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feat(solver): added CVODE solver from SUNDIALS

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This commit is contained in:
Emily Boudreaux
2025-08-15 12:11:32 -04:00
parent 0b77f2e269
commit ed1c5a1ac7
16 changed files with 588 additions and 62 deletions
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1
.gitignore vendored
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@@ -78,6 +78,7 @@ subprojects/eigen-*/
subprojects/fourdst/
subprojects/libplugin/
subprojects/minizip-ng-4.0.10/
subprojects/cvode-*/
*.fbundle
*.csv

47
build-config/cvode/meson.build Normal file
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@@ -0,0 +1,47 @@
cmake = import('cmake')
cvode_cmake_options = cmake.subproject_options()
cvode_cmake_options.add_cmake_defines({
'CMAKE_CXX_FLAGS' : '-Wno-deprecated-declarations',
'CMAKE_C_FLAGS' : '-Wno-deprecated-declarations',
'BUILD_SHARED_LIBS' : 'ON',
'BUILD_STATIC_LIBS' : 'OFF',
})
cvode_cmake_options.add_cmake_defines({
'CMAKE_INSTALL_LIBDIR': get_option('libdir'),
'CMAKE_INSTALL_INCLUDEDIR': get_option('includedir')
})
cvode_sp = cmake.subproject(
'cvode',
options: cvode_cmake_options,
)
# For the core SUNDIALS library (SUNContext, etc.)
sundials_core_dep = cvode_sp.dependency('sundials_core_shared')
# For the CVODE integrator library
sundials_cvode_dep = cvode_sp.dependency('sundials_cvode_shared')
# For the serial NVector library
sundials_nvecserial_dep = cvode_sp.dependency('sundials_nvecserial_shared')
# For the dense matrix library
sundials_sunmatrixdense_dep = cvode_sp.dependency('sundials_sunmatrixdense_shared')
# For the dense linear solver library
sundials_sunlinsoldense_dep = cvode_sp.dependency('sundials_sunlinsoldense_shared')
sundials_dep = declare_dependency(
dependencies: [
sundials_core_dep,
sundials_cvode_dep,
sundials_nvecserial_dep,
sundials_sunmatrixdense_dep,
sundials_sunlinsoldense_dep,
],
)

2
build-config/meson.build
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@@ -3,6 +3,8 @@ cmake = import('cmake')
subdir('fourdst')
subdir('libplugin')
subdir('cvode')
subdir('boost')
subdir('cppad')
subdir('xxHash')

8
meson.build
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@@ -45,20 +45,28 @@ llevel = get_option('log_level')
logbase='QUILL_COMPILE_ACTIVE_LOG_LEVEL_'
if (llevel == 'traceL3')
message('Setting log level to TRACE_L3')
log_argument = logbase + 'TRACE_L3'
elif (llevel == 'traceL2')
message('Setting log level to TRACE_L2')
log_argument = logbase + 'TRACE_L2'
elif (llevel == 'traceL1')
message('Setting log level to TRACE_L1')
log_argument = logbase + 'TRACE_L1'
elif (llevel == 'debug')
message('Setting log level to DEBUG')
log_argument = logbase + 'DEBUG'
elif (llevel == 'info')
message('Setting log level to INFO')
log_argument = logbase + 'INFO'
elif (llevel == 'warning')
message('Setting log level to WARNING')
log_argument = logbase + 'WARNING'
elif (llevel == 'error')
message('Setting log level to ERROR')
log_argument = logbase + 'ERROR'
elif (llevel == 'critical')
message('Setting log level to CRITICAL')
log_argument = logbase + 'CRITICAL'
endif

4
src/include/gridfire/screening/screening_weak.h
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@@ -187,13 +187,13 @@ namespace gridfire::screening {
reactants[1] == reactants[2]
);
if (reactants.size() == 2) {
LOG_TRACE_L3(m_logger, "Calculating screening factor for reaction: {}", reaction.peName());
LOG_TRACE_L3(m_logger, "Calculating screening factor for reaction: {}", reaction->id());
const T Z1 = static_cast<T>(reactants[0].m_z);
const T Z2 = static_cast<T>(reactants[1].m_z);
H_12 = prefactor * Z1 * Z2;
}
else if (isTripleAlpha) {
LOG_TRACE_L3(m_logger, "Special case for triple alpha process in reaction: {}", reaction.peName());
LOG_TRACE_L3(m_logger, "Special case for triple alpha process in reaction: {}", reaction->id());
// Special case for triple alpha process
const T Z_alpha = static_cast<T>(2.0);
const T H_alpha_alpha = prefactor * Z_alpha * Z_alpha;

