fix(wheels): system to continue if wheel build fails

Also added more explicit error handeling to ensure that users know what to do when the thread count exceeds the compiled maximum

.gitignore

@@ -107,6 +107,8 @@ glaze.wrap
 tomlplusplus.wrap
 
 .vscode/
+*.trace/
+conanfile.py
 
 *.log
 mpi-install-log.txt
@@ -130,3 +132,8 @@ meson-boost-test/
 cross/python_includes
 
 *.whl
+*.pdf
+
+*pynuc.txt
+*.dat
+*pynucastro_network.py

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         = v0.7.4_rc2
+PROJECT_NUMBER         = v1.0.1
 
 # 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

README.md

@@ -152,149 +152,80 @@ the same for the other shared object file (make sure to count the duplicate rpat
 We also include a script at `pip_install_mac_patch.sh` which will do this automatically for you.
 
 ## Automatic Build and Installation
-### Script Build and Installation Instructions
-
-The easiest way to build GridFire is using the `install.sh` or `install-tui.sh`
-scripts in the root directory. To use these scripts, simply run:
-
-```bash
-./install.sh
-# or
-./install-tui.sh
-```
-The regular installation script will select a standard "ideal" set of build
-options for you. If you want more control over the build options, you can use
-the `install-tui.sh` script, which will provide a text-based user interface to
-select the build options you want.
-
-Generally, both are intended to be easy to use and will prompt you
-automatically to install any missing dependencies.
-
-
 ### Currently, known good platforms
 The installation script has been tested and found to work on clean
 installations of the following platforms:
 - MacOS 15.3.2 (Apple Silicon + brew installed)
 - Fedora 42.0 (aarch64)
-- Ubuntu 25.04 (aarch64)
-- Ubuntu 22.04 (X86_64)
-
-> **Note:** On Ubuntu 22.04 the user needs to install boost libraries manually
-> as the versions in the Ubuntu repositories
-> are too old. The installer automatically detects this and will instruct the
-> user in how to do this.
+- Ubuntu 24.04 (X86_64)
 
 ## Manual Build Instructions
 
-### Prerequisites
-These only need to be manually installed if the user is not making use of the
-`install.sh` or `install-tui.sh`
-
 #### Required
 - C++ compiler supporting C++23 standard
+  - clang >= 17.0.0
+  - gcc >= 14.0
 - Meson build system (>= 1.5.0)
 - Python 3.8 or newer
 - CMake 3.20 or newer
 - ninja 1.10.0 or newer
 - Python packages: `meson-python>=0.15.0`
-- Boost libraries (>= 1.83.0) installed system-wide (or at least findable by
-  meson with pkg-config)
-
-#### Optional
-- dialog (used by the `install.sh` script, not needed if using pip or meson
-  directly)
-- pip (used by the `install.sh` script or by calling pip directly, not needed
-  if using meson directly)
-
-> **Note:** Boost is the only external library dependency used by GridFire directly.
 
 > **Note:** Windows is not supported at this time and *there are no plans to
 > support it in the future*. Windows users are encouraged to use WSL2 or a
 > Linux VM.
 
-> **Note:** If `install-tui.sh` is not able to find a usable version of boost
-> it will provide directions to fetch, compile, and install a usable version.
-
-### Install Scripts
-GridFire ships with an installer (`install.sh`) which is intended to make the
-process of installation both easier and more repeatable.
-
-#### Ease of Installation
-Both scripts are intended to automate installation more or less completely. This
-includes dependency checking. In the event that a dependency cannot be found
-they try to install (after explicitly asking for user permission). If that does
-not work they will provide a clear message as to what went wrong.
-
-#### Reproducibility
-The TUI mode provides easy modification of meson build system and compiler
-settings which can then be saved to a config file. This config file can then be
-loaded by either tui mode or cli mode (with the `--config`) flag meaning that
-build configurations can be made and reused. Note that this is **not** a
-deterministically reproducible build system as it does not interact with any
-system dependencies or settings, only meson and compiler settings.
-
-#### Examples
-
-##### TUI config and saving
-[![asciicast](https://asciinema.org/a/ahIrQPL71ErZv5EKKujfO1ZEW.svg)](https://asciinema.org/a/ahIrQPL71ErZv5EKKujfO1ZEW)
-
-##### TUI config loading and meson setup
-[![asciicast](https://asciinema.org/a/zGdzt9kYsETltG0TJKC50g3BK.svg)](https://asciinema.org/a/zGdzt9kYsETltG0TJKC50g3BK)
-
-##### CLI config loading, setup, and build
-[![asciicast](https://asciinema.org/a/GYaWTXZbDJRD4ohde0s3DkFMC.svg)](https://asciinema.org/a/GYaWTXZbDJRD4ohde0s3DkFMC)
-
-
-> **Note:** `install-tui.sh` is simply a script which calls `install.sh` with
-> the `--tui` flag. You can get the exact same results by running `install.sh
-> --tui`.
-
-> **Note:** Call `install.sh` with the `--help` or `--h` flag to see command
-> line options
-
-> **Note:** `clang` tends to compile GridFire much faster than `gcc` thus why I
-> select it in the above asciinema recording.
 
 ### Dependency Installation on Common Platforms
 
 - **Ubuntu/Debian:**
 ```bash
 sudo apt-get update
-sudo apt-get install -y build-essential meson python3 python3-pip libboost-all-dev
+sudo apt install pipx pkg-config gcc-14 g++-14
+pipx install meson ninja cmake
+pipx ensurepath
 ```
-
-> **Note:** Depending on the ubuntu version you have the libboost-all-dev
-> libraries may be too old. If this is the case refer to the boost
-> documentation for how to download and install a version `>=1.83.0`
-
-> **Note:** On recent versions of ubuntu python has switched to being
-> externally managed by the system. We **strongly** recommend that if you
-> install manually all python packages are installed inside some kind of
-> virtual environment (e.g. `pyenv`, `conda`, `python-venv`, etc...). When using
-> the installer script this is handled automatically using `python-venv`.
+> Note: Ubuntu tends to ship with older versions of compilers, you may need to adjust the specific compiler name
+> or add additional repositories if you are running a version of ubuntu older than 24.04 LTS
 
 - **Fedora/CentOS/RHEL:**
 ```bash
-sudo dnf install -y gcc-c++ meson python3 python3-pip boost-devel
+sudo dnf install pkgconf-pkg-config meson ninja-build cmake
+```
+
+- **Arch:**
+```bash
+sudo pacman -Syu pkgconf meson ninja cmake
 ```
 
 - **macOS (Homebrew):**
 ```bash
 brew update
-brew install boost meson python
+brew install pkg-config meson ninja cmake gcc
 ```
 
+> Note: macos >= 15.2.0 ships with a version of clang which works for compilation (and therefore you dont need gcc. I have not tested on versions of macos prior to this).
+
 ### Building the C++ Library
 ```bash
 meson setup build
 meson compile -C build
 ```
 
+> Note: On Ubuntu (or any system which does not have a supported version of the compiler as the default) you should use
+> ```bash
+> CC=gcc-14 CXX=g++-14 meson setup build
+> meson compile -C build
+> ```
+
 #### Clang vs. GCC
 As noted above `clang` tends to compile GridFire much faster than `gcc`. If
 your system has both `clang` and `gcc` installed you may force meson to use
 clang via environmental variables
 
