void CVodesIntegrator::setMaxSteps(int nmax)
{
m_maxsteps = nmax;
if (m_cvode_mem) {
CVodeSetMaxNumSteps(m_cvode_mem, m_maxsteps);
}
}
inline void cvodes_set_options(void* cvodes_mem,
double rel_tol, double abs_tol,
// NOLINTNEXTLINE(runtime/int)
long int max_num_steps) {
// forward CVode errors to noop error handler
CVodeSetErrHandlerFn(cvodes_mem, cvodes_silent_err_handler, 0);
// Initialize solver parameters
cvodes_check_flag(CVodeSStolerances(cvodes_mem, rel_tol, abs_tol),
"CVodeSStolerances");
cvodes_check_flag(CVodeSetMaxNumSteps(cvodes_mem, max_num_steps),
"CVodeSetMaxNumSteps");
double init_step = 0;
cvodes_check_flag(CVodeSetInitStep(cvodes_mem, init_step),
"CVodeSetInitStep");
long int max_err_test_fails = 20; // NOLINT(runtime/int)
cvodes_check_flag(CVodeSetMaxErrTestFails(cvodes_mem, max_err_test_fails),
"CVodeSetMaxErrTestFails");
long int max_conv_fails = 50; // NOLINT(runtime/int)
cvodes_check_flag(CVodeSetMaxConvFails(cvodes_mem, max_conv_fails),
"CVodeSetMaxConvFails");
}
void ode_solver_init(ode_solver* solver, const double t0, double* y0, int lenY, double* p, int lenP ){
int i,flag;
/* Get parameters */
if (p != 0){
if (lenP != solver->odeModel->P) {
fprintf(stderr,"ode_solver_init: lenP must be equal %d, the number of parameters in the ode model.\n",solver->odeModel->P);
return ;
}
for(i = 0; i < solver->odeModel->P; i++)
solver->params[i] = p[i];
}
/* Get initial conditions */
if(y0 != 0){
if( lenY != solver->odeModel->N ){
fprintf(stderr,"ode_solver_init: lenY must be equal %d, the number of variables in the ode model.\n",solver->odeModel->N);
return ;
}
NV_DATA_S(solver->y) = y0;
}
/* initialise */
flag = CVodeInit(solver->cvode_mem, solver->odeModel->vf_eval, t0, solver->y);
flag = CVodeSetUserData(solver->cvode_mem, solver->params);
flag = CVDense(solver->cvode_mem, solver->odeModel->N);
flag = CVDlsSetDenseJacFn(solver->cvode_mem, solver->odeModel->vf_jac);
flag = CVodeSStolerances(solver->cvode_mem, ODE_SOLVER_REL_ERR, ODE_SOLVER_ABS_ERR);
flag = CVodeSetMaxNumSteps(solver->cvode_mem, ODE_SOLVER_MX_STEPS);
}
void OpenSMOKE_CVODE_Sundials<T>::AnalyzeUserOptions()
{
/*
TODO
if (this->iSetMaximumNumberOfPrints_) iwork_[6] = this->maximumNumberOfPrints_;
if (this->iSetMaximumOrder_) iwork_[8] = this->maximumOrder_;
*/
if (this->iSetMaximumNumberOfSteps_)
{
int flag = CVodeSetMaxNumSteps(cvode_mem_, this->maximumNumberOfSteps_);
if (check_flag(&flag, std::string("CVodeSetMaxNumSteps"), 1)) exit(-1);
}
if (this->iSetMaximumStep_)
{
int flag = CVodeSetMaxStep(cvode_mem_, this->maximumStep_);
if (check_flag(&flag, std::string("CVodeSetMaxStep"), 1)) exit(-1);
}
if (this->iSetMinimumStep_)
{
int flag = CVodeSetMinStep(cvode_mem_, this->minimumStep_);
if (check_flag(&flag, std::string("CVodeSetMinStep"), 1)) exit(-1);
}
if (this->iSetFirstStep_)
{
int flag = CVodeSetInitStep(cvode_mem_, this->firstStep_);
if (check_flag(&flag, std::string("CVodeSetInitStep"), 1)) exit(-1);
}
}
int CVodeSetMaxNumStepsB(void *cvadj_mem, long int mxstepsB)
{
CVadjMem ca_mem;
void *cvode_mem;
int flag;
ca_mem = (CVadjMem) cvadj_mem;
cvode_mem = (void *)ca_mem->cvb_mem;
flag = CVodeSetMaxNumSteps(cvode_mem, mxstepsB);
return(flag);
}
int CVodeSetMaxNumStepsB(void *cvadj_mem, long int mxstepsB)
{
CVadjMem ca_mem;
void *cvode_mem;
int flag;
if (cvadj_mem == NULL) {
CVProcessError(NULL, CV_ADJMEM_NULL, "CVODEA", "CVodeSetMaxNumStepsB", MSGAM_NULL_CAMEM);
return(CV_ADJMEM_NULL);
}
ca_mem = (CVadjMem) cvadj_mem;
cvode_mem = (void *)ca_mem->cvb_mem;
flag = CVodeSetMaxNumSteps(cvode_mem, mxstepsB);
return(flag);
}
void CVodesIntegrator::applyOptions()
{
if (m_type == DENSE + NOJAC) {
sd_size_t N = static_cast<sd_size_t>(m_neq);
#if SUNDIALS_USE_LAPACK
CVLapackDense(m_cvode_mem, N);
#else
CVDense(m_cvode_mem, N);
#endif
} else if (m_type == DIAG) {
CVDiag(m_cvode_mem);
} else if (m_type == GMRES) {
CVSpgmr(m_cvode_mem, PREC_NONE, 0);
} else if (m_type == BAND + NOJAC) {
sd_size_t N = static_cast<sd_size_t>(m_neq);
long int nu = m_mupper;
long int nl = m_mlower;
#if SUNDIALS_USE_LAPACK
CVLapackBand(m_cvode_mem, N, nu, nl);
#else
CVBand(m_cvode_mem, N, nu, nl);
#endif
} else {
throw CanteraError("CVodesIntegrator::applyOptions",
"unsupported option");
}
if (m_maxord > 0) {
CVodeSetMaxOrd(m_cvode_mem, m_maxord);
}
if (m_maxsteps > 0) {
CVodeSetMaxNumSteps(m_cvode_mem, m_maxsteps);
}
if (m_hmax > 0) {
CVodeSetMaxStep(m_cvode_mem, m_hmax);
}
if (m_hmin > 0) {
CVodeSetMinStep(m_cvode_mem, m_hmin);
}
if (m_maxErrTestFails > 0) {
CVodeSetMaxErrTestFails(m_cvode_mem, m_maxErrTestFails);
}
}
int CVodeSetMaxNumStepsB(void *cvode_mem, int which, long int mxstepsB)
{
CVodeMem cv_mem;
CVadjMem ca_mem;
CVodeBMem cvB_mem;
void *cvodeB_mem;
int flag;
/* Check if cvode_mem exists */
if (cvode_mem == NULL) {
cvProcessError(NULL, CV_MEM_NULL, "CVODEA", "CVodeSetMaxNumStepsB", MSGCV_NO_MEM);
return(CV_MEM_NULL);
}
cv_mem = (CVodeMem) cvode_mem;
/* Was ASA initialized? */
if (cv_mem->cv_adjMallocDone == FALSE) {
cvProcessError(cv_mem, CV_NO_ADJ, "CVODEA", "CVodeSetMaxNumStepsB", MSGCV_NO_ADJ);
return(CV_NO_ADJ);
}
ca_mem = cv_mem->cv_adj_mem;
/* Check which */
if ( which >= nbckpbs ) {
cvProcessError(cv_mem, CV_ILL_INPUT, "CVODEA", "CVodeSetMaxNumStepsB", MSGCV_BAD_WHICH);
return(CV_ILL_INPUT);
}
/* Find the CVodeBMem entry in the linked list corresponding to which */
cvB_mem = ca_mem->cvB_mem;
while (cvB_mem != NULL) {
if ( which == cvB_mem->cv_index ) break;
cvB_mem = cvB_mem->cv_next;
}
cvodeB_mem = (void *) (cvB_mem->cv_mem);
flag = CVodeSetMaxNumSteps(cvodeB_mem, mxstepsB);
return(flag);
}
void FCV_SETIIN(char key_name[], long int *ival, int *ier)
{
if (!strncmp(key_name,"MAX_ORD",7))
*ier = CVodeSetMaxOrd(CV_cvodemem, (int) *ival);
else if (!strncmp(key_name,"MAX_NSTEPS",10))
*ier = CVodeSetMaxNumSteps(CV_cvodemem, (long int) *ival);
else if (!strncmp(key_name,"MAX_ERRFAIL",11))
*ier = CVodeSetMaxErrTestFails(CV_cvodemem, (int) *ival);
else if (!strncmp(key_name,"MAX_NITERS",10))
*ier = CVodeSetMaxNonlinIters(CV_cvodemem, (int) *ival);
else if (!strncmp(key_name,"MAX_CONVFAIL",12))
*ier = CVodeSetMaxConvFails(CV_cvodemem, (int) *ival);
else if (!strncmp(key_name,"HNIL_WARNS",10))
*ier = CVodeSetMaxHnilWarns(CV_cvodemem, (int) *ival);
else if (!strncmp(key_name,"STAB_LIM",8))
*ier = CVodeSetStabLimDet(CV_cvodemem, (booleantype) *ival);
else {
*ier = -99;
fprintf(stderr, "FCVSETIIN: Unrecognized key.\n\n");
}
}
int run_rate_state_sim(std::vector<std::vector<realtype> > &results, RSParams ¶ms) {
realtype long_term_reltol, event_reltol, t, tout, tbase=0;
N_Vector y, long_term_abstol, event_abstol;
unsigned int i, n;
int flag, err_code;
void *long_term_cvode, *event_cvode, *current_cvode;
// Create serial vector of length NEQ for I.C. and abstol
y = N_VNew_Serial(params.num_eqs()*params.num_blocks());
if (check_flag((void *)y, "N_VNew_Serial", 0)) return(1);
long_term_abstol = N_VNew_Serial(params.num_eqs()*params.num_blocks());
if (check_flag((void *)long_term_abstol, "N_VNew_Serial", 0)) return(1);
event_abstol = N_VNew_Serial(params.num_eqs()*params.num_blocks());
if (check_flag((void *)event_abstol, "N_VNew_Serial", 0)) return(1);
// Initialize y
for (i=0;i<params.num_blocks();++i) {
NV_Ith_S(y,i*params.num_eqs()+EQ_X) = params.init_val(i, EQ_X);
NV_Ith_S(y,i*params.num_eqs()+EQ_V) = params.init_val(i, EQ_V);
NV_Ith_S(y,i*params.num_eqs()+EQ_H) = params.init_val(i, EQ_H);
}
/* Initialize interactions */
/*interaction = new realtype[NBLOCKS*NBLOCKS];
double int_level = 1e-2;
double dropoff = 1.1;
for (i=0;i<NBLOCKS;++i) {
for (n=0;n<NBLOCKS;++n) {
interaction[i*NBLOCKS+n] = (i==n?(1.0-int_level):int_level);
}
}*/
/* Set the scalar relative tolerance */
long_term_reltol = RCONST(1.0e-12);
event_reltol = RCONST(1.0e-12);
/* Set the vector absolute tolerance */
for (i=0;i<params.num_blocks();++i) {
Xth(long_term_abstol,i) = RCONST(1.0e-12);
Vth(long_term_abstol,i) = RCONST(1.0e-12);
Hth(long_term_abstol,i) = RCONST(1.0e-12);
Xth(event_abstol,i) = RCONST(1.0e-12);
Vth(event_abstol,i) = RCONST(1.0e-12);
Hth(event_abstol,i) = RCONST(1.0e-12);
}
/* Call CVodeCreate to create the solver memory and specify the
* Backward Differentiation Formula and the use of a Newton iteration */
long_term_cvode = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void *)long_term_cvode, "CVodeCreate", 0)) return(1);
event_cvode = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void *)event_cvode, "CVodeCreate", 0)) return(1);
// Turn off error messages
//CVodeSetErrFile(long_term_cvode, NULL);
//CVodeSetErrFile(event_cvode, NULL);
/* Call CVodeInit to initialize the integrator memory and specify the
* user's right hand side function in y'=f(t,y), the inital time T0, and
* the initial dependent variable vector y. */
flag = CVodeInit(long_term_cvode, func, T0, y);
if (check_flag(&flag, "CVodeInit", 1)) return(1);
flag = CVodeInit(event_cvode, func, T0, y);
if (check_flag(&flag, "CVodeInit", 1)) return(1);
/* Call CVodeSVtolerances to specify the scalar relative tolerance
* and vector absolute tolerances */
flag = CVodeSVtolerances(long_term_cvode, long_term_reltol, long_term_abstol);
if (check_flag(&flag, "CVodeSVtolerances", 1)) return(1);
flag = CVodeSVtolerances(event_cvode, event_reltol, event_abstol);
if (check_flag(&flag, "CVodeSVtolerances", 1)) return(1);
/* Set the root finding function */
//flag = CVodeRootInit(long_term_cvode, params.num_blocks(), vel_switch_finder);
//flag = CVodeRootInit(event_cvode, params.num_blocks(), vel_switch_finder);
//if (check_flag(&flag, "CVodeRootInit", 1)) return(1);
/* Call CVDense to specify the CVDENSE dense linear solver */
//flag = CVSpbcg(cvode_mem, PREC_NONE, 0);
//if (check_flag(&flag, "CVSpbcg", 1)) return(1);
//flag = CVSpgmr(cvode_mem, PREC_NONE, 0);
//if (check_flag(&flag, "CVSpgmr", 1)) return(1);
flag = CVDense(long_term_cvode, params.num_eqs()*params.num_blocks());
if (check_flag(&flag, "CVDense", 1)) return(1);
flag = CVDense(event_cvode, params.num_eqs()*params.num_blocks());
if (check_flag(&flag, "CVDense", 1)) return(1);
flag = CVodeSetUserData(long_term_cvode, ¶ms);
if (check_flag(&flag, "CVodeSetUserData", 1)) return(1);
flag = CVodeSetUserData(event_cvode, ¶ms);
if (check_flag(&flag, "CVodeSetUserData", 1)) return(1);
CVodeSetMaxNumSteps(long_term_cvode, 100000);
CVodeSetMaxNumSteps(event_cvode, 100000);
/* Set the Jacobian routine to Jac (user-supplied) */
flag = CVDlsSetDenseJacFn(long_term_cvode, Jac);
if (check_flag(&flag, "CVDlsSetDenseJacFn", 1)) return(1);
flag = CVDlsSetDenseJacFn(event_cvode, Jac);
if (check_flag(&flag, "CVDlsSetDenseJacFn", 1)) return(1);
/* In loop, call CVode, print results, and test for error.
