Exemplo n.º 1
0
void CVodesIntegrator::sensInit(double t0, FuncEval& func)
{
    m_np = func.nparams();
    size_t nv = func.neq();
    m_sens_ok = false;

    doublereal* data;
    N_Vector y;
    y = N_VNew_Serial(static_cast<sd_size_t>(nv));
    m_yS = N_VCloneVectorArray_Serial(static_cast<sd_size_t>(m_np), y);
    for (size_t n = 0; n < m_np; n++) {
        data = NV_DATA_S(m_yS[n]);
        for (size_t j = 0; j < nv; j++) {
            data[j] =0.0;
        }
    }

    int flag = CVodeSensInit(m_cvode_mem, static_cast<sd_size_t>(m_np),
                             CV_STAGGERED, CVSensRhsFn(0), m_yS);

    if (flag != CV_SUCCESS) {
        throw CVodesErr("Error in CVodeSensMalloc");
    }
    vector_fp atol(m_np, m_abstolsens);
    double rtol = m_reltolsens;
    flag = CVodeSensSStolerances(m_cvode_mem, rtol, atol.data());

}
void CVodesIntegrator::sensInit(double t0, FuncEval& func)
{
    m_np = func.nparams();
    m_sens_ok = false;

    N_Vector y = N_VNew_Serial(static_cast<sd_size_t>(func.neq()));
    m_yS = N_VCloneVectorArray_Serial(static_cast<sd_size_t>(m_np), y);
    for (size_t n = 0; n < m_np; n++) {
        N_VConst(0.0, m_yS[n]);
    }
    N_VDestroy_Serial(y);

    int flag = CVodeSensInit(m_cvode_mem, static_cast<sd_size_t>(m_np),
                             CV_STAGGERED, CVSensRhsFn(0), m_yS);

    if (flag != CV_SUCCESS) {
        throw CanteraError("CVodesIntegrator::sensInit", "Error in CVodeSensInit");
    }
    vector_fp atol(m_np);
    for (size_t n = 0; n < m_np; n++) {
        // This scaling factor is tuned so that reaction and species enthalpy
        // sensitivities can be computed simultaneously with the same abstol.
        atol[n] = m_abstolsens / func.m_paramScales[n];
    }
    flag = CVodeSensSStolerances(m_cvode_mem, m_reltolsens, atol.data());
}
Exemplo n.º 3
0
  void CVodesIntegrator::sensInit(double t0, FuncEval& func) {
    m_np = func.nparams();
    long int nv = func.neq();

    doublereal* data;
    int n, j;
    N_Vector y;
    y = N_VNew_Serial(nv);
    m_yS = N_VCloneVectorArray_Serial(m_np, y);
    for (n = 0; n < m_np; n++) {
      data = NV_DATA_S(m_yS[n]);
      for (j = 0; j < nv; j++) {
	data[j] =0.0;
      }
    }

    int flag;

#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23)
    flag = CVodeSensMalloc(m_cvode_mem, m_np, CV_STAGGERED, m_yS);
    if (flag != CV_SUCCESS) {
      throw CVodesErr("Error in CVodeSensMalloc");
    }
    vector_fp atol(m_np, m_abstolsens);
    double rtol = m_reltolsens;
    flag = CVodeSetSensTolerances(m_cvode_mem, CV_SS, rtol, DATA_PTR(atol));
#elif defined(SUNDIALS_VERSION_24)
    flag = CVodeSensInit(m_cvode_mem, m_np, CV_STAGGERED,
			 CVSensRhsFn (0), m_yS);

    if (flag != CV_SUCCESS) {
      throw CVodesErr("Error in CVodeSensMalloc");
    }
    vector_fp atol(m_np, m_abstolsens);
    double rtol = m_reltolsens;
    flag = CVodeSensSStolerances(m_cvode_mem, rtol, DATA_PTR(atol));

