N_Vector N_VClone_Parallel(N_Vector w)
{
N_Vector v;
realtype *data;
long int local_length;
v = NULL;
v = N_VCloneEmpty_Parallel(w);
if (v == NULL) return(NULL);
local_length = NV_LOCLENGTH_P(w);
/* Create data */
if(local_length > 0) {
/* Allocate memory */
data = NULL;
data = (realtype *) malloc(local_length * sizeof(realtype));
if(data == NULL) { N_VDestroy_Parallel(v); return(NULL); }
/* Attach data */
NV_OWN_DATA_P(v) = TRUE;
NV_DATA_P(v) = data;
}
return(v);
}
N_Vector N_VNew_Parallel(MPI_Comm comm,
long int local_length,
long int global_length)
{
N_Vector v;
realtype *data;
v = NULL;
v = N_VNewEmpty_Parallel(comm, local_length, global_length);
if (v == NULL) return(NULL);
/* Create data */
if(local_length > 0) {
/* Allocate memory */
data = NULL;
data = (realtype *) malloc(local_length * sizeof(realtype));
if(data == NULL) { N_VDestroy_Parallel(v); return(NULL); }
/* Attach data */
NV_OWN_DATA_P(v) = TRUE;
NV_DATA_P(v) = data;
}
return(v);
}
static void FreeUserData(UserData webdata)
{
int ix, jy;
for (ix = 0; ix < MXSUB; ix++) {
for (jy = 0; jy < MYSUB; jy++) {
destroyMat((webdata->PP)[ix][jy]);
destroyArray((webdata->pivot)[ix][jy]);
}
}
destroyMat(webdata->acoef);
N_VDestroy_Parallel(webdata->rates);
N_VDestroy_Parallel(webdata->ewt);
free(webdata);
}
void N_VDestroyVectorArray_Parallel(N_Vector *vs, int count)
{
int j;
for (j = 0; j < count; j++) N_VDestroy_Parallel(vs[j]);
free(vs); vs = NULL;
return;
}
static void FreeUserData(UserData data)
{
destroyMat(acoef);
free(bcoef);
free(cox); free(coy);
N_VDestroy_Parallel(data->rates);
free(data);
}
static void FreeUserData(UserData data)
{
int jx, jy;
for (jx = 0; jx < MXSUB; jx++) {
for (jy = 0; jy < MYSUB; jy++) {
denfree((data->P)[jx][jy]);
denfreepiv((data->pivot)[jx][jy]);
}
}
denfree(acoef);
free(bcoef);
free(cox);
free(coy);
N_VDestroy_Parallel(data->rates);
free(data);
}
void FNV_FREEP(void)
{
N_VDestroy_Parallel(F2C_vec);
}
int main(int argc, char *argv[])
{
MPI_Comm comm;
void *mem;
UserData webdata;
long int SystemSize, local_N, mudq, mldq, mukeep, mlkeep;
realtype rtol, atol, t0, tout, tret;
N_Vector cc, cp, res, id;
int thispe, npes, maxl, iout, retval;
cc = cp = res = id = NULL;
webdata = NULL;
mem = NULL;
/* Set communicator, and get processor number and total number of PE's. */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_rank(comm, &thispe);
MPI_Comm_size(comm, &npes);
if (npes != NPEX*NPEY) {
if (thispe == 0)
fprintf(stderr,
"\nMPI_ERROR(0): npes = %d not equal to NPEX*NPEY = %d\n",
npes, NPEX*NPEY);
MPI_Finalize();
return(1);
}
/* Set local length (local_N) and global length (SystemSize). */
local_N = MXSUB*MYSUB*NUM_SPECIES;
SystemSize = NEQ;
/* Set up user data block webdata. */
webdata = (UserData) malloc(sizeof *webdata);
webdata->rates = N_VNew_Parallel(comm, local_N, SystemSize);
webdata->acoef = newDenseMat(NUM_SPECIES, NUM_SPECIES);
InitUserData(webdata, thispe, npes, comm);
/* Create needed vectors, and load initial values.
The vector res is used temporarily only. */
cc = N_VNew_Parallel(comm, local_N, SystemSize);
if(check_flag((void *)cc, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
cp = N_VNew_Parallel(comm, local_N, SystemSize);
if(check_flag((void *)cp, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
res = N_VNew_Parallel(comm, local_N, SystemSize);
if(check_flag((void *)res, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
id = N_VNew_Parallel(comm, local_N, SystemSize);
if(check_flag((void *)id, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
SetInitialProfiles(cc, cp, id, res, webdata);
N_VDestroy_Parallel(res);
/* Set remaining inputs to IDAMalloc. */
t0 = ZERO;
rtol = RTOL;
atol = ATOL;
/* Call IDACreate and IDAMalloc to initialize solution */
mem = IDACreate();
if(check_flag((void *)mem, "IDACreate", 0, thispe)) MPI_Abort(comm, 1);
retval = IDASetUserData(mem, webdata);
if(check_flag(&retval, "IDASetUserData", 1, thispe)) MPI_Abort(comm, 1);
retval = IDASetId(mem, id);
if(check_flag(&retval, "IDASetId", 1, thispe)) MPI_Abort(comm, 1);
retval = IDAInit(mem, resweb, t0, cc, cp);
if(check_flag(&retval, "IDAInit", 1, thispe)) MPI_Abort(comm, 1);
retval = IDASStolerances(mem, rtol, atol);
if(check_flag(&retval, "IDASStolerances", 1, thispe)) MPI_Abort(comm, 1);
/* Call IDASpgmr to specify the IDA linear solver IDASPGMR */
maxl = 16;
retval = IDASpgmr(mem, maxl);
if(check_flag(&retval, "IDASpgmr", 1, thispe)) MPI_Abort(comm, 1);
/* Call IDABBDPrecInit to initialize the band-block-diagonal preconditioner.
