void FCV_REINIT(realtype *t0, realtype *y0,
int *iatol, realtype *rtol, realtype *atol,
int *ier)
{
N_Vector Vatol;
*ier = 0;
/* Initialize all pointers to NULL */
Vatol = NULL;
/* Set data in F2C_CVODE_vec to y0 */
N_VSetArrayPointer(y0, F2C_CVODE_vec);
/* Call CVReInit */
*ier = CVodeReInit(CV_cvodemem, *t0, F2C_CVODE_vec);
/* Reset data pointers */
N_VSetArrayPointer(NULL, F2C_CVODE_vec);
/* On failure, exit */
if (*ier != CV_SUCCESS) {
*ier = -1;
return;
}
/* Set tolerances */
switch (*iatol) {
case 1:
*ier = CVodeSStolerances(CV_cvodemem, *rtol, *atol);
break;
case 2:
Vatol = NULL;
Vatol = N_VCloneEmpty(F2C_CVODE_vec);
if (Vatol == NULL) {
*ier = -1;
return;
}
N_VSetArrayPointer(atol, Vatol);
*ier = CVodeSVtolerances(CV_cvodemem, *rtol, Vatol);
N_VDestroy(Vatol);
break;
}
/* On failure, exit */
if (*ier != CV_SUCCESS) {
*ier = -1;
return;
}
return;
}
void ode_solver_setErrTol(ode_solver* solver, const double rel_tol, double* abs_tol, const int abs_tol_len){
if( (abs_tol_len != 1) && (abs_tol_len != solver->odeModel->N)){
fprintf(stderr,"ode_solver_setErrTol: length of abs_tol must be 1 or equal to the number of variables in the ode model.\n");
return ;
}
/* set tollerances to the cvode_mem internal structure */
if ( abs_tol_len == 1 )
CVodeSStolerances(solver->cvode_mem, rel_tol, abs_tol[0]);
else{
N_Vector abs_tol_vec = N_VNewEmpty_Serial(abs_tol_len); /* alloc */
NV_DATA_S(abs_tol_vec) = abs_tol;
CVodeSVtolerances(solver->cvode_mem, rel_tol, abs_tol_vec);
N_VDestroy_Serial(abs_tol_vec); /* free */
}
}
int main(int narg, char **args)
{
realtype reltol, t, tout;
N_Vector state, abstol;
void *cvode_mem;
int flag, flagr;
int rootsfound[NRF];
int rootdir[] = {1,};
FILE *pout;
if(!(pout = fopen("results/iaf_v.dat", "w"))){
fprintf(stderr, "Cannot open file results/iaf_v.dat. Are you trying to write to a non-existent directory? Exiting...\n");
exit(1);
}
state = abstol = NULL;
cvode_mem = NULL;
state = N_VNew_Serial(NEQ);
if (check_flag((void *)state, "N_VNew_Serial", 0)) return(1);
abstol = N_VNew_Serial(NEQ);
if (check_flag((void *)abstol, "N_VNew_Serial", 0)) return(1);
realtype reset = -0.07;
realtype C = 3.2e-12;
realtype thresh = -0.055;
realtype gleak = 2e-10;
realtype eleak = -0.053;
realtype p[] = {reset, C, thresh, gleak, eleak, };
realtype v = reset;
NV_Ith_S(state, 0) = reset;
reltol = RTOL;
NV_Ith_S(abstol,0) = ATOL0;
/* Allocations and initializations */
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1);
flag = CVodeInit(cvode_mem, dstate_dt, T0, state);
if (check_flag(&flag, "CVodeInit", 1)) return(1);
flag = CVodeSetUserData(cvode_mem, p);
if (check_flag(&flag, "CVodeSetUserData", 1)) return(1);
flag = CVodeSVtolerances(cvode_mem, reltol, abstol);
if (check_flag(&flag, "CVodeSVtolerances", 1)) return(1);
flag = CVodeRootInit(cvode_mem, NRF, root_functions);
if (check_flag(&flag, "CVodeRootInit", 1)) return(1);
CVodeSetRootDirection(cvode_mem, rootdir);
if (check_flag(&flag, "CVodeSetRootDirection", 1)) return(1);
flag = CVDense(cvode_mem, NEQ);
if (check_flag(&flag, "CVDense", 1)) return(1);
printf(" \n Integrating iaf \n\n");
printf("#t v, \n");
PrintOutput(pout, t, state);
tout = DT;
while(1) {
flag = CVode(cvode_mem, tout, state, &t, CV_NORMAL);
if(flag == CV_ROOT_RETURN) {
/* Event detected */
flagr = CVodeGetRootInfo(cvode_mem, rootsfound);
if (check_flag(&flagr, "CVodeGetRootInfo", 1)) return(1);
PrintRootInfo(t, state, rootsfound);
if(rootsfound[0]){
//condition_0
v = NV_Ith_S(state, 0);
NV_Ith_S(state, 0) = reset;
}
/* Restart integration with event-corrected state */
flag = CVodeSetUserData(cvode_mem, p);
if (check_flag(&flag, "CVodeSetUserData", 1)) return(1);
