/* yS0 in row major order */
void ode_solver_init_sens(ode_solver* solver, double* yS0, int lenP, int lenY){
/* change: lenP may now be shorter than P if you dpn't want to
* calculate all sensitivities. This is important for the correct
* treatment of input parameters, i.e. experimental conditions u
* (since we don't require sensitivities with repsect to them).
*/
int i,flag;
int N = solver->odeModel->N;
int P = solver->odeModel->P;
if (solver->odeModel->vf_sens == 0) {
fprintf(stderr,"ode_solver_init_sens: no sensitivities defined for this model.\n");
return;
}
solver->yS = N_VCloneVectorArrayEmpty_Serial(lenP, solver->y); /* alloc */
double tmp[N];
if(yS0 !=0 ){
if ( (lenY != N) ) {
fprintf(stderr,"ode_solver_init_sens: lenY must be equal to %d the number of parameters and variables in the ode model.\n",solver->odeModel->N);
return ;
}
for(i = 0; i < lenP; i++)
NV_DATA_S(solver->yS[i]) = &yS0[i*lenY];
}
else{
for (i=0; i < N ; i++)
tmp[i] = 0.0;
for (i = 0; i < lenP; i++)
NV_DATA_S(solver->yS[i]) = tmp;
}
flag = CVodeSensInit1(solver->cvode_mem, lenP, CV_STAGGERED1, solver->odeModel->vf_sens, solver->yS);
flag = CVodeSetSensErrCon(solver->cvode_mem, TRUE);
flag = CVodeSensEEtolerances(solver->cvode_mem);
/* set parameters scale for error corection */
double scale_p[lenP];
for (i=0; i<lenP; i++) {
/* order of magnitude can be found from the actual parameter value */
/* if zero then set to the default relative error */
if (solver->params[i] != 0.0){
scale_p[i] = solver->params[i];
}
else {
scale_p[i] = ODE_SOLVER_REL_ERR;
}
}
flag = CVodeSetSensParams(solver->cvode_mem, solver->params, scale_p, NULL);
}
int main(int argc, char *argv[])
{
void *cvode_mem;
UserData data;
realtype t, tout;
N_Vector y;
int iout, flag, nthreads, nnz;
realtype pbar[NS];
int is;
N_Vector *yS;
booleantype sensi, err_con;
int sensi_meth;
cvode_mem = NULL;
data = NULL;
y = NULL;
yS = NULL;
/* Process arguments */
ProcessArgs(argc, argv, &sensi, &sensi_meth, &err_con);
/* User data structure */
data = (UserData) malloc(sizeof *data);
if (check_flag((void *)data, "malloc", 2)) return(1);
data->p[0] = RCONST(0.04);
data->p[1] = RCONST(1.0e4);
data->p[2] = RCONST(3.0e7);
/* Initial conditions */
y = N_VNew_Serial(NEQ);
if (check_flag((void *)y, "N_VNew_Serial", 0)) return(1);
Ith(y,1) = Y1;
Ith(y,2) = Y2;
Ith(y,3) = Y3;
/* Call CVodeCreate to create the solver memory and specify the
Backward Differentiation Formula and the use of a Newton iteration */
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1);
/* Call CVodeInit to initialize the integrator memory and specify the
user's right hand side function in y'=f(t,y), the initial time T0, and
the initial dependent variable vector y. */
flag = CVodeInit(cvode_mem, f, T0, y);
if (check_flag(&flag, "CVodeInit", 1)) return(1);
/* Call CVodeWFtolerances to specify a user-supplied function ewt that sets
the multiplicative error weights W_i for use in the weighted RMS norm */
flag = CVodeWFtolerances(cvode_mem, ewt);
if (check_flag(&flag, "CVodeSetEwtFn", 1)) return(1);
/* Attach user data */
flag = CVodeSetUserData(cvode_mem, data);
if (check_flag(&flag, "CVodeSetUserData", 1)) return(1);
/* Call CVKLU to specify the CVKLU sparse direct linear solver */
nthreads = 1; /* no. of threads to use when factoring the system*/
nnz = NEQ * NEQ; /* max no. of nonzeros entries in the Jac */
flag = CVSuperLUMT(cvode_mem, nthreads, NEQ, nnz);
if (check_flag(&flag, "CVSuperLUMT", 1)) return(1);
/* Set the Jacobian routine to Jac (user-supplied) */
flag = CVSlsSetSparseJacFn(cvode_mem, Jac);
if (check_flag(&flag, "CVSlsSetSparseJacFn", 1)) return(1);
printf("\n3-species chemical kinetics problem\n");
/* Sensitivity-related settings */
if (sensi) {
/* Set parameter scaling factor */
pbar[0] = data->p[0];
pbar[1] = data->p[1];
pbar[2] = data->p[2];
/* Set sensitivity initial conditions */
yS = N_VCloneVectorArray_Serial(NS, y);
if (check_flag((void *)yS, "N_VCloneVectorArray_Serial", 0)) return(1);
for (is=0;is<NS;is++) N_VConst(ZERO, yS[is]);
/* Call CVodeSensInit1 to activate forward sensitivity computations
and allocate internal memory for COVEDS related to sensitivity
calculations. Computes the right-hand sides of the sensitivity
ODE, one at a time */
flag = CVodeSensInit1(cvode_mem, NS, sensi_meth, fS, yS);
if(check_flag(&flag, "CVodeSensInit", 1)) return(1);