Break out of loop when NOUT preset output times have been reached. */
tout = T0+params.time_step();
err_code = 0;
int mode = 0;
int num_res_vals = params.num_eqs()*params.num_blocks();
while(t+tbase < params.end_time()) {
switch (mode) {
case 0:
current_cvode = long_term_cvode;
break;
case 1:
current_cvode = event_cvode;
break;
}
flag = CVode(current_cvode, tout, y, &t, CV_NORMAL);
record_results(results, y, t, tbase, num_res_vals);
if (check_flag(&flag, "CVode", 1)) {
err_code = flag;
break;
}
if (flag == CV_ROOT_RETURN) {
int flagr;
int rootsfound[params.num_blocks()];
flagr = CVodeGetRootInfo(current_cvode, rootsfound);
if (check_flag(&flagr, "CVodeGetRootInfo", 1)) return(1);
//mode = !mode;
//std::cerr << rootsfound[0] << std::endl;
}
if (flag == CV_SUCCESS) tout += params.time_step();
if (t > 10) {
t -= 10;
tout -= 10;
Xth(y,0) -= 10;
tbase += 10;
CVodeReInit(current_cvode, t, y);
}
}
std::cerr << err_code <<
" X:" << Xth(y,0) <<
" V:" << Vth(y,0) <<
" H:" << Hth(y,0) <<
" F:" << F(0,Vth(y,0),Hth(y,0),params) <<
" dV:" << (Xth(y,0)-t-params.param(0, K_PARAM)*F(0,Vth(y,0),Hth(y,0),params))/params.param(0, R_PARAM) <<
" dH:" << -Hth(y,0)*Vth(y,0)*log(Hth(y,0)*Vth(y,0)) << std::endl;
/* Print some final statistics */
//PrintFinalStats(cvode_mem);
/* Free y and abstol vectors */
N_VDestroy_Serial(y);
N_VDestroy_Serial(long_term_abstol);
N_VDestroy_Serial(event_abstol);
/* Free integrator memory */
CVodeFree(&long_term_cvode);
return err_code;
}
/*
* Functions to use CVODES
*
*/
struct Integrator* CreateIntegrator(struct Simulation* sim,
class ExecutableModel* em)
{
if (!(sim && em))
{
ERROR("CreateIntegrator","Invalid arguments when creating integrator");
return((struct Integrator*)NULL);
}
int flag,mlmm,miter;
struct Integrator* integrator =
(struct Integrator*)malloc(sizeof(struct Integrator));
integrator->y = NULL;
integrator->cvode_mem = NULL;
integrator->simulation = simulationClone(sim);
// FIXME: really need to handle this properly, but for now simply grabbing a handle.
integrator->em = em;
/* Check for errors in the simulation */
if (simulationGetATolLength(integrator->simulation) < 1)
{
ERROR("CreateIntegrator","Absolute tolerance(s) not set\n");
DestroyIntegrator(&integrator);
return(NULL);
}
/* Would be good if we didn't require the specification of the
tabulation step size, but for now it is required so we should
check that it has a sensible value */
if (!simulationIsBvarTabStepSet(integrator->simulation))
{
ERROR("CreateIntegrator","Tabulation step size must be set\n");
DestroyIntegrator(&integrator);
return(NULL);
}
/* start and end also needs to be set */
if (!simulationIsBvarStartSet(integrator->simulation))
{
ERROR("CreateIntegrator","Bound variable interval start must be set\n");
DestroyIntegrator(&integrator);
return(NULL);
}
if (!simulationIsBvarEndSet(integrator->simulation))
{
ERROR("CreateIntegrator","Bound variable interval end must be set\n");
DestroyIntegrator(&integrator);
return(NULL);
}
/* Create serial vector of length NR for I.C. */
integrator->y = N_VNew_Serial(em->nRates);
if (check_flag((void *)(integrator->y),"N_VNew_Serial",0))
{
DestroyIntegrator(&integrator);
return(NULL);
}
/* Initialize y */
realtype* yD = NV_DATA_S(integrator->y);
int i;
for (i=0;i<(em->nRates);i++) yD[i] = (realtype)(em->states[i]);
/* adjust parameters accordingly */
switch (simulationGetMultistepMethod(integrator->simulation))
{
case ADAMS:
{
mlmm = CV_ADAMS;
break;
}
case BDF:
{
mlmm = CV_BDF;
break;
}
default:
{
ERROR("CreateIntegrator","Invalid multistep method choice\n");
DestroyIntegrator(&integrator);
return(NULL);
}
}
switch (simulationGetIterationMethod(integrator->simulation))
{
case FUNCTIONAL:
{
miter = CV_FUNCTIONAL;
break;
}
case NEWTON:
{
miter = CV_NEWTON;
break;
}
default:
{
ERROR("CreateIntegrator","Invalid iteration method choice\n");
DestroyIntegrator(&integrator);
return(NULL);
}
}
/*
Call CVodeCreate to create the solver memory:
A pointer to the integrator problem memory is returned and
stored in cvode_mem.
*/
integrator->cvode_mem = CVodeCreate(mlmm,miter);
if (check_flag((void *)(integrator->cvode_mem),"CVodeCreate",0))
{
DestroyIntegrator(&integrator);
return(NULL);
}
/*
Call CVodeMalloc to initialize the integrator memory:
cvode_mem is the pointer to the integrator memory returned by CVodeCreate
f is the user's right hand side function in y'=f(t,y)
tStart is the initial time
y is the initial dependent variable vector
CV_SS specifies scalar relative and absolute tolerances
reltol the scalar relative tolerance
&abstol is the absolute tolerance vector
*/
flag = CVodeInit(integrator->cvode_mem,f,
simulationGetBvarStart(integrator->simulation),integrator->y);
if (check_flag(&flag,"CVodeMalloc",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
double* atol = simulationGetATol(integrator->simulation);
if (simulationGetATolLength(integrator->simulation) == 1)
{
flag = CVodeSStolerances(integrator->cvode_mem,simulationGetRTol(integrator->simulation),atol[0]);
if (check_flag(&flag,"CVodeSStolerances",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
}
else
{
ERROR("CreateIntegrator", "array abstol not supported yet.");
DestroyIntegrator(&integrator);
return(NULL);
}
free(atol);
/* if using Newton iteration need a linear solver */
if (simulationGetIterationMethod(integrator->simulation) == NEWTON)
{
switch (simulationGetLinearSolver(integrator->simulation))
{
case DENSE:
{
/* Call CVDense to specify the CVDENSE dense linear solver */
flag = CVDense(integrator->cvode_mem,em->nRates);
if (check_flag(&flag,"CVDense",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
} break;
case BAND:
{
/* Call CVBand to specify the CVBAND linear solver */
long int upperBW = em->nRates - 1; /* FIXME: This probably doesn't make */
long int lowerBW = em->nRates - 1; /* any sense, but should do until I */
/* fix it */
flag = CVBand(integrator->cvode_mem,em->nRates,upperBW,lowerBW);
if (check_flag(&flag,"CVBand",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
} break;
case DIAG:
{
/* Call CVDiag to specify the CVDIAG linear solver */
flag = CVDiag(integrator->cvode_mem);
if (check_flag(&flag,"CVDiag",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
} break;
case SPGMR:
{
/* Call CVSpgmr to specify the linear solver CVSPGMR
with no preconditioning and the maximum Krylov dimension maxl */
flag = CVSpgmr(integrator->cvode_mem,PREC_NONE,0);
if(check_flag(&flag,"CVSpgmr",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
} break;
case SPBCG:
{
/* Call CVSpbcg to specify the linear solver CVSPBCG
with no preconditioning and the maximum Krylov dimension maxl */
flag = CVSpbcg(integrator->cvode_mem,PREC_NONE,0);
if(check_flag(&flag,"CVSpbcg",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
} break;
case SPTFQMR:
{
/* Call CVSptfqmr to specify the linear solver CVSPTFQMR
with no preconditioning and the maximum Krylov dimension maxl */
flag = CVSptfqmr(integrator->cvode_mem,PREC_NONE,0);
if(check_flag(&flag,"CVSptfqmr",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
} break;
default:
{
ERROR("CreateIntegrator",
"Must specify a valid linear solver when using "
"Newton iteration\n");
DestroyIntegrator(&integrator);
return(NULL);
}
}
}
/* Pass through the executable model to f */
// FIXME: really need to handle this properly, but for now simply grabbing a handle.
