Date: 2022-08-02T03:15:17+00:00

Actual source code: flow.c

      2: static char help[] = "FUN3D - 3-D, Unstructured Incompressible Euler Solver.\n\
      3: originally written by W. K. Anderson of NASA Langley, \n\
      4: and ported into PETSc by D. K. Kaushik, ODU and ICASE.\n\n";

      6: #include <petscsnes.h>
      7: #include <petsctime.h>
      8: #include <petscao.h>
      9: #include "user.h"
     10: #if defined(_OPENMP)
     11: #include "omp.h"
     12: #if !defined(HAVE_REDUNDANT_WORK)
     13: #include "metis.h"
     14: #endif
     15: #endif

     17: #define ICALLOC(size,y) PetscMalloc1(PetscMax(size,1),y);
     18: #define FCALLOC(size,y) PetscMalloc1(PetscMax(size,1),y);

     20: typedef struct {
     21:   Vec    qnew,qold,func;
     22:   double fnorm_ini,dt_ini,cfl_ini;
     23:   double ptime;
     24:   double cfl_max,max_time;
     25:   double fnorm,dt,cfl;
     26:   double fnorm_ratio;
     27:   int    ires,iramp,itstep;
     28:   int    max_steps,print_freq;
     29:   int    LocalTimeStepping;
     30: } TstepCtx;

     32: typedef struct {                               /*============================*/
     33:   GRID      *grid;                                 /* Pointer to Grid info       */
     34:   TstepCtx  *tsCtx;                                /* Pointer to Time Stepping Context */
     35:   PetscBool PreLoading;
     36: } AppCtx;                                      /*============================*/

     38: extern int  FormJacobian(SNES,Vec,Mat,Mat,void*),
     39:             FormFunction(SNES,Vec,Vec,void*),
     40:             FormInitialGuess(SNES,GRID*),
     41:             Update(SNES,void*),
     42:             ComputeTimeStep(SNES,int,void*),
     43:             GetLocalOrdering(GRID*),
     44:             SetPetscDS(GRID *,TstepCtx*);
     45: static PetscErrorCode WritePVTU(AppCtx*,const char*,PetscBool);
     46: #if defined(_OPENMP) && defined(HAVE_EDGE_COLORING)
     47: int EdgeColoring(int nnodes,int nedge,int *e2n,int *eperm,int *ncolor,int *ncount);
     48: #endif
     49: /* Global Variables */

     51:                                                /*============================*/
     52: CINFO  *c_info;                                /* Pointer to COMMON INFO     */
     53: CRUNGE *c_runge;                               /* Pointer to COMMON RUNGE    */
     54: CGMCOM *c_gmcom;                               /* Pointer to COMMON GMCOM    */
     55:                                                /*============================*/
     56: int  rank,size,rstart;
     57: REAL memSize = 0.0,grad_time = 0.0;
     58: #if defined(_OPENMP)
     59: int max_threads = 2,tot_threads,my_thread_id;
     60: #endif

     62: #if defined(PARCH_IRIX64) && defined(USE_HW_COUNTERS)
     63: int       event0,event1;
     64: Scalar    time_counters;
     65: long long counter0,counter1;
     66: #endif
     67: int  ntran[max_nbtran];        /* transition stuff put here to make global */
     68: REAL dxtran[max_nbtran];

     70: /* ======================== MAIN ROUTINE =================================== */
     71: /*                                                                           */
     72: /* Finite volume flux split solver for general polygons                      */
     73: /*                                                                           */
     74: /*===========================================================================*/

     76: int main(int argc,char **args)
     77: {
     78:   AppCtx      user;
     79:   GRID        f_pntr;
     80:   TstepCtx    tsCtx;
     81:   SNES        snes;                    /* nonlinear solver context */
     82:   Mat         Jpc;                     /* Jacobian and Preconditioner matrices */
     83:   PetscScalar *qnode;
     84:   int         ierr;
     85:   PetscBool   flg,write_pvtu,pvtu_base64;
     86:   MPI_Comm    comm;
     87:   PetscInt    maxfails                       = 10000;
     88:   char        pvtu_fname[PETSC_MAX_PATH_LEN] = "incomp";

     90:   PetscInitialize(&argc,&args,NULL,help);
     91:   PetscInitializeFortran();
     92:   PetscOptionsInsertFile(PETSC_COMM_WORLD,"petsc.opt",PETSC_FALSE);

     94:   comm = PETSC_COMM_WORLD;
     95:   f77FORLINK();                               /* Link FORTRAN and C COMMONS */

     97:   MPI_Comm_rank(comm,&rank);
     98:   MPI_Comm_size(comm,&size);

    100:   flg  = PETSC_FALSE;
    101:   PetscOptionsGetBool(NULL,NULL,"-mem_use",&flg,NULL);
    102:   if (flg) PetscMemorySetGetMaximumUsage();

    104:   /*======================================================================*/
    105:   /* Initilize stuff related to time stepping */
    106:   /*======================================================================*/
    107:   tsCtx.fnorm_ini         = 0.0;  tsCtx.cfl_ini     = 50.0;    tsCtx.cfl_max = 1.0e+05;
    108:   tsCtx.max_steps         = 50;   tsCtx.max_time    = 1.0e+12; tsCtx.iramp   = -50;
    109:   tsCtx.dt                = -5.0; tsCtx.fnorm_ratio = 1.0e+10;
    110:   tsCtx.LocalTimeStepping = 1;
    111:   PetscOptionsGetInt(NULL,NULL,"-max_st",&tsCtx.max_steps,NULL);
    112:   PetscOptionsGetReal(NULL,"-ts_rtol",&tsCtx.fnorm_ratio,NULL);
    113:   PetscOptionsGetReal(NULL,"-cfl_ini",&tsCtx.cfl_ini,NULL);
    114:   PetscOptionsGetReal(NULL,"-cfl_max",&tsCtx.cfl_max,NULL);
    115:   tsCtx.print_freq        = tsCtx.max_steps;
    116:   PetscOptionsGetInt(NULL,NULL,"-print_freq",&tsCtx.print_freq,&flg);
    117:   PetscOptionsGetString(NULL,NULL,"-pvtu",pvtu_fname,sizeof(pvtu_fname),&write_pvtu);
    118:   pvtu_base64             = PETSC_FALSE;
    119:   PetscOptionsGetBool(NULL,NULL,"-pvtu_base64",&pvtu_base64,NULL);

    121:   c_info->alpha = 3.0;
    122:   c_info->beta  = 15.0;
    123:   c_info->ivisc = 0;

    125:   c_gmcom->ilu0  = 1;
    126:   c_gmcom->nsrch = 10;

    128:   c_runge->nitfo = 0;

    130:   PetscMemzero(&f_pntr,sizeof(f_pntr));
    131:   f_pntr.jvisc  = c_info->ivisc;
    132:   f_pntr.ileast = 4;
    133:   PetscOptionsGetReal(NULL,"-alpha",&c_info->alpha,NULL);
    134:   PetscOptionsGetReal(NULL,"-beta",&c_info->beta,NULL);

    136:   /*======================================================================*/

    138:   /*Set the maximum number of threads for OpenMP */
    139: #if defined(_OPENMP)
    140:   PetscOptionsGetInt(NULL,NULL,"-max_threads",&max_threads,&flg);
    141:   omp_set_num_threads(max_threads);
    142:   PetscPrintf(comm,"Using %d threads for each MPI process\n",max_threads);
    143: #endif

    145:   /* Get the grid information into local ordering */
    146:   GetLocalOrdering(&f_pntr);

    148:   /* Allocate Memory for Some Other Grid Arrays */
    149:   set_up_grid(&f_pntr);

    151:   /* If using least squares for the gradients,calculate the r's */
    152:   if (f_pntr.ileast == 4) f77SUMGS(&f_pntr.nnodesLoc,&f_pntr.nedgeLoc,f_pntr.eptr,f_pntr.xyz,f_pntr.rxy,&rank,&f_pntr.nvertices);

    154:   user.grid  = &f_pntr;
    155:   user.tsCtx = &tsCtx;

    157:   /* SAWs Stuff */

    159:   /*
    160:     Preload the executable to get accurate timings. This runs the following chunk of
    161:     code twice, first to get the executable pages into memory and the second time for
    162:     accurate timings.
    163:   */
    164:   PetscPreLoadBegin(PETSC_TRUE,"Time integration");
    165:   user.PreLoading = PetscPreLoading;

    167:   /* Create nonlinear solver */
    168:   SetPetscDS(&f_pntr,&tsCtx);
    169:   SNESCreate(comm,&snes);
    170:   SNESSetType(snes,"newtonls");

    172:   /* Set various routines and options */
    173:   SNESSetFunction(snes,user.grid->res,FormFunction,&user);
    174:   flg  = PETSC_FALSE;
    175:   PetscOptionsGetBool(NULL,NULL,"-matrix_free",&flg,NULL);
    176:   if (flg) {
    177:     /* Use matrix-free to define Newton system; use explicit (approx) Jacobian for preconditioner */
    178:     MatCreateSNESMF(snes,&Jpc);
    179:     SNESSetJacobian(snes,Jpc,user.grid->A,FormJacobian,&user);
    180:   } else {
    181:     /* Use explicit (approx) Jacobian to define Newton system and preconditioner */
    182:     SNESSetJacobian(snes,user.grid->A,user.grid->A,FormJacobian,&user);
    183:   }

    185:   SNESSetMaxLinearSolveFailures(snes,maxfails);
    186:   SNESSetFromOptions(snes);

    188:   /* Initialize the flowfield */
    189:   FormInitialGuess(snes,user.grid);

    191:   /* Solve nonlinear system */
    192:   Update(snes,&user);

    194:   /* Write restart file */
    195:   VecGetArray(user.grid->qnode,&qnode);
    196:   /*f77WREST(&user.grid->nnodes,qnode,user.grid->turbre,user.grid->amut);*/

    198:   /* Write Tecplot solution file */
    199: #if 0
    200:   if (rank == 0)
    201:     f77TECFLO(&user.grid->nnodes,
    202:               &user.grid->nnbound,&user.grid->nvbound,&user.grid->nfbound,
    203:               &user.grid->nnfacet,&user.grid->nvfacet,&user.grid->nffacet,
    204:               &user.grid->nsnode, &user.grid->nvnode, &user.grid->nfnode,
    205:               c_info->title,
    206:               user.grid->x,       user.grid->y,       user.grid->z,
    207:               qnode,
    208:               user.grid->nnpts,   user.grid->nntet,   user.grid->nvpts,
    209:               user.grid->nvtet,   user.grid->nfpts,   user.grid->nftet,
    210:               user.grid->f2ntn,   user.grid->f2ntv,   user.grid->f2ntf,
    211:               user.grid->isnode,  user.grid->ivnode,  user.grid->ifnode,
    212:               &rank);
    213: #endif
    214:   if (write_pvtu) WritePVTU(&user,pvtu_fname,pvtu_base64);

    216:   /* Write residual,lift,drag,and moment history file */
    217:   /*
    218:     if (rank == 0) f77PLLAN(&user.grid->nnodes,&rank);
    219:   */

    221:   VecRestoreArray(user.grid->qnode,&qnode);
    222:   flg  = PETSC_FALSE;
    223:   PetscOptionsGetBool(NULL,NULL,"-mem_use",&flg,NULL);
    224:   if (flg) {
    225:     PetscMemoryView(PETSC_VIEWER_STDOUT_WORLD,"Memory usage before destroying\n");
    226:   }

    228:   VecDestroy(&user.grid->qnode);
    229:   VecDestroy(&user.grid->qnodeLoc);
    230:   VecDestroy(&user.tsCtx->qold);
    231:   VecDestroy(&user.tsCtx->func);
    232:   VecDestroy(&user.grid->res);
    233:   VecDestroy(&user.grid->grad);
    234:   VecDestroy(&user.grid->gradLoc);
    235:   MatDestroy(&user.grid->A);
    236:   flg  = PETSC_FALSE;
    237:   PetscOptionsGetBool(NULL,NULL,"-matrix_free",&flg,NULL);
    238:   if (flg) MatDestroy(&Jpc);
    239:   SNESDestroy(&snes);
    240:   VecScatterDestroy(&user.grid->scatter);
    241:   VecScatterDestroy(&user.grid->gradScatter);
    242:   flg  = PETSC_FALSE;
    243:   PetscOptionsGetBool(NULL,NULL,"-mem_use",&flg,NULL);
    244:   if (flg) {
    245:     PetscMemoryView(PETSC_VIEWER_STDOUT_WORLD,"Memory usage after destroying\n");
    246:   }
    247:   PetscPreLoadEnd();

    249:   /* allocated in set_up_grid() */
    250:   PetscFree(user.grid->isface);
    251:   PetscFree(user.grid->ivface);
    252:   PetscFree(user.grid->ifface);
    253:   PetscFree(user.grid->us);
    254:   PetscFree(user.grid->vs);
    255:   PetscFree(user.grid->as);

    257:   /* Allocated in GetLocalOrdering() */
    258:   PetscFree(user.grid->eptr);
    259:   PetscFree(user.grid->ia);
    260:   PetscFree(user.grid->ja);
    261:   PetscFree(user.grid->loc2glo);
    262:   PetscFree(user.grid->loc2pet);
    263:   PetscFree(user.grid->xyzn);
    264: #if defined(_OPENMP)
    265: #  if defined(HAVE_REDUNDANT_WORK)
    266:   PetscFree(user.grid->resd);
    267: #  else
    268:   PetscFree(user.grid->part_thr);
    269:   PetscFree(user.grid->nedge_thr);
    270:   PetscFree(user.grid->edge_thr);
    271:   PetscFree(user.grid->xyzn_thr);
    272: #  endif
    273: #endif
    274:   PetscFree(user.grid->xyz);
    275:   PetscFree(user.grid->area);

    277:   PetscFree(user.grid->nntet);
    278:   PetscFree(user.grid->nnpts);
    279:   PetscFree(user.grid->f2ntn);
    280:   PetscFree(user.grid->isnode);
    281:   PetscFree(user.grid->sxn);
    282:   PetscFree(user.grid->syn);
    283:   PetscFree(user.grid->szn);
    284:   PetscFree(user.grid->sa);
    285:   PetscFree(user.grid->sface_bit);

    287:   PetscFree(user.grid->nvtet);
    288:   PetscFree(user.grid->nvpts);
    289:   PetscFree(user.grid->f2ntv);
    290:   PetscFree(user.grid->ivnode);
    291:   PetscFree(user.grid->vxn);
    292:   PetscFree(user.grid->vyn);
    293:   PetscFree(user.grid->vzn);
    294:   PetscFree(user.grid->va);
    295:   PetscFree(user.grid->vface_bit);

    297:   PetscFree(user.grid->nftet);
    298:   PetscFree(user.grid->nfpts);
    299:   PetscFree(user.grid->f2ntf);
    300:   PetscFree(user.grid->ifnode);
    301:   PetscFree(user.grid->fxn);
    302:   PetscFree(user.grid->fyn);
    303:   PetscFree(user.grid->fzn);
    304:   PetscFree(user.grid->fa);
    305:   PetscFree(user.grid->cdt);
    306:   PetscFree(user.grid->phi);
    307:   PetscFree(user.grid->rxy);

    309:   PetscPrintf(comm,"Time taken in gradient calculation %g sec.\n",grad_time);

    311:   PetscFinalize();
    312:   return 0;
    313: }

    315: /*---------------------------------------------------------------------*/
    316: /* ---------------------  Form initial approximation ----------------- */
    317: int FormInitialGuess(SNES snes,GRID *grid)
    318: /*---------------------------------------------------------------------*/
    319: {
    320:   int         ierr;
    321:   PetscScalar *qnode;