/* Call CVodeSensEEtolerances to estimate tolerances for sensitivity
variables based on the rolerances supplied for states variables and
the scaling factor pbar */
flag = CVodeSensEEtolerances(cvode_mem);
if(check_flag(&flag, "CVodeSensEEtolerances", 1)) return(1);
/* Set sensitivity analysis optional inputs */
/* Call CVodeSetSensErrCon to specify the error control strategy for
sensitivity variables */
flag = CVodeSetSensErrCon(cvode_mem, err_con);
if (check_flag(&flag, "CVodeSetSensErrCon", 1)) return(1);
/* Call CVodeSetSensParams to specify problem parameter information for
sensitivity calculations */
flag = CVodeSetSensParams(cvode_mem, NULL, pbar, NULL);
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("===========================================");
printf("============================\n");
printf(" T Q H NST y1");
printf(" y2 y3 \n");
printf("===========================================");
printf("============================\n");
for (iout=1, tout=T1; iout <= NOUT; iout++, tout *= TMULT) {
flag = CVode(cvode_mem, tout, y, &t, CV_NORMAL);
if (check_flag(&flag, "CVode", 1)) break;
PrintOutput(cvode_mem, t, y);
/* Call CVodeGetSens to get the sensitivity solution vector after a
successful return from CVode */
if (sensi) {
flag = CVodeGetSens(cvode_mem, &t, yS);
if (check_flag(&flag, "CVodeGetSens", 1)) break;
PrintOutputS(yS);
}
printf("-----------------------------------------");
printf("------------------------------\n");
}
/* Print final statistics */
PrintFinalStats(cvode_mem, sensi);
/* Free memory */
N_VDestroy_Serial(y); /* Free y vector */
if (sensi) {
N_VDestroyVectorArray_Serial(yS, NS); /* Free yS vector */
}
free(data); /* Free user data */
CVodeFree(&cvode_mem); /* Free CVODES memory */
return(0);
}
/* creates CVODES forward sensitivity solver structures
return 1 => success
return 0 => failure
*/
int
IntegratorInstance_createCVODESSolverStructures(integratorInstance_t *engine)
{
int i, j, flag, neq, ns;
realtype *ydata, *abstoldata, *ySdata, *senstoldata;
odeModel_t *om = engine->om;
cvodeData_t *data = engine->data;
cvodeSolver_t *solver = engine->solver;
cvodeSettings_t *opt = engine->opt;
/* realtype pbar[data->nsens+1]; */
/*int *plist; removed by AMF 8/11/05
realtype *pbar;
ASSIGN_NEW_MEMORY_BLOCK(plist, data->nsens+1, int, 0)
ASSIGN_NEW_MEMORY_BLOCK(pbar, data->nsens+1, realtype, 0)*/
/***** adding sensitivity specific structures ******/
/**
* construct sensitivity related structures
*/
/* free sensitivity from former runs (changed for non-default cases!) */
ODEModel_freeSensitivity(om);
/* if jacobian matrix has been constructed successfully,
construct sensitivity matrix dx/dp, sets om->sensitivity
to 1 if successful, 0 otherwise */
/*!!! this function will require additional input for
non-default case, via sensitivity input settings! !!!*/
if ( om->jacobian )
ODEModel_constructSensitivity(om);
else {
om->sensitivity = 0;
om->jacob_sens = NULL;
om->nsens = om->nconst;
ASSIGN_NEW_MEMORY_BLOCK(om->index_sens, om->nsens, int, 0);
/*!!! non-default case:
these values should be passed for other cases !!!*/
for ( i=0; i<om->nsens; i++ )
om->index_sens[i] = om->neq + om->nass + i;
}
engine->solver->nsens = data->nsens;
solver->yS = N_VNewVectorArray_Serial(data->nsens, data->neq);
if (check_flag((void *)solver->yS, "N_VNewVectorArray_Serial",
1, stderr))
return(0);
/*
* (re)initialize ySdata sensitivities
*/
/* absolute tolerance for sensitivity error control */
solver->senstol = N_VNew_Serial(data->nsens);
abstoldata = NV_DATA_S(solver->senstol);
for ( j=0; j<data->nsens; j++ ) {
abstoldata[j] = 1e-4;
ySdata = NV_DATA_S(solver->yS[j]);
for ( i=0; i<data->neq; i++ )
ySdata[i] = data->sensitivity[i][j];
}
/*
* set method
*/
if ( opt->SensMethod == 0 )
flag =CVodeSensMalloc(solver->cvode_mem,data->nsens,
CV_SIMULTANEOUS, solver->yS);
else if ( opt->SensMethod == 1 )
flag = CVodeSensMalloc(solver->cvode_mem, data->nsens,
CV_STAGGERED, solver->yS);
else if ( opt->SensMethod == 2 )
flag = CVodeSensMalloc(solver->cvode_mem, data->nsens,
CV_STAGGERED1, solver->yS);
if(check_flag(&flag, "CVodeSensMalloc", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
/* *** set parameter values or R.H.S function fS *****/
/* NOTES: */
/* !!! plist could later be used to specify requested parameters
for sens.analysis !!! */
/* was construction of Jacobian and
