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feat(MultiscalePartitioningEngineView): added *much* more robust qse group identifiction and solving

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This commit is contained in:
Emily Boudreaux
2025-07-10 09:36:05 -04:00
parent 1ac6b451b8
commit 7012eb819a
23 changed files with 1863 additions and 378 deletions
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238
src/network/lib/engine/views/engine_defined.cpp
View File

@@ -1,32 +1,88 @@
#include "gridfire/engine/views/engine_defined.h"
#include <ranges>
#include "quill/LogMacros.h"
#include <string>
#include <vector>
#include <unordered_set>
#include <stdexcept>
#include <unordered_map>
#include <utility>
namespace gridfire {
using fourdst::atomic::Species;
FileDefinedEngineView::FileDefinedEngineView(
DynamicEngine &baseEngine,
const std::string &fileName,
const io::NetworkFileParser &parser
):
m_baseEngine(baseEngine),
m_fileName(fileName),
m_parser(parser),
m_activeSpecies(baseEngine.getNetworkSpecies()),
m_activeReactions(baseEngine.getNetworkReactions()) {
buildFromFile(fileName);
DefinedEngineView::DefinedEngineView(const std::vector<std::string>& peNames, DynamicEngine& baseEngine) :
m_baseEngine(baseEngine) {
m_activeReactions.clear();
m_activeSpecies.clear();
std::unordered_set<Species> seenSpecies;
const auto& fullNetworkReactionSet = m_baseEngine.getNetworkReactions();
for (const auto& peName : peNames) {
if (!fullNetworkReactionSet.contains(peName)) {
LOG_ERROR(m_logger, "Reaction with name '{}' not found in the base engine's network reactions. Aborting...", peName);
m_logger->flush_log();
throw std::runtime_error("Reaction with name '" + std::string(peName) + "' not found in the base engine's network reactions.");
}
auto reaction = fullNetworkReactionSet[peName];
for (const auto& reactant : reaction.reactants()) {
if (!seenSpecies.contains(reactant)) {
seenSpecies.insert(reactant);
m_activeSpecies.push_back(reactant);
}
}
for (const auto& product : reaction.products()) {
if (!seenSpecies.contains(product)) {
seenSpecies.insert(product);
m_activeSpecies.push_back(product);
}
}
m_activeReactions.add_reaction(reaction);
}
LOG_TRACE_L1(m_logger, "DefinedEngineView built with {} active species and {} active reactions.", m_activeSpecies.size(), m_activeReactions.size());
LOG_DEBUG(m_logger, "Active species: {}", [this]() -> std::string {
std::string result;
for (const auto& species : m_activeSpecies) {
result += std::string(species.name()) + ", ";
}
if (!result.empty()) {
result.pop_back(); // Remove last space
result.pop_back(); // Remove last comma
}
return result;
}());
LOG_DEBUG(m_logger, "Active reactions: {}", [this]() -> std::string {
std::string result;
for (const auto& reaction : m_activeReactions) {
result += std::string(reaction.id()) + ", ";
}
if (!result.empty()) {
result.pop_back(); // Remove last space
result.pop_back(); // Remove last comma
}
return result;
}());
m_speciesIndexMap = constructSpeciesIndexMap();
m_reactionIndexMap = constructReactionIndexMap();
m_isStale = false;
}
const DynamicEngine & FileDefinedEngineView::getBaseEngine() const {
const DynamicEngine & DefinedEngineView::getBaseEngine() const {
return m_baseEngine;
}
const std::vector<Species> & FileDefinedEngineView::getNetworkSpecies() const {
const std::vector<Species> & DefinedEngineView::getNetworkSpecies() const {
return m_activeSpecies;
}
StepDerivatives<double> FileDefinedEngineView::calculateRHSAndEnergy(
