annotated_dup =
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       ] ],
+      [ "policy", "namespacegridfire_1_1policy.html", [
+        [ "CNOChainPolicy", "classgridfire_1_1policy_1_1_c_n_o_chain_policy.html", "classgridfire_1_1policy_1_1_c_n_o_chain_policy" ],
+        [ "CNOIChainPolicy", "classgridfire_1_1policy_1_1_c_n_o_i_chain_policy.html", "classgridfire_1_1policy_1_1_c_n_o_i_chain_policy" ],
+        [ "CNOIIChainPolicy", "classgridfire_1_1policy_1_1_c_n_o_i_i_chain_policy.html", "classgridfire_1_1policy_1_1_c_n_o_i_i_chain_policy" ],
+        [ "CNOIIIChainPolicy", "classgridfire_1_1policy_1_1_c_n_o_i_i_i_chain_policy.html", "classgridfire_1_1policy_1_1_c_n_o_i_i_i_chain_policy" ],
+        [ "CNOIVChainPolicy", "classgridfire_1_1policy_1_1_c_n_o_i_v_chain_policy.html", "classgridfire_1_1policy_1_1_c_n_o_i_v_chain_policy" ],
+        [ "HotCNOChainPolicy", "classgridfire_1_1policy_1_1_hot_c_n_o_chain_policy.html", "classgridfire_1_1policy_1_1_hot_c_n_o_chain_policy" ],
+        [ "HotCNOIChainPolicy", "classgridfire_1_1policy_1_1_hot_c_n_o_i_chain_policy.html", "classgridfire_1_1policy_1_1_hot_c_n_o_i_chain_policy" ],
+        [ "HotCNOIIChainPolicy", "classgridfire_1_1policy_1_1_hot_c_n_o_i_i_chain_policy.html", "classgridfire_1_1policy_1_1_hot_c_n_o_i_i_chain_policy" ],
+        [ "HotCNOIIIChainPolicy", "classgridfire_1_1policy_1_1_hot_c_n_o_i_i_i_chain_policy.html", "classgridfire_1_1policy_1_1_hot_c_n_o_i_i_i_chain_policy" ],
+        [ "MainSequencePolicy", "classgridfire_1_1policy_1_1_main_sequence_policy.html", "classgridfire_1_1policy_1_1_main_sequence_policy" ],
+        [ "MainSequenceReactionChainPolicy", "classgridfire_1_1policy_1_1_main_sequence_reaction_chain_policy.html", "classgridfire_1_1policy_1_1_main_sequence_reaction_chain_policy" ],
+        [ "MultiReactionChainPolicy", "classgridfire_1_1policy_1_1_multi_reaction_chain_policy.html", "classgridfire_1_1policy_1_1_multi_reaction_chain_policy" ],
+        [ "NetworkPolicy", "classgridfire_1_1policy_1_1_network_policy.html", "classgridfire_1_1policy_1_1_network_policy" ],
+        [ "ProtonProtonChainPolicy", "classgridfire_1_1policy_1_1_proton_proton_chain_policy.html", "classgridfire_1_1policy_1_1_proton_proton_chain_policy" ],
+        [ "ProtonProtonIChainPolicy", "classgridfire_1_1policy_1_1_proton_proton_i_chain_policy.html", "classgridfire_1_1policy_1_1_proton_proton_i_chain_policy" ],
+        [ "ProtonProtonIIChainPolicy", "classgridfire_1_1policy_1_1_proton_proton_i_i_chain_policy.html", "classgridfire_1_1policy_1_1_proton_proton_i_i_chain_policy" ],
+        [ "ProtonProtonIIIChainPolicy", "classgridfire_1_1policy_1_1_proton_proton_i_i_i_chain_policy.html", "classgridfire_1_1policy_1_1_proton_proton_i_i_i_chain_policy" ],
+        [ "ReactionChainPolicy", "classgridfire_1_1policy_1_1_reaction_chain_policy.html", "classgridfire_1_1policy_1_1_reaction_chain_policy" ],
+        [ "TemperatureDependentChainPolicy", "classgridfire_1_1policy_1_1_temperature_dependent_chain_policy.html", "classgridfire_1_1policy_1_1_temperature_dependent_chain_policy" ],
+        [ "TripleAlphaChainPolicy", "classgridfire_1_1policy_1_1_triple_alpha_chain_policy.html", "classgridfire_1_1policy_1_1_triple_alpha_chain_policy" ]
+      ] ],
+      [ "rates", "namespacegridfire_1_1rates.html", [
+        [ "weak", "namespacegridfire_1_1rates_1_1weak.html", [
+          [ "BoundsErrorInfo", "structgridfire_1_1rates_1_1weak_1_1_bounds_error_info.html", "structgridfire_1_1rates_1_1weak_1_1_bounds_error_info" ],
+          [ "InterpolationError", "structgridfire_1_1rates_1_1weak_1_1_interpolation_error.html", "structgridfire_1_1rates_1_1weak_1_1_interpolation_error" ],
+          [ "IsotopeGrid", "structgridfire_1_1rates_1_1weak_1_1_isotope_grid.html", "structgridfire_1_1rates_1_1weak_1_1_isotope_grid" ],
+          [ "RateDataRow", "structgridfire_1_1rates_1_1weak_1_1_rate_data_row.html", "structgridfire_1_1rates_1_1weak_1_1_rate_data_row" ],
+          [ "WeakRateDerivatives", "structgridfire_1_1rates_1_1weak_1_1_weak_rate_derivatives.html", "structgridfire_1_1rates_1_1weak_1_1_weak_rate_derivatives" ],
+          [ "WeakRateInterpolator", "classgridfire_1_1rates_1_1weak_1_1_weak_rate_interpolator.html", "classgridfire_1_1rates_1_1weak_1_1_weak_rate_interpolator" ],
+          [ "WeakRatePayload", "structgridfire_1_1rates_1_1weak_1_1_weak_rate_payload.html", "structgridfire_1_1rates_1_1weak_1_1_weak_rate_payload" ],
+          [ "WeakReaction", "classgridfire_1_1rates_1_1weak_1_1_weak_reaction.html", "classgridfire_1_1rates_1_1weak_1_1_weak_reaction" ],
+          [ "WeakReactionEntry", "structgridfire_1_1rates_1_1weak_1_1_weak_reaction_entry.html", "structgridfire_1_1rates_1_1weak_1_1_weak_reaction_entry" ],
+          [ "WeakReactionMap", "classgridfire_1_1rates_1_1weak_1_1_weak_reaction_map.html", "classgridfire_1_1rates_1_1weak_1_1_weak_reaction_map" ]
+        ] ]
+      ] ],
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         [ "ReactionRecord", "structgridfire_1_1reaclib_1_1_reaction_record.html", "structgridfire_1_1reaclib_1_1_reaction_record" ]
       ] ],
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+        [ "LogicalReaclibReaction", "classgridfire_1_1reaction_1_1_logical_reaclib_reaction.html", "classgridfire_1_1reaction_1_1_logical_reaclib_reaction" ],
         [ "RateCoefficientSet", "structgridfire_1_1reaction_1_1_rate_coefficient_set.html", "structgridfire_1_1reaction_1_1_rate_coefficient_set" ],
+        [ "ReaclibReaction", "classgridfire_1_1reaction_1_1_reaclib_reaction.html", "classgridfire_1_1reaction_1_1_reaclib_reaction" ],