The half-bandwidths for the difference quotient evaluation are exact
for the system Jacobian, but only a 5-diagonal band matrix is retained. */
mudq = mldq = NSMXSUB;
mukeep = mlkeep = 2;
retval = IDABBDPrecInit(mem, local_N, mudq, mldq, mukeep, mlkeep,
ZERO, reslocal, NULL);
if(check_flag(&retval, "IDABBDPrecInit", 1, thispe)) MPI_Abort(comm, 1);
/* Call IDACalcIC (with default options) to correct the initial values. */
tout = RCONST(0.001);
retval = IDACalcIC(mem, IDA_YA_YDP_INIT, tout);
if(check_flag(&retval, "IDACalcIC", 1, thispe)) MPI_Abort(comm, 1);
/* On PE 0, print heading, basic parameters, initial values. */
if (thispe == 0) PrintHeader(SystemSize, maxl,
mudq, mldq, mukeep, mlkeep,
rtol, atol);
PrintOutput(mem, cc, t0, webdata, comm);
/* Call IDA in tout loop, normal mode, and print selected output. */
for (iout = 1; iout <= NOUT; iout++) {
retval = IDASolve(mem, tout, &tret, cc, cp, IDA_NORMAL);
if(check_flag(&retval, "IDASolve", 1, thispe)) MPI_Abort(comm, 1);
PrintOutput(mem, cc, tret, webdata, comm);
if (iout < 3) tout *= TMULT;
else tout += TADD;
}
/* On PE 0, print final set of statistics. */
if (thispe == 0) PrintFinalStats(mem);
/* Free memory. */
N_VDestroy_Parallel(cc);
N_VDestroy_Parallel(cp);
N_VDestroy_Parallel(id);
IDAFree(&mem);
destroyMat(webdata->acoef);
N_VDestroy_Parallel(webdata->rates);
free(webdata);
MPI_Finalize();
return(0);
}
int main(int argc, char *argv[])
{
MPI_Comm comm;
void *kmem;
UserData data;
N_Vector cc, sc, constraints;
int globalstrategy;
long int Nlocal;
realtype fnormtol, scsteptol, dq_rel_uu;
int flag, maxl, maxlrst;
long int mudq, mldq, mukeep, mlkeep;
int my_pe, npes, npelast = NPEX*NPEY-1;
data = NULL;
kmem = NULL;
cc = sc = constraints = NULL;
/* Get processor number and total number of pe's */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_size(comm, &npes);
MPI_Comm_rank(comm, &my_pe);
if (npes != NPEX*NPEY) {
if (my_pe == 0)
printf("\nMPI_ERROR(0): npes=%d is not equal to NPEX*NPEY=%d\n", npes,
NPEX*NPEY);
return(1);
}
/* Allocate memory, and set problem data, initial values, tolerances */
/* Set local length */
Nlocal = NUM_SPECIES*MXSUB*MYSUB;
/* Allocate and initialize user data block */
data = AllocUserData();
if (check_flag((void *)data, "AllocUserData", 2, my_pe)) MPI_Abort(comm, 1);
InitUserData(my_pe, Nlocal, comm, data);
/* Choose global strategy */
globalstrategy = KIN_NONE;
/* Allocate and initialize vectors */
cc = N_VNew_Parallel(comm, Nlocal, NEQ);
if (check_flag((void *)cc, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
sc = N_VNew_Parallel(comm, Nlocal, NEQ);
if (check_flag((void *)sc, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
data->rates = N_VNew_Parallel(comm, Nlocal, NEQ);
if (check_flag((void *)data->rates, "N_VNew_Parallel", 0, my_pe))
MPI_Abort(comm, 1);
constraints = N_VNew_Parallel(comm, Nlocal, NEQ);
if (check_flag((void *)constraints, "N_VNew_Parallel", 0, my_pe))
MPI_Abort(comm, 1);
N_VConst(ZERO, constraints);
SetInitialProfiles(cc, sc);
fnormtol = FTOL; scsteptol = STOL;
/* Call KINCreate/KINInit to initialize KINSOL:
nvSpec points to machine environment data
A pointer to KINSOL problem memory is returned and stored in kmem. */
kmem = KINCreate();
if (check_flag((void *)kmem, "KINCreate", 0, my_pe)) MPI_Abort(comm, 1);
/* Vector cc passed as template vector. */
flag = KINInit(kmem, func, cc);
if (check_flag(&flag, "KINInit", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetUserData(kmem, data);
if (check_flag(&flag, "KINSetUserData", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetConstraints(kmem, constraints);
if (check_flag(&flag, "KINSetConstraints", 1, my_pe)) MPI_Abort(comm, 1);
/* We no longer need the constraints vector since KINSetConstraints
creates a private copy for KINSOL to use. */
N_VDestroy_Parallel(constraints);
flag = KINSetFuncNormTol(kmem, fnormtol);
if (check_flag(&flag, "KINSetFuncNormTol", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetScaledStepTol(kmem, scsteptol);
if (check_flag(&flag, "KINSetScaledStepTol", 1, my_pe)) MPI_Abort(comm, 1);
/* Call KINBBDPrecInit to initialize and allocate memory for the
band-block-diagonal preconditioner, and specify the local and
communication functions func_local and gcomm=NULL (all communication
needed for the func_local is already done in func). */
dq_rel_uu = ZERO;
mudq = mldq = 2*NUM_SPECIES - 1;
mukeep = mlkeep = NUM_SPECIES;
/* Call KINBBDSpgmr to specify the linear solver KINSPGMR */
maxl = 20; maxlrst = 2;
flag = KINSpgmr(kmem, maxl);
if (check_flag(&flag, "KINSpgmr", 1, my_pe)) MPI_Abort(comm, 1);
/* Initialize BBD preconditioner */
flag = KINBBDPrecInit(kmem, Nlocal, mudq, mldq, mukeep, mlkeep,
dq_rel_uu, func_local, NULL);
if (check_flag(&flag, "KINBBDPrecInit", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSpilsSetMaxRestarts(kmem, maxlrst);
if (check_flag(&flag, "KINSpilsSetMaxRestarts", 1, my_pe))
MPI_Abort(comm, 1);
/* Print out the problem size, solution parameters, initial guess. */
if (my_pe == 0)
PrintHeader(globalstrategy, maxl, maxlrst, mudq, mldq, mukeep,
mlkeep, fnormtol, scsteptol);
/* call KINSol and print output concentration profile */
flag = KINSol(kmem, /* KINSol memory block */
cc, /* initial guesss on input; solution vector */
globalstrategy, /* global stragegy choice */
sc, /* scaling vector, for the variable cc */
sc); /* scaling vector for function values fval */
if (check_flag(&flag, "KINSol", 1, my_pe)) MPI_Abort(comm, 1);
if (my_pe == 0) printf("\n\nComputed equilibrium species concentrations:\n");
if (my_pe == 0 || my_pe==npelast) PrintOutput(my_pe, comm, cc);
/* Print final statistics and free memory */
if (my_pe == 0)
PrintFinalStats(kmem);
N_VDestroy_Parallel(cc);
N_VDestroy_Parallel(sc);
KINFree(&kmem);
FreeUserData(data);
MPI_Finalize();
return(0);
}
int main(int argc, char *argv[])
{
realtype dx, reltol, abstol, t, tout, umax;
N_Vector u;
UserData data;
void *cvode_mem;
int iout, flag, my_pe, npes;
long int local_N, nperpe, nrem, my_base, 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_flag((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_flag((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:
CV_ADAMS specifies the Adams Method
CV_FUNCTIONAL specifies functional iteration
A pointer to the integrator memory is returned and stored in cvode_mem.