parametric matrix successfull ? */
if ( om->sensitivity && om->jacobian ) {
flag = CVodeSetSensRhs1Fn(solver->cvode_mem, fS);
if (check_flag(&flag, "CVodeSetSensRhs1Fn", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
flag = CVodeSetSensFdata(solver->cvode_mem, data);
if (check_flag(&flag, "CVodeSetSensFdata", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
data->p = NULL;
}
else {
ASSIGN_NEW_MEMORY_BLOCK(data->p, data->nsens, realtype, 0);
for ( i=0; i<data->nsens; i++ ) {
/* data->p is only required if R.H.S. fS cannot be supplied */
/* plist[i] = i+1; */
data->p[i] = data->value[om->index_sens[i]];
/* pbar[i] = abs(data->p[i]); */ /*??? WHAT IS PBAR ???*/
}
flag = CVodeSetSensParams(solver->cvode_mem, data->p, NULL, NULL);
if (check_flag(&flag, "CVodeSetSensParams", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
flag = CVodeSetSensRho(solver->cvode_mem, 0.0); /* what is it? */
if (check_flag(&flag, "CVodeSetSensRhs1Fn", 1, stderr)) {
/* ERROR HANDLING CODE if failes */
return 0;
}
}
/* CVodeSetSensTolerances(solver->cvode_mem, CV_SS, */
/* solver->reltol, &solver->senstol); */
/* difference FALSE/TRUE ? */
flag = CVodeSetSensErrCon(solver->cvode_mem, FALSE);
if (check_flag(&flag, "CVodeSetSensFdata", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
return 1; /* OK */
}
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);
}
int main(int argc, char *argv[])
{
void *cvode_mem;
UserData data;
realtype t, tout;
N_Vector y;
int iout, flag;
realtype pbar[NS];
int is;
N_Vector *yS;
booleantype sensi, err_con;
int sensi_meth;
cvode_mem = NULL;
data = NULL;
y = NULL;
yS = NULL;
/* Process arguments */
ProcessArgs(argc, argv, &sensi, &sensi_meth, &err_con);
/* User data structure */
data = (UserData) malloc(sizeof *data);
if (check_flag((void *)data, "malloc", 2)) return(1);
data->p[0] = RCONST(0.04);
data->p[1] = RCONST(1.0e4);
data->p[2] = RCONST(3.0e7);
/* Initial conditions */
y = N_VNew_Serial(NEQ);
if (check_flag((void *)y, "N_VNew_Serial", 0)) return(1);
Ith(y,1) = Y1;
Ith(y,2) = Y2;
Ith(y,3) = Y3;
/* Create CVODES object */
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1);
/* Allocate space for CVODES */
flag = CVodeMalloc(cvode_mem, f, T0, y, CV_WF, 0.0, NULL);
if (check_flag(&flag, "CVodeMalloc", 1)) return(1);
/* Use private function to compute error weights */
flag = CVodeSetEwtFn(cvode_mem, ewt, NULL);
if (check_flag(&flag, "CVodeSetEwtFn", 1)) return(1);
/* Attach user data */
flag = CVodeSetFdata(cvode_mem, data);
if (check_flag(&flag, "CVodeSetFdata", 1)) return(1);
/* Attach linear solver */
flag = CVDense(cvode_mem, NEQ);
if (check_flag(&flag, "CVDense", 1)) return(1);
flag = CVDenseSetJacFn(cvode_mem, Jac, data);
if (check_flag(&flag, "CVDenseSetJacFn", 1)) return(1);
printf("\n3-species chemical kinetics problem\n");
/* Sensitivity-related settings */
if (sensi) {
pbar[0] = data->p[0];
pbar[1] = data->p[1];
pbar[2] = data->p[2];
yS = N_VNewVectorArray_Serial(NS, NEQ);
if (check_flag((void *)yS, "N_VNewVectorArray_Serial", 0)) return(1);
for (is=0;is<NS;is++) N_VConst(ZERO, yS[is]);
flag = CVodeSensMalloc(cvode_mem, NS, sensi_meth, yS);
if(check_flag(&flag, "CVodeSensMalloc", 1)) return(1);
flag = CVodeSetSensRhs1Fn(cvode_mem, fS);
if (check_flag(&flag, "CVodeSetSensRhs1Fn", 1)) return(1);
flag = CVodeSetSensErrCon(cvode_mem, err_con);
if (check_flag(&flag, "CVodeSetSensFdata", 1)) return(1);
flag = CVodeSetSensFdata(cvode_mem, data);
if (check_flag(&flag, "CVodeSetSensFdata", 1)) return(1);
flag = CVodeSetSensParams(cvode_mem, NULL, pbar, NULL);
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("===================================================");
printf("============================\n");
printf(" T Q H NST y1");
printf(" y2 y3 \n");
printf("===================================================");
printf("============================\n");
for (iout=1, tout=T1; iout <= NOUT; iout++, tout *= TMULT) {
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, yS);
if (check_flag(&flag, "CVodeGetSens", 1)) break;
PrintOutputS(yS);
}
printf("-------------------------------------------------");
printf("------------------------------\n");
}
/* Print final statistics */
PrintFinalStats(cvode_mem, sensi);
/* Free memory */
N_VDestroy_Serial(y); /* Free y vector */
if (sensi) {
N_VDestroyVectorArray_Serial(yS, NS); /* Free yS vector */
}
