feat(network): started adding GraphNetwork
GraphNetwork is intended to be a more general, reaclib based, network when compared to approx8 (which is also approx8 based but limited to a specific composition)
This commit is contained in:
@@ -1,12 +1,14 @@
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# Define the library
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network_sources = files(
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'private/network.cpp',
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'private/approx8.cpp'
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'private/approx8.cpp',
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'private/netgraph.cpp'
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)
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network_headers = files(
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'public/network.h',
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'public/approx8.h'
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'public/approx8.h',
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'public/netgraph.h',
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)
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dependencies = [
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@@ -1,3 +1,256 @@
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//
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// Created by Emily Boudreaux on 6/19/25.
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//
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#include "netgraph.h"
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#include "atomicSpecies.h"
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#include "reaclib.h"
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#include "network.h"
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#include "species.h"
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#include "quill/LogMacros.h"
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#include <set>
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#include <unordered_map>
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#include <string>
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#include <vector>
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#include <stdexcept>
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#include <string_view>
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#include <cstdint>
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#include <iostream>
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namespace serif::network {
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GraphNetwork::GraphNetwork(
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const serif::composition::Composition &composition
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):
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Network(REACLIB),
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m_reactions(build_reaclib_nuclear_network(composition)),
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m_initialComposition(composition),
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m_currentComposition(composition),
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m_cullingThreshold(0),
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m_T9(0) {
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syncInternalMaps();
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}
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GraphNetwork::GraphNetwork(
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const serif::composition::Composition &composition,
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const double cullingThreshold,
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const double T9
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):
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Network(REACLIB),
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m_reactions(build_reaclib_nuclear_network(composition, cullingThreshold, T9)),
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m_initialComposition(composition),
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m_currentComposition(composition),
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m_cullingThreshold(cullingThreshold),
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m_T9(T9) {
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syncInternalMaps();
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}
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void GraphNetwork::syncInternalMaps() {
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collectNetworkSpecies();
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populateReactionIDMap();
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populateSpeciesToIndexMap();
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}
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// --- Network Graph Construction Methods ---
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void GraphNetwork::collectNetworkSpecies() {
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m_networkSpecies.clear();
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m_networkSpeciesMap.clear();
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std::set<std::string_view> uniqueSpeciesNames;
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for (const auto& reaction: m_reactions) {
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for (const auto& reactant: reaction.reactants()) {
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uniqueSpeciesNames.insert(reactant.name());
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}
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for (const auto& product: reaction.products()) {
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uniqueSpeciesNames.insert(product.name());
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}
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}
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for (const auto& name: uniqueSpeciesNames) {
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auto it = serif::atomic::species.find(name);
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if (it != serif::atomic::species.end()) {
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m_networkSpecies.push_back(it->second);
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m_networkSpeciesMap.insert({name, it->second});
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} else {
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LOG_ERROR(m_logger, "Species '{}' not found in global atomic species database.", name);
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throw std::runtime_error("Species not found in global atomic species database: " + std::string(name));
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}
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}
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}
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void GraphNetwork::populateReactionIDMap() {
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LOG_INFO(m_logger, "Populating reaction ID map for REACLIB graph network (serif::network::GraphNetwork)...");
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m_reactionIDMap.clear();
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for (const auto& reaction: m_reactions) {
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m_reactionIDMap.insert({reaction.id(), reaction});
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}
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LOG_INFO(m_logger, "Populated {} reactions in the reaction ID map.", m_reactionIDMap.size());
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}
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void GraphNetwork::populateSpeciesToIndexMap() {
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m_speciesToIndexMap.clear();
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for (size_t i = 0; i < m_networkSpecies.size(); ++i) {
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m_speciesToIndexMap.insert({m_networkSpecies[i], i});
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}
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}
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void GraphNetwork::buildNetworkGraph() {
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LOG_INFO(m_logger, "Building network graph...");
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m_reactions = build_reaclib_nuclear_network(m_initialComposition, m_cullingThreshold, m_T9);
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syncInternalMaps();
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LOG_INFO(m_logger, "Network graph built with {} reactions and {} species.", m_reactions.size(), m_networkSpecies.size());
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}
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// --- Basic Accessors and Queries ---
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const std::vector<serif::atomic::Species>& GraphNetwork::getNetworkSpecies() const {
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// Returns a constant reference to the vector of unique species in the network.
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LOG_DEBUG(m_logger, "Providing access to network species vector. Size: {}.", m_networkSpecies.size());
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return m_networkSpecies;
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}
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const reaclib::REACLIBReactionSet& GraphNetwork::getNetworkReactions() const {
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// Returns a constant reference to the set of reactions in the network.
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LOG_DEBUG(m_logger, "Providing access to network reactions set. Size: {}.", m_reactions.size());
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return m_reactions;
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}
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bool GraphNetwork::involvesSpecies(const serif::atomic::Species& species) const {
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// Checks if a given species is present in the network's species map for efficient lookup.