flag = CVodeSetUserData(integrator->cvode_mem,(void*)(em));
if (check_flag(&flag,"CVodeSetUserData",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
/* Set the maximum time step size if it looks valid */
double mxD = simulationGetBvarMaxStep(integrator->simulation);
double tbD = simulationGetBvarTabStep(integrator->simulation);
double maxStep;
if (simulationIsBvarMaxStepSet(integrator->simulation))
{
flag = CVodeSetMaxStep(integrator->cvode_mem,
(realtype)mxD);
maxStep = mxD;
if (check_flag(&flag,"CVodeSetMaxStep (max)",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
}
else
{
flag = CVodeSetMaxStep(integrator->cvode_mem,
(realtype)tbD);
maxStep = tbD;
if (check_flag(&flag,"CVodeSetMaxStep (tab)",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
}
simulationSetBvarMaxStep(integrator->simulation,maxStep);
simulationSetBvarMaxStep(sim,maxStep);
/* try and make a sensible guess at the maximal number of steps to
get to tout to take into account case where we simply want to
integrate over a large time period in small steps (why?) */
double tout = simulationGetBvarStart(integrator->simulation)+
simulationGetBvarTabStep(integrator->simulation);
if (simulationIsBvarEndSet(integrator->simulation))
{
double end = simulationGetBvarEnd(integrator->simulation);
if (tout > end) tout = end;
}
long int maxsteps = (long int)ceil(tout/maxStep) * 100;
if (maxsteps < 500) maxsteps = 500; /* default value */
flag = CVodeSetMaxNumSteps(integrator->cvode_mem,maxsteps);
if (check_flag(&flag,"CVodeSetMaxNumSteps",1))
{
DestroyIntegrator(&integrator);
return(NULL);
}
return(integrator);
}
int main(int argc, char *argv[])
{
void *cvode_mem;
UserData data;
realtype abstol, reltol, t, tout;
N_Vector y;
int iout, flag;
realtype *pbar;
int is, *plist;
N_Vector *uS;
booleantype sensi, err_con;
int sensi_meth;
pbar = NULL;
plist = NULL;
uS = NULL;
y = NULL;
data = NULL;
cvode_mem = NULL;
/* Process arguments */
ProcessArgs(argc, argv, &sensi, &sensi_meth, &err_con);
/* Problem parameters */
data = AllocUserData();
if(check_flag((void *)data, "AllocUserData", 2)) return(1);
InitUserData(data);
/* Initial states */
y = N_VNew_Serial(NEQ);
if(check_flag((void *)y, "N_VNew_Serial", 0)) return(1);
SetInitialProfiles(y, data->dx, data->dz);
/* Tolerances */
abstol=ATOL;
reltol=RTOL;
/* Create CVODES object */
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if(check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1);
flag = CVodeSetFdata(cvode_mem, data);
if(check_flag(&flag, "CVodeSetFdata", 1)) return(1);
flag = CVodeSetMaxNumSteps(cvode_mem, 2000);
if(check_flag(&flag, "CVodeSetMaxNumSteps", 1)) return(1);
/* Allocate CVODES memory */
flag = CVodeMalloc(cvode_mem, f, T0, y, CV_SS, reltol, &abstol);
if(check_flag(&flag, "CVodeMalloc", 1)) return(1);
/* Attach CVSPGMR linear solver */
flag = CVSpgmr(cvode_mem, PREC_LEFT, 0);
if(check_flag(&flag, "CVSpgmr", 1)) return(1);
flag = CVSpilsSetPreconditioner(cvode_mem, Precond, PSolve, data);
if(check_flag(&flag, "CVSpilsSetPreconditioner", 1)) return(1);
printf("\n2-species diurnal advection-diffusion problem\n");
/* Forward sensitivity analysis */
if(sensi) {
plist = (int *) malloc(NS * sizeof(int));
if(check_flag((void *)plist, "malloc", 2)) return(1);
for(is=0; is<NS; is++) plist[is] = is;
pbar = (realtype *) malloc(NS * sizeof(realtype));
if(check_flag((void *)pbar, "malloc", 2)) return(1);
for(is=0; is<NS; is++) pbar[is] = data->p[plist[is]];
uS = N_VCloneVectorArray_Serial(NS, y);
if(check_flag((void *)uS, "N_VCloneVectorArray_Serial", 0)) return(1);
for(is=0;is<NS;is++)
N_VConst(ZERO,uS[is]);
flag = CVodeSensMalloc(cvode_mem, NS, sensi_meth, uS);
if(check_flag(&flag, "CVodeSensMalloc", 1)) return(1);
flag = CVodeSetSensErrCon(cvode_mem, err_con);
if(check_flag(&flag, "CVodeSetSensErrCon", 1)) return(1);
flag = CVodeSetSensRho(cvode_mem, ZERO);
if(check_flag(&flag, "CVodeSetSensRho", 1)) return(1);
flag = CVodeSetSensParams(cvode_mem, data->p, pbar, plist);
if(check_flag(&flag, "CVodeSetSensParams", 1)) return(1);
printf("Sensitivity: YES ");
if(sensi_meth == CV_SIMULTANEOUS)
printf("( SIMULTANEOUS +");
else
if(sensi_meth == CV_STAGGERED) printf("( STAGGERED +");
else printf("( STAGGERED1 +");
if(err_con) printf(" FULL ERROR CONTROL )");
else printf(" PARTIAL ERROR CONTROL )");
} else {
printf("Sensitivity: NO ");
}
/* In loop over output points, call CVode, print results, test for error */
printf("\n\n");
printf("========================================================================\n");
printf(" T Q H NST Bottom left Top right \n");
printf("========================================================================\n");
for (iout=1, tout = TWOHR; iout <= NOUT; iout++, tout += TWOHR) {
flag = CVode(cvode_mem, tout, y, &t, CV_NORMAL);
if(check_flag(&flag, "CVode", 1)) break;
PrintOutput(cvode_mem, t, y);
if (sensi) {
flag = CVodeGetSens(cvode_mem, t, uS);
if(check_flag(&flag, "CVodeGetSens", 1)) break;
PrintOutputS(uS);
}
printf("------------------------------------------------------------------------\n");
}
/* Print final statistics */
PrintFinalStats(cvode_mem, sensi);
/* Free memory */
N_VDestroy_Serial(y);
if (sensi) {
N_VDestroyVectorArray_Serial(uS, NS);
free(pbar);
free(plist);
}
FreeUserData(data);
CVodeFree(&cvode_mem);
return(0);
}
void SundialsCvode::initialize()
{
int flag = 0;
if (_initialized) {
// Starting over with a new IC, but the same ODE
flag = CVodeReInit(sundialsMem, t0, y.forSundials());
if (check_flag(&flag, "CVodeReInit", 1)) {
throw DebugException("SundialsCvode::reInitialize: error in CVodeReInit");
}
CVodeSetMaxNumSteps(sundialsMem, maxNumSteps);
CVodeSetMinStep(sundialsMem, minStep);
return;
}
// On the first call to initialize, need to allocate and set up
// the Sundials solver, set tolerances and link the ODE functions
sundialsMem = CVodeCreate(linearMultistepMethod, nonlinearSolverMethod);
if (check_flag((void *)sundialsMem, "CVodeCreate", 0)) {
throw DebugException("SundialsCvode::initialize: error in CVodeCreate");
}
flag = CVodeInit(sundialsMem, f, t0, y.forSundials());
if (check_flag(&flag, "CVodeMalloc", 1)) {
throw DebugException("SundialsCvode::initialize: error in CVodeMalloc");
}
CVodeSVtolerances(sundialsMem, reltol, abstol.forSundials());
CVodeSetUserData(sundialsMem, theODE);
CVodeSetMaxNumSteps(sundialsMem, maxNumSteps);
CVodeSetMinStep(sundialsMem, minStep);
if (findRoots) {
rootsFound.resize(nRoots);
// Call CVodeRootInit to specify the root function g with nRoots components
flag = CVodeRootInit(sundialsMem, nRoots, g);
if (check_flag(&flag, "CVodeRootInit", 1)) {
throw DebugException("SundialsCvode::initialize: error in CVodeRootInit");
}
}
if (bandwidth_upper == -1 && bandwidth_lower == -1) {
// Call CVDense to specify the CVDENSE dense linear solver
flag = CVDense(sundialsMem, nEq);
if (check_flag(&flag, "CVDense", 1)) {
throw DebugException("SundialsCvode::initialize: error in CVDense");
}
// Set the Jacobian routine to denseJac (user-supplied)
flag = CVDlsSetDenseJacFn(sundialsMem, denseJac);
if (check_flag(&flag, "CVDlsSetDenseJacFn", 1)) {
throw DebugException("SundialsCvode::initialize: error in CVDlsSetDenseJacFn");
}
} else {
// Call CVDense to specify the CVBAND Banded linear solver
flag = CVBand(sundialsMem, nEq, bandwidth_upper, bandwidth_lower);
if (check_flag(&flag, "CVBand", 1)) {
throw DebugException("SundialsCvode::initialize: error in CVBand");
}
// Set the Jacobian routine to bandJac (user-supplied)
flag = CVDlsSetBandJacFn(sundialsMem, bandJac);
if (check_flag(&flag, "CVDlsSetBandJacFn", 1)) {
throw DebugException("SundialsCvode::initialize: error in CVDlsSetBandJacFn");
}
}
_initialized = true;
}
void CvodeSolver::initialize(const double &pVoiStart,
const int &pRatesStatesCount, double *pConstants,
double *pRates, double *pStates,
double *pAlgebraic,
ComputeRatesFunction pComputeRates)
{
if (!mSolver) {
// Retrieve some of the CVODE properties
double maximumStep = MaximumStepDefaultValue;
int maximumNumberOfSteps = MaximumNumberOfStepsDefaultValue;
QString integrationMethod = IntegrationMethodDefaultValue;
QString iterationType = IterationTypeDefaultValue;
QString linearSolver = LinearSolverDefaultValue;
QString preconditioner = PreconditionerDefaultValue;
int upperHalfBandwidth = UpperHalfBandwidthDefaultValue;
int lowerHalfBandwidth = LowerHalfBandwidthDefaultValue;
double relativeTolerance = RelativeToleranceDefaultValue;
double absoluteTolerance = AbsoluteToleranceDefaultValue;
if (mProperties.contains(MaximumStepId)) {
maximumStep = mProperties.value(MaximumStepId).toDouble();
} else {
emit error(QObject::tr("the 'maximum step' property value could not be retrieved"));
return;
}
if (mProperties.contains(MaximumNumberOfStepsId)) {
maximumNumberOfSteps = mProperties.value(MaximumNumberOfStepsId).toInt();
} else {
emit error(QObject::tr("the 'maximum number of steps' property value could not be retrieved"));
return;
}
if (mProperties.contains(IntegrationMethodId)) {
integrationMethod = mProperties.value(IntegrationMethodId).toString();
} else {
emit error(QObject::tr("the 'integration method' property value could not be retrieved"));
return;
}
if (mProperties.contains(IterationTypeId)) {
iterationType = mProperties.value(IterationTypeId).toString();
if (!iterationType.compare(NewtonIteration)) {
// We are dealing with a Newton iteration, so retrieve and check
// its linear solver
if (mProperties.contains(LinearSolverId)) {
linearSolver = mProperties.value(LinearSolverId).toString();
bool needUpperAndLowerHalfBandwidths = false;
if ( !linearSolver.compare(DenseLinearSolver)
|| !linearSolver.compare(DiagonalLinearSolver)) {
// We are dealing with a dense/diagonal linear solver,
// so nothing more to do
} else if (!linearSolver.compare(BandedLinearSolver)) {
// We are dealing with a banded linear solver, so we
// need both an upper and a lower half bandwidth
needUpperAndLowerHalfBandwidths = true;
} else {
// We are dealing with a GMRES/Bi-CGStab/TFQMR linear
// solver, so retrieve and check its preconditioner
if (mProperties.contains(PreconditionerId)) {
preconditioner = mProperties.value(PreconditionerId).toString();
} else {
emit error(QObject::tr("the 'preconditioner' property value could not be retrieved"));
return;
}
if (!preconditioner.compare(BandedPreconditioner)) {
// We are dealing with a banded preconditioner, so
// we need both an upper and a lower half bandwidth
needUpperAndLowerHalfBandwidths = true;
}
}
if (needUpperAndLowerHalfBandwidths) {
if (mProperties.contains(UpperHalfBandwidthId)) {
upperHalfBandwidth = mProperties.value(UpperHalfBandwidthId).toInt();
if ( (upperHalfBandwidth < 0)
|| (upperHalfBandwidth >= pRatesStatesCount)) {
emit error(QObject::tr("the 'upper half-bandwidth' property must have a value between 0 and %1").arg(pRatesStatesCount-1));
return;
}
} else {
emit error(QObject::tr("the 'upper half-bandwidth' property value could not be retrieved"));
return;
}
if (mProperties.contains(LowerHalfBandwidthId)) {
lowerHalfBandwidth = mProperties.value(LowerHalfBandwidthId).toInt();
if ( (lowerHalfBandwidth < 0)
|| (lowerHalfBandwidth >= pRatesStatesCount)) {