free(data); /* Free user data */
CVodeFree(cvode_mem); /* Free CVODES memory */
return(0);
}
int main(int argc, char *argv[])
{
SUNMatrix A;
SUNLinearSolver LS;
void *cvode_mem;
UserData data;
realtype t, tout;
N_Vector y, constraints;
int iout, retval;
realtype pbar[NS];
int is;
N_Vector *yS;
booleantype sensi, err_con;
int sensi_meth;
cvode_mem = NULL;
data = NULL;
y = NULL;
yS = NULL;
A = NULL;
LS = NULL;
constraints = NULL;
/* Process arguments */
ProcessArgs(argc, argv, &sensi, &sensi_meth, &err_con);
/* User data structure */
data = (UserData) malloc(sizeof *data);
if (check_retval((void *)data, "malloc", 2)) return(1);
data->p[0] = RCONST(0.04);
data->p[1] = RCONST(1.0e4);
data->p[2] = RCONST(3.0e7);
/* Initial conditions */
y = N_VNew_Serial(NEQ);
if (check_retval((void *)y, "N_VNew_Serial", 0)) return(1);
Ith(y,1) = Y1;
Ith(y,2) = Y2;
Ith(y,3) = Y3;
/* Set constraints to all 1's for nonnegative solution values. */
constraints = N_VNew_Serial(NEQ);
if(check_retval((void *)constraints, "N_VNew_Serial", 0)) return(1);
N_VConst(ONE, constraints);
/* Create CVODES object */
cvode_mem = CVodeCreate(CV_BDF);
if (check_retval((void *)cvode_mem, "CVodeCreate", 0)) return(1);
/* Allocate space for CVODES */
retval = CVodeInit(cvode_mem, f, T0, y);
if (check_retval(&retval, "CVodeInit", 1)) return(1);
/* Use private function to compute error weights */
retval = CVodeWFtolerances(cvode_mem, ewt);
if (check_retval(&retval, "CVodeSetEwtFn", 1)) return(1);
/* Attach user data */
retval = CVodeSetUserData(cvode_mem, data);
if (check_retval(&retval, "CVodeSetUserData", 1)) return(1);
/* Call CVodeSetConstraints to initialize constraints */
retval = CVodeSetConstraints(cvode_mem, constraints);
if(check_retval(&retval, "CVodeSetConstraints", 1)) return(1);
N_VDestroy(constraints);
/* Create dense SUNMatrix */
A = SUNDenseMatrix(NEQ, NEQ);
if (check_retval((void *)A, "SUNDenseMatrix", 0)) return(1);
/* Create dense SUNLinearSolver */
LS = SUNLinSol_Dense(y, A);
if (check_retval((void *)LS, "SUNLinSol_Dense", 0)) return(1);
/* Attach the matrix and linear solver */
retval = CVDlsSetLinearSolver(cvode_mem, LS, A);
if (check_retval(&retval, "CVDlsSetLinearSolver", 1)) return(1);
/* Set the user-supplied Jacobian routine Jac */
retval = CVDlsSetJacFn(cvode_mem, Jac);
if (check_retval(&retval, "CVDlsSetJacFn", 1)) return(1);
printf("\n3-species chemical kinetics problem\n");
/* Sensitivity-related settings */
if (sensi) {
/* Set parameter scaling factor */
pbar[0] = data->p[0];
pbar[1] = data->p[1];
pbar[2] = data->p[2];
/* Set sensitivity initial conditions */
yS = N_VCloneVectorArray(NS, y);
if (check_retval((void *)yS, "N_VCloneVectorArray", 0)) return(1);
for (is=0;is<NS;is++) N_VConst(ZERO, yS[is]);
/* Call CVodeSensInit1 to activate forward sensitivity computations
and allocate internal memory for COVEDS related to sensitivity
calculations. Computes the right-hand sides of the sensitivity
ODE, one at a time */
retval = CVodeSensInit1(cvode_mem, NS, sensi_meth, fS, yS);
if(check_retval(&retval, "CVodeSensInit", 1)) return(1);
/* Call CVodeSensEEtolerances to estimate tolerances for sensitivity
variables based on the rolerances supplied for states variables and
the scaling factor pbar */
retval = CVodeSensEEtolerances(cvode_mem);
if(check_retval(&retval, "CVodeSensEEtolerances", 1)) return(1);
/* Set sensitivity analysis optional inputs */
/* Call CVodeSetSensErrCon to specify the error control strategy for
sensitivity variables */
retval = CVodeSetSensErrCon(cvode_mem, err_con);
if (check_retval(&retval, "CVodeSetSensErrCon", 1)) return(1);
/* Call CVodeSetSensParams to specify problem parameter information for
sensitivity calculations */
retval = CVodeSetSensParams(cvode_mem, NULL, pbar, NULL);
if (check_retval(&retval, "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("===========================================");
printf("============================\n");
printf(" T Q H NST y1");
printf(" y2 y3 \n");
printf("===========================================");
printf("============================\n");
for (iout=1, tout=T1; iout <= NOUT; iout++, tout *= TMULT) {
retval = CVode(cvode_mem, tout, y, &t, CV_NORMAL);
if (check_retval(&retval, "CVode", 1)) break;
PrintOutput(cvode_mem, t, y);
/* Call CVodeGetSens to get the sensitivity solution vector after a
successful return from CVode */