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const bool found = m_networkSpeciesMap.contains(species.name());
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LOG_DEBUG(m_logger, "Checking if species '{}' is involved in the network: {}.", species.name(), found ? "Yes" : "No");
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return found;
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}
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std::unordered_map<serif::atomic::Species, int> GraphNetwork::getNetReactionStoichiometry(const reaclib::REACLIBReaction& reaction) const {
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// Calculates the net stoichiometric coefficients for species in a given reaction.
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std::unordered_map<serif::atomic::Species, int> stoichiometry;
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// Iterate through reactants, decrementing their counts
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for (const auto& reactant : reaction.reactants()) {
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auto it = m_networkSpeciesMap.find(reactant.name());
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if (it != m_networkSpeciesMap.end()) {
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stoichiometry[it->second]--; // Copy Species by value (PERF: Future performance improvements by using pointers or references)
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} else {
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LOG_WARNING(m_logger, "Reactant species '{}' in reaction '{}' not found in network species map during stoichiometry calculation.",
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reactant.name(), reaction.id());
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}
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}
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// Iterate through products, incrementing their counts
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for (const auto& product : reaction.products()) {
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auto it = m_networkSpeciesMap.find(product.name());
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if (it != m_networkSpeciesMap.end()) {
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stoichiometry[it->second]++; // Copy Species by value (PERF: Future performance improvements by using pointers or references)
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} else {
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LOG_WARNING(m_logger, "Product species '{}' in reaction '{}' not found in network species map during stoichiometry calculation.",
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product.name(), reaction.id());
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}
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}
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LOG_DEBUG(m_logger, "Calculated net stoichiometry for reaction '{}'. Total unique species in stoichiometry: {}.", reaction.id(), stoichiometry.size());
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return stoichiometry;
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}
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// --- Validation Methods ---
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bool GraphNetwork::validateConservation() const {
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LOG_INFO(m_logger, "Validating mass (A) and charge (Z) conservation across all reactions in the network.");
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for (const auto& reaction : m_reactions) {
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uint64_t totalReactantA = 0;
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uint64_t totalReactantZ = 0;
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uint64_t totalProductA = 0;
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uint64_t totalProductZ = 0;
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// Calculate total A and Z for reactants
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for (const auto& reactant : reaction.reactants()) {
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auto it = m_networkSpeciesMap.find(reactant.name());
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if (it != m_networkSpeciesMap.end()) {
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totalReactantA += it->second.a();
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totalReactantZ += it->second.z();
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} else {
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// This scenario indicates a severe data integrity issue:
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// a reactant is part of a reaction but not in the network's species map.
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LOG_ERROR(m_logger, "CRITICAL ERROR: Reactant species '{}' in reaction '{}' not found in network species map during conservation validation.",
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reactant.name(), reaction.id());
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return false;
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}
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}
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// Calculate total A and Z for products
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for (const auto& product : reaction.products()) {
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auto it = m_networkSpeciesMap.find(product.name());
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if (it != m_networkSpeciesMap.end()) {
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totalProductA += it->second.a();
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totalProductZ += it->second.z();
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} else {
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// Similar critical error for product species
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LOG_ERROR(m_logger, "CRITICAL ERROR: Product species '{}' in reaction '{}' not found in network species map during conservation validation.",
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product.name(), reaction.id());
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return false;
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}
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}
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// Compare totals for conservation
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if (totalReactantA != totalProductA) {
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LOG_ERROR(m_logger, "Mass number (A) not conserved for reaction '{}': Reactants A={} vs Products A={}.",
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reaction.id(), totalReactantA, totalProductA);
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return false;
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}
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if (totalReactantZ != totalProductZ) {
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LOG_ERROR(m_logger, "Atomic number (Z) not conserved for reaction '{}': Reactants Z={} vs Products Z={}.",
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reaction.id(), totalReactantZ, totalProductZ);
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return false;
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}
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}
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LOG_INFO(m_logger, "Mass (A) and charge (Z) conservation validated successfully for all reactions.");
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return true; // All reactions passed the conservation check
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}
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// --- Generate Stoichiometry Matrix ---
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void GraphNetwork::generateStoichiometryMatrix() {
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LOG_INFO(m_logger, "Generating stoichiometry matrix...");
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// Task 1: Set dimensions and initialize the matrix
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size_t numSpecies = m_networkSpecies.size();
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size_t numReactions = m_reactions.size();
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m_stoichiometryMatrix.resize(numSpecies, numReactions, false);
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LOG_INFO(m_logger, "Stoichiometry matrix initialized with dimensions: {} rows (species) x {} columns (reactions).",
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numSpecies, numReactions);
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// Task 2: Populate the stoichiometry matrix
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// Iterate through all reactions, assign them a column index, and fill in their stoichiometric coefficients.
