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solver.cpp
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#include "amici/solver.h"
#include "amici/exception.h"
#include "amici/misc.h"
#include "amici/model.h"
#include "amici/rdata.h"
#include <cstdio>
#include <cstring>
#include <ctime>
#include <memory>
namespace amici {
Solver::Solver(AmiciApplication *app) : app(app)
{
}
Solver::Solver(const Solver &other)
: ism_(other.ism_), lmm_(other.lmm_), iter_(other.iter_),
interp_type_(other.interp_type_), maxsteps_(other.maxsteps_),
maxtime_(other.maxtime_), starttime_(other.starttime_),
sensi_meth_(other.sensi_meth_), sensi_meth_preeq_(other.sensi_meth_preeq_),
stldet_(other.stldet_), ordering_(other.ordering_),
newton_maxsteps_(other.newton_maxsteps_),
newton_damping_factor_mode_(other.newton_damping_factor_mode_),
newton_damping_factor_lower_bound_(other.newton_damping_factor_lower_bound_),
linsol_(other.linsol_), atol_(other.atol_), rtol_(other.rtol_),
atol_fsa_(other.atol_fsa_), rtol_fsa_(other.rtol_fsa_),
atolB_(other.atolB_), rtolB_(other.rtolB_), quad_atol_(other.quad_atol_),
quad_rtol_(other.quad_rtol_), ss_atol_(other.ss_atol_),
ss_rtol_(other.ss_rtol_), ss_atol_sensi_(other.ss_atol_sensi_),
ss_rtol_sensi_(other.ss_rtol_sensi_), rdata_mode_(other.rdata_mode_),
newton_step_steadystate_conv_(other.newton_step_steadystate_conv_),
check_sensi_steadystate_conv_(other.check_sensi_steadystate_conv_),
maxstepsB_(other.maxstepsB_), sensi_(other.sensi_)
{}
void Solver::apply_max_num_steps() const {
// set remaining steps, setMaxNumSteps only applies to a single call of solve
long int cursteps;
getNumSteps(solver_memory_.get(), &cursteps);
if (maxsteps_ <= cursteps)
throw AmiException("Reached maximum number of steps %ld before reaching "
"tout at t=%g.", maxsteps_, t_);
setMaxNumSteps(maxsteps_ - cursteps);
}
void Solver::apply_max_num_steps_B() const {
// set remaining steps, setMaxNumSteps only applies to a single call of solve
long int curstepsB;
auto maxstepsB = (maxstepsB_ == 0) ? maxsteps_ * 100 : maxstepsB_;
for (int i_mem_b = 0; i_mem_b < (int)solver_memory_B_.size(); ++i_mem_b) {
if (solver_memory_B_.at(i_mem_b)) {
getNumSteps(solver_memory_B_.at(i_mem_b).get(), &curstepsB);
if (maxstepsB <= curstepsB)
throw AmiException("Reached maximum number of steps %ld before "
"reaching tout at t=%g in backward "
"problem %i.", maxstepsB_, t_, i_mem_b);
setMaxNumStepsB(i_mem_b, maxstepsB - curstepsB);
}
}
}
int Solver::run(const realtype tout) const {
setStopTime(tout);
clock_t starttime = clock();
int status = AMICI_SUCCESS;
apply_max_num_steps();
if (nx() > 0) {
if (getAdjInitDone()) {
status = solveF(tout, AMICI_NORMAL, &ncheckPtr_);
} else {
status = solve(tout, AMICI_NORMAL);
}
} else {
t_ = tout;
}
cpu_time_ += (realtype)((clock() - starttime) * 1000) / CLOCKS_PER_SEC;
return status;
}
int Solver::step(const realtype tout) const {
int status = AMICI_SUCCESS;
apply_max_num_steps();
if (nx() > 0) {
if (getAdjInitDone()) {
status = solveF(tout, AMICI_ONE_STEP, &ncheckPtr_);
} else {
status = solve(tout, AMICI_ONE_STEP);
}
} else {
t_ = tout;
}
return status;
}
void Solver::runB(const realtype tout) const {
clock_t starttime = clock();
apply_max_num_steps_B();
if (nx() > 0) {
solveB(tout, AMICI_NORMAL);
}
cpu_timeB_ += (realtype)((clock() - starttime) * 1000) / CLOCKS_PER_SEC;
t_ = tout;
}
void Solver::setup(const realtype t0, Model *model, const AmiVector &x0,