*/
cvode_mem = CVodeCreate(CV_ADAMS, CV_FUNCTIONAL);
if(check_flag((void *)cvode_mem, "CVodeCreate", 0, my_pe)) MPI_Abort(comm, 1);
flag = CVodeSetFdata(cvode_mem, data);
if(check_flag(&flag, "CVodeSetFdata", 1, my_pe)) MPI_Abort(comm, 1);
/*
Call CVodeMalloc to initialize the integrator memory:
cvode_mem is the pointer to the integrator memory returned by CVodeCreate
f is the user's right hand side function in y'=f(t,y)
T0 is the initial time
u is the initial dependent variable vector
CV_SS specifies scalar relative and absolute tolerances
reltol is the relative tolerance
&abstol is a pointer to the scalar absolute tolerance
*/
flag = CVodeMalloc(cvode_mem, f, T0, u, CV_SS, reltol, &abstol);
if(check_flag(&flag, "CVodeMalloc", 1, my_pe)) MPI_Abort(comm, 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) {
flag = CVode(cvode_mem, tout, u, &t, CV_NORMAL);
if(check_flag(&flag, "CVode", 1, my_pe)) break;
umax = N_VMaxNorm(u);
flag = CVodeGetNumSteps(cvode_mem, &nst);
check_flag(&flag, "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);
}
int main(int argc, char *argv[])
{
ProblemData d;
MPI_Comm comm;
int npes, npes_needed;
int myId;
long int neq, l_neq;
void *cvode_mem;
N_Vector y, q;
realtype abstol, reltol, abstolQ, reltolQ;
long int mudq, mldq, mukeep, mlkeep;
int indexB;
N_Vector yB, qB;
realtype abstolB, reltolB, abstolQB, reltolQB;
long int mudqB, mldqB, mukeepB, mlkeepB;
realtype tret, *qdata, G;
int ncheckpnt, flag;
booleantype output;
/* Initialize MPI and set Ids */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_rank(comm, &myId);
/* Check number of processes */
npes_needed = NPX * NPY;
#ifdef USE3D
npes_needed *= NPZ;
#endif
MPI_Comm_size(comm, &npes);
if (npes_needed != npes) {
if (myId == 0)
fprintf(stderr,"I need %d processes but I only got %d\n",
npes_needed, npes);
MPI_Abort(comm, EXIT_FAILURE);
}
/* Test if matlab output is requested */
if (argc > 1) output = TRUE;
else output = FALSE;
/* Allocate and set problem data structure */
d = (ProblemData) malloc(sizeof *d);
SetData(d, comm, npes, myId, &neq, &l_neq);
if (myId == 0) PrintHeader();
/*--------------------------
Forward integration phase
--------------------------*/
/* Allocate space for y and set it with the I.C. */
y = N_VNew_Parallel(comm, l_neq, neq);
N_VConst(ZERO, y);
/* Allocate and initialize qB (local contribution to cost) */
q = N_VNew_Parallel(comm, 1, npes);
N_VConst(ZERO, q);
/* Create CVODES object, attach user data, and allocate space */
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
flag = CVodeSetUserData(cvode_mem, d);
flag = CVodeInit(cvode_mem, f, ti, y);
abstol = ATOL;
reltol = RTOL;
flag = CVodeSStolerances(cvode_mem, reltol, abstol);
/* attach linear solver */
flag = CVSpgmr(cvode_mem, PREC_LEFT, 0);
/* Attach preconditioner and linear solver modules */
mudq = mldq = d->l_m[0]+1;
mukeep = mlkeep = 2;
flag = CVBBDPrecInit(cvode_mem, l_neq, mudq, mldq,
mukeep, mlkeep, ZERO,
f_local, NULL);
/* Initialize quadrature calculations */
abstolQ = ATOL_Q;
reltolQ = RTOL_Q;
flag = CVodeQuadInit(cvode_mem, fQ, q);
flag = CVodeQuadSStolerances(cvode_mem, reltolQ, abstolQ);
flag = CVodeSetQuadErrCon(cvode_mem, TRUE);
/* Allocate space for the adjoint calculation */
flag = CVodeAdjInit(cvode_mem, STEPS, CV_HERMITE);
/* Integrate forward in time while storing check points */
if (myId == 0) printf("Begin forward integration... ");
flag = CVodeF(cvode_mem, tf, y, &tret, CV_NORMAL, &ncheckpnt);
if (myId == 0) printf("done. ");
/* Extract quadratures */
flag = CVodeGetQuad(cvode_mem, &tret, q);
qdata = NV_DATA_P(q);
MPI_Allreduce(&qdata[0], &G, 1, PVEC_REAL_MPI_TYPE, MPI_SUM, comm);
#if defined(SUNDIALS_EXTENDED_PRECISION)
if (myId == 0) printf(" G = %Le\n",G);
#elif defined(SUNDIALS_DOUBLE_PRECISION)
if (myId == 0) printf(" G = %e\n",G);
#else
if (myId == 0) printf(" G = %e\n",G);
#endif
/* Print statistics for forward run */
if (myId == 0) PrintFinalStats(cvode_mem);
/*--------------------------
Backward integration phase
--------------------------*/
/* Allocate and initialize yB */
yB = N_VNew_Parallel(comm, l_neq, neq);
N_VConst(ZERO, yB);
/* Allocate and initialize qB (gradient) */
qB = N_VNew_Parallel(comm, l_neq, neq);
N_VConst(ZERO, qB);
/* Create and allocate backward CVODE memory */
flag = CVodeCreateB(cvode_mem, CV_BDF, CV_NEWTON, &indexB);
flag = CVodeSetUserDataB(cvode_mem, indexB, d);
flag = CVodeInitB(cvode_mem, indexB, fB, tf, yB);
abstolB = ATOL_B;
reltolB = RTOL_B;
flag = CVodeSStolerancesB(cvode_mem, indexB, reltolB, abstolB);
/* Attach preconditioner and linear solver modules */
flag = CVSpgmrB(cvode_mem, indexB, PREC_LEFT, 0);
mudqB = mldqB = d->l_m[0]+1;
mukeepB = mlkeepB = 2;
flag = CVBBDPrecInitB(cvode_mem, indexB, l_neq, mudqB, mldqB,
mukeepB, mlkeepB, ZERO, fB_local, NULL);
/* Initialize quadrature calculations */
abstolQB = ATOL_QB;
reltolQB = RTOL_QB;
flag = CVodeQuadInitB(cvode_mem, indexB, fQB, qB);
flag = CVodeQuadSStolerancesB(cvode_mem, indexB, reltolQB, abstolQB);
flag = CVodeSetQuadErrConB(cvode_mem, indexB, TRUE);
/* Integrate backwards */
if (myId == 0) printf("Begin backward integration... ");
flag = CVodeB(cvode_mem, ti, CV_NORMAL);
if (myId == 0) printf("done.\n");
/* Extract solution */
flag = CVodeGetB(cvode_mem, indexB, &tret, yB);
/* Extract quadratures */
flag = CVodeGetQuadB(cvode_mem, indexB, &tret, qB);
/* Print statistics for backward run */
if (myId == 0) {
PrintFinalStats(CVodeGetAdjCVodeBmem(cvode_mem, indexB));
}
/* Process 0 collects the gradient components and prints them */
if (output) {
OutputGradient(myId, qB, d);
if (myId == 0) printf("Wrote matlab file 'grad.m'.\n");
}
/* Free memory */
N_VDestroy_Parallel(y);
N_VDestroy_Parallel(q);
N_VDestroy_Parallel(qB);
N_VDestroy_Parallel(yB);
CVodeFree(&cvode_mem);
MPI_Finalize();
return(0);
}
int main(int argc, char *argv[])
{
int globalstrategy;
long int local_N;
realtype fnormtol, scsteptol;
N_Vector cc, sc, constraints;
UserData data;
int flag, maxl, maxlrst;
int my_pe, npes, npelast = NPEX*NPEY-1;
void *kmem;
MPI_Comm comm;
cc = sc = constraints = NULL;
data = NULL;
kmem = NULL;
/* Get processor number and total number of pe's */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_size(comm, &npes);
MPI_Comm_rank(comm, &my_pe);