emit error(QObject::tr("the 'lower half-bandwidth' property must have a value between 0 and %1").arg(pRatesStatesCount-1));
return;
}
} else {
emit error(QObject::tr("the 'lower half-bandwidth' property value could not be retrieved"));
return;
}
}
} else {
emit error(QObject::tr("the 'linear solver' property value could not be retrieved"));
return;
}
}
} else {
emit error(QObject::tr("the 'iteration type' property value could not be retrieved"));
return;
}
if (mProperties.contains(RelativeToleranceId)) {
relativeTolerance = mProperties.value(RelativeToleranceId).toDouble();
if (relativeTolerance < 0) {
emit error(QObject::tr("the 'relative tolerance' property must have a value greater than or equal to 0"));
return;
}
} else {
emit error(QObject::tr("the 'relative tolerance' property value could not be retrieved"));
return;
}
if (mProperties.contains(AbsoluteToleranceId)) {
absoluteTolerance = mProperties.value(AbsoluteToleranceId).toDouble();
if (absoluteTolerance < 0) {
emit error(QObject::tr("the 'absolute tolerance' property must have a value greater than or equal to 0"));
return;
}
} else {
emit error(QObject::tr("the 'absolute tolerance' property value could not be retrieved"));
return;
}
if (mProperties.contains(InterpolateSolutionId)) {
mInterpolateSolution = mProperties.value(InterpolateSolutionId).toBool();
} else {
emit error(QObject::tr("the 'interpolate solution' property value could not be retrieved"));
return;
}
// Initialise the ODE solver itself
OpenCOR::Solver::OdeSolver::initialize(pVoiStart, pRatesStatesCount,
pConstants, pRates, pStates,
pAlgebraic, pComputeRates);
// Create the states vector
mStatesVector = N_VMake_Serial(pRatesStatesCount, pStates);
// Create the CVODE solver
bool newtonIteration = !iterationType.compare(NewtonIteration);
mSolver = CVodeCreate(!integrationMethod.compare(BdfMethod)?CV_BDF:CV_ADAMS,
newtonIteration?CV_NEWTON:CV_FUNCTIONAL);
// Use our own error handler
CVodeSetErrHandlerFn(mSolver, errorHandler, this);
// Initialise the CVODE solver
CVodeInit(mSolver, rhsFunction, pVoiStart, mStatesVector);
// Set some user data
mUserData = new CvodeSolverUserData(pConstants, pAlgebraic,
pComputeRates);
CVodeSetUserData(mSolver, mUserData);
// Set the maximum step
CVodeSetMaxStep(mSolver, maximumStep);
// Set the maximum number of steps
CVodeSetMaxNumSteps(mSolver, maximumNumberOfSteps);
// Set the linear solver, if needed
if (newtonIteration) {
if (!linearSolver.compare(DenseLinearSolver)) {
CVDense(mSolver, pRatesStatesCount);
} else if (!linearSolver.compare(BandedLinearSolver)) {
CVBand(mSolver, pRatesStatesCount, upperHalfBandwidth, lowerHalfBandwidth);
} else if (!linearSolver.compare(DiagonalLinearSolver)) {
CVDiag(mSolver);
} else {
// We are dealing with a GMRES/Bi-CGStab/TFQMR linear solver
if (!preconditioner.compare(BandedPreconditioner)) {
if (!linearSolver.compare(GmresLinearSolver))
CVSpgmr(mSolver, PREC_LEFT, 0);
else if (!linearSolver.compare(BiCgStabLinearSolver))
CVSpbcg(mSolver, PREC_LEFT, 0);
else
CVSptfqmr(mSolver, PREC_LEFT, 0);
CVBandPrecInit(mSolver, pRatesStatesCount, upperHalfBandwidth, lowerHalfBandwidth);
} else {
if (!linearSolver.compare(GmresLinearSolver))
CVSpgmr(mSolver, PREC_NONE, 0);
else if (!linearSolver.compare(BiCgStabLinearSolver))
CVSpbcg(mSolver, PREC_NONE, 0);
else
CVSptfqmr(mSolver, PREC_NONE, 0);
}
}
}
// Set the relative and absolute tolerances
CVodeSStolerances(mSolver, relativeTolerance, absoluteTolerance);
} else {
// Reinitialise the CVODE object
CVodeReInit(mSolver, pVoiStart, mStatesVector);
}
}
int calculate_abundances_(realtype *abundance, realtype *rate, realtype *density,
realtype *temperature, int *npart, int *nspec, int *nreac)
{
int neq = *nspec-1; /* Number of ODEs in the system */
realtype t0, t, tout; /* Initial, current and output times */
realtype *data; /* Array pointer to access data stored in vectors*/
N_Vector y; /* Vector of dependent variables that CVODE is to solve */
User_Data user_data; /* Data to be passed to the solver routines */
FILE *cvoderr; /* Log file for CVODE error messages */
void *cvode_mem; /* Memory allocated to the CVODE solver */
long int mxstep; /* Maximum number of internal steps */
int flag, status, nfails; /* CVODE return flag, status and failure counter */
/* Define the necessary external variables contained within the Fortran module CHEMISTRY_MODULE */
extern realtype chemistry_module_mp_relative_abundance_tolerance_ ; /* Relative error tolerance */
extern realtype chemistry_module_mp_absolute_abundance_tolerance_ ; /* Absolute error tolerance */
/* Define the necessary external variables contained within the Fortran module GLOBAL_MODULE */
extern realtype global_module_mp_start_time_; /* Start time for the chemical evolution (yr) */
extern realtype global_module_mp_end_time_; /* End time for the chemical evolution (yr) */
extern int global_module_mp_nelect_; /* Species index number for electron */
realtype reltol = chemistry_module_mp_relative_abundance_tolerance_;
realtype abstol = chemistry_module_mp_absolute_abundance_tolerance_;
realtype start_time = global_module_mp_start_time_;
realtype end_time = global_module_mp_end_time_;
realtype seconds_in_year = RCONST(3.1556926e7); /* Convert from years to seconds */
int nelect = global_module_mp_nelect_-1;
double cpu_start, cpu_end; /* CPU times */
#ifdef OPENMP
int nthread, thread; /* Number of threads and current thread number */
#endif
int n, i;
/* Open the error log files */
stderr = fopen("main.log", "a");
cvoderr = fopen("cvode.log", "a");
/* Specify the maximum number of internal steps */
mxstep = 10000000;
/* Initialize the global status flag */
status = 0;
#ifdef OPENMP
cpu_start = omp_get_wtime();
#else
cpu_start = clock();
#endif
#pragma omp parallel for default(none) schedule(dynamic) \
shared(npart, nspec, nreac, nelect, nthread, abundance, rate, density, temperature) \
shared(neq, start_time, end_time, reltol, abstol, mxstep, status, cvoderr, stderr) \
shared(seconds_in_year) \
private(i, t0, tout, t, y, data, user_data, cvode_mem, flag, nfails)
for (n = 0; n < *npart; n++) {
/* Store the number of threads being used */
#ifdef OPENMP
if (n == 0) nthread = omp_get_num_threads();
#endif
/* Reset the integration failure counter */
nfails = 0;
/* Specify the start and end time of the integration (in seconds) */
t0 = start_time*seconds_in_year;
tout = end_time*seconds_in_year;
/* Create a serial vector of length NEQ to contain the abundances */
y = NULL;
y = N_VNew_Serial(neq);
if (check_flag((void *)y, "N_VNew_Serial", 0)) status = 1;
/* Initialize y from the abundance array */
data = NV_DATA_S(y);
for (i = 0; i < neq; i++) {
#ifdef LOG_ODES
if (abundance[n*(*nspec)+i] > 0) data[i] = log(abundance[n*(*nspec)+i]);
else data[i] = log(abstol*abstol);
#else
data[i] = abundance[n*(*nspec)+i];
#endif
}
/* Create and allocate memory to user_data to contain the rates */
user_data = NULL;
user_data = (User_Data) malloc(sizeof *user_data);
if(check_flag((void *)user_data, "malloc", 2)) status = 1;
/* Initialize user_data with the array of reaction rate coefficients,
* the total number density, gas temperature and electron abundance */
user_data->rate = &rate[n*(*nreac)];
user_data->n_H = density[n];
user_data->T_g = temperature[n];
user_data->x_e = abundance[n*(*nspec)+nelect];
/* Call CVodeCreate to create the solver memory and specify the
* use of Backward Differentiation Formula and Newton iteration */
cvode_mem = NULL;
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void *)cvode_mem, "CVodeCreate", 0)) status = 1;
/* Call CVodeSetErrFile to direct all error messages to the log file */
flag = CVodeSetErrFile(cvode_mem, cvoderr);
if (check_flag(&flag, "CVodeSetErrFile", 1)) status = 1;
/* Call CVodeInit to initialize the integrator memory and specify the
* right hand side function in ydot = f(t,y), the inital time t0, and
* the initial dependent variable vector y */
flag = CVodeInit(cvode_mem, f, t0, y);
if (check_flag(&flag, "CVodeInit", 1)) status = 1;
/* Call CVodeSStolerances to set the relative and absolute tolerances */
flag = CVodeSStolerances(cvode_mem, reltol, abstol);
if (check_flag(&flag, "CVodeSStolerances", 1)) status = 1;
/* Call CVodeSetMaxNumSteps to set the maximum number of steps */
flag = CVodeSetMaxNumSteps(cvode_mem, mxstep);
if (check_flag(&flag, "CVodeSetMaxNumSteps", 1)) status = 1;
/* Specify the user-defined data to be passed to the various routines */
flag = CVodeSetUserData(cvode_mem, user_data);
if (check_flag(&flag, "CVodeSetUserData", 1)) status = 1;
/* Specify that the CVDense direct dense linear solver is to be used */
flag = CVDense(cvode_mem, neq);
if (check_flag(&flag, "CVDense", 1)) status = 1;
/* Specify that a user-supplied Jacobian routine (Jac) is to be used */
/* flag = CVDlsSetDenseJacFn(cvode_mem, Jac); */
/* if (check_flag(&flag, "CVDlsSetDenseJacFn", 1)) status = 1; */
tout = 1.0e-4*seconds_in_year;
do { /* Call CVode, check the return status and loop until the end time is reached */
flag = CVode(cvode_mem, tout, y, &t, CV_NORMAL);
#pragma omp critical (status)
if (flag == 0) {
if (nfails > 0) {
fprintf(cvoderr, "Call to CVODE successful: particle = %d, t = %8.2le yr, # steps = %ld\n\n", n, t/seconds_in_year, mxstep);
}
}
else {
nfails++;
if (flag == -1) {
if (nfails < 5) {
fprintf(cvoderr, " Particle %d: Doubling mxstep and continuing the integration.\n\n", n);
flag = CVodeSetMaxNumSteps(cvode_mem, mxstep);
if (check_flag(&flag, "CVodeSetMaxNumSteps", 1)) status = 1;
}
else {
fprintf(stderr, " WARNING! CVODE solver failed: flag = %d\n", flag);
fprintf(cvoderr, "ERROR! Fifth failure - aborting integration\n\n");
fprintf(cvoderr, "-----------------------------------------------\n");
fprintf(cvoderr, "CVODE Parameters:\n\n");
fprintf(cvoderr, "Particle %d\n\n", n);
fprintf(cvoderr, "Before:\n");
fprintf(cvoderr, "flag = %d\n", 0);
fprintf(cvoderr, "t = %8.2le yr\n", start_time);
fprintf(cvoderr, "tout = %8.2le yr\n", end_time);
fprintf(cvoderr, "dt = %8.2le yr\n\n", end_time-start_time);
fprintf(cvoderr, "After:\n");
fprintf(cvoderr, "flag = %d\n", flag);
fprintf(cvoderr, "t = %8.2le yr\n", t/seconds_in_year);
fprintf(cvoderr, "tout = %8.2le yr\n", tout/seconds_in_year);
fprintf(cvoderr, "dt = %8.2le yr\n", (tout-t)/seconds_in_year);
fprintf(cvoderr, "-----------------------------------------------\n\n");
status = flag;
}
}
else if (flag == -4) {
if (nfails < 5) {
fprintf(cvoderr, " Particle %d: Attempting to continue the integration using the same parameters.\n\n", n);
}
else {
fprintf(stderr, " WARNING! CVODE solver failed: flag = %d\n", flag);
fprintf(cvoderr, "ERROR! Fifth failure - aborting integration\n\n");
fprintf(cvoderr, "-----------------------------------------------\n");
fprintf(cvoderr, "CVODE Parameters:\n\n");
fprintf(cvoderr, "Particle %d\n\n", n);
fprintf(cvoderr, "Before:\n");
fprintf(cvoderr, "flag = %d\n", 0);
fprintf(cvoderr, "t = %8.2le yr\n", start_time);
fprintf(cvoderr, "tout = %8.2le yr\n", end_time);
fprintf(cvoderr, "dt = %8.2le yr\n\n", end_time-start_time);
fprintf(cvoderr, "After:\n");
fprintf(cvoderr, "flag = %d\n", flag);