const AmiVector &dx0, const AmiVectorArray &sx0,
const AmiVectorArray &sdx0) const {
if (nx() != model->nx_solver || nplist() != model->nplist() ||
nquad() != model->nJ * model->nplist()) {
resetMutableMemory(model->nx_solver, model->nplist(),
model->nJ * model->nplist());
}
/* Create solver memory object if necessary */
allocateSolver();
if (!solver_memory_)
throw AmiException("Failed to allocated solver memory!");
/* Initialize CVodes/IDAs solver*/
init(t0, x0, dx0);
/* Clear diagnosis storage */
resetDiagnosis();
/* Apply stored tolerances to sundials solver */
applyTolerances();
/* Set optional inputs */
setErrHandlerFn();
/* Attaches userdata */
user_data = std::make_pair(model, this);
setUserData();
/* activates stability limit detection */
setStabLimDet(stldet_);
rootInit(model->ne);
if (nx() == 0)
return;
initializeLinearSolver(model);
initializeNonLinearSolver();
if (sensi_ >= SensitivityOrder::first &&
sensi_meth_ > SensitivityMethod::none && model->nx_solver > 0) {
auto plist = model->getParameterList();
sensInit1(sx0, sdx0);
if (sensi_meth_ == SensitivityMethod::forward && !plist.empty()) {
/* Set sensitivity analysis optional inputs */
auto par = model->getUnscaledParameters();
/* Activate sensitivity calculations and apply tolerances */
initializeNonLinearSolverSens(model);
setSensParams(par.data(), nullptr, plist.data());
applyTolerancesFSA();
} else {
/* Allocate space for the adjoint computation */
adjInit();
}
}
setId(model);
setSuppressAlg(true);
/* calculate consistent DAE initial conditions (no effect for ODE) */
if (model->nt() > 1)
calcIC(model->getTimepoint(1));
}
void Solver::setupB(int *which, const realtype tf, Model *model,
const AmiVector &xB0, const AmiVector &dxB0,
const AmiVector &xQB0) const {
if (!solver_memory_)
throw AmiException(
"Solver for the forward problem must be setup first");
/* allocate memory for the backward problem */
allocateSolverB(which);
/* initialise states */
binit(*which, tf, xB0, dxB0);
/* Attach user data */
setUserDataB(*which);
if (nx() == 0)
return;
initializeLinearSolverB(model, *which);
initializeNonLinearSolverB(*which);
/* Initialise quadrature calculation */
qbinit(*which, xQB0);
applyTolerancesASA(*which);
applyQuadTolerancesASA(*which);
setStabLimDetB(*which, stldet_);
}
void Solver::setupSteadystate(const realtype t0, Model *model, const AmiVector &x0,
const AmiVector &dx0, const AmiVector &xB0,
const AmiVector &dxB0, const AmiVector &xQ0) const {
/* Initialize CVodes/IDAs solver with steadystate RHS function */
initSteadystate(t0, x0, dx0);
/* Allocate space for forward quadratures */
quadInit(xQ0);
/* Apply tolerances */
applyQuadTolerances();
/* Check linear solver (works only with KLU atm) */
if (linsol_ != LinearSolver::KLU)
throw AmiException("Backward steady state computation via integration "
"is currently only implemented for KLU linear solver");
/* Set Jacobian function and initialize values */
setSparseJacFn_ss();
model->writeSteadystateJB(t0, 0, x0, dx0, xB0, dxB0, xB0);
}
void Solver::updateAndReinitStatesAndSensitivities(Model *model) const {
model->fx0_fixedParameters(x_);
reInit(t_, x_, dx_);
if (getSensitivityOrder() >= SensitivityOrder::first) {
model->fsx0_fixedParameters(sx_, x_);
if (getSensitivityMethod() == SensitivityMethod::forward)
sensReInit(sx_, sdx_);
}
}
void Solver::resetDiagnosis() const {
ns_.clear();
nrhs_.clear();
netf_.clear();
