tboudreaux/GridFire
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

feat(network): added half lifes, spin flip parity, better reaction acritecture

Browse Source
This commit is contained in:
Emily Boudreaux
2025-06-29 14:53:39 -04:00
parent 2a410dc3fd
commit 29af4c3bab
14 changed files with 2270 additions and 637 deletions
Download Patch File Download Diff File Expand all files Collapse all files

83
src/network/lib/engine/engine_graph.cpp
View File

@@ -18,7 +18,6 @@
#include <vector>
#include <fstream>
#include <boost/numeric/ublas/vector.hpp>
#include <boost/numeric/odeint.hpp>
@@ -30,7 +29,7 @@ namespace gridfire {
syncInternalMaps();
}
GraphEngine::GraphEngine(reaction::REACLIBLogicalReactionSet reactions) :
GraphEngine::GraphEngine(reaction::LogicalReactionSet reactions) :
m_reactions(std::move(reactions)) {
syncInternalMaps();
}
@@ -61,21 +60,22 @@ namespace gridfire {
std::set<std::string_view> uniqueSpeciesNames;
for (const auto& reaction: m_reactions) {
for (const auto& reactant: reaction->reactants()) {
for (const auto& reactant: reaction.reactants()) {
uniqueSpeciesNames.insert(reactant.name());
}
for (const auto& product: reaction->products()) {
for (const auto& product: reaction.products()) {
uniqueSpeciesNames.insert(product.name());
}
}
for (const auto& name: uniqueSpeciesNames) {
auto it = fourdst::atomic::species.find(name);
auto it = fourdst::atomic::species.find(std::string(name));
if (it != fourdst::atomic::species.end()) {
m_networkSpecies.push_back(it->second);
m_networkSpeciesMap.insert({name, it->second});
} else {
LOG_ERROR(m_logger, "Species '{}' not found in global atomic species database.", name);
m_logger->flush_log();
throw std::runtime_error("Species not found in global atomic species database: " + std::string(name));
}
}
@@ -85,8 +85,8 @@ namespace gridfire {
void GraphEngine::populateReactionIDMap() {
LOG_TRACE_L1(m_logger, "Populating reaction ID map for REACLIB graph network (serif::network::GraphNetwork)...");
m_reactionIDMap.clear();
for (const auto& reaction: m_reactions) {
m_reactionIDMap.emplace(reaction->id(), reaction.get());
for (auto& reaction: m_reactions) {
m_reactionIDMap.emplace(reaction.id(), &reaction);
}
LOG_TRACE_L1(m_logger, "Populated {} reactions in the reaction ID map.", m_reactionIDMap.size());
}
@@ -111,13 +111,13 @@ namespace gridfire {
// --- Basic Accessors and Queries ---
const std::vector<fourdst::atomic::Species>& GraphEngine::getNetworkSpecies() const {
// Returns a constant reference to the vector of unique species in the network.
LOG_DEBUG(m_logger, "Providing access to network species vector. Size: {}.", m_networkSpecies.size());
LOG_TRACE_L3(m_logger, "Providing access to network species vector. Size: {}.", m_networkSpecies.size());
return m_networkSpecies;
}
const reaction::REACLIBLogicalReactionSet& GraphEngine::getNetworkReactions() const {
const reaction::LogicalReactionSet& GraphEngine::getNetworkReactions() const {
// Returns a constant reference to the set of reactions in the network.
LOG_DEBUG(m_logger, "Providing access to network reactions set. Size: {}.", m_reactions.size());
LOG_TRACE_L3(m_logger, "Providing access to network reactions set. Size: {}.", m_reactions.size());
return m_reactions;
}
@@ -139,7 +139,7 @@ namespace gridfire {
uint64_t totalProductZ = 0;
// Calculate total A and Z for reactants
for (const auto& reactant : reaction->reactants()) {
for (const auto& reactant : reaction.reactants()) {
auto it = m_networkSpeciesMap.find(reactant.name());
if (it != m_networkSpeciesMap.end()) {
totalReactantA += it->second.a();
@@ -148,13 +148,13 @@ namespace gridfire {
// This scenario indicates a severe data integrity issue:
// a reactant is part of a reaction but not in the network's species map.