if (npes != NPEX*NPEY) {
if (my_pe == 0)
fprintf(stderr, "\nMPI_ERROR(0); npes = %d is not equal to NPEX*NPEY = %d\n",
npes,NPEX*NPEY);
MPI_Finalize();
return(1);
}
/* Allocate memory, and set problem data, initial values, tolerances */
/* Set local vector length */
local_N = NUM_SPECIES*MXSUB*MYSUB;
/* Allocate and initialize user data block */
data = AllocUserData();
if (check_flag((void *)data, "AllocUserData", 0, my_pe)) MPI_Abort(comm, 1);
InitUserData(my_pe, comm, data);
/* Set global strategy flag */
globalstrategy = KIN_NONE;
/* Allocate and initialize vectors */
cc = N_VNew_Parallel(comm, local_N, NEQ);
if (check_flag((void *)cc, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
sc = N_VNew_Parallel(comm, local_N, NEQ);
if (check_flag((void *)sc, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
data->rates = N_VNew_Parallel(comm, local_N, NEQ);
if (check_flag((void *)data->rates, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
constraints = N_VNew_Parallel(comm, local_N, NEQ);
if (check_flag((void *)constraints, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
N_VConst(ZERO, constraints);
SetInitialProfiles(cc, sc);
fnormtol=FTOL; scsteptol=STOL;
/* Call KINCreate/KINMalloc to initialize KINSOL:
nvSpec is the nvSpec pointer used in the parallel version
A pointer to KINSOL problem memory is returned and stored in kmem. */
kmem = KINCreate();
if (check_flag((void *)kmem, "KINCreate", 0, my_pe)) MPI_Abort(comm, 1);
/* Vector cc passed as template vector. */
flag = KINMalloc(kmem, funcprpr, cc);
if (check_flag(&flag, "KINMalloc", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetNumMaxIters(kmem, 250);
if (check_flag(&flag, "KINSetNumMaxIters", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetFdata(kmem, data);
if (check_flag(&flag, "KINSetFdata", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetConstraints(kmem, constraints);
if (check_flag(&flag, "KINSetConstraints", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetFuncNormTol(kmem, fnormtol);
if (check_flag(&flag, "KINSetFuncNormTol", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetScaledStepTol(kmem, scsteptol);
if (check_flag(&flag, "KINSetScaledStepTop", 1, my_pe)) MPI_Abort(comm, 1);
/* We no longer need the constraints vector since KINSetConstraints
creates a private copy for KINSOL to use. */
N_VDestroy_Parallel(constraints);
/* Call KINSpgmr to specify the linear solver KINSPGMR with preconditioner
routines Precondbd and PSolvebd, and the pointer to the user data block. */
maxl = 20; maxlrst = 2;
flag = KINSpgmr(kmem, maxl);
if (check_flag(&flag, "KINSpgmr", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSpilsSetMaxRestarts(kmem, maxlrst);
if (check_flag(&flag, "KINSpilsSetMaxRestarts", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSpilsSetPreconditioner(kmem,
Precondbd,
PSolvebd,
data);
if (check_flag(&flag, "KINSpilsSetPreconditioner", 1, my_pe)) MPI_Abort(comm, 1);
/* Print out the problem size, solution parameters, initial guess. */
if (my_pe == 0)
PrintHeader(globalstrategy, maxl, maxlrst, fnormtol, scsteptol);
/* Call KINSol and print output concentration profile */
flag = KINSol(kmem, /* KINSol memory block */
cc, /* initial guess on input; solution vector */
globalstrategy, /* global stragegy choice */
sc, /* scaling vector for the variable cc */
sc); /* scaling vector for function values fval */
if (check_flag(&flag, "KINSol", 1, my_pe)) MPI_Abort(comm, 1);
if (my_pe == 0)
printf("\n\nComputed equilibrium species concentrations:\n");
if (my_pe == 0 || my_pe == npelast)
PrintOutput(my_pe, comm, cc);
/* Print final statistics and free memory */
if (my_pe == 0)
PrintFinalStats(kmem);
N_VDestroy_Parallel(cc);
N_VDestroy_Parallel(sc);
KINFree(&kmem);
FreeUserData(data);
MPI_Finalize();
return(0);
}
int main(int argc, char *argv[])
{
MPI_Comm comm;
void *mem;
UserData webdata;
long int SystemSize, local_N;
realtype rtol, atol, t0, tout, tret;
N_Vector cc, cp, res, id;
int thispe, npes, maxl, iout, flag;
cc = cp = res = id = NULL;
webdata = NULL;
mem = NULL;
/* Set communicator, and get processor number and total number of PE's. */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_rank(comm, &thispe);
MPI_Comm_size(comm, &npes);
if (npes != NPEX*NPEY) {
if (thispe == 0)
fprintf(stderr,
"\nMPI_ERROR(0): npes = %d not equal to NPEX*NPEY = %d\n",
npes, NPEX*NPEY);
MPI_Finalize();
return(1);
}
/* Set local length (local_N) and global length (SystemSize). */
local_N = MXSUB*MYSUB*NUM_SPECIES;
SystemSize = NEQ;
/* Set up user data block webdata. */
webdata = AllocUserData(comm, local_N, SystemSize);
if (check_flag((void *)webdata, "AllocUserData", 0, thispe)) MPI_Abort(comm, 1);
InitUserData(webdata, thispe, npes, comm);
/* Create needed vectors, and load initial values.
The vector res is used temporarily only. */
cc = N_VNew_Parallel(comm, local_N, SystemSize);
if (check_flag((void *)cc, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
cp = N_VNew_Parallel(comm, local_N, SystemSize);
if (check_flag((void *)cp, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
res = N_VNew_Parallel(comm, local_N, SystemSize);
if (check_flag((void *)res, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
id = N_VNew_Parallel(comm, local_N, SystemSize);
if (check_flag((void *)id, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
SetInitialProfiles(cc, cp, id, res, webdata);
N_VDestroy(res);
/* Set remaining inputs to IDAMalloc. */
t0 = ZERO;
rtol = RTOL;
atol = ATOL;
/* Call IDACreate and IDAMalloc to initialize IDA.
A pointer to IDA problem memory is returned and stored in idamem. */
mem = IDACreate();
if (check_flag((void *)mem, "IDACreate", 0, thispe)) MPI_Abort(comm, 1);
flag = IDASetUserData(mem, webdata);
if (check_flag(&flag, "IDASetUserData", 1, thispe)) MPI_Abort(comm, 1);
flag = IDASetId(mem, id);
if (check_flag(&flag, "IDASetId", 1, thispe)) MPI_Abort(comm, 1);
flag = IDAInit(mem, resweb, t0, cc, cp);
if (check_flag(&flag, "IDAinit", 1, thispe)) MPI_Abort(comm, 1);
flag = IDASStolerances(mem, rtol, atol);
if (check_flag(&flag, "IDASStolerances", 1, thispe)) MPI_Abort(comm, 1);
webdata->ida_mem = mem;
/* Call IDASpgmr to specify the IDA linear solver IDASPGMR and specify
the preconditioner routines supplied (Precondbd and PSolvebd).