CVodeReInit(cvode_mem, t, state);
//PrintRootInfo(t, state, rootsfound);
}
else
{
PrintOutput(pout, t, state);
if(check_flag(&flag, "CVode", 1)) break;
if(flag == CV_SUCCESS) {
tout += DT;
}
if (t >= T1) break;
}
}
PrintFinalStats(cvode_mem);
N_VDestroy_Serial(state);
N_VDestroy_Serial(abstol);
CVodeFree(&cvode_mem);
fclose(pout);
return(0);
}
int do_integrate(float t_start, float t_stop, int n_points)
{
realtype reltol, t;
N_Vector y, abstol;
void *cvode_mem;
int flag, flagr, iout;
y = abstol = NULL;
cvode_mem = NULL;
/* Create serial vector of length NEQ for I.C. and abstol */
y = N_VNew_Serial(NEQ);
if (check_flag((void *)y, "N_VNew_Serial", 0)) return(1);
abstol = N_VNew_Serial(NEQ);
if (check_flag((void *)abstol, "N_VNew_Serial", 0)) return(1);
//Setup the initial state values:
setup_initial_states(y);
setup_tolerances(abstol);
/* Set the scalar relative tolerance */
reltol = RTOL;
/* 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 inital time T0, and
* the initial dependent variable vector y. */
flag = CVodeInit(cvode_mem, f, t_start, y);
if (check_flag(&flag, "CVodeInit", 1)) return(1);
/* Call CVodeSVtolerances to specify the scalar relative tolerance
* and vector absolute tolerances */
flag = CVodeSVtolerances(cvode_mem, reltol, abstol);
if (check_flag(&flag, "CVodeSVtolerances", 1)) return(1);
/* Call CVDense to specify the CVDENSE dense linear solver */
flag = CVDense(cvode_mem, NEQ);
if (check_flag(&flag, "CVDense", 1)) return(1);
/* Set the Jacobian routine to Jac (user-supplied) */
flag = CVDlsSetDenseJacFn(cvode_mem, Jac);
if (check_flag(&flag, "CVDlsSetDenseJacFn", 1)) return(1);
/* In loop, call CVode, print results, and test for error.*/
printf(" \n3-species kinetics problem\n\n");
iout = 0;
int i=0;
for(i=1;i< n_points; i++)
{
float t_next = t_start + (t_stop-t_start)/n_points * i;
printf("Advancing to: %f", t_next);
flag = CVode(cvode_mem, t_next, y, &t, CV_NORMAL);
loop_function(t,y);
PrintOutput(t, Ith(y,1), Ith(y,2), Ith(y,3));
//printf("MH: %d %f",iout,t_next);
if (check_flag(&flag, "CVode", 1)) break;
assert(flag==CV_SUCCESS);
}
/* Print some final statistics */
PrintFinalStats(cvode_mem);
/* Free y and abstol vectors */
N_VDestroy_Serial(y);
N_VDestroy_Serial(abstol);
/* Free integrator memory */
CVodeFree(&cvode_mem);
return(0);
}
int main()
{
realtype reltol, t, tout;
N_Vector y, abstol;
void *cvode_mem;
int flag, flagr, iout, nnz;
int rootsfound[2];
y = abstol = NULL;
cvode_mem = NULL;
/* Create serial vector of length NEQ for I.C. and abstol */
y = N_VNew_Serial(NEQ);
if (check_flag((void *)y, "N_VNew_Serial", 0)) return(1);
abstol = N_VNew_Serial(NEQ);
if (check_flag((void *)abstol, "N_VNew_Serial", 0)) return(1);
/* Initialize y */
Ith(y,1) = Y1;
Ith(y,2) = Y2;
Ith(y,3) = Y3;
/* Set the scalar relative tolerance */
reltol = RTOL;
/* Set the vector absolute tolerance */
Ith(abstol,1) = ATOL1;
Ith(abstol,2) = ATOL2;
Ith(abstol,3) = ATOL3;
/* 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 inital 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 CVodeSVtolerances to specify the scalar relative tolerance
* and vector absolute tolerances */
flag = CVodeSVtolerances(cvode_mem, reltol, abstol);
if (check_flag(&flag, "CVodeSVtolerances", 1)) return(1);
/* Call CVodeRootInit to specify the root function g with 2 components */
flag = CVodeRootInit(cvode_mem, 2, g);
if (check_flag(&flag, "CVodeRootInit", 1)) return(1);
/* Call CVSuperLUMT to specify the CVSuperLUMT sparse direct linear solver */
nnz = NEQ * NEQ;
flag = CVSuperLUMT(cvode_mem, 1, 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);
/* In loop, call CVode, print results, and test for error.