+> Note: There is an issue I have not resolved on ubuntu 24.04 where clang++-18 fails to find the expected header
+> therefore we reccomend the use of gcc-14 and g++-14 on ubuntu 24.04
+
 ```bash
 CC=clang CXX=clang++ meson setup build_clang
 meson compile -C build_clang
@@ -308,7 +239,7 @@ meson install -C build
 ### Minimum compiler versions
 GridFire uses C++23 features and therefore only compilers and standard library
 implementations which support C++23 are supported. Generally we have found that
-`gcc >= 13.0.0` or `clang >= 16.0.0` work well.
+`gcc >= 14.0.0` or `clang >= 17.0.0` work well.
 
 
 ## Code Architecture and Logical Flow
@@ -447,7 +378,6 @@ likely to be one of adding new `EngineViews`.
 
 | View Name                        | Purpose                                                                           | Algorithm / Reference                                                                                      | When to Use                                                       |
 |----------------------------------|-----------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------|
-| AdaptiveEngineView               | Dynamically culls low-flow species and reactions during runtime                   | Iterative flux thresholding to remove reactions below a flow threshold                                     | Large networks to reduce computational cost                       |
 | DefinedEngineView                | Restricts the network to a user-specified subset of species and reactions         | Static network masking based on user-provided species/reaction lists                                       | Targeted pathway studies or code-to-code comparisons              |
 | FileDefinedEngineView            | Load a defined engine view from a file using some parser                          | Same as DefinedEngineView but loads from a file                                                            | Same as DefinedEngineView                                         |
 | MultiscalePartitioningEngineView | Partitions the network into fast and slow subsets based on reaction timescales    | Network partitioning following Hix & Thielemann Silicon Burning I & II (DOI:10.1086/177016,10.1086/306692) | Stiff, multi-scale networks requiring tailored integration        |
@@ -523,7 +453,7 @@ A `NetOut` struct contains
 - The total specific energy lost to neutrinos while evolving to `tMax` (`NetOut::total_neutrino_loss`) [erg/g]
 - The total flux of neutrinos while evolving to `tMax` (`NetOut::total_neutrino_flux`)
 
-### CVODESolverStrategy
+### PointSolver
 
 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.

benchmarks/Memory/main.cpp

@@ -0,0 +1,151 @@
+// ReSharper disable CppUnusedIncludeDirective
+#include <iostream>
+#include <fstream>
+#include <chrono>
+#include <thread>
+#include <format>
+
+#include <cppad/utility/thread_alloc.hpp> // Required for parallel_setup
+
+#include "fourdst/logging/logging.h"
+#include "fourdst/atomic/species.h"
+#include "fourdst/composition/utils/utils.h"
+
+#include "quill/Logger.h"
+#include "quill/Backend.h"
+#include "CLI/CLI.hpp"
+
+#include <clocale>
+
+#include "gridfire/gridfire.h"
+#include "fourdst/composition/composition.h"
+#include "gridfire/utils/gf_omp.h"
+
+#include <atomic>
+#include <new>
+#include <cstdlib>
+
+static std::atomic<size_t> g_allocated_bytes{0};
+
+void* operator new(std::size_t size) {
+    g_allocated_bytes += size;
+    if (void* ptr = std::malloc(size)) {
+        return ptr;
+    }
+    throw std::bad_alloc();
+}
+
+void operator delete(void* ptr, std::size_t size) {
+    g_allocated_bytes -= size;
+    std::free(ptr);
+}
+
+void operator delete(void* ptr) {
+    std::free(ptr);
+}
+
+struct MemoryScopeTracker {
+    size_t start_bytes;
+    MemoryScopeTracker() : start_bytes(g_allocated_bytes.load()) {}
+    size_t bytes_allocated() const {
+        return g_allocated_bytes.load() - start_bytes;
+    }
+
+    void reset_tracking() {
+        start_bytes = 0;
+        g_allocated_bytes = 0;
+    }
+};
+
+
+static std::terminate_handler g_previousHandler = nullptr;
+void quill_terminate_handler();
+
+gridfire::NetIn init(const double temp, const double rho, const double tMax) {
+    std::setlocale(LC_ALL, "");
+    g_previousHandler = std::set_terminate(quill_terminate_handler);
+    quill::Logger* logger = fourdst::logging::LogManager::getInstance().getLogger("log");
+    logger->set_log_level(quill::LogLevel::Info);
+
+    using namespace gridfire;
+    const std::vector<double> X            = {0.7081145999999999, 2.94e-5, 0.276, 0.003, 0.0011, 9.62e-3, 1.62e-3, 5.16e-4};
+    const std::vector<std::string> symbols = {"H-1", "He-3", "He-4", "C-12", "N-14", "O-16", "Ne-20", "Mg-24"};
+
+
+    const fourdst::composition::Composition composition = fourdst::composition::buildCompositionFromMassFractions(symbols, X);
+
+    NetIn netIn;
+    netIn.composition = composition;
+    netIn.temperature = temp;
+    netIn.density = rho;
+    netIn.energy = 0;
+
+    netIn.tMax = tMax;
+    netIn.dt0 = 1e-12;
+
+    return netIn;
+}
+
+void quill_terminate_handler()
+{
+    quill::Backend::stop();
+    if (g_previousHandler)
+        g_previousHandler();
+    else
+        std::abort();
+}
+
+
+int main(int argc, char* argv[]) {
+    using namespace gridfire;
+
+    double temp = 1.5e7;
+    double rho = 1.6e2;
+    double tMax = 3e17;
+    std::string output_filename = "gf_mem.csv";
+
+    CLI::App app("GridFire Memory Benchmarks");
+    app.add_option("--temperature", temp, "Temperature in degrees")->default_val(std::format("{:5.2E}", temp));
+    app.add_option("--density", rho, "Density in Kg")->default_val(std::format("{:5.2E}", rho));
+    app.add_option("--tmax", tMax, "Maximum time in seconds")->default_val(std::format("{:5.2E}", tMax));
+    app.add_option("--output", output_filename, "Output filename for intermediate results")->default_val("gf_mem.csv");
+
+    CLI11_PARSE(app, argc, argv);
+
+    const NetIn netIn = init(temp, rho, tMax);
+
+    std::unique_ptr<engine::GraphEngine> engine;
+
+    int prev_reactions = 0;
+    int prev_species = 0;
+    engine = std::make_unique<engine::GraphEngine>(netIn.composition, 1);
+
+    MemoryScopeTracker tracker;
+    std::ofstream mem_file(output_filename, std::ios::out);
+    mem_file << "depth,species,reactions,engine_memory_bytes,solver_memory_bytes\n";
+    for (int depth = 1; depth <= 100; depth++) {
+        tracker.reset_tracking();
+        engine = std::make_unique<engine::GraphEngine>(netIn.composition, depth);
+        auto blob = engine->constructStateBlob();
+        size_t engine_usage = tracker.bytes_allocated();
+
+        size_t current_num_species = engine->getNetworkSpecies(*blob).size();
+        size_t current_num_reactions = engine->getNetworkReactions(*blob).size();
+
+        if (prev_reactions == current_num_reactions && prev_species == current_num_species) {
+            std::println("Found end of useful graph traversal at a depth of {}", depth);
+            break;
+        }
+        tracker.reset_tracking();
+        const solver::PointSolver localSolver(*engine);
+        solver::PointSolverContext solverCtx(*blob);
+        size_t solver_usage = tracker.bytes_allocated();
+
+        mem_file << std::format("{},{},{},{},{}\n", depth, current_num_species, current_num_reactions, engine_usage, solver_usage);
+
+        prev_reactions = current_num_reactions;
+        prev_species = current_num_species;
+    }
+    mem_file.close();
+    std::println("Memory benchmarks results written to {}", output_filename);
+}

benchmarks/Memory/meson.build

@@ -0,0 +1,5 @@
+executable(
+    'gf_bench_memory',
+    'main.cpp',
+    dependencies: [gridfire_dep, cli11_dep],
+)

benchmarks/SingleZoneSolver/gf_wall_vs_temp.cpp

@@ -0,0 +1,134 @@
+// ReSharper disable CppUnusedIncludeDirective
+#include <iostream>
+#include <fstream>
+#include <chrono>
+#include <thread>
+#include <format>
+
+#include "gridfire/gridfire.h"
+#include <cppad/utility/thread_alloc.hpp> // Required for parallel_setup
+
+#include "fourdst/composition/composition.h"
+#include "fourdst/logging/logging.h"
+#include "fourdst/atomic/species.h"
+#include "fourdst/composition/utils/utils.h"
+
+#include "quill/Logger.h"
+#include "quill/Backend.h"
+
+#include <clocale>
+
+#include "gridfire/reaction/reaclib.h"
+#include "gridfire/utils/gf_omp.h"
+
+template <std::floating_point T>
+[[nodiscard]] constexpr auto linspace(T start, T end, std::size_t num_points) -> std::vector<T> {
+    if (num_points == 0) {
+        return {};
+    }
+    
+    if (num_points == 1) {
+        return {start};
+    }
+
+    return std::views::iota(0uz, num_points) 
+        | std::views::transform([=](std::size_t i) -> T {
+            const T t = static_cast<T>(i) / static_cast<T>(num_points - 1);
+            
+            return std::lerp(start, end, t);
+        }) 
+        | std::ranges::to<std::vector<T>>(); 
+}
+
+gridfire::NetIn init(const double temp, const double rho, const double tMax) {
+    std::setlocale(LC_ALL, "");
+    quill::Logger* logger = fourdst::logging::LogManager::getInstance().getLogger("log");
+    logger->set_log_level(quill::LogLevel::TraceL2);
+
+    using namespace gridfire;
+    const std::vector<double> X            = {0.7081145999999999, 2.94e-5, 0.276, 0.003, 0.0011, 9.62e-3, 1.62e-3, 5.16e-4};
+    const std::vector<std::string> symbols = {"H-1", "He-3", "He-4", "C-12", "N-14", "O-16", "Ne-20", "Mg-24"};
+
+
+    const fourdst::composition::Composition composition = fourdst::composition::buildCompositionFromMassFractions(symbols, X);
+
+    NetIn netIn;
+    netIn.composition = composition;
+    netIn.temperature = temp;
+    netIn.density = rho;
+    netIn.energy = 0;
+
+    netIn.tMax = tMax;
+    netIn.dt0 = 1e-12;
+
+    return netIn;
+}
+
+
+int main() {
+    GF_PAR_INIT()
+    using namespace gridfire;
+
+    constexpr double temp_init = 1.5e7;
+    constexpr double rho_init = 1.5e2;
+    constexpr double tMax = 3.1536e+12;
+
+    NetIn netIn = init(temp_init, rho_init, tMax);
+
+    policy::MainSequencePolicy stellarPolicy(netIn.composition);
+    const policy::ConstructionResults construct = stellarPolicy.construct();
+    std::println("Sandbox Engine Stack: {}", stellarPolicy);
+    std::println("Scratch Blob State: {}", *construct.scratch_blob);
+
+
+    // arrays to store timings
+
+    // Total number of interpolated data points
+    constexpr size_t N = 20;
+    std::array<double, N*N> eval_times{};
+    auto density = linspace(10.0, 5.0e2, N);
+    auto temperature = linspace(4e6,3e7, N);
+
+    solver::PointSolverContext solverCtx(*construct.scratch_blob);
+    solverCtx.set_stdout_logging(false);
+    solver::PointSolver solver(construct.engine);
+
+    auto startTime = std::chrono::high_resolution_clock::now();
+
+
+    size_t i = 0;
+    for (const auto temp : temperature) {
+        for (const auto dens : density) {
+            std::println("Evaluation {:3}/{:5} ({:3.0f}%): ρ = {:10.4E}, T = {:10.4E}", i + 1, N*N, 100.0*((static_cast<double>(i)+1.0)/(N*N)), dens, temp);
+            netIn.temperature = temp;
+            netIn.density = dens;
+            try {
+                auto start_eval_time = std::chrono::high_resolution_clock::now();
+                const NetOut netOut = solver.evaluate(solverCtx, netIn);
+                auto end_eval_time = std::chrono::high_resolution_clock::now();
+                std::chrono::duration<double> eval_elapsed = end_eval_time - start_eval_time;
+                eval_times[i] = eval_elapsed.count();
+            } catch (const gridfire::exceptions::GridFireError& e) {
+                std::cerr << "Error during evaluation " << (i + 1) << ": " << e.what() << std::endl;
+                eval_times[i] = std::numeric_limits<double>::quiet_NaN();
+            }
+            i++;
+        }
+    }
+    auto endTime = std::chrono::high_resolution_clock::now();
+
+    std::println("Total time for {} evaluations: {} seconds", N, (endTime - startTime).count());
+    for (size_t j = 0; j < static_cast<size_t>(N*N); ++j) {
+        std::println("Evaluation {}: {} seconds", j + 1, eval_times[j]);
+    }
+
+    std::ofstream outfile("gf_wall_vs_temp_results.csv");
+    outfile << "Evaluation,Density,Temperature,TimeSeconds\n";
+    size_t j = 0;
+    for (const auto temp: temperature) {
+        for (const auto dens: density ) {
+            outfile << (j + 1) << "," << dens << ","<< temp << "," << eval_times[j] << "\n";
+            j++;
+        }
+    }
+}

benchmarks/SingleZoneSolver/main.cpp

@@ -11,15 +11,19 @@
 #include "fourdst/composition/composition.h"
 #include "fourdst/logging/logging.h"
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
+#include "fourdst/composition/utils/utils.h"
 
 #include "quill/Logger.h"
 #include "quill/Backend.h"
+#include "nlohmann/json.hpp"
 
 #include <clocale>
 
+#include <sys/utsname.h>
+
 #include "gridfire/reaction/reaclib.h"
 #include "gridfire/utils/gf_omp.h"
+#include "gridfire/utils/config.h"
 
 gridfire::NetIn init(const double temp, const double rho, const double tMax) {
     std::setlocale(LC_ALL, "");
@@ -63,97 +67,157 @@ int main() {
     std::println("Scratch Blob State: {}", *construct.scratch_blob);
 
 
-    constexpr size_t runs = 10;
-    auto startTime = std::chrono::high_resolution_clock::now();
+    constexpr size_t runs = 100;
+    nlohmann::json results;
+    nlohmann::json metadata;
 
-    // arrays to store timings
-    std::array<std::chrono::duration<double>, runs> setup_times;
-    std::array<std::chrono::duration<double>, runs> eval_times;
-    std::array<NetOut, runs> serial_results;
-    for (size_t i = 0; i < runs; ++i) {
-        auto start_setup_time = std::chrono::high_resolution_clock::now();
-        solver::PointSolverContext solverCtx(*construct.scratch_blob);
-        solverCtx.set_stdout_logging(false);
-        solver::PointSolver solver(construct.engine);
-        auto end_setup_time = std::chrono::high_resolution_clock::now();
-        std::chrono::duration<double> setup_elapsed = end_setup_time - start_setup_time;
-        setup_times[i] = setup_elapsed;
+    const auto now = std::chrono::system_clock::now();
+    std::string now_str = std::format("{:%Y-%m-%d %H:%M:%S}", now);
 
-        auto start_eval_time = std::chrono::high_resolution_clock::now();
-        const NetOut netOut = solver.evaluate(solverCtx, netIn);
-        auto end_eval_time = std::chrono::high_resolution_clock::now();
-        serial_results[i] = netOut;
-        std::chrono::duration<double> eval_elapsed = end_eval_time - start_eval_time;
-        eval_times[i] = eval_elapsed;
-    }
-    auto endTime = std::chrono::high_resolution_clock::now();
-    std::chrono::duration<double> elapsed = endTime - startTime;
-    std::println("");
+    metadata["Datetime"] = now_str;
+    metadata["GF_Version"] = version::toString();
 
-    // Summarize serial timings
-    double total_setup_time = 0.0;
-    double total_eval_time = 0.0;
-    for (size_t i = 0; i < runs; ++i) {
-        total_setup_time += setup_times[i].count();
-        total_eval_time += eval_times[i].count();
-    }
-    std::println("Average Setup Time over {} runs: {:.6f} seconds", runs, total_setup_time / runs);
-    std::println("Average Evaluation Time over {} runs: {:.6f} seconds", runs, total_eval_time / runs);
-    std::println("Total Time for {} runs: {:.6f} seconds", runs, elapsed.count());
-
-
-    std::array<NetOut, runs> parallelResults;
-    std::array<std::chrono::duration<double>, runs> setupTimes;
-    std::array<std::chrono::duration<double>, runs> evalTimes;
-    std::array<std::unique_ptr<gridfire::engine::scratch::StateBlob>, runs> workspaces;
-    for (size_t i = 0; i < runs; ++i) {
-        workspaces[i] = construct.scratch_blob->clone_structure();
+    utsname buffer{};
+    if (uname(&buffer) == 0) {
+        std::string osName = buffer.sysname;
+#ifdef __APPLE__
+        if (osName == "Darwin") osName = "macOS";
+#endif
+        metadata["OS"] = osName;
+        metadata["OS Version"] = buffer.release;
+        metadata["Architecture"] = buffer.machine;
+    } else {
+        metadata["OS"] = "Unknown";
     }
 
+#if defined(__clang__)
+    metadata["Compiler"] = "Clang " __clang_version__;
+#elif defined(__GNUC__)
+    metadata["Compiler"] = "GCC " __VERSION__;
+#else
+    metadata["Compiler"] = "Unknown";
+#endif
 
-    // Parallel runs
-    startTime = std::chrono::high_resolution_clock::now();
+    // metadata["Threads"] = omp_get_max_threads();
+    metadata["Runs"] = runs;
+    metadata["Temperature"] = temp;
+    metadata["Density"] = rho;
+    metadata["tMax_per_run_s"] = tMax;
 
-    GF_OMP(parallel for, for (size_t i = 0; i < runs; ++i)) {
-        auto start_setup_time = std::chrono::high_resolution_clock::now();
-        solver::PointSolverContext solverCtx(*construct.scratch_blob);
-        solverCtx.set_stdout_logging(false);
-        solver::PointSolver solver(construct.engine);
-        auto end_setup_time = std::chrono::high_resolution_clock::now();
-        std::chrono::duration<double> setup_elapsed = end_setup_time - start_setup_time;
-        setupTimes[i] = setup_elapsed;
-        auto start_eval_time = std::chrono::high_resolution_clock::now();
-        parallelResults[i] = solver.evaluate(solverCtx, netIn);
-        auto end_eval_time = std::chrono::high_resolution_clock::now();
-        std::chrono::duration<double> eval_elapsed = end_eval_time - start_eval_time;
-        evalTimes[i] = eval_elapsed;
-    }
-    endTime = std::chrono::high_resolution_clock::now();
-    elapsed = endTime - startTime;
-    std::println("");
+    results["Metadata"] = metadata;
 
-    // Summarize parallel timings
-    total_setup_time = 0.0;
-    total_eval_time = 0.0;
-    for (size_t i = 0; i < runs; ++i) {
-        total_setup_time += setupTimes[i].count();
-        total_eval_time += evalTimes[i].count();
+    for (size_t rID = 0; rID < runs; rID++) {
+        nlohmann::json run_result;
+        nlohmann::json run_metadata;
+        run_metadata["num_zones"] = rID;
+        run_result["metadata"] = run_metadata;
+
+
+        auto startTime = std::chrono::high_resolution_clock::now();
+
+        // arrays to store timings
+        std::array<std::chrono::duration<double>, runs> setup_times{};
+        std::array<std::chrono::duration<double>, runs> eval_times{};
+        std::array<NetOut, runs> serial_results;
+        for (size_t i = 0; i < rID; ++i) {
+            auto start_setup_time = std::chrono::high_resolution_clock::now();
+            solver::PointSolverContext solverCtx(*construct.scratch_blob);
+            solverCtx.set_stdout_logging(false);
+            solver::PointSolver solver(construct.engine);
+            auto end_setup_time = std::chrono::high_resolution_clock::now();
+            std::chrono::duration<double> setup_elapsed = end_setup_time - start_setup_time;
+            setup_times[i] = setup_elapsed;
+
+            auto start_eval_time = std::chrono::high_resolution_clock::now();
+            const NetOut netOut = solver.evaluate(solverCtx, netIn);
+            auto end_eval_time = std::chrono::high_resolution_clock::now();
+            serial_results[i] = netOut;
+            std::chrono::duration<double> eval_elapsed = end_eval_time - start_eval_time;
+            eval_times[i] = eval_elapsed;
+        }
+        auto endTime = std::chrono::high_resolution_clock::now();
+        std::chrono::duration<double> elapsed = endTime - startTime;
+        std::println("");
+
+        nlohmann::json point_solver_time_results;
+        point_solver_time_results["total_time_s"] = elapsed.count();
+        run_result["Serial"] = point_solver_time_results;
+
+        // Summarize serial timings
+        double total_setup_time = 0.0;
+        double total_eval_time = 0.0;
+        for (size_t i = 0; i < rID; ++i) {
+            total_setup_time += setup_times[i].count();
+            total_eval_time += eval_times[i].count();
+        }
+        std::println("Average Setup Time over {} runs: {:.6f} seconds", runs, total_setup_time / runs);
+        std::println("Average Evaluation Time over {} runs: {:.6f} seconds", runs, total_eval_time / runs);
+        std::println("Total Time for {} runs: {:.6f} seconds", runs, elapsed.count());
+
+
+        std::array<NetOut, runs> parallelResults;
+        std::array<std::chrono::duration<double>, runs> setupTimes;
+        std::array<std::chrono::duration<double>, runs> evalTimes;
+        std::array<std::unique_ptr<gridfire::engine::scratch::StateBlob>, runs> workspaces;
+        for (size_t i = 0; i < rID; ++i) {
+            workspaces[i] = construct.scratch_blob->clone_structure();
+        }
+
+
+        // Parallel runs
+        startTime = std::chrono::high_resolution_clock::now();
+
+        GF_OMP(parallel for, for (size_t i = 0; i < rID; ++i)) {
+            auto start_setup_time = std::chrono::high_resolution_clock::now();
+            solver::PointSolverContext solverCtx(*construct.scratch_blob);
+            solverCtx.set_stdout_logging(false);
+            solver::PointSolver solver(construct.engine);
+            auto end_setup_time = std::chrono::high_resolution_clock::now();
+            std::chrono::duration<double> setup_elapsed = end_setup_time - start_setup_time;
+            setupTimes[i] = setup_elapsed;
+            auto start_eval_time = std::chrono::high_resolution_clock::now();
+            parallelResults[i] = solver.evaluate(solverCtx, netIn);
+            auto end_eval_time = std::chrono::high_resolution_clock::now();
+            std::chrono::duration<double> eval_elapsed = end_eval_time - start_eval_time;
+            evalTimes[i] = eval_elapsed;
+        }
+        endTime = std::chrono::high_resolution_clock::now();
+        elapsed = endTime - startTime;
+        std::println("");
+
+        nlohmann::json grid_solver_results;
+        grid_solver_results["total_time_s"] = elapsed.count();
+        run_result["Parallel"] = grid_solver_results;
+
+        // Summarize parallel timings
+        total_setup_time = 0.0;
+        total_eval_time = 0.0;
+        for (size_t i = 0; i < runs; ++i) {
+            total_setup_time += setupTimes[i].count();
+            total_eval_time += evalTimes[i].count();
+        }
+
+        std::println("Average Parallel Setup Time over {} runs: {:.6f} seconds", runs, total_setup_time / runs);
+        std::println("Average Parallel Evaluation Time over {} runs: {:.6f} seconds", runs, total_eval_time / runs);
+        std::println("Total Parallel Time for {} runs: {:.6f} seconds", runs, elapsed.count());
+
+        std::println("========== Summary ==========");
+        std::println("Serial Runs:");
+        std::println("  Average Setup Time: {:.6f} seconds", total_setup_time / runs);
+        std::println("  Average Evaluation Time: {:.6f} seconds", total_eval_time / runs);
+        std::println("Parallel Runs:");
+        std::println("  Average Setup Time: {:.6f} seconds", total_setup_time / runs);
+        std::println("  Average Evaluation Time: {:.6f} seconds", total_eval_time / runs);
+        std::println("Difference:");
+        std::println("  Setup Time Difference: {:.6f} seconds", (total_setup_time / runs) - (total_setup_time / runs));
+        std::println("  Evaluation Time Difference: {:.6f} seconds", (total_eval_time / runs) - (total_eval_time / runs));
+        std::println("  Setup Time Fractional Difference: {:.2f}%", ((total_setup_time / runs) - (total_setup_time / runs)) / (total_setup_time / runs) * 100.0);
+        std::println("  Evaluation Time Fractional Difference: {:.2f}%", ((total_eval_time / runs) - (total_eval_time / runs)) / (total_eval_time / runs) * 100.0);
+
+        results[std::format("Run_{}", rID)] = run_result;
     }
 
-    std::println("Average Parallel Setup Time over {} runs: {:.6f} seconds", runs, total_setup_time / runs);
-    std::println("Average Parallel Evaluation Time over {} runs: {:.6f} seconds", runs, total_eval_time / runs);
-    std::println("Total Parallel Time for {} runs: {:.6f} seconds", runs, elapsed.count());
-
-    std::println("========== Summary ==========");
-    std::println("Serial Runs:");
-    std::println("  Average Setup Time: {:.6f} seconds", total_setup_time / runs);
-    std::println("  Average Evaluation Time: {:.6f} seconds", total_eval_time / runs);
-    std::println("Parallel Runs:");
-    std::println("  Average Setup Time: {:.6f} seconds", total_setup_time / runs);
-    std::println("  Average Evaluation Time: {:.6f} seconds", total_eval_time / runs);
-    std::println("Difference:");
-    std::println("  Setup Time Difference: {:.6f} seconds", (total_setup_time / runs) - (total_setup_time / runs));
-    std::println("  Evaluation Time Difference: {:.6f} seconds", (total_eval_time / runs) - (total_eval_time / runs));
-    std::println("  Setup Time Fractional Difference: {:.2f}%", ((total_setup_time / runs) - (total_setup_time / runs)) / (total_setup_time / runs) * 100.0);
-    std::println("  Evaluation Time Fractional Difference: {:.2f}%", ((total_eval_time / runs) - (total_eval_time / runs)) / (total_eval_time / runs) * 100.0);
-}
+    std::ofstream o("gf_single_zone_solver_benchmark_results.json");
+    o << std::setw(4) << results << std::endl;
+    o.close();
+}

benchmarks/SingleZoneSolver/meson.build

@@ -3,3 +3,9 @@ executable(
     'main.cpp',
     dependencies: [gridfire_dep],
 )
+
+executable(
+    'gf_wall_vs_temp',
+    'gf_wall_vs_temp.cpp',
+    dependencies: [gridfire_dep]
+)

benchmarks/Timing/main.cpp

@@ -0,0 +1,147 @@
+// ReSharper disable CppUnusedIncludeDirective
+#include <iostream>
+#include <fstream>
+#include <chrono>
+#include <thread>
+#include <format>
+
+#include "fourdst/logging/logging.h"
+#include "fourdst/atomic/species.h"
+#include "fourdst/composition/utils/utils.h"
+
+#include "quill/Logger.h"
+#include "quill/Backend.h"
+#include "CLI/CLI.hpp"
+
+#include <clocale>
+
+#include "gridfire/gridfire.h"
+#include "fourdst/composition/composition.h"
+#include "gridfire/utils/gf_omp.h"
+
+#include <atomic>
+#include <new>
+#include <cstdlib>
+
+static std::terminate_handler g_previousHandler = nullptr;
+void quill_terminate_handler();
+
+gridfire::NetIn init(const double temp, const double rho, const double tMax) {
+    std::setlocale(LC_ALL, "");
+    g_previousHandler = std::set_terminate(quill_terminate_handler);
+    quill::Logger* logger = fourdst::logging::LogManager::getInstance().getLogger("log");
+    logger->set_log_level(quill::LogLevel::Info);
+
+    using namespace gridfire;