    323:   VecGetArray(grid->qnode,&qnode);
    324:   f77INIT(&grid->nnodesLoc,qnode,grid->turbre,grid->amut,&grid->nvnodeLoc,grid->ivnode,&rank);
    325:   VecRestoreArray(grid->qnode,&qnode);
    326:   return 0;
    327: }

    329: /*---------------------------------------------------------------------*/
    330: /* ---------------------  Evaluate Function F(x) --------------------- */
    331: int FormFunction(SNES snes,Vec x,Vec f,void *dummy)
    332: /*---------------------------------------------------------------------*/
    333: {
    334:   AppCtx      *user  = (AppCtx*) dummy;
    335:   GRID        *grid  = user->grid;
    336:   TstepCtx    *tsCtx = user->tsCtx;
    337:   PetscScalar *qnode,*res,*qold;
    338:   PetscScalar *grad;
    339:   PetscScalar temp;
    340:   VecScatter  scatter     = grid->scatter;
    341:   VecScatter  gradScatter = grid->gradScatter;
    342:   Vec         localX      = grid->qnodeLoc;
    343:   Vec         localGrad   = grid->gradLoc;
    344:   int         i,j,in,ierr;
    345:   int         nbface,ires;
    346:   PetscScalar time_ini,time_fin;

    348:   /* Get X into the local work vector */
    349:   VecScatterBegin(scatter,x,localX,INSERT_VALUES,SCATTER_FORWARD);
    350:   VecScatterEnd(scatter,x,localX,INSERT_VALUES,SCATTER_FORWARD);
    351:   /* VecCopy(x,localX); */
    352:   /* access the local work f,grad,and input */
    353:   VecGetArray(f,&res);
    354:   VecGetArray(grid->grad,&grad);
    355:   VecGetArray(localX,&qnode);
    356:   ires = tsCtx->ires;

    358:   PetscTime(&time_ini);
    359:   f77LSTGS(&grid->nnodesLoc,&grid->nedgeLoc,grid->eptr,qnode,grad,grid->xyz,grid->rxy,
    360:            &rank,&grid->nvertices);
    361:   PetscTime(&time_fin);
    362:   grad_time += time_fin - time_ini;
    363:   VecRestoreArray(grid->grad,&grad);

    365:   VecScatterBegin(gradScatter,grid->grad,localGrad,INSERT_VALUES,SCATTER_FORWARD);
    366:   VecScatterEnd(gradScatter,grid->grad,localGrad,INSERT_VALUES,SCATTER_FORWARD);
    367:   /*VecCopy(grid->grad,localGrad);*/

    369:   VecGetArray(localGrad,&grad);
    370:   nbface = grid->nsface + grid->nvface + grid->nfface;
    371:   f77GETRES(&grid->nnodesLoc,&grid->ncell,  &grid->nedgeLoc,  &grid->nsface,
    372:             &grid->nvface,&grid->nfface, &nbface,
    373:             &grid->nsnodeLoc,&grid->nvnodeLoc, &grid->nfnodeLoc,
    374:             grid->isface, grid->ivface,  grid->ifface, &grid->ileast,
    375:             grid->isnode, grid->ivnode,  grid->ifnode,
    376:             &grid->nnfacetLoc,grid->f2ntn,  &grid->nnbound,
    377:             &grid->nvfacetLoc,grid->f2ntv,  &grid->nvbound,
    378:             &grid->nffacetLoc,grid->f2ntf,  &grid->nfbound,
    379:             grid->eptr,
    380:             grid->sxn,    grid->syn,     grid->szn,
    381:             grid->vxn,    grid->vyn,     grid->vzn,
    382:             grid->fxn,    grid->fyn,     grid->fzn,
    383:             grid->xyzn,
    384:             qnode,        grid->cdt,
    385:             grid->xyz,    grid->area,
    386:             grad, res,
    387:             grid->turbre,
    388:             grid->slen,   grid->c2n,
    389:             grid->c2e,
    390:             grid->us,     grid->vs,      grid->as,
    391:             grid->phi,
    392:             grid->amut,   &ires,
    393: #if defined(_OPENMP)
    394:             &max_threads,
    395: #if defined(HAVE_EDGE_COLORING)
    396:             &grid->ncolor, grid->ncount,
    397: #elif defined(HAVE_REDUNDANT_WORK)
    398:             grid->resd,
    399: #else
    400:             &grid->nedgeAllThr,
    401:             grid->part_thr,grid->nedge_thr,grid->edge_thr,grid->xyzn_thr,
    402: #endif
    403: #endif
    404:             &tsCtx->LocalTimeStepping,&rank,&grid->nvertices);

    406: /* Add the contribution due to time stepping */
    407:   if (ires == 1) {
    408:     VecGetArray(tsCtx->qold,&qold);
    409: #if defined(INTERLACING)
    410:     for (i = 0; i < grid->nnodesLoc; i++) {
    411:       temp = grid->area[i]/(tsCtx->cfl*grid->cdt[i]);
    412:       for (j = 0; j < 4; j++) {
    413:         in       = 4*i + j;
    414:         res[in] += temp*(qnode[in] - qold[in]);
    415:       }
    416:     }
    417: #else
    418:     for (j = 0; j < 4; j++) {
    419:       for (i = 0; i < grid->nnodesLoc; i++) {
    420:         temp     = grid->area[i]/(tsCtx->cfl*grid->cdt[i]);
    421:         in       = grid->nnodesLoc*j + i;
    422:         res[in] += temp*(qnode[in] - qold[in]);
    423:       }
    424:     }
    425: #endif
    426:     VecRestoreArray(tsCtx->qold,&qold);
    427:   }
    428:   VecRestoreArray(localX,&qnode);
    429:   VecRestoreArray(f,&res);
    430:   VecRestoreArray(localGrad,&grad);
    431:   return 0;
    432: }

    434: /*---------------------------------------------------------------------*/
    435: /* --------------------  Evaluate Jacobian F'(x) -------------------- */

    437: int FormJacobian(SNES snes,Vec x,Mat Jac,Mat pc_mat,void *dummy)
    438: /*---------------------------------------------------------------------*/
    439: {
    440:   AppCtx      *user  = (AppCtx*) dummy;
    441:   GRID        *grid  = user->grid;
    442:   TstepCtx    *tsCtx = user->tsCtx;
    443:   Vec         localX = grid->qnodeLoc;
    444:   PetscScalar *qnode;
    445:   int         ierr;

    447:   /*  VecScatterBegin(scatter,x,localX,INSERT_VALUES,SCATTER_FORWARD);
    448:       VecScatterEnd(scatter,x,localX,INSERT_VALUES,SCATTER_FORWARD); */
    449:   /* VecCopy(x,localX); */
    450:   MatSetUnfactored(pc_mat);

    452:   VecGetArray(localX,&qnode);
    453:   f77FILLA(&grid->nnodesLoc,&grid->nedgeLoc,grid->eptr,
    454:            &grid->nsface,
    455:             grid->isface,grid->fxn,grid->fyn,grid->fzn,
    456:             grid->sxn,grid->syn,grid->szn,
    457:            &grid->nsnodeLoc,&grid->nvnodeLoc,&grid->nfnodeLoc,grid->isnode,
    458:             grid->ivnode,grid->ifnode,qnode,&pc_mat,grid->cdt,
    459:             grid->area,grid->xyzn,&tsCtx->cfl,
    460:            &rank,&grid->nvertices);
    461:   VecRestoreArray(localX,&qnode);
    462:   MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY);
    463:   MatAssemblyEnd(Jac,MAT_FINAL_ASSEMBLY);
    464: #if defined(MATRIX_VIEW)
    465:   if ((tsCtx->itstep != 0) &&(tsCtx->itstep % tsCtx->print_freq) == 0) {
    466:     PetscViewer viewer;
    467:     char mat_file[PETSC_MAX_PATH_LEN];
    468:     sprintf(mat_file,"mat_bin.%d",tsCtx->itstep);
    469:     PetscViewerBinaryOpen(MPI_COMM_WORLD,mat_file,FILE_MODE_WRITE,&viewer);
    470:     MatView(pc_mat,viewer);
    471:     PetscViewerDestroy(&viewer);
    472:   }
    473: #endif
    474:   return 0;
    475: }

    477: /*---------------------------------------------------------------------*/
    478: int Update(SNES snes,void *ctx)
    479: /*---------------------------------------------------------------------*/
    480: {
    481:   AppCtx      *user   = (AppCtx*) ctx;
    482:   GRID        *grid   = user->grid;
    483:   TstepCtx    *tsCtx  = user->tsCtx;
    484:   VecScatter  scatter = grid->scatter;
    485:   Vec         localX  = grid->qnodeLoc;
    486:   PetscScalar *qnode,*res;
    487:   PetscScalar clift,cdrag,cmom;
    488:   int         ierr,its;
    489:   PetscScalar fratio;
    490:   PetscScalar time1,time2,cpuloc,cpuglo;
    491:   int         max_steps;
    492:   PetscBool   print_flag = PETSC_FALSE;
    493:   FILE        *fptr      = 0;
    494:   int         nfailsCum  = 0,nfails = 0;
    495:   /*Scalar         cpu_ini,cpu_fin,cpu_time;*/
    496:   /*int            event0 = 14,event1 = 25,gen_start,gen_read;
    497:   PetscScalar    time_start_counters,time_read_counters;
    498:   long long      counter0,counter1;*/

    500:   PetscOptionsGetBool(NULL,NULL,"-print",&print_flag,NULL);
    501:   if (print_flag) {
    502:     PetscFOpen(PETSC_COMM_WORLD,"history.out","w",&fptr);
    503:     PetscFPrintf(PETSC_COMM_WORLD,fptr,"VARIABLES = iter,cfl,fnorm,clift,cdrag,cmom,cpu\n");
    504:   }
    505:   if (user->PreLoading) max_steps = 1;
    506:   else max_steps = tsCtx->max_steps;
    507:   fratio = 1.0;
    508:   /*tsCtx->ptime = 0.0;*/
    509:   VecCopy(grid->qnode,tsCtx->qold);
    510:   PetscTime(&time1);
    511: #if defined(PARCH_IRIX64) && defined(USE_HW_COUNTERS)
    512:   /* if (!user->PreLoading) {
    513:     PetscBool  flg = PETSC_FALSE;
    514:     PetscOptionsGetInt(NULL,NULL,"-e0",&event0,&flg);
    515:     PetscOptionsGetInt(NULL,NULL,"-e1",&event1,&flg);
    516:     PetscTime(&time_start_counters);
    517:     if ((gen_start = start_counters(event0,event1)) < 0)
    518:     SETERRQ(PETSC_COMM_SELF,1,>"Error in start_counters");
    519:   }*/
    520: #endif
    521:   /*cpu_ini = PetscGetCPUTime();*/
    522:   for (tsCtx->itstep = 0; (tsCtx->itstep < max_steps) &&
    523:         (fratio <= tsCtx->fnorm_ratio); tsCtx->itstep++) {
    524:     ComputeTimeStep(snes,tsCtx->itstep,user);
    525:     /*tsCtx->ptime +=  tsCtx->dt;*/

    527:     SNESSolve(snes,NULL,grid->qnode);
    528:     SNESGetIterationNumber(snes,&its);

    530:     SNESGetNonlinearStepFailures(snes,&nfails);
    531:     nfailsCum += nfails; nfails = 0;
    533:     if (print_flag) {
    534:       PetscPrintf(PETSC_COMM_WORLD,"At Time Step %d cfl = %g and fnorm = %g\n",
    535:                          tsCtx->itstep,tsCtx->cfl,tsCtx->fnorm);
    536:     }
    537:     VecCopy(grid->qnode,tsCtx->qold);

    539:     c_info->ntt = tsCtx->itstep+1;
    540:     PetscTime(&time2);
    541:     cpuloc      = time2-time1;
    542:     cpuglo      = 0.0;
    543:     MPI_Allreduce(&cpuloc,&cpuglo,1,MPIU_REAL,MPIU_MAX,PETSC_COMM_WORLD);
    544:     c_info->tot = cpuglo;    /* Total CPU time used upto this time step */

    546:     VecScatterBegin(scatter,grid->qnode,localX,INSERT_VALUES,SCATTER_FORWARD);
    547:     VecScatterEnd(scatter,grid->qnode,localX,INSERT_VALUES,SCATTER_FORWARD);
    548:     /* VecCopy(grid->qnode,localX); */

    550:     VecGetArray(grid->res,&res);
    551:     VecGetArray(localX,&qnode);

    553:     f77FORCE(&grid->nnodesLoc,&grid->nedgeLoc,
    554:               grid->isnode, grid->ivnode,
    555:              &grid->nnfacetLoc,grid->f2ntn,&grid->nnbound,
    556:              &grid->nvfacetLoc,grid->f2ntv,&grid->nvbound,
    557:               grid->eptr,   qnode,
    558:               grid->xyz,
    559:               grid->sface_bit,grid->vface_bit,
    560:               &clift,&cdrag,&cmom,&rank,&grid->nvertices);
    561:     if (print_flag) {
    562:       PetscPrintf(PETSC_COMM_WORLD,"%d\t%g\t%g\t%g\t%g\t%g\n",tsCtx->itstep,
    563:                         tsCtx->cfl,tsCtx->fnorm,clift,cdrag,cmom);
    564:       PetscPrintf(PETSC_COMM_WORLD,"Wall clock time needed %g seconds for %d time steps\n",
    565:                         cpuglo,tsCtx->itstep);
    566:       PetscFPrintf(PETSC_COMM_WORLD,fptr,"%d\t%g\t%g\t%g\t%g\t%g\t%g\n",
    567:                           tsCtx->itstep,tsCtx->cfl,tsCtx->fnorm,clift,cdrag,cmom,cpuglo);
    568:     }
    569:     VecRestoreArray(localX,&qnode);
    570:     VecRestoreArray(grid->res,&res);
    571:     fratio = tsCtx->fnorm_ini/tsCtx->fnorm;
    572:     MPI_Barrier(PETSC_COMM_WORLD);

    574:   } /* End of time step loop */

    576: #if defined(PARCH_IRIX64) && defined(USE_HW_COUNTERS)
    577:   if (!user->PreLoading) {
    578:     int  eve0,eve1;
    579:     FILE *cfp0,*cfp1;
    580:     char str[256];
    581:     /* if ((gen_read = read_counters(event0,&counter0,event1,&counter1)) < 0)
    582:     SETERRQ(PETSC_COMM_SELF,1,"Error in read_counter");
    583:     PetscTime(&time_read_counters);
    584:     if (gen_read != gen_start) {
    585:     SETERRQ(PETSC_COMM_SELF,1,"Lost Counters!! Aborting ...");
    586:     }*/
    587:     /*sprintf(str,"counters%d_and_%d",event0,event1);
    588:     cfp0 = fopen(str,"a");*/
    589:     /*print_counters(event0,counter0,event1,counter1);*/
    590:     /*fprintf(cfp0,"%lld %lld %g\n",counter0,counter1,
    591:                   time_counters);
    592:     fclose(cfp0);*/
    593:   }
    594: #endif
    595:   PetscPrintf(PETSC_COMM_WORLD,"Total wall clock time needed %g seconds for %d time steps\n",
    596:                      cpuglo,tsCtx->itstep);
    597:   PetscPrintf(PETSC_COMM_WORLD,"cfl = %g fnorm = %g\n",tsCtx->cfl,tsCtx->fnorm);
    598:   PetscPrintf(PETSC_COMM_WORLD,"clift = %g cdrag = %g cmom = %g\n",clift,cdrag,cmom);