Break out of loop when NOUT preset output times have been reached. */
printf(" \n3-species kinetics problem\n\n");
iout = 0; tout = T1;
while(1) {
flag = CVode(cvode_mem, tout, y, &t, CV_NORMAL);
PrintOutput(t, Ith(y,1), Ith(y,2), Ith(y,3));
if (flag == CV_ROOT_RETURN) {
flagr = CVodeGetRootInfo(cvode_mem, rootsfound);
if (check_flag(&flagr, "CVodeGetRootInfo", 1)) return(1);
PrintRootInfo(rootsfound[0],rootsfound[1]);
}
if (check_flag(&flag, "CVode", 1)) break;
if (flag == CV_SUCCESS) {
iout++;
tout *= TMULT;
}
if (iout == NOUT) break;
}
/* Print some final statistics */
PrintFinalStats(cvode_mem);
/* Free y and abstol vectors */
N_VDestroy_Serial(y);
N_VDestroy_Serial(abstol);
/* Free integrator memory */
CVodeFree(&cvode_mem);
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);
}
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);
}
int main(int narg, char **args)
{
realtype reltol, t, tout;
N_Vector state, abstol;
void *cvode_mem;
int flag, flagr;
int rootsfound[NRF];
int rootdir[] = {1,1,1,};
FILE *pout;
pout = stdout;
state = abstol = NULL;
cvode_mem = NULL;
state = N_VNew_Serial(NEQ);
if (check_flag((void *)state, "N_VNew_Serial", 0)) return(1);
abstol = N_VNew_Serial(NEQ);
if (check_flag((void *)abstol, "N_VNew_Serial", 0)) return(1);
realtype a = 0.02;
realtype b = 0.2;
realtype c = -50;
realtype d = 2;
realtype I = 0;
realtype v0 = -70;
realtype p[] = {a, b, c, d, I, v0, };
realtype v = v0;
realtype u = b * v0;
NV_Ith_S(state, 0) = v0;
NV_Ith_S(state, 1) = b * v0;
reltol = RTOL;
NV_Ith_S(abstol,0) = ATOL0;
NV_Ith_S(abstol,1) = ATOL1;
/* Allocations and initializations */
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1);
flag = CVodeInit(cvode_mem, dstate_dt, T0, state);
if (check_flag(&flag, "CVodeInit", 1)) return(1);
flag = CVodeSetUserData(cvode_mem, p);
if (check_flag(&flag, "CVodeSetUserData", 1)) return(1);
flag = CVodeSVtolerances(cvode_mem, reltol, abstol);
if (check_flag(&flag, "CVodeSVtolerances", 1)) return(1);
flag = CVodeRootInit(cvode_mem, NRF, root_functions);
if (check_flag(&flag, "CVodeRootInit", 1)) return(1);
CVodeSetRootDirection(cvode_mem, rootdir);
if (check_flag(&flag, "CVodeSetRootDirection", 1)) return(1);
flag = CVDense(cvode_mem, NEQ);
if (check_flag(&flag, "CVDense", 1)) return(1);
printf(" \n Integrating izhikevich_burster \n\n");
printf("#t v, u, \n");
PrintOutput(pout, t, state);
tout = DT;
while(1) {
flag = CVode(cvode_mem, tout, state, &t, CV_NORMAL);
if(flag == CV_ROOT_RETURN) {
/* Event detected */
flagr = CVodeGetRootInfo(cvode_mem, rootsfound);
if (check_flag(&flagr, "CVodeGetRootInfo", 1)) return(1);
PrintRootInfo(t, state, rootsfound);
if(rootsfound[0]){
//spike
v = NV_Ith_S(state, 0);
u = NV_Ith_S(state, 1);
NV_Ith_S(state, 0) = c;
NV_Ith_S(state, 1) = u + d;
}
if(rootsfound[1]){
//start_inj
I = 5;
p[0] = a;
p[1] = b;
p[2] = c;
p[3] = d;
p[4] = I;
p[5] = v0;
}
if(rootsfound[2]){
//end_inj
I = 0;
p[0] = a;
p[1] = b;
p[2] = c;
p[3] = d;
p[4] = I;
p[5] = v0;