StepDerivatives<double> DefinedEngineView::calculateRHSAndEnergy(
const std::vector<double> &Y_defined,
const double T9,
const double rho
@@ -42,18 +98,18 @@ namespace gridfire {
return definedResults;
}
void FileDefinedEngineView::generateJacobianMatrix(
const std::vector<double> &Y_defined,
void DefinedEngineView::generateJacobianMatrix(
const std::vector<double> &Y_dynamic,
const double T9,
const double rho
) {
validateNetworkState();
const auto Y_full = mapViewToFull(Y_defined);
const auto Y_full = mapViewToFull(Y_dynamic);
m_baseEngine.generateJacobianMatrix(Y_full, T9, rho);
}
double FileDefinedEngineView::getJacobianMatrixEntry(
double DefinedEngineView::getJacobianMatrixEntry(
const int i_defined,
const int j_defined
) const {
@@ -65,13 +121,13 @@ namespace gridfire {
return m_baseEngine.getJacobianMatrixEntry(i_full, j_full);
}
void FileDefinedEngineView::generateStoichiometryMatrix() {
void DefinedEngineView::generateStoichiometryMatrix() {
validateNetworkState();
m_baseEngine.generateStoichiometryMatrix();
}
int FileDefinedEngineView::getStoichiometryMatrixEntry(
int DefinedEngineView::getStoichiometryMatrixEntry(
const int speciesIndex_defined,
const int reactionIndex_defined
) const {
@@ -82,7 +138,7 @@ namespace gridfire {
return m_baseEngine.getStoichiometryMatrixEntry(i_full, j_full);
}
double FileDefinedEngineView::calculateMolarReactionFlow(
double DefinedEngineView::calculateMolarReactionFlow(
const reaction::Reaction &reaction,
const std::vector<double> &Y_defined,
const double T9,
@@ -91,7 +147,7 @@ namespace gridfire {
validateNetworkState();
if (!m_activeReactions.contains(reaction)) {
LOG_ERROR(m_logger, "Reaction '{}' is not part of the active reactions in the file defined engine view.", reaction.id());
LOG_ERROR(m_logger, "Reaction '{}' is not part of the active reactions in the DefinedEngineView.", reaction.id());
m_logger -> flush_log();
throw std::runtime_error("Reaction not found in active reactions: " + std::string(reaction.id()));
}
@@ -99,13 +155,13 @@ namespace gridfire {
return m_baseEngine.calculateMolarReactionFlow(reaction, Y_full, T9, rho);
}
const reaction::LogicalReactionSet & FileDefinedEngineView::getNetworkReactions() const {
const reaction::LogicalReactionSet & DefinedEngineView::getNetworkReactions() const {
validateNetworkState();
return m_activeReactions;
}
std::unordered_map<Species, double> FileDefinedEngineView::getSpeciesTimescales(
std::unordered_map<Species, double> DefinedEngineView::getSpeciesTimescales(
const std::vector<double> &Y_defined,
const double T9,
const double rho
@@ -124,28 +180,45 @@ namespace gridfire {
return definedTimescales;
}
void FileDefinedEngineView::update(const NetIn &netIn) {
if (m_isStale) {
buildFromFile(m_fileName);
}
void DefinedEngineView::update(const NetIn &netIn) {
return;
}
void FileDefinedEngineView::setNetworkFile(const std::string &fileName) {
m_isStale = true;
m_fileName = fileName;
LOG_DEBUG(m_logger, "File '{}' set to '{}'. FileDefinedNetworkView is now stale! You MUST call update() before you use it!", m_fileName, fileName);
}
void FileDefinedEngineView::setScreeningModel(const screening::ScreeningType model) {
void DefinedEngineView::setScreeningModel(const screening::ScreeningType model) {
m_baseEngine.setScreeningModel(model);
}
screening::ScreeningType FileDefinedEngineView::getScreeningModel() const {
screening::ScreeningType DefinedEngineView::getScreeningModel() const {
return m_baseEngine.getScreeningModel();
}