if (sensi) {
retval = CVodeGetSens(cvode_mem, &t, yS);
if (check_retval(&retval, "CVodeGetSens", 1)) break;
PrintOutputS(yS);
}
printf("-----------------------------------------");
printf("------------------------------\n");
}
/* Print final statistics */
PrintFinalStats(cvode_mem, sensi);
/* Free memory */
N_VDestroy(y); /* Free y vector */
if (sensi) {
N_VDestroyVectorArray(yS, NS); /* Free yS vector */
}
free(data); /* Free user data */
CVodeFree(&cvode_mem); /* Free CVODES memory */
SUNLinSolFree(LS); /* Free the linear solver memory */
SUNMatDestroy(A); /* Free the matrix memory */
return(0);
}
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);
}
int main(int argc, char *argv[])
{
void *cvode_mem;
UserData data;
realtype dx, reltol, abstol, t, tout;
N_Vector u;
int iout, flag;
realtype *pbar;
int is, *plist;
N_Vector *uS;
booleantype sensi, err_con;
int sensi_meth;
cvode_mem = NULL;
data = NULL;
u = NULL;
pbar = NULL;
plist = NULL;
uS = NULL;
/* Process arguments */
ProcessArgs(argc, argv, &sensi, &sensi_meth, &err_con);
/* Set user data */
data = (UserData) malloc(sizeof *data); /* Allocate data memory */
if(check_flag((void *)data, "malloc", 2)) return(1);
data->p = (realtype *) malloc(NP * sizeof(realtype));
dx = data->dx = XMAX/((realtype)(MX+1));
data->p[0] = RCONST(1.0);
data->p[1] = RCONST(0.5);
/* Allocate and set initial states */
u = N_VNew_Serial(NEQ);
if(check_flag((void *)u, "N_VNew_Serial", 0)) return(1);
SetIC(u, dx);
/* Set integration tolerances */
reltol = ZERO;
abstol = ATOL;
/* Create CVODES object */
cvode_mem = CVodeCreate(CV_ADAMS, CV_FUNCTIONAL);
if(check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1);
flag = CVodeSetUserData(cvode_mem, data);
if(check_flag(&flag, "CVodeSetUserData", 1)) return(1);
/* Allocate CVODES memory */
flag = CVodeInit(cvode_mem, f, T0, u);
if(check_flag(&flag, "CVodeInit", 1)) return(1);
flag = CVodeSStolerances(cvode_mem, reltol, abstol);
if(check_flag(&flag, "CVodeSStolerances", 1)) return(1);
printf("\n1-D advection-diffusion equation, mesh size =%3d\n", MX);
/* Sensitivity-related settings */
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, u);
if(check_flag((void *)uS, "N_VCloneVectorArray_Serial", 0)) return(1);
for(is=0;is<NS;is++)
N_VConst(ZERO, uS[is]);
flag = CVodeSensInit1(cvode_mem, NS, sensi_meth, NULL, uS);
if(check_flag(&flag, "CVodeSensInit1", 1)) return(1);
flag = CVodeSensEEtolerances(cvode_mem);
if(check_flag(&flag, "CVodeSensEEtolerances", 1)) return(1);
flag = CVodeSetSensErrCon(cvode_mem, err_con);
if(check_flag(&flag, "CVodeSetSensErrCon", 1)) return(1);
flag = CVodeSetSensDQMethod(cvode_mem, CV_CENTERED, ZERO);
if(check_flag(&flag, "CVodeSetSensDQMethod", 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 Max norm \n");
printf("============================================================\n");
for (iout=1, tout=T1; iout <= NOUT; iout++, tout += DTOUT) {
flag = CVode(cvode_mem, tout, u, &t, CV_NORMAL);
if(check_flag(&flag, "CVode", 1)) break;
PrintOutput(cvode_mem, t, u);
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(u);
if (sensi) {
N_VDestroyVectorArray_Serial(uS, NS);
free(plist);
free(pbar);
}
free(data);
CVodeFree(&cvode_mem);
return(0);
}
/**
* Solves an initial value problem using CVODES to integrate over a system of
* ODEs with optional forward sensitivity analysis. The initial conditions for
* the system and for the sensitivity analysis are expected to be in the first
* rows of simdata and sensitivities, respectively.
*
* @param [in] rhs the right-hand side of the system of ODEs
* @param [in] num_timepoints the number of timepoints
* @param [in] num_species the number of independent variables
* @param [in] num_sens the number of parameters to compute sensitivities
* for (set to zero to disable sensitivity
* calculations)
* @param [in] timepoints the timepoints at which data is to be returned
* @param [in] params parameters
* @param [in] sensi the indices of the parameters to compute the
* sensitivities for (may be NULL to compute the
* sensitivities for all parameters)
* @param [in] options additional options for the integrator
* @param [out] simdata contains the state values for each species at
* each timepoint in column-major order.
* @param [out] sensitivities sensitivities of each parameter in sensi
* with respect to each independent variable.