}
/* Restart integration with event-corrected state */
flag = CVodeSetUserData(cvode_mem, p);
if (check_flag(&flag, "CVodeSetUserData", 1)) return(1);
CVodeReInit(cvode_mem, t, state);
//PrintRootInfo(t, state, rootsfound);
}
else
{
PrintOutput(pout, t, state);
if(check_flag(&flag, "CVode", 1)) break;
if(flag == CV_SUCCESS) {
tout += DT;
}
if (t >= T1) break;
}
}
PrintFinalStats(cvode_mem);
N_VDestroy_Serial(state);
N_VDestroy_Serial(abstol);
CVodeFree(&cvode_mem);
fclose(pout);
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 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);
}
}
/** \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;
}
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;
}
int main(int narg, char **args)
{
realtype reltol, t, tout;
N_Vector state, abstol;
void *cvode_mem;
int flag, flagr;
FILE *pout;
if(!(pout = fopen("Locke2008_Circadian_Clock.dat", "w"))){
fprintf(stderr, "Cannot open file Locke2008_Circadian_Clock.dat. Are you trying to write to a non-existent directory? Exiting...\n");
exit(1);
}
state = abstol = NULL;
cvode_mem = NULL;
state = N_VNew_Serial(NEQ);
if (check_flag((void *)state, "N_VNew_Serial", 0)) return(1);
abstol = N_VNew_Serial(NEQ);
if (check_flag((void *)abstol, "N_VNew_Serial", 0)) return(1);
realtype Kc = 4.8283;
realtype v_4 = 1.0841;
realtype v_6 = 4.6645;
realtype vc = 6.7924;
realtype v_1 = 6.8355;
realtype v_2 = 8.4297;
realtype K = 1.0;
realtype v_8 = 3.5216;
realtype L = 0.0;
realtype n = 5.6645;
realtype k3 = 0.1177;
realtype K2 = 0.291;
realtype K1 = 2.7266;
realtype k7 = 0.2282;
realtype K6 = 9.9849;
realtype k5 = 0.3352;
realtype K4 = 8.1343;
realtype K8 = 7.4519;
realtype init_X1 = 4.25;
realtype tscale = 1.0;
realtype init_Z1 = 2.25;
realtype init_Z2 = 0.0;
realtype init_V1 = 2.5;
realtype init_V2 = 0.0;
realtype init_X2 = 0.0;
realtype compartment = 1.0;
realtype init_Y1 = 3.25;
realtype init_Y2 = 0.0;
realtype p[] = {Kc, v_4, v_6, vc, v_1, v_2, K, v_8, L, n, k3, K2, K1, k7, K6, k5, K4, K8, init_X1, tscale, init_Z1, init_Z2, init_V1, init_V2, init_X2, compartment, init_Y1, init_Y2, };
realtype X1 = init_X1;
realtype X2 = init_X2;
realtype V1 = init_V1;
realtype V2 = init_V2;
realtype Y1 = init_Y1;
realtype Y2 = init_Y2;
realtype Z1 = init_Z1;
realtype Z2 = init_Z2;
NV_Ith_S(state, 0) = init_Y2;
NV_Ith_S(state, 1) = init_V1;
NV_Ith_S(state, 2) = init_Y1;
NV_Ith_S(state, 3) = init_V2;
NV_Ith_S(state, 4) = init_X2;
NV_Ith_S(state, 5) = init_X1;
NV_Ith_S(state, 6) = init_Z1;
NV_Ith_S(state, 7) = init_Z2;
reltol = RTOL;
NV_Ith_S(abstol,0) = ATOL0;
NV_Ith_S(abstol,1) = ATOL1;
NV_Ith_S(abstol,2) = ATOL2;
NV_Ith_S(abstol,3) = ATOL3;
NV_Ith_S(abstol,4) = ATOL4;
NV_Ith_S(abstol,5) = ATOL5;
NV_Ith_S(abstol,6) = ATOL6;
NV_Ith_S(abstol,7) = ATOL7;
/* Allocations and initializations */
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1);
flag = CVodeInit(cvode_mem, dstate_dt, T0, state);
if (check_flag(&flag, "CVodeInit", 1)) return(1);