#endif
 
  }
Exemplo n.º 4
0
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);
}
Exemplo n.º 5
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_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]);

    flag = CVodeSensMalloc(cvode_mem, NS, sensi_meth, yS);
    if(check_flag(&flag, "CVodeSensMalloc", 1)) return(1);

    flag = CVodeSetSensRhs1Fn(cvode_mem, fS, data);
    if (check_flag(&flag, "CVodeSetSensRhs1Fn", 1)) return(1);
    flag = CVodeSetSensErrCon(cvode_mem, err_con);
    if (check_flag(&flag, "CVodeSetSensErrCon", 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);
}
Exemplo n.º 6
0
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);
}
Exemplo n.º 7
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);
}
Exemplo n.º 8
0
int main(void)
{
  UserData data;

  void *mem;
  N_Vector yy, yp, id, q, *yyS, *ypS, *qS;
  realtype tret;
  realtype pbar[2];
  realtype dp, G, Gm[2], Gp[2];
  int flag, is;
  realtype atolS[NP];

  id = N_VNew_Serial(NEQ);
  yy = N_VNew_Serial(NEQ);
  yp = N_VNew_Serial(NEQ);
  q = N_VNew_Serial(1);

  yyS= N_VCloneVectorArray(NP,yy);
  ypS= N_VCloneVectorArray(NP,yp);
  qS = N_VCloneVectorArray_Serial(NP, q);

  data = (UserData) malloc(sizeof *data);

  data->a = 0.5;   /* half-length of crank */
  data->J1 = 1.0;  /* crank moment of inertia */
  data->m2 = 1.0;  /* mass of connecting rod */
  data->m1 = 1.0;
  data->J2 = 2.0;  /* moment of inertia of connecting rod */
  data->params[0] = 1.0;   /* spring constant */
  data->params[1] = 1.0;   /* damper constant */
  data->l0 = 1.0;  /* spring free length */
  data->F = 1.0;   /* external constant force */

  N_VConst(ONE, id);
  NV_Ith_S(id, 9) = ZERO;
  NV_Ith_S(id, 8) = ZERO;
  NV_Ith_S(id, 7) = ZERO;
  NV_Ith_S(id, 6) = ZERO;
  
  printf("\nSlider-Crank example for IDAS:\n");

  /* Consistent IC*/
  setIC(yy, yp, data);

  for (is=0;is<NP;is++) {
    N_VConst(ZERO, yyS[is]);
    N_VConst(ZERO, ypS[is]);
  }

  /* IDA initialization */
  mem = IDACreate();
  flag = IDAInit(mem, ressc, TBEGIN, yy, yp);
  flag = IDASStolerances(mem, RTOLF, ATOLF);
  flag = IDASetUserData(mem, data);
  flag = IDASetId(mem, id);
  flag = IDASetSuppressAlg(mem, TRUE);
  flag = IDASetMaxNumSteps(mem, 20000);

  /* Call IDADense and set up the linear solver. */
  flag = IDADense(mem, NEQ);

  flag = IDASensInit(mem, NP, IDA_SIMULTANEOUS, NULL, yyS, ypS);
  pbar[0] = data->params[0];pbar[1] = data->params[1];
  flag = IDASetSensParams(mem, data->params, pbar, NULL);
  flag = IDASensEEtolerances(mem);
  IDASetSensErrCon(mem, TRUE);
  
  N_VConst(ZERO, q);
  flag = IDAQuadInit(mem, rhsQ, q);
  flag = IDAQuadSStolerances(mem, RTOLQ, ATOLQ);
  flag = IDASetQuadErrCon(mem, TRUE);
  
  N_VConst(ZERO, qS[0]);
  flag = IDAQuadSensInit(mem, rhsQS, qS);
  atolS[0] = atolS[1] = ATOLQ;
  flag = IDAQuadSensSStolerances(mem, RTOLQ, atolS);
  flag = IDASetQuadSensErrCon(mem, TRUE);  
  

  /* Perform forward run */
  printf("\nForward integration ... ");

  flag = IDASolve(mem, TEND, &tret, yy, yp, IDA_NORMAL);
  if (check_flag(&flag, "IDASolve", 1)) return(1);

  printf("done!\n");

  PrintFinalStats(mem);

  IDAGetQuad(mem, &tret, q);
  printf("--------------------------------------------\n");
  printf("  G = %24.16f\n", Ith(q,1));
  printf("--------------------------------------------\n\n");
  
  IDAGetQuadSens(mem, &tret, qS);
  printf("-------------F O R W A R D------------------\n");
  printf("   dG/dp:  %12.4le %12.4le\n", Ith(qS[0],1), Ith(qS[1],1));
  printf("--------------------------------------------\n\n");