136
src/include/gridfire/solver/strategies/CVODE_solver_strategy.h Normal file
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@@ -0,0 +1,136 @@
#pragma once
#include "gridfire/solver/solver.h"
#include "gridfire/engine/engine_abstract.h"
#include "gridfire/network.h"
#include "gridfire/exceptions/exceptions.h"
#include "fourdst/composition/atomicSpecies.h"
#include "fourdst/config/config.h"
#include <functional>
#include <any>
#include <string>
#include <vector>
#include <tuple>
// SUNDIALS/CVODE headers
#include <cvode/cvode.h>
#include <sundials/sundials_types.h>
// Include headers for linear solvers and N_Vectors
// We will use preprocessor directives to select the correct ones
#include <cvode/cvode.h> // For CVDls (serial dense linear solver)
#include <sundials/sundials_context.h>
#include <sunmatrix/sunmatrix_dense.h>
#include <sunlinsol/sunlinsol_dense.h>
#ifdef SUNDIALS_HAVE_OPENMP
#include <nvector/nvector_openmp.h>
#endif
#ifdef SUNDIALS_HAVE_PTHREADS
#include <nvector/nvector_pthreads.hh>
#endif
// Default to serial if no parallelism is enabled
#ifndef SUNDIALS_HAVE_OPENMP
#ifndef SUNDIALS_HAVE_PTHREADS
#include <nvector/nvector_serial.h>
#endif
#endif
namespace gridfire::solver {
class CVODESolverStrategy final : public DynamicNetworkSolverStrategy {
public:
explicit CVODESolverStrategy(DynamicEngine& engine);
~CVODESolverStrategy() override;
// Make the class non-copyable and non-movable to prevent shallow copies of CVODE pointers
CVODESolverStrategy(const CVODESolverStrategy&) = delete;
CVODESolverStrategy& operator=(const CVODESolverStrategy&) = delete;
CVODESolverStrategy(CVODESolverStrategy&&) = delete;
CVODESolverStrategy& operator=(CVODESolverStrategy&&) = delete;
NetOut evaluate(const NetIn& netIn) override;
void set_callback(const std::any &callback) override;
bool get_stdout_logging_enabled() const;
void set_stdout_logging_enabled(const bool value);
[[nodiscard]] std::vector<std::tuple<std::string, std::string>> describe_callback_context() const override;
struct TimestepContext final : public SolverContextBase {
// This struct can be identical to the one in DirectNetworkSolver
const double t;
const N_Vector& state; // Note: state is now an N_Vector
const double dt;
const double last_step_time;
const double T9;
const double rho;
const int num_steps;
const DynamicEngine& engine;
const std::vector<fourdst::atomic::Species>& networkSpecies;
// Constructor
TimestepContext(
double t, const N_Vector& state, double dt, double last_step_time,
double t9, double rho, int num_steps, const DynamicEngine& engine,
const std::vector<fourdst::atomic::Species>& networkSpecies
);
[[nodiscard]] std::vector<std::tuple<std::string, std::string>> describe() const override;
};
using TimestepCallback = std::function<void(const TimestepContext& context)>; ///< Type alias for a timestep callback function.
private:
/**
* @struct CVODEUserData
* @brief A helper struct to pass C++ context to C-style CVODE callbacks.
*
* CVODE callbacks are C functions and use a void* pointer to pass user data.
* This struct bundles all the necessary C++ objects (like 'this', engine references, etc.)
* to be accessed safely within those static C wrappers.
*/
struct CVODEUserData {
CVODESolverStrategy* solver_instance; // Pointer back to the class instance
DynamicEngine* engine;
double T9;
double rho;
const std::vector<fourdst::atomic::Species>* networkSpecies;
std::unique_ptr<exceptions::StaleEngineTrigger> captured_exception = nullptr;
};
private:
Config& m_config = Config::getInstance();
static int cvode_rhs_wrapper(sunrealtype t, N_Vector y, N_Vector ydot, void *user_data);
static int cvode_jac_wrapper(sunrealtype t, N_Vector y, N_Vector ydot, SUNMatrix J, void *user_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3);
int calculate_rhs(sunrealtype t, N_Vector y, N_Vector ydot, const CVODEUserData* data) const;
void initialize_cvode_integration_resources(
uint64_t N,
size_t numSpecies,
double current_time,
const fourdst::composition::Composition& composition,
double absTol,
double relTol,
double accumulatedEnergy
);
void cleanup_cvode_resources(bool memFree);
private:
SUNContext m_sun_ctx = nullptr;
void* m_cvode_mem = nullptr;
N_Vector m_Y = nullptr;
SUNMatrix m_J = nullptr;
SUNLinearSolver m_LS = nullptr;
TimestepCallback m_callback;
int m_num_steps = 0;
bool m_stdout_logging_enabled = true;
};
}