flag = CVodeSetUserData(cvode_mem, p);
if (check_flag(&flag, "CVodeSetUserData", 1)) return(1);
flag = CVodeSVtolerances(cvode_mem, reltol, abstol);
if (check_flag(&flag, "CVodeSVtolerances", 1)) return(1);
flag = CVDense(cvode_mem, NEQ);
if (check_flag(&flag, "CVDense", 1)) return(1);
printf(" \n Integrating Locke2008_Circadian_Clock_0 \n\n");
printf("#t Y2, V1, Y1, V2, X2, X1, Z1, Z2, \n");
PrintOutput(pout, t, state);
tout = DT;
while(1) {
flag = CVode(cvode_mem, tout, state, &t, CV_NORMAL);
{
PrintOutput(pout, t, state);
if(check_flag(&flag, "CVode", 1)) break;
if(flag == CV_SUCCESS) {
tout += DT;
}
if (t >= T1) break;
}
}
PrintFinalStats(cvode_mem);
N_VDestroy_Serial(state);
N_VDestroy_Serial(abstol);
CVodeFree(&cvode_mem);
fclose(pout);
return(0);
}
void FCV_MALLOC(realtype *t0, realtype *y0,
int *meth, int *iatol,
realtype *rtol, realtype *atol,
long int *iout, realtype *rout,
long int *ipar, realtype *rpar,
int *ier)
{
int lmm;
N_Vector Vatol;
FCVUserData CV_userdata;
*ier = 0;
/* Check for required vector operations */
if(F2C_CVODE_vec->ops->nvgetarraypointer == NULL ||
F2C_CVODE_vec->ops->nvsetarraypointer == NULL) {
*ier = -1;
fprintf(stderr, "A required vector operation is not implemented.\n\n");
return;
}
/* Initialize all pointers to NULL */
CV_cvodemem = NULL;
Vatol = NULL;
FCVNullNonlinSol();
/* initialize global constants to disable each option */
CV_nrtfn = 0;
CV_ls = -1;
/* Create CVODE object */
lmm = (*meth == 1) ? CV_ADAMS : CV_BDF;
CV_cvodemem = CVodeCreate(lmm);
if (CV_cvodemem == NULL) {
*ier = -1;
return;
}
/* Set and attach user data */
CV_userdata = NULL;
CV_userdata = (FCVUserData) malloc(sizeof *CV_userdata);
if (CV_userdata == NULL) {
*ier = -1;
return;
}
CV_userdata->rpar = rpar;
CV_userdata->ipar = ipar;
*ier = CVodeSetUserData(CV_cvodemem, CV_userdata);
if(*ier != CV_SUCCESS) {
free(CV_userdata); CV_userdata = NULL;
*ier = -1;
return;
}
/* Set data in F2C_CVODE_vec to y0 */
N_VSetArrayPointer(y0, F2C_CVODE_vec);
/* Call CVodeInit */
*ier = CVodeInit(CV_cvodemem, FCVf, *t0, F2C_CVODE_vec);
/* Reset data pointers */
N_VSetArrayPointer(NULL, F2C_CVODE_vec);
/* On failure, exit */
if(*ier != CV_SUCCESS) {
free(CV_userdata); CV_userdata = NULL;
*ier = -1;
return;
}
/* Set tolerances */
switch (*iatol) {
case 1:
*ier = CVodeSStolerances(CV_cvodemem, *rtol, *atol);
break;
case 2:
Vatol = NULL;
Vatol = N_VCloneEmpty(F2C_CVODE_vec);
if (Vatol == NULL) {
free(CV_userdata); CV_userdata = NULL;
*ier = -1;
return;
}
N_VSetArrayPointer(atol, Vatol);
*ier = CVodeSVtolerances(CV_cvodemem, *rtol, Vatol);
N_VDestroy(Vatol);
break;
}
/* On failure, exit */
if(*ier != CV_SUCCESS) {
free(CV_userdata); CV_userdata = NULL;
*ier = -1;
return;
}
/* Grab optional output arrays and store them in global variables */
CV_iout = iout;
CV_rout = rout;
/* Store the unit roundoff in rout for user access */
CV_rout[5] = UNIT_ROUNDOFF;
return;
}
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;
}
