void ode_solver_free(ode_solver* solver){
free(solver->params);
CVodeFree(&(solver->cvode_mem));
if (solver->yS != 0) {
N_VDestroyVectorArray_Serial(solver->yS, solver->odeModel->P);
}
N_VDestroy_Serial(solver->y);
free(solver);
}
CVodesIntegrator::~CVodesIntegrator()
{
if (m_cvode_mem) {
if (m_np > 0) {
CVodeSensFree(m_cvode_mem);
}
CVodeFree(&m_cvode_mem);
}
if (m_y) {
N_VDestroy_Serial(m_y);
}
if (m_abstol) {
N_VDestroy_Serial(m_abstol);
}
if (m_yS) {
N_VDestroyVectorArray_Serial(m_yS, static_cast<sd_size_t>(m_np));
}
}
N_Vector *N_VNewVectorArrayEmpty_Serial(int count, long int length)
{
N_Vector *vs;
int j;
if (count <= 0) return(NULL);
vs = (N_Vector *) malloc(count * sizeof(N_Vector));
if(vs == NULL) return(NULL);
for (j=0; j<count; j++) {
vs[j] = N_VNewEmpty_Serial(length);
if (vs[j] == NULL) {
N_VDestroyVectorArray_Serial(vs, j-1);
return(NULL);
}
}
return(vs);
}
N_Vector *N_VCloneVectorArrayEmpty_Serial(int count, N_Vector w)
{
N_Vector *vs;
int j;
if (count <= 0) return(NULL);
vs = NULL;
vs = (N_Vector *) malloc(count * sizeof(N_Vector));
if(vs == NULL) return(NULL);
for (j = 0; j < count; j++) {
vs[j] = NULL;
vs[j] = N_VCloneEmpty_Serial(w);
if (vs[j] == NULL) {
N_VDestroyVectorArray_Serial(vs, j-1);
return(NULL);
}
}
return(vs);
}
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);
}
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);
}
void handleError( void *cvode_mem, N_Vector y0, int flag, mxArray *plhs[], int nrhs, int sensitivity, N_Vector *yS0, realtype *sensitivities, struct mData *data ) {
#ifdef DEBUG
long int temp;
realtype tempreal;
#endif
#ifdef DEBUG
printf( "<<< DEBUG OUTPUT >>>\n" );
printf( "PARAMETERS: \n" );
for ( temp = 0; temp < N_PARAMS; temp++ ) {
printf( "P(%d) = %f\n", temp, data->p[ temp ] );
}
CVodeGetNumSteps(cvode_mem, &temp);
printf( "Number of steps taken by the solver: %d\n", temp );
CVodeGetNumErrTestFails(cvode_mem, &temp);
printf( "Number of local error test failures: %d\n", temp );
CVodeGetLastStep(cvode_mem, &tempreal);
printf( "Last stepsize: %f\n", tempreal );
CVodeGetCurrentStep(cvode_mem, &tempreal);
printf( "Last step: %f\n", tempreal );
#endif
if ( sensitivity == 1 ) {
if ( nrhs < 7 ) free( sensitivities );
free( data->p );
N_VDestroyVectorArray_Serial( yS0, N_STATES + N_PARAMS );
if ( plhs[2] != NULL ) mxDestroyArray(plhs[2]);
}
if ( plhs[1] != NULL ) mxDestroyArray(plhs[1]);
if ( plhs[0] != NULL ) mxDestroyArray(plhs[0]);
N_VDestroy_Serial( y0 );
/*printf( "Freeing..." );*/
/*CVodeFree( &cvode_mem );*/
/*printf( "Success!\n" );*/
switch( flag ) {
case CV_MEM_NULL:
printf( "ERROR: No memory was allocated for cvode_mem\n" );
break;
case CV_NO_MALLOC:
printf( "ERROR: Forgot or failed CVodeInit\n" );
break;
case CV_ILL_INPUT:
printf( "ERROR: Input for CVode was illegal\n" );
break;
case CV_TOO_CLOSE:
printf( "ERROR: Initial time too close to final time\n" );
break;
case CV_TOO_MUCH_WORK:
printf( "ERROR: Solver took maximum number of internal steps, but hasn't reached t_out\n" );
break;
case CV_TOO_MUCH_ACC:
printf( "ERROR: Could not attain desired accuracy\n" );
break;
case CV_ERR_FAILURE:
printf( "ERROR: Error tests failed too many times\n" );
break;
case CV_CONV_FAILURE:
printf( "ERROR: Convergence failure in solving the linear system\n" );
break;
case CV_LINIT_FAIL:
printf( "ERROR: Linear solver failed to initialize\n" );
break;
case CV_LSETUP_FAIL:
printf( "ERROR: Linear solver setup failed\n" );
break;
case CV_RHSFUNC_FAIL:
printf( "ERROR: Right hand side failed in an unrecoverable manner\n" );
break;
case CV_REPTD_RHSFUNC_ERR:
printf( "ERROR: Convergence test failures occured too many times in RHS\n" );
break;
case CV_UNREC_RHSFUNC_ERR:
printf( "ERROR: Unrecoverable error in the RHS\n" );
break;
case CV_RTFUNC_FAIL:
printf( "ERROR: Rootfinding function failed!\n" );
break;
default:
printf( "ERROR: I have no idea what's going on :(\n" );
break;
}
mexErrMsgTxt( "Aborting" );
}
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 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;
}