nnlscf_.clear();
order_.clear();
nsB_.clear();
nrhsB_.clear();
netfB_.clear();
nnlscfB_.clear();
}
void Solver::storeDiagnosis() const {
if (!solver_was_called_F_ || !solver_memory_) {
ns_.push_back(0);
nrhs_.push_back(0);
netf_.push_back(0);
nnlscf_.push_back(0);
order_.push_back(0);
return;
}
long int lnumber;
getNumSteps(solver_memory_.get(), &lnumber);
ns_.push_back(static_cast<int>(lnumber));
getNumRhsEvals(solver_memory_.get(), &lnumber);
nrhs_.push_back(static_cast<int>(lnumber));
getNumErrTestFails(solver_memory_.get(), &lnumber);
netf_.push_back(static_cast<int>(lnumber));
getNumNonlinSolvConvFails(solver_memory_.get(), &lnumber);
nnlscf_.push_back(static_cast<int>(lnumber));
int number;
getLastOrder(solver_memory_.get(), &number);
order_.push_back(number);
}
void Solver::storeDiagnosisB(const int which) const {
if (!solver_was_called_B_ || !solver_memory_B_.at(which)) {
nsB_.push_back(0);
nrhsB_.push_back(0);
netfB_.push_back(0);
nnlscfB_.push_back(0);
return;
}
long int number;
getNumSteps(solver_memory_B_.at(which).get(), &number);
nsB_.push_back(static_cast<int>(number));
getNumRhsEvals(solver_memory_B_.at(which).get(), &number);
nrhsB_.push_back(static_cast<int>(number));
getNumErrTestFails(solver_memory_B_.at(which).get(), &number);
netfB_.push_back(static_cast<int>(number));
getNumNonlinSolvConvFails(solver_memory_B_.at(which).get(), &number);
nnlscfB_.push_back(static_cast<int>(number));
}
void Solver::initializeLinearSolver(const Model *model) const {
switch (linsol_) {
/* DIRECT SOLVERS */
case LinearSolver::dense:
linear_solver_ = std::make_unique<SUNLinSolDense>(x_);
setLinearSolver();
setDenseJacFn();
break;
case LinearSolver::band:
linear_solver_ =
std::make_unique<SUNLinSolBand>(x_, model->ubw, model->lbw);
setLinearSolver();
setBandJacFn();
break;
case LinearSolver::LAPACKDense:
throw AmiException("Solver currently not supported!");
case LinearSolver::LAPACKBand:
throw AmiException("Solver currently not supported!");
case LinearSolver::diag:
diag();
setDenseJacFn();
break;
/* ITERATIVE SOLVERS */
case LinearSolver::SPGMR:
linear_solver_ = std::make_unique<SUNLinSolSPGMR>(x_);
setLinearSolver();
setJacTimesVecFn();
break;
case LinearSolver::SPBCG:
linear_solver_ = std::make_unique<SUNLinSolSPBCGS>(x_);
setLinearSolver();
setJacTimesVecFn();
break;
case LinearSolver::SPTFQMR:
linear_solver_ = std::make_unique<SUNLinSolSPTFQMR>(x_);
setLinearSolver();
setJacTimesVecFn();
break;
/* SPARSE SOLVERS */
case LinearSolver::KLU:
linear_solver_ = std::make_unique<SUNLinSolKLU>(
x_, model->nnz, CSC_MAT,
static_cast<SUNLinSolKLU::StateOrdering>(getStateOrdering()));
setLinearSolver();
setSparseJacFn();
break;
#ifdef SUNDIALS_SUPERLUMT
case LinearSolver::SuperLUMT:
// TODO state ordering
linearSolver = std::make_unique<SUNLinSolSuperLUMT>(
*x, model->nnz, CSC_MAT,
static_cast<SUNLinSolSuperLUMT::StateOrdering>(getStateOrdering()));
setLinearSolver();
setSparseJacFn();
break;
#endif
default:
throw AmiException("Invalid choice of solver: %d",
static_cast<int>(linsol_));
}
}
void Solver::initializeNonLinearSolver() const {
switch (iter_) {
case NonlinearSolverIteration::newton:
non_linear_solver_ = std::make_unique<SUNNonLinSolNewton>(x_.getNVector());
break;
case NonlinearSolverIteration::fixedpoint:
non_linear_solver_ =
std::make_unique<SUNNonLinSolFixedPoint>(x_.getNVector());
break;
default:
throw AmiException("Invalid non-linear solver specified (%d).",