fprintf(cvoderr, "t = %8.2le yr\n", t/seconds_in_year);
fprintf(cvoderr, "tout = %8.2le yr\n", tout/seconds_in_year);
fprintf(cvoderr, "dt = %8.2le yr\n", (tout-t)/seconds_in_year);
fprintf(cvoderr, "-----------------------------------------------\n\n");
status = flag;
}
}
else {
fprintf(stderr, " WARNING! CVODE solver failed: flag = %d\n", flag);
fprintf(cvoderr, "ERROR! CVODE failed with the following parameters:\n\n");
fprintf(cvoderr, "-----------------------------------------------\n");
fprintf(cvoderr, "CVODE Parameters:\n\n");
fprintf(cvoderr, "Particle %d\n\n", n);
fprintf(cvoderr, "Before:\n");
fprintf(cvoderr, "flag = %d\n", 0);
fprintf(cvoderr, "t = %8.2le yr\n", start_time);
fprintf(cvoderr, "tout = %8.2le yr\n", end_time);
fprintf(cvoderr, "dt = %8.2le yr\n\n", end_time-start_time);
fprintf(cvoderr, "After:\n");
fprintf(cvoderr, "flag = %d\n", flag);
fprintf(cvoderr, "t = %8.2le yr\n", t/seconds_in_year);
fprintf(cvoderr, "tout = %8.2le yr\n", tout/seconds_in_year);
fprintf(cvoderr, "dt = %8.2le yr\n", (tout-t)/seconds_in_year);
fprintf(cvoderr, "-----------------------------------------------\n\n");
status = flag;
nfails = 5;
}
}
tout = tout*10;
if (tout > end_time*seconds_in_year) tout = end_time*seconds_in_year;
} while (t < tout && nfails < 5);
/* Store the output values in the abundance array */
data = NV_DATA_S(y);
for (i = 0; i < neq; i++) {
#ifdef LOG_ODES
abundance[n*(*nspec)+i] = exp(data[i]);
#else
abundance[n*(*nspec)+i] = data[i];
#endif
if(abundance[n*(*nspec)+i] < abstol) abundance[n*(*nspec)+i] = 0;
}
abundance[n*(*nspec)+nelect] = user_data->x_e;
/* Free y vector memory allocation */
N_VDestroy_Serial(y);
/* Free user_data memory allocation */
free(user_data);
/* Free integrator memory allocation */
CVodeFree(&cvode_mem);
} /* End of for-loop over particles */
#ifdef OPENMP
cpu_end = omp_get_wtime();
#else
cpu_end = clock();
#endif
/* Close the error log files */
fclose(cvoderr);
fclose(stderr);
if (status != 0) {
fprintf(stdout, "\n ERROR! Calculation of abundances failed with status = %d\n\n", status);
#ifdef DEBUG
fprintf(stdout, " Elapsed time = %0.3f seconds\n", cpu_end-cpu_start);
#ifdef OPENMP
fprintf(stdout, " Threads used = %d (maximum %d)\n\n", nthread, omp_get_max_threads());
#endif
#endif
}
else {
#ifdef DEBUG
fprintf(stdout, " --> Elapsed time = %0.3f seconds\n", cpu_end-cpu_start);
#ifdef OPENMP
fprintf(stdout, " --> Threads used = %d (maximum %d)\n", nthread, omp_get_max_threads());
#endif
#endif
}
return(status);
}
void CVodesIntegrator::initialize(double t0, FuncEval& func)
{
m_neq = func.neq();
m_t0 = t0;
if (m_y) {
N_VDestroy_Serial(nv(m_y)); // free solution vector if already allocated
}
m_y = reinterpret_cast<void*>(N_VNew_Serial(m_neq)); // allocate solution vector
for (int i=0; i<m_neq; i++) {
NV_Ith_S(nv(m_y), i) = 0.0;
}
// check abs tolerance array size
if (m_itol == CV_SV && m_nabs < m_neq)
throw CVodesErr("not enough absolute tolerance values specified.");
func.getInitialConditions(m_t0, m_neq, NV_DATA_S(nv(m_y)));
if (m_cvode_mem) CVodeFree(&m_cvode_mem);
/*
* Specify the method and the iteration type:
* Cantera Defaults:
* CV_BDF - Use BDF methods
* CV_NEWTON - use newton's method
*/
m_cvode_mem = CVodeCreate(m_method, m_iter);
if (!m_cvode_mem) throw CVodesErr("CVodeCreate failed.");
int flag = 0;
#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23)
if (m_itol == CV_SV) {
// vector atol
flag = CVodeMalloc(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y), m_itol,
m_reltol, nv(m_abstol));
}
else {
// scalar atol
flag = CVodeMalloc(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y), m_itol,
m_reltol, &m_abstols);
}
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CVodesErr("Memory allocation failed.");
}
else if (flag == CV_ILL_INPUT) {
throw CVodesErr("Illegal value for CVodeMalloc input argument.");
}
else
throw CVodesErr("CVodeMalloc failed.");
}
#elif defined(SUNDIALS_VERSION_24)
flag = CVodeInit(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y));
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CVodesErr("Memory allocation failed.");
} else if (flag == CV_ILL_INPUT) {
throw CVodesErr("Illegal value for CVodeInit input argument.");
} else {
throw CVodesErr("CVodeInit failed.");
}
}
if (m_itol == CV_SV) {
flag = CVodeSVtolerances(m_cvode_mem, m_reltol, nv(m_abstol));
} else {
flag = CVodeSStolerances(m_cvode_mem, m_reltol, m_abstols);
}
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CVodesErr("Memory allocation failed.");
} else if (flag == CV_ILL_INPUT) {
throw CVodesErr("Illegal value for CVodeInit input argument.");
} else {
throw CVodesErr("CVodeInit failed.");
}
}
#else
printf("unknown sundials verson\n");
exit(-1);
#endif
if (m_type == DENSE + NOJAC) {
long int N = m_neq;
CVDense(m_cvode_mem, N);
}
else if (m_type == DIAG) {
CVDiag(m_cvode_mem);
}
else if (m_type == GMRES) {
CVSpgmr(m_cvode_mem, PREC_NONE, 0);
}
else if (m_type == BAND + NOJAC) {
long int N = m_neq;
long int nu = m_mupper;
long int nl = m_mlower;
CVBand(m_cvode_mem, N, nu, nl);
}
else {
throw CVodesErr("unsupported option");
}
// pass a pointer to func in m_data
m_fdata = new FuncData(&func, func.nparams());
//m_data = (void*)&func;
#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23)
flag = CVodeSetFdata(m_cvode_mem, (void*)m_fdata);
if (flag != CV_SUCCESS) {
throw CVodesErr("CVodeSetFdata failed.");
}
#elif defined(SUNDIALS_VERSION_24)
flag = CVodeSetUserData(m_cvode_mem, (void*)m_fdata);
if (flag != CV_SUCCESS) {
throw CVodesErr("CVodeSetUserData failed.");
}
#endif
if (func.nparams() > 0) {
sensInit(t0, func);
flag = CVodeSetSensParams(m_cvode_mem, DATA_PTR(m_fdata->m_pars),
NULL, NULL);
}
// set options
if (m_maxord > 0)
flag = CVodeSetMaxOrd(m_cvode_mem, m_maxord);
if (m_maxsteps > 0)
flag = CVodeSetMaxNumSteps(m_cvode_mem, m_maxsteps);
if (m_hmax > 0)
flag = CVodeSetMaxStep(m_cvode_mem, m_hmax);
}
void CVodesIntegrator::reinitialize(double t0, FuncEval& func)
{
m_t0 = t0;
//try {
func.getInitialConditions(m_t0, m_neq, NV_DATA_S(nv(m_y)));
//}
//catch (CanteraError) {
//showErrors();
//error("Teminating execution");
//}
int result, flag;
#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23)
if (m_itol == CV_SV) {
result = CVodeReInit(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y),
m_itol, m_reltol,
nv(m_abstol));
}
else {
result = CVodeReInit(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y),
m_itol, m_reltol,
&m_abstols);
}
if (result != CV_SUCCESS) {
throw CVodesErr("CVodeReInit failed. result = "+int2str(result));
}
#elif defined(SUNDIALS_VERSION_24)
result = CVodeReInit(m_cvode_mem, m_t0, nv(m_y));
if (result != CV_SUCCESS) {
throw CVodesErr("CVodeReInit failed. result = "+int2str(result));
}
#endif
if (m_type == DENSE + NOJAC) {
long int N = m_neq;
CVDense(m_cvode_mem, N);
}
else if (m_type == DIAG) {
CVDiag(m_cvode_mem);
}
else if (m_type == BAND + NOJAC) {
long int N = m_neq;
long int nu = m_mupper;
long int nl = m_mlower;
CVBand(m_cvode_mem, N, nu, nl);
}
else if (m_type == GMRES) {
CVSpgmr(m_cvode_mem, PREC_NONE, 0);
}
else {
throw CVodesErr("unsupported option");
}
// set options
if (m_maxord > 0)
flag = CVodeSetMaxOrd(m_cvode_mem, m_maxord);
if (m_maxsteps > 0)
flag = CVodeSetMaxNumSteps(m_cvode_mem, m_maxsteps);
if (m_hmax > 0)
flag = CVodeSetMaxStep(m_cvode_mem, m_hmax);
}
/** \brief Call the ODE solver.
*
* \param neq The number of equations.
* \param x_f A pointer to a vector of \c neq variables, giving the
* initial state vector on entry and the final state vector on exit.
* \param abstol_f A pointer to a vector of \c neq variables, giving
* the absolute error tolerance for the corresponding state vector
* component.
* \param reltol_f The scalar relative tolerance.
* \param t_initial_f The initial time (s).
* \param t_final_f The final time (s).
* \return A result code (0 is success).
*/
int condense_solver(int neq, double *x_f, double *abstol_f, double reltol_f,
double t_initial_f, double t_final_f)
{
realtype reltol, t_initial, t_final, t, tout;
N_Vector y, abstol;
void *cvode_mem;
CVodeMem cv_mem;
int flag, i, pretype, maxl;
realtype *y_data, *abstol_data;
y = abstol = NULL;
cvode_mem = NULL;
y = N_VNew_Serial(neq);
if (condense_check_flag((void *)y, "N_VNew_Serial", 0))
return PMC_CONDENSE_SOLVER_INIT_Y;
abstol = N_VNew_Serial(neq);
if (condense_check_flag((void *)abstol, "N_VNew_Serial", 0))
return PMC_CONDENSE_SOLVER_INIT_ABSTOL;
y_data = NV_DATA_S(y);
abstol_data = NV_DATA_S(abstol);
for (i = 0; i < neq; i++) {
y_data[i] = x_f[i];
abstol_data[i] = abstol_f[i];
}
reltol = reltol_f;
t_initial = t_initial_f;
t_final = t_final_f;
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if (condense_check_flag((void *)cvode_mem, "CVodeCreate", 0))
return PMC_CONDENSE_SOLVER_INIT_CVODE_MEM;
flag = CVodeInit(cvode_mem, condense_vf, t_initial, y);
if (condense_check_flag(&flag, "CVodeInit", 1))
return PMC_CONDENSE_SOLVER_INIT_CVODE;
flag = CVodeSVtolerances(cvode_mem, reltol, abstol);
if (condense_check_flag(&flag, "CVodeSVtolerances", 1))
return PMC_CONDENSE_SOLVER_SVTOL;
flag = CVodeSetMaxNumSteps(cvode_mem, 100000);
if (condense_check_flag(&flag, "CVodeSetMaxNumSteps", 1))
return PMC_CONDENSE_SOLVER_SET_MAX_STEPS;
/*******************************************************/
// dense solver
//flag = CVDense(cvode_mem, neq);
//if (condense_check_flag(&flag, "CVDense", 1)) return(1);
/*******************************************************/
/*******************************************************/
// iterative solver
//pretype = PREC_LEFT;
//maxl = 0;
//flag = CVSptfqmr(cvode_mem, pretype, maxl);
//if (condense_check_flag(&flag, "CVSptfqmr", 1)) return(1);
//flag = CVSpilsSetJacTimesVecFn(cvode_mem, condense_jtimes);
//if (condense_check_flag(&flag, "CVSpilsSetJacTimesVecFn", 1)) return(1);
//flag = CVSpilsSetPreconditioner(cvode_mem, NULL, condense_prec);
//if (condense_check_flag(&flag, "CVSpilsSetPreconditioner", 1)) return(1);
/*******************************************************/
/*******************************************************/
// explicit solver
cv_mem = (CVodeMem)cvode_mem;
cv_mem->cv_linit = condense_solver_Init;
cv_mem->cv_lsetup = condense_solver_Setup;
cv_mem->cv_lsolve = condense_solver_Solve;
cv_mem->cv_lfree = condense_solver_Free;
/*******************************************************/
t = t_initial;
flag = CVode(cvode_mem, t_final, y, &t, CV_NORMAL);
if (condense_check_flag(&flag, "CVode", 1))
return PMC_CONDENSE_SOLVER_FAIL;
for (i = 0; i < neq; i++) {
x_f[i] = y_data[i];
}
N_VDestroy_Serial(y);
N_VDestroy_Serial(abstol);
CVodeFree(&cvode_mem);
return PMC_CONDENSE_SOLVER_SUCCESS;
}
Bloch_McConnell_CV_Model::Bloch_McConnell_CV_Model () {
m_world->solverSettings = new bmnvec;
/* for (int i=0;i<OPT_SIZE;i++) {m_iopt[i]=0; m_ropt[i]=0.0;}
m_iopt[MXSTEP] = 1000000;
m_ropt[HMAX] = 10000.0;// the maximum stepsize in msec of the integrator*/
m_reltol = RTOL;
//cvode2.5:
// create cvode memory pointer; no mallocs done yet.
// m_cvode_mem = CVodeCreate(CV_BDF,CV_NEWTON);
m_cvode_mem = CVodeCreate(CV_ADAMS,CV_FUNCTIONAL);
// cvode allocate memory.