4
src/lib/engine/procedures/construction.cpp
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@@ -48,7 +48,7 @@ namespace gridfire {
if (depth == static_cast<int>(NetworkBuildDepth::Full)) {
LOG_INFO(logger, "Building full nuclear network with a total of {} reactions.", allReactions.size());
const ReactionSet reactionSet(remainingReactions);
return reaction::packReactionSet(reactionSet);
return reactionSet;
}
std::unordered_set<Species> availableSpecies;
@@ -104,7 +104,7 @@ namespace gridfire {
LOG_INFO(logger, "Network construction completed with {} reactions collected.", collectedReactions.size());
const ReactionSet reactionSet(collectedReactions);
return reaction::packReactionSet(reactionSet);
return reactionSet;
}
}

6
src/lib/engine/procedures/priming.cpp
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@@ -116,7 +116,7 @@ namespace gridfire {
LOG_TRACE_L3(logger, "Found equilibrium for {}: X_eq = {:.4e}", primingSpecies.name(), equilibriumMassFraction);
if (const reaction::Reaction* dominantChannel = findDominantCreationChannel(primer, primingSpecies, Y, T9, rho)) {
LOG_TRACE_L3(logger, "Dominant creation channel for {}: {}", primingSpecies.name(), dominantChannel->peName());
LOG_TRACE_L3(logger, "Dominant creation channel for {}: {}", primingSpecies.name(), dominantChannel->id());
double totalReactantMass = 0.0;
for (const auto& reactant : dominantChannel->reactants()) {
@@ -209,7 +209,7 @@ namespace gridfire {
double calculateCreationRate(
const DynamicEngine& engine,
const fourdst::atomic::Species& species,
const Species& species,
const std::vector<double>& Y,
const double T9,
const double rho
@@ -218,6 +218,8 @@ namespace gridfire {
for (const auto& reaction: engine.getNetworkReactions()) {
const int stoichiometry = reaction->stoichiometry(species);
if (stoichiometry > 0) {
if (engine.calculateMolarReactionFlow(*reaction, Y, T9, rho) > 0.0) {
}
creationRate += stoichiometry * engine.calculateMolarReactionFlow(*reaction, Y, T9, rho);
}
}

4
src/lib/engine/views/engine_adaptive.cpp
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@@ -385,7 +385,7 @@ namespace gridfire {
for (const auto& reaction : fullReactionSet) {
const double flow = m_baseEngine.calculateMolarReactionFlow(*reaction, out_Y_Full, T9, rho);
reactionFlows.push_back({reaction.get(), flow});
LOG_TRACE_L1(m_logger, "Reaction '{}' has flow rate: {:0.3E} [mol/s/g]", reaction.id(), flow);
LOG_TRACE_L1(m_logger, "Reaction '{}' has flow rate: {:0.3E} [mol/s/g]", reaction->id(), flow);
}
return reactionFlows;
}
@@ -423,7 +423,7 @@ namespace gridfire {
if (!reachable.contains(product)) {
reachable.insert(product);
new_species_found_in_pass = true;
LOG_TRACE_L2(m_logger, "Network Connectivity Analysis: Species '{}' is reachable via reaction '{}'.", product.name(), reaction.id());
LOG_TRACE_L2(m_logger, "Network Connectivity Analysis: Species '{}' is reachable via reaction '{}'.", product.name(), reaction->id());
}
}
}

2
src/lib/engine/views/engine_defined.cpp
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@@ -358,7 +358,7 @@ namespace gridfire {
LOG_TRACE_L3(m_logger, "Active reactions: {}", [this]() -> std::string {
std::string result;
for (const auto& reaction : m_activeReactions) {
result += std::string(reaction.id()) + ", ";
result += std::string(reaction->id()) + ", ";
}
if (!result.empty()) {
result.pop_back(); // Remove last space

