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reaclib.cpp
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#include "fourdst/composition/atomicSpecies.h"
#include "fourdst/composition/species.h"
#include "gridfire/reaction/reaclib.h"
#include "gridfire/reaction/reactions_data.h"
#include "gridfire/network.h"
#include <stdexcept>
#include <sstream>
#include <vector>
#include <string>
std::string trim_whitespace(const std::string& str) {
auto startIt = str.begin();
const auto endIt = str.end();
while (startIt != endIt && std::isspace(static_cast<unsigned char>(*startIt))) {
++startIt;
}
if (startIt == endIt) {
return "";
}
const auto ritr = std::find_if(str.rbegin(), std::string::const_reverse_iterator(startIt),
[](const unsigned char ch){ return !std::isspace(ch); });
return std::string(startIt, ritr.base());
}
namespace gridfire::reaclib {
static reaction::LogicalReactionSet* s_all_reaclib_reactions_ptr = nullptr;
#pragma pack(push, 1)
struct ReactionRecord {
int32_t chapter;
double qValue;
double coeffs[7];
bool reverse;
char label[8];
char rpName[64];
char reactants_str[128];
char products_str[128];
};
#pragma pack(pop)
std::ostream& operator<<(std::ostream& os, const ReactionRecord& r) {
os << "Chapter: " << r.chapter
<< ", Q-value: " << r.qValue
<< ", Coefficients: [" << r.coeffs[0] << ", " << r.coeffs[1] << ", "
<< r.coeffs[2] << ", " << r.coeffs[3] << ", " << r.coeffs[4] << ", "
<< r.coeffs[5] << ", " << r.coeffs[6] << "]"
<< ", Reverse: " << (r.reverse ? "true" : "false")
<< ", Label: '" << std::string(r.label, strnlen(r.label, sizeof(r.label))) << "'"
<< ", RP Name: '" << std::string(r.rpName, strnlen(r.rpName, sizeof(r.rpName))) << "'"
<< ", Reactants: '" << std::string(r.reactants_str, strnlen(r.reactants_str, sizeof(r.reactants_str))) << "'"
<< ", Products: '" << std::string(r.products_str, strnlen(r.products_str, sizeof(r.products_str))) << "'";
return os;
}
static std::vector<fourdst::atomic::Species> parseSpeciesString(const std::string_view str) {
std::vector<fourdst::atomic::Species> result;
std::stringstream ss{std::string(str)};
std::string name;
while (ss >> name) {
// Trim whitespace that might be left over from the fixed-width char arrays
const auto trimmed_name = trim_whitespace(name);
if (trimmed_name.empty()) continue;
auto it = fourdst::atomic::species.find(trimmed_name);
if (it != fourdst::atomic::species.end()) {
result.push_back(it->second);
} else {
// If a species is not found, it's a critical data error.
throw std::runtime_error("Unknown species in reaction data: " + std::string(trimmed_name));
}
}
return result;
}
static void initializeAllReaclibReactions() {
if (s_initialized) {
return;
}
// Cast the raw byte data to our structured record format.
const auto* records = reinterpret_cast<const ReactionRecord*>(raw_reactions_data);
constexpr size_t num_reactions = raw_reactions_data_len / sizeof(ReactionRecord);
std::vector<reaction::Reaction> reaction_list;
reaction_list.reserve(num_reactions);
for (size_t i = 0; i < num_reactions; ++i) {
const auto&[chapter, qValue, coeffs, reverse, label, rpName, reactants_str, products_str] = records[i];
// The char arrays from the binary are not guaranteed to be null-terminated
// if the string fills the entire buffer. We create null-terminated string_views.
const std::string_view label_sv(label, strnlen(label, sizeof(label)));
const std::string_view rpName_sv(rpName, strnlen(rpName, sizeof(rpName)));
const std::string_view reactants_sv(reactants_str, strnlen(reactants_str, sizeof(reactants_str)));
const std::string_view products_sv(products_str, strnlen(products_str, sizeof(products_str)));
auto reactants = parseSpeciesString(reactants_sv);
auto products = parseSpeciesString(products_sv);
const reaction::RateCoefficientSet rate_coeffs = {
coeffs[0], coeffs[1], coeffs[2],
coeffs[3], coeffs[4], coeffs[5],
coeffs[6]
};
// Construct the Reaction object. We use rpName for both the unique ID and the human-readable name.