         [ "Reaction", "classgridfire_1_1reaction_1_1_reaction.html", "classgridfire_1_1reaction_1_1_reaction" ],
-        [ "TemplatedReactionSet", "classgridfire_1_1reaction_1_1_templated_reaction_set.html", "classgridfire_1_1reaction_1_1_templated_reaction_set" ]
+        [ "ReactionSet", "classgridfire_1_1reaction_1_1_reaction_set.html", "classgridfire_1_1reaction_1_1_reaction_set" ]
       ] ],
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         [ "BareScreeningModel", "classgridfire_1_1screening_1_1_bare_screening_model.html", "classgridfire_1_1screening_1_1_bare_screening_model" ],
+        [ "IntermediateScreeningModel", "classgridfire_1_1screening_1_1_intermediate_screening_model.html", "classgridfire_1_1screening_1_1_intermediate_screening_model" ],
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-        [ "SolverContextBase", "structgridfire_1_1solver_1_1_solver_context_base.html", "structgridfire_1_1solver_1_1_solver_context_base" ]
+        [ "SolverContextBase", "classgridfire_1_1solver_1_1_solver_context_base.html", "classgridfire_1_1solver_1_1_solver_context_base" ]
+      ] ],
+      [ "trigger", "namespacegridfire_1_1trigger.html", [
+        [ "solver", "namespacegridfire_1_1trigger_1_1solver.html", [
+          [ "CVODE", "namespacegridfire_1_1trigger_1_1solver_1_1_c_v_o_d_e.html", [
+            [ "ConvergenceFailureTrigger", "classgridfire_1_1trigger_1_1solver_1_1_c_v_o_d_e_1_1_convergence_failure_trigger.html", "classgridfire_1_1trigger_1_1solver_1_1_c_v_o_d_e_1_1_convergence_failure_trigger" ],
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+          ] ]
+        ] ],
+        [ "AndTrigger", "classgridfire_1_1trigger_1_1_and_trigger.html", "classgridfire_1_1trigger_1_1_and_trigger" ],
+        [ "EveryNthTrigger", "classgridfire_1_1trigger_1_1_every_nth_trigger.html", "classgridfire_1_1trigger_1_1_every_nth_trigger" ],
+        [ "LogicalTrigger", "classgridfire_1_1trigger_1_1_logical_trigger.html", null ],
+        [ "NotTrigger", "classgridfire_1_1trigger_1_1_not_trigger.html", "classgridfire_1_1trigger_1_1_not_trigger" ],
+        [ "OrTrigger", "classgridfire_1_1trigger_1_1_or_trigger.html", "classgridfire_1_1trigger_1_1_or_trigger" ],
+        [ "Trigger", "classgridfire_1_1trigger_1_1_trigger.html", "classgridfire_1_1trigger_1_1_trigger" ],
+        [ "TriggerResult", "structgridfire_1_1trigger_1_1_trigger_result.html", "structgridfire_1_1trigger_1_1_trigger_result" ]
+      ] ],
+      [ "utils", "namespacegridfire_1_1utils.html", [
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+        [ "ColumnBase", "classgridfire_1_1utils_1_1_column_base.html", "classgridfire_1_1utils_1_1_column_base" ],
+        [ "Table", "classgridfire_1_1utils_1_1_table.html", "classgridfire_1_1utils_1_1_table" ],
+        [ "TableBase", "classgridfire_1_1utils_1_1_table_base.html", "classgridfire_1_1utils_1_1_table_base" ]
       ] ],
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 <div class="textblock"><code>#include &lt;variant&gt;</code><br />
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+</div>
+</div><div class="textblock"><div class="dynheader">
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+<div class="dyncontent">
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+<div class="textblock"><code>#include &quot;<a class="el" href="policy__abstract_8h.html">gridfire/policy/policy_abstract.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="policy__logical_8h.html">gridfire/policy/policy_logical.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="chains_8h.html">gridfire/policy/chains.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="error__policy_8h.html">gridfire/exceptions/error_policy.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="hashing_8h.html">gridfire/utils/hashing.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="reaclib_8h.html">gridfire/reaction/reaclib.h</a>&quot;</code><br />
+<code>#include &quot;xxhash64.h&quot;</code><br />
+</div><div class="textblock"><div class="dynheader">
+Include dependency graph for chains.cpp:</div>
+<div class="dyncontent">
+<div class="center"><div class="zoom"><iframe scrolling="no" frameborder="0" src="chains_8cpp__incl.svg" width="100%" height="600"><p><b>This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead.</b></p></iframe></div></div>
+</div>
+</div><table class="memberdecls">
+<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="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="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="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_0751b490135a42d238fc345542daa4c3.html">policy</a></li><li class="navelem"><a class="el" href="chains_8cpp.html">chains.cpp</a></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
+  </ul>
+</div>
+</body>
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+<p>Concrete implementations of ReactionChainPolicy for key stellar reaction chains.  
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+<div class="textblock"><code>#include &quot;<a class="el" href="policy__abstract_8h.html">gridfire/policy/policy_abstract.h</a>&quot;</code><br />
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+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<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="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>
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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>
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docs/html/chains_8h__incl.md5