// do CVodeMalloc with dummy values y0,abstol once here;
// -> CVodeReInit can later be used
//HACK
int pools = m_world->GetNoOfCompartments();
N_Vector y0,abstol;
y0 = N_VNew_Serial(NEQ*pools);
abstol = N_VNew_Serial(NEQ*pools);
((bmnvec*) (m_world->solverSettings))->abstol = N_VNew_Serial(pools*NEQ);
for(int i = 0; i< pools*NEQ; i+=NEQ){
NV_Ith_S(y0,AMPL+i) = 0.0; NV_Ith_S(y0,PHASE+i) = 0.0; NV_Ith_S(y0,ZC+i) = 0.0;
NV_Ith_S(abstol,AMPL+i) = ATOL1; NV_Ith_S(abstol,PHASE+i) = ATOL2; NV_Ith_S(abstol,ZC+i) = ATOL3;
}
#ifndef CVODE26
if(CVodeMalloc(m_cvode_mem,bloch,0,y0,CV_SV,m_reltol,abstol) != CV_SUCCESS ) {
cout << "CVodeMalloc failed! aborting..." << endl;exit (-1);
}
if(CVodeSetFdata(m_cvode_mem, (void *) m_world) !=CV_SUCCESS) {
cout << "CVode function data could not be set. Panic!" << endl;exit (-1);
}
#else
if(CVodeInit(m_cvode_mem,bloch,0,y0) != CV_SUCCESS ) {
cout << "CVodeInit failed! aborting..." << endl;exit (-1);
}
if(CVodeSVtolerances(m_cvode_mem, m_reltol, abstol)!= CV_SUCCESS){
cout << "CVodeSVtolerances failed! aborting..." << endl;exit (-1);
}
if(CVodeSetUserData(m_cvode_mem, (void *) m_world) !=CV_SUCCESS) {
cout << "CVode function data could not be set. Panic!" << endl;exit (-1);
}
#endif
/* int flag;
int blub = (3*pools);
flag = CVDense(m_cvode_mem, blub);
if (flag == CVDENSE_SUCCESS)
cout<< "great" <<endl;
else
cout<< "bad" <<endl;
*/
N_VDestroy_Serial(y0);
N_VDestroy_Serial(abstol);
/*if(CVodeSetFdata(m_cvode_mem, (void *) m_world) !=CV_SUCCESS) {
cout << "CVode function data could not be set. Panic!" << endl;
exit (-1);
}
// set CVODE initial step size
// CVodeSetInitStep(m_cvode_mem, 1e-4);
// set CVODE maximum step size
CVodeSetMaxErrTestFails(m_cvode_mem, 10);
// set CVODE minimum step size
CVodeSetMinStep(m_cvode_mem, 1e-15);
*/
CVodeSetMaxNumSteps(m_cvode_mem, 10000000);
// maximum number of warnings t+h = t (if number negative -> no warnings are issued )
CVodeSetMaxHnilWarns(m_cvode_mem,2);
}
void FCV_REINIT(realtype *t0, realtype *y0, int *iatol, realtype *rtol,
realtype *atol, int *optin, long int *iopt,
realtype *ropt, int *ier)
{
int itol;
void *atolptr;
atolptr = NULL;
N_VSetArrayPointer(y0, F2C_vec);
switch (*iatol) {
case 1:
itol = CV_SS;
atolptr = (void *) atol;
break;
case 2:
F2C_atolvec = N_VClone(F2C_vec);
data_F2C_atolvec = N_VGetArrayPointer(F2C_atolvec);
N_VSetArrayPointer(atol, F2C_atolvec);
itol = CV_SV;
atolptr = (void *) F2C_atolvec;
break;
case 3:
itol = CV_WF;
}
/*
Call CVodeSet* and CVReInit to re-initialize CVODE:
CVf is the user's right-hand side function in y'=f(t,y)
t0 is the initial time
F2C_vec is the initial dependent variable vector
itol specifies tolerance type
rtol is the scalar relative tolerance
atolptr is the absolute tolerance pointer (to scalar or vector or function)
*/
if (*optin == 1) {
CV_optin = TRUE;
if (iopt[0] > 0) CVodeSetMaxOrd(CV_cvodemem, (int)iopt[0]);
if (iopt[1] > 0) CVodeSetMaxNumSteps(CV_cvodemem, iopt[1]);
if (iopt[2] > 0) CVodeSetMaxHnilWarns(CV_cvodemem, (int)iopt[2]);
if (iopt[13] > 0) CVodeSetStabLimDet(CV_cvodemem, TRUE);
if (iopt[21] > 0) CVodeSetMaxErrTestFails(CV_cvodemem, (int)iopt[21]);
if (iopt[22] > 0) CVodeSetMaxNonlinIters(CV_cvodemem, (int)iopt[22]);
if (iopt[23] > 0) CVodeSetMaxConvFails(CV_cvodemem, (int)iopt[23]);
if (ropt[0] != ZERO) CVodeSetInitStep(CV_cvodemem, ropt[0]);
if (ropt[1] > ZERO) CVodeSetMaxStep(CV_cvodemem, ropt[1]);
if (ropt[2] > ZERO) CVodeSetMinStep(CV_cvodemem, ropt[2]);
if (ropt[7] != ZERO) CVodeSetStopTime(CV_cvodemem, ropt[7]);
if (ropt[8] > ZERO) CVodeSetNonlinConvCoef(CV_cvodemem, ropt[8]);
} else {
CV_optin = FALSE;
}
*ier = CVodeReInit(CV_cvodemem, FCVf, *t0, F2C_vec, itol, *rtol, atolptr);
/* reset data pointer into F2C_vec */
N_VSetArrayPointer(data_F2C_vec, F2C_vec);
/* destroy F2C_atolvec if allocated */
if (F2C_atolvec != NULL) {
N_VSetArrayPointer(data_F2C_atolvec, F2C_atolvec);
N_VDestroy(F2C_atolvec);
}
if (*ier != CV_SUCCESS) {
*ier = -1;
return;
}
CV_iopt = iopt;
CV_ropt = ropt;
return;
}
PetscErrorCode TSSetUp_Sundials(TS ts)
{
TS_Sundials *cvode = (TS_Sundials*)ts->data;
PetscErrorCode ierr;
PetscInt glosize,locsize,i,flag;
PetscScalar *y_data,*parray;
void *mem;
PC pc;
PCType pctype;
PetscBool pcnone;
PetscFunctionBegin;
/* get the vector size */
ierr = VecGetSize(ts->vec_sol,&glosize);CHKERRQ(ierr);
ierr = VecGetLocalSize(ts->vec_sol,&locsize);CHKERRQ(ierr);
/* allocate the memory for N_Vec y */
cvode->y = N_VNew_Parallel(cvode->comm_sundials,locsize,glosize);
if (!cvode->y) SETERRQ(PETSC_COMM_SELF,1,"cvode->y is not allocated");
/* initialize N_Vec y: copy ts->vec_sol to cvode->y */
ierr = VecGetArray(ts->vec_sol,&parray);CHKERRQ(ierr);
y_data = (PetscScalar*) N_VGetArrayPointer(cvode->y);
for (i = 0; i < locsize; i++) y_data[i] = parray[i];
ierr = VecRestoreArray(ts->vec_sol,NULL);CHKERRQ(ierr);
ierr = VecDuplicate(ts->vec_sol,&cvode->update);CHKERRQ(ierr);
ierr = VecDuplicate(ts->vec_sol,&cvode->ydot);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)ts,(PetscObject)cvode->update);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)ts,(PetscObject)cvode->ydot);CHKERRQ(ierr);
/*
Create work vectors for the TSPSolve_Sundials() routine. Note these are
allocated with zero space arrays because the actual array space is provided
by Sundials and set using VecPlaceArray().
*/
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)ts),1,locsize,PETSC_DECIDE,0,&cvode->w1);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)ts),1,locsize,PETSC_DECIDE,0,&cvode->w2);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)ts,(PetscObject)cvode->w1);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)ts,(PetscObject)cvode->w2);CHKERRQ(ierr);
/* Call CVodeCreate to create the solver memory and the use of a Newton iteration */
mem = CVodeCreate(cvode->cvode_type, CV_NEWTON);
if (!mem) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_MEM,"CVodeCreate() fails");
cvode->mem = mem;
/* Set the pointer to user-defined data */
flag = CVodeSetUserData(mem, ts);
if (flag) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVodeSetUserData() fails");
/* Sundials may choose to use a smaller initial step, but will never use a larger step. */
flag = CVodeSetInitStep(mem,(realtype)ts->time_step);
if (flag) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_LIB,"CVodeSetInitStep() failed");
if (cvode->mindt > 0) {
flag = CVodeSetMinStep(mem,(realtype)cvode->mindt);
if (flag) {
if (flag == CV_MEM_NULL) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_LIB,"CVodeSetMinStep() failed, cvode_mem pointer is NULL");
else if (flag == CV_ILL_INPUT) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_LIB,"CVodeSetMinStep() failed, hmin is nonpositive or it exceeds the maximum allowable step size");
else SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_LIB,"CVodeSetMinStep() failed");
}
}
if (cvode->maxdt > 0) {
flag = CVodeSetMaxStep(mem,(realtype)cvode->maxdt);
if (flag) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_LIB,"CVodeSetMaxStep() failed");
}
/* Call CVodeInit to initialize the integrator memory and specify the
* user's right hand side function in u'=f(t,u), the inital time T0, and
* the initial dependent variable vector cvode->y */
flag = CVodeInit(mem,TSFunction_Sundials,ts->ptime,cvode->y);
if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVodeInit() fails, flag %d",flag);
/* specifies scalar relative and absolute tolerances */
flag = CVodeSStolerances(mem,cvode->reltol,cvode->abstol);
if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVodeSStolerances() fails, flag %d",flag);
/* Specify max num of steps to be taken by cvode in its attempt to reach the next output time */
flag = CVodeSetMaxNumSteps(mem,ts->max_steps);
/* call CVSpgmr to use GMRES as the linear solver. */
/* setup the ode integrator with the given preconditioner */
ierr = TSSundialsGetPC(ts,&pc);CHKERRQ(ierr);
ierr = PCGetType(pc,&pctype);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)pc,PCNONE,&pcnone);CHKERRQ(ierr);
if (pcnone) {
flag = CVSpgmr(mem,PREC_NONE,0);
if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVSpgmr() fails, flag %d",flag);
} else {
flag = CVSpgmr(mem,PREC_LEFT,cvode->maxl);
if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVSpgmr() fails, flag %d",flag);
/* Set preconditioner and solve routines Precond and PSolve,
and the pointer to the user-defined block data */
flag = CVSpilsSetPreconditioner(mem,TSPrecond_Sundials,TSPSolve_Sundials);
if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVSpilsSetPreconditioner() fails, flag %d", flag);
}
flag = CVSpilsSetGSType(mem, MODIFIED_GS);
if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVSpgmrSetGSType() fails, flag %d",flag);
PetscFunctionReturn(0);
}
int Solver::init(rhsfunc f, int argc, char **argv, bool restarting, int nout, real tstep)
{
#ifdef CHECK
int msg_point = msg_stack.push("Initialising CVODE solver");
#endif
/// Call the generic initialisation first
if(GenericSolver::init(f, argc, argv, restarting, nout, tstep))
return 1;
// Save nout and tstep for use in run
NOUT = nout;
TIMESTEP = tstep;
output.write("Initialising SUNDIALS' CVODE solver\n");
// Set the rhs solver function
func = f;
// Calculate number of variables (in generic_solver)
int local_N = getLocalN();
// Get total problem size
int neq;
if(MPI_Allreduce(&local_N, &neq, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD)) {
output.write("\tERROR: MPI_Allreduce failed!\n");
return 1;
}
output.write("\t3d fields = %d, 2d fields = %d neq=%d, local_N=%d\n",
n3Dvars(), n2Dvars(), neq, local_N);
// Allocate memory
if((uvec = N_VNew_Parallel(MPI_COMM_WORLD, local_N, neq)) == NULL)
bout_error("ERROR: SUNDIALS memory allocation failed\n");
// Put the variables into uvec
if(save_vars(NV_DATA_P(uvec)))
bout_error("\tERROR: Initial variable value not set\n");
/// Get options
real abstol, reltol;
int maxl;
int mudq, mldq;
int mukeep, mlkeep;
bool use_precon, use_jacobian;
real max_timestep;
bool adams_moulton, func_iter; // Time-integration method
options.setSection("solver");
options.get("mudq", mudq, n3Dvars()*(MXSUB+2));