    600:   if (rank == 0 && print_flag) fclose(fptr);
    601:   if (user->PreLoading) {
    602:     tsCtx->fnorm_ini = 0.0;
    603:     PetscPrintf(PETSC_COMM_WORLD,"Preloading done ...\n");
    604:   }
    605:   return 0;
    606: }

    608: /*---------------------------------------------------------------------*/
    609: int ComputeTimeStep(SNES snes,int iter,void *ctx)
    610: /*---------------------------------------------------------------------*/
    611: {
    612:   AppCtx      *user  = (AppCtx*) ctx;
    613:   TstepCtx    *tsCtx = user->tsCtx;
    614:   Vec         func   = tsCtx->func;
    615:   PetscScalar inc    = 1.1;
    616:   PetscScalar newcfl;
    617:   int         ierr;
    618:   /*int       iramp = tsCtx->iramp;*/

    620:   tsCtx->ires = 0;
    621:   FormFunction(snes,tsCtx->qold,func,user);
    622:   tsCtx->ires = 1;
    623:   VecNorm(func,NORM_2,&tsCtx->fnorm);
    624:   /* first time through so compute initial function norm */
    625:   if (tsCtx->fnorm_ini == 0.0) {
    626:     tsCtx->fnorm_ini = tsCtx->fnorm;
    627:     tsCtx->cfl       = tsCtx->cfl_ini;
    628:   } else {
    629:     newcfl     = inc*tsCtx->cfl_ini*tsCtx->fnorm_ini/tsCtx->fnorm;
    630:     tsCtx->cfl = PetscMin(newcfl,tsCtx->cfl_max);
    631:   }

    633:   /* if (iramp < 0) {
    634:    newcfl = inc*tsCtx->cfl_ini*tsCtx->fnorm_ini/tsCtx->fnorm;
    635:   } else {
    636:    if (tsCtx->dt < 0 && iramp > 0)
    637:     if (iter > iramp) newcfl = tsCtx->cfl_max;
    638:     else newcfl = tsCtx->cfl_ini + (tsCtx->cfl_max - tsCtx->cfl_ini)*
    639:                                 (double) iter/(double) iramp;
    640:   }
    641:   tsCtx->cfl = MIN(newcfl,tsCtx->cfl_max);*/
    642:   /*printf("In ComputeTime Step - fnorm is %f\n",tsCtx->fnorm);*/
    643:   /*VecDestroy(&func);*/
    644:   return 0;
    645: }

    647: /*---------------------------------------------------------------------*/
    648: int GetLocalOrdering(GRID *grid)
    649: /*---------------------------------------------------------------------*/
    650: {
    651:   int         ierr,i,j,k,inode,isurf,nte,nb,node1,node2,node3;
    652:   int         nnodes,nedge,nnz,jstart,jend;
    653:   int         nnodesLoc,nvertices,nedgeLoc,nnodesLocEst;
    654:   int         nedgeLocEst,remEdges,readEdges,remNodes,readNodes;
    655:   int         nnfacet,nvfacet,nffacet;
    656:   int         nnfacetLoc,nvfacetLoc,nffacetLoc;
    657:   int         nsnode,nvnode,nfnode;
    658:   int         nsnodeLoc,nvnodeLoc,nfnodeLoc;
    659:   int         nnbound,nvbound,nfbound;
    660:   int         bs = 4;
    661:   int         fdes = 0;
    662:   off_t       currentPos  = 0,newPos = 0;
    663:   int         grid_param  = 13;
    664:   int         cross_edges = 0;
    665:   int         *edge_bit,*pordering;
    666:   int         *l2p,*l2a,*p2l,*a2l,*v2p,*eperm;
    667:   int         *tmp,*tmp1,*tmp2;
    668:   PetscScalar time_ini,time_fin;
    669:   PetscScalar *ftmp,*ftmp1;
    670:   char        mesh_file[PETSC_MAX_PATH_LEN] = "";
    671:   AO          ao;
    672:   FILE        *fptr,*fptr1;
    673:   PetscBool   flg;
    674:   MPI_Comm    comm = PETSC_COMM_WORLD;

    676:   /* Read the integer grid parameters */
    677:   ICALLOC(grid_param,&tmp);
    678:   if (rank == 0) {
    679:     PetscBool exists;
    680:     PetscOptionsGetString(NULL,NULL,"-mesh",mesh_file,sizeof(mesh_file),&flg);
    681:     PetscTestFile(mesh_file,'r',&exists);
    682:     if (!exists) { /* try uns3d.msh as the file name */
    683:       PetscStrcpy(mesh_file,"uns3d.msh");
    684:     }
    685:     PetscBinaryOpen(mesh_file,FILE_MODE_READ,&fdes);
    686:   }
    687:   PetscBinarySynchronizedRead(comm,fdes,tmp,grid_param,PETSC_INT);
    688:   grid->ncell   = tmp[0];
    689:   grid->nnodes  = tmp[1];
    690:   grid->nedge   = tmp[2];
    691:   grid->nnbound = tmp[3];
    692:   grid->nvbound = tmp[4];
    693:   grid->nfbound = tmp[5];
    694:   grid->nnfacet = tmp[6];
    695:   grid->nvfacet = tmp[7];
    696:   grid->nffacet = tmp[8];
    697:   grid->nsnode  = tmp[9];
    698:   grid->nvnode  = tmp[10];
    699:   grid->nfnode  = tmp[11];
    700:   grid->ntte    = tmp[12];
    701:   grid->nsface  = 0;
    702:   grid->nvface  = 0;
    703:   grid->nfface  = 0;
    704:   PetscFree(tmp);
    705:   PetscPrintf(comm,"nnodes = %d,nedge = %d,nnfacet = %d,nsnode = %d,nfnode = %d\n",
    706:                               grid->nnodes,grid->nedge,grid->nnfacet,grid->nsnode,grid->nfnode);

    708:   nnodes  = grid->nnodes;
    709:   nedge   = grid->nedge;
    710:   nnfacet = grid->nnfacet;
    711:   nvfacet = grid->nvfacet;
    712:   nffacet = grid->nffacet;
    713:   nnbound = grid->nnbound;
    714:   nvbound = grid->nvbound;
    715:   nfbound = grid->nfbound;
    716:   nsnode  = grid->nsnode;
    717:   nvnode  = grid->nvnode;
    718:   nfnode  = grid->nfnode;

    720:   /* Read the partitioning vector generated by MeTiS */
    721:   ICALLOC(nnodes,&l2a);
    722:   ICALLOC(nnodes,&v2p);
    723:   ICALLOC(nnodes,&a2l);
    724:   nnodesLoc = 0;

    726:   for (i = 0; i < nnodes; i++) a2l[i] = -1;
    727:   PetscTime(&time_ini);

    729:   if (rank == 0) {
    730:     if (size == 1) {
    731:       PetscMemzero(v2p,nnodes*sizeof(int));
    732:     } else {
    733:       char      spart_file[PETSC_MAX_PATH_LEN],part_file[PETSC_MAX_PATH_LEN];
    734:       PetscBool exists;

    736:       PetscOptionsGetString(NULL,NULL,"-partition",spart_file,sizeof(spart_file),&flg);
    737:       PetscTestFile(spart_file,'r',&exists);
    738:       if (!exists) { /* try appending the number of processors */
    739:         sprintf(part_file,"part_vec.part.%d",size);
    740:         PetscStrcpy(spart_file,part_file);
    741:       }
    742:       fptr = fopen(spart_file,"r");
    744:       for (inode = 0; inode < nnodes; inode++) {
    745:         fscanf(fptr,"%d\n",&node1);
    746:         v2p[inode] = node1;
    747:       }
    748:       fclose(fptr);
    749:     }
    750:   }
    751:   MPI_Bcast(v2p,nnodes,MPI_INT,0,comm);
    752:   for (inode = 0; inode < nnodes; inode++) {
    753:     if (v2p[inode] == rank) {
    754:       l2a[nnodesLoc] = inode;
    755:       a2l[inode]     = nnodesLoc;
    756:       nnodesLoc++;
    757:     }
    758:   }

    760:   PetscTime(&time_fin);
    761:   time_fin -= time_ini;
    762:   PetscPrintf(comm,"Partition Vector read successfully\n");
    763:   PetscPrintf(comm,"Time taken in this phase was %g\n",time_fin);

    765:   MPI_Scan(&nnodesLoc,&rstart,1,MPI_INT,MPI_SUM,comm);
    766:   rstart -= nnodesLoc;
    767:   ICALLOC(nnodesLoc,&pordering);
    768:   for (i=0; i < nnodesLoc; i++) pordering[i] = rstart + i;
    769:   AOCreateBasic(comm,nnodesLoc,l2a,pordering,&ao);
    770:   PetscFree(pordering);

    772:   /* Now count the local number of edges - including edges with
    773:    ghost nodes but edges between ghost nodes are NOT counted */
    774:   nedgeLoc  = 0;
    775:   nvertices = nnodesLoc;
    776:   /* Choose an estimated number of local edges. The choice
    777:    nedgeLocEst = 1000000 looks reasonable as it will read
    778:    the edge and edge normal arrays in 8 MB chunks */
    779:   /*nedgeLocEst = nedge/size;*/
    780:   nedgeLocEst = PetscMin(nedge,1000000);
    781:   remEdges    = nedge;
    782:   ICALLOC(2*nedgeLocEst,&tmp);
    783:   PetscBinarySynchronizedSeek(comm,fdes,0,PETSC_BINARY_SEEK_CUR,&currentPos);
    784:   PetscTime(&time_ini);
    785:   while (remEdges > 0) {
    786:     readEdges = PetscMin(remEdges,nedgeLocEst);
    787:     /*time_ini = PetscTime();*/
    788:     PetscBinarySynchronizedRead(comm,fdes,tmp,readEdges,PETSC_INT);
    789:     PetscBinarySynchronizedSeek(comm,fdes,(nedge-readEdges)*PETSC_BINARY_INT_SIZE,PETSC_BINARY_SEEK_CUR,&newPos);
    790:     PetscBinarySynchronizedRead(comm,fdes,tmp+readEdges,readEdges,PETSC_INT);
    791:     PetscBinarySynchronizedSeek(comm,fdes,-nedge*PETSC_BINARY_INT_SIZE,PETSC_BINARY_SEEK_CUR,&newPos);
    792:     /*time_fin += PetscTime()-time_ini;*/
    793:     for (j = 0; j < readEdges; j++) {
    794:       node1 = tmp[j]-1;
    795:       node2 = tmp[j+readEdges]-1;
    796:       if ((v2p[node1] == rank) || (v2p[node2] == rank)) {
    797:         nedgeLoc++;
    798:         if (a2l[node1] == -1) {
    799:           l2a[nvertices] = node1;
    800:           a2l[node1]     = nvertices;
    801:           nvertices++;
    802:         }
    803:         if (a2l[node2] == -1) {
    804:           l2a[nvertices] = node2;
    805:           a2l[node2]     = nvertices;
    806:           nvertices++;
    807:         }
    808:       }
    809:     }
    810:     remEdges = remEdges - readEdges;
    811:     MPI_Barrier(comm);
    812:   }
    813:   PetscTime(&time_fin);
    814:   time_fin -= time_ini;
    815:   PetscPrintf(comm,"Local edges counted with MPI_Bcast %d\n",nedgeLoc);
    816:   PetscPrintf(comm,"Local vertices counted %d\n",nvertices);
    817:   PetscPrintf(comm,"Time taken in this phase was %g\n",time_fin);

    819:   /* Now store the local edges */
    820:   ICALLOC(2*nedgeLoc,&grid->eptr);
    821:   ICALLOC(nedgeLoc,&edge_bit);
    822:   ICALLOC(nedgeLoc,&eperm);
    823:   i = 0; j = 0; k = 0;
    824:   remEdges   = nedge;
    825:   PetscBinarySynchronizedSeek(comm,fdes,currentPos,PETSC_BINARY_SEEK_SET,&newPos);
    826:   currentPos = newPos;

    828:   PetscTime(&time_ini);
    829:   while (remEdges > 0) {
    830:     readEdges = PetscMin(remEdges,nedgeLocEst);
    831:     PetscBinarySynchronizedRead(comm,fdes,tmp,readEdges,PETSC_INT);
    832:     PetscBinarySynchronizedSeek(comm,fdes,(nedge-readEdges)*PETSC_BINARY_INT_SIZE,PETSC_BINARY_SEEK_CUR,&newPos);
    833:     PetscBinarySynchronizedRead(comm,fdes,tmp+readEdges,readEdges,PETSC_INT);
    834:     PetscBinarySynchronizedSeek(comm,fdes,-nedge*PETSC_BINARY_INT_SIZE,PETSC_BINARY_SEEK_CUR,&newPos);
    835:     for (j = 0; j < readEdges; j++) {
    836:       node1 = tmp[j]-1;
    837:       node2 = tmp[j+readEdges]-1;
    838:       if ((v2p[node1] == rank) || (v2p[node2] == rank)) {
    839:         grid->eptr[k]          = a2l[node1];
    840:         grid->eptr[k+nedgeLoc] = a2l[node2];
    841:         edge_bit[k]            = i; /* Record global file index of the edge */
    842:         eperm[k]               = k;
    843:         k++;
    844:       }
    845:       i++;
    846:     }
    847:     remEdges = remEdges - readEdges;
    848:     MPI_Barrier(comm);
    849:   }
    850:   PetscBinarySynchronizedSeek(comm,fdes,currentPos+2*nedge*PETSC_BINARY_INT_SIZE,PETSC_BINARY_SEEK_SET,&newPos);
    851:   PetscTime(&time_fin);
    852:   time_fin -= time_ini;
    853:   PetscPrintf(comm,"Local edges stored\n");
    854:   PetscPrintf(comm,"Time taken in this phase was %g\n",time_fin);