maxl (max. Krylov subspace dim.) is set to 16. */
maxl = 16;
flag = IDASpgmr(mem, maxl);
if (check_flag(&flag, "IDASpgmr", 1, thispe))
MPI_Abort(comm, 1);
flag = IDASpilsSetPreconditioner(mem, Precondbd, PSolvebd);
if (check_flag(&flag, "IDASpilsSetPreconditioner", 1, thispe))
MPI_Abort(comm, 1);
/* Call IDACalcIC (with default options) to correct the initial values. */
tout = RCONST(0.001);
flag = IDACalcIC(mem, IDA_YA_YDP_INIT, tout);
if (check_flag(&flag, "IDACalcIC", 1, thispe))
MPI_Abort(comm, 1);
/* On PE 0, print heading, basic parameters, initial values. */
if (thispe == 0) PrintHeader(SystemSize, maxl, rtol, atol);
PrintOutput(mem, cc, t0, webdata, comm);
/* Loop over iout, call IDASolve (normal mode), print selected output. */
for (iout = 1; iout <= NOUT; iout++) {
flag = IDASolve(mem, tout, &tret, cc, cp, IDA_NORMAL);
if (check_flag(&flag, "IDASolve", 1, thispe)) MPI_Abort(comm, 1);
PrintOutput(mem, cc, tret, webdata, comm);
if (iout < 3) tout *= TMULT;
else tout += TADD;
}
/* On PE 0, print final set of statistics. */
if (thispe == 0) PrintFinalStats(mem);
/* Free memory. */
N_VDestroy_Parallel(cc);
N_VDestroy_Parallel(cp);
N_VDestroy_Parallel(id);
IDAFree(&mem);
FreeUserData(webdata);
MPI_Finalize();
return(0);
}
int main(int argc, char *argv[])
{
MPI_Comm comm;
void *mem;
UserData data;
int thispe, iout, ier, npes;
int Neq, local_N, mudq, mldq, mukeep, mlkeep;
realtype rtol, atol, t0, t1, tout, tret;
N_Vector uu, up, constraints, id, res;
realtype *pbar;
int is;
N_Vector *uuS, *upS;
booleantype sensi, err_con;
int sensi_meth;
mem = NULL;
data = NULL;
uu = up = constraints = id = res = NULL;
uuS = upS = NULL;
/* Get processor number and total number of pe's. */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_size(comm, &npes);
MPI_Comm_rank(comm, &thispe);
if (npes != NPEX*NPEY) {
if (thispe == 0)
fprintf(stderr,
"\nMPI_ERROR(0): npes = %d is not equal to NPEX*NPEY = %d\n",
npes,NPEX*NPEY);
MPI_Finalize();
return(1);
}
/* Process arguments */
ProcessArgs(argc, argv, thispe, &sensi, &sensi_meth, &err_con);
/* Set local length local_N and global length Neq. */
local_N = MXSUB*MYSUB;
Neq = MX * MY;
/* Allocate N-vectors. */
uu = N_VNew_Parallel(comm, local_N, Neq);
if(check_flag((void *)uu, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
up = N_VNew_Parallel(comm, local_N, Neq);
if(check_flag((void *)up, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
res = N_VNew_Parallel(comm, local_N, Neq);
if(check_flag((void *)res, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
constraints = N_VNew_Parallel(comm, local_N, Neq);
if(check_flag((void *)constraints, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
id = N_VNew_Parallel(comm, local_N, Neq);
if(check_flag((void *)id, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
/* Allocate and initialize the data structure. */
data = (UserData) malloc(sizeof *data);
if(check_flag((void *)data, "malloc", 2, thispe)) MPI_Abort(comm, 1);
InitUserData(thispe, comm, data);
/* Initialize the uu, up, id, and constraints profiles. */
SetInitialProfile(uu, up, id, res, data);
N_VConst(ONE, constraints);
t0 = ZERO; t1 = RCONST(0.01);
/* Scalar relative and absolute tolerance. */
rtol = ZERO;
atol = RCONST(1.0e-3);
/* Call IDACreate and IDAInit to initialize solution and various
IDASet*** functions to specify optional inputs:
- indicate which variables are differential and which are algebraic
- exclude algebraic variables from error test
- specify additional constraints on solution components */
mem = IDACreate();
if(check_flag((void *)mem, "IDACreate", 0, thispe)) MPI_Abort(comm, 1);
ier = IDASetUserData(mem, data);
if(check_flag(&ier, "IDASetUserData", 1, thispe)) MPI_Abort(comm, 1);
ier = IDASetSuppressAlg(mem, TRUE);
if(check_flag(&ier, "IDASetSuppressAlg", 1, thispe)) MPI_Abort(comm, 1);
ier = IDASetId(mem, id);
if(check_flag(&ier, "IDASetId", 1, thispe)) MPI_Abort(comm, 1);
ier = IDASetConstraints(mem, constraints);
if(check_flag(&ier, "IDASetConstraints", 1, thispe)) MPI_Abort(comm, 1);
N_VDestroy_Parallel(constraints);
ier = IDAInit(mem, heatres, t0, uu, up);
if(check_flag(&ier, "IDAInit", 1, thispe)) MPI_Abort(comm, 1);
/* Specify state tolerances (scalar relative and absolute tolerances) */
ier = IDASStolerances(mem, rtol, atol);
if(check_flag(&ier, "IDASStolerances", 1, thispe)) MPI_Abort(comm, 1);
/* Call IDASpgmr to specify the linear solver. */
ier = IDASpgmr(mem, 12);
if(check_flag(&ier, "IDASpgmr", 1, thispe)) MPI_Abort(comm, 1);
/* Call IDABBDPrecInit to initialize BBD preconditioner. */
mudq = MXSUB;
mldq = MXSUB;
mukeep = 1;
mlkeep = 1;
ier = IDABBDPrecInit(mem, local_N, mudq, mldq, mukeep, mlkeep,
ZERO, reslocal, NULL);
if(check_flag(&ier, "IDABBDPrecInit", 1, thispe)) MPI_Abort(comm, 1);
/* Sensitivity-related settings */
if( sensi) {
/* Allocate and set pbar, the vector with order of magnitude
information for the problem parameters. (Note: this is
done here as an illustration only, as the default values
for pbar, if pbar is not supplied, are anyway 1.0) */
pbar = (realtype *) malloc(NS*sizeof(realtype));
if (check_flag((void *)pbar, "malloc", 2, thispe)) MPI_Abort(comm, 1);
for (is=0; is<NS; is++) pbar[is] = data->p[is];
/* Allocate sensitivity solution vectors uuS and upS and set them
to an initial guess for the sensitivity ICs (the IC for uuS are
0.0 since the state IC do not depend on the porblem parameters;
however, the derivatives upS may not and therefore we will have
to call IDACalcIC to find them) */
uuS = N_VCloneVectorArray_Parallel(NS, uu);
if (check_flag((void *)uuS, "N_VCloneVectorArray_Parallel", 0, thispe)) MPI_Abort(comm, 1);
for (is = 0; is < NS; is++) N_VConst(ZERO,uuS[is]);
upS = N_VCloneVectorArray_Parallel(NS, uu);
if (check_flag((void *)upS, "N_VCloneVectorArray_Parallel", 0, thispe)) MPI_Abort(comm, 1);
for (is = 0; is < NS; is++) N_VConst(ZERO,upS[is]);
/* Initialize FSA using the default internal sensitivity residual function
(Note that this requires specifying the problem parameters -- see below) */
ier = IDASensInit(mem, NS, sensi_meth, NULL, uuS, upS);
if(check_flag(&ier, "IDASensInit", 1, thispe)) MPI_Abort(comm, 1);
/* Indicate the use of internally estimated tolerances for the sensitivity
variables (based on the tolerances provided for the states and the
pbar values) */
ier = IDASensEEtolerances(mem);
if(check_flag(&ier, "IDASensEEtolerances", 1, thispe)) MPI_Abort(comm, 1);
/* Specify whether the sensitivity variables are included in the error
test or not */
ier = IDASetSensErrCon(mem, err_con);
