本文整理汇总了C++中CVode函数的典型用法代码示例。如果您正苦于以下问题：C++ CVode函数的具体用法？C++ CVode怎么用？C++ CVode使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了CVode函数的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的C++代码示例。
示例1: cvode_eval
int cvode_eval(solver_props *props, unsigned int modelid){
cvode_mem *mem = props->mem;
mem = &mem[modelid];
// Stop the solver if the stop time has been reached
props->running[modelid] = (props->time[modelid] + props->timestep) < props->stoptime;
if(!props->running[modelid])
return 0;
// if a positive dt is specified, then we will have this function return after it reaches the next time point,
// otherwise, it will just run one iteration and return
if(props->timestep > 0) {
// Reinitialize the function at each step
if(CVodeReInit(mem->cvmem, props->time[modelid], mem->y0) != CV_SUCCESS) {
PRINTF( "CVODE failed to reinitialize");
}
CDATAFORMAT stop_time = MIN(props->time[modelid] + props->timestep, props->stoptime);
mem->first_iteration = TRUE;
if(CVode(mem->cvmem, stop_time, mem->y0, &(props->next_time[modelid]), CV_NORMAL) != CV_SUCCESS){
PRINTF( "CVODE failed to make a fixed step in model %d.\n", modelid);
return 1;
}
}
else {
mem->first_iteration = TRUE;
if(CVode(mem->cvmem, props->stoptime, mem->y0, &(props->next_time[modelid]), CV_ONE_STEP) != CV_SUCCESS){
PRINTF( "CVODE failed to make a step in model %d.\n", modelid);
return 1;
}
}
return 0;
}
开发者ID:joshuaecook，项目名称:simengine，代码行数:34，代码来源:cvode.c
示例2: CVode
void CVodeInt::integrate(double tout)
{
double t;
int flag;
flag = CVode(m_cvode_mem, tout, nv(m_y), &t, NORMAL);
if (flag != SUCCESS)
throw CVodeErr(" CVode error encountered.");
}
开发者ID:hkmoffat，项目名称:cantera，代码行数:8，代码来源:CVodeInt.cpp
示例3: CVode
double CVodesIntegrator::step(double tout)
{
double t;
int flag;
flag = CVode(m_cvode_mem, tout, nv(m_y), &t, CV_ONE_STEP);
if (flag != CV_SUCCESS)
throw CVodesErr(" CVodes error encountered.");
return t;
}
开发者ID:anujg1991，项目名称:cantera，代码行数:9，代码来源:CVodesIntegrator.cpp
示例4: CVode
void CVodesIntegrator::integrate(double tout)
{
int flag = CVode(m_cvode_mem, tout, m_y, &m_time, CV_NORMAL);
if (flag != CV_SUCCESS) {
throw CVodesErr("CVodes error encountered. Error code: " + int2str(flag) + "\n" + m_error_message +
"\nComponents with largest weighted error estimates:\n" + getErrorInfo(10));
}
m_sens_ok = false;
}
开发者ID:thomasfiala，项目名称:cantera，代码行数:9，代码来源:CVodesIntegrator.cpp
示例5: CVode
double CVodesIntegrator::step(double tout)
{
int flag = CVode(m_cvode_mem, tout, m_y, &m_time, CV_ONE_STEP);
if (flag != CV_SUCCESS) {
throw CanteraError("CVodesIntegrator::step",
"CVodes error encountered. Error code: {}\n{}\n"
"Components with largest weighted error estimates:\n{}",
flag, m_error_message, getErrorInfo(10));
}
m_sens_ok = false;
return m_time;
}
开发者ID:Niemeyer-Research-Group，项目名称:cantera，代码行数:13，代码来源:CVodesIntegrator.cpp
示例6: ode_solver_solve
int ode_solver_solve(ode_solver* solver, const double t, double* y, double* tout){
double lTout;
/* Advance the solution */
NV_DATA_S(solver->y) = y;
int flag = CVode(solver->cvode_mem,t, solver->y, &lTout, CV_NORMAL);
if(tout)
*tout = lTout;
return flag;
}
开发者ID:BioinformaticsArchive，项目名称:mcmc_clib，代码行数:13，代码来源:ode_model.c
示例7: SOLVER
int SOLVER(cvode, eval, TARGET, SIMENGINE_STORAGE, cvode_mem *mem, unsigned int modelid) {
// Stop the solver if the stop time has been reached
mem->props->running[modelid] = mem->props->time[modelid] < mem->props->stoptime;