    856:   PetscFree(tmp);
    857:   ICALLOC(2*nedgeLoc,&tmp);
    858:   PetscMemcpy(tmp,grid->eptr,2*nedgeLoc*sizeof(int));
    859: #if defined(_OPENMP) && defined(HAVE_EDGE_COLORING)
    860:   EdgeColoring(nvertices,nedgeLoc,grid->eptr,eperm,&grid->ncolor,grid->ncount);
    861: #else
    862:   /* Now reorder the edges for better cache locality */
    863:   /*
    864:   tmp[0]=7;tmp[1]=6;tmp[2]=3;tmp[3]=9;tmp[4]=2;tmp[5]=0;
    865:   PetscSortIntWithPermutation(6,tmp,eperm);
    866:   for (i=0; i<6; i++)
    867:    printf("%d %d %d\n",i,tmp[i],eperm[i]);
    868:   */
    869:   flg  = PETSC_FALSE;
    870:   PetscOptionsGetBool(0,"-no_edge_reordering",&flg,NULL);
    871:   if (!flg) {
    872:     PetscSortIntWithPermutation(nedgeLoc,tmp,eperm);
    873:   }
    874: #endif
    875:   PetscMallocValidate(__LINE__,PETSC_FUNCTION_NAME,__FILE__);
    876:   k    = 0;
    877:   for (i = 0; i < nedgeLoc; i++) {
    878:     int cross_node=nnodesLoc/2;
    879:     node1 = tmp[eperm[i]] + 1;
    880:     node2 = tmp[nedgeLoc+eperm[i]] + 1;
    881: #if defined(INTERLACING)
    882:     grid->eptr[k++] = node1;
    883:     grid->eptr[k++] = node2;
    884: #else
    885:     grid->eptr[i]          = node1;
    886:     grid->eptr[nedgeLoc+i] = node2;
    887: #endif
    888:     /* if (node1 > node2)
    889:      printf("On processor %d, for edge %d node1 = %d, node2 = %d\n",
    890:             rank,i,node1,node2);*/
    891:     if ((node1 <= cross_node) && (node2 > cross_node)) cross_edges++;
    892:   }
    893:   PetscPrintf(comm,"Number of cross edges %d\n", cross_edges);
    894:   PetscFree(tmp);
    895: #if defined(_OPENMP) && !defined(HAVE_REDUNDANT_WORK) && !defined(HAVE_EDGE_COLORING)
    896:   /* Now make the local 'ia' and 'ja' arrays */
    897:   ICALLOC(nvertices+1,&grid->ia);
    898:   /* Use tmp for a work array */
    899:   ICALLOC(nvertices,&tmp);
    900:   f77GETIA(&nvertices,&nedgeLoc,grid->eptr,grid->ia,tmp,&rank);
    901:   nnz = grid->ia[nvertices] - 1;
    902:   ICALLOC(nnz,&grid->ja);
    903:   f77GETJA(&nvertices,&nedgeLoc,grid->eptr,grid->ia,grid->ja,tmp,&rank);
    904:   PetscFree(tmp);
    905: #else
    906:   /* Now make the local 'ia' and 'ja' arrays */
    907:   ICALLOC(nnodesLoc+1,&grid->ia);
    908:   /* Use tmp for a work array */
    909:   ICALLOC(nnodesLoc,&tmp);
    910:   f77GETIA(&nnodesLoc,&nedgeLoc,grid->eptr,grid->ia,tmp,&rank);
    911:   nnz = grid->ia[nnodesLoc] - 1;
    912: #if defined(BLOCKING)
    913:   PetscPrintf(comm,"The Jacobian has %d non-zero blocks with block size = %d\n",nnz,bs);
    914: #else
    915:   PetscPrintf(comm,"The Jacobian has %d non-zeros\n",nnz);
    916: #endif
    917:   ICALLOC(nnz,&grid->ja);
    918:   f77GETJA(&nnodesLoc,&nedgeLoc,grid->eptr,grid->ia,grid->ja,tmp,&rank);
    919:   PetscFree(tmp);
    920: #endif
    921:   ICALLOC(nvertices,&grid->loc2glo);
    922:   PetscMemcpy(grid->loc2glo,l2a,nvertices*sizeof(int));
    923:   PetscFree(l2a);
    924:   l2a  = grid->loc2glo;
    925:   ICALLOC(nvertices,&grid->loc2pet);
    926:   l2p  = grid->loc2pet;
    927:   PetscMemcpy(l2p,l2a,nvertices*sizeof(int));
    928:   AOApplicationToPetsc(ao,nvertices,l2p);

    930:   /* Renumber unit normals of dual face (from node1 to node2)
    931:       and the area of the dual mesh face */
    932:   FCALLOC(nedgeLocEst,&ftmp);
    933:   FCALLOC(nedgeLoc,&ftmp1);
    934:   FCALLOC(4*nedgeLoc,&grid->xyzn);
    935:   /* Do the x-component */
    936:   i = 0; k = 0;
    937:   remEdges = nedge;
    938:   PetscTime(&time_ini);
    939:   while (remEdges > 0) {
    940:     readEdges = PetscMin(remEdges,nedgeLocEst);
    941:     PetscBinarySynchronizedRead(comm,fdes,ftmp,readEdges,PETSC_SCALAR);
    942:     for (j = 0; j < readEdges; j++)
    943:       if (edge_bit[k] == (i+j)) {
    944:         ftmp1[k] = ftmp[j];
    945:         k++;
    946:       }
    947:     i       += readEdges;
    948:     remEdges = remEdges - readEdges;
    949:     MPI_Barrier(comm);
    950:   }
    951:   for (i = 0; i < nedgeLoc; i++)
    952: #if defined(INTERLACING)
    953:     grid->xyzn[4*i] = ftmp1[eperm[i]];
    954: #else
    955:     grid->xyzn[i] = ftmp1[eperm[i]];
    956: #endif
    957:   /* Do the y-component */
    958:   i = 0; k = 0;
    959:   remEdges = nedge;
    960:   while (remEdges > 0) {
    961:     readEdges = PetscMin(remEdges,nedgeLocEst);
    962:     PetscBinarySynchronizedRead(comm,fdes,ftmp,readEdges,PETSC_SCALAR);
    963:     for (j = 0; j < readEdges; j++)
    964:       if (edge_bit[k] == (i+j)) {
    965:         ftmp1[k] = ftmp[j];
    966:         k++;
    967:       }
    968:     i       += readEdges;
    969:     remEdges = remEdges - readEdges;
    970:     MPI_Barrier(comm);
    971:   }
    972:   for (i = 0; i < nedgeLoc; i++)
    973: #if defined(INTERLACING)
    974:     grid->xyzn[4*i+1] = ftmp1[eperm[i]];
    975: #else
    976:     grid->xyzn[nedgeLoc+i] = ftmp1[eperm[i]];
    977: #endif
    978:   /* Do the z-component */
    979:   i = 0; k = 0;
    980:   remEdges = nedge;
    981:   while (remEdges > 0) {
    982:     readEdges = PetscMin(remEdges,nedgeLocEst);
    983:     PetscBinarySynchronizedRead(comm,fdes,ftmp,readEdges,PETSC_SCALAR);
    984:     for (j = 0; j < readEdges; j++)
    985:       if (edge_bit[k] == (i+j)) {
    986:         ftmp1[k] = ftmp[j];
    987:         k++;
    988:       }
    989:     i       += readEdges;
    990:     remEdges = remEdges - readEdges;
    991:     MPI_Barrier(comm);
    992:   }
    993:   for (i = 0; i < nedgeLoc; i++)
    994: #if defined(INTERLACING)
    995:     grid->xyzn[4*i+2] = ftmp1[eperm[i]];
    996: #else
    997:     grid->xyzn[2*nedgeLoc+i] = ftmp1[eperm[i]];
    998: #endif
    999:   /* Do the area */
    1000:   i = 0; k = 0;
    1001:   remEdges = nedge;
    1002:   while (remEdges > 0) {
    1003:     readEdges = PetscMin(remEdges,nedgeLocEst);
    1004:     PetscBinarySynchronizedRead(comm,fdes,ftmp,readEdges,PETSC_SCALAR);
    1005:     for (j = 0; j < readEdges; j++)
    1006:       if (edge_bit[k] == (i+j)) {
    1007:         ftmp1[k] = ftmp[j];
    1008:         k++;
    1009:       }
    1010:     i       += readEdges;
    1011:     remEdges = remEdges - readEdges;
    1012:     MPI_Barrier(comm);
    1013:   }
    1014:   for (i = 0; i < nedgeLoc; i++)
    1015: #if defined(INTERLACING)
    1016:     grid->xyzn[4*i+3] = ftmp1[eperm[i]];
    1017: #else
    1018:     grid->xyzn[3*nedgeLoc+i] = ftmp1[eperm[i]];
    1019: #endif

    1021:   PetscFree(edge_bit);
    1022:   PetscFree(eperm);
    1023:   PetscFree(ftmp);
    1024:   PetscFree(ftmp1);
    1025:   PetscTime(&time_fin);
    1026:   time_fin -= time_ini;
    1027:   PetscPrintf(comm,"Edge normals partitioned\n");
    1028:   PetscPrintf(comm,"Time taken in this phase was %g\n",time_fin);
    1029: #if defined(_OPENMP)
    1030:   /*Arrange for the division of work among threads*/
    1031: #if defined(HAVE_EDGE_COLORING)
    1032: #elif defined(HAVE_REDUNDANT_WORK)
    1033:   FCALLOC(4*nnodesLoc,   &grid->resd);
    1034: #else
    1035:   {
    1036:     /* Get the local adjacency structure of the graph for partitioning the local
    1037:       graph into max_threads pieces */
    1038:     int *ia,*ja,*vwtg=0,*adjwgt=0,options[5];
    1039:     int numflag = 0, wgtflag = 0, edgecut;
    1040:     int thr1,thr2,nedgeAllThreads,ned1,ned2;
    1041:     ICALLOC((nvertices+1),&ia);
    1042:     ICALLOC((2*nedgeLoc),&ja);
    1043:     ia[0] = 0;
    1044:     for (i = 1; i <= nvertices; i++) ia[i] = grid->ia[i]-i-1;
    1045:     for (i = 0; i < nvertices; i++) {
    1046:       int jstart,jend;
    1047:       jstart = grid->ia[i]-1;
    1048:       jend   = grid->ia[i+1]-1;
    1049:       k      = ia[i];
    1050:       for (j=jstart; j < jend; j++) {
    1051:         inode = grid->ja[j]-1;
    1052:         if (inode != i) ja[k++] = inode;
    1053:       }
    1054:     }
    1055:     ICALLOC(nvertices,&grid->part_thr);
    1056:     PetscMemzero(grid->part_thr,nvertices*sizeof(int));
    1057:     options[0] = 0;
    1058:     /* Call the pmetis library routine */
    1059:     if (max_threads > 1)
    1060:       METIS_PartGraphRecursive(&nvertices,ia,ja,vwtg,adjwgt,
    1061:                                &wgtflag,&numflag,&max_threads,options,&edgecut,grid->part_thr);
    1062:     PetscPrintf(MPI_COMM_WORLD,"The number of cut edges is %d\n", edgecut);
    1063:     /* Write the partition vector to disk */
    1064:     flg  = PETSC_FALSE;
    1065:     PetscOptionsGetBool(0,"-omp_partitioning",&flg,NULL);
    1066:     if (flg) {
    1067:       int  *partv_loc, *partv_glo;
    1068:       int  *disp,*counts,*loc2glo_glo;
    1069:       char part_file[PETSC_MAX_PATH_LEN];
    1070:       FILE *fp;

    1072:       ICALLOC(nnodes, &partv_glo);
    1073:       ICALLOC(nnodesLoc, &partv_loc);
    1074:       for (i = 0; i < nnodesLoc; i++)
    1075:         /*partv_loc[i] = grid->part_thr[i]*size + rank;*/
    1076:         partv_loc[i] = grid->part_thr[i] + max_threads*rank;
    1077:       ICALLOC(size,&disp);
    1078:       ICALLOC(size,&counts);
    1079:       MPI_Allgather(&nnodesLoc,1,MPI_INT,counts,1,MPI_INT,MPI_COMM_WORLD);
    1080:       disp[0] = 0;
    1081:       for (i = 1; i < size; i++) disp[i] = counts[i-1] + disp[i-1];
    1082:       ICALLOC(nnodes, &loc2glo_glo);
    1083:       MPI_Gatherv(grid->loc2glo,nnodesLoc,MPI_INT,loc2glo_glo,counts,disp,MPI_INT,0,MPI_COMM_WORLD);
    1084:       MPI_Gatherv(partv_loc,nnodesLoc,MPI_INT,partv_glo,counts,disp,MPI_INT,0,MPI_COMM_WORLD);
    1085:       if (rank == 0) {
    1086:         PetscSortIntWithArray(nnodes,loc2glo_glo,partv_glo);
    1087:         sprintf(part_file,"hyb_part_vec.%d",2*size);
    1088:         fp = fopen(part_file,"w");
    1089:         for (i = 0; i < nnodes; i++) fprintf(fp,"%d\n",partv_glo[i]);
    1090:         fclose(fp);
    1091:       }
    1092:       PetscFree(partv_loc);
    1093:       PetscFree(partv_glo);
    1094:       PetscFree(disp);
    1095:       PetscFree(counts);
    1096:       PetscFree(loc2glo_glo);
    1097:     }

    1099:     /* Divide the work among threads */
    1100:     k = 0;
    1101:     ICALLOC((max_threads+1),&grid->nedge_thr);
    1102:     PetscMemzero(grid->nedge_thr,(max_threads+1)*sizeof(int));
    1103:     cross_edges = 0;
    1104:     for (i = 0; i < nedgeLoc; i++) {
    1105:       node1 = grid->eptr[k++]-1;
    1106:       node2 = grid->eptr[k++]-1;
    1107:       thr1  = grid->part_thr[node1];
    1108:       thr2  = grid->part_thr[node2];
    1109:       grid->nedge_thr[thr1]+=1;
    1110:       if (thr1 != thr2) {
    1111:         grid->nedge_thr[thr2]+=1;
    1112:         cross_edges++;
    1113:       }
    1114:     }
    1115:     PetscPrintf(MPI_COMM_WORLD,"The number of cross edges after Metis partitioning is %d\n",cross_edges);
    1116:     ned1 = grid->nedge_thr[0];
    1117:     grid->nedge_thr[0] = 1;
    1118:     for (i = 1; i <= max_threads; i++) {
    1119:       ned2 = grid->nedge_thr[i];
    1120:       grid->nedge_thr[i] = grid->nedge_thr[i-1]+ned1;
    1121:       ned1 = ned2;
    1122:     }
    1123:     /* Allocate a shared edge array. Note that a cut edge is evaluated
    1124:         by both the threads but updates are done only for the locally
    1125:         owned node */
    1126:     grid->nedgeAllThr = nedgeAllThreads = grid->nedge_thr[max_threads]-1;
    1127:     ICALLOC(2*nedgeAllThreads, &grid->edge_thr);
    1128:     ICALLOC(max_threads,&tmp);
    1129:     FCALLOC(4*nedgeAllThreads,&grid->xyzn_thr);
    1130:     for (i = 0; i < max_threads; i++) tmp[i] = grid->nedge_thr[i]-1;
    1131:     k = 0;
    1132:     for (i = 0; i < nedgeLoc; i++) {
    1133:       int ie1,ie2,ie3;
    1134:       node1 = grid->eptr[k++];
    1135:       node2 = grid->eptr[k++];
    1136:       thr1  = grid->part_thr[node1-1];
    1137:       thr2  = grid->part_thr[node2-1];
    1138:       ie1   = 2*tmp[thr1];
    1139:       ie2   = 4*tmp[thr1];
    1140:       ie3   = 4*i;

    1142:       grid->edge_thr[ie1]   = node1;
    1143:       grid->edge_thr[ie1+1] = node2;
    1144:       grid->xyzn_thr[ie2]   = grid->xyzn[ie3];
    1145:       grid->xyzn_thr[ie2+1] = grid->xyzn[ie3+1];
    1146:       grid->xyzn_thr[ie2+2] = grid->xyzn[ie3+2];
    1147:       grid->xyzn_thr[ie2+3] = grid->xyzn[ie3+3];

    1149:       tmp[thr1]+=1;
    1150:       if (thr1 != thr2) {
    1151:         ie1 = 2*tmp[thr2];
    1152:         ie2 = 4*tmp[thr2];

    1154:         grid->edge_thr[ie1]   = node1;
    1155:         grid->edge_thr[ie1+1] = node2;
    1156:         grid->xyzn_thr[ie2]   = grid->xyzn[ie3];
    1157:         grid->xyzn_thr[ie2+1] = grid->xyzn[ie3+1];
    1158:         grid->xyzn_thr[ie2+2] = grid->xyzn[ie3+2];
    1159:         grid->xyzn_thr[ie2+3] = grid->xyzn[ie3+3];

    1161:         tmp[thr2]+=1;
    1162:       }
    1163:     }
    1164:   }
    1165: #endif
    1166: #endif