+    const std::vector<double> X            = {0.7081145999999999, 2.94e-5, 0.276, 0.003, 0.0011, 9.62e-3, 1.62e-3, 5.16e-4};
+    const std::vector<std::string> symbols = {"H-1", "He-3", "He-4", "C-12", "N-14", "O-16", "Ne-20", "Mg-24"};
+
+
+    const fourdst::composition::Composition composition = fourdst::composition::buildCompositionFromMassFractions(symbols, X);
+
+    NetIn netIn;
+    netIn.composition = composition;
+    netIn.temperature = temp;
+    netIn.density = rho;
+    netIn.energy = 0;
+
+    netIn.tMax = tMax;
+    netIn.dt0 = 1e-12;
+
+    return netIn;
+}
+
+
+void quill_terminate_handler()
+{
+    quill::Backend::stop();
+    if (g_previousHandler)
+        g_previousHandler();
+    else
+        std::abort();
+}
+
+int main(int argc, char* argv[]) {
+    using namespace gridfire;
+
+    double temp = 1.5e7;
+    double rho = 1.6e2;
+    double tMax = 3e17;
+
+    std::string output_filename = "gridfire_timings.csv";
+
+    CLI::App app("GridFire Timeing Benchmarks");
+    app.add_option("--temperature", temp, "Temperature in degrees")->default_val(std::format("{:5.2E}", temp));
+    app.add_option("--density", rho, "Density in Kg")->default_val(std::format("{:5.2E}", rho));
+    app.add_option("--tmax", tMax, "Maximum time in seconds")->default_val(std::format("{:5.2E}", tMax));
+    app.add_option("--output", output_filename, "Output filename for intermediate results")->default_val("gridfire_timings.csv");
+
+    CLI11_PARSE(app, argc, argv);
+
+    const NetIn netIn = init(temp, rho, tMax);
+
+    std::unique_ptr<engine::GraphEngine> engine;
+
+
+    struct TimingInfo  {
+        double depth;
+        int num_reactions;
+        int num_species;
+        double timing;
+    };
+
+    std::vector<TimingInfo> timings;
+
+    int prev_reactions = 0;
+    int prev_species = 0;
+    engine = std::make_unique<engine::GraphEngine>(netIn.composition, 1);
+    for (int depth = 1; depth <= 100; depth++) {
+        engine = std::make_unique<engine::GraphEngine>(netIn.composition, depth);
+        auto blob = engine->constructStateBlob();
+
+        TimingInfo info;
+        info.depth = depth;
+        info.num_species = engine->getNetworkSpecies(*blob).size();
+        info.num_reactions = engine->getNetworkReactions(*blob).size();
+
+        if (prev_reactions == info.num_reactions && prev_species == info.num_species) {
+            std::println("Found end of useful graph traversal at a depth of {}", depth);
+            break;
+        }
+        const solver::PointSolver localSolver(*engine);
+        solver::PointSolverContext solverCtx(*blob);
+
+
+        solverCtx.stdout_logging = true;
+
+        try {
+            auto start = std::chrono::high_resolution_clock::now();
+            auto result = localSolver.evaluate(solverCtx, netIn, false, false);
+            auto end = std::chrono::high_resolution_clock::now();
+
+            double ns = std::chrono::duration<double>(end - start).count();
+
+            info.timing = ns;
+
+        prev_reactions = info.num_reactions;
+        prev_species = info.num_species;
+
+            timings.push_back(info);
+        } catch (gridfire::exceptions::CVODESolverFailureError& e) {
+            continue;
+        }
+    }
+
+    std::ofstream csvFile(output_filename, std::ios::out);
+    csvFile << std::format("# Temperature (K): {}", temp);
+    csvFile << std::format("# Density: {}", rho);
+    csvFile << std::format("# TMax: {}", tMax);
+    csvFile << "depth,reactions,species,time\n";
+    for (const auto& [depth, numReactions, numSpecies, ns]: timings) {
+        std::string line = std::format("{},{},{},{}\n", depth, numReactions, numSpecies, ns);
+        csvFile << line;
+    }
+    csvFile.close();
+
+    std::println("Timeing Benchmarks results written to {}", output_filename);
+}

benchmarks/Timing/meson.build

@@ -0,0 +1,5 @@
+executable(
+    'gf_bench_timeing',
+    'main.cpp',
+    dependencies: [gridfire_dep, cli11_dep],
+)

benchmarks/meson.build

@@ -1,3 +1,5 @@
 if get_option('build_benchmarks')
   subdir('SingleZoneSolver')
+  subdir('Memory')
+  subdir('Timing')
 endif

build-check/CPPC/meson.build

@@ -1,39 +1,184 @@
 cppc = meson.get_compiler('cpp')
+fs = import('fs')
 
-if cppc.get_id() == 'clang'
+# --- minimum supported versions ------------------------------------------
+gridfire_gcc_min        = '14.0'   # g++
+gridfire_clang_min      = '17.0'   # upstream LLVM clang++
+gridfire_appleclang_min = '16.0'   # Apple clang (Xcode 16 toolchain)
+
+# --- identify the active toolchain ----------------------------------------
+compiler_id = cppc.get_id()
+compiler_version = cppc.version()
+
+is_apple_clang = false
+if compiler_id == 'clang' and cppc.get_define('__apple_build_version__') != ''
+    is_apple_clang = true
+endif
+
+if is_apple_clang
+    toolchain_desc = 'Apple clang (Xcode) ' + compiler_version
+    required_min = gridfire_appleclang_min
+elif compiler_id == 'clang'
+    toolchain_desc = 'LLVM clang ' + compiler_version
+    required_min = gridfire_clang_min
+elif compiler_id == 'gcc'
+    toolchain_desc = 'GCC ' + compiler_version
+    required_min = gridfire_gcc_min
+else
+    toolchain_desc = compiler_id + ' ' + compiler_version
+    required_min = ''
+    warning('GridFire is developed and tested with GCC and Clang; compiler "'
+            + compiler_id + '" is untested. Proceeding, but the capability '
+            + 'checks below must pass.')
+endif
+
+message('C++ toolchain: ' + toolchain_desc)
+message('C++ standard set to: ' + get_option('cpp_std'))
+
+# --- per-compiler warning tweaks (unchanged behavior) ----------------------
+if compiler_id == 'clang'
     message('disabling bitwise-instead-of-logical warnings for clang')
     add_project_arguments('-Wno-bitwise-instead-of-logical', language: 'cpp')
 endif
-
-if cppc.get_id() == 'gcc'
+if compiler_id == 'gcc'
     message('disabling psabi warnings for gcc')
     add_project_arguments('-Wno-psabi', language: 'cpp')
-    
-    if (cppc.version().version_compare('<14.0'))
-      error('g++ version must be at least 14.0, found ' + cppc.version())
+endif
+
+# --- functional capability probes (authoritative) --------------------------
+have_print_hdr  = cppc.has_header('print')
+have_format_hdr = cppc.has_header('format')
+println_works = cppc.compiles(
+    '''#include <print>
+       #include <format>
+       int main() { std::println("gridfire toolchain probe {}", 23); }''',
+    args: ['-std=c++23'],
+    name: 'std::println usable at -std=c++23',
+)
+
+toolchain_functional = have_print_hdr and have_format_hdr and println_works
+version_sufficient = required_min == '' ? true : compiler_version.version_compare('>=' + required_min)
+
+# --- failure analysis and reporting ----------------------------------------
+if toolchain_functional and not version_sufficient
+    warning(toolchain_desc + ' is below the minimum GridFire tests against ('
+            + required_min + '), but all C++23 capability probes passed. '
+            + 'Proceeding; if you hit compiler errors deep in the build, '
+            + 'upgrade your toolchain before reporting a bug.')
+endif
+
+if not toolchain_functional
+    failure_detail = ''
+    if not have_print_hdr
+        failure_detail += '\n  * C++ standard library header <print> not found.'
     endif
+    if not have_format_hdr
+        failure_detail += '\n  * C++ standard library header <format> not found.'
+    endif
+    if have_print_hdr and have_format_hdr and not println_works
+        failure_detail += '\n  * Headers exist but std::println failed to compile at -std=c++23 (incomplete library support).'
+    endif
+    if not version_sufficient
+        failure_detail += '\n  * ' + toolchain_desc + ' is below the required minimum (' + required_min + ').'
+    elif compiler_id == 'clang' and not is_apple_clang
+        failure_detail += ('\n  * clang itself is new enough; on Linux clang uses the system '
+            + 'libstdc++, so the GNU C++ runtime is likely too old. Install GCC >= '
+            + gridfire_gcc_min + ' (clang will pick up its libstdc++), or use -Dcpp_args=-stdlib=libc++ with libc++ >= 17 installed.')
+    endif
+
+    candidate_names = []
+    if compiler_id == 'gcc'
+        candidate_names += ['g++-16', 'g++-15', 'g++-14', 'clang++-21', 'clang++-20', 'clang++-19', 'clang++-18', 'clang++-17']
+    else
+        candidate_names += ['clang++-21', 'clang++-20', 'clang++-19', 'clang++-18', 'clang++-17', 'g++-16', 'g++-15', 'g++-14']
+    endif
+    if host_machine.system() == 'darwin'
+        candidate_names += [
+            '/opt/homebrew/opt/llvm/bin/clang++',
+            '/usr/local/opt/llvm/bin/clang++',
+        ]
+    endif
+
+    suitable_cxx = ''
+    candidates_report = ''
+    foreach cand : candidate_names
+        p = find_program(cand, required: false)
+        if p.found()
+            cand_ver = p.version()
+            cand_min = cand.contains('clang') ? gridfire_clang_min : gridfire_gcc_min
+            if cand_ver != 'unknown' and cand_ver.version_compare('>=' + cand_min)
+                candidates_report += '\n  [OK]       ' + p.full_path() + '  (version ' + cand_ver + ')'
+                if suitable_cxx == ''
+                    suitable_cxx = p.full_path()
+                endif
+            else
+                candidates_report += '\n  [too old]  ' + p.full_path() + '  (version ' + cand_ver + ')'
+            endif
+        endif
+    endforeach
+
+    os_help = ''
+    if host_machine.system() == 'darwin'
+        os_help = '''
+How to get a suitable compiler on macOS:
+  * Apple clang: update Xcode / Command Line Tools to Xcode 16 or newer
+      softwareupdate --list   (or install from developer.apple.com)
+  * Homebrew LLVM:   brew install llvm     -> /opt/homebrew/opt/llvm/bin/clang++
+  * Homebrew GCC:    brew install gcc      -> g++-14 (or newer) on your PATH'''
+    elif host_machine.system() == 'linux'
+        distro_hint = ''
+        if fs.exists('/etc/os-release')
+            os_release = fs.read('/etc/os-release')
+            if os_release.contains('ubuntu') or os_release.contains('debian')
+                distro_hint = '''
+  Detected Debian/Ubuntu:
+      sudo apt install g++-14            (or newer)
+      sudo apt install clang-18 libstdc++-14-dev   (clang needs a modern libstdc++ too)'''
+            elif os_release.contains('fedora') or os_release.contains('rhel') or os_release.contains('centos')
+                distro_hint = '''
+  Detected Fedora/RHEL family:
+      sudo dnf install gcc-c++           (Fedora 40+ ships GCC 14)
+      sudo dnf install clang'''
+            elif os_release.contains('arch')
+                distro_hint = '''
+  Detected Arch:
+      sudo pacman -S gcc clang           (both current in the repos)'''
+            endif
+        endif
+        os_help = '''
+How to get a suitable compiler on Linux:''' + distro_hint + '''
+  Generic: install GCC >= ''' + gridfire_gcc_min + ''' or LLVM clang >= ''' + gridfire_clang_min + ''' from your
+  package manager; many distros package versioned binaries (g++-14, clang++-18).'''
+    else
+        os_help = '\nInstall GCC >= ' + gridfire_gcc_min + ' or LLVM clang >= ' + gridfire_clang_min + ' for your platform.'
+    endif
+
+    if suitable_cxx != ''
+        action = ('\nA suitable compiler IS already installed. Meson cannot switch compilers '
+            + 'after configuration starts, so re-run setup pointing at it:\n\n'
+            + '    CXX=' + suitable_cxx + ' meson setup --wipe <builddir>\n')
+    else
+        action = ('\nNo suitable alternate compiler was found on this system.\n' + os_help + '\n\n'
+            + 'After installing one, configure with:\n\n'
+            + '    CXX=<new compiler> meson setup --wipe <builddir>\n')
+    endif
+
+    scanned = candidates_report == '' ? '\n  (none of the common versioned compiler names were found on PATH)' : candidates_report
+
+    error('GridFire requires a C++23 toolchain (GCC >= ' + gridfire_gcc_min
+          + ', LLVM clang >= ' + gridfire_clang_min + ', or Apple clang >= ' + gridfire_appleclang_min + ').\n'
+          + 'Active compiler: ' + toolchain_desc + '\n'
+          + '\nProblems detected:' + failure_detail + '\n'
+          + '\nAlternate compilers scanned:' + scanned + '\n'
+          + action)
 endif
 
-if not cppc.has_header('print')
-    error('C++ standard library header <print> not found. Please ensure your compiler and standard library supports C++23. We have already validated your compiler version so this is likely an issue with your standard library installation.')
-endif
-if not cppc.has_header('format')
-    error('C++ standard library header <format> not found. Please ensure your compiler and standard library supports C++23. We have already validated your compiler version so this is likely an issue with your standard library installation.')
-endif
 
-# For Eigen
 add_project_arguments('-Wno-deprecated-declarations', language: 'cpp')
-
-if get_option('build_python')
-    message('enabling hidden visibility for C++ symbols when building Python extension. This reduces the size of the resulting shared library.')
-    add_project_arguments('-fvisibility=hidden', language: 'cpp')
-else
-    message('enabling default visibility for C++ symbols')
-    add_project_arguments('-fvisibility=default', language: 'cpp')
-endif
+add_project_arguments('-fvisibility=default', language: 'cpp')
 
 if get_option('openmp_support')
-    add_project_arguments('-DGF_USE_OPENMP', language: 'cpp')
+    gridfire_args += ['-DGF_USE_OPENMP']
 endif
 
 if get_option('asan') and get_option('buildtype') != 'debug' and get_option('buildtype') != 'debugoptimized'

build-check/meson.build

@@ -5,8 +5,10 @@ cc = meson.get_compiler('c')
 
 ignore_unused_args = '-Wno-unused-command-line-argument'
 
-add_global_arguments(ignore_unused_args, language: 'cpp')
-add_global_arguments(ignore_unused_args, language: 'c')
+if not meson.is_subproject()
+  add_global_arguments(ignore_unused_args, language: 'cpp')
+  add_global_arguments(ignore_unused_args, language: 'c')
+endif
 
 
 subdir('CPPC')

build-config/cppad/meson.build

@@ -1,23 +1,12 @@
-#cppad_inc = include_directories('include', is_system: true)
-#cppad_dep = declare_dependency(
-#  include_directories: cppad_inc,
-#)
-#
-#message('Registering CppAD headers for installation...')
-#install_subdir('include/cppad', install_dir: get_option('includedir'))
-#message('Done registering CppAD headers for installation!')
-#
-
-
 cppad_cmake_options = cmake.subproject_options()
 
 cppad_cmake_options.add_cmake_defines({
-    'cppad_static_lib': 'true',
-    'cpp_mas_num_threads': '10',
-    'cppad_debug_and_release': 'false',
-    'include_doc': 'false'
-})
-
+                                          'cppad_static_lib': 'true',
+                                          'cppad_max_num_threads': '512',
+                                          'cppad_debug_and_release': 'false',
+                                          'include_doc': 'false',
+                                          'CMAKE_POSITION_INDEPENDENT_CODE': true
+                                      })
 cppad_cmake_options.set_install(false)
 
 cppad_sp = cmake.subproject(
@@ -25,4 +14,41 @@ cppad_sp = cmake.subproject(
     options: cppad_cmake_options,
 )
 
-cppad_dep = cppad_sp.dependency('cppad_lib').as_system()
+cppad_target = cppad_sp.target('cppad_lib')
+cppad_objs = [cppad_target.extract_all_objects(recursive: true)]
+cppad_incs = cppad_sp.include_directories('cppad_lib')
+
+empty_cppad_file = configure_file(output: 'cppad_dummy_ar.cpp', command: ['echo'], capture: true)
+
+libcppad_static = static_library(
+    'cppad-static',
+    empty_cppad_file,
+    objects: cppad_objs,
+    include_directories: cppad_incs,
+    pic: true,
+    install: false
+)
+
+dl_dep = dependency('dl', required: false)
+if not dl_dep.found()
+    dl_dep = cpp.find_library('dl', required: false)
+endif
+
+cppad_dep = declare_dependency(
+    include_directories: cppad_incs,
+    dependencies: dl_dep.found() ? [dl_dep] : [],
+)
+
+message('Staging vendored CppAD headers for ' + gridfire_vendor_includedir)
+
+custom_target(
+    'vendor_cppad_headers',
+    command: copytree_cmd + [
+        meson.project_source_root() / 'subprojects' / 'CppAD-20250000.2' / 'include' / 'cppad',
+        '@OUTPUT@',
+    ],
+    output: 'cppad',
+    depends: libcppad_static,
+    install: true,
+    install_dir: gridfire_vendor_includedir,
+)

build-config/eigen/meson.build

@@ -1,5 +1,13 @@
-eigen_dep = dependency(
-    'eigen3',
-    version : '>=3.3',
-    fallback : ['eigen', 'eigen_dep']
-).as_system()
+eigen_sp = subproject('eigen')
+eigen_dep = eigen_sp.get_variable('eigen_dep').as_system()
+
+custom_target(
+    'vendor_eigen_headers',
+    command: copytree_cmd + [
+        meson.project_source_root() / 'subprojects' / 'eigen-3.4.0' / 'Eigen',
+        '@OUTPUT@',
+    ],
+    output: 'Eigen',
+    install: true,
+    install_dir: gridfire_vendor_includedir,
+)

build-config/fourdst/meson.build

@@ -1,38 +1,74 @@
-# bring in all of the fourdst utility repositories
+if get_option('build_python')
+    fourdst_inc_probe = run_command(py_installation, '-c',
+                                    'import fourdst; print("\\n".join(fourdst.get_include_dirs()))',
+                                    check: false)
+    if fourdst_inc_probe.returncode() != 0
+        error('Could not interrogate the fourdst wheel:\n' + fourdst_inc_probe.stderr()
+              + '\nIs fourdst installed in the build environment?')
+    endif
+    fourdst_inc_dirs = fourdst_inc_probe.stdout().strip().split('\n')
 
-fourdst_build_lib_all = true
-if not get_option('plugin_support')
-    fourdst_build_lib_all=false
-    message('Disabling fourdst plugin support as per user request.')
-endif
-
-fourdst_sp = subproject('fourdst',
-                        default_options:
-                            ['build_tests=' + get_option('build_tests').to_string(),
-                             'build_python=' + get_option('build_python').to_string(),
-                             'build_lib_all=' + fourdst_build_lib_all.to_string(),
-                             'build_lib_comp=true',
-                             'build_lib_config=true',
-                             'build_lib_log=true',
-                             'build_lib_const=true',
-                             'pkg_config=' + get_option('pkg_config').to_string(),
-                            ]
-)
-
-composition_dep = fourdst_sp.get_variable('composition_dep')
-log_dep = fourdst_sp.get_variable('log_dep')
-const_dep = fourdst_sp.get_variable('const_dep')
-config_dep = fourdst_sp.get_variable('config_dep')
-if get_option('plugin_support')
-    warning('Including plugin library from fourdst. Note this will bring in minizip-ng and openssl, which can cause build issues with cross compilation due to their complexity.')
-    plugin_dep = fourdst_sp.get_variable('plugin_dep')
-endif
-
-libcomposition = fourdst_sp.get_variable('libcomposition')
-libconst = fourdst_sp.get_variable('libconst')
-liblogging = fourdst_sp.get_variable('liblogging')
-
-if get_option('plugin_support')
-    warning('Including plugin library from fourdst. Note this will bring in minizip-ng and openssl, which can cause build issues with cross compilation due to their complexity.')
-    libplugin = fourdst_sp.get_variable('libplugin')
+    fourdst_lib_probe = run_command(py_installation, '-c',
+                                    'import fourdst; print("\\n".join(fourdst.get_lib_dirs()))',
+                                    check: false)
+    if fourdst_lib_probe.returncode() != 0
+        error('Could not interrogate the fourdst wheel:\n' + fourdst_lib_probe.stderr())
+    endif
+    fourdst_lib_dirs = fourdst_lib_probe.stdout().strip().split('\n')
+    fourdst_inc_args = []
+    foreach d : fourdst_inc_dirs
+        fourdst_inc_args += ['-I' + d]
+    endforeach
+
+    cpp = meson.get_compiler('cpp')
+    comp_lib  = cpp.find_library('composition', dirs: fourdst_lib_dirs)
+    log_lib   = cpp.find_library('logging',     dirs: fourdst_lib_dirs)
+    const_lib = cpp.find_library('const',       dirs: fourdst_lib_dirs)
+    refl_lib  = cpp.find_library('reflect_cpp', dirs: fourdst_lib_dirs)
+
+    composition_dep = declare_dependency(compile_args: fourdst_inc_args, dependencies: [comp_lib, refl_lib])
+    log_dep         = declare_dependency(compile_args: fourdst_inc_args, dependencies: log_lib)
+    const_dep       = declare_dependency(compile_args: fourdst_inc_args, dependencies: const_lib)
+    config_dep      = declare_dependency(compile_args: fourdst_inc_args)   # header-only libconfig
+else
+    fourdst_build_lib_all = true
+    if not get_option('plugin_support')
+        fourdst_build_lib_all=false
+        message('Disabling fourdst plugin support as per user request.')
+    endif
+
+    fourdst_default_options = [
+        'build_tests=' + get_option('build_tests').to_string(),
+        'build_python=' + get_option('build_python').to_string(),
+        'build_lib_all=' + fourdst_build_lib_all.to_string(),
+        'build_lib_comp=true',
+        'build_lib_config=true',
+        'build_lib_log=true',
+        'build_lib_const=true',
+        'pkg_config=' + get_option('pkg_config').to_string(),
+    ]
+
+    if get_option('build_python')
+        fourdst_default_options += ['default_library=static']
+    endif
+
+    fourdst_sp = subproject('fourdst', default_options: fourdst_default_options)
+
+    composition_dep = fourdst_sp.get_variable('composition_dep')
+    log_dep = fourdst_sp.get_variable('log_dep')
+    const_dep = fourdst_sp.get_variable('const_dep')
+    config_dep = fourdst_sp.get_variable('config_dep')
+    if get_option('plugin_support')
+        warning('Including plugin library from fourdst. Note this will bring in minizip-ng and openssl, which can cause build issues with cross compilation due to their complexity.')
+        plugin_dep = fourdst_sp.get_variable('plugin_dep')
+    endif
+
+    libcomposition = fourdst_sp.get_variable('libcomposition')
+    libconst = fourdst_sp.get_variable('libconst')
+    liblogging = fourdst_sp.get_variable('liblogging')
+
+    if get_option('plugin_support')
+        warning('Including plugin library from fourdst. Note this will bring in minizip-ng and openssl, which can cause build issues with cross compilation due to their complexity.')
+        libplugin = fourdst_sp.get_variable('libplugin')
+    endif
 endif

build-config/json/meson.build

@@ -1,3 +1,9 @@
 json_dep = declare_dependency(
     include_directories: include_directories('include')
 )
+
+install_subdir(
+    'include',
+    install_dir: gridfire_vendor_includedir,
+    strip_directory: true,
+)

build-config/meson.build

@@ -4,6 +4,41 @@ if get_option('build_python')
   subdir('python')
   subdir('pybind')
 endif
+
+if get_option('build_python')
+  gridfire_pkg_dir    = py_installation.get_install_dir() / 'gridfire'
+  gridfire_includedir = gridfire_pkg_dir / 'include'
+  gridfire_libdir     = gridfire_pkg_dir / 'lib'
+  gridfire_pcdir      = gridfire_libdir / 'pkgconfig'
+else
+  gridfire_includedir = get_option('includedir')
+  gridfire_libdir     = get_option('libdir')
+  gridfire_pcdir      = get_option('libdir') / 'pkgconfig'
+endif
+
+gridfire_vendor_includedir = gridfire_includedir / 'gridfire' / 'vendor'
+
+gridfire_fourdst_vendor_includedir = gridfire_includedir / 'fourdst' / 'vendor'
+
+vendor_py = import('python').find_installation('python3')
+copytree_cmd = [
+  vendor_py, '-c',
+  '''import sys, os, stat, shutil
+src, dst = sys.argv[1], sys.argv[2]
+shutil.rmtree(dst, ignore_errors=True)
+shutil.copytree(src, dst)
+for root, dirs, files in os.walk(dst):
+    os.chmod(root, 0o755)
+    for f in files:
+        p = os.path.join(root, f)
+        os.chmod(p, os.stat(p).st_mode | 0o644)
+''',
+]
+copyfiles_cmd = [
+  vendor_py, '-c',
+  'import sys, shutil; [shutil.copy2(p, sys.argv[-1]) for p in sys.argv[1:-1]]',
+]
+
 subdir('fourdst')
 subdir('sundials')
 
@@ -14,7 +49,6 @@ subdir('eigen')
 subdir('json')
 
 subdir('CLI11')
-subdir('unordered_dense')
 
 if get_option('use_mimalloc')
   subdir('mimalloc')

build-config/python/meson.build

@@ -1,16 +1,15 @@
 py_installation = import('python').find_installation('python3', pure: false)
 
-
 if meson.is_cross_build() and host_machine.system() == 'darwin'
-  py_ver = get_option('python-target-version')
+  py_ver = get_option('python_target_version')
   message('Cross build on Darwin, using python version ' + py_ver)
   py_inc_dir = include_directories('../../cross/python_includes/python-' + py_ver + '/include/python' + py_ver)
   py_dep = declare_dependency(include_directories: py_inc_dir)
   py_module_prefix = ''
-  py_module_suffic = 'so'
+  py_module_suffix = 'so'
   meson.override_dependency('python3', py_dep)
 else
   py_dep = py_installation.dependency()
   py_module_prefix = ''
-  py_module_suffic = 'so'
+  py_module_suffix = 'so'
 endif

build-config/sundials/cvode/meson.build

@@ -1,31 +1,34 @@
 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' : 'OFF',
-    'BUILD_STATIC_LIBS' : 'ON',
-    'EXAMPLES_ENABLE_C' : 'OFF',
-    'CMAKE_POSITION_INDEPENDENT_CODE': true,
-    'CMAKE_PLATFORM_NO_VERSIONED_SONAME': 'ON'
-
-})
+sundials_hidden_flags = '-Wno-deprecated-declarations -fvisibility=hidden -fvisibility-inlines-hidden'
 
 cvode_cmake_options.add_cmake_defines({
-    'CMAKE_INSTALL_LIBDIR': get_option('libdir'),
-    'CMAKE_INSTALL_INCLUDEDIR': get_option('includedir')
-})
+                                          'CMAKE_CXX_FLAGS'   : sundials_hidden_flags,
+                                          'CMAKE_C_FLAGS'     : sundials_hidden_flags,
+                                          'BUILD_SHARED_LIBS' : 'OFF',
+                                          'BUILD_STATIC_LIBS' : 'ON',
+                                          'EXAMPLES_ENABLE_C' : 'OFF',
+                                          'CMAKE_POSITION_INDEPENDENT_CODE': true,
+                                          'CMAKE_PLATFORM_NO_VERSIONED_SONAME': 'ON',
+                                          'SUNDIALS_LOGGING_LEVEL': 1
+
+                                      })
+
+cvode_cmake_options.add_cmake_defines({
+                                          'CMAKE_INSTALL_LIBDIR': get_option('libdir'),
+                                          'CMAKE_INSTALL_INCLUDEDIR': get_option('includedir')
+                                      })
 
 cvode_cmake_options.set_install(false)
 
 if meson.is_cross_build() and host_machine.system() == 'emscripten'