static_cast<int>(iter_));
}
setNonLinearSolver();
}
void Solver::initializeLinearSolverB(const Model *model,
const int which) const {
switch (linsol_) {
/* DIRECT SOLVERS */
case LinearSolver::dense:
linear_solver_B_ = std::make_unique<SUNLinSolDense>(xB_);
setLinearSolverB(which);
setDenseJacFnB(which);
break;
case LinearSolver::band:
linear_solver_B_ =
std::make_unique<SUNLinSolBand>(xB_, model->ubw, model->lbw);
setLinearSolverB(which);
setBandJacFnB(which);
break;
case LinearSolver::LAPACKDense:
throw AmiException("Solver currently not supported!");
case LinearSolver::LAPACKBand:
throw AmiException("Solver currently not supported!");
case LinearSolver::diag:
diagB(which);
setDenseJacFnB(which);
break;
/* ITERATIVE SOLVERS */
case LinearSolver::SPGMR:
linear_solver_B_ = std::make_unique<SUNLinSolSPGMR>(xB_);
setLinearSolverB(which);
setJacTimesVecFnB(which);
break;
case LinearSolver::SPBCG:
linear_solver_B_ = std::make_unique<SUNLinSolSPBCGS>(xB_);
setLinearSolverB(which);
setJacTimesVecFnB(which);
break;
case LinearSolver::SPTFQMR:
linear_solver_B_ = std::make_unique<SUNLinSolSPTFQMR>(xB_);
setLinearSolverB(which);
setJacTimesVecFnB(which);
break;
/* SPARSE SOLVERS */
case LinearSolver::KLU:
linear_solver_B_ = std::make_unique<SUNLinSolKLU>(
xB_, model->nnz, CSC_MAT,
static_cast<SUNLinSolKLU::StateOrdering>(getStateOrdering()));
setLinearSolverB(which);
setSparseJacFnB(which);
break;
#ifdef SUNDIALS_SUPERLUMT
case LinearSolver::SuperLUMT:
linearSolverB = std::make_unique<SUNLinSolSuperLUMT>(
*xB, model->nnz, CSC_MAT,
static_cast<SUNLinSolSuperLUMT::StateOrdering>(getStateOrdering()));
setLinearSolverB(which);
setSparseJacFnB(which);
break;
#endif
default:
throw AmiException("Invalid choice of solver: %d",
static_cast<int>(linsol_));
}
}
void Solver::initializeNonLinearSolverB(const int which) const {
switch (iter_) {
case NonlinearSolverIteration::newton:
non_linear_solver_B_ =
std::make_unique<SUNNonLinSolNewton>(xB_.getNVector());
break;
case NonlinearSolverIteration::fixedpoint:
non_linear_solver_B_ =
std::make_unique<SUNNonLinSolFixedPoint>(xB_.getNVector());
break;
default:
throw AmiException("Invalid non-linear solver specified (%d).",
static_cast<int>(iter_));
}
setNonLinearSolverB(which);
}
bool operator==(const Solver &a, const Solver &b) {
if (typeid(a) != typeid(b))
return false;
return (a.interp_type_ == b.interp_type_) && (a.lmm_ == b.lmm_) &&
(a.iter_ == b.iter_) && (a.stldet_ == b.stldet_) &&
(a.ordering_ == b.ordering_) &&
(a.newton_maxsteps_ == b.newton_maxsteps_) &&
(a.newton_damping_factor_mode_ == b.newton_damping_factor_mode_) &&
(a.newton_damping_factor_lower_bound_ == b.newton_damping_factor_lower_bound_) &&
(a.ism_ == b.ism_) &&
(a.linsol_ == b.linsol_) && (a.atol_ == b.atol_) && (a.rtol_ == b.rtol_) &&
(a.maxsteps_ == b.maxsteps_) && (a.maxstepsB_ == b.maxstepsB_) &&
(a.quad_atol_ == b.quad_atol_) && (a.quad_rtol_ == b.quad_rtol_) &&
(a.maxtime_ == b.maxtime_) &&
(a.getAbsoluteToleranceSteadyState() ==
b.getAbsoluteToleranceSteadyState()) &&
(a.getRelativeToleranceSteadyState() ==
b.getRelativeToleranceSteadyState()) &&
(a.getAbsoluteToleranceSteadyStateSensi() ==
b.getAbsoluteToleranceSteadyStateSensi()) &&
(a.getRelativeToleranceSteadyStateSensi() ==
b.getRelativeToleranceSteadyStateSensi()) &&
(a.rtol_fsa_ == b.rtol_fsa_ ||
(isNaN(a.rtol_fsa_) && isNaN(b.rtol_fsa_))) &&
(a.atol_fsa_ == b.atol_fsa_ ||