if(check_flag(&ier, "IDASetSensErrCon", 1, thispe)) MPI_Abort(comm, 1);
/* Specify the problem parameters and their order of magnitude
(Note that we do not specify the index array plist and therefore
IDAS will compute sensitivities w.r.t. the first NS parameters) */
ier = IDASetSensParams(mem, data->p, pbar, NULL);
if(check_flag(&ier, "IDASetSensParams", 1, thispe)) MPI_Abort(comm, 1);
/* Compute consistent initial conditions (Note that this is required
only if performing SA since uu and up already contain consistent
initial conditions for the states) */
ier = IDACalcIC(mem, IDA_YA_YDP_INIT, t1);
if(check_flag(&ier, "IDACalcIC", 1, thispe)) MPI_Abort(comm, 1);
}
/* Print problem description */
if (thispe == 0 ) PrintHeader(Neq, rtol, atol, mudq, mukeep,
sensi, sensi_meth, err_con);
/* Loop over tout, call IDASolve, print output. */
for (tout = t1, iout = 1; iout <= NOUT; iout++, tout *= TWO) {
ier = IDASolve(mem, tout, &tret, uu, up, IDA_NORMAL);
if(check_flag(&ier, "IDASolve", 1, thispe)) MPI_Abort(comm, 1);
if (sensi) {
ier = IDAGetSens(mem, &tret, uuS);
if(check_flag(&ier, "IDAGetSens", 1, thispe)) MPI_Abort(comm, 1);
}
PrintOutput(thispe, mem, tret, uu, sensi, uuS);
}
/* Print final statistics */
if (thispe == 0) PrintFinalStats(mem);
/* Free Memory */
IDAFree(&mem);
free(data);
N_VDestroy_Parallel(id);
N_VDestroy_Parallel(res);
N_VDestroy_Parallel(up);
N_VDestroy_Parallel(uu);
MPI_Finalize();
return(0);
}
int main(int argc, char *argv[])
{
UserData data;
void *cvode_mem;
realtype abstol, reltol, t, tout;
N_Vector u;
int iout, my_pe, npes, flag, jpre;
long int neq, local_N, mudq, mldq, mukeep, mlkeep;
MPI_Comm comm;
data = NULL;
cvode_mem = NULL;
u = NULL;
/* Set problem size neq */
neq = NVARS*MX*MY;
/* Get processor number and total number of pe's */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_size(comm, &npes);
MPI_Comm_rank(comm, &my_pe);
if (npes != NPEX*NPEY) {
if (my_pe == 0)
fprintf(stderr, "\nMPI_ERROR(0): npes = %d is not equal to NPEX*NPEY = %d\n\n",
npes, NPEX*NPEY);
MPI_Finalize();
return(1);
}
/* Set local length */
local_N = NVARS*MXSUB*MYSUB;
/* Allocate and load user data block */
data = (UserData) malloc(sizeof *data);
if(check_flag((void *)data, "malloc", 2, my_pe)) MPI_Abort(comm, 1);
InitUserData(my_pe, local_N, comm, data);
/* Allocate and initialize u, and set tolerances */
u = N_VNew_Parallel(comm, local_N, neq);
if(check_flag((void *)u, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
SetInitialProfiles(u, data);
abstol = ATOL;
reltol = RTOL;
/* Call CVodeCreate to create the solver memory and specify the
* Backward Differentiation Formula and the use of a Newton iteration */
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if(check_flag((void *)cvode_mem, "CVodeCreate", 0, my_pe)) MPI_Abort(comm, 1);
/* Set the pointer to user-defined data */
flag = CVodeSetUserData(cvode_mem, data);
if(check_flag(&flag, "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. */
flag = CVodeInit(cvode_mem, f, T0, u);
if(check_flag(&flag, "CVodeInit", 1, my_pe)) return(1);
/* Call CVodeSStolerances to specify the scalar relative tolerance
* and scalar absolute tolerances */
flag = CVodeSStolerances(cvode_mem, reltol, abstol);
if (check_flag(&flag, "CVodeSStolerances", 1, my_pe)) return(1);
/* Call CVSpgmr to specify the linear solver CVSPGMR with left
preconditioning and the default maximum Krylov dimension maxl */
flag = CVSpgmr(cvode_mem, PREC_LEFT, 0);
if(check_flag(&flag, "CVBBDSpgmr", 1, my_pe)) MPI_Abort(comm, 1);
/* Initialize BBD preconditioner */
mudq = mldq = NVARS*MXSUB;
mukeep = mlkeep = NVARS;
flag = CVBBDPrecInit(cvode_mem, local_N, mudq, mldq,
mukeep, mlkeep, ZERO, flocal, NULL);
if(check_flag(&flag, "CVBBDPrecAlloc", 1, my_pe)) MPI_Abort(comm, 1);
/* Print heading */
if (my_pe == 0) PrintIntro(npes, mudq, mldq, mukeep, mlkeep);
/* Loop over jpre (= PREC_LEFT, PREC_RIGHT), and solve the problem */
for (jpre = PREC_LEFT; jpre <= PREC_RIGHT; jpre++) {
/* On second run, re-initialize u, the integrator, CVBBDPRE, and CVSPGMR */
if (jpre == PREC_RIGHT) {
SetInitialProfiles(u, data);
flag = CVodeReInit(cvode_mem, T0, u);
if(check_flag(&flag, "CVodeReInit", 1, my_pe)) MPI_Abort(comm, 1);
flag = CVBBDPrecReInit(cvode_mem, mudq, mldq, ZERO);
if(check_flag(&flag, "CVBBDPrecReInit", 1, my_pe)) MPI_Abort(comm, 1);
flag = CVSpilsSetPrecType(cvode_mem, PREC_RIGHT);
check_flag(&flag, "CVSpilsSetPrecType", 1, my_pe);
if (my_pe == 0) {
printf("\n\n-------------------------------------------------------");
printf("------------\n");
}
}
if (my_pe == 0) {
printf("\n\nPreconditioner type is: jpre = %s\n\n",
(jpre == PREC_LEFT) ? "PREC_LEFT" : "PREC_RIGHT");
}
/* In loop over output points, call CVode, print results, test for error */
for (iout = 1, tout = TWOHR; iout <= NOUT; iout++, tout += TWOHR) {
flag = CVode(cvode_mem, tout, u, &t, CV_NORMAL);
if(check_flag(&flag, "CVode", 1, my_pe)) break;
PrintOutput(cvode_mem, my_pe, comm, u, t);
}
/* Print final statistics */
if (my_pe == 0) PrintFinalStats(cvode_mem);
} /* End of jpre loop */
/* Free memory */
N_VDestroy_Parallel(u);
free(data);
CVodeFree(&cvode_mem);
MPI_Finalize();
return(0);
}
int main(int argc, char *argv[])
{
realtype abstol, reltol, t, tout;
N_Vector u;
UserData data;
PreconData predata;
void *cvode_mem;
int iout, flag, my_pe, npes;
long int neq, local_N;
MPI_Comm comm;
u = NULL;
data = NULL;
predata = NULL;
cvode_mem = NULL;
/* Set problem size neq */
neq = NVARS*MX*MY;
/* Get processor number and total number of pe's */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_size(comm, &npes);
MPI_Comm_rank(comm, &my_pe);
if (npes != NPEX*NPEY) {
if (my_pe == 0)
fprintf(stderr, "\nMPI_ERROR(0): npes = %d is not equal to NPEX*NPEY = %d\n\n",
npes,NPEX*NPEY);
MPI_Finalize();
return(1);
}
/* Set local length */
local_N = NVARS*MXSUB*MYSUB;
/* Allocate and load user data block; allocate preconditioner block */
data = (UserData) malloc(sizeof *data);
if (check_flag((void *)data, "malloc", 2, my_pe)) MPI_Abort(comm, 1);
InitUserData(my_pe, comm, data);
predata = AllocPreconData (data);
/* Allocate u, and set initial values and tolerances */
u = N_VNew_Parallel(comm, local_N, neq);
if (check_flag((void *)u, "N_VNew", 0, my_pe)) MPI_Abort(comm, 1);
SetInitialProfiles(u, data);
abstol = ATOL; reltol = RTOL;
/*
Call CVodeCreate to create the solver memory:
CV_BDF specifies the Backward Differentiation Formula
CV_NEWTON specifies a Newton iteration
A pointer to the integrator memory is returned and stored in cvode_mem.