    1168:   /* Remap coordinates */
    1169:   /*nnodesLocEst = nnodes/size;*/
    1170:   nnodesLocEst = PetscMin(nnodes,500000);
    1171:   FCALLOC(nnodesLocEst,&ftmp);
    1172:   FCALLOC(3*nvertices,&grid->xyz);
    1173:   remNodes = nnodes;
    1174:   i        = 0;
    1175:   PetscTime(&time_ini);
    1176:   while (remNodes > 0) {
    1177:     readNodes = PetscMin(remNodes,nnodesLocEst);
    1178:     PetscBinarySynchronizedRead(comm,fdes,ftmp,readNodes,PETSC_SCALAR);
    1179:     for (j = 0; j < readNodes; j++) {
    1180:       if (a2l[i+j] >= 0) {
    1181: #if defined(INTERLACING)
    1182:         grid->xyz[3*a2l[i+j]] = ftmp[j];
    1183: #else
    1184:         grid->xyz[a2l[i+j]] = ftmp[j];
    1185: #endif
    1186:       }
    1187:     }
    1188:     i        += nnodesLocEst;
    1189:     remNodes -= nnodesLocEst;
    1190:     MPI_Barrier(comm);
    1191:   }

    1193:   remNodes = nnodes;
    1194:   i = 0;
    1195:   while (remNodes > 0) {
    1196:     readNodes = PetscMin(remNodes,nnodesLocEst);
    1197:     PetscBinarySynchronizedRead(comm,fdes,ftmp,readNodes,PETSC_SCALAR);
    1198:     for (j = 0; j < readNodes; j++) {
    1199:       if (a2l[i+j] >= 0) {
    1200: #if defined(INTERLACING)
    1201:         grid->xyz[3*a2l[i+j]+1] = ftmp[j];
    1202: #else
    1203:         grid->xyz[nnodesLoc+a2l[i+j]] = ftmp[j];
    1204: #endif
    1205:       }
    1206:     }
    1207:     i        += nnodesLocEst;
    1208:     remNodes -= nnodesLocEst;
    1209:     MPI_Barrier(comm);
    1210:   }

    1212:   remNodes = nnodes;
    1213:   i        = 0;
    1214:   while (remNodes > 0) {
    1215:     readNodes = PetscMin(remNodes,nnodesLocEst);
    1216:     PetscBinarySynchronizedRead(comm,fdes,ftmp,readNodes,PETSC_SCALAR);
    1217:     for (j = 0; j < readNodes; j++) {
    1218:       if (a2l[i+j] >= 0) {
    1219: #if defined(INTERLACING)
    1220:         grid->xyz[3*a2l[i+j]+2] = ftmp[j];
    1221: #else
    1222:         grid->xyz[2*nnodesLoc+a2l[i+j]] = ftmp[j];
    1223: #endif
    1224:       }
    1225:     }
    1226:     i        += nnodesLocEst;
    1227:     remNodes -= nnodesLocEst;
    1228:     MPI_Barrier(comm);
    1229:   }

    1231:   /* Renumber dual volume "area" */
    1232:   FCALLOC(nvertices,&grid->area);
    1233:   remNodes = nnodes;
    1234:   i        = 0;
    1235:   while (remNodes > 0) {
    1236:     readNodes = PetscMin(remNodes,nnodesLocEst);
    1237:     PetscBinarySynchronizedRead(comm,fdes,ftmp,readNodes,PETSC_SCALAR);
    1238:     for (j = 0; j < readNodes; j++)
    1239:       if (a2l[i+j] >= 0)
    1240:         grid->area[a2l[i+j]] = ftmp[j];
    1241:     i        += nnodesLocEst;
    1242:     remNodes -= nnodesLocEst;
    1243:     MPI_Barrier(comm);
    1244:   }

    1246:   PetscFree(ftmp);
    1247:   PetscTime(&time_fin);
    1248:   time_fin -= time_ini;
    1249:   PetscPrintf(comm,"Coordinates remapped\n");
    1250:   PetscPrintf(comm,"Time taken in this phase was %g\n",time_fin);

    1252: /* Now,handle all the solid boundaries - things to be done :
    1253:  * 1. Identify the nodes belonging to the solid
    1254:  *    boundaries and count them.
    1255:  * 2. Put proper indices into f2ntn array,after making it
    1256:  *    of suitable size.
    1257:  * 3. Remap the normals and areas of solid faces (sxn,syn,szn,
    1258:  *    and sa arrays).
    1259:  */
    1260:   ICALLOC(nnbound,  &grid->nntet);
    1261:   ICALLOC(nnbound,  &grid->nnpts);
    1262:   ICALLOC(4*nnfacet,&grid->f2ntn);
    1263:   ICALLOC(nsnode,&grid->isnode);
    1264:   FCALLOC(nsnode,&grid->sxn);
    1265:   FCALLOC(nsnode,&grid->syn);
    1266:   FCALLOC(nsnode,&grid->szn);
    1267:   FCALLOC(nsnode,&grid->sa);
    1268:   PetscBinarySynchronizedRead(comm,fdes,grid->nntet,nnbound,PETSC_INT);
    1269:   PetscBinarySynchronizedRead(comm,fdes,grid->nnpts,nnbound,PETSC_INT);
    1270:   PetscBinarySynchronizedRead(comm,fdes,grid->f2ntn,4*nnfacet,PETSC_INT);
    1271:   PetscBinarySynchronizedRead(comm,fdes,grid->isnode,nsnode,PETSC_INT);
    1272:   PetscBinarySynchronizedRead(comm,fdes,grid->sxn,nsnode,PETSC_SCALAR);
    1273:   PetscBinarySynchronizedRead(comm,fdes,grid->syn,nsnode,PETSC_SCALAR);
    1274:   PetscBinarySynchronizedRead(comm,fdes,grid->szn,nsnode,PETSC_SCALAR);

    1276:   isurf      = 0;
    1277:   nsnodeLoc  = 0;
    1278:   nnfacetLoc = 0;
    1279:   nb         = 0;
    1280:   nte        = 0;
    1281:   ICALLOC(3*nnfacet,&tmp);
    1282:   ICALLOC(nsnode,&tmp1);
    1283:   ICALLOC(nnodes,&tmp2);
    1284:   FCALLOC(4*nsnode,&ftmp);
    1285:   PetscMemzero(tmp,3*nnfacet*sizeof(int));
    1286:   PetscMemzero(tmp1,nsnode*sizeof(int));
    1287:   PetscMemzero(tmp2,nnodes*sizeof(int));

    1289:   j = 0;
    1290:   for (i = 0; i < nsnode; i++) {
    1291:     node1 = a2l[grid->isnode[i] - 1];
    1292:     if (node1 >= 0) {
    1293:       tmp1[nsnodeLoc] = node1;
    1294:       tmp2[node1]     = nsnodeLoc;
    1295:       ftmp[j++]       = grid->sxn[i];
    1296:       ftmp[j++]       = grid->syn[i];
    1297:       ftmp[j++]       = grid->szn[i];
    1298:       ftmp[j++]       = grid->sa[i];
    1299:       nsnodeLoc++;
    1300:     }
    1301:   }
    1302:   for (i = 0; i < nnbound; i++) {
    1303:     for (j = isurf; j < isurf + grid->nntet[i]; j++) {
    1304:       node1 = a2l[grid->isnode[grid->f2ntn[j] - 1] - 1];
    1305:       node2 = a2l[grid->isnode[grid->f2ntn[nnfacet + j] - 1] - 1];
    1306:       node3 = a2l[grid->isnode[grid->f2ntn[2*nnfacet + j] - 1] - 1];

    1308:       if ((node1 >= 0) && (node2 >= 0) && (node3 >= 0)) {
    1309:         nnfacetLoc++;
    1310:         nte++;
    1311:         tmp[nb++] = tmp2[node1];
    1312:         tmp[nb++] = tmp2[node2];
    1313:         tmp[nb++] = tmp2[node3];
    1314:       }
    1315:     }
    1316:     isurf += grid->nntet[i];
    1317:     /*printf("grid->nntet[%d] before reordering is %d\n",i,grid->nntet[i]);*/
    1318:     grid->nntet[i] = nte;
    1319:     /*printf("grid->nntet[%d] after reordering is %d\n",i,grid->nntet[i]);*/
    1320:     nte = 0;
    1321:   }
    1322:   PetscFree(grid->f2ntn);
    1323:   PetscFree(grid->isnode);
    1324:   PetscFree(grid->sxn);
    1325:   PetscFree(grid->syn);
    1326:   PetscFree(grid->szn);
    1327:   PetscFree(grid->sa);
    1328:   ICALLOC(4*nnfacetLoc,&grid->f2ntn);
    1329:   ICALLOC(nsnodeLoc,&grid->isnode);
    1330:   FCALLOC(nsnodeLoc,&grid->sxn);
    1331:   FCALLOC(nsnodeLoc,&grid->syn);
    1332:   FCALLOC(nsnodeLoc,&grid->szn);
    1333:   FCALLOC(nsnodeLoc,&grid->sa);
    1334:   j = 0;
    1335:   for (i = 0; i < nsnodeLoc; i++) {
    1336:     grid->isnode[i] = tmp1[i] + 1;
    1337:     grid->sxn[i]    = ftmp[j++];
    1338:     grid->syn[i]    = ftmp[j++];
    1339:     grid->szn[i]    = ftmp[j++];
    1340:     grid->sa[i]     = ftmp[j++];
    1341:   }
    1342:   j = 0;
    1343:   for (i = 0; i < nnfacetLoc; i++) {
    1344:     grid->f2ntn[i]              = tmp[j++] + 1;
    1345:     grid->f2ntn[nnfacetLoc+i]   = tmp[j++] + 1;
    1346:     grid->f2ntn[2*nnfacetLoc+i] = tmp[j++] + 1;
    1347:   }
    1348:   PetscFree(tmp);
    1349:   PetscFree(tmp1);
    1350:   PetscFree(tmp2);
    1351:   PetscFree(ftmp);

    1353: /* Now identify the triangles on which the current processor
    1354:    would perform force calculation */
    1355:   ICALLOC(nnfacetLoc,&grid->sface_bit);
    1356:   PetscMemzero(grid->sface_bit,nnfacetLoc*sizeof(int));
    1357:   for (i = 0; i < nnfacetLoc; i++) {
    1358:     node1 = l2a[grid->isnode[grid->f2ntn[i] - 1] - 1];
    1359:     node2 = l2a[grid->isnode[grid->f2ntn[nnfacetLoc + i] - 1] - 1];
    1360:     node3 = l2a[grid->isnode[grid->f2ntn[2*nnfacetLoc + i] - 1] - 1];
    1361:     if (((v2p[node1] >= rank) && (v2p[node2] >= rank)
    1362:          && (v2p[node3] >= rank)) &&
    1363:         ((v2p[node1] == rank) || (v2p[node2] == rank)
    1364:          || (v2p[node3] == rank)))
    1365:       grid->sface_bit[i] = 1;
    1366:   }
    1367:   /*printf("On processor %d total solid triangles = %d,locally owned = %d alpha = %d\n",rank,totTr,myTr,alpha);*/
    1368:   PetscPrintf(comm,"Solid boundaries partitioned\n");

    1370: /* Now,handle all the viscous boundaries - things to be done :
    1371:  * 1. Identify the nodes belonging to the viscous
    1372:  *    boundaries and count them.
    1373:  * 2. Put proper indices into f2ntv array,after making it
    1374:  *    of suitable size
    1375:  * 3. Remap the normals and areas of viscous faces (vxn,vyn,vzn,
    1376:  *    and va arrays).
    1377:  */
    1378:   ICALLOC(nvbound,  &grid->nvtet);
    1379:   ICALLOC(nvbound,  &grid->nvpts);
    1380:   ICALLOC(4*nvfacet,&grid->f2ntv);
    1381:   ICALLOC(nvnode,&grid->ivnode);
    1382:   FCALLOC(nvnode,&grid->vxn);
    1383:   FCALLOC(nvnode,&grid->vyn);
    1384:   FCALLOC(nvnode,&grid->vzn);
    1385:   FCALLOC(nvnode,&grid->va);
    1386:   PetscBinarySynchronizedRead(comm,fdes,grid->nvtet,nvbound,PETSC_INT);
    1387:   PetscBinarySynchronizedRead(comm,fdes,grid->nvpts,nvbound,PETSC_INT);
    1388:   PetscBinarySynchronizedRead(comm,fdes,grid->f2ntv,4*nvfacet,PETSC_INT);
    1389:   PetscBinarySynchronizedRead(comm,fdes,grid->ivnode,nvnode,PETSC_INT);
    1390:   PetscBinarySynchronizedRead(comm,fdes,grid->vxn,nvnode,PETSC_SCALAR);
    1391:   PetscBinarySynchronizedRead(comm,fdes,grid->vyn,nvnode,PETSC_SCALAR);
    1392:   PetscBinarySynchronizedRead(comm,fdes,grid->vzn,nvnode,PETSC_SCALAR);

    1394:   isurf      = 0;
    1395:   nvnodeLoc  = 0;
    1396:   nvfacetLoc = 0;
    1397:   nb         = 0;
    1398:   nte        = 0;
    1399:   ICALLOC(3*nvfacet,&tmp);
    1400:   ICALLOC(nvnode,&tmp1);
    1401:   ICALLOC(nnodes,&tmp2);
    1402:   FCALLOC(4*nvnode,&ftmp);
    1403:   PetscMemzero(tmp,3*nvfacet*sizeof(int));
    1404:   PetscMemzero(tmp1,nvnode*sizeof(int));
    1405:   PetscMemzero(tmp2,nnodes*sizeof(int));

    1407:   j = 0;
    1408:   for (i = 0; i < nvnode; i++) {
    1409:     node1 = a2l[grid->ivnode[i] - 1];
    1410:     if (node1 >= 0) {
    1411:       tmp1[nvnodeLoc] = node1;
    1412:       tmp2[node1]     = nvnodeLoc;
    1413:       ftmp[j++]       = grid->vxn[i];
    1414:       ftmp[j++]       = grid->vyn[i];
    1415:       ftmp[j++]       = grid->vzn[i];
    1416:       ftmp[j++]       = grid->va[i];
    1417:       nvnodeLoc++;
    1418:     }
    1419:   }
    1420:   for (i = 0; i < nvbound; i++) {
    1421:     for (j = isurf; j < isurf + grid->nvtet[i]; j++) {
    1422:       node1 = a2l[grid->ivnode[grid->f2ntv[j] - 1] - 1];
    1423:       node2 = a2l[grid->ivnode[grid->f2ntv[nvfacet + j] - 1] - 1];
    1424:       node3 = a2l[grid->ivnode[grid->f2ntv[2*nvfacet + j] - 1] - 1];
    1425:       if ((node1 >= 0) && (node2 >= 0) && (node3 >= 0)) {
    1426:         nvfacetLoc++;
    1427:         nte++;
    1428:         tmp[nb++] = tmp2[node1];
    1429:         tmp[nb++] = tmp2[node2];
    1430:         tmp[nb++] = tmp2[node3];
    1431:       }
    1432:     }
    1433:     isurf         += grid->nvtet[i];
    1434:     grid->nvtet[i] = nte;
    1435:     nte            = 0;
    1436:   }
    1437:   PetscFree(grid->f2ntv);
    1438:   PetscFree(grid->ivnode);
    1439:   PetscFree(grid->vxn);
    1440:   PetscFree(grid->vyn);
    1441:   PetscFree(grid->vzn);
    1442:   PetscFree(grid->va);
    1443:   ICALLOC(4*nvfacetLoc,&grid->f2ntv);
    1444:   ICALLOC(nvnodeLoc,&grid->ivnode);
    1445:   FCALLOC(nvnodeLoc,&grid->vxn);
    1446:   FCALLOC(nvnodeLoc,&grid->vyn);
    1447:   FCALLOC(nvnodeLoc,&grid->vzn);
    1448:   FCALLOC(nvnodeLoc,&grid->va);
    1449:   j = 0;
    1450:   for (i = 0; i < nvnodeLoc; i++) {
    1451:     grid->ivnode[i] = tmp1[i] + 1;
    1452:     grid->vxn[i]    = ftmp[j++];
    1453:     grid->vyn[i]    = ftmp[j++];
    1454:     grid->vzn[i]    = ftmp[j++];
    1455:     grid->va[i]     = ftmp[j++];
    1456:   }
    1457:   j = 0;
    1458:   for (i = 0; i < nvfacetLoc; i++) {
    1459:     grid->f2ntv[i]              = tmp[j++] + 1;
    1460:     grid->f2ntv[nvfacetLoc+i]   = tmp[j++] + 1;
    1461:     grid->f2ntv[2*nvfacetLoc+i] = tmp[j++] + 1;
    1462:   }
    1463:   PetscFree(tmp);
    1464:   PetscFree(tmp1);
    1465:   PetscFree(tmp2);
    1466:   PetscFree(ftmp);