(isNaN(a.atol_fsa_) && isNaN(b.atol_fsa_))) &&
(a.rtolB_ == b.rtolB_ || (isNaN(a.rtolB_) && isNaN(b.rtolB_))) &&
(a.atolB_ == b.atolB_ || (isNaN(a.atolB_) && isNaN(b.atolB_))) &&
(a.sensi_ == b.sensi_) && (a.sensi_meth_ == b.sensi_meth_) &&
(a.newton_step_steadystate_conv_ == b.newton_step_steadystate_conv_) &&
(a.check_sensi_steadystate_conv_ == b.check_sensi_steadystate_conv_) &&
(a.rdata_mode_ == b.rdata_mode_);
}
void Solver::applyTolerances() const {
if (!getInitDone())
throw AmiException("Solver instance was not yet set up, the "
"tolerances cannot be applied yet!");
setSStolerances(rtol_, atol_);
}
void Solver::applyTolerancesFSA() const {
if (!getInitDone())
throw AmiException("Solver instance was not yet set up, the "
"tolerances cannot be applied yet!");
if (sensi_ < SensitivityOrder::first)
return;
if (nplist()) {
std::vector<realtype> atols(nplist(), getAbsoluteToleranceFSA());
setSensSStolerances(getRelativeToleranceFSA(), atols.data());
setSensErrCon(true);
}
}
void Solver::applyTolerancesASA(const int which) const {
if (!getAdjInitDone())
throw AmiException("Adjoint solver instance was not yet set up, the "
"tolerances cannot be applied yet!");
if (sensi_ < SensitivityOrder::first)
return;
/* specify integration tolerances for backward problem */
setSStolerancesB(which, getRelativeToleranceB(), getAbsoluteToleranceB());
}
void Solver::applyQuadTolerancesASA(const int which) const {
if (!getAdjInitDone())
throw AmiException("Adjoint solver instance was not yet set up, the "
"tolerances cannot be applied yet!");
if (sensi_ < SensitivityOrder::first)
return;
realtype quad_rtol = isNaN(quad_rtol_) ? rtol_ : quad_rtol_;
realtype quad_atol = isNaN(quad_atol_) ? atol_ : quad_atol_;
/* Enable Quadrature Error Control */
setQuadErrConB(which, !std::isinf(quad_atol) && !std::isinf(quad_rtol));
quadSStolerancesB(which, quad_rtol, quad_atol);
}
void Solver::applyQuadTolerances() const {
if (!getQuadInitDone())
throw AmiException("Quadratures were not initialized, the "
"tolerances cannot be applied yet!");
if (sensi_ < SensitivityOrder::first)
return;
realtype quad_rtolF = isNaN(quad_rtol_) ? rtol_ : quad_rtol_;
realtype quad_atolF = isNaN(quad_atol_) ? atol_ : quad_atol_;
/* Enable Quadrature Error Control */
setQuadErrCon(!std::isinf(quad_atolF) && !std::isinf(quad_rtolF));
quadSStolerances(quad_rtolF, quad_atolF);
}
void Solver::applySensitivityTolerances() const {
if (sensi_ < SensitivityOrder::first)
return;
if (sensi_meth_ == SensitivityMethod::forward)
applyTolerancesFSA();
else if (sensi_meth_ == SensitivityMethod::adjoint && getAdjInitDone()) {
for (int iMem = 0; iMem < (int)solver_memory_B_.size(); ++iMem)
applyTolerancesASA(iMem);
}
}
SensitivityMethod Solver::getSensitivityMethod() const { return sensi_meth_; }
SensitivityMethod Solver::getSensitivityMethodPreequilibration() const { return sensi_meth_preeq_; }
void Solver::setSensitivityMethod(const SensitivityMethod sensi_meth) {
checkSensitivityMethod(sensi_meth, false);
this->sensi_meth_ = sensi_meth;
}
void Solver::setSensitivityMethodPreequilibration(const SensitivityMethod sensi_meth_preeq) {
checkSensitivityMethod(sensi_meth_preeq, true);
sensi_meth_preeq_ = sensi_meth_preeq;
}
void Solver::checkSensitivityMethod(const SensitivityMethod sensi_meth,
bool preequilibration) const {
if (rdata_mode_ == RDataReporting::residuals &&
sensi_meth == SensitivityMethod::adjoint)