@@ -0,0 +1 @@
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docs/html/class_py_dynamic_engine-members.html

@@ -29,7 +29,7 @@
  <tbody>
  <tr id="projectrow">
   <td id="projectalign">
-   <div id="projectname">GridFire<span id="projectnumber">&#160;0.6.0</span>
+   <div id="projectname">GridFire<span id="projectnumber">&#160;v0.7.0-alpha</span>
    </div>
    <div id="projectbrief">General Purpose Nuclear Network</div>
   </td>
@@ -105,29 +105,31 @@ $(function(){initNavTree('class_py_dynamic_engine.html',''); initResizable(true)
 
 <p>This is the complete list of members for <a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a>, including all inherited members.</p>
 <table class="directory">
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a6224f546ba66b1257506b1fc9f47195a">calculateMolarReactionFlow</a>(const gridfire::reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a09eb8874b0c687aacc84a7bc7a5e2330">calculateEpsDerivatives</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a5b7f0cfe327c634ec125303256de8b9a">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.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="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a5bd40c752db1badcd600797c9113121d">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a339e7238d290665ae9823c701e0ba32e">calculateRHSAndEnergy</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#aa0f1fd3f0c0185395193d1b6897d64c5">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const gridfire::SparsityPattern &amp;sparsityPattern) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a6c5397f57fb9e115495188a1d2296147">collectComposition</a>(fourdst::composition::Composition &amp;comp) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2066649ca11a869c054079ea12d8d0e9">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2a63d0132254983a2143f31e863a5c18">generateJacobianMatrix</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#adba68716d832b6100e08d32fbc36f13c">getDepth</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2c0a465848ed6da8d3aaef5f6824375d">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="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a1c888bbc0618f1ae02d9a53e45f3c159">getJacobianMatrixEntry</a>(int i, int j) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a36f2dbd2278608fe8a4ef7f08d7e4963">generateJacobianMatrix</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho, const gridfire::SparsityPattern &amp;sparsityPattern) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a5988cfba247631ba6c00795cafda9a38">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2066649ca11a869c054079ea12d8d0e9">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#afc745e7ab5da5d8b3cf916044515cd7d">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#adba68716d832b6100e08d32fbc36f13c">getDepth</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ab4cfdca5e15957c5cef75ffa6dedeee5">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a63bbe8f6d3849e99dd41b6d9613ff1f0">getJacobianMatrixEntry</a>(const fourdst::atomic::Species &amp;rowSpecies, const fourdst::atomic::Species &amp;colSpecies) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a020044829e0146427ed4830e5b02c4f3">getSpeciesDestructionTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a1d5143640666631501cf229bc491516e">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2ee1d745c1c21b9fcb652c96c42f1091">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#afc745e7ab5da5d8b3cf916044515cd7d">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a02a4c86c9637a3c9c9ca8ddd82ecff22">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ab4cfdca5e15957c5cef75ffa6dedeee5">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ab48ef6db18da20024aa563a91fa16f83">getStoichiometryMatrixEntry</a>(int speciesIndex, int reactionIndex) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a16c27e5af29ddf187e5ab82a6e6db57b">getSpeciesDestructionTimescales</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a55bf19ed7534a312a36faf74753f7b14">isStale</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a95d10a7b240d543a1bc6c67ddf2dc8e0">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2246382b1c98ba69cdb419bba63a6d03">m_species_cache</a></td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a8bbf2956e0a3d01065c14e74cdc71626">getSpeciesTimescales</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a61bb4b430fe740cfb2c24e5cc673e4ac">mapNetInToMolarAbundanceVector</a>(const gridfire::NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.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="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
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+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a55bf19ed7534a312a36faf74753f7b14">isStale</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
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+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2246382b1c98ba69cdb419bba63a6d03">m_species_cache</a></td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
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+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a61bb4b430fe740cfb2c24e5cc673e4ac">mapNetInToMolarAbundanceVector</a>(const gridfire::NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
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+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ac22a10412be6649bf379e6d61113c878">primeEngine</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
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+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a8e39a86c2ba1ac7f1669362554f07fcf">rebuild</a>(const fourdst::composition::CompositionAbstract &amp;comp, gridfire::BuildDepthType depth) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
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+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#af469cba3be850d53f659ec173f0eb4e4">setNetworkReactions</a>(const gridfire::reaction::ReactionSet &amp;reactions) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
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+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#af8e6a8cd44f278535d7bcc9a896d6da8">update</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
 </table></div><!-- contents -->
 </div><!-- doc-content -->
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docs/html/class_py_dynamic_engine.html