  IDAFree(&mem);



  /* Finite differences for dG/dp */
  dp = 0.00001;
  data->params[0] = ONE;
  data->params[1] = ONE;

  mem = IDACreate();

  setIC(yy, yp, data);
  flag = IDAInit(mem, ressc, TBEGIN, yy, yp);
  flag = IDASStolerances(mem, RTOLFD, ATOLFD);
  flag = IDASetUserData(mem, data);
  flag = IDASetId(mem, id);
  flag = IDASetSuppressAlg(mem, TRUE);
  /* Call IDADense and set up the linear solver. */
  flag = IDADense(mem, NEQ);

  N_VConst(ZERO, q);
  IDAQuadInit(mem, rhsQ, q);
  IDAQuadSStolerances(mem, RTOLQ, ATOLQ);
  IDASetQuadErrCon(mem, TRUE);

  IDASolve(mem, TEND, &tret, yy, yp, IDA_NORMAL);

  IDAGetQuad(mem,&tret,q);
  G = Ith(q,1);
  /*printf("  G  =%12.6e\n", Ith(q,1));*/

  /******************************
  * BACKWARD for k
  ******************************/
  data->params[0] -= dp;
  setIC(yy, yp, data);

  IDAReInit(mem, TBEGIN, yy, yp);

  N_VConst(ZERO, q);
  IDAQuadReInit(mem, q);

  IDASolve(mem, TEND, &tret, yy, yp, IDA_NORMAL);
  IDAGetQuad(mem, &tret, q);
  Gm[0] = Ith(q,1);
  /*printf("Gm[0]=%12.6e\n", Ith(q,1));*/

  /****************************
  * FORWARD for k *
  ****************************/
  data->params[0] += (TWO*dp);
  setIC(yy, yp, data);
  IDAReInit(mem, TBEGIN, yy, yp);

  N_VConst(ZERO, q);
  IDAQuadReInit(mem, q);

  IDASolve(mem, TEND, &tret, yy, yp, IDA_NORMAL);
  IDAGetQuad(mem, &tret, q);
  Gp[0] = Ith(q,1);
  /*printf("Gp[0]=%12.6e\n", Ith(q,1));*/


  /* Backward for c */
  data->params[0] = ONE;
  data->params[1] -= dp;
  setIC(yy, yp, data);
  IDAReInit(mem, TBEGIN, yy, yp);

  N_VConst(ZERO, q);
  IDAQuadReInit(mem, q);

  IDASolve(mem, TEND, &tret, yy, yp, IDA_NORMAL);
  IDAGetQuad(mem, &tret, q);
  Gm[1] = Ith(q,1);

  /* Forward for c */
  data->params[1] += (TWO*dp);
  setIC(yy, yp, data);
  IDAReInit(mem, TBEGIN, yy, yp);

  N_VConst(ZERO, q);
  IDAQuadReInit(mem, q);

  IDASolve(mem, TEND, &tret, yy, yp, IDA_NORMAL);
  IDAGetQuad(mem, &tret, q);
  Gp[1] = Ith(q,1);

  IDAFree(&mem);

  printf("\n\n   Checking using Finite Differences \n\n");

  printf("---------------BACKWARD------------------\n");
  printf("   dG/dp:  %12.4le %12.4le\n", (G-Gm[0])/dp, (G-Gm[1])/dp);
  printf("-----------------------------------------\n\n");

  printf("---------------FORWARD-------------------\n");
  printf("   dG/dp:  %12.4le %12.4le\n", (Gp[0]-G)/dp, (Gp[1]-G)/dp);
  printf("-----------------------------------------\n\n");

  printf("--------------CENTERED-------------------\n");
  printf("   dG/dp:  %12.4le %12.4le\n", (Gp[0]-Gm[0])/(TWO*dp) ,(Gp[1]-Gm[1])/(TWO*dp));
  printf("-----------------------------------------\n\n");


  /* Free memory */
  free(data);

  N_VDestroy(id);
  N_VDestroy_Serial(yy);
  N_VDestroy_Serial(yp);
  N_VDestroy_Serial(q);
  return(0);
  
}
Exemplo n.º 9
0
Arquivo: cvodes.c Projeto: UCL/GMCMC
/**
 * 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;
}