-  cvode_cmake_options.add_cmake_defines({
-      'CMAKE_C_FLAGS': '-s MEMORY64=1 -s ALLOW_MEMORY_GROWTH=1',
-      'CMAKE_CXX_FLAGS': '-s MEMORY64=1 -s ALLOW_MEMORY_GROWTH=1',
-      'CMAKE_SHARED_LINKER_FLAGS': '-s MEMORY64=1 -s ALLOW_MEMORY_GROWTH=1',
-      'CMAKE_EXE_LINKER_FLAGS': '-s MEMORY64=1 -s ALLOW_MEMORY_GROWTH=1'
-  })
+    cvode_cmake_options.add_cmake_defines({
+                                              'CMAKE_C_FLAGS': '-s MEMORY64=1 -s ALLOW_MEMORY_GROWTH=1',
+                                              'CMAKE_CXX_FLAGS': '-s MEMORY64=1 -s ALLOW_MEMORY_GROWTH=1',
+                                              'CMAKE_SHARED_LINKER_FLAGS': '-s MEMORY64=1 -s ALLOW_MEMORY_GROWTH=1',
+                                              'CMAKE_EXE_LINKER_FLAGS': '-s MEMORY64=1 -s ALLOW_MEMORY_GROWTH=1'
+                                          })
 endif
 
 cvode_sp = cmake.subproject(
@@ -40,11 +43,11 @@ sundials_sunmatrixdense_tgt = cvode_sp.target('sundials_sunmatrixdense_static')
 sundials_sunlinsoldense_tgt = cvode_sp.target('sundials_sunlinsoldense_static')
 
 cvode_objs = [
-  sundials_core_tgt.extract_all_objects(recursive: true),
-  sundials_cvode_tgt.extract_all_objects(recursive: true),
-  sundials_nvecserial_tgt.extract_all_objects(recursive: true),
-  sundials_sunmatrixdense_tgt.extract_all_objects(recursive: true),
-  sundials_sunlinsoldense_tgt.extract_all_objects(recursive: true),
+    sundials_core_tgt.extract_all_objects(recursive: true),
+    sundials_cvode_tgt.extract_all_objects(recursive: true),
+    sundials_nvecserial_tgt.extract_all_objects(recursive: true),
+    sundials_sunmatrixdense_tgt.extract_all_objects(recursive: true),
+    sundials_sunlinsoldense_tgt.extract_all_objects(recursive: true),
 ]
 
 sundials_core_includes = cvode_sp.include_directories('sundials_core_static')
@@ -54,35 +57,29 @@ sundials_sunmatrixdense_includes = cvode_sp.include_directories('sundials_sunmat
 sundials_sunlinsoldense_includes = cvode_sp.include_directories('sundials_sunlinsoldense_static')
 
 cvode_includes = [
-  sundials_core_includes,
-  sundials_cvode_includes,
-  sundials_nvecserial_includes,
-  sundials_sunmatrixdense_includes,
-  sundials_sunlinsoldense_includes
+    sundials_core_includes,
+    sundials_cvode_includes,
+    sundials_nvecserial_includes,
+    sundials_sunmatrixdense_includes,
+    sundials_sunlinsoldense_includes
 ]
 
-
 empty_cvode_file = configure_file(
-  output: 'cvode_dummy_ar.cpp',
-  command: ['echo'],
-  capture: true
-  )
-
+    output: 'cvode_dummy_ar.cpp',
+    command: ['echo'],
+    capture: true
+)
 
 
 libcvode_static = static_library(
-   'cvode-static',
-   empty_cvode_file,
-   objects: cvode_objs,
-   include_directories: cvode_includes,
-   pic: true,
-   install: false
+    'cvode-static',
+    empty_cvode_file,
+    objects: cvode_objs,
+    include_directories: cvode_includes,
+    pic: true,
+    install: false
 )
 
-
 cvode_dep = declare_dependency(
-  link_with: libcvode_static,
-  include_directories: cvode_includes,
+    include_directories: cvode_includes,
 )
-
-

build-config/sundials/kinsol/meson.build

@@ -3,19 +3,20 @@ 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' : 'OFF',
-    'BUILD_STATIC_LIBS' : 'ON',
-    'EXAMPLES_ENABLE_C' : 'OFF',
-    'CMAKE_POSITION_INDEPENDENT_CODE': true,
-    'CMAKE_PLATFORM_NO_VERSIONED_SONAME': 'ON'
-})
+                                           'CMAKE_CXX_FLAGS'   : '-Wno-deprecated-declarations -fvisibility=hidden -fvisibility-inlines-hidden',
+                                           'CMAKE_C_FLAGS'     : '-Wno-deprecated-declarations -fvisibility=hidden -fvisibility-inlines-hidden',
+                                           'BUILD_SHARED_LIBS' : 'OFF',
+                                           'BUILD_STATIC_LIBS' : 'ON',
+                                           'EXAMPLES_ENABLE_C' : 'OFF',
+                                           'CMAKE_POSITION_INDEPENDENT_CODE': true,
+                                           'CMAKE_PLATFORM_NO_VERSIONED_SONAME': 'ON',
+                                           'SUNDIALS_LOGGING_LEVEL': 1
+                                       })
 
 kinsol_cmake_options.add_cmake_defines({
-    'CMAKE_INSTALL_LIBDIR': get_option('libdir'),
-    'CMAKE_INSTALL_INCLUDEDIR': get_option('includedir')
-})
+                                           'CMAKE_INSTALL_LIBDIR': get_option('libdir'),
+                                           'CMAKE_INSTALL_INCLUDEDIR': get_option('includedir')
+                                       })
 
 kinsol_cmake_options.set_install(false)
 
@@ -30,25 +31,22 @@ kinsol_includes = kinsol_sp.include_directories('sundials_kinsol_obj_static')
 kinsol_objs = [sundials_kinsol_static_tgt.extract_all_objects(recursive: false)]
 
 empty_kinsol_file = configure_file(
-  output: 'kinsol_dummy_ar.cpp',
-  command: ['echo'],
-  capture: true
-  )
+    output: 'kinsol_dummy_ar.cpp',
+    command: ['echo'],
+    capture: true
+)
 
 
 libkinsol_static = static_library(
-  'kinsol_static',
-  empty_kinsol_file,
-  objects: kinsol_objs,
-  include_directories: kinsol_includes,
-  pic: true,
-  install: false
+    'kinsol_static',
+    empty_kinsol_file,
+    objects: kinsol_objs,
+    include_directories: kinsol_includes,
+    pic: true,
+    install: false
 )
 
 
 kinsol_dep = declare_dependency(
-  link_with: libkinsol_static,
-  include_directories: kinsol_includes
+    include_directories: kinsol_includes
 )
-
-

build-config/sundials/meson.build

@@ -7,3 +7,11 @@ sundials_dep = declare_dependency(
         kinsol_dep,
     ],
 )
+
+# Vendor the SUNDIALS public headers (see vendor/meson.build). GridFire's
+# installed public headers #include <sundials/...> etc., so consumers of
+# gridfire.pc must compile against exactly the headers this build used --
+# never whatever SUNDIALS happens to be in /usr/local/include (which may be
+# a different version or configuration, e.g. an MPI-enabled build whose
+# sundials_config.h pulls in <mpi.h>).
+subdir('vendor')

build-config/sundials/vendor/meson.build

@@ -0,0 +1,46 @@
+sundials_src_include = meson.project_source_root() / 'subprojects' / 'cvode-7.5.0' / 'include'
+kinsol_src_include   = meson.project_source_root() / 'subprojects' / 'kinsol-7.5.0' / 'include'
+
+sundials_vendor_dirs = [
+    'sundials',           # core (includes sundials/priv/)
+    'cvode',
+    'nvector',
+    'sunmatrix',
+    'sunlinsol',
+    'sunnonlinsol',
+    'sunmemory',
+    'sunadaptcontroller',
+]
+
+foreach d : sundials_vendor_dirs
+    custom_target(
+        'vendor_sundials_' + d,
+        command: copytree_cmd + [sundials_src_include / d, '@OUTPUT@'],
+        output: d,
+        install: true,
+        install_dir: gridfire_vendor_includedir,
+    )
+endforeach
+
+custom_target(
+    'vendor_sundials_kinsol',
+    command: copytree_cmd + [kinsol_src_include / 'kinsol', '@OUTPUT@'],
+    output: 'kinsol',
+    install: true,
+    install_dir: gridfire_vendor_includedir,
+)
+
+sundials_cmake_include = meson.global_build_root() / 'subprojects' / 'cvode-7.5.0' / '__CMake_build' / 'include' / 'sundials'
+
+custom_target(
+    'vendor_sundials_generated',
+    command: copyfiles_cmd + [
+        sundials_cmake_include / 'sundials_config.h',
+        sundials_cmake_include / 'sundials_export.h',
+        '@OUTDIR@',
+    ],
+    output: ['sundials_config.h', 'sundials_export.h'],
+    depends: libcvode_static,
+    install: true,
+    install_dir: gridfire_vendor_includedir / 'sundials',
+)

build-config/xxHash/meson.build

@@ -1,4 +1,9 @@
-
 xxhash_dep = declare_dependency(
     include_directories: include_directories('include')
 )
+
+install_subdir(
+    'include',
+    install_dir: gridfire_vendor_includedir,
+    strip_directory: true,
+)

build-extra/log-level/meson.build

@@ -29,4 +29,4 @@ elif (llevel == 'critical')
 endif
 
 log_argument = '-DQUILL_COMPILE_ACTIVE_LOG_LEVEL=' + log_argument
-add_project_arguments(log_argument, language: 'cpp')
+gridfire_args += [log_argument]

build-extra/pkg-config/gridfire-wheel.pc.in

@@ -0,0 +1,9 @@
+prefix=${pcfiledir}/../..
+includedir=${prefix}/include
+libdir=${prefix}/lib
+
+Name: gridfire
+Description: GridFire nuclear reaction network solver (bundled with the gridfire Python wheel)
+Version: @VERSION@
+Cflags: -I${includedir} -I${includedir}/gridfire/vendor -I${includedir}/fourdst/vendor
+Libs: -L${libdir} -lgridfire -Wl,-rpath,${libdir}

build-extra/pkg-config/meson.build

@@ -1,18 +1,24 @@
-if get_option('pkg_config')
+if get_option('build_python')
+    message('Generating wheel-relocatable pkg-config file for GridFire...')
+    wheel_pc_conf = configuration_data()
+    wheel_pc_conf.set('VERSION', meson.project_version())
+    configure_file(
+        input: 'gridfire-wheel.pc.in',
+        output: 'gridfire.pc',
+        configuration: wheel_pc_conf,
+        install: true,
+        install_dir: gridfire_pcdir,
+    )
+elif get_option('pkg_config')
     message('Generating pkg-config file for GridFire...')
     pkg = import('pkgconfig')
     pkg.generate(
         name: 'gridfire',
         description: 'GridFire nuclear reaction network solver',
-        version: meson.project_version(),
-        libraries: [
-            libgridfire,
-            libcomposition,
-            libconst,
-            liblogging
-        ],
-        subdirs: ['gridfire'],
         filebase: 'gridfire',
-        install_dir: join_paths(get_option('libdir'), 'pkgconfig')
+        subdirs: ['gridfire'],
+        libraries: [libgridfire, '-Wl,-rpath,${libdir}'],
+        requires: ['fourdst_composition', 'fourdst_config', 'fourdst_constants', 'fourdst_logging'],
+        extra_cflags: ['-I${includedir}' / 'gridfire' / 'vendor'],
     )
 endif

build-python/meson.build

@@ -1,99 +1,92 @@
 if get_option('build_python')
-  message('Building Python bindings...')
+    message('Building Python bindings...')
 
-  gridfire_py_deps = [
-      py_dep,
-      pybind11_dep,
-      const_dep,
-      config_dep,
-      composition_dep,
-      gridfire_dep
-  ]
+    gridfire_py_deps = [
+        py_dep,
+        pybind11_dep,
+        gridfire_dep
+    ]
 
-  py_sources =  [
-          meson.project_source_root() + '/src/python/bindings.cpp',
-          meson.project_source_root() + '/src/python/types/bindings.cpp',
-          meson.project_source_root() + '/src/python/partition/bindings.cpp',
-          meson.project_source_root() + '/src/python/partition/trampoline/py_partition.cpp',
-          meson.project_source_root() + '/src/python/reaction/bindings.cpp',
-          meson.project_source_root() + '/src/python/screening/bindings.cpp',
-          meson.project_source_root() + '/src/python/screening/trampoline/py_screening.cpp',
-          meson.project_source_root() + '/src/python/io/bindings.cpp',
-          meson.project_source_root() + '/src/python/io/trampoline/py_io.cpp',
-          meson.project_source_root() + '/src/python/exceptions/bindings.cpp',
-          meson.project_source_root() + '/src/python/engine/bindings.cpp',
-          meson.project_source_root() + '/src/python/engine/trampoline/py_engine.cpp',
-          meson.project_source_root() + '/src/python/solver/bindings.cpp',
-          meson.project_source_root() + '/src/python/solver/trampoline/py_solver.cpp',
-          meson.project_source_root() + '/src/python/policy/bindings.cpp',
-          meson.project_source_root() + '/src/python/policy/trampoline/py_policy.cpp',
-          meson.project_source_root() + '/src/python/utils/bindings.cpp',
-          meson.project_source_root() + '/src/python/config/bindings.cpp',
-          meson.project_source_root() + '/src/python/engine/scratchpads/bindings.cpp',
-      ]
+    if host_machine.system() == 'darwin'
+        gridfire_ext_rpath = '@loader_path/lib'
+    else
+        gridfire_ext_rpath = '$ORIGIN/lib'
+    endif
+
+    py_sources =  [
+        meson.project_source_root() + '/src/python/bindings.cpp',
+        meson.project_source_root() + '/src/python/types/bindings.cpp',
+        meson.project_source_root() + '/src/python/partition/bindings.cpp',
+        meson.project_source_root() + '/src/python/partition/trampoline/py_partition.cpp',
+        meson.project_source_root() + '/src/python/reaction/bindings.cpp',
+        meson.project_source_root() + '/src/python/screening/bindings.cpp',
+        meson.project_source_root() + '/src/python/screening/trampoline/py_screening.cpp',
+        meson.project_source_root() + '/src/python/io/bindings.cpp',
+        meson.project_source_root() + '/src/python/io/trampoline/py_io.cpp',
+        meson.project_source_root() + '/src/python/exceptions/bindings.cpp',
+        meson.project_source_root() + '/src/python/engine/bindings.cpp',
+        meson.project_source_root() + '/src/python/engine/trampoline/py_engine.cpp',
+        meson.project_source_root() + '/src/python/solver/bindings.cpp',
+        meson.project_source_root() + '/src/python/solver/trampoline/py_solver.cpp',
+        meson.project_source_root() + '/src/python/policy/bindings.cpp',
+        meson.project_source_root() + '/src/python/policy/trampoline/py_policy.cpp',
+        meson.project_source_root() + '/src/python/utils/bindings.cpp',
+        meson.project_source_root() + '/src/python/config/bindings.cpp',
+        meson.project_source_root() + '/src/python/engine/scratchpads/bindings.cpp',
+    ]
 
 
-  if meson.is_cross_build() and host_machine.system() == 'darwin'
-    py_mod = shared_module(
-      '_gridfire',
-      sources: py_sources,
-      dependencies: gridfire_py_deps,
-      name_prefix: '',
-      name_suffix: 'so',
-      install: true,
-      install_dir: py_installation.get_install_dir() + '/gridfire'
-      )
-  else
     py_mod = py_installation.extension_module(
-        '_gridfire', # Name of the generated .so/.pyd file (without extension)
+        '_gridfire',
         sources: py_sources,
-        dependencies : gridfire_py_deps,
-        install : true,
+        dependencies: gridfire_py_deps,
+        install: true,
+        link_args: gridfire_ext_rpath_args,
+        build_rpath: gridfire_ext_rpath,
+        install_rpath: gridfire_ext_rpath,
         subdir: 'gridfire',
     )
-  endif
 
+    py_installation.install_sources(
+        files(
+            meson.project_source_root() + '/src/python/gridfire/__init__.py',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/__init__.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/config.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/exceptions.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/partition.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/reaction.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/screening.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/io.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/solver.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/policy.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/type.pyi'
+        ),
+        subdir: 'gridfire',
+    )
 
-  py_installation.install_sources(
-      files(
-          meson.project_source_root() + '/src/python/gridfire/__init__.py',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/__init__.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/config.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/exceptions.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/partition.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/reaction.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/screening.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/io.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/solver.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/policy.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/type.pyi'
-      ),
-      subdir: 'gridfire',
-  )
+    py_installation.install_sources(
+        files(
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/engine/__init__.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/engine/diagnostics.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/engine/scratchpads.pyi'
+        ),
+        subdir: 'gridfire/engine',
+    )
 
-  py_installation.install_sources(
-      files(
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/engine/__init__.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/engine/diagnostics.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/engine/scratchpads.pyi'
-      ),
-      subdir: 'gridfire/engine',
-  )
+    py_installation.install_sources(
+        files(
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/utils/__init__.pyi',
+        ),
+        subdir: 'gridfire/utils',
+    )
 
-  py_installation.install_sources(
-      files(
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/utils/__init__.pyi',
-      ),
-      subdir: 'gridfire/utils',
-  )
-
-  py_installation.install_sources(
-      files(
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/utils/hashing/__init__.pyi',
-          meson.project_source_root() + '/stubs/gridfire/_gridfire/utils/hashing/reaction.pyi',
-      ),
-      subdir: 'gridfire/utils/hashing',
-  )
+    py_installation.install_sources(
+        files(
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/utils/hashing/__init__.pyi',
+            meson.project_source_root() + '/stubs/gridfire/_gridfire/utils/hashing/reaction.pyi',
+        ),
+        subdir: 'gridfire/utils/hashing',
+    )
 else
-  message('Python bindings disabled')
+    message('Python bindings disabled')
 endif

check.sh

@@ -0,0 +1,392 @@
+#!/usr/bin/env bash
+#
+# install.sh -- GridFire build-dependency checker.
+#
+# This script does NOT install anything. It detects your operating system,
+# checks each build dependency, and prints the exact commands to run if
+# something is missing or too old. Nothing on your system is modified.
+#
+# Dependencies checked:
+#   1. Meson      >= 1.6.0
+#   2. Ninja      (any recent)
+#   3. CMake      >= 3.16
+#   4. pkg-config (or pkgconf)
+#   5. A C and C++ toolchain: GCC >= 14  OR  Clang >= 17  (either is fine),
+#      with a working C++23 standard library
+#   6. Fortran (gfortran >= 14) -- only when --fortran is passed
+#
+# Supported platforms: Linux (apt / dnf / pacman / zypper) and macOS on
+# Apple Silicon. macOS x86_64 and Windows are NOT supported.
+#
+# Usage:
+#   ./install.sh            check core dependencies
+#   ./install.sh --fortran  also check for a Fortran compiler
+#   ./install.sh --help     show this help
+
+set -u
+
+MESON_MIN="1.6.0"
+CMAKE_MIN="3.16"
+GCC_MIN="14"
+CLANG_MIN="17"
+GFORTRAN_MIN="14"
+
+if [ -t 1 ]; then
+  RED=$'\033[0;31m'; GREEN=$'\033[0;32m'; YELLOW=$'\033[1;33m'
+  BLUE=$'\033[0;34m'; BOLD=$'\033[1m'; NC=$'\033[0m'
+else
+  RED=""; GREEN=""; YELLOW=""; BLUE=""; BOLD=""; NC=""
+fi
+
+ok()    { printf '  %s[ OK ]%s %s\n' "$GREEN" "$NC" "$1"; }
+bad()   { printf '  %s[FAIL]%s %s\n' "$RED" "$NC" "$1"; }
+warn()  { printf '  %s[WARN]%s %s\n' "$YELLOW" "$NC" "$1"; }
+info()  { printf '  %s[INFO]%s %s\n' "$BLUE" "$NC" "$1"; }
+hdr()   { printf '\n%s%s%s\n' "$BOLD" "$1" "$NC"; }
+
+FIX_NOTES=""
+FAIL_COUNT=0
+add_fix() { FIX_NOTES="${FIX_NOTES}$1\n"; }
+note_fail() { FAIL_COUNT=$((FAIL_COUNT + 1)); }
+
+WANT_FORTRAN=0
+for arg in "$@"; do
+  case "$arg" in
+    --fortran) WANT_FORTRAN=1 ;;
+    -h|--help) sed -n '2,/^$/p' "$0" | sed 's/^# \{0,1\}//'; exit 0 ;;
+    *) printf '%sUnknown argument: %s%s\n' "$RED" "$arg" "$NC"; exit 2 ;;
+  esac
+done
+
+version_ge() {
+  local a b ai bi n i
+  IFS='.' read -ra a <<< "$1"
+  IFS='.' read -ra b <<< "$2"
+  n=${#a[@]}; [ ${#b[@]} -gt "$n" ] && n=${#b[@]}
+  for ((i=0; i<n; i++)); do
+    ai=${a[i]:-0}; bi=${b[i]:-0}
+    ai=${ai%%[!0-9]*}; bi=${bi%%[!0-9]*}
+    ai=${ai:-0}; bi=${bi:-0}
+    if ((10#$ai > 10#$bi)); then return 0; fi
+    if ((10#$ai < 10#$bi)); then return 1; fi
+  done
+  return 0
+}
+
+extract_version() {
+  printf '%s' "$1" | grep -oE '[0-9]+(\.[0-9]+){0,3}' | head -n1
+}
+
+OS="$(uname -s)"
+ARCH="$(uname -m)"
+PKG_MGR=""
+DISTRO_NAME=""
+
+detect_platform() {
+  case "$OS" in
+    Darwin)
+      if [ "$ARCH" != "arm64" ]; then
+        printf '%sUnsupported platform.%s\n' "$RED" "$NC"
+        printf 'GridFire supports macOS on Apple Silicon (arm64) only; detected macOS on %s.\n' "$ARCH"
+        printf 'macOS x86_64 (Intel) is not supported.\n'
+        exit 1
+      fi
+      DISTRO_NAME="macOS (Apple Silicon)"
+      if command -v brew >/dev/null 2>&1; then
+        PKG_MGR="brew"
+      else
+        PKG_MGR="brew-missing"
+      fi
+      ;;
+    Linux)
+      if command -v apt-get >/dev/null 2>&1; then PKG_MGR="apt"
+      elif command -v dnf >/dev/null 2>&1; then PKG_MGR="dnf"
+      elif command -v pacman >/dev/null 2>&1; then PKG_MGR="pacman"
+      elif command -v zypper >/dev/null 2>&1; then PKG_MGR="zypper"
+      else PKG_MGR="unknown"; fi
+      if [ -r /etc/os-release ]; then
+        # shellcheck disable=SC1091
+        DISTRO_NAME="$(. /etc/os-release; printf '%s' "${PRETTY_NAME:-Linux}")"
+      else
+        DISTRO_NAME="Linux"
+      fi
+      ;;
+    *)
+      printf '%sUnsupported platform: %s.%s\n' "$RED" "$OS" "$NC"
+      printf 'GridFire supports Linux and macOS (Apple Silicon). Windows is not supported.\n'
+      printf 'On Windows, use WSL2 with a supported Linux distribution.\n'
+      exit 1
+      ;;
+  esac
+}
+
+pkg_cmd() {
+  case "$PKG_MGR" in
+    apt)
+      case "$1" in
+        ninja)     echo "sudo apt install ninja-build" ;;
+        cmake)     echo "sudo apt install cmake" ;;
+        pkgconfig) echo "sudo apt install pkg-config" ;;
+        gcc)       echo "sudo apt install g++-14 gcc-14" ;;
+        clang)     echo "sudo apt install clang-18 libstdc++-14-dev" ;;
+        gfortran)  echo "sudo apt install gfortran-14" ;;
+      esac ;;
+    dnf)
+      case "$1" in
+        ninja)     echo "sudo dnf install ninja-build" ;;
+        cmake)     echo "sudo dnf install cmake" ;;
+        pkgconfig) echo "sudo dnf install pkgconf-pkg-config" ;;
+        gcc)       echo "sudo dnf install gcc-c++" ;;
+        clang)     echo "sudo dnf install clang" ;;
+        gfortran)  echo "sudo dnf install gcc-gfortran" ;;
+      esac ;;
+    pacman)
+      case "$1" in
+        ninja)     echo "sudo pacman -S ninja" ;;
+        cmake)     echo "sudo pacman -S cmake" ;;
+        pkgconfig) echo "sudo pacman -S pkgconf" ;;
+        gcc)       echo "sudo pacman -S gcc" ;;
+        clang)     echo "sudo pacman -S clang" ;;
+        gfortran)  echo "sudo pacman -S gcc-fortran" ;;
+      esac ;;
+    zypper)
+      case "$1" in
+        ninja)     echo "sudo zypper install ninja" ;;
+        cmake)     echo "sudo zypper install cmake" ;;
+        pkgconfig) echo "sudo zypper install pkg-config" ;;
+        gcc)       echo "sudo zypper install gcc14-c++" ;;
+        clang)     echo "sudo zypper install clang" ;;
+        gfortran)  echo "sudo zypper install gcc14-fortran" ;;
+      esac ;;
+    brew|brew-missing)
+      case "$1" in
+        ninja)     echo "brew install ninja" ;;
+        cmake)     echo "brew install cmake" ;;
+        pkgconfig) echo "brew install pkg-config" ;;
+        gcc)       echo "brew install gcc" ;;
+        clang)     echo "brew install llvm   # then use /opt/homebrew/opt/llvm/bin/clang++" ;;
+        gfortran)  echo "brew install gcc    # provides gfortran" ;;
+      esac ;;
+    *)
+      echo "(install '$1' using your system package manager)" ;;
+  esac
+}
+
+check_meson() {
+  if command -v meson >/dev/null 2>&1; then
+    local v; v="$(extract_version "$(meson --version 2>/dev/null)")"
+    if [ -n "$v" ] && version_ge "$v" "$MESON_MIN"; then
+      ok "Meson $v (>= $MESON_MIN)"
+    else
+      bad "Meson ${v:-?} found but GridFire needs >= $MESON_MIN"
+      note_fail
+      add_fix "Meson upgrade (isolated, recommended):\n    pipx upgrade meson || pipx install meson\n  or with pip:\n    python3 -m pip install --user --upgrade meson"
+    fi
+  else
+    bad "Meson not found (need >= $MESON_MIN)"
+    note_fail
+    add_fix "Install Meson (isolated, recommended):\n    pipx install meson\n  If pipx is unavailable:\n    python3 -m pip install --user meson\n  (pipx itself: ${PKG_MGR/brew-missing/brew} install pipx; on Linux: python3 -m pip install --user pipx)"
+  fi
+}
+
+check_ninja() {
+  if command -v ninja >/dev/null 2>&1; then
+    ok "Ninja $(extract_version "$(ninja --version 2>/dev/null)")"
+  elif command -v samu >/dev/null 2>&1; then
+    ok "samurai (ninja-compatible) found"
+  else
+    bad "Ninja not found"
+    note_fail
+    add_fix "Install Ninja (isolated, recommended):\n    pipx inject meson ninja   # if meson via pipx\n  or:\n    python3 -m pip install --user ninja\n  or via system packages:\n    $(pkg_cmd ninja)"
+  fi
+}
+
+check_cmake() {
+  if command -v cmake >/dev/null 2>&1; then
+    local v; v="$(extract_version "$(cmake --version 2>/dev/null)")"
+    if [ -n "$v" ] && version_ge "$v" "$CMAKE_MIN"; then
+      ok "CMake $v (>= $CMAKE_MIN)"
+    else
+      bad "CMake ${v:-?} found but >= $CMAKE_MIN required (SUNDIALS/CppAD subprojects)"
+      note_fail
+      add_fix "Upgrade CMake:\n    $(pkg_cmd cmake)\n  or isolated:  python3 -m pip install --user --upgrade cmake"
+    fi
+  else
+    bad "CMake not found (required to build the SUNDIALS and CppAD subprojects)"
+    note_fail
+    add_fix "Install CMake:\n    $(pkg_cmd cmake)\n  or isolated:  python3 -m pip install --user cmake"
+  fi
+}
+
+check_pkgconfig() {
+  if command -v pkg-config >/dev/null 2>&1; then
+    ok "pkg-config $(extract_version "$(pkg-config --version 2>/dev/null)")"
+  elif command -v pkgconf >/dev/null 2>&1; then
+    ok "pkgconf $(extract_version "$(pkgconf --version 2>/dev/null)") (pkg-config compatible)"
+  else
+    bad "pkg-config not found"
+    note_fail
+    add_fix "Install pkg-config:\n    $(pkg_cmd pkgconfig)"
+  fi
+}
+
+probe_cxx23() {
+  local cxx="$1" dir src out rc
+  command -v "$cxx" >/dev/null 2>&1 || return 2
+  dir="$(mktemp -d 2>/dev/null)" || return 3
+  src="$dir/gf_probe.cpp"
+  out="$dir/gf_probe.out"
+  cat > "$src" <<'EOF'
+#include <print>
+#include <format>
+#include <expected>
+int main() {
+  std::println("ok {}", 23);
+  std::expected<int, int> test;
+}
+EOF
+  "$cxx" -std=c++23 "$src" -o "$out" >/dev/null 2>&1
+  rc=$?
+  rm -rf "$dir"
+  return $rc
+}
+check_toolchain() {
+  local found_ok=0 detail=""
+
+  local candidates=()
+  [ -n "${CXX:-}" ] && candidates+=("$CXX")
+  candidates+=(clang++ clang++-21 clang++-20 clang++-19 clang++-18 clang++-17 g++ g++-16 g++-15 g++-14)
+  if [ "$OS" = "Darwin" ]; then