LOG_ERROR(m_logger, "CRITICAL ERROR: Reactant species '{}' in reaction '{}' not found in network species map during conservation validation.",
reactant.name(), reaction->id());
reactant.name(), reaction.id());
return false;
}
}
// Calculate total A and Z for products
for (const auto& product : reaction->products()) {
for (const auto& product : reaction.products()) {
auto it = m_networkSpeciesMap.find(product.name());
if (it != m_networkSpeciesMap.end()) {
totalProductA += it->second.a();
@@ -162,7 +162,7 @@ namespace gridfire {
} else {
// Similar critical error for product species
LOG_ERROR(m_logger, "CRITICAL ERROR: Product species '{}' in reaction '{}' not found in network species map during conservation validation.",
product.name(), reaction->id());
product.name(), reaction.id());
return false;
}
}
@@ -170,12 +170,12 @@ namespace gridfire {
// Compare totals for conservation
if (totalReactantA != totalProductA) {
LOG_ERROR(m_logger, "Mass number (A) not conserved for reaction '{}': Reactants A={} vs Products A={}.",
reaction->id(), totalReactantA, totalProductA);
reaction.id(), totalReactantA, totalProductA);
return false;
}
if (totalReactantZ != totalProductZ) {
LOG_ERROR(m_logger, "Atomic number (Z) not conserved for reaction '{}': Reactants Z={} vs Products Z={}.",
reaction->id(), totalReactantZ, totalProductZ);
reaction.id(), totalReactantZ, totalProductZ);
return false;
}
}
@@ -187,7 +187,7 @@ namespace gridfire {
void GraphEngine::validateComposition(const fourdst::composition::Composition &composition, double culling, double T9) {
// Check if the requested network has already been cached.
// PERF: Rebuilding this should be pretty fast but it may be a good point of optimization in the future.
const reaction::REACLIBLogicalReactionSet validationReactionSet = build_reaclib_nuclear_network(composition, false);
const reaction::LogicalReactionSet validationReactionSet = build_reaclib_nuclear_network(composition, false);
// TODO: need some more robust method here to
// A. Build the basic network from the composition's species with non zero mass fractions.
// B. rebuild a new composition from the reaction set's reactants + products (with the mass fractions from the things that are only products set to 0)
@@ -199,7 +199,7 @@ namespace gridfire {
// This allows for dynamic network modification while retaining caching for networks which are very similar.
if (validationReactionSet != m_reactions) {
LOG_DEBUG(m_logger, "Reaction set not cached. Rebuilding the reaction set for T9={} and culling={}.", T9, culling);
m_reactions = validationReactionSet;
m_reactions = std::move(validationReactionSet);
syncInternalMaps(); // Re-sync internal maps after updating reactions. Note this will also retrace the AD tape.
}
}
@@ -221,7 +221,7 @@ namespace gridfire {
size_t reactionColumnIndex = 0;
for (const auto& reaction : m_reactions) {
// Get the net stoichiometry for the current reaction
std::unordered_map<fourdst::atomic::Species, int> netStoichiometry = reaction->stoichiometry();
std::unordered_map<fourdst::atomic::Species, int> netStoichiometry = reaction.stoichiometry();
// Iterate through the species and their coefficients in the stoichiometry map
for (const auto& [species, coefficient] : netStoichiometry) {
@@ -234,7 +234,8 @@ namespace gridfire {
} else {
// This scenario should ideally not happen if m_networkSpeciesMap and m_speciesToIndexMap are correctly synced
LOG_ERROR(m_logger, "CRITICAL ERROR: Species '{}' from reaction '{}' stoichiometry not found in species to index map.",
species.name(), reaction->id());
species.name(), reaction.id());
m_logger -> flush_log();
throw std::runtime_error("Species not found in species to index map: " + std::string(species.name()));
}
}
@@ -255,8 +256,8 @@ namespace gridfire {
StepDerivatives<ADDouble> GraphEngine::calculateAllDerivatives(
const std::vector<ADDouble> &Y_in,
const ADDouble T9,
const ADDouble rho
const ADDouble &T9,
const ADDouble &rho
) const {
return calculateAllDerivatives<ADDouble>(Y_in, T9, rho);
}
@@ -300,7 +301,7 @@ namespace gridfire {
}
}
}
LOG_DEBUG(m_logger, "Jacobian matrix generated with dimensions: {} rows x {} columns.", m_jacobianMatrix.size1(), m_jacobianMatrix.size2());
LOG_TRACE_L1(m_logger, "Jacobian matrix generated with dimensions: {} rows x {} columns.", m_jacobianMatrix.size1(), m_jacobianMatrix.size2());