throw AmiException("Adjoint Sensitivity Analysis is not compatible with"
" only reporting residuals!");
if (!preequilibration && sensi_meth != sensi_meth_)
resetMutableMemory(nx(), nplist(), nquad());
}
int Solver::getNewtonMaxSteps() const { return newton_maxsteps_; }
void Solver::setNewtonMaxSteps(const int newton_maxsteps) {
if (newton_maxsteps < 0)
throw AmiException("newton_maxsteps must be a non-negative number");
newton_maxsteps_ = newton_maxsteps;
}
NewtonDampingFactorMode Solver::getNewtonDampingFactorMode() const { return newton_damping_factor_mode_; }
void Solver::setNewtonDampingFactorMode(NewtonDampingFactorMode dampingFactorMode) {
newton_damping_factor_mode_ = dampingFactorMode;
}
double Solver::getNewtonDampingFactorLowerBound() const { return newton_damping_factor_lower_bound_; }
void Solver::setNewtonDampingFactorLowerBound(double dampingFactorLowerBound) {
newton_damping_factor_lower_bound_ = dampingFactorLowerBound;
}
SensitivityOrder Solver::getSensitivityOrder() const { return sensi_; }
void Solver::setSensitivityOrder(const SensitivityOrder sensi) {
if (sensi_ != sensi)
resetMutableMemory(nx(), nplist(), nquad());
sensi_ = sensi;
if (getInitDone())
applySensitivityTolerances();
}
double Solver::getRelativeTolerance() const {
return static_cast<double>(rtol_);
}
void Solver::setRelativeTolerance(const double rtol) {
if (rtol < 0)
throw AmiException("rtol must be a non-negative number");
rtol_ = static_cast<realtype>(rtol);
if (getInitDone()) {
applyTolerances();
applySensitivityTolerances();
}
}
double Solver::getAbsoluteTolerance() const {
return static_cast<double>(atol_);
}
void Solver::setAbsoluteTolerance(double atol) {
if (atol < 0)
throw AmiException("atol must be a non-negative number");
atol_ = static_cast<realtype>(atol);
if (getInitDone()) {
applyTolerances();
applySensitivityTolerances();
}
}
double Solver::getRelativeToleranceFSA() const {
return static_cast<double>(isNaN(rtol_fsa_) ? rtol_ : rtol_fsa_);
}
void Solver::setRelativeToleranceFSA(const double rtol) {
if (rtol < 0)
throw AmiException("rtol must be a non-negative number");
rtol_fsa_ = static_cast<realtype>(rtol);
if (getInitDone()) {
applySensitivityTolerances();
}
}
double Solver::getAbsoluteToleranceFSA() const {
return static_cast<double>(isNaN(atol_fsa_) ? atol_ : atol_fsa_);
}
void Solver::setAbsoluteToleranceFSA(const double atol) {
if (atol < 0)
throw AmiException("atol must be a non-negative number");
atol_fsa_ = static_cast<realtype>(atol);
if (getInitDone()) {
applySensitivityTolerances();
}
}
double Solver::getRelativeToleranceB() const {
return static_cast<double>(isNaN(rtolB_) ? rtol_ : rtolB_);
}
void Solver::setRelativeToleranceB(const double rtol) {
if (rtol < 0)
throw AmiException("rtol must be a non-negative number");
rtolB_ = static_cast<realtype>(rtol);
if (getInitDone()) {
applySensitivityTolerances();
}
}
double Solver::getAbsoluteToleranceB() const {
return static_cast<double>(isNaN(atolB_) ? atol_ : atolB_);
}
void Solver::setAbsoluteToleranceB(const double atol) {
if (atol < 0)
throw AmiException("atol must be a non-negative number");
atolB_ = static_cast<realtype>(atol);
if (getInitDone()) {
applySensitivityTolerances();
}
}
double Solver::getRelativeToleranceQuadratures() const {
return static_cast<double>(quad_rtol_);
}
void Solver::setRelativeToleranceQuadratures(const double rtol) {
if (rtol < 0)