+    candidates+=(/opt/homebrew/opt/llvm/bin/clang++ /usr/local/opt/llvm/bin/clang++)
+  fi
+
+  local seen="" cxx ver id minreq
+  for cxx in "${candidates[@]}"; do
+    command -v "$cxx" >/dev/null 2>&1 || continue
+    local rp; rp="$(command -v "$cxx")"
+    case " $seen " in *" $rp "*) continue ;; esac
+    seen="$seen $rp"
+
+    ver="$("$cxx" --version 2>/dev/null | head -n1)"
+    if printf '%s' "$ver" | grep -qiE 'clang'; then
+      id="clang"; minreq="$CLANG_MIN"
+    elif printf '%s' "$ver" | grep -qiE 'g\+\+|gcc|free software foundation'; then
+      id="gcc"; minreq="$GCC_MIN"
+    else
+      id="unknown"; minreq=""
+    fi
+    local vnum; vnum="$(extract_version "$ver")"
+
+    if probe_cxx23 "$cxx"; then
+      if [ -n "$minreq" ] && [ -n "$vnum" ] && ! version_ge "$vnum" "$minreq"; then
+        warn "$cxx ($id $vnum): C++23 probe passed but below tested floor ($minreq) -- usable, upgrade if you hit errors"
+      else
+        ok "$cxx ($id ${vnum:-?}): C++23 standard library working"
+      fi
+      found_ok=1
+      [ -z "${WORKING_CXX:-}" ] && WORKING_CXX="$rp"
+    else
+      detail="${detail}\n    - $cxx ($id ${vnum:-?}): present but failed the C++23 compile probe"
+    fi
+  done
+
+  local have_cc=0
+  for c in "${CC:-}" cc gcc clang; do
+    [ -n "$c" ] && command -v "$c" >/dev/null 2>&1 && { have_cc=1; break; }
+  done
+
+  if [ "$found_ok" -eq 1 ] && [ "$have_cc" -eq 1 ]; then
+    ok "C toolchain present"
+    [ -n "${WORKING_CXX:-}" ] && info "Suggested: CXX=$WORKING_CXX meson setup build"
+    return
+  fi
+
+  if [ "$found_ok" -ne 1 ]; then
+    bad "No C++ compiler with working C++23 support found (need GCC >= $GCC_MIN or Clang >= $CLANG_MIN)"
+    note_fail
+    [ -n "$detail" ] && printf '       Compilers seen but rejected:%b\n' "$detail"
+  fi
+  if [ "$have_cc" -ne 1 ]; then
+    bad "No C compiler found"
+    note_fail
+  fi
+
+
+  local fix="Install a C/C++ toolchain (Clang >= $CLANG_MIN or GCC >= $GCC_MIN):\n    $(pkg_cmd clang)\n  or GCC:\n    $(pkg_cmd gcc)"
+  # local fix="Install a C/C++ toolchain (GCC >= $GCC_MIN or Clang >= $CLANG_MIN):\n    $(pkg_cmd gcc)\n  or Clang:\n    $(pkg_cmd clang)"
+  if [ "$OS" = "Linux" ]; then
+    fix="$fix\n  Note: on Linux, Clang uses the system libstdc++ -- if a new Clang fails the\n  C++23 probe, install a newer libstdc++ (e.g. via g++-14) and Clang will use it."
+  elif [ "$OS" = "Darwin" ]; then
+    fix="$fix\n  Apple Clang: update Xcode / Command Line Tools to Xcode 16+\n    xcode-select --install   (or update via the App Store)"
+  fi
+  add_fix "$fix"
+}
+
+check_fortran() {
+  [ "$WANT_FORTRAN" -eq 1 ] || return 0
+  if command -v gfortran >/dev/null 2>&1; then
+    local v; v="$(extract_version "$(gfortran --version 2>/dev/null | head -n1)")"
+    if [ -n "$v" ] && version_ge "$v" "$GFORTRAN_MIN"; then
+      ok "gfortran $v (>= $GFORTRAN_MIN)"
+    else
+      bad "gfortran ${v:-?} found but >= $GFORTRAN_MIN required"
+      note_fail
+      add_fix "Upgrade gfortran:\n    $(pkg_cmd gfortran)"
+    fi
+  else
+    bad "gfortran not found (required by --fortran / -Dbuild_fortran=true)"
+    note_fail
+    add_fix "Install gfortran:\n    $(pkg_cmd gfortran)\n  (GridFire only supports gfortran; other Fortran compilers need -Dunsafe_fortran=true)"
+  fi
+}
+
+printf '%s======================================================%s\n' "$BOLD" "$NC"
+printf '%s  GridFire build-dependency check%s\n' "$BOLD" "$NC"
+printf '%s======================================================%s\n' "$BOLD" "$NC"
+
+detect_platform
+info "Platform: $DISTRO_NAME ($ARCH)"
+case "$PKG_MGR" in
+  brew-missing)
+    warn "Homebrew not found. Install it first: https://brew.sh"
+    warn "All macOS remediation commands below assume Homebrew." ;;
+  unknown)
+    warn "Could not identify a supported package manager (apt/dnf/pacman/zypper)." ;;
+  *) info "Package manager: $PKG_MGR" ;;
+esac
+
+hdr "Build tools"
+check_meson
+check_ninja
+check_cmake
+check_pkgconfig
+
+hdr "Compiler toolchain"
+check_toolchain
+
+if [ "$WANT_FORTRAN" -eq 1 ]; then
+  hdr "Fortran (requested via --fortran)"
+  check_fortran
+fi
+
+printf '\n%s======================================================%s\n' "$BOLD" "$NC"
+if [ "$FAIL_COUNT" -eq 0 ]; then
+  printf '%s  All dependencies satisfied.%s\n' "$GREEN" "$NC"
+  printf '%s======================================================%s\n' "$BOLD" "$NC"
+  printf '\nYou can build GridFire with:\n\n'
+  if [ -n "${WORKING_CXX:-}" ]; then
+    printf '    CXX=%s meson setup build\n' "$WORKING_CXX"
+  else
+    printf '    meson setup build\n'
+  fi
+  printf '    meson compile -C build\n'
+  printf '    sudo meson install -C build\n\n'
+  exit 0
+else
+  printf '%s  %d dependency problem(s) found -- see below.%s\n' "$RED" "$FAIL_COUNT" "$NC"
+  printf '%s======================================================%s\n' "$BOLD" "$NC"
+  printf '\n%sThis script does not install anything. Run the commands below yourself:%s\n\n' "$BOLD" "$NC"
+  printf '%b\n' "$FIX_NOTES"
+  printf 'Re-run %s./install.sh%s after installing to confirm.\n\n' "$BOLD" "$NC"
+  exit 1
+fi

docs/html/____init_____8py.html

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 <head>
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 <meta http-equiv="X-UA-Compatible" content="IE=11"/>
-<meta name="generator" content="Doxygen 1.9.8"/>
+<meta name="generator" content="Doxygen 1.13.2"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
 <title>GridFire: src/python/gridfire/__init__.py File Reference</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>
+<script type="text/javascript" src="clipboard.js"></script>
 <link href="navtree.css" rel="stylesheet" type="text/css"/>
-<script type="text/javascript" src="resize.js"></script>
 <script type="text/javascript" src="navtreedata.js"></script>
 <script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="cookie.js"></script>
 <link href="search/search.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="search/searchdata.js"></script>
 <script type="text/javascript" src="search/search.js"></script>
@@ -27,7 +29,7 @@
  <tbody>
  <tr id="projectrow">
   <td id="projectalign">
-   <div id="projectname">GridFire<span id="projectnumber">&#160;v0.7.1_rc2</span>
+   <div id="projectname">GridFire<span id="projectnumber">&#160;v0.7.6rc4.0</span>
    </div>
    <div id="projectbrief">General Purpose Nuclear Network</div>
   </td>
@@ -36,19 +38,24 @@
 </table>
 </div>
 <!-- end header part -->
-<!-- Generated by Doxygen 1.9.8 -->
+<!-- Generated by Doxygen 1.13.2 -->
 <script type="text/javascript">
 /* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
 var searchBox = new SearchBox("searchBox", "search/",'.html');
 /* @license-end */
 </script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() { codefold.init(0); });
+/* @license-end */
+</script>
 <script type="text/javascript" src="menudata.js"></script>
 <script type="text/javascript" src="menu.js"></script>
 <script type="text/javascript">
 /* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
 $(function() {
-  initMenu('',true,false,'search.php','Search');
-  $(document).ready(function() { init_search(); });
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
 });
 /* @license-end */
 </script>
@@ -66,7 +73,7 @@ $(function() {
 </div>
 <script type="text/javascript">
 /* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
-$(document).ready(function(){initNavTree('____init_____8py.html',''); initResizable(); });
+$(function(){initNavTree('____init_____8py.html',''); initResizable(true); });
 /* @license-end */
 </script>
 <div id="doc-content">
@@ -94,6 +101,7 @@ $(document).ready(function(){initNavTree('____init_____8py.html',''); initResiza
 <div class="header">
   <div class="summary">
 <a href="#namespaces">Namespaces</a> &#124;
+<a href="#func-members">Functions</a> &#124;
 <a href="#var-members">Variables</a>  </div>
   <div class="headertitle"><div class="title">__init__.py File Reference</div></div>
 </div><!--header-->
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+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
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+<tr class="separator:a0ee5ace587287cdba8f9755a0ef0b498"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a45c5e5933ef14301b6f7ec2fff6a0966" id="r_a45c5e5933ef14301b6f7ec2fff6a0966"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire.html#a45c5e5933ef14301b6f7ec2fff6a0966">gridfire.gf_version</a> ()</td></tr>
+<tr class="separator:a45c5e5933ef14301b6f7ec2fff6a0966"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a1de3db5e65a2e834c55f458307cab68e" id="r_a1de3db5e65a2e834c55f458307cab68e"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire.html#a1de3db5e65a2e834c55f458307cab68e">gridfire.gf_author</a> ()</td></tr>
+<tr class="separator:a1de3db5e65a2e834c55f458307cab68e"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="separator:ae6f8e40e5233e5c98c9c4290f518b72d"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+</table><table class="memberdecls">
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+  <div class="headertitle"><div class="title">PointSolver.cpp File Reference</div></div>
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+<div class="textblock"><code>#include &quot;<a class="el" href="_point_solver_8h.html">gridfire/solver/strategies/PointSolver.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="types_2types_8h.html">gridfire/types/types.h</a>&quot;</code><br />
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+<code>#include &quot;quill/LogMacros.h&quot;</code><br />
+<code>#include &quot;fourdst/composition/composition.h&quot;</code><br />
+<code>#include &lt;cstdint&gt;</code><br />
+<code>#include &lt;limits&gt;</code><br />
+<code>#include &lt;string&gt;</code><br />
+<code>#include &lt;unordered_map&gt;</code><br />
+<code>#include &lt;stdexcept&gt;</code><br />
+<code>#include &lt;algorithm&gt;</code><br />
+<code>#include &quot;fourdst/atomic/species.h&quot;</code><br />
+<code>#include &quot;fourdst/composition/exceptions/exceptions_composition.h&quot;</code><br />
+<code>#include &quot;<a class="el" href="engine__graph_8h.html">gridfire/engine/engine_graph.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="engine__partitioning__trigger_8h.html">gridfire/solver/strategies/triggers/engine_partitioning_trigger.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="trigger__pprint_8h.html">gridfire/trigger/procedures/trigger_pprint.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="error__solver_8h.html">gridfire/exceptions/error_solver.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="sundials_8h.html">gridfire/utils/sundials.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="config_8h.html">gridfire/config/config.h</a>&quot;</code><br />
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+   <div id="projectname">GridFire<span id="projectnumber">&#160;v0.7.6rc4.0</span>
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+  <div class="summary">
+<a href="#nested-classes">Classes</a> &#124;
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+  <div class="headertitle"><div class="title">PointSolver.h File Reference</div></div>
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+<div class="contents">
+<div class="textblock"><code>#include &quot;<a class="el" href="strategy__abstract_8h.html">gridfire/solver/strategies/strategy_abstract.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="engine__abstract_8h.html">gridfire/engine/engine_abstract.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="types_2types_8h.html">gridfire/types/types.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="exceptions_8h.html">gridfire/exceptions/exceptions.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="config_8h.html">gridfire/config/config.h</a>&quot;</code><br />
+<code>#include &quot;fourdst/atomic/atomicSpecies.h&quot;</code><br />
+<code>#include &quot;fourdst/config/config.h&quot;</code><br />
+<code>#include &lt;functional&gt;</code><br />
+<code>#include &lt;any&gt;</code><br />
+<code>#include &lt;string&gt;</code><br />
+<code>#include &lt;vector&gt;</code><br />
+<code>#include &lt;tuple&gt;</code><br />
+<code>#include &lt;cvode/cvode.h&gt;</code><br />
+<code>#include &lt;sundials/sundials_types.h&gt;</code><br />
+<code>#include &lt;sundials/sundials_context.h&gt;</code><br />
+<code>#include &lt;sunmatrix/sunmatrix_dense.h&gt;</code><br />
+<code>#include &lt;sunlinsol/sunlinsol_dense.h&gt;</code><br />
+<code>#include &lt;nvector/nvector_serial.h&gt;</code><br />
+</div><div class="textblock"><div class="dynheader">
+Include dependency graph for PointSolver.h:</div>
+<div class="dyncontent">
+<div class="center"><div class="zoom"><iframe scrolling="no" frameborder="0" src="_point_solver_8h__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><div class="textblock"><div class="dynheader">
+This graph shows which files directly or indirectly include this file:</div>
+<div class="dyncontent">
+<div class="center"><div class="zoom"><iframe scrolling="no" frameborder="0" src="_point_solver_8h__dep__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>
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+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="nested-classes" name="nested-classes"></a>
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-<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span><span onclick="javascript:toggleLevel(4);">4</span><span onclick="javascript:toggleLevel(5);">5</span>]</div><table class="directory">
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-<tr id="row_0_1_14_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1MissingSeedSpeciesError.html" target="_self">MissingSeedSpeciesError</a></td><td class="desc">Exception thrown when a required seed species is not found in the initial composition </td></tr>
-<tr id="row_0_1_15_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1NetworkResizedError.html" target="_self">NetworkResizedError</a></td><td class="desc">Exception for errors during network resizing </td></tr>
-<tr id="row_0_1_16_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1PolicyError.html" target="_self">PolicyError</a></td><td class="desc">Base class for all exceptions related to network policy operations </td></tr>
-<tr id="row_0_1_17_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1ReactionError.html" target="_self">ReactionError</a></td><td class="desc">Base class for all exceptions related to reaction operations </td></tr>
-<tr id="row_0_1_18_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1ReactionParsingError.html" target="_self">ReactionParsingError</a></td><td class="desc"></td></tr>
-<tr id="row_0_1_19_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1SingularJacobianError.html" target="_self">SingularJacobianError</a></td><td class="desc">Exception thrown when the Jacobian matrix is singular </td></tr>
-<tr id="row_0_1_20_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1SolverError.html" target="_self">SolverError</a></td><td class="desc">Base class for all exceptions related to solver operations </td></tr>
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-<tr id="row_0_1_22_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1SUNDIALSError.html" target="_self">SUNDIALSError</a></td><td class="desc">Base class for exceptions related to SUNDIALS solver operations </td></tr>
-<tr id="row_0_1_23_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1UnableToSetNetworkReactionsError.html" target="_self">UnableToSetNetworkReactionsError</a></td><td class="desc">Exception for failures in setting network reactions </td></tr>
-<tr id="row_0_1_24_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1exceptions_1_1UninitializedJacobianError.html" target="_self">UninitializedJacobianError</a></td><td class="desc">Exception for uninitialized Jacobian matrix access </td></tr>
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-<tr id="row_0_5_0_" class="odd" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_5_0_" class="arrow" onclick="toggleFolder('0_5_0_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1rates_1_1weak.html" target="_self">weak</a></td><td class="desc"></td></tr>
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-<tr id="row_0_5_0_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_1rates_1_1weak_1_1InterpolationError.html" target="_self">InterpolationError</a></td><td class="desc">Interpolation error with optional per-axis bounds details </td></tr>
-<tr id="row_0_5_0_2_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1rates_1_1weak_1_1IsotopeGrid.html" target="_self">IsotopeGrid</a></td><td class="desc">Regular 2D grid and payloads for a single isotope (A,Z) </td></tr>
-<tr id="row_0_5_0_3_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1rates_1_1weak_1_1RateDataRow.html" target="_self">RateDataRow</a></td><td class="desc">One row of the unified weak-rate data table for a specific isotope and state </td></tr>
-<tr id="row_0_5_0_4_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1rates_1_1weak_1_1WeakRateDerivatives.html" target="_self">WeakRateDerivatives</a></td><td class="desc">Partial derivatives of the log10() fields w.r.t. (T9, log10(rho*Ye)) </td></tr>
-<tr id="row_0_5_0_5_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1rates_1_1weak_1_1WeakRateInterpolator.html" target="_self">WeakRateInterpolator</a></td><td class="desc">3D table interpolator for tabulated weak reaction data by isotope </td></tr>
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+<tr id="row_0_0_5_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1config_1_1_point_solver_config.html" target="_self">PointSolverConfig</a></td><td class="desc"></td></tr>
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+<tr id="row_0_1_1_0_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_1engine_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_2_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1_defined_engine_view.html" target="_self">DefinedEngineView</a></td><td class="desc"></td></tr>
+<tr id="row_0_1_3_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html" target="_self">DynamicEngine</a></td><td class="desc">Abstract class for engines supporting Jacobian and stoichiometry operations </td></tr>
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+<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_1engine_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_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_1engine_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>
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+<tr id="row_0_1_8_0_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1engine_1_1_graph_engine_1_1_atomic_reverse_rate.html" target="_self">AtomicReverseRate</a></td><td class="desc"></td></tr>
+<tr id="row_0_1_8_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_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_2_9_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_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_2_10_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_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_2_11_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="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_2_12_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="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_2_13_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_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_2_14_" 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_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_2_15_" 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_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_2_16_" 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_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_2_17_" 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_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_2_18_" 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_1exceptions_1_1_reaction_parsing_error.html" target="_self">ReactionParsingError</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_19_" 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_1exceptions_1_1_scratch_pad_error.html" target="_self">ScratchPadError</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_20_" 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_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_2_21_" 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_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_2_22_" 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_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_2_23_" 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_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_2_24_" 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_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_2_25_" 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_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_2_26_" 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_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_2_27_" 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_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_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_1io.html" target="_self">io</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_0_" class="odd" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_3_0_" class="arrow" onclick="dynsection.toggleFolder('0_3_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_3_0_0_" class="odd" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_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>
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+<tr id="row_0_3_2_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_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>
+<tr id="row_0_3_3_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_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>
+<tr id="row_0_4_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_4_" class="arrow" onclick="dynsection.toggleFolder('0_4_')">&#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_4_0_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_4_0_" class="arrow" onclick="dynsection.toggleFolder('0_4_0_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1partition_1_1record.html" target="_self">record</a></td><td class="desc"></td></tr>
+<tr id="row_0_4_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_1partition_1_1record_1_1_rauscher_thielemann_partition_data_record.html" target="_self">RauscherThielemannPartitionDataRecord</a></td><td class="desc">Packed binary record of Rauscher-Thielemann partition function data for an isotope </td></tr>
+<tr id="row_0_4_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_1partition_1_1_composite_partition_function.html" target="_self">CompositePartitionFunction</a></td><td class="desc">Combines multiple <a class="el" href="classgridfire_1_1partition_1_1_partition_function.html" title="Abstract interface for evaluating nuclear partition functions.">PartitionFunction</a> instances into a single composite strategy </td></tr>
+<tr id="row_0_4_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_1partition_1_1_ground_state_partition_function.html" target="_self">GroundStatePartitionFunction</a></td><td class="desc">Partition function implementation for nuclear ground states </td></tr>
+<tr id="row_0_4_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_1partition_1_1_partition_function.html" target="_self">PartitionFunction</a></td><td class="desc">Abstract interface for evaluating nuclear partition functions </td></tr>
+<tr id="row_0_4_4_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_4_4_" class="arrow" onclick="dynsection.toggleFolder('0_4_4_')">&#9658;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1partition_1_1_rauscher_thielemann_partition_function.html" target="_self">RauscherThielemannPartitionFunction</a></td><td class="desc">Partition function using Rauscher-Thielemann tabulated normalized G-values </td></tr>
+<tr id="row_0_4_4_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_1partition_1_1_rauscher_thielemann_partition_function_1_1_identified_isotope.html" target="_self">IdentifiedIsotope</a></td><td class="desc"></td></tr>
+<tr id="row_0_4_4_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_1partition_1_1_rauscher_thielemann_partition_function_1_1_interpolation_points.html" target="_self">InterpolationPoints</a></td><td class="desc"></td></tr>
+<tr id="row_0_4_4_2_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgridfire_1_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_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_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1policy.html" target="_self">policy</a></td><td class="desc"></td></tr>
+<tr id="row_0_5_0_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1policy_1_1_c_n_o_chain_policy.html" target="_self">CNOChainPolicy</a></td><td class="desc">CNO Chain Policy </td></tr>
+<tr id="row_0_5_1_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1policy_1_1_c_n_o_i_chain_policy.html" target="_self">CNOIChainPolicy</a></td><td class="desc">CNO I Chain Policy </td></tr>
+<tr id="row_0_5_2_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1policy_1_1_c_n_o_i_i_chain_policy.html" target="_self">CNOIIChainPolicy</a></td><td class="desc">CNO II Chain Policy </td></tr>
+<tr id="row_0_5_3_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1policy_1_1_c_n_o_i_i_i_chain_policy.html" target="_self">CNOIIIChainPolicy</a></td><td class="desc">CNO III Chain Policy </td></tr>
+<tr id="row_0_5_4_" class="odd" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1policy_1_1_c_n_o_i_v_chain_policy.html" target="_self">CNOIVChainPolicy</a></td><td class="desc">CNO IV Chain Policy </td></tr>
+<tr id="row_0_5_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="structgridfire_1_1policy_1_1_construction_results.html" target="_self">ConstructionResults</a></td><td class="desc"></td></tr>
+<tr id="row_0_5_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_1policy_1_1_hot_c_n_o_chain_policy.html" target="_self">HotCNOChainPolicy</a></td><td class="desc">Hot CNO Chain Policy </td></tr>
+<tr id="row_0_5_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_1policy_1_1_hot_c_n_o_i_chain_policy.html" target="_self">HotCNOIChainPolicy</a></td><td class="desc">Hot CNO I Chain Policy </td></tr>