    1468: /* Now identify the triangles on which the current processor
    1469:    would perform force calculation */
    1470:   ICALLOC(nvfacetLoc,&grid->vface_bit);
    1471:   PetscMemzero(grid->vface_bit,nvfacetLoc*sizeof(int));
    1472:   for (i = 0; i < nvfacetLoc; i++) {
    1473:     node1 = l2a[grid->ivnode[grid->f2ntv[i] - 1] - 1];
    1474:     node2 = l2a[grid->ivnode[grid->f2ntv[nvfacetLoc + i] - 1] - 1];
    1475:     node3 = l2a[grid->ivnode[grid->f2ntv[2*nvfacetLoc + i] - 1] - 1];
    1476:     if (((v2p[node1] >= rank) && (v2p[node2] >= rank)
    1477:          && (v2p[node3] >= rank)) &&
    1478:         ((v2p[node1] == rank) || (v2p[node2] == rank)
    1479:         || (v2p[node3] == rank))) {
    1480:          grid->vface_bit[i] = 1;
    1481:     }
    1482:   }
    1483:   PetscFree(v2p);
    1484:   PetscPrintf(comm,"Viscous boundaries partitioned\n");

    1486: /* Now,handle all the free boundaries - things to be done :
    1487:  * 1. Identify the nodes belonging to the free
    1488:  *    boundaries and count them.
    1489:  * 2. Put proper indices into f2ntf array,after making it
    1490:  *    of suitable size
    1491:  * 3. Remap the normals and areas of free bound. faces (fxn,fyn,fzn,
    1492:  *    and fa arrays).
    1493:  */

    1495:   ICALLOC(nfbound,  &grid->nftet);
    1496:   ICALLOC(nfbound,  &grid->nfpts);
    1497:   ICALLOC(4*nffacet,&grid->f2ntf);
    1498:   ICALLOC(nfnode,&grid->ifnode);
    1499:   FCALLOC(nfnode,&grid->fxn);
    1500:   FCALLOC(nfnode,&grid->fyn);
    1501:   FCALLOC(nfnode,&grid->fzn);
    1502:   FCALLOC(nfnode,&grid->fa);
    1503:   PetscBinarySynchronizedRead(comm,fdes,grid->nftet,nfbound,PETSC_INT);
    1504:   PetscBinarySynchronizedRead(comm,fdes,grid->nfpts,nfbound,PETSC_INT);
    1505:   PetscBinarySynchronizedRead(comm,fdes,grid->f2ntf,4*nffacet,PETSC_INT);
    1506:   PetscBinarySynchronizedRead(comm,fdes,grid->ifnode,nfnode,PETSC_INT);
    1507:   PetscBinarySynchronizedRead(comm,fdes,grid->fxn,nfnode,PETSC_SCALAR);
    1508:   PetscBinarySynchronizedRead(comm,fdes,grid->fyn,nfnode,PETSC_SCALAR);
    1509:   PetscBinarySynchronizedRead(comm,fdes,grid->fzn,nfnode,PETSC_SCALAR);

    1511:   isurf      = 0;
    1512:   nfnodeLoc  = 0;
    1513:   nffacetLoc = 0;
    1514:   nb         = 0;
    1515:   nte        = 0;
    1516:   ICALLOC(3*nffacet,&tmp);
    1517:   ICALLOC(nfnode,&tmp1);
    1518:   ICALLOC(nnodes,&tmp2);
    1519:   FCALLOC(4*nfnode,&ftmp);
    1520:   PetscMemzero(tmp,3*nffacet*sizeof(int));
    1521:   PetscMemzero(tmp1,nfnode*sizeof(int));
    1522:   PetscMemzero(tmp2,nnodes*sizeof(int));

    1524:   j = 0;
    1525:   for (i = 0; i < nfnode; i++) {
    1526:     node1 = a2l[grid->ifnode[i] - 1];
    1527:     if (node1 >= 0) {
    1528:       tmp1[nfnodeLoc] = node1;
    1529:       tmp2[node1]     = nfnodeLoc;
    1530:       ftmp[j++]       = grid->fxn[i];
    1531:       ftmp[j++]       = grid->fyn[i];
    1532:       ftmp[j++]       = grid->fzn[i];
    1533:       ftmp[j++]       = grid->fa[i];
    1534:       nfnodeLoc++;
    1535:     }
    1536:   }
    1537:   for (i = 0; i < nfbound; i++) {
    1538:     for (j = isurf; j < isurf + grid->nftet[i]; j++) {
    1539:       node1 = a2l[grid->ifnode[grid->f2ntf[j] - 1] - 1];
    1540:       node2 = a2l[grid->ifnode[grid->f2ntf[nffacet + j] - 1] - 1];
    1541:       node3 = a2l[grid->ifnode[grid->f2ntf[2*nffacet + j] - 1] - 1];
    1542:       if ((node1 >= 0) && (node2 >= 0) && (node3 >= 0)) {
    1543:         nffacetLoc++;
    1544:         nte++;
    1545:         tmp[nb++] = tmp2[node1];
    1546:         tmp[nb++] = tmp2[node2];
    1547:         tmp[nb++] = tmp2[node3];
    1548:       }
    1549:     }
    1550:     isurf         += grid->nftet[i];
    1551:     grid->nftet[i] = nte;
    1552:     nte            = 0;
    1553:   }
    1554:   PetscFree(grid->f2ntf);
    1555:   PetscFree(grid->ifnode);
    1556:   PetscFree(grid->fxn);
    1557:   PetscFree(grid->fyn);
    1558:   PetscFree(grid->fzn);
    1559:   PetscFree(grid->fa);
    1560:   ICALLOC(4*nffacetLoc,&grid->f2ntf);
    1561:   ICALLOC(nfnodeLoc,&grid->ifnode);
    1562:   FCALLOC(nfnodeLoc,&grid->fxn);
    1563:   FCALLOC(nfnodeLoc,&grid->fyn);
    1564:   FCALLOC(nfnodeLoc,&grid->fzn);
    1565:   FCALLOC(nfnodeLoc,&grid->fa);
    1566:   j = 0;
    1567:   for (i = 0; i < nfnodeLoc; i++) {
    1568:     grid->ifnode[i] = tmp1[i] + 1;
    1569:     grid->fxn[i]    = ftmp[j++];
    1570:     grid->fyn[i]    = ftmp[j++];
    1571:     grid->fzn[i]    = ftmp[j++];
    1572:     grid->fa[i]     = ftmp[j++];
    1573:   }
    1574:   j = 0;
    1575:   for (i = 0; i < nffacetLoc; i++) {
    1576:     grid->f2ntf[i]              = tmp[j++] + 1;
    1577:     grid->f2ntf[nffacetLoc+i]   = tmp[j++] + 1;
    1578:     grid->f2ntf[2*nffacetLoc+i] = tmp[j++] + 1;
    1579:   }

    1581:   PetscFree(tmp);
    1582:   PetscFree(tmp1);
    1583:   PetscFree(tmp2);
    1584:   PetscFree(ftmp);
    1585:   PetscPrintf(comm,"Free boundaries partitioned\n");

    1587:   flg  = PETSC_FALSE;
    1588:   PetscOptionsGetBool(0,"-mem_use",&flg,NULL);
    1589:   if (flg) {
    1590:     PetscMemoryView(PETSC_VIEWER_STDOUT_WORLD,"Memory usage after partitioning\n");
    1591:   }

    1593:   /* Put different mappings and other info into grid */
    1594:   /* ICALLOC(nvertices,&grid->loc2pet);
    1595:    ICALLOC(nvertices,&grid->loc2glo);
    1596:    PetscMemcpy(grid->loc2pet,l2p,nvertices*sizeof(int));
    1597:    PetscMemcpy(grid->loc2glo,l2a,nvertices*sizeof(int));
    1598:    PetscFree(l2a);
    1599:    PetscFree(l2p);*/

    1601:   grid->nnodesLoc  = nnodesLoc;
    1602:   grid->nedgeLoc   = nedgeLoc;
    1603:   grid->nvertices  = nvertices;
    1604:   grid->nsnodeLoc  = nsnodeLoc;
    1605:   grid->nvnodeLoc  = nvnodeLoc;
    1606:   grid->nfnodeLoc  = nfnodeLoc;
    1607:   grid->nnfacetLoc = nnfacetLoc;
    1608:   grid->nvfacetLoc = nvfacetLoc;
    1609:   grid->nffacetLoc = nffacetLoc;
    1610: /*
    1611:  * FCALLOC(nvertices*4, &grid->gradx);
    1612:  * FCALLOC(nvertices*4, &grid->grady);
    1613:  * FCALLOC(nvertices*4, &grid->gradz);
    1614:  */
    1615:   FCALLOC(nvertices,   &grid->cdt);
    1616:   FCALLOC(nvertices*4, &grid->phi);
    1617: /*
    1618:    FCALLOC(nvertices,   &grid->r11);
    1619:    FCALLOC(nvertices,   &grid->r12);
    1620:    FCALLOC(nvertices,   &grid->r13);
    1621:    FCALLOC(nvertices,   &grid->r22);
    1622:    FCALLOC(nvertices,   &grid->r23);
    1623:    FCALLOC(nvertices,   &grid->r33);
    1624: */
    1625:   FCALLOC(7*nnodesLoc,   &grid->rxy);

    1627: /* Map the 'ja' array in petsc ordering */
    1628:   for (i = 0; i < nnz; i++) grid->ja[i] = l2a[grid->ja[i] - 1];
    1629:   AOApplicationToPetsc(ao,nnz,grid->ja);
    1630:   AODestroy(&ao);

    1632: /* Print the different mappings
    1633:  *
    1634:  */
    1635:   {
    1636:     int partLoc[7],partMax[7],partMin[7],partSum[7];
    1637:     partLoc[0] = nnodesLoc;
    1638:     partLoc[1] = nvertices;
    1639:     partLoc[2] = nedgeLoc;
    1640:     partLoc[3] = nnfacetLoc;
    1641:     partLoc[4] = nffacetLoc;
    1642:     partLoc[5] = nsnodeLoc;
    1643:     partLoc[6] = nfnodeLoc;
    1644:     for (i = 0; i < 7; i++) {
    1645:       partMin[i] = 0;
    1646:       partMax[i] = 0;
    1647:       partSum[i] = 0;
    1648:     }

    1650:     MPI_Allreduce(partLoc,partMax,7,MPI_INT,MPI_MAX,comm);
    1651:     MPI_Allreduce(partLoc,partMin,7,MPI_INT,MPI_MIN,comm);
    1652:     MPI_Allreduce(partLoc,partSum,7,MPI_INT,MPI_SUM,comm);
    1653:     PetscPrintf(comm,"==============================\n");
    1654:     PetscPrintf(comm,"Partitioning quality info ....\n");
    1655:     PetscPrintf(comm,"==============================\n");
    1656:     PetscPrintf(comm,"------------------------------------------------------------\n");
    1657:     PetscPrintf(comm,"Item                    Min        Max    Average      Total\n");
    1658:     PetscPrintf(comm,"------------------------------------------------------------\n");
    1659:     PetscPrintf(comm,"Local Nodes       %9d  %9d  %9d  %9d\n",
    1660:                        partMin[0],partMax[0],partSum[0]/size,partSum[0]);
    1661:     PetscPrintf(comm,"Local+Ghost Nodes %9d  %9d  %9d  %9d\n",
    1662:                        partMin[1],partMax[1],partSum[1]/size,partSum[1]);
    1663:     PetscPrintf(comm,"Local Edges       %9d  %9d  %9d  %9d\n",
    1664:                        partMin[2],partMax[2],partSum[2]/size,partSum[2]);
    1665:     PetscPrintf(comm,"Local solid faces %9d  %9d  %9d  %9d\n",
    1666:                        partMin[3],partMax[3],partSum[3]/size,partSum[3]);
    1667:     PetscPrintf(comm,"Local free faces  %9d  %9d  %9d  %9d\n",
    1668:                        partMin[4],partMax[4],partSum[4]/size,partSum[4]);
    1669:     PetscPrintf(comm,"Local solid nodes %9d  %9d  %9d  %9d\n",
    1670:                        partMin[5],partMax[5],partSum[5]/size,partSum[5]);
    1671:     PetscPrintf(comm,"Local free nodes  %9d  %9d  %9d  %9d\n",
    1672:                        partMin[6],partMax[6],partSum[6]/size,partSum[6]);
    1673:     PetscPrintf(comm,"------------------------------------------------------------\n");
    1674:   }
    1675:   flg  = PETSC_FALSE;
    1676:   PetscOptionsGetBool(0,"-partition_info",&flg,NULL);
    1677:   if (flg) {
    1678:     char part_file[PETSC_MAX_PATH_LEN];
    1679:     sprintf(part_file,"output.%d",rank);
    1680:     fptr1 = fopen(part_file,"w");

    1682:     fprintf(fptr1,"---------------------------------------------\n");
    1683:     fprintf(fptr1,"Local and Global Grid Parameters are :\n");
    1684:     fprintf(fptr1,"---------------------------------------------\n");
    1685:     fprintf(fptr1,"Local\t\t\t\tGlobal\n");
    1686:     fprintf(fptr1,"nnodesLoc = %d\t\tnnodes = %d\n",nnodesLoc,nnodes);
    1687:     fprintf(fptr1,"nedgeLoc = %d\t\t\tnedge = %d\n",nedgeLoc,nedge);
    1688:     fprintf(fptr1,"nnfacetLoc = %d\t\tnnfacet = %d\n",nnfacetLoc,nnfacet);
    1689:     fprintf(fptr1,"nvfacetLoc = %d\t\t\tnvfacet = %d\n",nvfacetLoc,nvfacet);
    1690:     fprintf(fptr1,"nffacetLoc = %d\t\t\tnffacet = %d\n",nffacetLoc,nffacet);
    1691:     fprintf(fptr1,"nsnodeLoc = %d\t\t\tnsnode = %d\n",nsnodeLoc,nsnode);
    1692:     fprintf(fptr1,"nvnodeLoc = %d\t\t\tnvnode = %d\n",nvnodeLoc,nvnode);
    1693:     fprintf(fptr1,"nfnodeLoc = %d\t\t\tnfnode = %d\n",nfnodeLoc,nfnode);
    1694:     fprintf(fptr1,"\n");
    1695:     fprintf(fptr1,"nvertices = %d\n",nvertices);
    1696:     fprintf(fptr1,"nnbound = %d\n",nnbound);
    1697:     fprintf(fptr1,"nvbound = %d\n",nvbound);
    1698:     fprintf(fptr1,"nfbound = %d\n",nfbound);
    1699:     fprintf(fptr1,"\n");