* The sensitivity of parameter j with respect to
* variable k at timepoint i is stored at
* (j * num_species + k) * lds + i.
* May be NULL if sensitivities are not to be
* calculated.
* @param [in] lds leading dimension of simdata and sensitivities
*
* @return 0 on success,
* GMCMC_ENOMEM if there was not enough memory to create the solver,
* GMCMC_EINVAL if there was an invalid argument to the function,
* GMCMC_ELINAL if the solution could not be found.
*/
int cvodes_solve(gmcmc_ode_rhs rhs, size_t num_timepoints, size_t num_species, size_t num_params, size_t num_sens, const double * timepoints, const double * params, const size_t * sensi, const cvodes_options * options, double * simdata, double * sensitivities, size_t lds) {
int error;
// Set vector of initial values
N_Vector y = N_VNew_Serial((long int)num_species);
for (size_t j = 0; j < num_species; j++)
NV_Ith_S(y, j) = simdata[j * lds];
// Create CVODES object
void * cvode_mem;
if ((cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON)) == NULL)
GMCMC_ERROR("Failed to allocate ODE solver", GMCMC_ENOMEM);
// Initialise CVODES solver
if ((error = CVodeInit(cvode_mem, cvodes_rhs, timepoints[0], y)) != CV_SUCCESS) {
CVodeFree(&cvode_mem);
GMCMC_ERROR("Failed to initialise ODE solver", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM);
}
// Set integration tolerances
if ((error = CVodeSStolerances(cvode_mem, options->reltol, options->abstol)) != CV_SUCCESS) {
CVodeFree(&cvode_mem);
GMCMC_ERROR("Failed to set ODE solver integration tolerances", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM);
}
// Create a copy of the parameters in case CVODES modifies them
realtype * sens_params;
if ((sens_params = malloc(num_params * sizeof(realtype))) == NULL) {
CVodeFree(&cvode_mem);
GMCMC_ERROR("Failed to allocate copy of parameter vector for sensitivity analysis", GMCMC_ENOMEM);
}
for (size_t i = 0; i < num_params; i++)
sens_params[i] = (realtype)params[i];
// Set optional inputs
cvodes_userdata userdata = { rhs, sens_params };
if ((error = CVodeSetUserData(cvode_mem, &userdata)) != CV_SUCCESS) {
CVodeFree(&cvode_mem);
free(sens_params);
GMCMC_ERROR("Failed to set ODE solver user data", GMCMC_EINVAL);
}
// Attach linear solver module
if ((error = CVLapackDense(cvode_mem, (int)num_species)) != CV_SUCCESS) {
CVodeFree(&cvode_mem);
free(sens_params);
GMCMC_ERROR("Failed to attach ODE solver module", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM);
}
N_Vector * yS = NULL;
int * plist = NULL;
if (num_sens > 0) {
// Set sensitivity initial conditions
yS = N_VCloneVectorArray_Serial((int)num_sens, y);
for (size_t j = 0; j < num_sens; j++) {
for (size_t i = 0; i < num_species; i++)
NV_Ith_S(yS[j], i) = sensitivities[(j * num_species + i) * lds];
}
// Activate sensitivity calculations
// Use default finite differences
if ((error = CVodeSensInit(cvode_mem, (int)num_sens, CV_SIMULTANEOUS, NULL, yS)) != CV_SUCCESS) {
CVodeFree(&cvode_mem);
free(sens_params);
GMCMC_ERROR("Failed to activate ODE solver sensitivity calculations", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM);
}
// Set sensitivity tolerances
if ((error = CVodeSensEEtolerances(cvode_mem)) != CV_SUCCESS) {
CVodeFree(&cvode_mem);
free(sens_params);
GMCMC_ERROR("Failed to set ODE solver sensitivity tolerances", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM);
}
if (sensi != NULL) {
if ((plist = malloc(num_sens * sizeof(int))) == NULL) {
CVodeFree(&cvode_mem);
free(sens_params);
GMCMC_ERROR("Failed to allocate sensitivity parameter list", GMCMC_ENOMEM);
}
for (size_t i = 0; i < num_sens; i++)
plist[i] = (int)sensi[i];
}
// Set sensitivity analysis optional inputs
if ((error = CVodeSetSensParams(cvode_mem, sens_params, NULL, plist)) != CV_SUCCESS) {
CVodeFree(&cvode_mem);
free(plist);
free(sens_params);
GMCMC_ERROR("Failed to set ODE solver sensitivity parameters", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM);
}
}
// Advance solution in time
realtype tret;
for (size_t i = 1; i < num_timepoints; i++) {
if ((error = CVode(cvode_mem, timepoints[i], y, &tret, CV_NORMAL)) != CV_SUCCESS) {
free(plist);
free(sens_params);
CVodeFree(&cvode_mem);
GMCMC_ERROR("Failed to advance ODE solution", GMCMC_ELINAL);