+<tr id="row_0_5_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_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>
+<tr id="row_0_5_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_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>
+<tr id="row_0_5_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_1policy_1_1_main_sequence_policy.html" target="_self">MainSequencePolicy</a></td><td class="desc">A <a class="el" href="classgridfire_1_1policy_1_1_network_policy.html" title="Abstract interface for policies that construct DynamicEngine networks from a seed composition.">NetworkPolicy</a> for building reaction networks suitable for low-mass main-sequence stars </td></tr>
+<tr id="row_0_5_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_1policy_1_1_main_sequence_reaction_chain_policy.html" target="_self">MainSequenceReactionChainPolicy</a></td><td class="desc">Main Sequence Reaction Chain Policy </td></tr>
+<tr id="row_0_5_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_1policy_1_1_multi_reaction_chain_policy.html" target="_self">MultiReactionChainPolicy</a></td><td class="desc">A <a class="el" href="classgridfire_1_1policy_1_1_reaction_chain_policy.html" title="Abstract interface encapsulating a set of reactions representing a single chain or pathway.">ReactionChainPolicy</a> composed of multiple child <a class="el" href="classgridfire_1_1policy_1_1_reaction_chain_policy.html" title="Abstract interface encapsulating a set of reactions representing a single chain or pathway.">ReactionChainPolicy</a> instances </td></tr>
+<tr id="row_0_5_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_1policy_1_1_network_policy.html" target="_self">NetworkPolicy</a></td><td class="desc">Abstract interface for policies that construct DynamicEngine networks from a seed composition </td></tr>
+<tr id="row_0_5_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_1policy_1_1_proton_proton_chain_policy.html" target="_self">ProtonProtonChainPolicy</a></td><td class="desc">Proton-Proton Chain Policy </td></tr>
+<tr id="row_0_5_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_1policy_1_1_proton_proton_i_chain_policy.html" target="_self">ProtonProtonIChainPolicy</a></td><td class="desc">Proton-Proton I Chain Policy </td></tr>
+<tr id="row_0_5_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_1policy_1_1_proton_proton_i_i_chain_policy.html" target="_self">ProtonProtonIIChainPolicy</a></td><td class="desc">Proton-Proton II Chain Policy </td></tr>
+<tr id="row_0_5_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_1policy_1_1_proton_proton_i_i_i_chain_policy.html" target="_self">ProtonProtonIIIChainPolicy</a></td><td class="desc">Proton-Proton III Chain Policy </td></tr>
+<tr id="row_0_5_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_1policy_1_1_reaction_chain_policy.html" target="_self">ReactionChainPolicy</a></td><td class="desc">Abstract interface encapsulating a set of reactions representing a single chain or pathway </td></tr>
+<tr id="row_0_5_19_" class="odd" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_5_19_" class="arrow" onclick="dynsection.toggleFolder('0_5_19_')">&#9658;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1policy_1_1_temperature_dependent_chain_policy.html" target="_self">TemperatureDependentChainPolicy</a></td><td class="desc">Base class for reaction chain policies that are active only within specific temperature ranges </td></tr>
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+<tr id="row_0_8_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_8_" class="arrow" onclick="dynsection.toggleFolder('0_8_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1reaction.html" target="_self">reaction</a></td><td class="desc"></td></tr>
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+<tr id="row_0_8_4_" 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_1reaction_1_1_reaction_set.html" target="_self">ReactionSet</a></td><td class="desc"></td></tr>
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+<tr id="row_0_11_0_" class="odd" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_0_11_0_" class="arrow" onclick="dynsection.toggleFolder('0_11_0_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacegridfire_1_1trigger_1_1solver.html" target="_self">solver</a></td><td class="desc"></td></tr>
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+<tr id="row_0_11_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="structgridfire_1_1trigger_1_1_trigger_result.html" target="_self">TriggerResult</a></td><td class="desc"></td></tr>
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+<tr id="row_0_12_0_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgridfire_1_1utils_1_1_column.html" target="_self">Column</a></td><td class="desc"></td></tr>
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+        [ "GroundStatePartitionFunction", "classgridfire_1_1partition_1_1_ground_state_partition_function.html", "classgridfire_1_1partition_1_1_ground_state_partition_function" ],
+        [ "PartitionFunction", "classgridfire_1_1partition_1_1_partition_function.html", "classgridfire_1_1partition_1_1_partition_function" ],
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+        [ "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" ],
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+        [ "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" ],
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+          [ "RateDataRow", "structgridfire_1_1rates_1_1weak_1_1_rate_data_row.html", "structgridfire_1_1rates_1_1weak_1_1_rate_data_row" ],
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+          [ "WeakRatePayload", "structgridfire_1_1rates_1_1weak_1_1_weak_rate_payload.html", "structgridfire_1_1rates_1_1weak_1_1_weak_rate_payload" ],
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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" ],
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+<g id="a_Node000009"><a xlink:href="io_2bindings_8h.html" target="_top" xlink:title=" ">
+<polygon fill="white" stroke="#666666" points="760.33,-80.12 689.58,-80.12 689.58,-60.88 760.33,-60.88 760.33,-80.12"/>
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+<g id="a_Node000011"><a xlink:href="screening_2bindings_8h.html" target="_top" xlink:title=" ">
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-<text xml:space="preserve" text-anchor="middle" x="1043.36" y="-61" font-family="Helvetica,sans-Serif" font-size="10.00">utils/bindings.h</text>
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+<polygon fill="white" stroke="#666666" points="1106.7,-80.12 1017.2,-80.12 1017.2,-60.88 1106.7,-60.88 1106.7,-80.12"/>
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+<g id="a_Node000013"><a xlink:href="utils_2bindings_8h.html" target="_top" xlink:title=" ">
+<polygon fill="white" stroke="#666666" points="1205.58,-80.12 1124.33,-80.12 1124.33,-60.88 1205.58,-60.88 1205.58,-80.12"/>
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+<!-- Node14 -->
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+</a>
+</g>
+</g>
+<!-- Node1&#45;&gt;Node14 -->
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+<title>Node1&#45;&gt;Node14</title>
+<g id="a_edge23_Node000001_Node000014"><a xlink:title=" ">
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+<!-- Node15 -->
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+</a>
+</g>
+</g>
+<!-- Node1&#45;&gt;Node15 -->
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+<title>Node1&#45;&gt;Node15</title>
+<g id="a_edge25_Node000001_Node000015"><a xlink:title=" ">
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+   </div>
+   <div id="projectbrief">General Purpose Nuclear Network</div>
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+  <div class="summary">
+<a href="#nested-classes">Classes</a> &#124;
+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#concepts">Concepts</a>  </div>
+  <div class="headertitle"><div class="title">blob.h File Reference</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>Container class for managing multiple scratchpad instances.  
+<a href="#details">More...</a></p>
+<div class="textblock"><code>#include &quot;<a class="el" href="scratchpad__abstract_8h.html">gridfire/engine/scratchpads/scratchpad_abstract.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="engine_2scratchpads_2types_8h.html">gridfire/engine/scratchpads/types.h</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="error__scratchpad_8h.html">gridfire/exceptions/error_scratchpad.h</a>&quot;</code><br />
+<code>#include &lt;unordered_map&gt;</code><br />
+<code>#include &lt;memory&gt;</code><br />
+<code>#include &lt;expected&gt;</code><br />
+<code>#include &lt;unordered_set&gt;</code><br />
+</div><div class="textblock"><div class="dynheader">
+Include dependency graph for blob.h:</div>
+<div class="dyncontent">
+<div class="center"><div class="zoom"><iframe scrolling="no" frameborder="0" src="blob_8h__incl.svg" width="100%" height="527"><p><b>This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead.</b></p></iframe></div></div>
+</div>
+</div><div class="textblock"><div class="dynheader">
+This graph shows which files directly or indirectly include this file:</div>
+<div class="dyncontent">
+<div class="center"><div class="zoom"><iframe scrolling="no" frameborder="0" src="blob_8h__dep__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="nested-classes" name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a></td></tr>
+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Container for managing a collection of typed scratchpad instances.  <a href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#details">More...</a><br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="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_1engine.html">gridfire::engine</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_1engine_1_1scratch.html">gridfire::engine::scratch</a></td></tr>
+<tr class="memdesc:namespacegridfire_1_1engine_1_1scratch"><td class="mdescLeft">&#160;</td><td class="mdescRight">Scratchpad memory management for computational engines. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="concepts" name="concepts"></a>
+Concepts</h2></td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">concept &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="conceptgridfire_1_1engine_1_1scratch_1_1_is_scratch_pad.html">gridfire::engine::scratch::IsScratchPad</a></td></tr>
+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Concept that constrains types to valid scratchpad implementations. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><p>Container class for managing multiple scratchpad instances. </p>
+<p>This header defines the StateBlob class, which serves as a centralized registry for managing multiple scratchpad instances used by computational engines. It provides type-safe enrollment, retrieval, and cloning of scratchpads using compile-time type checking via C++20 concepts.</p>
+<dl class="section user"><dt>Purpose</dt><dd>The StateBlob provides:<ul>
+<li>A fixed-size array of scratchpad slots indexed by ScratchPadType</li>
+<li>Type-safe enrollment ensuring one instance per scratchpad type</li>
+<li>Compile-time verified retrieval with optional initialization checks</li>
+<li>Deep cloning of all enrolled scratchpads for parallel execution</li>
+<li>Status tracking for each scratchpad slot</li>
+</ul>
+</dd></dl>
+<dl class="section user"><dt>Examples</dt><dd><div class="fragment"><div class="line"><span class="preprocessor">#include &quot;<a class="code" href="blob_8h.html">gridfire/engine/scratchpads/blob.h</a>&quot;</span></div>
+<div class="line"><span class="preprocessor">#include &quot;<a class="code" href="engine__graph__scratchpad_8h.html">gridfire/engine/scratchpads/engine_graph_scratchpad.h</a>&quot;</span></div>
+<div class="line"> </div>
+<div class="line"><span class="keyword">using namespace </span><a class="code hl_namespace" href="namespacegridfire_1_1engine_1_1scratch.html">gridfire::engine::scratch</a>;</div>
+<div class="line"> </div>
+<div class="line"><span class="comment">// Create a StateBlob and enroll scratchpads</span></div>
+<div class="line"><a class="code hl_class" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">StateBlob</a> blob;</div>
+<div class="line">blob.<a class="code hl_function" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#aa06d7bb89e67c4b6fd584d8f32a251bf">enroll</a>&lt;<a class="code hl_struct" href="structgridfire_1_1engine_1_1scratch_1_1_graph_engine_scratch_pad.html">GraphEngineScratchPad</a>&gt;();</div>
+<div class="line"> </div>
+<div class="line"><span class="comment">// Retrieve a scratchpad (returns std::expected)</span></div>
+<div class="line"><span class="keyword">auto</span> result = blob.<a class="code hl_function" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#acedd28277e5c6805865a9baa3991686a">get</a>&lt;<a class="code hl_struct" href="structgridfire_1_1engine_1_1scratch_1_1_graph_engine_scratch_pad.html">GraphEngineScratchPad</a>&gt;();</div>
+<div class="line"><span class="keywordflow">if</span> (result.has_value()) {</div>
+<div class="line">    <a class="code hl_struct" href="structgridfire_1_1engine_1_1scratch_1_1_graph_engine_scratch_pad.html">GraphEngineScratchPad</a>* <a class="code hl_namespace" href="namespacegridfire_1_1engine_1_1scratch.html">scratch</a> = result.value();</div>
+<div class="line">    <a class="code hl_namespace" href="namespacegridfire_1_1engine_1_1scratch.html">scratch</a>-&gt;initialize(<a class="code hl_namespace" href="namespacegridfire_1_1engine.html">engine</a>);</div>
+<div class="line">}</div>
+<div class="line"> </div>
+<div class="line"><span class="comment">// Retrieve with initialization check</span></div>
+<div class="line"><span class="keyword">auto</span> checked = blob.<a class="code hl_function" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#acedd28277e5c6805865a9baa3991686a">get</a>&lt;<a class="code hl_struct" href="structgridfire_1_1engine_1_1scratch_1_1_graph_engine_scratch_pad.html">GraphEngineScratchPad</a>, <span class="keyword">true</span>&gt;();</div>
+<div class="line"><span class="keywordflow">if</span> (!checked.has_value()) {</div>
+<div class="line">    <span class="keywordflow">if</span> (checked.error() == <a class="code hl_enumvalue" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#a12f7a1fcb8bd6277f91b7ee08f267bd8abe3241d81779b1878546fba3b251eba3">StateBlob::Error::SCRATCHPAD_NOT_INITIALIZED</a>) {</div>
+<div class="line">        <span class="comment">// Handle uninitialized scratchpad</span></div>
+<div class="line">    }</div>
+<div class="line">}</div>
+<div class="line"> </div>
+<div class="line"><span class="comment">// Clone for parallel execution</span></div>
+<div class="line"><span class="keyword">auto</span> worker_blob = blob.<a class="code hl_function" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#aa45357f0c368d7403306452c5ea56af0">clone_structure</a>();</div>
+<div class="ttc" id="ablob_8h_html"><div class="ttname"><a href="blob_8h.html">blob.h</a></div><div class="ttdoc">Container class for managing multiple scratchpad instances.</div></div>
+<div class="ttc" id="aclassgridfire_1_1engine_1_1scratch_1_1_state_blob_html"><div class="ttname"><a href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a></div><div class="ttdoc">Container for managing a collection of typed scratchpad instances.</div><div class="ttdef"><b>Definition</b> blob.h:114</div></div>
+<div class="ttc" id="aclassgridfire_1_1engine_1_1scratch_1_1_state_blob_html_a12f7a1fcb8bd6277f91b7ee08f267bd8abe3241d81779b1878546fba3b251eba3"><div class="ttname"><a href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#a12f7a1fcb8bd6277f91b7ee08f267bd8abe3241d81779b1878546fba3b251eba3">gridfire::engine::scratch::StateBlob::Error::SCRATCHPAD_NOT_INITIALIZED</a></div><div class="ttdeci">@ SCRATCHPAD_NOT_INITIALIZED</div><div class="ttdoc">Scratchpad exists but is not initialized.</div><div class="ttdef"><b>Definition</b> blob.h:122</div></div>
+<div class="ttc" id="aclassgridfire_1_1engine_1_1scratch_1_1_state_blob_html_aa06d7bb89e67c4b6fd584d8f32a251bf"><div class="ttname"><a href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#aa06d7bb89e67c4b6fd584d8f32a251bf">gridfire::engine::scratch::StateBlob::enroll</a></div><div class="ttdeci">void enroll()</div><div class="ttdoc">Enroll a new scratchpad type into the blob.</div><div class="ttdef"><b>Definition</b> blob.h:196</div></div>
+<div class="ttc" id="aclassgridfire_1_1engine_1_1scratch_1_1_state_blob_html_aa45357f0c368d7403306452c5ea56af0"><div class="ttname"><a href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#aa45357f0c368d7403306452c5ea56af0">gridfire::engine::scratch::StateBlob::clone_structure</a></div><div class="ttdeci">std::unique_ptr&lt; StateBlob &gt; clone_structure() const</div><div class="ttdoc">Create a deep copy of this blob with all enrolled scratchpads.</div><div class="ttdef"><b>Definition</b> blob.h:361</div></div>
+<div class="ttc" id="aclassgridfire_1_1engine_1_1scratch_1_1_state_blob_html_acedd28277e5c6805865a9baa3991686a"><div class="ttname"><a href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#acedd28277e5c6805865a9baa3991686a">gridfire::engine::scratch::StateBlob::get</a></div><div class="ttdeci">std::expected&lt; CTX *, Error &gt; get() const</div><div class="ttdoc">Retrieve a scratchpad by type.</div><div class="ttdef"><b>Definition</b> blob.h:230</div></div>
+<div class="ttc" id="aengine__graph__scratchpad_8h_html"><div class="ttname"><a href="engine__graph__scratchpad_8h.html">engine_graph_scratchpad.h</a></div><div class="ttdoc">Scratchpad implementation for the GraphEngine using CppAD automatic differentiation.</div></div>
+<div class="ttc" id="anamespacegridfire_1_1engine_1_1scratch_html"><div class="ttname"><a href="namespacegridfire_1_1engine_1_1scratch.html">gridfire::engine::scratch</a></div><div class="ttdoc">Scratchpad memory management for computational engines.</div><div class="ttdef"><b>Definition</b> blob.h:69</div></div>
+<div class="ttc" id="anamespacegridfire_1_1engine_html"><div class="ttname"><a href="namespacegridfire_1_1engine.html">gridfire::engine</a></div><div class="ttdef"><b>Definition</b> dynamic_engine_diagnostics.h:39</div></div>
+<div class="ttc" id="astructgridfire_1_1engine_1_1scratch_1_1_graph_engine_scratch_pad_html"><div class="ttname"><a href="structgridfire_1_1engine_1_1scratch_1_1_graph_engine_scratch_pad.html">gridfire::engine::scratch::GraphEngineScratchPad</a></div><div class="ttdoc">Scratchpad for storing CppAD automatic differentiation state for GraphEngine.</div><div class="ttdef"><b>Definition</b> engine_graph_scratchpad.h:83</div></div>
+</div><!-- fragment --></dd></dl>
+<dl class="section user"><dt>Thread Safety</dt><dd>The StateBlob class is <b>not thread-safe</b>. Each thread should have its own StateBlob instance. Use clone_structure() to create independent copies for parallel workers. The cloned blob contains deep copies of all enrolled scratchpads.</dd></dl>
+<dl class="section see"><dt>See also</dt><dd>AbstractScratchPad </dd>
+<dd>
+ScratchPadType </dd></dl>
+</div></div><!-- contents -->
+</div><!-- doc-content -->
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 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="namespaces" name="namespaces"></a>
 Namespaces</h2></td></tr>
-<tr class="memitem:namespacegridfire" id="r_namespacegridfire"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire.html">gridfire</a></td></tr>
+<tr class="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:namespacegridfire_1_1policy" id="r_namespacegridfire_1_1policy"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire_1_1policy.html">gridfire::policy</a></td></tr>
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 </table>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Concrete implementations of ReactionChainPolicy for key stellar reaction chains. </p>
 <p>This file provides concrete policies for fundamental nuclear reaction chains, such as the Proton-Proton chain and the CNO cycle. These policies inherit from ReactionChainPolicy (see <code><a class="el" href="policy__abstract_8h.html" title="Abstract policy interfaces used to construct reaction networks (DynamicEngine) from seed compositions...">policy_abstract.h</a></code>) and provide a pre-defined set of reactions.</p>
 <p>They are typically used by higher-level NetworkPolicy implementations (e.g., <code>MainSequencePolicy</code> in <code><a class="el" href="stellar__policy_8h.html" title="High-level concrete NetworkPolicy for specific stellar environments.">stellar_policy.h</a></code>) to compose a complete set of required reactions for a particular stellar environment.</p>
-<dl class="section note"><dt>Note</dt><dd>Constructors for these policies may throw <code><a class="el" href="classgridfire_1_1exceptions_1_1MissingBaseReactionError.html" title="Exception thrown when a required reaction is missing from the underlying database (e....">gridfire::exceptions::MissingBaseReactionError</a></code> if a required reaction is not found in the underlying REACLIB database. This usually indicates an issue with the GridFire installation or the bundled reaction data. </dd></dl>
+<dl class="section note"><dt>Note</dt><dd>Constructors for these policies may throw <code><a class="el" href="classgridfire_1_1exceptions_1_1_missing_base_reaction_error.html" title="Exception thrown when a required reaction is missing from the underlying database (e....">gridfire::exceptions::MissingBaseReactionError</a></code> if a required reaction is not found in the underlying REACLIB database. This usually indicates an issue with the GridFire installation or the bundled reaction data. </dd></dl>
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-  <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"><span class="mlabel">virtual</span></td></tr>
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-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a204643754cac3cf37c550ecd32f659fe">generateJacobianMatrix</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho, const gridfire::engine::SparsityPattern &amp;sparsityPattern) const override</td><td class="entry"><a class="el" href="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"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a541cf022fe3253279f8f1309c10556d7">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#a1d5143640666631501cf229bc491516e">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#afc745e7ab5da5d8b3cf916044515cd7d">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ab4cfdca5e15957c5cef75ffa6dedeee5">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a8d34faa3d6ea804a3467979858d33535">getSpeciesDestructionTimescales</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"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><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"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2947824dca9662e113153de5c6516609">getSpeciesStatus</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#a71678a567bb0cedd8a97aff9ceddd814">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"><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"><span class="mlabel">virtual</span></td></tr>
-  <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"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a01c0ea8802358c2cbc6d8571a145775a">calculateEpsDerivatives</a>(gridfire::engine::scratch::StateBlob &amp;ctx, 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"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2f723f732e9a83c24c1e654885ec7eea">calculateMolarReactionFlow</a>(gridfire::engine::scratch::StateBlob &amp;ctx, 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"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a1331900141bb079e634151abdea075dc">calculateRHSAndEnergy</a>(gridfire::engine::scratch::StateBlob &amp;ctx, const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho, bool trust) 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#a60445db14a6bfd0eeef7c0a62d458a60">collectComposition</a>(gridfire::engine::scratch::StateBlob &amp;ctx, 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"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a6dc693583383d7237b3cede639b41f5f">constructStateBlob</a>(const gridfire::engine::scratch::StateBlob *blob) 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#a13b42a3a523e4c14e06820a43f15041b">generateJacobianMatrix</a>(gridfire::engine::scratch::StateBlob &amp;ctx, 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"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a5a2697b43cddeef2aeb40b604a0de933">generateJacobianMatrix</a>(gridfire::engine::scratch::StateBlob &amp;ctx, 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"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#af9c4725bfc2cc8c85c63790e2385d55b">generateJacobianMatrix</a>(gridfire::engine::scratch::StateBlob &amp;ctx, const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho, const gridfire::engine::SparsityPattern &amp;sparsityPattern) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#ac87099ff654ca30a8d8224f4779e1a15">getInactiveNetworkReactions</a>(scratch::StateBlob &amp;ctx) const</td><td class="entry"><a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html">gridfire::engine::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#adc0a33fa6e9d8de3b433fef55f3a6972">getInactiveReactionMolarReactionFlow</a>(scratch::StateBlob &amp;ctx, const reaction::Reaction &amp;reaction, const fourdst::composition::CompositionAbstract &amp;comp, const double T9, const double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html">gridfire::engine::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a6db6bfd45e74517f837c1b83a9919924">getMostRecentRHSCalculation</a>(gridfire::engine::scratch::StateBlob &amp;ctx) 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#a78d0b8501591667f8593a929a5439692">getNetworkReactions</a>(gridfire::engine::scratch::StateBlob &amp;ctx) 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#a75450cd1eee0d9d79b23eafbf452aa02">getNetworkSpecies</a>(gridfire::engine::scratch::StateBlob &amp;ctx) 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#ae36830f13ee730dccc3a5a8b3e4d603c">getScreeningModel</a>(gridfire::engine::scratch::StateBlob &amp;ctx) 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#af5f39c10cfc932d006c08e4bd1c1bcad">getSpeciesDestructionTimescales</a>(gridfire::engine::scratch::StateBlob &amp;ctx, 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"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#abd2f90dc6bd506c2fd92045ba2a9e6cf">getSpeciesIndex</a>(gridfire::engine::scratch::StateBlob &amp;ctx, const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ac7232a79df901309c8f8b0b78788afe8">getSpeciesStatus</a>(gridfire::engine::scratch::StateBlob &amp;ctx, 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#a688269fb742d37ce15926ced80fa3f70">getSpeciesTimescales</a>(gridfire::engine::scratch::StateBlob &amp;ctx, 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"><span class="mlabel">virtual</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"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a6118af81e45d2850f7a2517891147274">primeEngine</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a25e52496b36d731127603c31e9dcaa97">rebuild</a>(const fourdst::composition::CompositionAbstract &amp;comp, gridfire::engine::BuildDepthType depth) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