*/
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void *)cvode_mem, "CVodeCreate", 0, my_pe)) MPI_Abort(comm, 1);
/* Set the pointer to user-defined data */
flag = CVodeSetFdata(cvode_mem, data);
if (check_flag(&flag, "CVodeSetFdata", 1, my_pe)) MPI_Abort(comm, 1);
/*
Call CVodeMalloc to initialize the integrator memory:
cvode_mem is the pointer to the integrator memory returned by CVodeCreate
f is the user's right hand side function in y'=f(t,y)
T0 is the initial time
u is the initial dependent variable vector
CV_SS specifies scalar relative and absolute tolerances
reltol is the relative tolerance
&abstol is a pointer to the scalar absolute tolerance
*/
flag = CVodeMalloc(cvode_mem, f, T0, u, CV_SS, reltol, &abstol);
if (check_flag(&flag, "CVodeMalloc", 1, my_pe)) MPI_Abort(comm, 1);
/* Call CVSpgmr to specify the linear solver CVSPGMR
with left preconditioning and the maximum Krylov dimension maxl */
flag = CVSpgmr(cvode_mem, PREC_LEFT, 0);
if (check_flag(&flag, "CVSpgmr", 1, my_pe)) MPI_Abort(comm, 1);
/* Set preconditioner setup and solve routines Precond and PSolve,
and the pointer to the user-defined block data */
flag = CVSpilsSetPreconditioner(cvode_mem, Precond, PSolve, predata);
if (check_flag(&flag, "CVSpilsSetPreconditioner", 1, my_pe)) MPI_Abort(comm, 1);
if (my_pe == 0)
printf("\n2-species diurnal advection-diffusion problem\n\n");
/* In loop over output points, call CVode, print results, test for error */
for (iout=1, tout = TWOHR; iout <= NOUT; iout++, tout += TWOHR) {
flag = CVode(cvode_mem, tout, u, &t, CV_NORMAL);
if (check_flag(&flag, "CVode", 1, my_pe)) break;
PrintOutput(cvode_mem, my_pe, comm, u, t);
}
/* Print final statistics */
if (my_pe == 0) PrintFinalStats(cvode_mem);
/* Free memory */
N_VDestroy_Parallel(u);
free(data);
FreePreconData(predata);
CVodeFree(&cvode_mem);
MPI_Finalize();
return(0);
}
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);
}
int main(int argc, char *argv[])
{
MPI_Comm comm;
void *mem;
UserData data;
int thispe, iout, ier, npes;
long int Neq, local_N, mudq, mldq, mukeep, mlkeep;
realtype rtol, atol, t0, t1, tout, tret;
N_Vector uu, up, constraints, id, res;
mem = NULL;
data = NULL;
uu = up = constraints = id = res = NULL;
/* Get processor number and total number of pe's. */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_size(comm, &npes);
MPI_Comm_rank(comm, &thispe);
if (npes != NPEX*NPEY) {
if (thispe == 0)
fprintf(stderr,
"\nMPI_ERROR(0): npes = %d is not equal to NPEX*NPEY = %d\n",
npes,NPEX*NPEY);
MPI_Finalize();
return(1);
}
/* Set local length local_N and global length Neq. */
local_N = MXSUB*MYSUB;
Neq = MX * MY;
/* Allocate N-vectors. */
uu = N_VNew_Parallel(comm, local_N, Neq);
if(check_flag((void *)uu, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
up = N_VNew_Parallel(comm, local_N, Neq);
if(check_flag((void *)up, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
res = N_VNew_Parallel(comm, local_N, Neq);
if(check_flag((void *)res, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
constraints = N_VNew_Parallel(comm, local_N, Neq);
if(check_flag((void *)constraints, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
id = N_VNew_Parallel(comm, local_N, Neq);
if(check_flag((void *)id, "N_VNew_Parallel", 0, thispe)) MPI_Abort(comm, 1);
/* Allocate and initialize the data structure. */
data = (UserData) malloc(sizeof *data);
if(check_flag((void *)data, "malloc", 2, thispe)) MPI_Abort(comm, 1);
InitUserData(thispe, comm, data);
/* Initialize the uu, up, id, and constraints profiles. */
SetInitialProfile(uu, up, id, res, data);
N_VConst(ONE, constraints);
t0 = ZERO; t1 = RCONST(0.01);
/* Scalar relative and absolute tolerance. */
rtol = ZERO;
atol = RCONST(1.0e-3);
/* Call IDACreate and IDAMalloc to initialize solution */
mem = IDACreate();
if(check_flag((void *)mem, "IDACreate", 0, thispe)) MPI_Abort(comm, 1);
ier = IDASetUserData(mem, data);
if(check_flag(&ier, "IDASetUserData", 1, thispe)) MPI_Abort(comm, 1);
ier = IDASetSuppressAlg(mem, TRUE);
if(check_flag(&ier, "IDASetSuppressAlg", 1, thispe)) MPI_Abort(comm, 1);
ier = IDASetId(mem, id);
if(check_flag(&ier, "IDASetId", 1, thispe)) MPI_Abort(comm, 1);
ier = IDASetConstraints(mem, constraints);
if(check_flag(&ier, "IDASetConstraints", 1, thispe)) MPI_Abort(comm, 1);
N_VDestroy_Parallel(constraints);
ier = IDAInit(mem, heatres, t0, uu, up);
if(check_flag(&ier, "IDAInit", 1, thispe)) MPI_Abort(comm, 1);
ier = IDASStolerances(mem, rtol, atol);
if(check_flag(&ier, "IDASStolerances", 1, thispe)) MPI_Abort(comm, 1);
mudq = MXSUB;
mldq = MXSUB;
mukeep = 1;
mlkeep = 1;
/* Print problem description */
if (thispe == 0 ) PrintHeader(Neq, rtol, atol);
/*
* -----------------------------
* Case 1 -- mldq = mudq = MXSUB
* -----------------------------
*/
/* Call IDASpgmr to specify the linear solver. */
ier = IDASpgmr(mem, 0);
if(check_flag(&ier, "IDASpgmr", 1, thispe)) MPI_Abort(comm, 1);
/* Call IDABBDPrecInit to initialize BBD preconditioner. */
ier = IDABBDPrecInit(mem, local_N, mudq, mldq, mukeep, mlkeep,
ZERO, reslocal, NULL);
if(check_flag(&ier, "IDABBDPrecAlloc", 1, thispe)) MPI_Abort(comm, 1);
/* Print output heading (on processor 0 only) and initial solution. */
if (thispe == 0) PrintCase(1, mudq, mukeep);
/* Loop over tout, call IDASolve, print output. */
for (tout = t1, iout = 1; iout <= NOUT; iout++, tout *= TWO) {
ier = IDASolve(mem, tout, &tret, uu, up, IDA_NORMAL);
if(check_flag(&ier, "IDASolve", 1, thispe)) MPI_Abort(comm, 1);
PrintOutput(thispe, mem, tret, uu);
}
/* Print final statistics */
if (thispe == 0) PrintFinalStats(mem);
/*
* -----------------------------
* Case 2 -- mldq = mudq = 1
* -----------------------------
*/
mudq = 1;
mldq = 1;
/* Re-initialize the uu and up profiles. */
SetInitialProfile(uu, up, id, res, data);
/* Call IDAReInit to re-initialize IDA. */
ier = IDAReInit(mem, t0, uu, up);
if(check_flag(&ier, "IDAReInit", 1, thispe)) MPI_Abort(comm, 1);
/* Call IDABBDPrecReInit to re-initialize BBD preconditioner. */
ier = IDABBDPrecReInit(mem, mudq, mldq, ZERO);
if(check_flag(&ier, "IDABBDPrecReInit", 1, thispe)) MPI_Abort(comm, 1);