if(!mem->props->running[modelid])
return 0;
mem[modelid].first_iteration = TRUE;
if(CVode(mem[modelid].cvmem, mem[modelid].props->stoptime, ((N_Vector)(mem[modelid].y0)), &(mem[modelid].props->time[modelid]), CV_ONE_STEP) != CV_SUCCESS){
fprintf(stderr, "CVODE failed to make a step in model %d.\n", modelid);
return 1;
}
return 0;
}
开发者ID:joshuaecook，项目名称:simengine，代码行数:14，代码来源:cvode.c
示例8: MPI_Barrier
real Solver::run(real tout, int &ncalls, real &rhstime)
{
#ifdef CHECK
int msg_point = msg_stack.push("Running solver: solver::run(%e)", tout);
#endif
MPI_Barrier(MPI_COMM_WORLD);
rhs_wtime = 0.0;
rhs_ncalls = 0;
pre_Wtime = 0.0;
pre_ncalls = 0.0;
int flag = CVode(cvode_mem, tout, uvec, &simtime, CV_NORMAL);
ncalls = rhs_ncalls;
rhstime = rhs_wtime;
// Copy variables
load_vars(NV_DATA_P(uvec));
// Call rhs function to get extra variables at this time
real tstart = MPI_Wtime();
(*func)(simtime);
rhs_wtime += MPI_Wtime() - tstart;
rhs_ncalls++;
if(flag < 0) {
output.write("ERROR CVODE solve failed at t = %e, flag = %d\n", simtime, flag);
return -1.0;
}
#ifdef CHECK
msg_stack.pop(msg_point);
#endif
return simtime;
}
开发者ID:bendudson，项目名称:BOUT-0.8，代码行数:39，代码来源:sundials_solver.cpp
示例9: integrate
int integrate(struct Integrator* integrator, double tout, double* t)
{
if (integrator->em->nRates > 0)
{
/* need to integrate if we have any differential equations */
int flag;
/* Make sure we don't go past the specified end time - could run into
trouble if we're almost reaching a threshold */
flag = CVodeSetStopTime(integrator->cvode_mem,(realtype)tout);
if (check_flag(&flag,"CVode",1)) return(ERR);
flag = CVode(integrator->cvode_mem,tout,integrator->y,t,CV_NORMAL);
if (check_flag(&flag,"CVode",1)) return(ERR);
/* we also need to evaluate all the other variables that are not required
to be updated during integration */
integrator->em->evaluateVariables(*t);
}
else
{
/* no differential equations so just evaluate once */
integrator->em->computeRates(tout);
integrator->em->evaluateVariables(tout);
*t = tout;
}
/*
* Now that using CV_NORMAL_TSTOP this is no longer required?
*/
#ifdef OLD_CODE
/* only the y array is gonna be at the desired tout, so we need to also
update the full variables array */
ud->BOUND[0] = *t;
ud->methods->ComputeVariables(ud->BOUND,ud->RATES,ud->CONSTANTS,
ud->VARIABLES);
#endif
/* Make sure the outputs are up-to-date */
integrator->em->getOutputs(*t);
return(OK);
}
开发者ID:chrispbradley，项目名称:csim，代码行数:39，代码来源:integrator.cpp
示例10: CVAdataStore
int CVAdataStore(CVadjMem ca_mem, CkpntMem ck_mem)
{
CVodeMem cv_mem;
DtpntMem *dt_mem;
realtype t;
long int i;
int flag;
cv_mem = ca_mem->cv_mem;
dt_mem = ca_mem->dt_mem;
/* Initialize cv_mem with data from ck_mem */
flag = CVAckpntGet(cv_mem, ck_mem);
if (flag != CV_SUCCESS) return(CV_REIFWD_FAIL);
/* Set first structure in dt_mem[0] */
dt_mem[0]->t = t0_;
storePnt(cv_mem, dt_mem[0]);
/* Run CVode to set following structures in dt_mem[i] */
i = 1;
do {
flag = CVode(cv_mem, t1_, ytmp, &t, CV_ONE_STEP);
if (flag < 0) return(CV_FWD_FAIL);
dt_mem[i]->t = t;
storePnt(cv_mem, dt_mem[i]);
i++;
} while (t<t1_);
/* New data is now available */
ckpntData = ck_mem;
newData = TRUE;
np = i;
return(CV_SUCCESS);
}
开发者ID:igemsoftware，项目名称:USTC-Software_2011，代码行数:37，代码来源:cvodea.c
示例11: TSStep_Sundials
PetscErrorCode TSStep_Sundials(TS ts)
{
TS_Sundials *cvode = (TS_Sundials*)ts->data;