-  <tr class="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"><span class="mlabel">virtual</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#afa3abfd612033336a656f092721c14ac">setScreeningModel</a>(gridfire::screening::ScreeningType model) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="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"><span class="mlabel">virtual</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a25d827397e97c638cd87223684effebc">primeEngine</a>(gridfire::engine::scratch::StateBlob &amp;ctx, 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#abe31184ce7e63f7428b4a31ab39e7a8d">project</a>(gridfire::engine::scratch::StateBlob &amp;ctx, const gridfire::NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1engine_1_1_engine.html#af0ea99416c28933d364a872fc6aff556">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1engine_1_1_engine.html">gridfire::engine::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 </table></div><!-- contents -->
 </div><!-- doc-content -->

docs/html/class_py_dynamic_engine.html

@@ -29,7 +29,7 @@
  <tbody>
  <tr id="projectrow">
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@@ -121,78 +121,64 @@ Collaboration diagram for PyDynamicEngine:</div>
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 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
 Public Member Functions</h2></td></tr>
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+<tr class="memdesc:abd2f90dc6bd506c2fd92045ba2a9e6cf"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the index of a species in the network.  <br /></td></tr>
+<tr class="separator:abd2f90dc6bd506c2fd92045ba2a9e6cf"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="memdesc:a25d827397e97c638cd87223684effebc"><td class="mdescLeft">&#160;</td><td class="mdescRight">Prime the engine with initial conditions.  <br /></td></tr>
+<tr class="separator:a25d827397e97c638cd87223684effebc"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a01c0ea8802358c2cbc6d8571a145775a" id="r_a01c0ea8802358c2cbc6d8571a145775a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1engine_1_1_energy_derivatives.html">gridfire::engine::EnergyDerivatives</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a01c0ea8802358c2cbc6d8571a145775a">calculateEpsDerivatives</a> (<a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;ctx, const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td></tr>
+<tr class="memdesc:a01c0ea8802358c2cbc6d8571a145775a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the derivatives of the energy generation rate with respect to T and rho.  <br /></td></tr>
+<tr class="separator:a01c0ea8802358c2cbc6d8571a145775a"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a60445db14a6bfd0eeef7c0a62d458a60" id="r_a60445db14a6bfd0eeef7c0a62d458a60"><td class="memItemLeft" align="right" valign="top">fourdst::composition::Composition&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a60445db14a6bfd0eeef7c0a62d458a60">collectComposition</a> (<a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;ctx, const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td></tr>
+<tr class="memdesc:a60445db14a6bfd0eeef7c0a62d458a60"><td class="mdescLeft">&#160;</td><td class="mdescRight">Recursively collect composition from current engine and any sub engines if they exist.  <br /></td></tr>
+<tr class="separator:a60445db14a6bfd0eeef7c0a62d458a60"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ac7232a79df901309c8f8b0b78788afe8" id="r_ac7232a79df901309c8f8b0b78788afe8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1engine.html#a83c9d755597668bba3cf00cd0ea10ee3">gridfire::engine::SpeciesStatus</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ac7232a79df901309c8f8b0b78788afe8">getSpeciesStatus</a> (<a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;ctx, const fourdst::atomic::Species &amp;species) const override</td></tr>
+<tr class="memdesc:ac7232a79df901309c8f8b0b78788afe8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the status of a species in the network.  <br /></td></tr>
+<tr class="separator:ac7232a79df901309c8f8b0b78788afe8"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a6db6bfd45e74517f837c1b83a9919924" id="r_a6db6bfd45e74517f837c1b83a9919924"><td class="memItemLeft" align="right" valign="top">std::optional&lt; <a class="el" href="structgridfire_1_1engine_1_1_step_derivatives.html">gridfire::engine::StepDerivatives</a>&lt; double &gt; &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a6db6bfd45e74517f837c1b83a9919924">getMostRecentRHSCalculation</a> (<a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;ctx) const override</td></tr>
+<tr class="separator:a6db6bfd45e74517f837c1b83a9919924"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a6dc693583383d7237b3cede639b41f5f" id="r_a6dc693583383d7237b3cede639b41f5f"><td class="memItemLeft" align="right" valign="top">std::unique_ptr&lt; <a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a6dc693583383d7237b3cede639b41f5f">constructStateBlob</a> (const <a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> *blob) const override</td></tr>
+<tr class="separator:a6dc693583383d7237b3cede639b41f5f"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="inherit_header pub_methods_classgridfire_1_1engine_1_1_dynamic_engine"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1engine_1_1_dynamic_engine')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html">gridfire::engine::DynamicEngine</a></td></tr>
+<tr class="memitem:ac87099ff654ca30a8d8224f4779e1a15 inherit pub_methods_classgridfire_1_1engine_1_1_dynamic_engine" id="r_ac87099ff654ca30a8d8224f4779e1a15"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#ac87099ff654ca30a8d8224f4779e1a15">getInactiveNetworkReactions</a> (<a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">scratch::StateBlob</a> &amp;ctx) const</td></tr>
+<tr class="memdesc:ac87099ff654ca30a8d8224f4779e1a15 inherit pub_methods_classgridfire_1_1engine_1_1_dynamic_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the set of inactive reactions in the network.  <br /></td></tr>
+<tr class="separator:ac87099ff654ca30a8d8224f4779e1a15 inherit pub_methods_classgridfire_1_1engine_1_1_dynamic_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:adc0a33fa6e9d8de3b433fef55f3a6972 inherit pub_methods_classgridfire_1_1engine_1_1_dynamic_engine" id="r_adc0a33fa6e9d8de3b433fef55f3a6972"><td class="memItemLeft" align="right" valign="top">virtual double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#adc0a33fa6e9d8de3b433fef55f3a6972">getInactiveReactionMolarReactionFlow</a> (<a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">scratch::StateBlob</a> &amp;ctx, const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;reaction, const fourdst::composition::CompositionAbstract &amp;comp, const double T9, const double rho) const</td></tr>
+<tr class="separator:adc0a33fa6e9d8de3b433fef55f3a6972 inherit pub_methods_classgridfire_1_1engine_1_1_dynamic_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="inherit_header pub_methods_classgridfire_1_1engine_1_1_engine"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1engine_1_1_engine')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1engine_1_1_engine.html">gridfire::engine::Engine</a></td></tr>
 <tr class="memitem:af0ea99416c28933d364a872fc6aff556 inherit pub_methods_classgridfire_1_1engine_1_1_engine" id="r_af0ea99416c28933d364a872fc6aff556"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1_engine.html#af0ea99416c28933d364a872fc6aff556">~Engine</a> ()=default</td></tr>
 <tr class="memdesc:af0ea99416c28933d364a872fc6aff556 inherit pub_methods_classgridfire_1_1engine_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor.  <br /></td></tr>
@@ -204,8 +190,8 @@ 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="a6832a7898da51017a20f578e33cba729" name="a6832a7898da51017a20f578e33cba729"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a6832a7898da51017a20f578e33cba729">&#9670;&#160;</a></span>calculateEpsDerivatives()</h2>
+<a id="a01c0ea8802358c2cbc6d8571a145775a" name="a01c0ea8802358c2cbc6d8571a145775a"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a01c0ea8802358c2cbc6d8571a145775a">&#9670;&#160;</a></span>calculateEpsDerivatives()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -216,6 +202,11 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="memname"><a class="el" href="structgridfire_1_1engine_1_1_energy_derivatives.html">gridfire::engine::EnergyDerivatives</a> PyDynamicEngine::calculateEpsDerivatives </td>
           <td>(</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></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>
@@ -248,12 +239,12 @@ Private Attributes</h2></td></tr>
 <dl class="section return"><dt>Returns</dt><dd>EnergyDerivatives containing dEps/dT and dEps/dRho.</dd></dl>
 <p>This method computes the partial derivatives of the specific nuclear energy generation rate with respect to temperature and density for the current state. </p>
 
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#ada6a1295a92c2aede841672ecae0cede">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a3fd5d4f3c58d1790b7a517b5ef888eaf">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
 </div>
-<a id="a8facba88b6df6e016ce53a0ff3cff125" name="a8facba88b6df6e016ce53a0ff3cff125"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a8facba88b6df6e016ce53a0ff3cff125">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
+<a id="a2f723f732e9a83c24c1e654885ec7eea" name="a2f723f732e9a83c24c1e654885ec7eea"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a2f723f732e9a83c24c1e654885ec7eea">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -264,6 +255,11 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="memname">double PyDynamicEngine::calculateMolarReactionFlow </td>
           <td>(</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></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>, </td>
         </tr>
         <tr>
@@ -292,6 +288,7 @@ Private Attributes</h2></td></tr>
 <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">ctx</td><td>The scratchpad context for the current state. </td></tr>
     <tr><td class="paramname">reaction</td><td>The reaction for which to calculate the flow. </td></tr>
     <tr><td class="paramname">comp</td><td>Composition object containing current abundances. </td></tr>
     <tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
@@ -302,12 +299,12 @@ Private Attributes</h2></td></tr>
 <dl class="section return"><dt>Returns</dt><dd>Molar flow rate for the reaction (e.g., mol/g/s).</dd></dl>
 <p>This method computes the net rate at which the given reaction proceeds under the current state. </p>
 
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#aa57fa5e58b98a03fba31bcddda8001d4">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#abf0f13b9eae66da6119e6fca826379e8">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
 </div>
-<a id="aac1f2005c0a58befc4e01627c9357924" name="aac1f2005c0a58befc4e01627c9357924"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#aac1f2005c0a58befc4e01627c9357924">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
+<a id="a1331900141bb079e634151abdea075dc" name="a1331900141bb079e634151abdea075dc"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a1331900141bb079e634151abdea075dc">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -318,6 +315,11 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="memname">std::expected&lt; <a class="el" href="structgridfire_1_1engine_1_1_step_derivatives.html">gridfire::engine::StepDerivatives</a>&lt; double &gt;, <a class="el" href="namespacegridfire_1_1engine.html#a4d057e41b489bf20744dfa8d2958ad5a">gridfire::engine::EngineStatus</a> &gt; PyDynamicEngine::calculateRHSAndEnergy </td>
           <td>(</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em></em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></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>
@@ -328,7 +330,12 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">double</td>          <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</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">bool</td>          <td class="paramname"><span class="paramname"><em>trust</em></span>&#160;) const</td>
         </tr>
       </table>
   </td>
@@ -344,18 +351,19 @@ Private Attributes</h2></td></tr>
     <tr><td class="paramname">comp</td><td>Composition object containing 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>
+    <tr><td class="paramname">trust</td><td>If true, indicates that the engine should trust the passed composition has already been collected. </td></tr>
   </table>
   </dd>
 </dl>
 <dl class="section return"><dt>Returns</dt><dd>expected&lt;StepDerivatives&lt;double&gt;&gt; containing either dY/dt and energy generation rate or a stale engine error indicating that the engine must be updated</dd></dl>
 <p>This function must be implemented by derived classes to compute the time derivatives of all species and the specific nuclear energy generation rate for the current state. </p>
 
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_engine.html#a764fc091c72c12c8529105d7c96badb2">gridfire::engine::Engine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_engine.html#a71c9ed5e0810799cd6af1d8ffbc8a918">gridfire::engine::Engine</a>.</p>
 
 </div>
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-<a id="a239826d90cb5db236e68230f7ac84bcb" name="a239826d90cb5db236e68230f7ac84bcb"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a239826d90cb5db236e68230f7ac84bcb">&#9670;&#160;</a></span>collectComposition()</h2>
+<a id="a60445db14a6bfd0eeef7c0a62d458a60" name="a60445db14a6bfd0eeef7c0a62d458a60"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a60445db14a6bfd0eeef7c0a62d458a60">&#9670;&#160;</a></span>collectComposition()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -366,6 +374,11 @@ Private Attributes</h2></td></tr>
         <tr>
           <td class="memname">fourdst::composition::Composition PyDynamicEngine::collectComposition </td>
           <td>(</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></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>
@@ -392,6 +405,7 @@ Private Attributes</h2></td></tr>
 These methods return an unfinalized composition which must then be finalized by the caller </dd></dl>
 <dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
+    <tr><td class="paramname">ctx</td><td>The scratchpad context for the current state. </td></tr>
     <tr><td class="paramname">comp</td><td>Input composition to "normalize". </td></tr>
     <tr><td class="paramname">T9</td><td></td></tr>
     <tr><td class="paramname">rho</td><td></td></tr>
@@ -400,12 +414,39 @@ These methods return an unfinalized composition which must then be finalized by
 </dl>
 <dl class="section return"><dt>Returns</dt><dd>An updated composition which is a superset of comp. This may contain species which were culled, for example, by either QSE partitioning or reaction flow rate culling </dd></dl>
 
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a41877719ae5e8de53c1692c7cf9bfbfc">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a078a16d21f2d7de9636c5bc6a05ddfec">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
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-<h2 class="memtitle"><span class="permalink"><a href="#a298f700c647d2c3973d2a35d370c823e">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[1/3]</span></h2>
+<a id="a6dc693583383d7237b3cede639b41f5f" name="a6dc693583383d7237b3cede639b41f5f"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a6dc693583383d7237b3cede639b41f5f">&#9670;&#160;</a></span>constructStateBlob()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::unique_ptr&lt; <a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &gt; PyDynamicEngine::constructStateBlob </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> *</td>          <td class="paramname"><span class="paramname"><em>blob</em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a675024091dc64f8784204a78bab46d90">gridfire::engine::DynamicEngine</a>.</p>
+
+</div>
+</div>
+<a id="a13b42a3a523e4c14e06820a43f15041b" name="a13b42a3a523e4c14e06820a43f15041b"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a13b42a3a523e4c14e06820a43f15041b">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[1/3]</span></h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -416,6 +457,11 @@ These methods return an unfinalized composition which must then be finalized by
         <tr>
           <td class="memname"><a class="el" href="classgridfire_1_1engine_1_1_network_jacobian.html">gridfire::engine::NetworkJacobian</a> PyDynamicEngine::generateJacobianMatrix </td>
           <td>(</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></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>
@@ -439,6 +485,7 @@ These methods return an unfinalized composition which must then be finalized by
 <p>Generate the Jacobian matrix for the current state. </p>
 <dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
+    <tr><td class="paramname">ctx</td><td>The scratchpad context for the current state. </td></tr>
     <tr><td class="paramname">comp</td><td>Composition object containing 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>
@@ -447,12 +494,12 @@ These methods return an unfinalized composition which must then be finalized by
 </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 getJacobianMatrixEntry(). </p>
 
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a53276f09346b531f8676db355e1219eb">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#ab6d95491f017feb4c43d9fa05739fcd0">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
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-<h2 class="memtitle"><span class="permalink"><a href="#a204643754cac3cf37c550ecd32f659fe">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[2/3]</span></h2>
+<a id="af9c4725bfc2cc8c85c63790e2385d55b" name="af9c4725bfc2cc8c85c63790e2385d55b"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#af9c4725bfc2cc8c85c63790e2385d55b">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[2/3]</span></h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -463,6 +510,11 @@ These methods return an unfinalized composition which must then be finalized by
         <tr>
           <td class="memname"><a class="el" href="classgridfire_1_1engine_1_1_network_jacobian.html">gridfire::engine::NetworkJacobian</a> PyDynamicEngine::generateJacobianMatrix </td>
           <td>(</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></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>
@@ -491,6 +543,7 @@ These methods return an unfinalized composition which must then be finalized by
 <p>Generate the Jacobian matrix for the current state with a specified sparsity pattern. </p>
 <dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
+    <tr><td class="paramname">ctx</td><td>Get the scratchpad context for the current state. </td></tr>
     <tr><td class="paramname">comp</td><td>Composition object containing 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>
@@ -501,12 +554,12 @@ These methods return an unfinalized composition which must then be finalized by
 <p>This method must compute and store the Jacobian matrix (∂(dY/dt)_i/∂Y_j) for the current state using automatic differentiation, taking into account the provided sparsity pattern. The matrix can then be accessed via <code>getJacobianMatrixEntry()</code>.</p>
 <dl class="section see"><dt>See also</dt><dd>getJacobianMatrixEntry() </dd></dl>
 
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a51d55a21be28e372021b2b8e5ecdc551">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a78f7b315bfa0a1f34d8fd5ab652b6934">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
 </div>
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-<h2 class="memtitle"><span class="permalink"><a href="#a2b1c054b250abccc2af9a7275c68df4a">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[3/3]</span></h2>
+<a id="a5a2697b43cddeef2aeb40b604a0de933" name="a5a2697b43cddeef2aeb40b604a0de933"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a5a2697b43cddeef2aeb40b604a0de933">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[3/3]</span></h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -517,6 +570,11 @@ These methods return an unfinalized composition which must then be finalized by
         <tr>
           <td class="memname"><a class="el" href="classgridfire_1_1engine_1_1_network_jacobian.html">gridfire::engine::NetworkJacobian</a> PyDynamicEngine::generateJacobianMatrix </td>
           <td>(</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></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>
@@ -545,6 +603,7 @@ These methods return an unfinalized composition which must then be finalized by
 <p>Generate the Jacobian matrix for the current state using a subset of active species. </p>
 <dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
+    <tr><td class="paramname">ctx</td><td>The scratchpad context for the current state. </td></tr>
     <tr><td class="paramname">comp</td><td>Composition object containing 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>
@@ -554,12 +613,12 @@ These methods return an unfinalized composition which must then be finalized by
 </dl>
 <p>This method must compute and store the Jacobian matrix (∂(dY/dt)_i/∂Y_j) for the current state, considering only the specified subset of active species. The matrix can then be accessed via getJacobianMatrixEntry(). </p>
 
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a15d53dac8b622a3b7d0f928a3995dbde">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a983551b5fef4610799c062cb5be2b1c7">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
 </div>
-<a id="a2066649ca11a869c054079ea12d8d0e9" name="a2066649ca11a869c054079ea12d8d0e9"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a2066649ca11a869c054079ea12d8d0e9">&#9670;&#160;</a></span>generateStoichiometryMatrix()</h2>
+<a id="a6db6bfd45e74517f837c1b83a9919924" name="a6db6bfd45e74517f837c1b83a9919924"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a6db6bfd45e74517f837c1b83a9919924">&#9670;&#160;</a></span>getMostRecentRHSCalculation()</h2>
 
 <div class="memitem">
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@@ -568,10 +627,10 @@ These methods return an unfinalized composition which must then be finalized by
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">void PyDynamicEngine::generateStoichiometryMatrix </td>
+          <td class="memname">std::optional&lt; <a class="el" href="structgridfire_1_1engine_1_1_step_derivatives.html">gridfire::engine::StepDerivatives</a>&lt; double &gt; &gt; PyDynamicEngine::getMostRecentRHSCalculation </td>
           <td>(</td>
-          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
-          <td></td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span></td><td>)</td>
+          <td> const</td>
         </tr>
       </table>
   </td>
@@ -581,46 +640,12 @@ These methods return an unfinalized composition which must then be finalized by
 </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_1engine_1_1_dynamic_engine.html#a5e2c45a3e415b53e41def8f743f93464">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a30cc7809d53540bd3407d971de8eec48">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
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-<a id="a541cf022fe3253279f8f1309c10556d7" name="a541cf022fe3253279f8f1309c10556d7"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a541cf022fe3253279f8f1309c10556d7">&#9670;&#160;</a></span>getDepth()</h2>
-
-<div class="memitem">
-<div class="memproto">
-<table class="mlabels">
-  <tr>
-  <td class="mlabels-left">
-      <table class="memname">
-        <tr>
-          <td class="memname"><a class="el" href="namespacegridfire_1_1engine.html#a55cd7c313bbfafd5b6a1bcd6329ed99b">gridfire::engine::BuildDepthType</a> PyDynamicEngine::getDepth </td>
-          <td>(</td>
-          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
-          <td> const</td>
-        </tr>
-      </table>
-  </td>
-  <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</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_1engine_1_1_dynamic_engine.html#ac5a0def6b6af0bd93bf9057c25f048ff">gridfire::engine::DynamicEngine</a>.</p>
-
-</div>
-</div>
-<a id="a1d5143640666631501cf229bc491516e" name="a1d5143640666631501cf229bc491516e"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a1d5143640666631501cf229bc491516e">&#9670;&#160;</a></span>getNetworkReactions()</h2>
+<a id="a78d0b8501591667f8593a929a5439692" name="a78d0b8501591667f8593a929a5439692"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a78d0b8501591667f8593a929a5439692">&#9670;&#160;</a></span>getNetworkReactions()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -631,7 +656,7 @@ These methods return an unfinalized composition which must then be finalized by
         <tr>
           <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 class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span></td><td>)</td>
           <td> const</td>
         </tr>
       </table>
@@ -645,12 +670,12 @@ These methods return an unfinalized composition which must then be finalized by
 <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_1engine_1_1_dynamic_engine.html#a26b59a4c7622bf820c0eeec6a7522aa8">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a77a889cbc3791beca4abb95cb663a4d6">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
