/* yS0 in row major order */ void ode_solver_init_sens(ode_solver* solver, double* yS0, int lenP, int lenY){ /* change: lenP may now be shorter than P if you dpn't want to * calculate all sensitivities. This is important for the correct * treatment of input parameters, i.e. experimental conditions u * (since we don't require sensitivities with repsect to them). */ int i,flag; int N = solver->odeModel->N; int P = solver->odeModel->P; if (solver->odeModel->vf_sens == 0) { fprintf(stderr,"ode_solver_init_sens: no sensitivities defined for this model.\n"); return; } solver->yS = N_VCloneVectorArrayEmpty_Serial(lenP, solver->y); /* alloc */ double tmp[N]; if(yS0 !=0 ){ if ( (lenY != N) ) { fprintf(stderr,"ode_solver_init_sens: lenY must be equal to %d the number of parameters and variables in the ode model.\n",solver->odeModel->N); return ; } for(i = 0; i < lenP; i++) NV_DATA_S(solver->yS[i]) = &yS0[i*lenY]; } else{ for (i=0; i < N ; i++) tmp[i] = 0.0; for (i = 0; i < lenP; i++) NV_DATA_S(solver->yS[i]) = tmp; } flag = CVodeSensInit1(solver->cvode_mem, lenP, CV_STAGGERED1, solver->odeModel->vf_sens, solver->yS); flag = CVodeSetSensErrCon(solver->cvode_mem, TRUE); flag = CVodeSensEEtolerances(solver->cvode_mem); /* set parameters scale for error corection */ double scale_p[lenP]; for (i=0; i<lenP; i++) { /* order of magnitude can be found from the actual parameter value */ /* if zero then set to the default relative error */ if (solver->params[i] != 0.0){ scale_p[i] = solver->params[i]; } else { scale_p[i] = ODE_SOLVER_REL_ERR; } } flag = CVodeSetSensParams(solver->cvode_mem, solver->params, scale_p, NULL); }
int main(int argc, char *argv[]) { void *cvode_mem; UserData data; realtype t, tout; N_Vector y; int iout, flag, nthreads, nnz; realtype pbar[NS]; int is; N_Vector *yS; booleantype sensi, err_con; int sensi_meth; cvode_mem = NULL; data = NULL; y = NULL; yS = NULL; /* Process arguments */ ProcessArgs(argc, argv, &sensi, &sensi_meth, &err_con); /* User data structure */ data = (UserData) malloc(sizeof *data); if (check_flag((void *)data, "malloc", 2)) return(1); data->p[0] = RCONST(0.04); data->p[1] = RCONST(1.0e4); data->p[2] = RCONST(3.0e7); /* Initial conditions */ y = N_VNew_Serial(NEQ); if (check_flag((void *)y, "N_VNew_Serial", 0)) return(1); Ith(y,1) = Y1; Ith(y,2) = Y2; Ith(y,3) = Y3; /* Call CVodeCreate to create the solver memory and specify the Backward Differentiation Formula and the use of a Newton iteration */ cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON); if (check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1); /* Call CVodeInit to initialize the integrator memory and specify the user's right hand side function in y'=f(t,y), the initial time T0, and the initial dependent variable vector y. */ flag = CVodeInit(cvode_mem, f, T0, y); if (check_flag(&flag, "CVodeInit", 1)) return(1); /* Call CVodeWFtolerances to specify a user-supplied function ewt that sets the multiplicative error weights W_i for use in the weighted RMS norm */ flag = CVodeWFtolerances(cvode_mem, ewt); if (check_flag(&flag, "CVodeSetEwtFn", 1)) return(1); /* Attach user data */ flag = CVodeSetUserData(cvode_mem, data); if (check_flag(&flag, "CVodeSetUserData", 1)) return(1); /* Call CVKLU to specify the CVKLU sparse direct linear solver */ nthreads = 1; /* no. of threads to use when factoring the system*/ nnz = NEQ * NEQ; /* max