PetscErrorCode ierr;
PetscInt flag;
long int its,nsteps;
realtype t,tout;
PetscScalar *y_data;
void *mem;
PetscFunctionBegin;
mem = cvode->mem;
tout = ts->max_time;
ierr = VecGetArray(ts->vec_sol,&y_data);CHKERRQ(ierr);
N_VSetArrayPointer((realtype*)y_data,cvode->y);
ierr = VecRestoreArray(ts->vec_sol,NULL);CHKERRQ(ierr);
ierr = TSPreStep(ts);CHKERRQ(ierr);
/* We would like to call TSPreStep() when starting each step (including rejections) and TSPreStage() before each
* stage solve, but CVode does not appear to support this. */
if (cvode->monitorstep) flag = CVode(mem,tout,cvode->y,&t,CV_ONE_STEP);
else flag = CVode(mem,tout,cvode->y,&t,CV_NORMAL);
if (flag) { /* display error message */
switch (flag) {
case CV_ILL_INPUT:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_ILL_INPUT");
break;
case CV_TOO_CLOSE:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_TOO_CLOSE");
break;
case CV_TOO_MUCH_WORK: {
PetscReal tcur;
ierr = CVodeGetNumSteps(mem,&nsteps);CHKERRQ(ierr);
ierr = CVodeGetCurrentTime(mem,&tcur);CHKERRQ(ierr);
SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_TOO_MUCH_WORK. At t=%G, nsteps %D exceeds mxstep %D. Increase '-ts_max_steps <>' or modify TSSetDuration()",tcur,nsteps,ts->max_steps);
} break;
case CV_TOO_MUCH_ACC:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_TOO_MUCH_ACC");
break;
case CV_ERR_FAILURE:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_ERR_FAILURE");
break;
case CV_CONV_FAILURE:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_CONV_FAILURE");
break;
case CV_LINIT_FAIL:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_LINIT_FAIL");
break;
case CV_LSETUP_FAIL:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_LSETUP_FAIL");
break;
case CV_LSOLVE_FAIL:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_LSOLVE_FAIL");
break;
case CV_RHSFUNC_FAIL:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_RHSFUNC_FAIL");
break;
case CV_FIRST_RHSFUNC_ERR:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_FIRST_RHSFUNC_ERR");
break;
case CV_REPTD_RHSFUNC_ERR:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_REPTD_RHSFUNC_ERR");
break;
case CV_UNREC_RHSFUNC_ERR:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_UNREC_RHSFUNC_ERR");
break;
case CV_RTFUNC_FAIL:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, CV_RTFUNC_FAIL");
break;
default:
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVode() fails, flag %d",flag);
}
}
/* copy the solution from cvode->y to cvode->update and sol */
ierr = VecPlaceArray(cvode->w1,y_data);CHKERRQ(ierr);
ierr = VecCopy(cvode->w1,cvode->update);CHKERRQ(ierr);
ierr = VecResetArray(cvode->w1);CHKERRQ(ierr);
ierr = VecCopy(cvode->update,ts->vec_sol);CHKERRQ(ierr);
ierr = CVodeGetNumNonlinSolvIters(mem,&its);CHKERRQ(ierr);
ierr = CVSpilsGetNumLinIters(mem, &its);
ts->snes_its = its; ts->ksp_its = its;
ts->time_step = t - ts->ptime;
ts->ptime = t;
ts->steps++;
ierr = CVodeGetNumSteps(mem,&nsteps);CHKERRQ(ierr);
if (!cvode->monitorstep) ts->steps = nsteps;
PetscFunctionReturn(0);
}
开发者ID:hsahasra，项目名称:petsc-magma-dense-mat，代码行数:93，代码来源:sundials.c
示例12: main
int main()
{
realtype abstol=ATOL, reltol=RTOL, t, tout;
N_Vector c;
WebData wdata;
void *cvode_mem;
booleantype firstrun;
int jpre, gstype, flag;
int ns, mxns, iout;
c = NULL;
wdata = NULL;
cvode_mem = NULL;
/* Initializations */
c = N_VNew_Serial(NEQ);