options.get("mldq", mldq, n3Dvars()*(MXSUB+2));
options.get("mukeep", mukeep, n3Dvars()+n2Dvars());
options.get("mlkeep", mlkeep, n3Dvars()+n2Dvars());
options.get("ATOL", abstol, 1.0e-12);
options.get("RTOL", reltol, 1.0e-5);
options.get("maxl", maxl, 5);
options.get("use_precon", use_precon, false);
options.get("use_jacobian", use_jacobian, false);
options.get("max_timestep", max_timestep, -1.);
int mxsteps; // Maximum number of steps to take between outputs
options.get("pvode_mxstep", mxsteps, 500);
options.get("adams_moulton", adams_moulton, false);
int lmm = CV_BDF;
if(adams_moulton) {
// By default use functional iteration for Adams-Moulton
lmm = CV_ADAMS;
output.write("\tUsing Adams-Moulton implicit multistep method\n");
options.get("func_iter", func_iter, true);
}else {
output.write("\tUsing BDF method\n");
// Use Newton iteration for BDF
options.get("func_iter", func_iter, false);
}
int iter = CV_NEWTON;
if(func_iter)
iter = CV_FUNCTIONAL;
// Call CVodeCreate
if((cvode_mem = CVodeCreate(lmm, iter)) == NULL)
bout_error("ERROR: CVodeCreate failed\n");
if( CVodeSetUserData(cvode_mem, this) < 0 ) // For callbacks, need pointer to solver object
bout_error("ERROR: CVodeSetUserData failed\n");
if( CVodeInit(cvode_mem, cvode_rhs, simtime, uvec) < 0 )
bout_error("ERROR: CVodeInit failed\n");
if( CVodeSStolerances(cvode_mem, reltol, abstol) < 0 )
bout_error("ERROR: CVodeSStolerances failed\n");
CVodeSetMaxNumSteps(cvode_mem, mxsteps);
if(max_timestep > 0.0) {
// Setting a maximum timestep
CVodeSetMaxStep(cvode_mem, max_timestep);
}
/// Newton method can include Preconditioners and Jacobian function
if(!func_iter) {
output.write("\tUsing Newton iteration\n");
/// Set Preconditioner
if(use_precon) {
if( CVSpgmr(cvode_mem, PREC_LEFT, maxl) != CVSPILS_SUCCESS )
bout_error("ERROR: CVSpgmr failed\n");
if(prefunc == NULL) {
output.write("\tUsing BBD preconditioner\n");
if( CVBBDPrecInit(cvode_mem, local_N, mudq, mldq,
mukeep, mlkeep, ZERO, cvode_bbd_rhs, NULL) )
bout_error("ERROR: CVBBDPrecInit failed\n");
}else {
output.write("\tUsing user-supplied preconditioner\n");
if( CVSpilsSetPreconditioner(cvode_mem, NULL, cvode_pre) )
bout_error("ERROR: CVSpilsSetPreconditioner failed\n");
}
}else {
// Not using preconditioning
output.write("\tNo preconditioning\n");
if( CVSpgmr(cvode_mem, PREC_NONE, maxl) != CVSPILS_SUCCESS )
bout_error("ERROR: CVSpgmr failed\n");
}
/// Set Jacobian-vector multiplication function
if((use_jacobian) && (jacfunc != NULL)) {
output.write("\tUsing user-supplied Jacobian function\n");
if( CVSpilsSetJacTimesVecFn(cvode_mem, cvode_jac) != CVSPILS_SUCCESS )
bout_error("ERROR: CVSpilsSetJacTimesVecFn failed\n");
}else
output.write("\tUsing difference quotient approximation for Jacobian\n");
}else {
output.write("\tUsing Functional iteration\n");
}
#ifdef CHECK
msg_stack.pop(msg_point);
#endif
return(0);
}
void Cvode::initialize()
{
_properties = dynamic_cast<ISystemProperties*>(_system);
_continuous_system = dynamic_cast<IContinuous*>(_system);
_event_system = dynamic_cast<IEvent*>(_system);
_mixed_system = dynamic_cast<IMixedSystem*>(_system);
_time_system = dynamic_cast<ITime*>(_system);
IGlobalSettings* global_settings = dynamic_cast<ISolverSettings*>(_cvodesettings)->getGlobalSettings();
// Kennzeichnung, dass initialize()() (vor der Integration) aufgerufen wurde
_idid = 5000;
_tLastEvent = 0.0;
_event_n = 0;
SolverDefaultImplementation::initialize();
_dimSys = _continuous_system->getDimContinuousStates();
_dimZeroFunc = _event_system->getDimZeroFunc();
if (_dimSys == 0)
_dimSys = 1; // introduce dummy state
if (_dimSys <= 0)
{
_idid = -1;
throw ModelicaSimulationError(SOLVER,"Cvode::initialize()");
}
else
{
// Allocate state vectors, stages and temporary arrays
if (_z)
delete[] _z;
if (_zInit)
delete[] _zInit;
if (_zWrite)
delete[] _zWrite;
if (_zeroSign)
delete[] _zeroSign;
if (_absTol)
delete[] _absTol;
if(_delta)
delete [] _delta;
if(_deltaInv)
delete [] _deltaInv;
if(_ysave)
delete [] _ysave;
_z = new double[_dimSys];
_zInit = new double[_dimSys];
_zWrite = new double[_dimSys];
_zeroSign = new int[_dimZeroFunc];
_absTol = new double[_dimSys];
_delta =new double[_dimSys];
_deltaInv =new double[_dimSys];
_ysave =new double[_dimSys];
memset(_z, 0, _dimSys * sizeof(double));
memset(_zInit, 0, _dimSys * sizeof(double));
memset(_ysave, 0, _dimSys * sizeof(double));
// Counter initialisieren
_outStps = 0;
if (_cvodesettings->getDenseOutput())
{
// Ausgabeschrittweite
_hOut = global_settings->gethOutput();
}
// Allocate memory for the solver
_cvodeMem = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void*) _cvodeMem, "CVodeCreate", 0))
{
_idid = -5;
throw ModelicaSimulationError(SOLVER,/*_idid,_tCurrent,*/"Cvode::initialize()");
}
//
// Make Cvode ready for integration
//
// Set initial values for CVODE
_continuous_system->evaluateAll(IContinuous::CONTINUOUS);
_continuous_system->getContinuousStates(_zInit);
memcpy(_z, _zInit, _dimSys * sizeof(double));
// Get nominal values
_absTol[0] = 1.0; // in case of dummy state
_continuous_system->getNominalStates(_absTol);
for (int i = 0; i < _dimSys; i++)
_absTol[i] *= dynamic_cast<ISolverSettings*>(_cvodesettings)->getATol();
_CV_y0 = N_VMake_Serial(_dimSys, _zInit);
_CV_y = N_VMake_Serial(_dimSys, _z);
_CV_yWrite = N_VMake_Serial(_dimSys, _zWrite);
_CV_absTol = N_VMake_Serial(_dimSys, _absTol);
if (check_flag((void*) _CV_y0, "N_VMake_Serial", 0))
{
_idid = -5;
throw ModelicaSimulationError(SOLVER,"Cvode::initialize()");
}
// Initialize Cvode (Initial values are required)
_idid = CVodeInit(_cvodeMem, CV_fCallback, _tCurrent, _CV_y0);
if (_idid < 0)
{
_idid = -5;
throw ModelicaSimulationError(SOLVER,"Cvode::initialize()");
}
// Set Tolerances
_idid = CVodeSVtolerances(_cvodeMem, dynamic_cast<ISolverSettings*>(_cvodesettings)->getRTol(), _CV_absTol); // RTOL and ATOL
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"CVode::initialize()");
// Set the pointer to user-defined data
_idid = CVodeSetUserData(_cvodeMem, _data);
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"Cvode::initialize()");
_idid = CVodeSetInitStep(_cvodeMem, 1e-6); // INITIAL STEPSIZE
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"Cvode::initialize()");
_idid = CVodeSetMaxOrd(_cvodeMem, 5); // Max Order
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"CVoder::initialize()");
_idid = CVodeSetMaxConvFails(_cvodeMem, 100); // Maximale Fehler im Konvergenztest
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"CVoder::initialize()");
_idid = CVodeSetStabLimDet(_cvodeMem, TRUE); // Stability Detection
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"CVoder::initialize()");
_idid = CVodeSetMinStep(_cvodeMem, dynamic_cast<ISolverSettings*>(_cvodesettings)->getLowerLimit()); // MINIMUM STEPSIZE
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"CVode::initialize()");
_idid = CVodeSetMaxStep(_cvodeMem, global_settings->getEndTime() / 10.0); // MAXIMUM STEPSIZE
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"CVode::initialize()");
_idid = CVodeSetMaxNonlinIters(_cvodeMem, 5); // Max number of iterations
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"CVode::initialize()");
_idid = CVodeSetMaxErrTestFails(_cvodeMem, 100);
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"CVode::initialize()");
_idid = CVodeSetMaxNumSteps(_cvodeMem, 1e3); // Max Number of steps
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,/*_idid,_tCurrent,*/"Cvode::initialize()");
// Initialize linear solver
#ifdef USE_SUNDIALS_LAPACK
_idid = CVLapackDense(_cvodeMem, _dimSys);
#else
_idid = CVDense(_cvodeMem, _dimSys);
#endif
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"Cvode::initialize()");
// Use own jacobian matrix
// Check if Colored Jacobians are worth to use
#if SUNDIALS_MAJOR_VERSION >= 2 || (SUNDIALS_MAJOR_VERSION == 2 && SUNDIALS_MINOR_VERSION >= 4)
_maxColors = _system->getAMaxColors();
if(_maxColors < _dimSys && _continuous_system->getDimContinuousStates() > 0)
{
// _idid = CVDlsSetDenseJacFn(_cvodeMem, &CV_JCallback);
// initializeColoredJac();
}
#endif
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,"CVode::initialize()");
if (_dimZeroFunc)
{
_idid = CVodeRootInit(_cvodeMem, _dimZeroFunc, &CV_ZerofCallback);
memset(_zeroSign, 0, _dimZeroFunc * sizeof(int));
_idid = CVodeSetRootDirection(_cvodeMem, _zeroSign);
if (_idid < 0)
throw ModelicaSimulationError(SOLVER,/*_idid,_tCurrent,*/"CVode::initialize()");
memset(_zeroSign, -1, _dimZeroFunc * sizeof(int));
memset(_zeroVal, -1, _dimZeroFunc * sizeof(int));
}
_cvode_initialized = true;
LOGGER_WRITE("Cvode: initialized",LC_SOLV,LL_DEBUG);
}
}
void FCV_MALLOC(realtype *t0, realtype *y0,
int *meth, int *itmeth, int *iatol,
realtype *rtol, realtype *atol,
int *optin, long int *iopt, realtype *ropt,
int *ier)
{
int lmm, iter, itol;
void *atolptr;
atolptr = NULL;
if(F2C_vec->ops->nvgetarraypointer == NULL ||
F2C_vec->ops->nvsetarraypointer == NULL) {
*ier = -1;
printf("A required vector operation is not implemented.\n\n");
return;
}
/* Save the data array in F2C_vec into data_F2C_vec and then
overwrite it with y0 */
data_F2C_vec = N_VGetArrayPointer(F2C_vec);
N_VSetArrayPointer(y0, F2C_vec);
lmm = (*meth == 1) ? CV_ADAMS : CV_BDF;
iter = (*itmeth == 1) ? CV_FUNCTIONAL : CV_NEWTON;
switch (*iatol) {
case 1:
F2C_atolvec = NULL;
itol = CV_SS;
atolptr = (void *) atol;
break;
case 2:
F2C_atolvec = N_VClone(F2C_vec);
data_F2C_atolvec = N_VGetArrayPointer(F2C_atolvec);
N_VSetArrayPointer(atol, F2C_atolvec);
itol = CV_SV;
atolptr = (void *) F2C_atolvec;
break;
case 3:
F2C_atolvec = NULL;
itol = CV_WF;
break;
}
/*
Call CVodeCreate, CVodeSet*, and CVodeMalloc to initialize CVODE:
lmm is the method specifier
iter is the iteration method specifier
CVf is the user's right-hand side function in y'=f(t,y)
*t0 is the initial time
F2C_vec is the initial dependent variable vector
itol specifies tolerance type
rtol is the scalar relative tolerance
atolptr is the absolute tolerance pointer (to scalar or vector or function)
A pointer to CVODE problem memory is createded and stored in CV_cvodemem.