    1701:     fprintf(fptr1,"---------------------------------------------\n");
    1702:     fprintf(fptr1,"Different Orderings\n");
    1703:     fprintf(fptr1,"---------------------------------------------\n");
    1704:     fprintf(fptr1,"Local\t\tPETSc\t\tGlobal\n");
    1705:     fprintf(fptr1,"---------------------------------------------\n");
    1706:     for (i = 0; i < nvertices; i++) fprintf(fptr1,"%d\t\t%d\t\t%d\n",i,grid->loc2pet[i],grid->loc2glo[i]);
    1707:     fprintf(fptr1,"\n");

    1709:     fprintf(fptr1,"---------------------------------------------\n");
    1710:     fprintf(fptr1,"Solid Boundary Nodes\n");
    1711:     fprintf(fptr1,"---------------------------------------------\n");
    1712:     fprintf(fptr1,"Local\t\tPETSc\t\tGlobal\n");
    1713:     fprintf(fptr1,"---------------------------------------------\n");
    1714:     for (i = 0; i < nsnodeLoc; i++) {
    1715:       j = grid->isnode[i]-1;
    1716:       fprintf(fptr1,"%d\t\t%d\t\t%d\n",j,grid->loc2pet[j],grid->loc2glo[j]);
    1717:     }
    1718:     fprintf(fptr1,"\n");
    1719:     fprintf(fptr1,"---------------------------------------------\n");
    1720:     fprintf(fptr1,"f2ntn array\n");
    1721:     fprintf(fptr1,"---------------------------------------------\n");
    1722:     for (i = 0; i < nnfacetLoc; i++) {
    1723:       fprintf(fptr1,"%d\t\t%d\t\t%d\t\t%d\n",i,grid->f2ntn[i],
    1724:               grid->f2ntn[nnfacetLoc+i],grid->f2ntn[2*nnfacetLoc+i]);
    1725:     }
    1726:     fprintf(fptr1,"\n");

    1728:     fprintf(fptr1,"---------------------------------------------\n");
    1729:     fprintf(fptr1,"Viscous Boundary Nodes\n");
    1730:     fprintf(fptr1,"---------------------------------------------\n");
    1731:     fprintf(fptr1,"Local\t\tPETSc\t\tGlobal\n");
    1732:     fprintf(fptr1,"---------------------------------------------\n");
    1733:     for (i = 0; i < nvnodeLoc; i++) {
    1734:       j = grid->ivnode[i]-1;
    1735:       fprintf(fptr1,"%d\t\t%d\t\t%d\n",j,grid->loc2pet[j],grid->loc2glo[j]);
    1736:     }
    1737:     fprintf(fptr1,"\n");
    1738:     fprintf(fptr1,"---------------------------------------------\n");
    1739:     fprintf(fptr1,"f2ntv array\n");
    1740:     fprintf(fptr1,"---------------------------------------------\n");
    1741:     for (i = 0; i < nvfacetLoc; i++) {
    1742:       fprintf(fptr1,"%d\t\t%d\t\t%d\t\t%d\n",i,grid->f2ntv[i],
    1743:               grid->f2ntv[nvfacetLoc+i],grid->f2ntv[2*nvfacetLoc+i]);
    1744:     }
    1745:     fprintf(fptr1,"\n");

    1747:     fprintf(fptr1,"---------------------------------------------\n");
    1748:     fprintf(fptr1,"Free Boundary Nodes\n");
    1749:     fprintf(fptr1,"---------------------------------------------\n");
    1750:     fprintf(fptr1,"Local\t\tPETSc\t\tGlobal\n");
    1751:     fprintf(fptr1,"---------------------------------------------\n");
    1752:     for (i = 0; i < nfnodeLoc; i++) {
    1753:       j = grid->ifnode[i]-1;
    1754:       fprintf(fptr1,"%d\t\t%d\t\t%d\n",j,grid->loc2pet[j],grid->loc2glo[j]);
    1755:     }
    1756:     fprintf(fptr1,"\n");
    1757:     fprintf(fptr1,"---------------------------------------------\n");
    1758:     fprintf(fptr1,"f2ntf array\n");
    1759:     fprintf(fptr1,"---------------------------------------------\n");
    1760:     for (i = 0; i < nffacetLoc; i++) {
    1761:       fprintf(fptr1,"%d\t\t%d\t\t%d\t\t%d\n",i,grid->f2ntf[i],
    1762:               grid->f2ntf[nffacetLoc+i],grid->f2ntf[2*nffacetLoc+i]);
    1763:     }
    1764:     fprintf(fptr1,"\n");

    1766:     fprintf(fptr1,"---------------------------------------------\n");
    1767:     fprintf(fptr1,"Neighborhood Info In Various Ordering\n");
    1768:     fprintf(fptr1,"---------------------------------------------\n");
    1769:     ICALLOC(nnodes,&p2l);
    1770:     for (i = 0; i < nvertices; i++) p2l[grid->loc2pet[i]] = i;
    1771:     for (i = 0; i < nnodesLoc; i++) {
    1772:       jstart = grid->ia[grid->loc2glo[i]] - 1;
    1773:       jend   = grid->ia[grid->loc2glo[i]+1] - 1;
    1774:       fprintf(fptr1,"Neighbors of Node %d in Local Ordering are :",i);
    1775:       for (j = jstart; j < jend; j++) fprintf(fptr1,"%d ",p2l[grid->ja[j]]);
    1776:       fprintf(fptr1,"\n");

    1778:       fprintf(fptr1,"Neighbors of Node %d in PETSc ordering are :",grid->loc2pet[i]);
    1779:       for (j = jstart; j < jend; j++) fprintf(fptr1,"%d ",grid->ja[j]);
    1780:       fprintf(fptr1,"\n");

    1782:       fprintf(fptr1,"Neighbors of Node %d in Global Ordering are :",grid->loc2glo[i]);
    1783:       for (j = jstart; j < jend; j++) fprintf(fptr1,"%d ",grid->loc2glo[p2l[grid->ja[j]]]);
    1784:       fprintf(fptr1,"\n");

    1786:     }
    1787:     fprintf(fptr1,"\n");
    1788:     PetscFree(p2l);
    1789:     fclose(fptr1);
    1790:   }

    1792: /* Free the temporary arrays */
    1793:   PetscFree(a2l);
    1794:   MPI_Barrier(comm);
    1795:   return 0;
    1796: }

    1798: /*
    1799:   encode 3 8-bit binary bytes as 4 '6-bit' characters, len is the number of bytes remaining, at most 3 are used
    1800: */
    1801: void *base64_encodeblock(void *vout,const void *vin,int len)
    1802: {
    1803:   unsigned char *out = (unsigned char*)vout,in[3] = {0,0,0};
    1804:   /* Translation Table as described in RFC1113 */
    1805:   static const char cb64[]="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/";
    1806:   memcpy(in,vin,PetscMin(len,3));
    1807:   out[0] = cb64[in[0] >> 2];
    1808:   out[1] = cb64[((in[0] & 0x03) << 4) | ((in[1] & 0xf0) >> 4)];
    1809:   out[2] = (unsigned char) (len > 1 ? cb64[((in[1] & 0x0f) << 2) | ((in[2] & 0xc0) >> 6)] : '=');
    1810:   out[3] = (unsigned char) (len > 2 ? cb64[in[2] & 0x3f] : '=');
    1811:   return (void*)(out+4);
    1812: }

    1814: /* Write binary data, does not do byte swapping. */
    1815: static PetscErrorCode PetscFWrite_FUN3D(MPI_Comm comm,FILE *fp,void *data,PetscInt n,PetscDataType dtype,PetscBool base64)
    1816: {
    1817:   PetscMPIInt    rank;

    1820:   if (!n) return 0;
    1821:   MPI_Comm_rank(comm,&rank);
    1822:   if (rank == 0) {
    1823:     size_t count;
    1824:     int    bytes;
    1825:     switch (dtype) {
    1826:     case PETSC_DOUBLE:
    1827:       size = sizeof(double);
    1828:       break;
    1829:     case PETSC_FLOAT:
    1830:       size = sizeof(float);
    1831:       break;
    1832:     case PETSC_INT:
    1833:       size = sizeof(PetscInt);
    1834:       break;
    1835:     case PETSC_CHAR:
    1836:       size = sizeof(char);
    1837:       break;
    1838:     default: SETERRQ(comm,PETSC_ERR_SUP,"Data type not supported");
    1839:     }
    1840:     bytes = size*n;
    1841:     if (base64) {
    1842:       unsigned char *buf,*ptr;
    1843:       int           i;
    1844:       size_t        b64alloc = 9 + (n*size*4) / 3 + (n*size*4) % 3;
    1845:       PetscMalloc(b64alloc,&buf);
    1846:       ptr  = buf;
    1847:       ptr  = (unsigned char*)base64_encodeblock(ptr,&bytes,3);
    1848:       ptr  = (unsigned char*)base64_encodeblock(ptr,((char*)&bytes)+3,1);
    1849:       for (i=0; i<bytes; i+=3) {
    1850:         int left = bytes - i;
    1851:         ptr = (unsigned char*)base64_encodeblock(ptr,((char*)data)+i,left);
    1852:       }
    1853:       *ptr++ = '\n';
    1854:       /* printf("encoded 4+%d raw bytes in %zd base64 chars, allocated for %zd\n",bytes,ptr-buf,b64alloc); */
    1855:       count = fwrite(buf,1,ptr-buf,fp);
    1856:       if (count < (size_t)(ptr-buf)) {
    1857:         perror("");
    1858:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_WRITE,"Wrote %" PetscInt_FMT " of %" PetscInt_FMT " bytes",(PetscInt)count,(PetscInt)(ptr-buf));
    1859:       }
    1860:       PetscFree(buf);
    1861:     } else {
    1862:       count = fwrite(&bytes,sizeof(int),1,fp);
    1863:       if (count != 1) {
    1864:         perror("");
    1865:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_WRITE,"Error writing byte count");
    1866:       }
    1867:       count = fwrite(data,size,(size_t)n,fp);
    1868:       if ((int)count != n) {
    1869:         perror("");
    1870:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_WRITE,"Wrote %" PetscInt_FMT "/%" PetscInt_FMT " array members of size %" PetscInt_FMT,(PetscInt)count,n,(PetscInt)size);
    1871:       }
    1872:     }
    1873:   }
    1874:   return 0;
    1875: }

    1877: static void SortInt2(PetscInt *a,PetscInt *b)
    1878: {
    1879:   if (*b < *a) {
    1880:     PetscInt c = *b;
    1881:     *b = *a;
    1882:     *a = c;
    1883:   }
    1884: }

    1886: /* b = intersection(a,b) */
    1887: static PetscErrorCode IntersectInt(PetscInt na,const PetscInt *a,PetscInt *nb,PetscInt *b)
    1888: {
    1889:   PetscInt i,n,j;

    1891:   j = 0;
    1892:   n = 0;
    1893:   for (i=0; i<*nb; i++) {
    1894:     while (j<na && a[j]<b[i]) j++;
    1895:     if (j<na && a[j]==b[i]) {
    1896:       b[n++] = b[i];
    1897:       j++;
    1898:     }
    1899:   }
    1900:   *nb = n;
    1901:   return 0;
    1902: }

    1904: /*
    1905:   This function currently has a semantic bug: it only produces cells containing all local edges.  Since the local mesh
    1906:   does not even store edges between unowned nodes, primal cells that are effectively shared between processes will not
    1907:   be constructed. This causes visualization artifacts.

    1909:   This issue could be resolved by either (a) storing more edges from the original mesh or (b) communicating an extra
    1910:   layer of edges in this function.
    1911: */
    1912: static PetscErrorCode InferLocalCellConnectivity(PetscInt nnodes,PetscInt nedge,const PetscInt *eptr,PetscInt *incell,PetscInt **iconn)
    1913: {
    1914:   PetscInt       ncell,acell,(*conn)[4],node0,node1,node2,node3,i,j,k,l,rowmax;
    1915:   PetscInt       *ui,*uj,*utmp,*tmp1,*tmp2,*tmp3,ntmp1,ntmp2,ntmp3;
    1916: #if defined(INTERLACING)
    1917: #  define GetEdge(eptr,i,n1,n2) do { n1 = eptr[i*2+0]-1; n2 = eptr[i*2+1]-1; } while (0)
    1918: #else
    1919: #  define GetEdge(eptr,i,n1,n2) do { n1 = eptr[i+0*nedge]-1; n2 = eptr[i+1*nedge]-1; } while (0)
    1920: #endif

    1922:   *incell = -1;
    1923:   *iconn  = NULL;
    1924:   acell   = 100000;              /* allocate for this many cells */
    1925:   PetscMalloc1(acell,&conn);
    1926:   PetscMalloc2(nnodes+1,&ui,nedge,&uj);
    1927:   PetscCalloc1(nnodes,&utmp);
    1928:   /* count the number of edges in the upper-triangular matrix u */
    1929:   for (i=0; i<nedge; i++) {     /* count number of nonzeros in upper triangular matrix */
    1930:     GetEdge(eptr,i,node0,node1);
    1931:     utmp[PetscMin(node0,node1)]++;
    1932:   }
    1933:   rowmax = 0;
    1934:   ui[0]  = 0;
    1935:   for (i=0; i<nnodes; i++) {
    1936:     rowmax  = PetscMax(rowmax,utmp[i]);
    1937:     ui[i+1] = ui[i] + utmp[i]; /* convert from count to row offsets */
    1938:     utmp[i] = 0;
    1939:   }
    1940:   for (i=0; i<nedge; i++) {     /* assemble upper triangular matrix U */
    1941:     GetEdge(eptr,i,node0,node1);
    1942:     SortInt2(&node0,&node1);
    1943:     uj[ui[node0] + utmp[node0]++] = node1;
    1944:   }
    1945:   PetscFree(utmp);
    1946:   for (i=0; i<nnodes; i++) {    /* sort every row */
    1947:     PetscInt n = ui[i+1] - ui[i];
    1948:     PetscSortInt(n,&uj[ui[i]]);
    1949:   }