}
for (size_t j = 0; j < num_species; j++)
simdata[j * lds + i] = NV_Ith_S(y, j);
// Extract the sensitivity solution
if (yS != NULL) {
if ((error = CVodeGetSens(cvode_mem, &tret, yS)) != CV_SUCCESS) {
free(plist);
free(sens_params);
CVodeFree(&cvode_mem);
GMCMC_ERROR("Failed to extract ODE sensitivity solution", GMCMC_ELINAL);
}
for (size_t j = 0; j < num_sens; j++) {
for (size_t k = 0; k < num_species; k++)
sensitivities[(j * num_species + k) * lds + i] = NV_Ith_S(yS[j], k);
}
}
}
N_VDestroy(y);
if (yS != NULL)
N_VDestroyVectorArray_Serial(yS, (int)num_sens);
free(plist);
free(sens_params);
// Free solver memory
CVodeFree(&cvode_mem);
return 0;
}
int main(int argc, char *argv[])
{
realtype dx, reltol, abstol, t, tout;
N_Vector u;
UserData data;
void *cvode_mem;
int iout, flag, my_pe, npes;
long int local_N, nperpe, nrem, my_base;
realtype *pbar;
int is, *plist;
N_Vector *uS;
booleantype sensi, err_con;
int sensi_meth;
MPI_Comm comm;
u = NULL;
data = NULL;
cvode_mem = NULL;
pbar = NULL;
plist = NULL;
uS = NULL;
/* Get processor number, total number of pe's, and my_pe. */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_size(comm, &npes);
MPI_Comm_rank(comm, &my_pe);
/* Process arguments */
ProcessArgs(argc, argv, my_pe, &sensi, &sensi_meth, &err_con);
/* Set local vector length. */
nperpe = NEQ/npes;
nrem = NEQ - npes*nperpe;
local_N = (my_pe < nrem) ? nperpe+1 : nperpe;
my_base = (my_pe < nrem) ? my_pe*local_N : my_pe*nperpe + nrem;
/* USER DATA STRUCTURE */
data = (UserData) malloc(sizeof *data); /* Allocate data memory */
data->p = NULL;
if(check_flag((void *)data, "malloc", 2, my_pe)) MPI_Abort(comm, 1);
data->comm = comm;
data->npes = npes;
data->my_pe = my_pe;
data->p = (realtype *) malloc(NP * sizeof(realtype));
if(check_flag((void *)data->p, "malloc", 2, my_pe)) MPI_Abort(comm, 1);
dx = data->dx = XMAX/((realtype)(MX+1));
data->p[0] = RCONST(1.0);
data->p[1] = RCONST(0.5);
/* INITIAL STATES */
u = N_VNew_Parallel(comm, local_N, NEQ); /* Allocate u vector */
if(check_flag((void *)u, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
SetIC(u, dx, local_N, my_base); /* Initialize u vector */
/* TOLERANCES */
reltol = ZERO; /* Set the tolerances */
abstol = ATOL;
/* CVODE_CREATE & CVODE_MALLOC */
cvode_mem = CVodeCreate(CV_ADAMS, CV_FUNCTIONAL);
if(check_flag((void *)cvode_mem, "CVodeCreate", 0, my_pe)) MPI_Abort(comm, 1);
flag = CVodeSetUserData(cvode_mem, data);
if(check_flag(&flag, "CVodeSetUserData", 1, my_pe)) MPI_Abort(comm, 1);
flag = CVodeInit(cvode_mem, f, T0, u);
if(check_flag(&flag, "CVodeInit", 1, my_pe)) MPI_Abort(comm, 1);
flag = CVodeSStolerances(cvode_mem, reltol, abstol);
if(check_flag(&flag, "CVodeSStolerances", 1, my_pe)) MPI_Abort(comm, 1);
if (my_pe == 0) {
printf("\n1-D advection-diffusion equation, mesh size =%3d \n", MX);
printf("\nNumber of PEs = %3d \n",npes);
}
if(sensi) {
plist = (int *) malloc(NS * sizeof(int));
if(check_flag((void *)plist, "malloc", 2, my_pe)) MPI_Abort(comm, 1);
for(is=0; is<NS; is++)
plist[is] = is; /* sensitivity w.r.t. i-th parameter */
pbar = (realtype *) malloc(NS * sizeof(realtype));
if(check_flag((void *)pbar, "malloc", 2, my_pe)) MPI_Abort(comm, 1);
for(is=0; is<NS; is++) pbar[is] = data->p[plist[is]];
uS = N_VCloneVectorArray_Parallel(NS, u);
if(check_flag((void *)uS, "N_VCloneVectorArray_Parallel", 0, my_pe))
MPI_Abort(comm, 1);
for(is=0;is<NS;is++)
N_VConst(ZERO,uS[is]);
flag = CVodeSensInit1(cvode_mem, NS, sensi_meth, NULL, uS);
if(check_flag(&flag, "CVodeSensInit1", 1, my_pe)) MPI_Abort(comm, 1);
flag = CVodeSensEEtolerances(cvode_mem);
if(check_flag(&flag, "CVodeSensEEtolerances", 1, my_pe)) MPI_Abort(comm, 1);
flag = CVodeSetSensErrCon(cvode_mem, err_con);
if(check_flag(&flag, "CVodeSetSensErrCon", 1, my_pe)) MPI_Abort(comm, 1);
flag = CVodeSetSensDQMethod(cvode_mem, CV_CENTERED, ZERO);
if(check_flag(&flag, "CVodeSetSensDQMethod", 1, my_pe)) MPI_Abort(comm, 1);
flag = CVodeSetSensParams(cvode_mem, data->p, pbar, plist);
if(check_flag(&flag, "CVodeSetSensParams", 1, my_pe)) MPI_Abort(comm, 1);
if(my_pe == 0) {
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 {
if(my_pe == 0) printf("Sensitivity: NO ");
}