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size_t reactionColumnIndex = 0;
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for (const auto& reaction : m_reactions) {
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// Get the net stoichiometry for the current reaction
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std::unordered_map<serif::atomic::Species, int> netStoichiometry = getNetReactionStoichiometry(reaction);
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// Iterate through the species and their coefficients in the stoichiometry map
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for (const auto& pair : netStoichiometry) {
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const serif::atomic::Species& species = pair.first; // The Species object
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const int coefficient = pair.second; // The stoichiometric coefficient
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// Find the row index for this species
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auto it = m_speciesToIndexMap.find(species);
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if (it != m_speciesToIndexMap.end()) {
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const size_t speciesRowIndex = it->second;
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// Set the matrix element. Boost.uBLAS handles sparse insertion.
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m_stoichiometryMatrix(speciesRowIndex, reactionColumnIndex) = coefficient;
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} else {
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// This scenario should ideally not happen if m_networkSpeciesMap and m_speciesToIndexMap are correctly synced
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LOG_ERROR(m_logger, "CRITICAL ERROR: Species '{}' from reaction '{}' stoichiometry not found in species to index map.",
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species.name(), reaction.id());
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throw std::runtime_error("Species not found in species to index map: " + std::string(species.name()));
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}
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}
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reactionColumnIndex++; // Move to the next column for the next reaction
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}
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LOG_INFO(m_logger, "Stoichiometry matrix population complete. Number of non-zero elements: {}.",
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m_stoichiometryMatrix.nnz()); // Assuming nnz() exists for compressed_matrix
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}
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NetOut GraphNetwork::evaluate(const NetIn &netIn) {
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return Network::evaluate(netIn);
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}
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}
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@@ -1,8 +1,63 @@
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//
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// Created by Emily Boudreaux on 6/19/25.
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//
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#pragma once
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#ifndef NETGRAPH_H
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#define NETGRAPH_H
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#include "network.h"
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#include "reaclib.h"
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#include "atomicSpecies.h"
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#include "composition.h"
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#endif //NETGRAPH_H
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#include <unordered_map>
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#include <vector>
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#include <string>
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#include <boost/numeric/ublas/matrix_sparse.hpp>
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// PERF: The function getNetReactionStoichiometry returns a map of species to their stoichiometric coefficients for a given reaction.
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// this makes extra copies of the species, which is not ideal and could be optimized further.
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// Even more relevant is the member m_reactionIDMap which makes copies of a REACLIBReaction for each reaction ID.
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// REACLIBReactions are quite large data structures, so this could be a performance bottleneck.
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namespace serif::network {
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class GraphNetwork final : public Network {
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public:
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explicit GraphNetwork(const serif::composition::Composition &composition);
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explicit GraphNetwork(const serif::composition::Composition &composition, const double cullingThreshold, const double T9);
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NetOut evaluate(const NetIn &netIn) override;
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[[nodiscard]] const std::vector<serif::atomic::Species>& getNetworkSpecies() const;
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[[nodiscard]] const reaclib::REACLIBReactionSet& getNetworkReactions() const;
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[[nodiscard]] std::unordered_map<serif::atomic::Species, int> getNetReactionStoichiometry(const reaclib::REACLIBReaction& reaction) const;
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[[nodiscard]] bool involvesSpecies(const serif::atomic::Species& species) const;
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std::vector<std::vector<std::string>> detectCycles() const;
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std::vector<std::string> topologicalSortReactions() const;
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private:
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reaclib::REACLIBReactionSet m_reactions; ///< Set of REACLIB reactions for the network.
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serif::composition::Composition m_initialComposition;
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serif::composition::Composition m_currentComposition;
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double m_cullingThreshold; ///< Threshold for culling reactions.
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double m_T9; ///< Temperature in T9 units to evaluate culling.
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std::vector<serif::atomic::Species> m_networkSpecies; ///< The species in the network.
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std::unordered_map<std::string_view, serif::atomic::Species> m_networkSpeciesMap;
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std::unordered_map<std::string_view, const reaclib::REACLIBReaction> m_reactionIDMap; ///< Map of reaction IDs to REACLIB reactions.
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boost::numeric::ublas::compressed_matrix<int> m_stoichiometryMatrix; ///< Stoichiometry matrix for the network.
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std::unordered_map<serif::atomic::Species, size_t> m_speciesToIndexMap; ///< Map of species to their index in the stoichiometry matrix.
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private:
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void syncInternalMaps();
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void collectNetworkSpecies();
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void populateReactionIDMap();
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void populateSpeciesToIndexMap();
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void buildNetworkGraph();
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bool validateConservation() const;
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void generateStoichiometryMatrix();
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void pruneNetworkGraph();
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};
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};
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@@ -33,11 +33,13 @@ namespace serif::network {
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enum NetworkFormat {
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APPROX8, ///< Approx8 nuclear reaction network format.
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REACLIB, ///< General REACLIB nuclear reaction network format.
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UNKNOWN,
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};
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static inline std::unordered_map<NetworkFormat, std::string> FormatStringLookup = {
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{APPROX8, "Approx8"},
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{REACLIB, "REACLIB"},
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{UNKNOWN, "Unknown"}
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};
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