no. of nonzeros entries in the Jac */ flag = CVSuperLUMT(cvode_mem, nthreads, NEQ, nnz); if (check_flag(&flag, "CVSuperLUMT", 1)) return(1); /* Set the Jacobian routine to Jac (user-supplied) */ flag = CVSlsSetSparseJacFn(cvode_mem, Jac); if (check_flag(&flag, "CVSlsSetSparseJacFn", 1)) return(1); printf("\n3-species chemical kinetics problem\n"); /* Sensitivity-related settings */ if (sensi) { /* Set parameter scaling factor */ pbar[0] = data->p[0]; pbar[1] = data->p[1]; pbar[2] = data->p[2]; /* Set sensitivity initial conditions */ yS = N_VCloneVectorArray_Serial(NS, y); if (check_flag((void *)yS, "N_VCloneVectorArray_Serial", 0)) return(1); for (is=0;is<NS;is++) N_VConst(ZERO, yS[is]); /* Call CVodeSensInit1 to activate forward sensitivity computations and allocate internal memory for COVEDS related to sensitivity calculations. Computes the right-hand sides of the sensitivity ODE, one at a time */ flag = CVodeSensInit1(cvode_mem, NS, sensi_meth, fS, yS); if(check_flag(&flag, "CVodeSensInit", 1)) return(1); /* Call CVodeSensEEtolerances to estimate tolerances for sensitivity variables based on the rolerances supplied for states variables and the scaling factor pbar */ flag = CVodeSensEEtolerances(cvode_mem); if(check_flag(&flag, "CVodeSensEEtolerances", 1)) return(1); /* Set sensitivity analysis optional inputs */ /* Call CVodeSetSensErrCon to specify the error control strategy for sensitivity variables */ flag = CVodeSetSensErrCon(cvode_mem, err_con); if (check_flag(&flag, "CVodeSetSensErrCon", 1)) return(1); /* Call CVodeSetSensParams to specify problem parameter information for sensitivity calculations */ flag = CVodeSetSensParams(cvode_mem, NULL, pbar, NULL); if (check_flag(&flag, "CVodeSetSensParams", 1)) return(1); printf("Sensitivity: YES "); if(sensi_meth == CV_SIMULTANEOUS) printf("( SIMULTANEOUS +"); else if(sensi_meth == CV_STAGGERED) printf("( STAGGERED +"); else printf("( STAGGERED1 +"); if(err_con) printf(" FULL ERROR CONTROL )"); else printf(" PARTIAL ERROR CONTROL )"); } else { printf("Sensitivity: NO "); } /* In loop over output points, call CVode, print results, test for error */ printf("\n\n"); printf("==========================================="); printf("============================\n"); printf(" T Q H NST y1"); printf(" y2 y3 \n"); printf("==========================================="); printf("============================\n"); for (iout=1, tout=T1; iout <= NOUT; iout++, tout *= TMULT) { flag = CVode(cvode_mem, tout, y, &t, CV_NORMAL); if (check_flag(&flag, "CVode", 1)) break; PrintOutput(cvode_mem, t, y); /* Call CVodeGetSens to get the sensitivity solution vector after a successful return from CVode */ if (sensi) { flag = CVodeGetSens(cvode_mem, &t, yS); if (check_flag(&flag, "CVodeGetSens", 1)) break; PrintOutputS(yS); } printf("-----------------------------------------"); printf("------------------------------\n"); } /* Print final statistics */ PrintFinalStats(cvode_mem, sensi); /* Free memory */ N_VDestroy_Serial(y); /* Free y vector */ if (sensi) { N_VDestroyVectorArray_Serial(yS, NS); /* Free yS vector */ } free(data); /* Free user data */ CVodeFree(&cvode_mem); /* Free CVODES memory */ return(0); }