@@ -29,7 +29,7 @@
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 <table class="memberdecls">
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 Public Member Functions</h2></td></tr>
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-<tr class="memdesc:ab4cfdca5e15957c5cef75ffa6dedeee5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the current electron screening model.  <br /></td></tr>
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+<tr class="memitem:a95d10a7b240d543a1bc6c67ddf2dc8e0" id="r_a95d10a7b240d543a1bc6c67ddf2dc8e0"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a95d10a7b240d543a1bc6c67ddf2dc8e0">getSpeciesIndex</a> (const fourdst::atomic::Species &amp;species) const override</td></tr>
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+<tr class="separator:a95d10a7b240d543a1bc6c67ddf2dc8e0"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="separator:a2ee1d745c1c21b9fcb652c96c42f1091"><td class="memSeparator" colspan="2">&#160;</td></tr>
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-<tr class="memdesc:a61bb4b430fe740cfb2c24e5cc673e4ac"><td class="mdescLeft">&#160;</td><td class="mdescRight">Map a NetIn object to a vector of molar abundances.  <br /></td></tr>
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+<tr class="memitem:ac22a10412be6649bf379e6d61113c878" id="r_ac22a10412be6649bf379e6d61113c878"><td class="memItemLeft" align="right" valign="top">gridfire::PrimingReport&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ac22a10412be6649bf379e6d61113c878">primeEngine</a> (const <a class="el" href="structgridfire_1_1_net_in.html">gridfire::NetIn</a> &amp;netIn) override</td></tr>
-<tr class="memdesc:ac22a10412be6649bf379e6d61113c878"><td class="mdescLeft">&#160;</td><td class="mdescRight">Prime the engine with initial conditions.  <br /></td></tr>
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+<tr class="memitem:adba68716d832b6100e08d32fbc36f13c" id="r_adba68716d832b6100e08d32fbc36f13c"><td class="memItemLeft" align="right" valign="top">gridfire::BuildDepthType&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#adba68716d832b6100e08d32fbc36f13c">getDepth</a> () const override</td></tr>
-<tr class="memdesc:adba68716d832b6100e08d32fbc36f13c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the depth of the network.  <br /></td></tr>
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+<tr class="memitem:a8e39a86c2ba1ac7f1669362554f07fcf" id="r_a8e39a86c2ba1ac7f1669362554f07fcf"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a8e39a86c2ba1ac7f1669362554f07fcf">rebuild</a> (const fourdst::composition::CompositionAbstract &amp;comp, gridfire::BuildDepthType depth) override</td></tr>
-<tr class="memdesc:a3d30a9116825ab2c5c209bc2712126bc"><td class="mdescLeft">&#160;</td><td class="mdescRight">Rebuild the network with a specified depth.  <br /></td></tr>
+<tr class="separator:a8e39a86c2ba1ac7f1669362554f07fcf"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="separator:a3d30a9116825ab2c5c209bc2712126bc"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a09eb8874b0c687aacc84a7bc7a5e2330" id="r_a09eb8874b0c687aacc84a7bc7a5e2330"><td class="memItemLeft" align="right" valign="top">gridfire::EnergyDerivatives&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a09eb8874b0c687aacc84a7bc7a5e2330">calculateEpsDerivatives</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
-<tr class="inherit_header pub_methods_classgridfire_1_1_engine"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td></tr>
+<tr class="separator:a09eb8874b0c687aacc84a7bc7a5e2330"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" id="r_a2e7970bed2100699f226f4141d5db037"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a> ()=default</td></tr>
+<tr class="memitem:a6c5397f57fb9e115495188a1d2296147" id="r_a6c5397f57fb9e115495188a1d2296147"><td class="memItemLeft" align="right" valign="top">fourdst::composition::Composition&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a6c5397f57fb9e115495188a1d2296147">collectComposition</a> (fourdst::composition::Composition &amp;comp) const override</td></tr>
-<tr class="memdesc:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor.  <br /></td></tr>
+<tr class="separator:a6c5397f57fb9e115495188a1d2296147"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="separator:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
 Private Attributes</h2></td></tr>
@@ -191,8 +177,42 @@ Private Attributes</h2></td></tr>
 <tr class="separator:a2246382b1c98ba69cdb419bba63a6d03"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
 <h2 class="groupheader">Member Function Documentation</h2>
-<a id="a6224f546ba66b1257506b1fc9f47195a" name="a6224f546ba66b1257506b1fc9f47195a"></a>
+<a id="a09eb8874b0c687aacc84a7bc7a5e2330" name="a09eb8874b0c687aacc84a7bc7a5e2330"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a6224f546ba66b1257506b1fc9f47195a">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a09eb8874b0c687aacc84a7bc7a5e2330">&#9670;&#160;</a></span>calculateEpsDerivatives()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">gridfire::EnergyDerivatives PyDynamicEngine::calculateEpsDerivatives </td>
+          <td>(</td>
+          <td class="paramtype">const fourdst::composition::Composition &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+</div>
+</div>
+<a id="a8facba88b6df6e016ce53a0ff3cff125" name="a8facba88b6df6e016ce53a0ff3cff125"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a8facba88b6df6e016ce53a0ff3cff125">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -208,7 +228,7 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
+          <td class="paramtype">const fourdst::composition::CompositionAbstract &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
@@ -223,30 +243,15 @@ Private Attributes</h2></td></tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Calculate the molar reaction flow for a given reaction. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">reaction</td><td>The reaction for which to calculate the flow. </td></tr>
-    <tr><td class="paramname">Y</td><td>Vector of current abundances. </td></tr>
-    <tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
-    <tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
-  </table>
-  </dd>
-</dl>
-<dl class="section return"><dt>Returns</dt><dd>Molar flow rate for the reaction (e.g., mol/g/s).</dd></dl>
-<p>This method computes the net rate at which the given reaction proceeds under the current state. </p>
-
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine</a>.</p>
-
 </div>
 </div>
-<a id="a5b7f0cfe327c634ec125303256de8b9a" name="a5b7f0cfe327c634ec125303256de8b9a"></a>
+<a id="a339e7238d290665ae9823c701e0ba32e" name="a339e7238d290665ae9823c701e0ba32e"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a5b7f0cfe327c634ec125303256de8b9a">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a339e7238d290665ae9823c701e0ba32e">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
 