if(check_flag((void *)c, "N_VNew_Serial", 0)) return(1);
wdata = AllocUserData();
if(check_flag((void *)wdata, "AllocUserData", 2)) return(1);
InitUserData(wdata);
ns = wdata->ns;
mxns = wdata->mxns;
/* Print problem description */
PrintIntro();
/* Loop over jpre and gstype (four cases) */
for (jpre = PREC_LEFT; jpre <= PREC_RIGHT; jpre++) {
for (gstype = MODIFIED_GS; gstype <= CLASSICAL_GS; gstype++) {
/* Initialize c and print heading */
CInit(c, wdata);
PrintHeader(jpre, gstype);
/* Call CVodeInit or CVodeReInit, then CVSpgmr to set up problem */
firstrun = (jpre == PREC_LEFT) && (gstype == MODIFIED_GS);
if (firstrun) {
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if(check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1);
wdata->cvode_mem = cvode_mem;
flag = CVodeSetUserData(cvode_mem, wdata);
if(check_flag(&flag, "CVodeSetUserData", 1)) return(1);
flag = CVodeInit(cvode_mem, f, T0, c);
if(check_flag(&flag, "CVodeInit", 1)) return(1);
flag = CVodeSStolerances(cvode_mem, reltol, abstol);
if (check_flag(&flag, "CVodeSStolerances", 1)) return(1);
flag = CVSpgmr(cvode_mem, jpre, MAXL);
if(check_flag(&flag, "CVSpgmr", 1)) return(1);
flag = CVSpilsSetGSType(cvode_mem, gstype);
if(check_flag(&flag, "CVSpilsSetGSType", 1)) return(1);
flag = CVSpilsSetEpsLin(cvode_mem, DELT);
if(check_flag(&flag, "CVSpilsSetEpsLin", 1)) return(1);
flag = CVSpilsSetPreconditioner(cvode_mem, Precond, PSolve);
if(check_flag(&flag, "CVSpilsSetPreconditioner", 1)) return(1);
} else {
flag = CVodeReInit(cvode_mem, T0, c);
if(check_flag(&flag, "CVodeReInit", 1)) return(1);
flag = CVSpilsSetPrecType(cvode_mem, jpre);
check_flag(&flag, "CVSpilsSetPrecType", 1);
flag = CVSpilsSetGSType(cvode_mem, gstype);
if(check_flag(&flag, "CVSpilsSetGSType", 1)) return(1);
}
/* Print initial values */
if (firstrun) PrintAllSpecies(c, ns, mxns, T0);
/* Loop over output points, call CVode, print sample solution values. */
tout = T1;
for (iout = 1; iout <= NOUT; iout++) {
flag = CVode(cvode_mem, tout, c, &t, CV_NORMAL);
PrintOutput(cvode_mem, t);
if (firstrun && (iout % 3 == 0)) PrintAllSpecies(c, ns, mxns, t);
if(check_flag(&flag, "CVode", 1)) break;
if (tout > RCONST(0.9)) tout += DTOUT;
else tout *= TOUT_MULT;
}
/* Print final statistics, and loop for next case */
PrintFinalStats(cvode_mem);
}
}
/* Free all memory */
CVodeFree(&cvode_mem);
N_VDestroy_Serial(c);
FreeUserData(wdata);
//.........这里部分代码省略.........
开发者ID:aragilar，项目名称:debian-packaging-sundials，代码行数:101，代码来源:cvsKrylovDemo_prec.c
示例13: main
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);
//.........这里部分代码省略.........
开发者ID:luca-heltai，项目名称:sundials，代码行数:101，代码来源:cvsRoberts_FSA_sps.c
示例14: run_rate_state_sim
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);
//.........这里部分代码省略.........
开发者ID:eheien，项目名称:rs，代码行数:101，代码来源:RateState.cpp
示例15: main
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;
}
}
//.........这里部分代码省略.........
开发者ID:borismarin，项目名称:som-codegen，代码行数:101，代码来源:iaf.c
示例16: dynamixMain
int dynamixMain (int argc, char * argv[]) {
//// DECLARING VARIABLES
// Struct of parameters
PARAMETERS p;
// CVode variables
void * cvode_mem = NULL; // pointer to block of CVode memory
N_Vector y, yout; // arrays of populations
// arrays for energetic parameters
realtype ** V = NULL; // pointer to k-c coupling constants
realtype * Vbridge = NULL; // pointer to array of bridge coupling constants.