throw AmiException("rtol must be a non-negative number");
quad_rtol_ = static_cast<realtype>(rtol);
if (sensi_meth_ != SensitivityMethod::adjoint)
return;
for (int iMem = 0; iMem < (int)solver_memory_B_.size(); ++iMem)
if (solver_memory_B_.at(iMem))
applyQuadTolerancesASA(iMem);
}
double Solver::getAbsoluteToleranceQuadratures() const {
return static_cast<double>(quad_atol_);
}
void Solver::setAbsoluteToleranceQuadratures(const double atol) {
if (atol < 0)
throw AmiException("atol must be a non-negative number");
quad_atol_ = static_cast<realtype>(atol);
if (sensi_meth_ != SensitivityMethod::adjoint)
return;
for (int iMem = 0; iMem < (int)solver_memory_B_.size(); ++iMem)
if (solver_memory_B_.at(iMem))
applyTolerancesASA(iMem);
}
double Solver::getRelativeToleranceSteadyState() const {
return static_cast<double>(isNaN(ss_rtol_) ? rtol_ : ss_rtol_);
}
void Solver::setRelativeToleranceSteadyState(const double rtol) {
if (rtol < 0)
throw AmiException("rtol must be a non-negative number");
ss_rtol_ = static_cast<realtype>(rtol);
}
double Solver::getAbsoluteToleranceSteadyState() const {
return static_cast<double>(isNaN(ss_atol_) ? atol_ : ss_atol_);
}
void Solver::setAbsoluteToleranceSteadyState(const double atol) {
if (atol < 0)
throw AmiException("atol must be a non-negative number");
ss_atol_ = static_cast<realtype>(atol);
}
double Solver::getRelativeToleranceSteadyStateSensi() const {
return static_cast<double>(isNaN(ss_rtol_sensi_) ? rtol_ : ss_rtol_sensi_);
}
void Solver::setRelativeToleranceSteadyStateSensi(const double rtol) {
if (rtol < 0)
throw AmiException("rtol must be a non-negative number");
ss_rtol_sensi_ = static_cast<realtype>(rtol);
}
double Solver::getAbsoluteToleranceSteadyStateSensi() const {
return static_cast<double>(isNaN(ss_atol_sensi_) ? atol_ : ss_atol_sensi_);
}
void Solver::setAbsoluteToleranceSteadyStateSensi(const double atol) {
if (atol < 0)
throw AmiException("atol must be a non-negative number");
ss_atol_sensi_ = static_cast<realtype>(atol);
}
long int Solver::getMaxSteps() const { return maxsteps_; }
double Solver::getMaxTime() const { return maxtime_.count(); }
void Solver::setMaxTime(double maxtime)
{
maxtime_ = std::chrono::duration<double>(maxtime);
}
void Solver::startTimer() const
{
starttime_ = std::chrono::system_clock::now();
}
bool Solver::timeExceeded() const
{
return std::chrono::system_clock::now() - starttime_ > maxtime_;
}
void Solver::setMaxSteps(const long int maxsteps) {
if (maxsteps <= 0)
throw AmiException("maxsteps must be a positive number");
maxsteps_ = maxsteps;
if (getAdjInitDone())
resetMutableMemory(nx(), nplist(), nquad());
}
long int Solver::getMaxStepsBackwardProblem() const { return maxstepsB_; }
void Solver::setMaxStepsBackwardProblem(const long int maxsteps) {
if (maxsteps < 0)
throw AmiException("maxsteps must be a non-negative number");
maxstepsB_ = maxsteps;
}
LinearMultistepMethod Solver::getLinearMultistepMethod() const { return lmm_; }
void Solver::setLinearMultistepMethod(const LinearMultistepMethod lmm) {
if (solver_memory_)
resetMutableMemory(nx(), nplist(), nquad());
lmm_ = lmm;
}
NonlinearSolverIteration Solver::getNonlinearSolverIteration() const {
return iter_;
}
void Solver::setNonlinearSolverIteration(const NonlinearSolverIteration iter) {
if (solver_memory_)
resetMutableMemory(nx(), nplist(), nquad());
iter_ = iter;
}
InterpolationType Solver::getInterpolationType() const { return interp_type_; }