 <div class="memitem">
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@@ -255,9 +260,9 @@ Private Attributes</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">gridfire::StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">gridfire::expectations::StaleEngineError</a> &gt; PyDynamicEngine::calculateRHSAndEnergy </td>
+          <td class="memname">std::expected&lt; gridfire::StepDerivatives&lt; double &gt;, gridfire::expectations::StaleEngineError &gt; PyDynamicEngine::calculateRHSAndEnergy </td>
           <td>(</td>
-          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
+          <td class="paramtype">const fourdst::composition::CompositionAbstract &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
@@ -272,29 +277,40 @@ Private Attributes</h2></td></tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Calculate the right-hand side (dY/dt) and energy generation. </p>
+</div>
-<dl class="params"><dt>Parameters</dt><dd>
+</div>
-  <table class="params">
+<a id="a6c5397f57fb9e115495188a1d2296147" name="a6c5397f57fb9e115495188a1d2296147"></a>
-    <tr><td class="paramname">Y</td><td>Vector of current abundances for all species. </td></tr>
+<h2 class="memtitle"><span class="permalink"><a href="#a6c5397f57fb9e115495188a1d2296147">&#9670;&#160;</a></span>collectComposition()</h2>
-    <tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
+
-    <tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">fourdst::composition::Composition PyDynamicEngine::collectComposition </td>
+          <td>(</td>
+          <td class="paramtype">fourdst::composition::Composition &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
       </table>
-  </dd>
+  </td>
-</dl>
+  <td class="mlabels-right">
-<dl class="section return"><dt>Returns</dt><dd>StepDerivatives&lt;double&gt; containing dY/dt and energy generation rate.</dd></dl>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
-<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>
+  </tr>
-
+</table>
-<p>Implements <a class="el" href="classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb">gridfire::Engine</a>.</p>
+</div><div class="memdoc">
 
 </div>
 </div>
-<a id="a5bd40c752db1badcd600797c9113121d" name="a5bd40c752db1badcd600797c9113121d"></a>
+<a id="a2a63d0132254983a2143f31e863a5c18" name="a2a63d0132254983a2143f31e863a5c18"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a5bd40c752db1badcd600797c9113121d">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[1/2]</span></h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a2a63d0132254983a2143f31e863a5c18">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[1/3]</span></h2>
 
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@@ -305,7 +321,7 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="memname">void PyDynamicEngine::generateJacobianMatrix </td>
           <td>(</td>
-          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y_dynamic</em></span>, </td>
+          <td class="paramtype">const fourdst::composition::Composition &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
@@ -320,28 +336,15 @@ Private Attributes</h2></td></tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Generate the Jacobian matrix for the current state. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">Y_dynamic</td><td>Vector of current abundances. </td></tr>
-    <tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
-    <tr><td class="paramname">rho</td><td>Density in g/cm^3.</td></tr>
-  </table>
-  </dd>
-</dl>
-<p>This method must compute and store the Jacobian matrix (∂(dY/dt)_i/∂Y_j) for the current state. The matrix can then be accessed via <a class="el" href="#a1c888bbc0618f1ae02d9a53e45f3c159" title="Get an entry from the previously generated Jacobian matrix.">getJacobianMatrixEntry()</a>. </p>
-
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a29bdd4231c29c3a4e524ad6ca66a127d">gridfire::DynamicEngine</a>.</p>
-
 </div>
 </div>
-<a id="aa0f1fd3f0c0185395193d1b6897d64c5" name="aa0f1fd3f0c0185395193d1b6897d64c5"></a>
+<a id="a36f2dbd2278608fe8a4ef7f08d7e4963" name="a36f2dbd2278608fe8a4ef7f08d7e4963"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#aa0f1fd3f0c0185395193d1b6897d64c5">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[2/2]</span></h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a36f2dbd2278608fe8a4ef7f08d7e4963">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[2/3]</span></h2>
 