 </div>
-<a id="afc745e7ab5da5d8b3cf916044515cd7d" name="afc745e7ab5da5d8b3cf916044515cd7d"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#afc745e7ab5da5d8b3cf916044515cd7d">&#9670;&#160;</a></span>getNetworkSpecies()</h2>
+<a id="a75450cd1eee0d9d79b23eafbf452aa02" name="a75450cd1eee0d9d79b23eafbf452aa02"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a75450cd1eee0d9d79b23eafbf452aa02">&#9670;&#160;</a></span>getNetworkSpecies()</h2>
 
 <div class="memitem">
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@@ -661,7 +686,7 @@ These methods return an unfinalized composition which must then be finalized by
         <tr>
           <td class="memname">const std::vector&lt; fourdst::atomic::Species &gt; &amp; PyDynamicEngine::getNetworkSpecies </td>
           <td>(</td>
-          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span></td><td>)</td>
           <td> const</td>
         </tr>
       </table>
@@ -674,12 +699,12 @@ These methods return an unfinalized composition which must then be finalized by
 
 <p><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a> Implementation ///. </p>
 
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_engine.html#a3263c3fde2509d5d8ec4da3b6e946c48">gridfire::engine::Engine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_engine.html#afa8b1970e20f4bab61e4d31ead09f930">gridfire::engine::Engine</a>.</p>
 
 </div>
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-<h2 class="memtitle"><span class="permalink"><a href="#ab4cfdca5e15957c5cef75ffa6dedeee5">&#9670;&#160;</a></span>getScreeningModel()</h2>
+<a id="ae36830f13ee730dccc3a5a8b3e4d603c" name="ae36830f13ee730dccc3a5a8b3e4d603c"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ae36830f13ee730dccc3a5a8b3e4d603c">&#9670;&#160;</a></span>getScreeningModel()</h2>
 
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           <td class="memname"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">gridfire::screening::ScreeningType</a> PyDynamicEngine::getScreeningModel </td>
           <td>(</td>
-          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span></td><td>)</td>
           <td> const</td>
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       </table>
@@ -702,16 +727,22 @@ These methods return an unfinalized composition which must then be finalized by
 </div><div class="memdoc">
 
 <p>Get the current electron screening model. </p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">ctx</td><td>The scratchpad context for the current state.</td></tr>
+  </table>
+  </dd>
+</dl>
 <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_1engine_1_1_dynamic_engine.html#a24103027a38e02d4342161164554d332">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a60834e4bcfb2e4ec21a9cbf7bb9f7363">gridfire::engine::DynamicEngine</a>.</p>
 
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-<h2 class="memtitle"><span class="permalink"><a href="#a8d34faa3d6ea804a3467979858d33535">&#9670;&#160;</a></span>getSpeciesDestructionTimescales()</h2>
+<a id="af5f39c10cfc932d006c08e4bd1c1bcad" name="af5f39c10cfc932d006c08e4bd1c1bcad"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#af5f39c10cfc932d006c08e4bd1c1bcad">&#9670;&#160;</a></span>getSpeciesDestructionTimescales()</h2>
 
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           <td class="memname">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="namespacegridfire_1_1engine.html#a4d057e41b489bf20744dfa8d2958ad5a">gridfire::engine::EngineStatus</a> &gt; PyDynamicEngine::getSpeciesDestructionTimescales </td>
           <td>(</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></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>
@@ -745,6 +781,7 @@ These methods return an unfinalized composition which must then be finalized by
 <p>Compute destruction timescales for all species in the network. </p>
 <dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
+    <tr><td class="paramname">ctx</td><td>The scratchpad context for the current state. </td></tr>
     <tr><td class="paramname">comp</td><td>Composition object containing 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>
@@ -754,12 +791,12 @@ These methods return an unfinalized composition which must then be finalized by
 <dl class="section return"><dt>Returns</dt><dd>Map from Species to their destruction timescales (s).</dd></dl>
 <p>This method estimates the destruction timescale for each species, which can be useful for understanding reaction flows and equilibrium states. </p>
 
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#aefc5d0f7842b27a108ba1e4ca346e9a0">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a128dd0a7f738f93092c437eeda983fdf">gridfire::engine::DynamicEngine</a>.</p>
 
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-<h2 class="memtitle"><span class="permalink"><a href="#a95d10a7b240d543a1bc6c67ddf2dc8e0">&#9670;&#160;</a></span>getSpeciesIndex()</h2>
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           <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>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const fourdst::atomic::Species &amp;</td>          <td class="paramname"><span class="paramname"><em>species</em></span>&#160;) const</td>
         </tr>
       </table>
   </td>
@@ -784,18 +825,19 @@ These methods return an unfinalized composition which must then be finalized by
 <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">ctx</td><td>The scratchpad context for the current state. </td></tr>
     <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_1engine_1_1_dynamic_engine.html#ac0f40017603e8e6887b75dc7360d7c5e">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a16bd2fae51fa738da62f2a767f6875d2">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
 </div>
-<a id="a2947824dca9662e113153de5c6516609" name="a2947824dca9662e113153de5c6516609"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a2947824dca9662e113153de5c6516609">&#9670;&#160;</a></span>getSpeciesStatus()</h2>
+<a id="ac7232a79df901309c8f8b0b78788afe8" name="ac7232a79df901309c8f8b0b78788afe8"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ac7232a79df901309c8f8b0b78788afe8">&#9670;&#160;</a></span>getSpeciesStatus()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -806,8 +848,12 @@ These methods return an unfinalized composition which must then be finalized by
         <tr>
           <td class="memname"><a class="el" href="namespacegridfire_1_1engine.html#a83c9d755597668bba3cf00cd0ea10ee3">gridfire::engine::SpeciesStatus</a> PyDynamicEngine::getSpeciesStatus </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>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const fourdst::atomic::Species &amp;</td>          <td class="paramname"><span class="paramname"><em>species</em></span>&#160;) const</td>
         </tr>
       </table>
   </td>
@@ -827,12 +873,12 @@ These methods return an unfinalized composition which must then be finalized by
 <dl class="section return"><dt>Returns</dt><dd>SpeciesStatus indicating whether the species is active, inactive, or culled.</dd></dl>
 <p>This method allows querying the current status of a specific species within the engine's network. </p>
 
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a8aebefad50c1aa34207e118e92d7ccf0">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a1fefd34491959f9936b7a065fc2d6274">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
 </div>
-<a id="a71678a567bb0cedd8a97aff9ceddd814" name="a71678a567bb0cedd8a97aff9ceddd814"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a71678a567bb0cedd8a97aff9ceddd814">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
+<a id="a688269fb742d37ce15926ced80fa3f70" name="a688269fb742d37ce15926ced80fa3f70"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a688269fb742d37ce15926ced80fa3f70">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -843,6 +889,11 @@ These methods return an unfinalized composition which must then be finalized by
         <tr>
           <td class="memname">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="namespacegridfire_1_1engine.html#a4d057e41b489bf20744dfa8d2958ad5a">gridfire::engine::EngineStatus</a> &gt; PyDynamicEngine::getSpeciesTimescales </td>
           <td>(</td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></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>
@@ -875,133 +926,12 @@ These methods return an unfinalized composition which must then be finalized by
 <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_1engine_1_1_dynamic_engine.html#aef6ed91d922c0b1733fd7835e99d0efe">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a92be21f072b61fcf291559246045801f">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
 </div>
-<a id="a3dd5cf419f25e76e144af35df15a2067" name="a3dd5cf419f25e76e144af35df15a2067"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a3dd5cf419f25e76e144af35df15a2067">&#9670;&#160;</a></span>getStoichiometryMatrixEntry()</h2>
-
-<div class="memitem">
-<div class="memproto">
-<table class="mlabels">
-  <tr>
-  <td class="mlabels-left">
-      <table class="memname">
-        <tr>
-          <td class="memname">int PyDynamicEngine::getStoichiometryMatrixEntry </td>
-          <td>(</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">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>
-        </tr>
-      </table>
-  </td>
-  <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
-  </tr>
-</table>
-</div><div class="memdoc">
-
-<p>Get an entry from the stoichiometry matrix. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">species</td><td>species to look up stoichiometry for. </td></tr>
-    <tr><td class="paramname">reaction</td><td>reaction to find </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_1engine_1_1_dynamic_engine.html#a5ce6ff370e3f0964c6b2688fb3f4bb7e">gridfire::engine::DynamicEngine</a>.</p>
-
-</div>
-</div>
-<a id="a55bf19ed7534a312a36faf74753f7b14" name="a55bf19ed7534a312a36faf74753f7b14"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a55bf19ed7534a312a36faf74753f7b14">&#9670;&#160;</a></span>isStale()</h2>
-
-<div class="memitem">
-<div class="memproto">
-<table class="mlabels">
-  <tr>
-  <td class="mlabels-left">
-      <table class="memname">
-        <tr>
-          <td class="memname">bool PyDynamicEngine::isStale </td>
-          <td>(</td>
-          <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">gridfire::NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
-          <td></td>
-        </tr>
-      </table>
-  </td>
-  <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
-  </tr>
-</table>
-</div><div class="memdoc">
-
-<p>Check if the engine's internal state is stale. </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>
-<dl class="section return"><dt>Returns</dt><dd>True if the engine's state is stale and needs to be updated; false otherwise.</dd></dl>
-<p>This method allows derived classes to determine if their internal state is out-of-date with respect to the provided network conditions. If the engine is stale, it may require a call to <code><a class="el" href="#af8e6a8cd44f278535d7bcc9a896d6da8" title="Update the internal state of the engine.">update()</a></code> before performing calculations.</p>
-<dl class="section user"><dt>Usage Example:</dt><dd><div class="fragment"><div class="line">NetIn input = { ... };</div>
-<div class="line"><span class="keywordflow">if</span> (myEngine.isStale(input)) {</div>
-<div class="line">    <span class="comment">// Update the engine before proceeding</span></div>
-<div class="line">}</div>
-</div><!-- fragment --> </dd></dl>
-
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a79423b9f67b4cac702547b4f1d8bd14c">gridfire::engine::DynamicEngine</a>.</p>
-
-</div>
-</div>
-<a id="a61bb4b430fe740cfb2c24e5cc673e4ac" name="a61bb4b430fe740cfb2c24e5cc673e4ac"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a61bb4b430fe740cfb2c24e5cc673e4ac">&#9670;&#160;</a></span>mapNetInToMolarAbundanceVector()</h2>
-
-<div class="memitem">
-<div class="memproto">
-<table class="mlabels">
-  <tr>
-  <td class="mlabels-left">
-      <table class="memname">
-        <tr>
-          <td class="memname">std::vector&lt; double &gt; PyDynamicEngine::mapNetInToMolarAbundanceVector </td>
-          <td>(</td>
-          <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">gridfire::NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
-          <td> const</td>
-        </tr>
-      </table>
-  </td>
-  <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
-  </tr>
-</table>
-</div><div class="memdoc">
-
-<p>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_1engine_1_1_dynamic_engine.html#aa9d55b81c1963113aad86aa60c19676f">gridfire::engine::DynamicEngine</a>.</p>
-
-</div>
-</div>
-<a id="a6118af81e45d2850f7a2517891147274" name="a6118af81e45d2850f7a2517891147274"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a6118af81e45d2850f7a2517891147274">&#9670;&#160;</a></span>primeEngine()</h2>
+<a id="a25d827397e97c638cd87223684effebc" name="a25d827397e97c638cd87223684effebc"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a25d827397e97c638cd87223684effebc">&#9670;&#160;</a></span>primeEngine()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -1012,8 +942,12 @@ These methods return an unfinalized composition which must then be finalized by
         <tr>
           <td class="memname"><a class="el" href="structgridfire_1_1engine_1_1_priming_report.html">gridfire::engine::PrimingReport</a> 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>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></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>&#160;) const</td>
         </tr>
       </table>
   </td>
@@ -1026,6 +960,7 @@ These methods return an unfinalized composition which must then be finalized by
 <p>Prime the engine with initial conditions. </p>
 <dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
+    <tr><td class="paramname">ctx</td><td>The scratchpad context for the current state. </td></tr>
     <tr><td class="paramname">netIn</td><td>The input conditions for the network. </td></tr>
   </table>
   </dd>
@@ -1033,12 +968,12 @@ These methods return an unfinalized composition which must then be finalized by
 <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_1engine_1_1_dynamic_engine.html#a70e270bb50910c0055a75575c1ef1e95">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a30df09678c3de1a55b7c6ac5eae35004">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
 </div>
-<a id="a25e52496b36d731127603c31e9dcaa97" name="a25e52496b36d731127603c31e9dcaa97"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a25e52496b36d731127603c31e9dcaa97">&#9670;&#160;</a></span>rebuild()</h2>
+<a id="abe31184ce7e63f7428b4a31ab39e7a8d" name="abe31184ce7e63f7428b4a31ab39e7a8d"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#abe31184ce7e63f7428b4a31ab39e7a8d">&#9670;&#160;</a></span>project()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -1047,51 +982,14 @@ These methods return an unfinalized composition which must then be finalized by
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">void PyDynamicEngine::rebuild </td>
+          <td class="memname">fourdst::composition::Composition PyDynamicEngine::project </td>
           <td>(</td>
-          <td class="paramtype">const fourdst::composition::CompositionAbstract &amp;</td>          <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
+          <td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>ctx</em></span>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype"><a class="el" href="namespacegridfire_1_1engine.html#a55cd7c313bbfafd5b6a1bcd6329ed99b">gridfire::engine::BuildDepthType</a></td>          <td class="paramname"><span class="paramname"><em>depth</em></span>&#160;)</td>
-        </tr>
-      </table>
-  </td>
-  <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel inline">inline</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
-  </tr>
-</table>
-</div><div class="memdoc">
-
-<p>Rebuild the network with a specified depth. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">comp</td><td>The composition to rebuild the network with. </td></tr>
-    <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_1engine_1_1_dynamic_engine.html#a2444b9ed3bc61920ce23c546444269e4">gridfire::engine::DynamicEngine</a>.</p>
-
-</div>
-</div>
-<a id="af469cba3be850d53f659ec173f0eb4e4" name="af469cba3be850d53f659ec173f0eb4e4"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#af469cba3be850d53f659ec173f0eb4e4">&#9670;&#160;</a></span>setNetworkReactions()</h2>
-
-<div class="memitem">
-<div class="memproto">
-<table class="mlabels">
-  <tr>
-  <td class="mlabels-left">
-      <table class="memname">
-        <tr>
-          <td class="memname">void PyDynamicEngine::setNetworkReactions </td>
-          <td>(</td>
-          <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>
-          <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>&#160;) const</td>
         </tr>
       </table>
   </td>
@@ -1101,84 +999,10 @@ These methods return an unfinalized composition which must then be finalized by
 </table>
 </div><div class="memdoc">
 
-<p>Set the reactions for the network. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">reactions</td><td>The set of reactions to use in the network.</td></tr>
-  </table>
-  </dd>
-</dl>
-<p>This method replaces the current set of reactions in the network with the provided set. It marks the engine as stale, requiring regeneration of matrices and recalculation of rates. </p>
-
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#ab321170954bffc53b1bedaf54f6976be">gridfire::engine::DynamicEngine</a>.</p>
-
-</div>
-</div>
-<a id="afa3abfd612033336a656f092721c14ac" name="afa3abfd612033336a656f092721c14ac"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#afa3abfd612033336a656f092721c14ac">&#9670;&#160;</a></span>setScreeningModel()</h2>
-
-<div class="memitem">
-<div class="memproto">
-<table class="mlabels">
-  <tr>
-  <td class="mlabels-left">
-      <table class="memname">
-        <tr>
-          <td class="memname">void PyDynamicEngine::setScreeningModel </td>
-          <td>(</td>
-          <td class="paramtype"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">gridfire::screening::ScreeningType</a></td>          <td class="paramname"><span class="paramname"><em>model</em></span></td><td>)</td>
-          <td></td>
-        </tr>
-      </table>
-  </td>
-  <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
-  </tr>
-</table>
-</div><div class="memdoc">
-
-<p>Set the electron screening model. </p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">model</td><td>The type of screening model to use for reaction rate calculations.</td></tr>
-  </table>
-  </dd>
-</dl>
-<p>This method allows changing the screening model at runtime. Screening corrections account for the electrostatic shielding of nuclei by electrons, which affects reaction rates in dense stellar plasmas.</p>
-<dl class="section user"><dt>Usage Example:</dt><dd><div class="fragment"><div class="line">myEngine.setScreeningModel(screening::ScreeningType::WEAK);</div>
-</div><!-- fragment --></dd></dl>
-<dl class="section post"><dt>Postcondition</dt><dd>The engine will use the specified screening model for subsequent rate calculations. </dd></dl>
-
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a50e76977d0dc3cc23d52b51842d35003">gridfire::engine::DynamicEngine</a>.</p>
-
-</div>
-</div>
-<a id="af8e6a8cd44f278535d7bcc9a896d6da8" name="af8e6a8cd44f278535d7bcc9a896d6da8"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#af8e6a8cd44f278535d7bcc9a896d6da8">&#9670;&#160;</a></span>update()</h2>
-
-<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::update </td>
-          <td>(</td>
-          <td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">gridfire::NetIn</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
-          <td></td>
-        </tr>
-      </table>
-  </td>
-  <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span>  </td>
-  </tr>
-</table>
-</div><div class="memdoc">
-
-<p>Update the internal state of the engine. </p>
+<p>Update the thread local scratch pad state of a network. </p>
 <dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
+    <tr><td class="paramname">ctx</td><td>The scratchpad context for the current state. </td></tr>
     <tr><td class="paramname">netIn</td><td>A struct containing the current network input, such as temperature, density, and composition.</td></tr>
   </table>
   </dd>
@@ -1189,7 +1013,7 @@ These methods return an unfinalized composition which must then be finalized by
 </div><!-- fragment --></dd></dl>
 <dl class="section post"><dt>Postcondition</dt><dd>The internal state of the engine is updated to reflect the new conditions. </dd></dl>
 
-<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a8dd85442ec54f20d91743c72364e36ff">gridfire::engine::DynamicEngine</a>.</p>
+<p>Implements <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a260d36cc1e14ca8eda0309745e9134d9">gridfire::engine::DynamicEngine</a>.</p>
 
 </div>
 </div>

docs/html/class_py_dynamic_engine.js

@@ -1,28 +1,22 @@
 var class_py_dynamic_engine =
 [
-    [ "calculateEpsDerivatives", "class_py_dynamic_engine.html#a6832a7898da51017a20f578e33cba729", null ],
-    [ "calculateMolarReactionFlow", "class_py_dynamic_engine.html#a8facba88b6df6e016ce53a0ff3cff125", null ],
-    [ "calculateRHSAndEnergy", "class_py_dynamic_engine.html#aac1f2005c0a58befc4e01627c9357924", null ],
-    [ "collectComposition", "class_py_dynamic_engine.html#a239826d90cb5db236e68230f7ac84bcb", null ],
-    [ "generateJacobianMatrix", "class_py_dynamic_engine.html#a298f700c647d2c3973d2a35d370c823e", null ],
-    [ "generateJacobianMatrix", "class_py_dynamic_engine.html#a204643754cac3cf37c550ecd32f659fe", null ],
-    [ "generateJacobianMatrix", "class_py_dynamic_engine.html#a2b1c054b250abccc2af9a7275c68df4a", null ],
-    [ "generateStoichiometryMatrix", "class_py_dynamic_engine.html#a2066649ca11a869c054079ea12d8d0e9", null ],
-    [ "getDepth", "class_py_dynamic_engine.html#a541cf022fe3253279f8f1309c10556d7", null ],
-    [ "getNetworkReactions", "class_py_dynamic_engine.html#a1d5143640666631501cf229bc491516e", null ],
-    [ "getNetworkSpecies", "class_py_dynamic_engine.html#afc745e7ab5da5d8b3cf916044515cd7d", null ],
-    [ "getScreeningModel", "class_py_dynamic_engine.html#ab4cfdca5e15957c5cef75ffa6dedeee5", null ],
-    [ "getSpeciesDestructionTimescales", "class_py_dynamic_engine.html#a8d34faa3d6ea804a3467979858d33535", null ],
-    [ "getSpeciesIndex", "class_py_dynamic_engine.html#a95d10a7b240d543a1bc6c67ddf2dc8e0", null ],
-    [ "getSpeciesStatus", "class_py_dynamic_engine.html#a2947824dca9662e113153de5c6516609", null ],
-    [ "getSpeciesTimescales", "class_py_dynamic_engine.html#a71678a567bb0cedd8a97aff9ceddd814", null ],
-    [ "getStoichiometryMatrixEntry", "class_py_dynamic_engine.html#a3dd5cf419f25e76e144af35df15a2067", null ],
-    [ "isStale", "class_py_dynamic_engine.html#a55bf19ed7534a312a36faf74753f7b14", null ],
-    [ "mapNetInToMolarAbundanceVector", "class_py_dynamic_engine.html#a61bb4b430fe740cfb2c24e5cc673e4ac", null ],
-    [ "primeEngine", "class_py_dynamic_engine.html#a6118af81e45d2850f7a2517891147274", null ],
-    [ "rebuild", "class_py_dynamic_engine.html#a25e52496b36d731127603c31e9dcaa97", null ],
-    [ "setNetworkReactions", "class_py_dynamic_engine.html#af469cba3be850d53f659ec173f0eb4e4", null ],
-    [ "setScreeningModel", "class_py_dynamic_engine.html#afa3abfd612033336a656f092721c14ac", null ],
-    [ "update", "class_py_dynamic_engine.html#af8e6a8cd44f278535d7bcc9a896d6da8", null ],
+    [ "calculateEpsDerivatives", "class_py_dynamic_engine.html#a01c0ea8802358c2cbc6d8571a145775a", null ],
+    [ "calculateMolarReactionFlow", "class_py_dynamic_engine.html#a2f723f732e9a83c24c1e654885ec7eea", null ],
+    [ "calculateRHSAndEnergy", "class_py_dynamic_engine.html#a1331900141bb079e634151abdea075dc", null ],
+    [ "collectComposition", "class_py_dynamic_engine.html#a60445db14a6bfd0eeef7c0a62d458a60", null ],
+    [ "constructStateBlob", "class_py_dynamic_engine.html#a6dc693583383d7237b3cede639b41f5f", null ],
+    [ "generateJacobianMatrix", "class_py_dynamic_engine.html#a13b42a3a523e4c14e06820a43f15041b", null ],
+    [ "generateJacobianMatrix", "class_py_dynamic_engine.html#af9c4725bfc2cc8c85c63790e2385d55b", null ],
+    [ "generateJacobianMatrix", "class_py_dynamic_engine.html#a5a2697b43cddeef2aeb40b604a0de933", null ],
+    [ "getMostRecentRHSCalculation", "class_py_dynamic_engine.html#a6db6bfd45e74517f837c1b83a9919924", null ],
+    [ "getNetworkReactions", "class_py_dynamic_engine.html#a78d0b8501591667f8593a929a5439692", null ],
+    [ "getNetworkSpecies", "class_py_dynamic_engine.html#a75450cd1eee0d9d79b23eafbf452aa02", null ],
+    [ "getScreeningModel", "class_py_dynamic_engine.html#ae36830f13ee730dccc3a5a8b3e4d603c", null ],
+    [ "getSpeciesDestructionTimescales", "class_py_dynamic_engine.html#af5f39c10cfc932d006c08e4bd1c1bcad", null ],
+    [ "getSpeciesIndex", "class_py_dynamic_engine.html#abd2f90dc6bd506c2fd92045ba2a9e6cf", null ],
+    [ "getSpeciesStatus", "class_py_dynamic_engine.html#ac7232a79df901309c8f8b0b78788afe8", null ],
+    [ "getSpeciesTimescales", "class_py_dynamic_engine.html#a688269fb742d37ce15926ced80fa3f70", null ],
+    [ "primeEngine", "class_py_dynamic_engine.html#a25d827397e97c638cd87223684effebc", null ],
+    [ "project", "class_py_dynamic_engine.html#abe31184ce7e63f7428b4a31ab39e7a8d", null ],
     [ "m_species_cache", "class_py_dynamic_engine.html#a2246382b1c98ba69cdb419bba63a6d03", null ]
 ];

docs/html/class_py_dynamic_engine_view-members.html

@@ -29,7 +29,7 @@
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   <td id="projectalign">
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+   <div id="projectname">GridFire<span id="projectnumber">&#160;v0.7.6rc4.0</span>
    </div>
    <div id="projectbrief">General Purpose Nuclear Network</div>
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docs/html/class_py_dynamic_engine_view.html

@@ -29,7 +29,7 @@
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+   <div id="projectname">GridFire<span id="projectnumber">&#160;v0.7.6rc4.0</span>
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    <div id="projectbrief">General Purpose Nuclear Network</div>
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