std::vector<size_t> FileDefinedEngineView::constructSpeciesIndexMap() const {
LOG_TRACE_L1(m_logger, "Constructing species index map for file defined engine view...");
int DefinedEngineView::getSpeciesIndex(const Species &species) const {
validateNetworkState();
auto it = std::find(m_activeSpecies.begin(), m_activeSpecies.end(), species);
if (it != m_activeSpecies.end()) {
return static_cast<int>(std::distance(m_activeSpecies.begin(), it));
} else {
LOG_ERROR(m_logger, "Species '{}' not found in active species list.", species.name());
m_logger->flush_log();
throw std::runtime_error("Species not found in active species list: " + std::string(species.name()));
}
}
std::vector<double> DefinedEngineView::mapNetInToMolarAbundanceVector(const NetIn &netIn) const {
std::vector<double> Y(m_activeSpecies.size(), 0.0); // Initialize with zeros
for (const auto& [symbol, entry] : netIn.composition) {
auto it = std::ranges::find(m_activeSpecies, entry.isotope());
if (it != m_activeSpecies.end()) {
Y[getSpeciesIndex(entry.isotope())] = netIn.composition.getMolarAbundance(symbol); // Map species to their molar abundance
}
}
return Y; // Return the vector of molar abundances
}
std::vector<size_t> DefinedEngineView::constructSpeciesIndexMap() const {
LOG_TRACE_L1(m_logger, "Constructing species index map for DefinedEngineView...");
std::unordered_map<Species, size_t> fullSpeciesReverseMap;
const auto& fullSpeciesList = m_baseEngine.getNetworkSpecies();
@@ -173,8 +246,8 @@ namespace gridfire {
}
std::vector<size_t> FileDefinedEngineView::constructReactionIndexMap() const {
LOG_TRACE_L1(m_logger, "Constructing reaction index map for file defined engine view...");
std::vector<size_t> DefinedEngineView::constructReactionIndexMap() const {
LOG_TRACE_L1(m_logger, "Constructing reaction index map for DefinedEngineView...");
// --- Step 1: Create a reverse map using the reaction's unique ID as the key. ---
std::unordered_map<std::string_view, size_t> fullReactionReverseMap;
@@ -205,66 +278,7 @@ namespace gridfire {
return reactionIndexMap;
}
void FileDefinedEngineView::buildFromFile(const std::string &fileName) {
LOG_TRACE_L1(m_logger, "Building file defined engine view from {}...", fileName);
auto [reactionPENames] = m_parser.parse(fileName);
m_activeReactions.clear();
m_activeSpecies.clear();
std::unordered_set<Species> seenSpecies;
const auto& fullNetworkReactionSet = m_baseEngine.getNetworkReactions();
for (const auto& peName : reactionPENames) {
if (!fullNetworkReactionSet.contains(peName)) {
LOG_ERROR(m_logger, "Reaction with name '{}' not found in the base engine's network reactions. Aborting...", peName);
m_logger->flush_log();
throw std::runtime_error("Reaction with name '" + std::string(peName) + "' not found in the base engine's network reactions.");
}
auto reaction = fullNetworkReactionSet[peName];
for (const auto& reactant : reaction.reactants()) {
if (!seenSpecies.contains(reactant)) {
seenSpecies.insert(reactant);
m_activeSpecies.push_back(reactant);
}
}
for (const auto& product : reaction.products()) {
if (!seenSpecies.contains(product)) {
seenSpecies.insert(product);
m_activeSpecies.push_back(product);
}
}
m_activeReactions.add_reaction(reaction);
}
LOG_TRACE_L1(m_logger, "File defined engine view built with {} active species and {} active reactions.", m_activeSpecies.size(), m_activeReactions.size());
LOG_DEBUG(m_logger, "Active species: {}", [this]() -> std::string {
std::string result;
for (const auto& species : m_activeSpecies) {