 <div class="memitem">
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@@ -352,7 +355,7 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="memname">void PyDynamicEngine::generateJacobianMatrix </td>
           <td>(</td>
-          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y_dynamic</em></span>, </td>
+          <td class="paramtype">const fourdst::composition::Composition &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
@@ -367,17 +370,54 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">const <a class="el" href="namespacegridfire.html#a898dfe22579e649935645cbd6f073178">gridfire::SparsityPattern</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>sparsityPattern</em></span>&#160;) const</td>
+          <td class="paramtype">const gridfire::SparsityPattern &amp;</td>          <td class="paramname"><span class="paramname"><em>sparsityPattern</em></span>&#160;) const</td>
         </tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Reimplemented from <a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">gridfire::DynamicEngine</a>.</p>
+</div>
+</div>
+<a id="a2c0a465848ed6da8d3aaef5f6824375d" name="a2c0a465848ed6da8d3aaef5f6824375d"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a2c0a465848ed6da8d3aaef5f6824375d">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[3/3]</span></h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">void PyDynamicEngine::generateJacobianMatrix </td>
+          <td>(</td>
+          <td class="paramtype">const fourdst::composition::CompositionAbstract &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const std::vector&lt; fourdst::atomic::Species &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>activeSpecies</em></span>&#160;) const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
 
 </div>
 </div>
@@ -399,16 +439,11 @@ Private Attributes</h2></td></tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Generate the stoichiometry matrix for the network. </p>
-<p>This method must compute and store the stoichiometry matrix, which encodes the net change of each species in each reaction. </p>
-
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">gridfire::DynamicEngine</a>.</p>
-
 </div>
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@@ -421,7 +456,7 @@ Private Attributes</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname"><a class="el" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">gridfire::BuildDepthType</a> PyDynamicEngine::getDepth </td>
+          <td class="memname">gridfire::BuildDepthType PyDynamicEngine::getDepth </td>
           <td>(</td>
           <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
           <td> const</td>
@@ -429,21 +464,15 @@ Private Attributes</h2></td></tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Get the depth of the network. </p>
-<dl class="section return"><dt>Returns</dt><dd>The depth of the network, which may indicate the level of detail or complexity in the reaction network.</dd></dl>
-<p>This method is intended to provide information about the network's structure, such as how many layers of reactions or species are present. It can be useful for diagnostics and understanding the network's complexity. </p>
-
-<p>Reimplemented from <a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">gridfire::DynamicEngine</a>.</p>
-
 </div>
 </div>
-<a id="a1c888bbc0618f1ae02d9a53e45f3c159" name="a1c888bbc0618f1ae02d9a53e45f3c159"></a>
+<a id="a63bbe8f6d3849e99dd41b6d9613ff1f0" name="a63bbe8f6d3849e99dd41b6d9613ff1f0"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a1c888bbc0618f1ae02d9a53e45f3c159">&#9670;&#160;</a></span>getJacobianMatrixEntry()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a63bbe8f6d3849e99dd41b6d9613ff1f0">&#9670;&#160;</a></span>getJacobianMatrixEntry()</h2>
 
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@@ -454,38 +483,25 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="memname">double PyDynamicEngine::getJacobianMatrixEntry </td>
           <td>(</td>
-          <td class="paramtype">int</td>          <td class="paramname"><span class="paramname"><em>i</em></span>, </td>
+          <td class="paramtype">const fourdst::atomic::Species &amp;</td>          <td class="paramname"><span class="paramname"><em>rowSpecies</em></span>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">int</td>          <td class="paramname"><span class="paramname"><em>j</em></span>&#160;) const</td>
+          <td class="paramtype">const fourdst::atomic::Species &amp;</td>          <td class="paramname"><span class="paramname"><em>colSpecies</em></span>&#160;) const</td>
         </tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Get an entry from the previously generated Jacobian matrix. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">i</td><td>Row index (species index). </td></tr>
-    <tr><td class="paramname">j</td><td>Column index (species index). </td></tr>
-  </table>
-  </dd>
-</dl>
-<dl class="section return"><dt>Returns</dt><dd>Value of the Jacobian matrix at (i, j).</dd></dl>
-<p>The Jacobian must have been generated by <a class="el" href="#a5bd40c752db1badcd600797c9113121d" title="Generate the Jacobian matrix for the current state.">generateJacobianMatrix()</a> before calling this. </p>
-
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">gridfire::DynamicEngine</a>.</p>
-
 </div>
 </div>
-<a id="a5988cfba247631ba6c00795cafda9a38" name="a5988cfba247631ba6c00795cafda9a38"></a>
+<a id="a1d5143640666631501cf229bc491516e" name="a1d5143640666631501cf229bc491516e"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a5988cfba247631ba6c00795cafda9a38">&#9670;&#160;</a></span>getNetworkReactions()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a1d5143640666631501cf229bc491516e">&#9670;&#160;</a></span>getNetworkReactions()</h2>
 