8
src/lib/engine/views/engine_multiscale.cpp
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@@ -1020,7 +1020,7 @@ namespace gridfire {
LOG_TRACE_L3(
m_logger,
"Reaction {} is internal to the group containing {} and contributes to internal flux by {}",
reaction.id(),
reaction->id(),
[&]() -> std::string {
std::stringstream ss;
int count = 0;
@@ -1040,7 +1040,7 @@ namespace gridfire {
LOG_TRACE_L3(
m_logger,
"Reaction {} is external to the group containing {} and contributes to external flux by {}",
reaction.id(),
reaction->id(),
[&]() -> std::string {
std::stringstream ss;
int count = 0;
@@ -1406,13 +1406,13 @@ namespace gridfire {
for (const auto& reactant : reaction->reactants()) {
if (std::ranges::find(pool, m_baseEngine.getSpeciesIndex(reactant)) == pool.end()) {
has_external_reactant = true;
LOG_TRACE_L3(m_logger, "Found external reactant {} in reaction {} for species {}.", reactant.name(), reaction.id(), ash.name());
LOG_TRACE_L3(m_logger, "Found external reactant {} in reaction {} for species {}.", reactant.name(), reaction->id(), ash.name());
break; // Found an external reactant, no need to check further
}
}
if (has_external_reactant) {
double flow = std::abs(m_baseEngine.calculateMolarReactionFlow(*reaction, Y, T9, rho));
LOG_TRACE_L3(m_logger, "Found bridge reaction {} with flow {} for species {}.", reaction.id(), flow, ash.name());
LOG_TRACE_L3(m_logger, "Found bridge reaction {} with flow {} for species {}.", reaction->id(), flow, ash.name());
bridge_reactions.emplace_back(reaction.get(), flow);
}
}

8
src/lib/reaction/reaclib.cpp
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@@ -22,11 +22,11 @@ std::string trim_whitespace(const std::string& str) {
}
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());
return {startIt, ritr.base()};
}
namespace gridfire::reaclib {
static reaction::ReactionSet* s_all_reaclib_reactions_ptr = nullptr;
static std::unique_ptr<reaction::ReactionSet> s_all_reaclib_reactions_ptr = nullptr;
#pragma pack(push, 1)
struct ReactionRecord {
@@ -125,9 +125,7 @@ namespace gridfire::reaclib {
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::ReactionSet(
reaction::packReactionSet(reaction_set)
);
s_all_reaclib_reactions_ptr = std::make_unique<reaction::ReactionSet>(reaction::packReactionSet(reaction_set));
s_initialized = true;
}