int main(int argc, char *argv[]) { SUNMatrix A; SUNLinearSolver LS; void *cvode_mem; UserData data; realtype t, tout; N_Vector y, constraints; int iout, retval; realtype pbar[NS]; int is; N_Vector *yS; booleantype sensi, err_con; int sensi_meth; cvode_mem = NULL; data = NULL; y = NULL; yS = NULL; A = NULL; LS = NULL; constraints = NULL; /* Process arguments */ ProcessArgs(argc, argv, &sensi, &sensi_meth, &err_con); /* User data structure */ data = (UserData) malloc(sizeof *data); if (check_retval((void *)data, "malloc", 2)) return(1); data->p[0] = RCONST(0.04); data->p[1] = RCONST(1.0e4); data->p[2] = RCONST(3.0e7); /* Initial conditions */ y = N_VNew_Serial(NEQ); if (check_retval((void *)y, "N_VNew_Serial", 0)) return(1); Ith(y,1) = Y1; Ith(y,2) = Y2; Ith(y,3) = Y3; /* Set constraints to all 1's for nonnegative solution values. */ constraints = N_VNew_Serial(NEQ); if(check_retval((void *)constraints, "N_VNew_Serial", 0)) return(1); N_VConst(ONE, constraints); /* Create CVODES object */ cvode_mem = CVodeCreate(CV_BDF); if (check_retval((void *)cvode_mem, "CVodeCreate", 0)) return(1); /* Allocate space for CVODES */ retval = CVodeInit(cvode_mem, f, T0, y); if (check_retval(&retval, "CVodeInit", 1)) return(1); /* Use private function to compute error weights */ retval = CVodeWFtolerances(cvode_mem, ewt); if (check_retval(&retval, "CVodeSetEwtFn", 1)) return(1); /* Attach user data */ retval = CVodeSetUserData(cvode_mem, data); if (check_retval(&retval, "CVodeSetUserData", 1)) return(1); /* Call CVodeSetConstraints to initialize constraints */ retval = CVodeSetConstraints(cvode_mem, constraints); if(check_retval(&retval, "CVodeSetConstraints", 1)) return(1); N_VDestroy(constraints); /* Create dense SUNMatrix */ A = SUNDenseMatrix(NEQ, NEQ); if (check_retval((void *)A, "SUNDenseMatrix", 0)) return(1); /* Create dense SUNLinearSolver */ LS = SUNLinSol_Dense(y, A); if (check_retval((void *)LS, "SUNLinSol_Dense", 0)) return(1); /* Attach the matrix and linear solver */ retval = CVDlsSetLinearSolver(cvode_mem, LS, A); if (check_retval(&retval, "CVDlsSetLinearSolver", 1)) return(1); /* Set the user-supplied Jacobian routine Jac */ retval = CVDlsSetJacFn(cvode_mem, Jac); if (check_retval(&retval, "CVDlsSetJacFn", 1)) return(1); printf("\n3-species chemical kinetics problem\n"); /* Sensitivity-related settings */ if (sensi) { /* Set parameter scaling factor */ pbar[0] = data->p[0]; pbar[1] = data->p[1]; pbar[2] = data->p[2]; /* Set sensitivity initial conditions */ yS = N_VCloneVectorArray(NS, y); if (check_retval((void *)yS, "N_VCloneVectorArray", 0)) return(1); for (is=0;is<NS;is++) N_VConst(ZERO, yS[is]); /* Call CVodeSensInit1 to activate forward sensitivity computations and allocate internal memory for COVEDS related to sensitivity calculations. Computes the right-hand sides of the sensitivity ODE, one at a time */ retval = CVodeSensInit1(cvode_mem, NS, sensi_meth, fS, yS); if(check_retval(&retval, "CVodeSensInit", 1)) return(1); /* Call CVodeSensEEtolerances to estimate tolerances for sensitivity variables based on the rolerances supplied for states variables and the scaling factor pbar */ retval = CVodeSensEEtolerances(cvode_mem); if(check_retval(&retval, "CVodeSensEEtolerances", 1)) return(1); /* Set sensitivity analysis optional inputs */ /* Call CVodeSetSensErrCon to specify the error control strategy for sensitivity variables */ retval = CVodeSetSensErrCon(cvode_mem, err_con); if (check_retval(&retval, "CVodeSetSensErrCon", 1)) return(1); /* Call CVodeSetSensParams to specify problem parameter information for sensitivity