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@@ -494,7 +510,7 @@ Private Attributes</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a> &amp; PyDynamicEngine::getNetworkReactions </td>
+          <td class="memname">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">gridfire::reaction::ReactionSet</a> &amp; PyDynamicEngine::getNetworkReactions </td>
           <td>(</td>
           <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
           <td> const</td>
@@ -502,16 +518,11 @@ Private Attributes</h2></td></tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Get the set of logical reactions in the network. </p>
-<dl class="section return"><dt>Returns</dt><dd>Reference to the LogicalReactionSet containing all reactions. </dd></dl>
-
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">gridfire::DynamicEngine</a>.</p>
-
 </div>
 </div>
 <a id="afc745e7ab5da5d8b3cf916044515cd7d" name="afc745e7ab5da5d8b3cf916044515cd7d"></a>
@@ -532,15 +543,13 @@ Private Attributes</h2></td></tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
 <p><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a> Implementation ///. </p>
 
-<p>Implements <a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">gridfire::Engine</a>.</p>
-
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 </div>
 <a id="ab4cfdca5e15957c5cef75ffa6dedeee5" name="ab4cfdca5e15957c5cef75ffa6dedeee5"></a>
@@ -561,22 +570,15 @@ Private Attributes</h2></td></tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Get the current electron screening model. </p>
-<dl class="section return"><dt>Returns</dt><dd>The currently active screening model type.</dd></dl>
-<dl class="section user"><dt>Usage Example:</dt><dd><div class="fragment"><div class="line">screening::ScreeningType currentModel = myEngine.getScreeningModel();</div>
-</div><!-- fragment --> </dd></dl>
-
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">gridfire::DynamicEngine</a>.</p>
-
 </div>
 </div>
-<a id="a020044829e0146427ed4830e5b02c4f3" name="a020044829e0146427ed4830e5b02c4f3"></a>
+<a id="a16c27e5af29ddf187e5ab82a6e6db57b" name="a16c27e5af29ddf187e5ab82a6e6db57b"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a020044829e0146427ed4830e5b02c4f3">&#9670;&#160;</a></span>getSpeciesDestructionTimescales()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a16c27e5af29ddf187e5ab82a6e6db57b">&#9670;&#160;</a></span>getSpeciesDestructionTimescales()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -585,9 +587,9 @@ Private Attributes</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">gridfire::expectations::StaleEngineError</a> &gt; PyDynamicEngine::getSpeciesDestructionTimescales </td>
+          <td class="memname">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, gridfire::expectations::StaleEngineError &gt; PyDynamicEngine::getSpeciesDestructionTimescales </td>
           <td>(</td>
-          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
+          <td class="paramtype">const fourdst::composition::Composition &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
@@ -602,17 +604,15 @@ Private Attributes</h2></td></tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6ca0f315f75252ca505507a61556dda6">gridfire::DynamicEngine</a>.</p>
-
 </div>
 </div>
-<a id="a2ee1d745c1c21b9fcb652c96c42f1091" name="a2ee1d745c1c21b9fcb652c96c42f1091"></a>
+<a id="a95d10a7b240d543a1bc6c67ddf2dc8e0" name="a95d10a7b240d543a1bc6c67ddf2dc8e0"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a2ee1d745c1c21b9fcb652c96c42f1091">&#9670;&#160;</a></span>getSpeciesIndex()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a95d10a7b240d543a1bc6c67ddf2dc8e0">&#9670;&#160;</a></span>getSpeciesIndex()</h2>
 
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@@ -621,7 +621,7 @@ Private Attributes</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">int PyDynamicEngine::getSpeciesIndex </td>
+          <td class="memname">size_t PyDynamicEngine::getSpeciesIndex </td>
           <td>(</td>
           <td class="paramtype">const fourdst::atomic::Species &amp;</td>          <td class="paramname"><span class="paramname"><em>species</em></span></td><td>)</td>
           <td> const</td>
@@ -629,26 +629,15 @@ Private Attributes</h2></td></tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Get the index of a species in the network. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">species</td><td>The species to look up.</td></tr>
-  </table>
-  </dd>
-</dl>
-<p>This method allows querying the index of a specific species in the engine's internal representation. It is useful for accessing species data efficiently. </p>
-
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">gridfire::DynamicEngine</a>.</p>
-
 </div>
 </div>
-<a id="a02a4c86c9637a3c9c9ca8ddd82ecff22" name="a02a4c86c9637a3c9c9ca8ddd82ecff22"></a>
+<a id="a8bbf2956e0a3d01065c14e74cdc71626" name="a8bbf2956e0a3d01065c14e74cdc71626"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a02a4c86c9637a3c9c9ca8ddd82ecff22">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a8bbf2956e0a3d01065c14e74cdc71626">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
 
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@@ -657,9 +646,9 @@ Private Attributes</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">gridfire::expectations::StaleEngineError</a> &gt; PyDynamicEngine::getSpeciesTimescales </td>
+          <td class="memname">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, gridfire::expectations::StaleEngineError &gt; PyDynamicEngine::getSpeciesTimescales </td>
           <td>(</td>
-          <td class="paramtype">const std::vector&lt; double &gt; &amp;</td>          <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
+          <td class="paramtype">const fourdst::composition::CompositionAbstract &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
@@ -674,29 +663,15 @@ Private Attributes</h2></td></tr>
       </table>
   </td>
   <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
   </tr>
 </table>
 </div><div class="memdoc">
 