}
double GraphEngine::getJacobianMatrixEntry(const int i, const int j) const {
@@ -309,7 +310,7 @@ namespace gridfire {
std::unordered_map<fourdst::atomic::Species, int> GraphEngine::getNetReactionStoichiometry(
const reaction::Reaction &reaction
) const {
) {
return reaction.stoichiometry();
}
@@ -326,6 +327,7 @@ namespace gridfire {
std::ofstream dotFile(filename);
if (!dotFile.is_open()) {
LOG_ERROR(m_logger, "Failed to open file for writing: {}", filename);
m_logger->flush_log();
throw std::runtime_error("Failed to open file for writing: " + filename);
}
@@ -345,19 +347,19 @@ namespace gridfire {
dotFile << " // --- Reaction Edges ---\n";
for (const auto& reaction : m_reactions) {
// Create a unique ID for the reaction node
std::string reactionNodeId = "reaction_" + std::string(reaction->id());
std::string reactionNodeId = "reaction_" + std::string(reaction.id());
// Define the reaction node (small, black dot)
dotFile << " \"" << reactionNodeId << "\" [shape=point, fillcolor=black, width=0.1, height=0.1, label=\"\"];\n";
// Draw edges from reactants to the reaction node
for (const auto& reactant : reaction->reactants()) {
for (const auto& reactant : reaction.reactants()) {
dotFile << " \"" << reactant.name() << "\" -> \"" << reactionNodeId << "\";\n";
}
// Draw edges from the reaction node to products
for (const auto& product : reaction->products()) {
dotFile << " \"" << reactionNodeId << "\" -> \"" << product.name() << "\" [label=\"" << reaction->qValue() << " MeV\"];\n";
for (const auto& product : reaction.products()) {
dotFile << " \"" << reactionNodeId << "\" -> \"" << product.name() << "\" [label=\"" << reaction.qValue() << " MeV\"];\n";
}
dotFile << "\n";
}
@@ -373,36 +375,32 @@ namespace gridfire {
std::ofstream csvFile(filename, std::ios::out | std::ios::trunc);
if (!csvFile.is_open()) {
LOG_ERROR(m_logger, "Failed to open file for writing: {}", filename);
m_logger->flush_log();
throw std::runtime_error("Failed to open file for writing: " + filename);
}
csvFile << "Reaction;Reactants;Products;Q-value;sources;rates\n";
for (const auto& reaction : m_reactions) {
// Dynamic cast to REACLIBReaction to access specific properties
csvFile << reaction->id() << ";";
csvFile << reaction.id() << ";";
// Reactants
int count = 0;
for (const auto& reactant : reaction->reactants()) {
for (const auto& reactant : reaction.reactants()) {
csvFile << reactant.name();
if (++count < reaction->reactants().size()) {
if (++count < reaction.reactants().size()) {
csvFile << ",";
}
}
csvFile << ";";
count = 0;
for (const auto& product : reaction->products()) {
for (const auto& product : reaction.products()) {
csvFile << product.name();
if (++count < reaction->products().size()) {
if (++count < reaction.products().size()) {
csvFile << ",";
}
}
csvFile << ";" << reaction->qValue() << ";";
csvFile << ";" << reaction.qValue() << ";";
// Reaction coefficients
auto* reaclibReaction = dynamic_cast<const reaction::REACLIBLogicalReaction*>(reaction.get());
if (!reaclibReaction) {
LOG_ERROR(m_logger, "Failed to cast Reaction to REACLIBLogicalReaction in GraphNetwork::exportToCSV().");
throw std::runtime_error("Failed to cast Reaction to REACLIBLogicalReaction in GraphNetwork::exportToCSV(). This should not happen, please check your reaction setup.");
}
auto sources = reaclibReaction->sources();
auto sources = reaction.sources();
count = 0;
for (const auto& source : sources) {
csvFile << source;
@@ -413,9 +411,9 @@ namespace gridfire {
csvFile << ";";
// Reaction coefficients
count = 0;
for (const auto& rates : *reaclibReaction) {
for (const auto& rates : reaction) {
csvFile << rates;
if (++count < reaclibReaction->size()) {
if (++count < reaction.size()) {
csvFile << ",";
}
}
@@ -448,6 +446,7 @@ namespace gridfire {
const size_t numSpecies = m_networkSpecies.size();
if (numSpecies == 0) {
LOG_ERROR(m_logger, "Cannot record AD tape: No species in the network.");
m_logger->flush_log();
throw std::runtime_error("Cannot record AD tape: No species in the network.");
}
const size_t numADInputs = numSpecies + 2; // Note here that by not letting T9 and rho be independent variables, we are constraining the network to a constant temperature and density during each evaluation.