/* In loop over output points, call CVode, print results, test for error */
if(my_pe == 0) {
printf("\n\n");
printf("============================================================\n");
printf(" T Q H NST Max norm \n");
printf("============================================================\n");
}
for (iout=1, tout=T1; iout <= NOUT; iout++, tout += DTOUT) {
flag = CVode(cvode_mem, tout, u, &t, CV_NORMAL);
if(check_flag(&flag, "CVode", 1, my_pe)) break;
PrintOutput(cvode_mem, my_pe, t, u);
if (sensi) {
flag = CVodeGetSens(cvode_mem, &t, uS);
if(check_flag(&flag, "CVodeGetSens", 1, my_pe)) break;
PrintOutputS(my_pe, uS);
}
if (my_pe == 0)
printf("------------------------------------------------------------\n");
}
/* Print final statistics */
if (my_pe == 0)
PrintFinalStats(cvode_mem, sensi);
/* Free memory */
N_VDestroy(u); /* Free the u vector */
if (sensi)
N_VDestroyVectorArray(uS, NS); /* Free the uS vectors */
free(data->p); /* Free the p vector */
free(data); /* Free block of UserData */
CVodeFree(&cvode_mem); /* Free the CVODES problem memory */
free(pbar);
if(sensi) free(plist);
MPI_Finalize();
return(0);
}
void CVodesIntegrator::initialize(double t0, FuncEval& func)
{
m_neq = func.neq();
m_t0 = t0;
m_time = t0;
if (m_y) {
N_VDestroy_Serial(m_y); // free solution vector if already allocated
}
m_y = N_VNew_Serial(static_cast<sd_size_t>(m_neq)); // allocate solution vector
for (size_t i = 0; i < m_neq; i++) {
NV_Ith_S(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(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 = CVodeInit(m_cvode_mem, cvodes_rhs, m_t0, 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.");
}
}
CVodeSetErrHandlerFn(m_cvode_mem, &cvodes_err, this);
if (m_itol == CV_SV) {
flag = CVodeSVtolerances(m_cvode_mem, m_reltol, 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.");
}
}
// pass a pointer to func in m_data
m_fdata.reset(new FuncData(&func, func.nparams()));
flag = CVodeSetUserData(m_cvode_mem, m_fdata.get());
if (flag != CV_SUCCESS) {
throw CVodesErr("CVodeSetUserData failed.");
}
if (func.nparams() > 0) {
sensInit(t0, func);
flag = CVodeSetSensParams(m_cvode_mem, m_fdata->m_pars.data(),
NULL, NULL);
}
applyOptions();
}
void CVodesIntegrator::initialize(double t0, FuncEval& func)
{
m_neq = func.neq();
m_t0 = t0;
m_time = t0;
if (m_y) {
N_VDestroy_Serial(m_y); // free solution vector if already allocated
}
m_y = N_VNew_Serial(static_cast<sd_size_t>(m_neq)); // allocate solution vector
N_VConst(0.0, m_y);
// check abs tolerance array size
if (m_itol == CV_SV && m_nabs < m_neq) {
throw CanteraError("CVodesIntegrator::initialize",
"not enough absolute tolerance values specified.");
}
func.getState(NV_DATA_S(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 CanteraError("CVodesIntegrator::initialize",
"CVodeCreate failed.");
}
int flag = CVodeInit(m_cvode_mem, cvodes_rhs, m_t0, m_y);
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CanteraError("CVodesIntegrator::initialize",
"Memory allocation failed.");
} else if (flag == CV_ILL_INPUT) {
throw CanteraError("CVodesIntegrator::initialize",
"Illegal value for CVodeInit input argument.");
} else {
throw CanteraError("CVodesIntegrator::initialize",
"CVodeInit failed.");
}
}
CVodeSetErrHandlerFn(m_cvode_mem, &cvodes_err, this);
if (m_itol == CV_SV) {
flag = CVodeSVtolerances(m_cvode_mem, m_reltol, m_abstol);
} else {
flag = CVodeSStolerances(m_cvode_mem, m_reltol, m_abstols);
}
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CanteraError("CVodesIntegrator::initialize",
"Memory allocation failed.");
} else if (flag == CV_ILL_INPUT) {
throw CanteraError("CVodesIntegrator::initialize",
"Illegal value for CVodeInit input argument.");
} else {
throw CanteraError("CVodesIntegrator::initialize",
"CVodeInit failed.");
}
}
flag = CVodeSetUserData(m_cvode_mem, &func);
if (flag != CV_SUCCESS) {
throw CanteraError("CVodesIntegrator::initialize",
"CVodeSetUserData failed.");
}
if (func.nparams() > 0) {
sensInit(t0, func);
flag = CVodeSetSensParams(m_cvode_mem, func.m_sens_params.data(),
func.m_paramScales.data(), NULL);
if (flag != CV_SUCCESS) {
throw CanteraError("CVodesIntegrator::initialize",
"CVodeSetSensParams failed.");
}
}
applyOptions();
}