-<p>Compute timescales for all species in the network. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">Y</td><td>Vector of current abundances. </td></tr>
-    <tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
-    <tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
-  </table>
-  </dd>
-</dl>
-<dl class="section return"><dt>Returns</dt><dd>Map from Species to their characteristic timescales (s).</dd></dl>
-<p>This method estimates the timescale for abundance change of each species, which can be used for timestep control, diagnostics, and reaction network culling. </p>
-
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6772ac384b4c3d3e91712041e4aaa813">gridfire::DynamicEngine</a>.</p>
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           <td class="memname">int PyDynamicEngine::getStoichiometryMatrixEntry </td>
           <td>(</td>
-          <td class="paramtype">int</td>          <td class="paramname"><span class="paramname"><em>speciesIndex</em></span>, </td>
+          <td class="paramtype">const fourdst::atomic::Species &amp;</td>          <td class="paramname"><span class="paramname"><em>species</em></span>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">int</td>          <td class="paramname"><span class="paramname"><em>reactionIndex</em></span>&#160;) const</td>
+          <td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">gridfire::reaction::Reaction</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>reaction</em></span>&#160;) const</td>
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-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+<span class="mlabels"><span class="mlabel override">override</span></span>  </td>
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-<p>Get an entry from the stoichiometry matrix. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">speciesIndex</td><td>Index of the species. </td></tr>
-    <tr><td class="paramname">reactionIndex</td><td>Index of the reaction. </td></tr>
-  </table>
-  </dd>
-</dl>
-<dl class="section return"><dt>Returns</dt><dd>Stoichiometric coefficient for the species in the reaction.</dd></dl>
-<p>The stoichiometry matrix must have been generated by <a class="el" href="#a2066649ca11a869c054079ea12d8d0e9" title="Generate the stoichiometry matrix for the network.">generateStoichiometryMatrix()</a>. </p>
-
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">gridfire::DynamicEngine</a>.</p>
-
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-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a942e65ced17ca602482cc42e469d6398">gridfire::DynamicEngine</a>.</p>
-
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-<p>Map a NetIn object to a vector of molar abundances. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">netIn</td><td>The input conditions for the network. </td></tr>
-  </table>
-  </dd>
-</dl>
-<dl class="section return"><dt>Returns</dt><dd>A vector of molar abundances corresponding to the species in the network.</dd></dl>
-<p>This method converts the input conditions into a vector of molar abundances, which can be used for further calculations or diagnostics. </p>
-
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a55f1b7e5ebe2840e1d7c54665ca5411a">gridfire::DynamicEngine</a>.</p>
-
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-          <td class="memname"><a class="el" href="structgridfire_1_1_priming_report.html">gridfire::PrimingReport</a> PyDynamicEngine::primeEngine </td>
+          <td class="memname">gridfire::PrimingReport PyDynamicEngine::primeEngine </td>
           <td>(</td>
           <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">gridfire::NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
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-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
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-<p>Prime the engine with initial conditions. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">netIn</td><td>The input conditions for the network. </td></tr>
-  </table>
-  </dd>
-</dl>
-<dl class="section return"><dt>Returns</dt><dd>PrimingReport containing information about the priming process.</dd></dl>
-<p>This method is used to prepare the engine for calculations by setting up initial conditions, reactions, and species. It may involve compiling reaction rates, initializing internal data structures, and performing any necessary pre-computation. </p>
-
-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a21c34f59c080a853fafa38a25175124e">gridfire::DynamicEngine</a>.</p>
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-          <td class="paramtype">const fourdst::composition::Composition &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
+          <td class="paramtype">const fourdst::composition::CompositionAbstract &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
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+          <td class="paramtype">gridfire::BuildDepthType</td>          <td class="paramname"><span class="paramname"><em>depth</em></span>&#160;)</td>
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-<p>Rebuild the network with a specified depth. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
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-    <tr><td class="paramname">depth</td><td>The desired depth of the network.</td></tr>
-  </table>
-  </dd>
-</dl>
-<p>This method is intended to allow dynamic adjustment of the network's depth, which may involve adding or removing species and reactions based on the specified depth. However, not all engines support this operation. </p>
-
-<p>Reimplemented from <a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">gridfire::DynamicEngine</a>.</p>
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+          <td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">gridfire::reaction::ReactionSet</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>reactions</em></span></td><td>)</td>
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-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afb2ec904d88fc8aab516db4059d0e00f">gridfire::DynamicEngine</a>.</p>
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-<p>Set the electron screening model. </p>
-<dl class="params"><dt>Parameters</dt><dd>
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-    <tr><td class="paramname">model</td><td>The type of screening model to use for reaction rate calculations.</td></tr>
-  </table>
-  </dd>
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-</div><!-- fragment --></dd></dl>
-<dl class="section post"><dt>Postcondition</dt><dd>The engine will use the specified screening model for subsequent rate calculations. </dd></dl>
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-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">gridfire::DynamicEngine</a>.</p>
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-<p>Update the internal state of the engine. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">netIn</td><td>A struct containing the current network input, such as temperature, density, and composition.</td></tr>
-  </table>
-  </dd>
-</dl>
-<p>This method is intended to be implemented by derived classes to update their internal state based on the provided network conditions. For example, an adaptive engine might use this to re-evaluate which reactions and species are active. For other engines that do not support manually updating, this method might do nothing.</p>
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-<dl class="section post"><dt>Postcondition</dt><dd>The internal state of the engine is updated to reflect the new conditions. </dd></dl>
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-<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aa799ff785e7e79bf35b11efd55f6282a">gridfire::DynamicEngine</a>.</p>
-
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 </div>
 <h2 class="groupheader">Member Data Documentation</h2>

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docs/html/class_py_dynamic_network_solver_strategy-members.html

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docs/html/class_py_engine.html

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 <table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
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