calculations */ retval = CVodeSetSensParams(cvode_mem, NULL, pbar, NULL); if (check_retval(&retval, "CVodeSetSensParams", 1)) return(1); printf("Sensitivity: YES "); if(sensi_meth == CV_SIMULTANEOUS) printf("( SIMULTANEOUS +"); else if(sensi_meth == CV_STAGGERED) printf("( STAGGERED +"); else printf("( STAGGERED1 +"); if(err_con) printf(" FULL ERROR CONTROL )"); else printf(" PARTIAL ERROR CONTROL )"); } else { printf("Sensitivity: NO "); } /* In loop over output points, call CVode, print results, test for error */ printf("\n\n"); printf("==========================================="); printf("============================\n"); printf(" T Q H NST y1"); printf(" y2 y3 \n"); printf("==========================================="); printf("============================\n"); for (iout=1, tout=T1; iout <= NOUT; iout++, tout *= TMULT) { retval = CVode(cvode_mem, tout, y, &t, CV_NORMAL); if (check_retval(&retval, "CVode", 1)) break; PrintOutput(cvode_mem, t, y); /* Call CVodeGetSens to get the sensitivity solution vector after a successful return from CVode */ if (sensi) { retval = CVodeGetSens(cvode_mem, &t, yS); if (check_retval(&retval, "CVodeGetSens", 1)) break; PrintOutputS(yS); } printf("-----------------------------------------"); printf("------------------------------\n"); } /* Print final statistics */ PrintFinalStats(cvode_mem, sensi); /* Free memory */ N_VDestroy(y); /* Free y vector */ if (sensi) { N_VDestroyVectorArray(yS, NS); /* Free yS vector */ } free(data); /* Free user data */ CVodeFree(&cvode_mem); /* Free CVODES memory */ SUNLinSolFree(LS); /* Free the linear solver memory */ SUNMatDestroy(A); /* Free the matrix memory */ return(0); }
int main(int argc, char *argv[]) { void *cvode_mem; UserData data; realtype dx, reltol, abstol, t, tout; N_Vector u; int iout, flag; realtype *pbar; int is, *plist; N_Vector *uS; booleantype sensi, err_con; int sensi_meth; cvode_mem = NULL; data = NULL; u = NULL; pbar = NULL; plist = NULL; uS = NULL; /* Process arguments */ ProcessArgs(argc, argv, &sensi, &sensi_meth, &err_con); /* Set user data */ data = (UserData) malloc(sizeof *data); /* Allocate data memory */ if(check_flag((void *)data, "malloc", 2)) return(1); data->p = (realtype *) malloc(NP * sizeof(realtype)); dx = data->dx = XMAX/((realtype)(MX+1)); data->p[0] = RCONST(1.0); data->p[1] = RCONST(0.5); /* Allocate and set initial states */ u = N_VNew_Serial(NEQ); if(check_flag((void *)u, "N_VNew_Serial", 0)) return(1); SetIC(u, dx); /* Set integration tolerances */ reltol = ZERO; abstol = ATOL; /* Create CVODES object */ cvode_mem = CVodeCreate(CV_ADAMS, CV_FUNCTIONAL); if(check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1); flag = CVodeSetUserData(cvode_mem, data); if(check_flag(&flag, "CVodeSetUserData", 1)) return(1); /* Allocate CVODES memory */ flag = CVodeInit(cvode_mem, f, T0, u); if(check_flag(&flag, "CVodeInit", 1)) return(1); flag = CVodeSStolerances(cvode_mem, reltol, abstol); if(check_flag(&flag, "CVodeSStolerances", 1)) return(1); printf("\n1-D advection-diffusion equation, mesh size =%3d\n", MX); /* Sensitivity-related settings */ if(sensi) { plist = (int *) malloc(NS * sizeof(int)); if(check_flag((void *)plist, "malloc", 2)) return(1); for(is=0; is<NS; is++) plist[is] = is; pbar = (realtype *) malloc(NS * sizeof(realtype)); if(check_flag((void *)pbar, "malloc", 2)) return(1); for(is=0; is<NS; is++) pbar[is] = data->p[plist[is]]; uS = N_VCloneVectorArray_Serial(NS, u); if(check_flag((void *)uS, "N_VCloneVectorArray_Serial", 0)) return(1); for(is=0;is<NS;is++) N_VConst(ZERO, uS[is]); flag = CVodeSensInit1(cvode_mem, NS, sensi_meth, NULL, uS); if(check_flag(&flag, "CVodeSensInit1", 1)) return(1); flag = CVodeSensEEtolerances(cvode_mem); if(check_flag(&flag, "CVodeSensEEtolerances", 1)) return(1); flag = CVodeSetSensErrCon(cvode_mem, err_con); if(check_flag(&flag, "CVodeSetSensErrCon", 1)) return(1); flag = CVodeSetSensDQMethod(cvode_mem, CV_CENTERED, ZERO); if(check_flag(&flag, "CVodeSetSensDQMethod", 1)) return(1); flag = CVodeSetSensParams(cvode_mem, data->p, pbar, plist); if(check_flag(&flag, "CVodeSetSensParams", 1)) return(1); printf("Sensitivity: YES "); if(sensi_meth == CV_SIMULTANEOUS) printf("( SIMULTANEOUS +"); else if(sensi_meth == CV_STAGGERED) printf("( STAGGERED +"); else printf("( STAGGERED1 +"); if(err_con) printf(" FULL ERROR CONTROL )"); else printf(" PARTIAL ERROR CONTROL )"); } else { printf("Sensitivity: NO "); } /* In loop over output points, call CVode, print results, test for error */ printf("\n\n"); printf("============================================================\n"); printf(" T Q H NST Max norm \n"); printf("============================================================\n"); for (iout=1, tout=T1; iout <= NOUT; iout++, tout += DTOUT) { flag = CVode(cvode_mem, tout, u, &t, CV_NORMAL); if(check_flag(&flag, "CVode", 1)) break; PrintOutput(cvode_mem, t, u); if (sensi) { flag = CVodeGetSens(cvode_mem, &t, uS); if(check_flag(&flag, "CVodeGetSens", 1)) break; PrintOutputS(uS); } printf("------------------------------------------------------------\n"); } /* Print final statistics */ PrintFinalStats(cvode_mem, sensi); /* Free memory */ N_VDestroy_Serial(u); if (sensi) { N_VDestroyVectorArray_Serial(uS, NS); free(plist); free(pbar); } free(data); CVodeFree(&cvode_mem); return(0); }
/** * Solves an initial value problem using CVODES to integrate over a system of * ODEs with optional forward sensitivity analysis. The initial conditions for * the system and for the sensitivity analysis are expected to be in the first * rows of simdata and sensitivities, respectively. * * @param [in] rhs the right-hand side of the system of ODEs * @param [in] num_timepoints the number of timepoints * @param [in] num_species the number of independent variables * @param [in] num_sens the number of parameters to compute sensitivities * for (set to zero to disable sensitivity * calculations) * @param [in] timepoints the timepoints at which data is to be returned * @param [in] params parameters * @param [in] sensi the indices of the parameters to compute the * sensitivities for (may be NULL to compute the * sensitivities for all parameters) * @param [in] options additional options for the integrator * @param [out] simdata contains the state values for each species at * each timepoint in column-major order. * @param [out] sensitivities sensitivities of each parameter in sensi * with respect to each independent variable. * The sensitivity of parameter j with respect to * variable k at timepoint i is stored at * (j * num_species + k) * lds + i. * May be NULL if sensitivities are not to be * calculated. * @param [in] lds leading dimension of simdata and sensitivities * * @return 0 on success, * GMCMC_ENOMEM if there was not enough memory to create