362
src/lib/solver/strategies/CVODE_solver_strategy.cpp Normal file
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@@ -0,0 +1,362 @@
#include "gridfire/solver/strategies/CVODE_solver_strategy.h"
#include "gridfire/network.h"
#include "fourdst/composition/composition.h"
// ReSharper disable once CppUnusedIncludeDirective
#include <cstdint>
#include <limits>
#include <string>
#include <unordered_map>
#include <stdexcept>
namespace {
std::unordered_map<int, std::string> cvode_ret_code_map {
{0, "CV_SUCCESS: The solver succeeded."},
{1, "CV_TSTOP_RETURN: The solver reached the specified stopping time."},
{2, "CV_ROOT_RETURN: A root was found."},
{-99, "CV_WARNING: CVODE succeeded but in an unusual manner"},
{-1, "CV_TOO_MUCH_WORK: The solver took too many internal steps."},
{-2, "CV_TOO_MUCH_ACC: The solver could not satisfy the accuracy requested."},
{-3, "CV_ERR_FAILURE: The solver encountered a non-recoverable error."},
{-4, "CV_CONV_FAILURE: The solver failed to converge."},
{-5, "CV_LINIT_FAIL: The linear solver's initialization function failed."},
{-6, "CV_LSETUP_FAIL: The linear solver's setup function failed."},
{-7, "CV_LSOLVE_FAIL: The linear solver's solve function failed."},
{-8, "CV_RHSFUNC_FAIL: The right-hand side function failed in an unrecoverable manner."},
{-9, "CV_FIRST_RHSFUNC_ERR: The right-hand side function failed at the first call."},
{-10, "CV_REPTD_RHSFUNC_ERR: The right-hand side function repeatedly failed recoverable."},
{-11, "CV_UNREC_RHSFUNC_ERR: The right-hand side function failed unrecoverably."},
{-12, "CV_RTFUNC_FAIL: The rootfinding function failed in an unrecoverable manner."},
{-13, "CV_NLS_INIT_FAIL: The nonlinear solver's initialization function failed."},
{-14, "CV_NLS_SETUP_FAIL: The nonlinear solver's setup function failed."},
{-15, "CV_CONSTR_FAIL : The inequality constraint was violated and the solver was unable to recover."},
{-16, "CV_NLS_FAIL: The nonlinear solver's solve function failed."},
{-20, "CV_MEM_FAIL: Memory allocation failed."},
{-21, "CV_MEM_NULL: The CVODE memory structure is NULL."},
{-22, "CV_ILL_INPUT: An illegal input was detected."},
{-23, "CV_NO_MALLOC: The CVODE memory structure has not been allocated."},
{-24, "CV_BAD_K: The value of k is invalid."},
{-25, "CV_BAD_T: The value of t is invalid."},
{-26, "CV_BAD_DKY: The value of dky is invalid."},
{-27, "CV_TOO_CLOSE: The time points are too close together."},
{-28, "CV_VECTOROP_ERR: A vector operation failed."},
{-29, "CV_PROJ_MEM_NULL: The projection memory structure is NULL."},
{-30, "CV_PROJFUNC_FAIL: The projection function failed in an unrecoverable manner."},
{-31, "CV_REPTD_PROJFUNC_ERR: THe projection function has repeated recoverable errors."}
};
void check_cvode_flag(const int flag, const std::string& func_name) {
if (flag < 0) {
if (!cvode_ret_code_map.contains(flag)) {
throw std::runtime_error("CVODE error in " + func_name + ": Unknown error code: " + std::to_string(flag));
}
throw std::runtime_error("CVODE error in " + func_name + ": " + cvode_ret_code_map.at(flag));
}
}
N_Vector init_sun_vector(uint64_t size, SUNContext sun_ctx) {
#ifdef SUNDIALS_HAVE_OPENMP
N_Vector vec = N_VNew_OpenMP(size, 0, sun_ctx);
#elif SUNDIALS_HAVE_PTHREADS
N_Vector vec = N_VNew_Pthreads(size, sun_ctx);
#else
N_Vector vec = N_VNew_Serial(size, sun_ctx);
#endif
check_cvode_flag(vec == nullptr ? -1 : 0, "N_VNew");
return vec;
}
}
namespace gridfire::solver {
CVODESolverStrategy::CVODESolverStrategy(DynamicEngine &engine): NetworkSolverStrategy<DynamicEngine>(engine) {
// TODO: In order to support MPI this function must be changed
const int flag = SUNContext_Create(SUN_COMM_NULL, &m_sun_ctx);
if (flag < 0) {
throw std::runtime_error("Failed to create SUNDIALS context (Errno: " + std::to_string(flag) + ")");
}
}
CVODESolverStrategy::~CVODESolverStrategy() {
cleanup_cvode_resources(true);
if (m_sun_ctx) {
SUNContext_Free(&m_sun_ctx);
}
}
NetOut CVODESolverStrategy::evaluate(const NetIn& netIn) {
const double T9 = netIn.temperature / 1e9; // Convert temperature from Kelvin to T9 (T9 = T / 1e9)
const auto absTol = m_config.get<double>("gridfire:solver:CVODESolverStrategy:absTol", 1.0e-8);
const auto relTol = m_config.get<double>("gridfire:solver:CVODESolverStrategy:relTol", 1.0e-8);