*/
*ier = 0;
CV_cvodemem = CVodeCreate(lmm, iter);
if (CV_cvodemem == NULL) {
*ier = -1;
return;
}
if (*optin == 1) {
CV_optin = TRUE;
if (iopt[0] > 0) CVodeSetMaxOrd(CV_cvodemem, (int)iopt[0]);
if (iopt[1] > 0) CVodeSetMaxNumSteps(CV_cvodemem, iopt[1]);
if (iopt[2] > 0) CVodeSetMaxHnilWarns(CV_cvodemem, (int)iopt[2]);
if (iopt[13] > 0) CVodeSetStabLimDet(CV_cvodemem, TRUE);
if (iopt[21] > 0) CVodeSetMaxErrTestFails(CV_cvodemem, (int)iopt[21]);
if (iopt[22] > 0) CVodeSetMaxNonlinIters(CV_cvodemem, (int)iopt[22]);
if (iopt[23] > 0) CVodeSetMaxConvFails(CV_cvodemem, (int)iopt[23]);
if (ropt[0] != ZERO) CVodeSetInitStep(CV_cvodemem, ropt[0]);
if (ropt[1] > ZERO) CVodeSetMaxStep(CV_cvodemem, ropt[1]);
if (ropt[2] > ZERO) CVodeSetMinStep(CV_cvodemem, ropt[2]);
if (ropt[7] != ZERO) CVodeSetStopTime(CV_cvodemem, ropt[7]);
if (ropt[8] > ZERO) CVodeSetNonlinConvCoef(CV_cvodemem, ropt[8]);
} else {
CV_optin = FALSE;
}
*ier = CVodeMalloc(CV_cvodemem, FCVf, *t0, F2C_vec, itol, *rtol, atolptr);
/* reset data pointer into F2C_vec */
N_VSetArrayPointer(data_F2C_vec, F2C_vec);
/* destroy F2C_atolvec if allocated */
if (F2C_atolvec != NULL) {
N_VSetArrayPointer(data_F2C_atolvec, F2C_atolvec);
N_VDestroy(F2C_atolvec);
}
if(*ier != CV_SUCCESS) {
*ier = -1;
return;
}
/* Store the unit roundoff in ropt for user access */
ropt[9] = UNIT_ROUNDOFF;
CV_iopt = iopt;
CV_ropt = ropt;
return;
}
/*
** ========
** main MEX
** ========
*/
void mexFunction( int nlhs, mxArray * plhs[], int nrhs, const mxArray * prhs[] )
{
/* variables */
double * return_status;
double * species_out;
double * observables_out;
double * parameters;
double * species_init;
double * timepoints;
size_t n_timepoints;
size_t i;
size_t j;
/* intermediate data vectors */
N_Vector expressions;
N_Vector observables;
N_Vector ratelaws;
/* array to hold pointers to data vectors */
N_Vector temp_data[3];
/* CVODE specific variables */
realtype reltol;
realtype abstol;
realtype time;
N_Vector species;
void * cvode_mem;
int flag;
/* check number of input/output arguments */
if (nlhs != 3)
{ mexErrMsgTxt("syntax: [err_flag, species_out, obsv_out] = network_mex( timepoints, species_init, params )"); }
if (nrhs != 3)
{ mexErrMsgTxt("syntax: [err_flag, species_out, obsv_out] = network_mex( timepoints, species_init, params )"); }
/* make sure timepoints has correct dimensions */
if ( (mxGetM(prhs[0]) < 2) || (mxGetN(prhs[0]) != 1) )
{ mexErrMsgTxt("TIMEPOINTS must be a column vector with 2 or more elements."); }
/* make sure species_init has correct dimensions */
if ( (mxGetM(prhs[1]) != 1) || (mxGetN(prhs[1]) != __N_SPECIES__) )
{ mexErrMsgTxt("SPECIES_INIT must be a row vector with 7 elements."); }
/* make sure params has correct dimensions */
if ( (mxGetM(prhs[2]) != 1) || (mxGetN(prhs[2]) != __N_PARAMETERS__) )
{ mexErrMsgTxt("PARAMS must be a column vector with 4 elements."); }
/* get pointers to input arrays */
timepoints = mxGetPr(prhs[0]);
species_init = mxGetPr(prhs[1]);
parameters = mxGetPr(prhs[2]);
/* get number of timepoints */
n_timepoints = mxGetM(prhs[0]);
/* Create an mxArray for output trajectories */
plhs[0] = mxCreateDoubleMatrix(1, 1, mxREAL );
plhs[1] = mxCreateDoubleMatrix(n_timepoints, __N_SPECIES__, mxREAL);
plhs[2] = mxCreateDoubleMatrix(n_timepoints, __N_OBSERVABLES__, mxREAL);
/* get pointers to output arrays */
return_status = mxGetPr(plhs[0]);
species_out = mxGetPr(plhs[1]);
observables_out = mxGetPr(plhs[2]);
/* initialize intermediate data vectors */
expressions = NULL;
expressions = N_VNew_Serial(__N_EXPRESSIONS__);
if (check_flag((void *)expressions, "N_VNew_Serial", 0))
{
return_status[0] = 1;
return;
}
observables = NULL;
observables = N_VNew_Serial(__N_OBSERVABLES__);
if (check_flag((void *)observables, "N_VNew_Serial", 0))
{
N_VDestroy_Serial(expressions);
return_status[0] = 1;
return;
}
ratelaws = NULL;
ratelaws = N_VNew_Serial(__N_RATELAWS__);
if (check_flag((void *)ratelaws, "N_VNew_Serial", 0))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
return_status[0] = 1;
return;
}
/* set up pointers to intermediate data vectors */
temp_data[0] = expressions;
temp_data[1] = observables;
temp_data[2] = ratelaws;
/* calculate expressions (expressions are constant, so only do this once!) */
calc_expressions( expressions, parameters );
/* SOLVE model equations! */
species = NULL;
cvode_mem = NULL;
/* Set the scalar relative tolerance */
reltol = 1e-06;
abstol = 1e-06;
/* Create serial vector for Species */
species = N_VNew_Serial(__N_SPECIES__);
if (check_flag((void *)species, "N_VNew_Serial", 0))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
return_status[0] = 1;
return;
}
for ( i = 0; i < __N_SPECIES__; i++ )
{ NV_Ith_S(species,i) = species_init[i]; }
/* write initial species populations into species_out */
for ( i = 0; i < __N_SPECIES__; i++ )
{ species_out[i*n_timepoints] = species_init[i]; }
/* write initial observables populations into species_out */
calc_observables( observables, species, expressions );
for ( i = 0; i < __N_OBSERVABLES__; i++ )
{ observables_out[i*n_timepoints] = NV_Ith_S(observables,i); }
/* Call CVodeCreate to create the solver memory:
* CV_ADAMS or CV_BDF is the linear multistep method
* CV_FUNCTIONAL or CV_NEWTON is the nonlinear solver iteration
* A pointer to the integrator problem memory is returned and stored in cvode_mem.
*/
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void *)cvode_mem, "CVodeCreate", 0))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
N_VDestroy_Serial(species);
CVodeFree(&cvode_mem);
return_status[0] = 1;
return;
}
/* Call CVodeInit to initialize the integrator memory:
* cvode_mem is the pointer to the integrator memory returned by CVodeCreate
* rhs_func is the user's right hand side function in y'=f(t,y)
* T0 is the initial time
* y is the initial dependent variable vector
*/
flag = CVodeInit(cvode_mem, calc_species_deriv, timepoints[0], species);
if (check_flag(&flag, "CVodeInit", 1))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
N_VDestroy_Serial(species);
CVodeFree(&cvode_mem);
return_status[0] = 1;
return;
}
/* Set scalar relative and absolute tolerances */
flag = CVodeSStolerances(cvode_mem, reltol, abstol);
if (check_flag(&flag, "CVodeSStolerances", 1))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
N_VDestroy_Serial(species);
CVodeFree(&cvode_mem);
return_status[0] = 1;
return;
}
/* pass params to rhs_func */
flag = CVodeSetUserData(cvode_mem, &temp_data);
if (check_flag(&flag, "CVodeSetFdata", 1))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
N_VDestroy_Serial(species);
CVodeFree(&cvode_mem);
return_status[0] = 1;
return;
}
/* select linear solver */
flag = CVDense(cvode_mem, __N_SPECIES__);
if (check_flag(&flag, "CVDense", 1))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
N_VDestroy_Serial(species);
CVodeFree(&cvode_mem);
return_status[0] = 1;
return;
}
flag = CVodeSetMaxNumSteps(cvode_mem, 2000);
if (check_flag(&flag, "CVodeSetMaxNumSteps", 1))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
N_VDestroy_Serial(species);
CVodeFree(&cvode_mem);
return_status[0] = 1;
return;
}
flag = CVodeSetMaxErrTestFails(cvode_mem, 7);
if (check_flag(&flag, "CVodeSetMaxErrTestFails", 1))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
N_VDestroy_Serial(species);
CVodeFree(&cvode_mem);
return_status[0] = 1;
return;
}
flag = CVodeSetMaxConvFails(cvode_mem, 10);
if (check_flag(&flag, "CVodeSetMaxConvFails", 1))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
N_VDestroy_Serial(species);
CVodeFree(&cvode_mem);
return_status[0] = 1;
return;
}
flag = CVodeSetMaxStep(cvode_mem, 0.0);
if (check_flag(&flag, "CVodeSetMaxStep", 1))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
N_VDestroy_Serial(species);
CVodeFree(&cvode_mem);
return_status[0] = 1;
return;
}
/* integrate to each timepoint */
for ( i=1; i < n_timepoints; i++ )
{
flag = CVode(cvode_mem, timepoints[i], species, &time, CV_NORMAL);
if (check_flag(&flag, "CVode", 1))
{
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
N_VDestroy_Serial(species);
CVodeFree(&cvode_mem);
return_status[0] = 1;
return;
}
/* copy species output from nvector to matlab array */
for ( j = 0; j < __N_SPECIES__; j++ )
{ species_out[j*n_timepoints + i] = NV_Ith_S(species,j); }
/* copy observables output from nvector to matlab array */
calc_observables( observables, species, expressions );
for ( j = 0; j < __N_OBSERVABLES__; j++ )
{ observables_out[j*n_timepoints + i] = NV_Ith_S(observables,j); }
}
/* Free vectors */
N_VDestroy_Serial(expressions);
N_VDestroy_Serial(observables);
N_VDestroy_Serial(ratelaws);
N_VDestroy_Serial(species);
/* Free integrator memory */
CVodeFree(&cvode_mem);
return;
}
void CvodeSolver::initialize(const double &pVoiStart, const int &pStatesCount,
double *pConstants, double *pStates,
double *pRates, double *pAlgebraic,
ComputeRatesFunction pComputeRates)
{
if (!mSolver) {
// Initialise the ODE solver itself
OpenCOR::CoreSolver::CoreOdeSolver::initialize(pVoiStart, pStatesCount,
pConstants, pStates,
pRates, pAlgebraic,
pComputeRates);
// Retrieve some of the CVODE properties
if (mProperties.contains(MaximumStepProperty)) {
mMaximumStep = mProperties.value(MaximumStepProperty).toDouble();
} else {
emit error(QObject::tr("the 'maximum step' property value could not be retrieved"));
return;
}
if (mProperties.contains(MaximumNumberOfStepsProperty)) {
mMaximumNumberOfSteps = mProperties.value(MaximumNumberOfStepsProperty).toInt();
} else {
emit error(QObject::tr("the 'maximum number of steps' property value could not be retrieved"));
return;
}
if (mProperties.contains(RelativeToleranceProperty)) {
mRelativeTolerance = mProperties.value(RelativeToleranceProperty).toDouble();
} else {
emit error(QObject::tr("the 'relative tolerance' property value could not be retrieved"));
return;
}
if (mProperties.contains(AbsoluteToleranceProperty)) {
mAbsoluteTolerance = mProperties.value(AbsoluteToleranceProperty).toDouble();
} else {
emit error(QObject::tr("the 'absolute tolerance' property value could not be retrieved"));
return;
}
// Create the states vector
mStatesVector = N_VMake_Serial(pStatesCount, pStates);
// Create the CVODE solver
mSolver = CVodeCreate(CV_BDF, CV_NEWTON);
// Use our own error handler
CVodeSetErrHandlerFn(mSolver, errorHandler, this);
// Initialise the CVODE solver
CVodeInit(mSolver, rhsFunction, pVoiStart, mStatesVector);
// Set some user data
delete mUserData; // Just in case the solver got initialised before
mUserData = new CvodeSolverUserData(pConstants, pAlgebraic,
pComputeRates);
CVodeSetUserData(mSolver, mUserData);
// Set the linear solver
CVDense(mSolver, pStatesCount);
// Set the maximum step
CVodeSetMaxStep(mSolver, mMaximumStep);
// Set the maximum number of steps
CVodeSetMaxNumSteps(mSolver, mMaximumNumberOfSteps);
// Set the relative and absolute tolerances
CVodeSStolerances(mSolver, mRelativeTolerance, mAbsoluteTolerance);
} else {
// Reinitialise the CVODE object
CVodeReInit(mSolver, pVoiStart, mStatesVector);
}
}