reaction_list.emplace_back(
rpName_sv,
rpName_sv,
chapter,
reactants,
products,
qValue,
label_sv,
rate_coeffs,
reverse
);
}
// The ReactionSet takes the vector of all individual reactions.
const reaction::ReactionSet reaction_set(std::move(reaction_list));
// The LogicalReactionSet groups reactions by their peName, which is what we want.
s_all_reaclib_reactions_ptr = new reaction::LogicalReactionSet(
reaction::packReactionSetToLogicalReactionSet(reaction_set)
);
s_initialized = true;
}
// --- Public Interface Implementation ---
const reaction::LogicalReactionSet& get_all_reactions() {
// This ensures that the initialization happens only on the first call.
if (!s_initialized) {
initializeAllReaclibReactions();
}
if (s_all_reaclib_reactions_ptr == nullptr) {
throw std::runtime_error("Reaclib reactions have not been initialized.");
}
return *s_all_reaclib_reactions_ptr;
}
} // namespace gridfire::reaclib
gridfire::reaclib
Definition reaclib.h:5
gridfire::reaclib::initializeAllReaclibReactions
static void initializeAllReaclibReactions()
Definition reaclib.cpp:79
gridfire::reaclib::s_all_reaclib_reactions_ptr
static reaction::LogicalReactionSet * s_all_reaclib_reactions_ptr
Definition reaclib.cpp:29
gridfire::reaclib::operator<<
std::ostream & operator<<(std::ostream &os, const ReactionRecord &r)
Definition reaclib.cpp:44
gridfire::reaclib::get_all_reactions
const reaction::LogicalReactionSet & get_all_reactions()
Provides global access to the fully initialized REACLIB reaction set.
Definition reaclib.cpp:138
gridfire::reaclib::s_initialized
static bool s_initialized
Definition reaclib.h:7
gridfire::reaclib::parseSpeciesString
static std::vector< fourdst::atomic::Species > parseSpeciesString(const std::string_view str)
Definition reaclib.cpp:58
gridfire::reaction::LogicalReactionSet
TemplatedReactionSet< LogicalReaction > LogicalReactionSet
A set of logical reactions.
Definition reaction.h:563
gridfire::reaction::packReactionSetToLogicalReactionSet
LogicalReactionSet packReactionSetToLogicalReactionSet(const ReactionSet &reactionSet)
Definition reaction.cpp:273
gridfire::reaction::ReactionSet
TemplatedReactionSet< Reaction > ReactionSet
A set of reactions, typically from a single source like REACLIB.
Definition reaction.h:562
gridfire::trim_whitespace
std::string trim_whitespace(const std::string &str)
Definition network.cpp:65
network.h
trim_whitespace
std::string trim_whitespace(const std::string &str)
Definition reaclib.cpp:13
reaclib.h
reactions_data.h
raw_reactions_data_len
const size_t raw_reactions_data_len
Definition reactions_data.h:181934
raw_reactions_data
const unsigned char raw_reactions_data[]
Definition reactions_data.h:5
gridfire::reaclib::ReactionRecord
Definition reaclib.cpp:32
gridfire::reaclib::ReactionRecord::label
char label[8]
Definition reaclib.cpp:37
gridfire::reaclib::ReactionRecord::rpName
char rpName[64]
Definition reaclib.cpp:38
gridfire::reaclib::ReactionRecord::chapter
int32_t chapter
Definition reaclib.cpp:33
gridfire::reaclib::ReactionRecord::reactants_str
char reactants_str[128]
Definition reaclib.cpp:39
gridfire::reaclib::ReactionRecord::coeffs
double coeffs[7]
Definition reaclib.cpp:35
gridfire::reaclib::ReactionRecord::reverse
bool reverse
Definition reaclib.cpp:36
gridfire::reaclib::ReactionRecord::qValue
double qValue
Definition reaclib.cpp:34
gridfire::reaclib::ReactionRecord::products_str
char products_str[128]
Definition reaclib.cpp:40
gridfire::reaction::RateCoefficientSet
Holds the seven coefficients for the REACLIB rate equation.
Definition reaction.h:33