int jmi_ode_cvode_new(jmi_ode_cvode_t** integrator_ptr, jmi_ode_solver_t* solver) {
jmi_ode_cvode_t* integrator;
jmi_ode_problem_t* problem = solver -> ode_problem;
int flag = 0;
void* cvode_mem;
jmi_real_t* y;
jmi_real_t* atol_nv;
int i;
integrator = (jmi_ode_cvode_t*)calloc(1,sizeof(jmi_ode_cvode_t));
if(!integrator){
jmi_log_node(problem->log, logError, "Error", "Failed to allocate the internal CVODE struct.");
return -1;
}
/* DEFAULT VALUES NEEDS TO BE IMPROVED*/
integrator->lmm = CV_BDF;
integrator->iter = CV_NEWTON;
/* integrator->rtol = 1e-4; */
integrator->rtol = solver->rel_tol;
if (problem->n_real_x > 0) {
integrator->atol = N_VNew_Serial(problem->n_real_x);
} else {
integrator->atol = N_VNew_Serial(1);
}
atol_nv = NV_DATA_S(integrator->atol);
if (problem->n_real_x > 0) {
for (i = 0; i < problem->n_real_x; i++) {
atol_nv[i] = 0.01*integrator->rtol*problem->nominal[i];
}
}else{
atol_nv[0] = 0.01*integrator->rtol*1.0;
}
cvode_mem = CVodeCreate(integrator->lmm,integrator->iter);
if(!cvode_mem){
jmi_log_node(problem->log, logError, "Error", "Failed to allocate the CVODE struct.");
return -1;
}
/* Get the default values for the time and states */
if (problem->n_real_x > 0) {
integrator->y_work = N_VNew_Serial(problem->n_real_x);
y = NV_DATA_S(integrator->y_work);
memcpy (y, problem->states, problem->n_real_x*sizeof(jmi_real_t));
}else{
integrator->y_work = N_VNew_Serial(1);
y = NV_DATA_S(integrator->y_work);
y[0] = 0.0;
}
flag = CVodeInit(cvode_mem, cv_rhs, problem->time, integrator->y_work);
if(flag != 0) {
jmi_log_node(problem->log, logError, "Error", "Failed to initialize CVODE. Returned with <error_flag: %d>", flag);
return -1;
}
flag = CVodeSVtolerances(cvode_mem, integrator->rtol, integrator->atol);
if(flag!=0){
jmi_log_node(problem->log, logError, "Error", "Failed to specify the tolerances. Returned with <error_flag: %d>", flag);
return -1;
}
if (problem->n_real_x > 0) {
flag = CVDense(cvode_mem, problem->n_real_x);
}else{
flag = CVDense(cvode_mem, 1);
}
if(flag!=0){
jmi_log_node(problem->log, logError, "Error", "Failed to specify the linear solver. Returned with <error_flag: %d>", flag);
return -1;
}
flag = CVodeSetUserData(cvode_mem, (void*)solver);
if(flag!=0){
jmi_log_node(problem->log, logError, "Error", "Failed to specify the user data. Returned with <error_flag: %d>", flag);
return -1;
}
if (problem->n_sw > 0){
flag = CVodeRootInit(cvode_mem, problem->n_sw, cv_root);
if(flag!=0){
jmi_log_node(problem->log, logError, "Error", "Failed to specify the event indicator function. Returned with <error_flag: %d>", flag);
return -1;
}
}
flag = CVodeSetErrHandlerFn(cvode_mem, cv_err, (void*)solver);
if(flag!=0){
jmi_log_node(problem->log, logError, "Error", "Failed to specify the error handling function. Returned with <error_flag: %d>", flag);
return -1;
}
integrator->cvode_mem = cvode_mem;
*integrator_ptr = integrator;
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
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();
}