void Solver::setInterpolationType(const InterpolationType interpType) {
if (!solver_memory_B_.empty())
resetMutableMemory(nx(), nplist(), nquad());
interp_type_ = interpType;
}
int Solver::getStateOrdering() const { return ordering_; }
void Solver::setStateOrdering(int ordering) {
ordering_ = ordering;
if (solver_memory_ && linsol_ == LinearSolver::KLU) {
auto klu = dynamic_cast<SUNLinSolKLU *>(linear_solver_.get());
klu->setOrdering(static_cast<SUNLinSolKLU::StateOrdering>(ordering));
klu = dynamic_cast<SUNLinSolKLU *>(linear_solver_B_.get());
klu->setOrdering(static_cast<SUNLinSolKLU::StateOrdering>(ordering));
}
#ifdef SUNDIALS_SUPERLUMT
if (solverMemory && linsol == LinearSolver::SuperLUMT) {
auto klu = dynamic_cast<SUNLinSolSuperLUMT *>(linearSolver.get());
klu->setOrdering(
static_cast<SUNLinSolSuperLUMT::StateOrdering>(ordering));
klu = dynamic_cast<SUNLinSolSuperLUMT *>(linearSolverB.get());
klu->setOrdering(
static_cast<SUNLinSolSuperLUMT::StateOrdering>(ordering));
}
#endif
}
bool Solver::getStabilityLimitFlag() const { return stldet_; }
void Solver::setStabilityLimitFlag(const bool stldet) {
stldet_ = stldet;
if (solver_memory_) {
setStabLimDet(stldet);
for (int iMem = 0; iMem < (int)solver_memory_B_.size(); ++iMem)
if (solver_memory_B_.at(iMem))
setStabLimDetB(iMem, stldet);
}
}
LinearSolver Solver::getLinearSolver() const { return linsol_; }
void Solver::setLinearSolver(LinearSolver linsol) {
if (solver_memory_)
resetMutableMemory(nx(), nplist(), nquad());
linsol_ = linsol;
}
InternalSensitivityMethod Solver::getInternalSensitivityMethod() const {
return ism_;
}
void Solver::setInternalSensitivityMethod(const InternalSensitivityMethod ism) {
if (solver_memory_)
resetMutableMemory(nx(), nplist(), nquad());
ism_ = ism;
}
RDataReporting Solver::getReturnDataReportingMode() const {
return rdata_mode_;
};
void Solver::setReturnDataReportingMode(RDataReporting rdrm) {
if (rdrm == RDataReporting::residuals &&
sensi_meth_ == SensitivityMethod::adjoint)
throw AmiException("Adjoint Sensitivity Analysis cannot report "
"residuals!");
rdata_mode_ = rdrm;
}
void Solver::initializeNonLinearSolverSens(const Model *model) const {
switch (iter_) {
case NonlinearSolverIteration::newton:
switch (ism_) {
case InternalSensitivityMethod::staggered:
case InternalSensitivityMethod::simultaneous:
non_linear_solver_sens_ = std::make_unique<SUNNonLinSolNewton>(
1 + model->nplist(), x_.getNVector());
break;
case InternalSensitivityMethod::staggered1:
non_linear_solver_sens_ =
std::make_unique<SUNNonLinSolNewton>(x_.getNVector());
break;
default:
throw AmiException(
"Unsupported internal sensitivity method selected: %d", ism_);
}
break;
case NonlinearSolverIteration::fixedpoint:
switch (ism_) {
case InternalSensitivityMethod::staggered:
case InternalSensitivityMethod::simultaneous:
non_linear_solver_sens_ = std::make_unique<SUNNonLinSolFixedPoint>(
1 + model->nplist(), x_.getNVector());
break;
case InternalSensitivityMethod::staggered1:
non_linear_solver_sens_ =
std::make_unique<SUNNonLinSolFixedPoint>(x_.getNVector());
break;
default:
throw AmiException(
"Unsupported internal sensitivity method selected: %d", ism_);
}
break;
default:
throw AmiException("Invalid non-linear solver specified (%d).",
static_cast<int>(iter_));
}
setNonLinearSolverSens();
}
int Solver::nplist() const { return sx_.getLength(); }
int Solver::nx() const { return x_.getLength(); }