fourdst::composition::Composition equilibratedComposition = m_engine.update(netIn);
size_t numSpecies = m_engine.getNetworkSpecies().size();
uint64_t N = numSpecies + 1;
m_cvode_mem = CVodeCreate(CV_BDF, m_sun_ctx);
check_cvode_flag(m_cvode_mem == nullptr ? -1 : 0, "CVodeCreate");
initialize_cvode_integration_resources(N, numSpecies, 0.0, equilibratedComposition, absTol, relTol, 0.0);
CVODEUserData user_data;
user_data.solver_instance = this;
user_data.engine = &m_engine;
double current_time = 0;
[[maybe_unused]] double last_callback_time = 0;
m_num_steps = 0;
double accumulated_energy = 0.0;
while (current_time < netIn.tMax) {
try {
user_data.T9 = T9;
user_data.rho = netIn.density;
user_data.networkSpecies = &m_engine.getNetworkSpecies();
user_data.captured_exception.reset();
check_cvode_flag(CVodeSetUserData(m_cvode_mem, &user_data), "CVodeSetUserData");
int flag = -1;
if (m_stdout_logging_enabled) {
flag = CVode(m_cvode_mem, netIn.tMax, m_Y, &current_time, CV_ONE_STEP);
} else {
flag = CVode(m_cvode_mem, netIn.tMax, m_Y, &current_time, CV_NORMAL);
}
if (user_data.captured_exception){
std::rethrow_exception(std::make_exception_ptr(*user_data.captured_exception));
}
check_cvode_flag(flag, "CVode");
long int n_steps;
double last_step_size;
CVodeGetNumSteps(m_cvode_mem, &n_steps);
CVodeGetLastStep(m_cvode_mem, &last_step_size);
std::cout << std::scientific << std::setprecision(3) << "Step: " << std::setw(6) << n_steps << " | Time: " << current_time << " | Last Step Size: " << last_step_size << std::endl;
} catch (const exceptions::StaleEngineTrigger& e) {
exceptions::StaleEngineTrigger::state staleState = e.getState();
accumulated_energy += e.energy(); // Add the specific energy rate to the accumulated energy
// total_update_stages_triggered++;
fourdst::composition::Composition temp_comp;
std::vector<double> mass_fractions;
size_t num_species_at_stop = e.numSpecies();
if (num_species_at_stop != m_engine.getNetworkSpecies().size()) {
throw std::runtime_error(
"StaleEngineError state has a different number of species than the engine. This should not happen."
);
}
mass_fractions.reserve(num_species_at_stop);
for (size_t i = 0; i < num_species_at_stop; ++i) {
const auto& species = m_engine.getNetworkSpecies()[i];
temp_comp.registerSpecies(species);
mass_fractions.push_back(e.getMolarAbundance(i) * species.mass()); // Convert from molar abundance to mass fraction
}
temp_comp.setMassFraction(m_engine.getNetworkSpecies(), mass_fractions);
temp_comp.finalize(true);
NetIn netInTemp = netIn;
netInTemp.temperature = e.temperature();
netInTemp.density = e.density();
netInTemp.composition = temp_comp;
fourdst::composition::Composition currentComposition = m_engine.update(netInTemp);
numSpecies = m_engine.getNetworkSpecies().size();
N = numSpecies + 1;
initialize_cvode_integration_resources(N, numSpecies, current_time, temp_comp, absTol, relTol, accumulated_energy);
check_cvode_flag(CVodeReInit(m_cvode_mem, current_time, m_Y), "CVodeReInit");
}
}
sunrealtype* y_data = N_VGetArrayPointer(m_Y);
accumulated_energy += y_data[numSpecies];
std::vector<double> finalMassFractions(numSpecies);
for (size_t i = 0; i < numSpecies; ++i) {
const double molarMass = m_engine.getNetworkSpecies()[i].mass();
finalMassFractions[i] = y_data[i] * molarMass; // Convert from molar abundance to mass fraction
if (finalMassFractions[i] < MIN_ABUNDANCE_THRESHOLD) {
finalMassFractions[i] = 0.0;
}
}
std::vector<std::string> speciesNames;
speciesNames.reserve(numSpecies);
for (const auto& species : m_engine.getNetworkSpecies()) {
speciesNames.push_back(std::string(species.name()));
}
fourdst::composition::Composition outputComposition(speciesNames);
outputComposition.setMassFraction(speciesNames, finalMassFractions);
outputComposition.finalize(true);
NetOut netOut;
netOut.composition = std::move(outputComposition);
netOut.energy = accumulated_energy;
check_cvode_flag(CVodeGetNumSteps(m_cvode_mem, reinterpret_cast<long int *>(&netOut.num_steps)), "CVodeGetNumSteps");
return netOut;
}
void CVODESolverStrategy::set_callback(const std::any &callback) {
m_callback = std::any_cast<TimestepCallback>(callback);
}
bool CVODESolverStrategy::get_stdout_logging_enabled() const {
return m_stdout_logging_enabled;
}