result += std::string(species.name()) + ", ";
}
if (!result.empty()) {
result.pop_back(); // Remove last space
result.pop_back(); // Remove last comma
}
return result;
}());
LOG_DEBUG(m_logger, "Active reactions: {}", [this]() -> std::string {
std::string result;
for (const auto& reaction : m_activeReactions) {
result += std::string(reaction.id()) + ", ";
}
if (!result.empty()) {
result.pop_back(); // Remove last space
result.pop_back(); // Remove last comma
}
return result;
}());
m_speciesIndexMap = constructSpeciesIndexMap();
m_reactionIndexMap = constructReactionIndexMap();
m_isStale = false;
}
std::vector<double> FileDefinedEngineView::mapViewToFull(const std::vector<double>& culled) const {
std::vector<double> DefinedEngineView::mapViewToFull(const std::vector<double>& culled) const {
std::vector<double> full(m_baseEngine.getNetworkSpecies().size(), 0.0);
for (size_t i_culled = 0; i_culled < culled.size(); ++i_culled) {
const size_t i_full = m_speciesIndexMap[i_culled];
@@ -273,7 +287,7 @@ namespace gridfire {
return full;
}
std::vector<double> FileDefinedEngineView::mapFullToView(const std::vector<double>& full) const {
std::vector<double> DefinedEngineView::mapFullToView(const std::vector<double>& full) const {
std::vector<double> culled(m_activeSpecies.size(), 0.0);
for (size_t i_culled = 0; i_culled < m_activeSpecies.size(); ++i_culled) {
const size_t i_full = m_speciesIndexMap[i_culled];
@@ -282,7 +296,7 @@ namespace gridfire {
return culled;
}
size_t FileDefinedEngineView::mapViewToFullSpeciesIndex(size_t culledSpeciesIndex) const {
size_t DefinedEngineView::mapViewToFullSpeciesIndex(size_t culledSpeciesIndex) const {
if (culledSpeciesIndex < 0 || culledSpeciesIndex >= static_cast<int>(m_speciesIndexMap.size())) {
LOG_ERROR(m_logger, "Defined index {} is out of bounds for species index map of size {}.", culledSpeciesIndex, m_speciesIndexMap.size());
m_logger->flush_log();
@@ -291,7 +305,7 @@ namespace gridfire {
return m_speciesIndexMap[culledSpeciesIndex];
}
size_t FileDefinedEngineView::mapViewToFullReactionIndex(size_t culledReactionIndex) const {
size_t DefinedEngineView::mapViewToFullReactionIndex(size_t culledReactionIndex) const {
if (culledReactionIndex < 0 || culledReactionIndex >= static_cast<int>(m_reactionIndexMap.size())) {
LOG_ERROR(m_logger, "Defined index {} is out of bounds for reaction index map of size {}.", culledReactionIndex, m_reactionIndexMap.size());
m_logger->flush_log();
@@ -300,11 +314,25 @@ namespace gridfire {
return m_reactionIndexMap[culledReactionIndex];
}
void FileDefinedEngineView::validateNetworkState() const {
void DefinedEngineView::validateNetworkState() const {
if (m_isStale) {
LOG_ERROR(m_logger, "File defined engine view is stale. Please call update() with a valid NetIn object.");
LOG_ERROR(m_logger, "DefinedEngineView is stale. Please call update() with a valid NetIn object.");
m_logger->flush_log();
throw std::runtime_error("File defined engine view is stale. Please call update() with a valid NetIn object.");
throw std::runtime_error("DefinedEngineView is stale. Please call update() with a valid NetIn object.");
}
}
////////////////////////////////////////////
/// FileDefinedEngineView Implementation ///
/////////////////////////////////////////////
FileDefinedEngineView::FileDefinedEngineView(
DynamicEngine &baseEngine,
const std::string &fileName,
const io::NetworkFileParser &parser
):
DefinedEngineView(parser.parse(fileName), baseEngine),
m_fileName(fileName),
m_parser(parser) {}
}