/* Print output heading (on processor 0 only). */
if (thispe == 0) PrintCase(2, mudq, mukeep);
/* Loop over tout, call IDASolve, print output. */
for (tout = t1, iout = 1; iout <= NOUT; iout++, tout *= TWO) {
ier = IDASolve(mem, tout, &tret, uu, up, IDA_NORMAL);
if(check_flag(&ier, "IDASolve", 1, thispe)) MPI_Abort(comm, 1);
PrintOutput(thispe, mem, tret, uu);
}
/* Print final statistics */
if (thispe == 0) PrintFinalStats(mem);
/* Free Memory */
IDAFree(&mem);
free(data);
N_VDestroy_Parallel(id);
N_VDestroy_Parallel(res);
N_VDestroy_Parallel(up);
N_VDestroy_Parallel(uu);
MPI_Finalize();
return(0);
}
int main(int argc, char *argv[])
{
UserData data;
void *cvode_mem;
N_Vector u;
realtype reltol, abstol;
int indexB;
N_Vector uB;
realtype dx, t, g_val;
int retval, my_pe, nprocs, npes, ncheck;
sunindextype local_N=0, nperpe, nrem, my_base=-1;
SUNNonlinearSolver NLS, NLSB;
MPI_Comm comm;
data = NULL;
cvode_mem = NULL;
u = uB = NULL;
/*------------------------------------------------------
Initialize MPI and get total number of pe's, and my_pe
------------------------------------------------------*/
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_size(comm, &nprocs);
MPI_Comm_rank(comm, &my_pe);
npes = nprocs - 1; /* pe's dedicated to PDE integration */
if ( npes <= 0 ) {
if (my_pe == npes)
fprintf(stderr, "\nMPI_ERROR(%d): number of processes must be >= 2\n\n",
my_pe);
MPI_Finalize();
return(1);
}
/*-----------------------
Set local vector length
-----------------------*/
nperpe = NEQ/npes;
nrem = NEQ - npes*nperpe;
if (my_pe < npes) {
/* PDE vars. distributed to this proccess */
local_N = (my_pe < nrem) ? nperpe+1 : nperpe;
my_base = (my_pe < nrem) ? my_pe*local_N : my_pe*nperpe + nrem;
} else {
/* Make last process inactive for forward phase */
local_N = 0;
}
/*-------------------------------------
Allocate and load user data structure
-------------------------------------*/
data = (UserData) malloc(sizeof *data);
if (check_retval((void *)data , "malloc", 2, my_pe)) MPI_Abort(comm, 1);
data->p[0] = ONE;
data->p[1] = RCONST(0.5);
dx = data->dx = XMAX/((realtype)(MX+1));
data->hdcoef = data->p[0]/(dx*dx);
data->hacoef = data->p[1]/(TWO*dx);
data->comm = comm;
data->npes = npes;
data->my_pe = my_pe;
data->nperpe = nperpe;
data->nrem = nrem;
data->local_N = local_N;
/*-------------------------
Forward integration phase
-------------------------*/
/* Set relative and absolute tolerances for forward phase */
reltol = ZERO;
abstol = ATOL;
/* Allocate and initialize forward variables */
u = N_VNew_Parallel(comm, local_N, NEQ);
if (check_retval((void *)u, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
SetIC(u, dx, local_N, my_base);
/* Allocate CVODES memory for forward integration */
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);
retval = CVodeInit(cvode_mem, f, T0, u);
if (check_retval(&retval, "CVodeInit", 1, my_pe)) MPI_Abort(comm, 1);
retval = CVodeSStolerances(cvode_mem, reltol, abstol);
if (check_retval(&retval, "CVodeSStolerances", 1, my_pe)) MPI_Abort(comm, 1);
/* create fixed point nonlinear solver object */
NLS = SUNNonlinSol_FixedPoint(u, 0);
if(check_retval((void *)NLS, "SUNNonlinSol_FixedPoint", 0, my_pe)) MPI_Abort(comm, 1);
/* attach nonlinear solver object to CVode */
retval = CVodeSetNonlinearSolver(cvode_mem, NLS);
if(check_retval(&retval, "CVodeSetNonlinearSolver", 1, my_pe)) MPI_Abort(comm, 1);
/* Allocate combined forward/backward memory */
retval = CVodeAdjInit(cvode_mem, STEPS, CV_HERMITE);
if (check_retval(&retval, "CVadjInit", 1, my_pe)) MPI_Abort(comm, 1);
/* Integrate to TOUT and collect check point information */
retval = CVodeF(cvode_mem, TOUT, u, &t, CV_NORMAL, &ncheck);
if (check_retval(&retval, "CVodeF", 1, my_pe)) MPI_Abort(comm, 1);
/*---------------------------
Compute and value of g(t_f)
---------------------------*/
g_val = Compute_g(u, data);
/*--------------------------
Backward integration phase
--------------------------*/
if (my_pe == npes) {
/* Activate last process for integration of the quadrature equations */
local_N = NP;
} else {
/* Allocate work space */
data->z1 = (realtype *)malloc(local_N*sizeof(realtype));
if (check_retval((void *)data->z1, "malloc", 2, my_pe)) MPI_Abort(comm, 1);
data->z2 = (realtype *)malloc(local_N*sizeof(realtype));
if (check_retval((void *)data->z2, "malloc", 2, my_pe)) MPI_Abort(comm, 1);
}
/* Allocate and initialize backward variables */
uB = N_VNew_Parallel(comm, local_N, NEQ+NP);
if (check_retval((void *)uB, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
SetICback(uB, my_base);
/* Allocate CVODES memory for the backward integration */
retval = CVodeCreateB(cvode_mem, CV_ADAMS, &indexB);
if (check_retval(&retval, "CVodeCreateB", 1, my_pe)) MPI_Abort(comm, 1);
retval = CVodeSetUserDataB(cvode_mem, indexB, data);
if (check_retval(&retval, "CVodeSetUserDataB", 1, my_pe)) MPI_Abort(comm, 1);
retval = CVodeInitB(cvode_mem, indexB, fB, TOUT, uB);
if (check_retval(&retval, "CVodeInitB", 1, my_pe)) MPI_Abort(comm, 1);
retval = CVodeSStolerancesB(cvode_mem, indexB, reltol, abstol);
if (check_retval(&retval, "CVodeSStolerancesB", 1, my_pe)) MPI_Abort(comm, 1);
/* create fixed point nonlinear solver object */
NLSB = SUNNonlinSol_FixedPoint(uB, 0);
if(check_retval((void *)NLSB, "SUNNonlinSol_FixedPoint", 0, my_pe)) MPI_Abort(comm, 1);
/* attach nonlinear solver object to CVode */
retval = CVodeSetNonlinearSolverB(cvode_mem, indexB, NLSB);
if(check_retval(&retval, "CVodeSetNonlinearSolver", 1, my_pe)) MPI_Abort(comm, 1);
/* Integrate to T0 */
retval = CVodeB(cvode_mem, T0, CV_NORMAL);
if (check_retval(&retval, "CVodeB", 1, my_pe)) MPI_Abort(comm, 1);
retval = CVodeGetB(cvode_mem, indexB, &t, uB);
if (check_retval(&retval, "CVodeGetB", 1, my_pe)) MPI_Abort(comm, 1);
/* Print results (adjoint states and quadrature variables) */
PrintOutput(g_val, uB, data);
/* Free memory */
N_VDestroy_Parallel(u);
N_VDestroy_Parallel(uB);
CVodeFree(&cvode_mem);
SUNNonlinSolFree(NLS);
SUNNonlinSolFree(NLSB);
if (my_pe != npes) {
free(data->z1);
free(data->z2);
}
free(data);
MPI_Finalize();
return(0);
}