the solver, * GMCMC_EINVAL if there was an invalid argument to the function, * GMCMC_ELINAL if the solution could not be found. */ int cvodes_solve(gmcmc_ode_rhs rhs, size_t num_timepoints, size_t num_species, size_t num_params, size_t num_sens, const double * timepoints, const double * params, const size_t * sensi, const cvodes_options * options, double * simdata, double * sensitivities, size_t lds) { int error; // Set vector of initial values N_Vector y = N_VNew_Serial((long int)num_species); for (size_t j = 0; j < num_species; j++) NV_Ith_S(y, j) = simdata[j * lds]; // Create CVODES object void * cvode_mem; if ((cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON)) == NULL) GMCMC_ERROR("Failed to allocate ODE solver", GMCMC_ENOMEM); // Initialise CVODES solver if ((error = CVodeInit(cvode_mem, cvodes_rhs, timepoints[0], y)) != CV_SUCCESS) { CVodeFree(&cvode_mem); GMCMC_ERROR("Failed to initialise ODE solver", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM); } // Set integration tolerances if ((error = CVodeSStolerances(cvode_mem, options->reltol, options->abstol)) != CV_SUCCESS) { CVodeFree(&cvode_mem); GMCMC_ERROR("Failed to set ODE solver integration tolerances", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM); } // Create a copy of the parameters in case CVODES modifies them realtype * sens_params; if ((sens_params = malloc(num_params * sizeof(realtype))) == NULL) { CVodeFree(&cvode_mem); GMCMC_ERROR("Failed to allocate copy of parameter vector for sensitivity analysis", GMCMC_ENOMEM); } for (size_t i = 0; i < num_params; i++) sens_params[i] = (realtype)params[i]; // Set optional inputs cvodes_userdata userdata = { rhs, sens_params }; if ((error = CVodeSetUserData(cvode_mem, &userdata)) != CV_SUCCESS) { CVodeFree(&cvode_mem); free(sens_params); GMCMC_ERROR("Failed to set ODE solver user data", GMCMC_EINVAL); } // Attach linear solver module if ((error = CVLapackDense(cvode_mem, (int)num_species)) != CV_SUCCESS) { CVodeFree(&cvode_mem); free(sens_params); GMCMC_ERROR("Failed to attach ODE solver module", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM); } N_Vector * yS = NULL; int * plist = NULL; if (num_sens > 0) { // Set sensitivity initial conditions yS = N_VCloneVectorArray_Serial((int)num_sens, y); for (size_t j = 0; j < num_sens; j++) { for (size_t i = 0; i < num_species; i++) NV_Ith_S(yS[j], i) = sensitivities[(j * num_species + i) * lds]; } // Activate sensitivity calculations // Use default finite differences if ((error = CVodeSensInit(cvode_mem, (int)num_sens, CV_SIMULTANEOUS, NULL, yS)) != CV_SUCCESS) { CVodeFree(&cvode_mem); free(sens_params); GMCMC_ERROR("Failed to activate ODE solver sensitivity calculations", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM); } // Set sensitivity tolerances if ((error = CVodeSensEEtolerances(cvode_mem)) != CV_SUCCESS) { CVodeFree(&cvode_mem); free(sens_params); GMCMC_ERROR("Failed to set ODE solver sensitivity tolerances", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM); } if (sensi != NULL) { if ((plist = malloc(num_sens * sizeof(int))) == NULL) { CVodeFree(&cvode_mem); free(sens_params); GMCMC_ERROR("Failed to allocate sensitivity parameter list", GMCMC_ENOMEM); } for (size_t i = 0; i < num_sens; i++) plist[i] = (int)sensi[i]; } // Set sensitivity analysis optional inputs if ((error = CVodeSetSensParams(cvode_mem, sens_params, NULL, plist)) != CV_SUCCESS) { CVodeFree(&cvode_mem); free(plist); free(sens_params); GMCMC_ERROR("Failed to set ODE solver sensitivity parameters", (error == CV_ILL_INPUT) ? GMCMC_EINVAL : GMCMC_ENOMEM); } } // Advance solution in time realtype tret; for (size_t i = 1; i < num_timepoints; i++) { if ((error = CVode(cvode_mem, timepoints[i], y, &tret, CV_NORMAL)) != CV_SUCCESS) { free(plist); free(sens_params); CVodeFree(&cvode_mem); GMCMC_ERROR("Failed to advance ODE solution", GMCMC_ELINAL); } for (size_t j = 0; j < num_species; j++) simdata[j * lds + i] = NV_Ith_S(y, j); // Extract the sensitivity solution if (yS != NULL) { if ((error = CVodeGetSens(cvode_mem, &tret, yS)) != CV_SUCCESS) { free(plist); free(sens_params); CVodeFree(&cvode_mem); GMCMC_ERROR("Failed to extract ODE sensitivity solution", GMCMC_ELINAL); } for (size_t j = 0; j < num_sens; j++) { for (size_t k = 0; k < num_species; k++) sensitivities[(j * num_species + k) * lds + i] = NV_Ith_S(yS[j], k); } } } N_VDestroy(y); if (yS != NULL) N_VDestroyVectorArray_Serial(yS, (int)num_sens); free(plist); free(sens_params); // Free solver memory CVodeFree(&cvode_mem); return 0; }
int main(int argc, char *argv[]) { realtype dx, reltol, abstol, t, tout; N_Vector u; UserData data; void *cvode_mem; int iout, flag, my_pe, npes; long int local_N, nperpe, nrem, my_base; realtype *pbar; int is, *plist; N_Vector *uS; booleantype sensi, err_con; int sensi_meth; MPI_Comm comm; u = NULL; data = NULL; cvode_mem = NULL; pbar = NULL; plist = NULL; uS = NULL; /* Get processor number, total number of pe's, and my_pe. */ MPI_Init(&argc, &argv); comm = MPI_COMM_WORLD; MPI_Comm_size(comm, &npes); MPI_Comm_rank(comm, &my_pe); /* Process arguments */ ProcessArgs(argc, argv, my_pe, &sensi, &sensi_meth, &err_con); /* Set local vector length. */ nperpe = NEQ/npes; nrem = NEQ - npes*nperpe; local_N = (my_pe < nrem) ? nperpe+1 : nperpe; my_base = (my_pe < nrem) ? my_pe*local_N : my_pe*nperpe + nrem; /* USER DATA STRUCTURE */ data = (UserData) malloc(sizeof *data); /* Allocate data memory */ data->p = NULL; if(check_flag((void *)data, "malloc", 2, my_pe)) MPI_Abort(comm, 1); data->comm = comm; data->npes = npes; data->my_pe = my_pe; data->p = (realtype *) malloc(NP * sizeof(realtype)); if(check_flag((void *)data->p, "malloc", 2, my_pe)) MPI_Abort(comm, 1); dx = data->dx = XMAX/((realtype)(MX+1)); data->p[0] = RCONST(1.0); data->p[1] = RCONST(0.5); /* INITIAL STATES */ u = N_VNew_Parallel(comm, local_N, NEQ); /* Allocate u vector */ if(check_flag((void *)u, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1); SetIC(u, dx, local_N, my_base); /* Initialize u vector */ /* TOLERANCES */ reltol = ZERO; /* Set the tolerances */ abstol = ATOL; /* CVODE_CREATE & CVODE_MALLOC */ cvode_mem = CVodeCreate(CV_ADAMS, CV_FUNCTIONAL); if(check_flag((void *)cvode_mem, "CVodeCreate", 0, my_pe)) MPI_Abort(comm, 1); flag = CVodeSetUserData(cvode_mem, data); if(check_flag(&flag, "CVodeSetUserData", 1, my_pe)) MPI_Abort(comm, 1); flag = CVodeInit(cvode_mem, f, T0, u); if(check_flag(&flag, "CVodeInit", 1, my_pe)) MPI_Abort(comm, 1); flag = CVodeSStolerances(cvode_mem, reltol, abstol); if(check_flag(&flag, "CVodeSStolerances", 1, my_pe)) MPI_Abort(comm, 1); if (my_pe == 0) { printf("\n1-D advection-diffusion equation, mesh size =%3d \n", MX); printf("\nNumber of PEs = %3d \n",npes); } if(sensi) { plist = (int *) malloc(NS * sizeof(int)); if(check_flag((void *)plist, "malloc", 2, my_pe)) MPI_Abort(comm, 1); for(is=0; is<NS; is++) plist[is] = is; /* sensitivity w.r.t. i-th parameter */ pbar = (realtype *) malloc(NS * sizeof(realtype)); if(check_flag((void *)pbar, "malloc", 2, my_pe)) MPI_Abort(comm, 1); for(is=0; is<NS; is++) pbar[is] = data->p[plist[is]]; uS = N_VCloneVectorArray_Parallel(NS, u); if(check_flag((void *)uS, "N_VCloneVectorArray_Parallel", 0, my_pe)) MPI_Abort(comm, 1); for(is=0;is<NS;is++) N_VConst(ZERO,uS[is]); flag = CVodeSensInit1(cvode_mem, NS, sensi_meth, NULL, uS); if(check_flag(&flag, "CVodeSensInit1", 1, my_pe)) MPI_Abort(comm, 1); flag = CVodeSensEEtolerances(cvode_mem); if(check_flag(&flag, "CVodeSensEEtolerances", 1, my_pe)) MPI_Abort(comm, 1); flag = CVodeSetSensErrCon(cvode_mem, err_con); if(check_flag(&flag, "CVodeSetSensErrCon", 1, my_pe)) MPI_Abort(comm, 1); flag = CVodeSetSensDQMethod(cvode_mem, CV_CENTERED, ZERO); if(check_flag(&flag, "CVodeSetSensDQMethod", 1, my_pe)) MPI_Abort(comm, 1); flag = CVodeSetSensParams(cvode_mem, data->p, pbar, plist); if(check_flag(&flag, "CVodeSetSensParams", 1, my_pe)) MPI_Abort(comm, 1); if(my_pe == 0) { printf("Sensitivity: YES "); if(sensi_meth == CV_SIMULTANEOUS) printf("( SIMULTANEOUS +"); else if(sensi_meth == CV_STAGGERED) printf("( STAGGERED +"); else printf("( STAGGERED1 +"); if(err_con) printf(" FULL ERROR CONTROL )"); else printf(" PARTIAL ERROR CONTROL )"); } } else { if(my_pe == 0) printf("Sensitivity: NO "); } /* In loop over output points, call CVode, print results, test for error */ if(my_pe == 0) { printf("\n\n"); printf("============================================================\n"); printf(" T Q H NST Max norm \n"); printf("============================================================\n"); } for (iout=1, tout=T1; iout <= NOUT; iout++, tout += DTOUT) { flag = CVode(cvode_mem, tout, u, &t, CV_NORMAL); if(check_flag(&flag, "CVode", 1, my_pe)) break; PrintOutput(cvode_mem, my_pe, t, u); if (sensi) { flag = CVodeGetSens(cvode_mem, &t, uS); if(check_flag(&flag, "CVodeGetSens", 1, my_pe)) break; PrintOutputS(my_pe, uS); } if (my_pe == 0) printf("------------------------------------------------------------\n"); } /* Print final statistics */ if (my_pe == 0) PrintFinalStats(cvode_mem, sensi); /* Free memory */ N_VDestroy(u); /* Free the u vector */ if (sensi) N_VDestroyVectorArray(uS, NS); /* Free the uS vectors */ free(data->p); /* Free the p vector */ free(data); /* Free block of UserData */ CVodeFree(&cvode_mem); /* Free the CVODES problem memory */ free(pbar); if(sensi) free(plist); MPI_Finalize(); return(0); }
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 = CVodeSetUserData(cvode_mem, data); if(check_flag(&flag, "CVodeSetUserData", 1)) return(1); flag = CVodeSetMaxNumSteps(cvode_mem, 2000); if(check_flag(&flag, "CVodeSetMaxNumSteps", 1)) return(1); /* Allocate CVODES memory */ flag = CVodeInit(cvode_mem, f, T0, y); if(check_flag(&flag, "CVodeInit", 1)) return(1); flag = CVodeSStolerances(cvode_mem, reltol, abstol); if(check_flag(&flag, "CVodeSStolerances", 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); 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 = CVodeSensInit1(cvode_mem, NS, sensi_meth, NULL, uS); if(check_flag(&flag, "CVodeSensInit", 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 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); }