// first element [0] is Vkb1, last [Nb] is VcbN
realtype * Vnobridge = NULL; // coupling constant when there is no bridge
//// Setting defaults for parameters to be read from input
//// done setting defaults
int flag;
realtype * k_pops = NULL; // pointers to arrays of populations
realtype * l_pops = NULL;
realtype * c_pops = NULL;
realtype * b_pops = NULL;
realtype * ydata = NULL; // pointer to ydata (contains all populations)
realtype * wavefunction = NULL; // (initial) wavefunction
realtype * dm = NULL; // density matrix
realtype * dmt = NULL; // density matrix in time
realtype * wfnt = NULL; // density matrix in time
realtype * k_energies = NULL; // pointers to arrays of energies
realtype * c_energies = NULL;
realtype * b_energies = NULL;
realtype * l_energies = NULL;
realtype t0 = 0.0; // initial time
realtype t = 0;
realtype tret = 0; // time returned by the solver
time_t startRun; // time at start of log
time_t endRun; // time at end of log
struct tm * currentTime = NULL; // time structure for localtime
#ifdef DEBUG
FILE * realImaginary; // file containing real and imaginary parts of the wavefunction
#endif
FILE * log; // log file with run times
realtype * tkprob = NULL; // total probability in k, l, c, b states at each timestep
realtype * tlprob = NULL;
realtype * tcprob = NULL;
realtype * tbprob = NULL;
double ** allprob = NULL; // populations in all states at all times
realtype * times = NULL;
realtype * qd_est = NULL;
realtype * qd_est_diag = NULL;
std::string inputFile = "ins/parameters.in"; // name of input file
std::string cEnergiesInput = "ins/c_energies.in";
std::string cPopsInput = "ins/c_pops.in";
std::string bEnergiesInput = "ins/b_energies.in";
std::string VNoBridgeInput = "ins/Vnobridge.in";
std::string VBridgeInput = "ins/Vbridge.in";
std::map<const std::string, bool> outs; // map of output file names to bool
// default output directory
p.outputDir = "outs/";
double summ = 0; // sum variable
// ---- process command line flags ---- //
opterr = 0;
int c;
std::string insDir;
/* process command line options */
while ((c = getopt(argc, argv, "i:o:")) != -1) {
switch (c) {
case 'i':
// check that it ends in a slash
std::cerr << "[dynamix]: assigning input directory" << std::endl;
insDir = optarg;
if (strcmp(&(insDir.at(insDir.length() - 1)), "/")) {
std::cerr << "ERROR: option -i requires argument ("
<< insDir << ") to have a trailing slash (/)." << std::endl;
return 1;
}
else {
// ---- assign input files ---- //
inputFile = insDir + "parameters.in";
cEnergiesInput = insDir + "c_energies.in";
cPopsInput = insDir + "c_pops.in";
bEnergiesInput = insDir + "b_energies.in";
VNoBridgeInput = insDir + "Vnobridge.in";
VBridgeInput = insDir + "Vbridge.in";
}
break;
case 'o':
std::cerr << "[dynamix]: assigning output directory" << std::endl;
p.outputDir = optarg;
break;
case '?':
if (optopt == 'i') {
fprintf(stderr, "Option -%c requires a directory argument.\n", optopt);
//.........这里部分代码省略.........
开发者ID:andyras，项目名称:GAlib-mpi，代码行数:101，代码来源:dynamix.cpp
示例17: main
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 ");
}
//.........这里部分代码省略.........
开发者ID:bareqsh，项目名称:SBML_odeSolver，代码行数:101，代码来源:cvfdx.c
示例18: main
int main(int argc, char *argv[])
{
realtype dx, reltol, abstol, t, tout, umax;
N_Vector u;
UserData data;
void *cvode_mem;
int iout, retval, my_pe, npes;
sunindextype local_N, nperpe, nrem, my_base;
long int nst;
MPI_Comm comm;
u = NULL;
data = NULL;
cvode_mem = 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);
/* 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;
data = (UserData) malloc(sizeof *data); /* Allocate data memory */
if(check_retval((void *)data, "malloc", 2, my_pe)) MPI_Abort(comm, 1);
data->comm = comm;
data->npes = npes;
