feat(GridFire): added weak electron screening
This commit is contained in:
@@ -1,3 +1,310 @@
|
||||
//
|
||||
// Created by Emily Boudreaux on 6/30/25.
|
||||
//
|
||||
#include "gridfire/engine/views/engine_defined.h"
|
||||
|
||||
#include "quill/LogMacros.h"
|
||||
|
||||
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);
|
||||
}
|
||||
|
||||
const DynamicEngine & FileDefinedEngineView::getBaseEngine() const {
|
||||
return m_baseEngine;
|
||||
}
|
||||
|
||||
const std::vector<Species> & FileDefinedEngineView::getNetworkSpecies() const {
|
||||
return m_activeSpecies;
|
||||
}
|
||||
|
||||
StepDerivatives<double> FileDefinedEngineView::calculateRHSAndEnergy(
|
||||
const std::vector<double> &Y_defined,
|
||||
const double T9,
|
||||
const double rho
|
||||
) const {
|
||||
validateNetworkState();
|
||||
|
||||
const auto Y_full = mapViewToFull(Y_defined);
|
||||
const auto [dydt, nuclearEnergyGenerationRate] = m_baseEngine.calculateRHSAndEnergy(Y_full, T9, rho);
|
||||
|
||||
StepDerivatives<double> definedResults;
|
||||
definedResults.nuclearEnergyGenerationRate = nuclearEnergyGenerationRate;
|
||||
definedResults.dydt = mapFullToView(dydt);
|
||||
return definedResults;
|
||||
}
|
||||
|
||||
void FileDefinedEngineView::generateJacobianMatrix(
|
||||
const std::vector<double> &Y_defined,
|
||||
const double T9,
|
||||
const double rho
|
||||
) {
|
||||
validateNetworkState();
|
||||
|
||||
const auto Y_full = mapViewToFull(Y_defined);
|
||||
m_baseEngine.generateJacobianMatrix(Y_full, T9, rho);
|
||||
}
|
||||
|
||||
double FileDefinedEngineView::getJacobianMatrixEntry(
|
||||
const int i_defined,
|
||||
const int j_defined
|
||||
) const {
|
||||
validateNetworkState();
|
||||
|
||||
const size_t i_full = mapViewToFullSpeciesIndex(i_defined);
|
||||
const size_t j_full = mapViewToFullSpeciesIndex(j_defined);
|
||||
|
||||
return m_baseEngine.getJacobianMatrixEntry(i_full, j_full);
|
||||
}
|
||||
|
||||
void FileDefinedEngineView::generateStoichiometryMatrix() {
|
||||
validateNetworkState();
|
||||
|
||||
m_baseEngine.generateStoichiometryMatrix();
|
||||
}
|
||||
|
||||
int FileDefinedEngineView::getStoichiometryMatrixEntry(
|
||||
const int speciesIndex_defined,
|
||||
const int reactionIndex_defined
|
||||
) const {
|
||||
validateNetworkState();
|
||||
|
||||
const size_t i_full = mapViewToFullSpeciesIndex(speciesIndex_defined);
|
||||
const size_t j_full = mapViewToFullReactionIndex(reactionIndex_defined);
|
||||
return m_baseEngine.getStoichiometryMatrixEntry(i_full, j_full);
|
||||
}
|
||||
|
||||
double FileDefinedEngineView::calculateMolarReactionFlow(
|
||||
const reaction::Reaction &reaction,
|
||||
const std::vector<double> &Y_defined,
|
||||
const double T9,
|
||||
const double rho
|
||||
) const {
|
||||
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());
|
||||
m_logger -> flush_log();
|
||||
throw std::runtime_error("Reaction not found in active reactions: " + std::string(reaction.id()));
|
||||
}
|
||||
const auto Y_full = mapViewToFull(Y_defined);
|
||||
return m_baseEngine.calculateMolarReactionFlow(reaction, Y_full, T9, rho);
|
||||
}
|
||||
|
||||
const reaction::LogicalReactionSet & FileDefinedEngineView::getNetworkReactions() const {
|
||||
validateNetworkState();
|
||||
|
||||
return m_activeReactions;
|
||||
}
|
||||
|
||||
std::unordered_map<Species, double> FileDefinedEngineView::getSpeciesTimescales(
|
||||
const std::vector<double> &Y_defined,
|
||||
const double T9,
|
||||
const double rho
|
||||
) const {
|
||||
validateNetworkState();
|
||||
|
||||
const auto Y_full = mapViewToFull(Y_defined);
|
||||
const auto fullTimescales = m_baseEngine.getSpeciesTimescales(Y_full, T9, rho);
|
||||
|
||||
std::unordered_map<Species, double> definedTimescales;
|
||||
for (const auto& active_species : m_activeSpecies) {
|
||||
if (fullTimescales.contains(active_species)) {
|
||||
definedTimescales[active_species] = fullTimescales.at(active_species);
|
||||
}
|
||||
}
|
||||
return definedTimescales;
|
||||
}
|
||||
|
||||
void FileDefinedEngineView::update(const NetIn &netIn) {
|
||||
if (m_isStale) {
|
||||
buildFromFile(m_fileName);
|
||||
}
|
||||
}
|
||||
|
||||