void CVODESolverStrategy::set_stdout_logging_enabled(const bool value) {
m_stdout_logging_enabled = value;
}
std::vector<std::tuple<std::string, std::string>> CVODESolverStrategy::describe_callback_context() const {
return {};
}
int CVODESolverStrategy::cvode_rhs_wrapper(
sunrealtype t,
N_Vector y,
N_Vector ydot,
void *user_data
) {
auto* data = static_cast<CVODEUserData*>(user_data);
auto* instance = data->solver_instance;
try {
return instance->calculate_rhs(t, y, ydot, data);
} catch (const exceptions::StaleEngineTrigger& e) {
data->captured_exception = std::make_unique<exceptions::StaleEngineTrigger>(e);
return 1; // 1 Indicates a recoverable error, CVODE will retry the step
} catch (...) {
return -1; // Some unrecoverable error
}
}
int CVODESolverStrategy::cvode_jac_wrapper(
sunrealtype t,
N_Vector y,
N_Vector ydot,
SUNMatrix J,
void *user_data,
N_Vector tmp1,
N_Vector tmp2,
N_Vector tmp3
) {
const auto* data = static_cast<CVODEUserData*>(user_data);
const auto* engine = data->engine;
const size_t numSpecies = engine->getNetworkSpecies().size();
sunrealtype* J_data = SUNDenseMatrix_Data(J);
const long int N = SUNDenseMatrix_Columns(J);
for (size_t j = 0; j < numSpecies; ++j) {
for (size_t i = 0; i < numSpecies; ++i) {
// J(i,j) = d(f_i)/d(y_j)
// Column-major order format for SUNDenseMatrix: J_data[j*N + i]
J_data[j * N + i] = engine->getJacobianMatrixEntry(i, j);
}
}
// For now assume that the energy derivatives wrt. abundances are zero
for (size_t i = 0; i < N; ++i) {
J_data[(N - 1) * N + i] = 0.0; // df(energy_dot)/df(y_i)
J_data[i * N + (N - 1)] = 0.0; // df(f_i)/df(energy_dot)
}
return 0;
}
int CVODESolverStrategy::calculate_rhs(
const sunrealtype t,
const N_Vector y,
const N_Vector ydot,
const CVODEUserData *data
) const {
const size_t numSpecies = m_engine.getNetworkSpecies().size();
sunrealtype* y_data = N_VGetArrayPointer(y);
std::vector<double> y_vec(y_data, y_data + numSpecies);
std::ranges::replace_if(y_vec, [](const double val) { return val < 0.0; }, 0.0);
const auto result = m_engine.calculateRHSAndEnergy(y_vec, data->T9, data->rho);
if (!result) {
throw exceptions::StaleEngineTrigger({data->T9, data->rho, y_vec, t, m_num_steps, y_data[numSpecies]});
}
sunrealtype* ydot_data = N_VGetArrayPointer(ydot);
const auto& [dydt, nuclearEnergyGenerationRate] = result.value();
for (size_t i = 0; i < numSpecies; ++i) {
ydot_data[i] = dydt[i];
}
ydot_data[numSpecies] = nuclearEnergyGenerationRate; // Set the last element to the specific energy rate
return 0;
}
void CVODESolverStrategy::initialize_cvode_integration_resources(
const uint64_t N,
const size_t numSpecies,
const double current_time,
const fourdst::composition::Composition &composition,
const double absTol,
const double relTol,
const double accumulatedEnergy
) {
cleanup_cvode_resources(false); // Cleanup any existing resources before initializing new ones
m_Y = init_sun_vector(N, m_sun_ctx);
sunrealtype *y_data = N_VGetArrayPointer(m_Y);
for (size_t i = 0; i < numSpecies; i++) {
const auto& species = m_engine.getNetworkSpecies()[i];
if (composition.contains(species)) {
y_data[i] = composition.getMolarAbundance(species);
} else {
y_data[i] = std::numeric_limits<double>::min(); // Species not in the composition, set to a small value
}
}
y_data[numSpecies] = accumulatedEnergy; // Specific energy rate, initialized to zero
check_cvode_flag(CVodeInit(m_cvode_mem, cvode_rhs_wrapper, current_time, m_Y), "CVodeInit");
check_cvode_flag(CVodeSStolerances(m_cvode_mem, relTol, absTol), "CVodeSStolerances");
m_J = SUNDenseMatrix(static_cast<sunindextype>(N), static_cast<sunindextype>(N), m_sun_ctx);
check_cvode_flag(m_J == nullptr ? -1 : 0, "SUNDenseMatrix");
m_LS = SUNLinSol_Dense(m_Y, m_J, m_sun_ctx);
check_cvode_flag(m_LS == nullptr ? -1 : 0, "SUNLinSol_Dense");
check_cvode_flag(CVodeSetLinearSolver(m_cvode_mem, m_LS, m_J), "CVodeSetLinearSolver");
check_cvode_flag(CVodeSetJacFn(m_cvode_mem, cvode_jac_wrapper), "CVodeSetJacFn");
}
void CVODESolverStrategy::cleanup_cvode_resources(const bool memFree) {
if (m_LS) SUNLinSolFree(m_LS);
if (m_J) SUNMatDestroy(m_J);
if (m_Y) N_VDestroy(m_Y);
m_LS = nullptr;
m_J = nullptr;
m_Y = nullptr;
if (memFree) {
if (m_cvode_mem) CVodeFree(&m_cvode_mem);
m_cvode_mem = nullptr;
}
}
}