data->my_pe = my_pe;
u = N_VNew_Parallel(comm, local_N, NEQ); /* Allocate u vector */
if(check_retval((void *)u, "N_VNew", 0, my_pe)) MPI_Abort(comm, 1);
reltol = ZERO; /* Set the tolerances */
abstol = ATOL;
dx = data->dx = XMAX/((realtype)(MX+1)); /* Set grid coefficients in data */
data->hdcoef = RCONST(1.0)/(dx*dx);
data->hacoef = RCONST(0.5)/(RCONST(2.0)*dx);
SetIC(u, dx, local_N, my_base); /* Initialize u vector */
/* Call CVodeCreate to create the solver memory and specify the
* Adams-Moulton LMM */
cvode_mem = CVodeCreate(CV_ADAMS);
if(check_retval((void *)cvode_mem, "CVodeCreate", 0, my_pe)) MPI_Abort(comm, 1);
retval = CVodeSetUserData(cvode_mem, data);
if(check_retval(&retval, "CVodeSetUserData", 1, my_pe)) MPI_Abort(comm, 1);
/* Call CVodeInit to initialize the integrator memory and specify the
* user's right hand side function in u'=f(t,u), the inital time T0, and
* the initial dependent variable vector u. */
retval = CVodeInit(cvode_mem, f, T0, u);
if(check_retval(&retval, "CVodeInit", 1, my_pe)) return(1);
/* Call CVodeSStolerances to specify the scalar relative tolerance
* and scalar absolute tolerances */
retval = CVodeSStolerances(cvode_mem, reltol, abstol);
if (check_retval(&retval, "CVodeSStolerances", 1, my_pe)) return(1);
/* Call CVDiag to create and attach CVODE-specific diagonal linear solver */
retval = CVDiag(cvode_mem);
if(check_retval(&retval, "CVDiag", 1, my_pe)) return(1);
if (my_pe == 0) PrintIntro(npes);
umax = N_VMaxNorm(u);
if (my_pe == 0) {
t = T0;
PrintData(t, umax, 0);
}
/* In loop over output points, call CVode, print results, test for error */
for (iout=1, tout=T1; iout <= NOUT; iout++, tout += DTOUT) {
retval = CVode(cvode_mem, tout, u, &t, CV_NORMAL);
if(check_retval(&retval, "CVode", 1, my_pe)) break;
umax = N_VMaxNorm(u);
retval = CVodeGetNumSteps(cvode_mem, &nst);
check_retval(&retval, "CVodeGetNumSteps", 1, my_pe);
if (my_pe == 0) PrintData(t, umax, nst);
}
if (my_pe == 0)
PrintFinalStats(cvode_mem); /* Print some final statistics */
N_VDestroy_Parallel(u); /* Free the u vector */
CVodeFree(&cvode_mem); /* Free the integrator memory */
free(data); /* Free user data */
MPI_Finalize();
return(0);
//.........这里部分代码省略.........
开发者ID:polymec，项目名称:polymec-dev，代码行数:101，代码来源:cvAdvDiff_diag_p.c
示例19: Problem2
static int Problem2(void)
{
realtype reltol=RTOL, abstol=ATOL, t, tout, er, erm, ero;
int miter, flag, temp_flag, nerr=0;
N_Vector y;
void *cvode_mem;
booleantype firstrun;
int qu, iout;
realtype hu;
y = NULL;
cvode_mem = NULL;
y = N_VNew_Serial(P2_NEQ);
if(check_flag((void *)y, "N_VNew", 0)) return(1);
PrintIntro2();
cvode_mem = CVodeCreate(CV_ADAMS, CV_FUNCTIONAL);
if(check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1);
for (miter=FUNC; miter <= BAND_DQ; miter++) {
if ((miter==DENSE_USER) || (miter==DENSE_DQ)) continue;
ero = ZERO;
N_VConst(ZERO, y);
NV_Ith_S(y,0) = ONE;
firstrun = (miter==FUNC);
if (firstrun) {
flag = CVodeMalloc(cvode_mem, f2, P2_T0, y, CV_SS, reltol, &abstol);
if(check_flag(&flag, "CVodeMalloc", 1)) return(1);
} else {
flag = CVodeSetIterType(cvode_mem, CV_NEWTON);
if(check_flag(&flag, "CVodeSetIterType", 1)) ++nerr;
flag = CVodeReInit(cvode_mem, f2, P2_T0, y, CV_SS, reltol, &abstol);
if(check_flag(&flag, "CVodeReInit", 1)) return(1);
}
flag = PrepareNextRun(cvode_mem, CV_ADAMS, miter, P2_MU, P2_ML);
if(check_flag(&flag, "PrepareNextRun", 1)) return(1);
PrintHeader2();
for(iout=1, tout=P2_T1; iout <= P2_NOUT; iout++, tout*=P2_TOUT_MULT) {
flag = CVode(cvode_mem, tout, y, &t, CV_NORMAL);
check_flag(&flag, "CVode", 1);
erm = MaxError(y, t);
temp_flag = CVodeGetLastOrder(cvode_mem, &qu);
if(check_flag(&temp_flag, "CVodeGetLastOrder", 1)) ++nerr;
temp_flag =
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