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) {
|
||||
m_baseEngine.setScreeningModel(model);
|
||||
}
|
||||
|
||||
screening::ScreeningType FileDefinedEngineView::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...");
|
||||
std::unordered_map<Species, size_t> fullSpeciesReverseMap;
|
||||
const auto& fullSpeciesList = m_baseEngine.getNetworkSpecies();
|
||||
|
||||
fullSpeciesReverseMap.reserve(fullSpeciesList.size());
|
||||
|
||||
for (size_t i = 0; i < fullSpeciesList.size(); ++i) {
|
||||
fullSpeciesReverseMap[fullSpeciesList[i]] = i;
|
||||
}
|
||||
|
||||
std::vector<size_t> speciesIndexMap;
|
||||
speciesIndexMap.reserve(m_activeSpecies.size());
|
||||
|
||||
for (const auto& active_species : m_activeSpecies) {
|
||||
auto it = fullSpeciesReverseMap.find(active_species);
|
||||
if (it != fullSpeciesReverseMap.end()) {
|
||||
speciesIndexMap.push_back(it->second);
|
||||
} else {
|
||||
LOG_ERROR(m_logger, "Species '{}' not found in full species map.", active_species.name());
|
||||
m_logger -> flush_log();
|
||||
throw std::runtime_error("Species not found in full species map: " + std::string(active_species.name()));
|
||||
}
|
||||
}
|
||||
LOG_TRACE_L1(m_logger, "Species index map constructed with {} entries.", speciesIndexMap.size());
|
||||
return speciesIndexMap;
|
||||
|
||||
}
|
||||
|
||||
std::vector<size_t> FileDefinedEngineView::constructReactionIndexMap() const {
|
||||
LOG_TRACE_L1(m_logger, "Constructing reaction index map for file defined engine view...");
|
||||
|
||||
// --- Step 1: Create a reverse map using the reaction's unique ID as the key. ---
|
||||
std::unordered_map<std::string_view, size_t> fullReactionReverseMap;
|
||||
const auto& fullReactionSet = m_baseEngine.getNetworkReactions();
|
||||
fullReactionReverseMap.reserve(fullReactionSet.size());
|
||||
|
||||
for (size_t i_full = 0; i_full < fullReactionSet.size(); ++i_full) {
|
||||
fullReactionReverseMap[fullReactionSet[i_full].id()] = i_full;
|
||||
}
|
||||
|
||||
// --- Step 2: Build the final index map using the active reaction set. ---
|
||||
std::vector<size_t> reactionIndexMap;
|
||||
reactionIndexMap.reserve(m_activeReactions.size());
|
||||
|
||||
for (const auto& active_reaction_ptr : m_activeReactions) {
|
||||
auto it = fullReactionReverseMap.find(active_reaction_ptr.id());
|
||||
|
||||
if (it != fullReactionReverseMap.end()) {
|
||||
reactionIndexMap.push_back(it->second);
|
||||
} else {
|
||||
LOG_ERROR(m_logger, "Active reaction '{}' not found in base engine during reaction index map construction.", active_reaction_ptr.id());
|
||||
m_logger->flush_log();
|
||||
throw std::runtime_error("Mismatch between active reactions and base engine.");
|
||||
}
|
||||
}
|
||||
|
||||
LOG_TRACE_L1(m_logger, "Reaction index map constructed with {} entries.", reactionIndexMap.size());
|
||||
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> 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];
|
||||
full[i_full] += culled[i_culled];
|
||||
}
|
||||
return full;
|
||||
}
|
||||
|
||||
std::vector<double> FileDefinedEngineView::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];
|
||||
culled[i_culled] = full[i_full];
|
||||
}
|
||||
return culled;
|
||||
}
|
||||
|
||||
size_t FileDefinedEngineView::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();
|
||||
throw std::out_of_range("Defined index " + std::to_string(culledSpeciesIndex) + " is out of bounds for species index map of size " + std::to_string(m_speciesIndexMap.size()) + ".");
|
||||
}
|
||||
return m_speciesIndexMap[culledSpeciesIndex];
|
||||
}
|
||||
|
||||
size_t FileDefinedEngineView::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();
|
||||
throw std::out_of_range("Defined index " + std::to_string(culledReactionIndex) + " is out of bounds for reaction index map of size " + std::to_string(m_reactionIndexMap.size()) + ".");
|
||||
}
|
||||
return m_reactionIndexMap[culledReactionIndex];
|
||||
}
|
||||
|
||||
void FileDefinedEngineView::validateNetworkState() const {
|
||||
if (m_isStale) {
|
||||
LOG_ERROR(m_logger, "File defined engine view 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.");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user