37
src/meson.build
View File

@@ -13,6 +13,7 @@ gridfire_sources = files(
'lib/reaction/reaclib.cpp',
'lib/io/network_file.cpp',
'lib/solver/solver.cpp',
'lib/solver/strategies/CVODE_solver_strategy.cpp',
'lib/screening/screening_types.cpp',
'lib/screening/screening_weak.cpp',
'lib/screening/screening_bare.cpp',
@@ -33,6 +34,7 @@ gridfire_build_dependencies = [
xxhash_dep,
eigen_dep,
plugin_dep,
sundials_dep,
]
# Define the libnetwork library so it can be linked against by other parts of the build system
@@ -49,39 +51,6 @@ gridfire_dep = declare_dependency(
dependencies: gridfire_build_dependencies,
)
# Make headers accessible
gridfire_headers = files(
'include/gridfire/network.h',
'include/gridfire/engine/engine_abstract.h',
'include/gridfire/engine/views/engine_view_abstract.h',
'include/gridfire/engine/engine_approx8.h',
'include/gridfire/engine/engine_graph.h',
'include/gridfire/engine/views/engine_adaptive.h',
'include/gridfire/engine/views/engine_defined.h',
'include/gridfire/engine/views/engine_multiscale.h',
'include/gridfire/engine/views/engine_priming.h',
'include/gridfire/engine/procedures/priming.h',
'include/gridfire/engine/procedures/construction.h',
'include/gridfire/reaction/reaction.h',
'include/gridfire/reaction/reaclib.h',
'include/gridfire/io/network_file.h',
'include/gridfire/solver/solver.h',
'include/gridfire/screening/screening_abstract.h',
'include/gridfire/screening/screening_bare.h',
'include/gridfire/screening/screening_weak.h',
'include/gridfire/screening/screening_types.h',
'include/gridfire/partition/partition_abstract.h',
'include/gridfire/partition/partition_rauscher_thielemann.h',
'include/gridfire/partition/partition_ground.h',
'include/gridfire/partition/composite/partition_composite.h',
'include/gridfire/utils/logging.h',
)
install_headers(gridfire_headers, subdir : 'gridfire')
solver_interface_headers = files(
'include/gridfire/interfaces/solver/solver_interfaces.h',
)
install_headers(solver_interface_headers, subdir : 'gridfire/interfaces/solver')
install_subdir('include/gridfire', install_dir: get_option('includedir'))
subdir('python')

6
subprojects/cvode.wrap Normal file
View File

@@ -0,0 +1,6 @@
[wrap-file]
directory = cvode-7.3.0
source_url = https://github.com/LLNL/sundials/releases/download/v7.3.0/cvode-7.3.0.tar.gz
source_filename = cvode-7.3.0.tar.gz
source_hash = 8b15a646882f2414b1915cad4d53136717a077539e7cfc480f2002c5898ae568

15
tests/graphnet_sandbox/main.cpp
View File

@@ -11,6 +11,7 @@
#include "gridfire/io/network_file.h"
#include "gridfire/solver/solver.h"
#include "gridfire/solver/strategies/CVODE_solver_strategy.h"
#include "gridfire/network.h"
@@ -42,8 +43,6 @@ void callback(const gridfire::solver::DirectNetworkSolver::TimestepContext& ctx)
std::cout << "Time: " << ctx.t << ", H-1: " << ctx.state(H1Index) << ", He-4: " << ctx.state(He4Index) << "\n";
size_t i = 0;
}
void measure_execution_time(const std::function<void()>& callback, const std::string& name)
@@ -100,8 +99,8 @@ int main(int argc, char* argv[]){
g_previousHandler = std::set_terminate(quill_terminate_handler);
quill::Logger* logger = fourdst::logging::LogManager::getInstance().getLogger("log");
logger->set_log_level(quill::LogLevel::Info);
LOG_DEBUG(logger, "Starting Adaptive Engine View Example...");
logger->set_log_level(quill::LogLevel::TraceL1);
LOG_INFO(logger, "Starting Adaptive Engine View Example...");
using namespace gridfire;
const std::vector<double> comp = {0.708, 2.94e-5, 0.276, 0.003, 0.0011, 9.62e-3, 1.62e-3, 5.16e-4};
@@ -129,14 +128,10 @@ int main(int argc, char* argv[]){
GraphEngine ReaclibEngine(composition, partitionFunction, NetworkBuildDepth::SecondOrder);
ReaclibEngine.setUseReverseReactions(false);
// ReaclibEngine.setScreeningModel(screening::ScreeningType::WEAK);
//
MultiscalePartitioningEngineView partitioningView(ReaclibEngine);
AdaptiveEngineView adaptiveView(partitioningView);
//
solver::DirectNetworkSolver solver(adaptiveView);
// consumptionFile << "t,X,a,b,c\n";
solver.set_callback(callback);
solver::CVODESolverStrategy solver(adaptiveView);
NetOut netOut;