    1951:   /* Infer cells */
    1952:   ncell = 0;
    1953:   PetscMalloc3(rowmax,&tmp1,rowmax,&tmp2,rowmax,&tmp3);
    1954:   for (i=0; i<nnodes; i++) {
    1955:     node0 = i;
    1956:     ntmp1 = ui[node0+1] - ui[node0]; /* Number of candidates for node1 */
    1957:     PetscMemcpy(tmp1,&uj[ui[node0]],ntmp1*sizeof(PetscInt));
    1958:     for (j=0; j<ntmp1; j++) {
    1959:       node1 = tmp1[j];
    1962:       ntmp2 = ui[node1+1] - ui[node1];
    1963:       PetscMemcpy(tmp2,&uj[ui[node1]],ntmp2*sizeof(PetscInt));
    1964:       IntersectInt(ntmp1,tmp1,&ntmp2,tmp2);
    1965:       for (k=0; k<ntmp2; k++) {
    1966:         node2 = tmp2[k];
    1969:         ntmp3 = ui[node2+1] - ui[node2];
    1970:         PetscMemcpy(tmp3,&uj[ui[node2]],ntmp3*sizeof(PetscInt));
    1971:         IntersectInt(ntmp2,tmp2,&ntmp3,tmp3);
    1972:         for (l=0; l<ntmp3; l++) {
    1973:           node3 = tmp3[l];
    1977:           if (ntmp3 < 3) continue;
    1978:           conn[ncell][0] = node0;
    1979:           conn[ncell][1] = node1;
    1980:           conn[ncell][2] = node2;
    1981:           conn[ncell][3] = node3;
    1982:           if (0) {
    1983:             PetscViewer viewer = PETSC_VIEWER_STDOUT_WORLD;
    1984:             PetscViewerASCIIPrintf(viewer,"created cell %d: %d %d %d %d\n",ncell,node0,node1,node2,node3);
    1985:             PetscIntView(ntmp1,tmp1,viewer);
    1986:             PetscIntView(ntmp2,tmp2,viewer);
    1987:             PetscIntView(ntmp3,tmp3,viewer);
    1988:             /* uns3d.msh has a handful of "tetrahedra" that overlap by violating the following condition. As far as I
    1989:              * can tell, that means it is an invalid mesh. I don't know what the intent was. */
    1991:           }
    1992:           ncell++;
    1993:         }
    1994:       }
    1995:     }
    1996:   }
    1997:   PetscFree3(tmp1,tmp2,tmp3);
    1998:   PetscFree2(ui,uj);

    2000:   PetscSynchronizedPrintf(PETSC_COMM_WORLD,"Inferred %" PetscInt_FMT " cells with nnodes=%" PetscInt_FMT " nedge=%" PetscInt_FMT "\n",ncell,nnodes,nedge);
    2001:   PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
    2002:   *incell = ncell;
    2003:   *iconn  = (PetscInt*)conn;
    2004:   return 0;
    2005: }

    2007: static PetscErrorCode GridCompleteOverlap(GRID *grid,PetscInt *invertices,PetscInt *inedgeOv,PetscInt **ieptrOv)
    2008: {
    2009:   PetscInt       nedgeLoc,nedgeOv,i,j,cnt,node0,node1,node0p,node1p,nnodes,nnodesLoc,nvertices,rstart,nodeEdgeCountAll,nodeEdgeRstart;
    2010:   PetscInt       *nodeEdgeCount,*nodeEdgeOffset,*eIdxOv,*p2l,*eptrOv;
    2011:   Vec            VNodeEdge,VNodeEdgeInfo,VNodeEdgeInfoOv,VNodeEdgeOv;
    2012:   PetscScalar    *vne,*vnei;
    2013:   IS             isglobal,isedgeOv;
    2014:   VecScatter     nescat,neiscat;
    2015:   PetscBool      flg;

    2017:   nnodes    = grid->nnodes;     /* Total number of global nodes */
    2018:   nnodesLoc = grid->nnodesLoc;  /* Number of owned nodes */
    2019:   nvertices = grid->nvertices;  /* Number of owned+ghosted nodes */
    2020:   nedgeLoc  = grid->nedgeLoc;   /* Number of edges connected to owned nodes */

    2022:   /* Count the number of neighbors of each owned node */
    2023:   MPI_Scan(&nnodesLoc,&rstart,1,MPIU_INT,MPI_SUM,PETSC_COMM_WORLD);
    2024:   rstart -= nnodesLoc;
    2025:   PetscMalloc2(nnodesLoc,&nodeEdgeCount,nnodesLoc,&nodeEdgeOffset);
    2026:   PetscMemzero(nodeEdgeCount,nnodesLoc*sizeof(*nodeEdgeCount));
    2027:   for (i=0; i<nedgeLoc; i++) {
    2028:     GetEdge(grid->eptr,i,node0,node1);
    2029:     node0p = grid->loc2pet[node0];
    2030:     node1p = grid->loc2pet[node1];
    2031:     if (rstart <= node0p && node0p < rstart+nnodesLoc) nodeEdgeCount[node0p-rstart]++;
    2032:     if (rstart <= node1p && node1p < rstart+nnodesLoc) nodeEdgeCount[node1p-rstart]++;
    2033:   }
    2034:   /* Get the offset in the node-based edge array */
    2035:   nodeEdgeOffset[0] = 0;
    2036:   for (i=0; i<nnodesLoc-1; i++) nodeEdgeOffset[i+1] = nodeEdgeOffset[i] + nodeEdgeCount[i];
    2037:   nodeEdgeCountAll = nodeEdgeCount[nnodesLoc-1] + nodeEdgeOffset[nnodesLoc-1];

    2039:   /* Pack a Vec by node of all the edges for that node. The nodes are stored by global index */
    2040:   VecCreateMPI(PETSC_COMM_WORLD,nodeEdgeCountAll,PETSC_DETERMINE,&VNodeEdge);
    2041:   PetscMemzero(nodeEdgeCount,nnodesLoc*sizeof(*nodeEdgeCount));
    2042:   VecGetArray(VNodeEdge,&vne);
    2043:   for (i=0; i<nedgeLoc; i++) {
    2044:     GetEdge(grid->eptr,i,node0,node1);
    2045:     node0p = grid->loc2pet[node0];
    2046:     node1p = grid->loc2pet[node1];
    2047:     if (rstart <= node0p && node0p < rstart+nnodesLoc) vne[nodeEdgeOffset[node0p-rstart] + nodeEdgeCount[node0p-rstart]++] = node1p;
    2048:     if (rstart <= node1p && node1p < rstart+nnodesLoc) vne[nodeEdgeOffset[node1p-rstart] + nodeEdgeCount[node1p-rstart]++] = node0p;
    2049:   }
    2050:   VecRestoreArray(VNodeEdge,&vne);
    2051:   VecGetOwnershipRange(VNodeEdge,&nodeEdgeRstart,NULL);

    2053:   /* Move the count and offset into a Vec so that we can use VecScatter, translating offset from local to global */
    2054:   VecCreate(PETSC_COMM_WORLD,&VNodeEdgeInfo);
    2055:   VecSetSizes(VNodeEdgeInfo,2*nnodesLoc,2*nnodes);
    2056:   VecSetBlockSize(VNodeEdgeInfo,2);
    2057:   VecSetType(VNodeEdgeInfo,VECMPI);

    2059:   VecGetArray(VNodeEdgeInfo,&vnei);
    2060:   for (i=0; i<nnodesLoc; i++) {
    2061:     vnei[i*2+0] = nodeEdgeCount[i];                   /* Total number of edges from this vertex */
    2062:     vnei[i*2+1] = nodeEdgeOffset[i] + nodeEdgeRstart; /* Now the global index in the next comm round */
    2063:   }
    2064:   VecRestoreArray(VNodeEdgeInfo,&vnei);
    2065:   PetscFree2(nodeEdgeCount,nodeEdgeOffset);

    2067:   /* Create a Vec to receive the edge count and global offset for each node in owned+ghosted, get them, and clean up */
    2068:   VecCreate(PETSC_COMM_SELF,&VNodeEdgeInfoOv);
    2069:   VecSetSizes(VNodeEdgeInfoOv,2*nvertices,2*nvertices);
    2070:   VecSetBlockSize(VNodeEdgeInfoOv,2);
    2071:   VecSetType(VNodeEdgeInfoOv,VECSEQ);

    2073:   ISCreateBlock(PETSC_COMM_WORLD,2,nvertices,grid->loc2pet,PETSC_COPY_VALUES,&isglobal); /* Address the nodes in overlap to get info from */
    2074:   VecScatterCreate(VNodeEdgeInfo,isglobal,VNodeEdgeInfoOv,NULL,&neiscat);
    2075:   VecScatterBegin(neiscat,VNodeEdgeInfo,VNodeEdgeInfoOv,INSERT_VALUES,SCATTER_FORWARD);
    2076:   VecScatterEnd(neiscat,VNodeEdgeInfo,VNodeEdgeInfoOv,INSERT_VALUES,SCATTER_FORWARD);
    2077:   VecScatterDestroy(&neiscat);
    2078:   VecDestroy(&VNodeEdgeInfo);
    2079:   ISDestroy(&isglobal);

    2081:   /* Create a Vec to receive the actual edges for all nodes (owned and ghosted), execute the scatter */
    2082:   nedgeOv = 0;                  /* First count the number of edges in the complete overlap */
    2083:   VecGetArray(VNodeEdgeInfoOv,&vnei);
    2084:   for (i=0; i<nvertices; i++) nedgeOv += (PetscInt)vnei[2*i+0];
    2085:   /* Allocate for the global indices in VNodeEdge of the edges to receive */
    2086:   PetscMalloc1(nedgeOv,&eIdxOv);
    2087:   for (i=0,cnt=0; i<nvertices; i++) {
    2088:     for (j=0; j<(PetscInt)vnei[2*i+0]; j++) eIdxOv[cnt++] = (PetscInt)vnei[2*i+1] + j;
    2089:   }
    2090:   VecRestoreArray(VNodeEdgeInfoOv,&vnei);
    2091:   ISCreateGeneral(PETSC_COMM_WORLD,nedgeOv,eIdxOv,PETSC_USE_POINTER,&isedgeOv);
    2092:   VecCreateSeq(PETSC_COMM_SELF,nedgeOv,&VNodeEdgeOv);
    2093:   VecScatterCreate(VNodeEdge,isedgeOv,VNodeEdgeOv,NULL,&nescat);
    2094:   VecScatterBegin(nescat,VNodeEdge,VNodeEdgeOv,INSERT_VALUES,SCATTER_FORWARD);
    2095:   VecScatterEnd(nescat,VNodeEdge,VNodeEdgeOv,INSERT_VALUES,SCATTER_FORWARD);
    2096:   VecScatterDestroy(&nescat);
    2097:   VecDestroy(&VNodeEdge);
    2098:   ISDestroy(&isedgeOv);
    2099:   PetscFree(eIdxOv);

    2101:   PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d] %s: number of edges before pruning: %" PetscInt_FMT ", half=%" PetscInt_FMT "\n",rank,PETSC_FUNCTION_NAME,nedgeOv,nedgeOv/2);

    2103:   /* Create the non-scalable global-to-local index map. Yuck, but it has already been used elsewhere. */
    2104:   PetscMalloc1(nnodes,&p2l);
    2105:   for (i=0; i<nnodes; i++) p2l[i] = -1;
    2106:   for (i=0; i<nvertices; i++) p2l[grid->loc2pet[i]] = i;
    2107:   if (1) {
    2108:     PetscInt m = 0;
    2109:     for (i=0; i<nnodes; i++) m += (p2l[i] >= 0);
    2110:     PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d] %s: number of global indices that map to local indices: %" PetscInt_FMT "; nvertices=%" PetscInt_FMT " nnodesLoc=%" PetscInt_FMT " nnodes=%" PetscInt_FMT "\n",rank,PETSC_FUNCTION_NAME,m,nvertices,nnodesLoc,nnodes);
    2111:   }

    2113:   /* Log each edge connecting nodes in owned+ghosted exactly once */
    2114:   VecGetArray(VNodeEdgeInfoOv,&vnei);
    2115:   VecGetArray(VNodeEdgeOv,&vne);
    2116:   /* First count the number of edges to keep */
    2117:   nedgeOv = 0;
    2118:   for (i=0,cnt=0; i<nvertices; i++) {
    2119:     PetscInt n = (PetscInt)vnei[2*i+0]; /* number of nodes connected to i */
    2120:     node0 = i;
    2121:     for (j=0; j<n; j++) {
    2122:       node1p = vne[cnt++];
    2123:       node1  = p2l[node1p];
    2124:       if (node0 < node1) nedgeOv++;
    2125:     }
    2126:   }
    2127:   /* Array of edges to keep */
    2128:   PetscMalloc1(2*nedgeOv,&eptrOv);
    2129:   nedgeOv = 0;
    2130:   for (i=0,cnt=0; i<nvertices; i++) {
    2131:     PetscInt n = (PetscInt)vnei[2*i+0]; /* number of nodes connected to i */
    2132:     node0 = i;
    2133:     for (j=0; j<n; j++) {
    2134:       node1p = vne[cnt++];
    2135:       node1  = p2l[node1p];
    2136:       if (node0 < node1) {
    2137:         eptrOv[2*nedgeOv+0] = node0;
    2138:         eptrOv[2*nedgeOv+1] = node1;
    2139:         nedgeOv++;
    2140:       }
    2141:     }
    2142:   }
    2143:   VecRestoreArray(VNodeEdgeInfoOv,&vnei);
    2144:   VecRestoreArray(VNodeEdgeOv,&vne);
    2145:   VecDestroy(&VNodeEdgeInfoOv);
    2146:   VecDestroy(&VNodeEdgeOv);
    2147:   PetscFree(p2l);

    2149:   PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d] %s: nedgeLoc=%" PetscInt_FMT " nedgeOv=%" PetscInt_FMT "\n",rank,PETSC_FUNCTION_NAME,nedgeLoc,nedgeOv);
    2150:   PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);

    2152:   flg  = PETSC_TRUE;
    2153:   PetscOptionsGetBool(NULL,NULL,"-complete_overlap",&flg,NULL);
    2154:   if (flg) {
    2155:     *invertices = grid->nvertices; /* We did not change the number of vertices */
    2156:     *inedgeOv   = nedgeOv;
    2157:     *ieptrOv    = eptrOv;
    2158:   } else {
    2159:     *invertices = grid->nvertices;
    2160:     *inedgeOv   = nedgeLoc;
    2161:     PetscFree(eptrOv);
    2162:     PetscMalloc1(2*nedgeLoc,&eptrOv);
    2163:     PetscMemcpy(eptrOv,grid->eptr,2*nedgeLoc*sizeof(PetscInt));
    2164:     *ieptrOv    = eptrOv;
    2165:   }
    2166:   return 0;
    2167: }

    2169: static PetscErrorCode WritePVTU(AppCtx *user,const char *fname,PetscBool base64)
    2170: {
    2171:   GRID              *grid  = user->grid;
    2172:   TstepCtx          *tsCtx = user->tsCtx;
    2173:   FILE              *vtu,*pvtu;
    2174:   char              pvtu_fname[PETSC_MAX_PATH_LEN],vtu_fname[PETSC_MAX_PATH_LEN];
    2175:   MPI_Comm          comm;
    2176:   PetscMPIInt       rank,size;
    2177:   PetscInt          i,nvertices = 0,nedgeLoc = 0,ncells,bs,nloc,boffset = 0,*eptr = NULL;
    2178:   PetscErrorCode    ierr;
    2179:   Vec               Xloc,Xploc,Xuloc;
    2180:   unsigned char     *celltype;
    2181:   int               *celloffset,*conn,*cellrank;
    2182:   const PetscScalar *x;
    2183:   PetscScalar       *xu,*xp;
    2184:   const char        *byte_order = PetscBinaryBigEndian() ? "BigEndian" : "LittleEndian";

    2186:   GridCompleteOverlap(user->grid,&nvertices,&nedgeLoc,&eptr);
    2187:   comm = PETSC_COMM_WORLD;
    2188:   MPI_Comm_rank(comm,&rank);
    2189:   MPI_Comm_size(comm,&size);
    2190: #if defined(PETSC_USE_COMPLEX) || !defined(PETSC_USE_REAL_DOUBLE) || defined(PETSC_USE_64BIT_INDICES)
    2191:   SETERRQ(comm,PETSC_ERR_SUP,"This function is only implemented for scalar-type=real precision=double, 32-bit indices");
    2192: #endif
    2193:   PetscSNPrintf(pvtu_fname,sizeof(pvtu_fname),"%s-%" PetscInt_FMT ".pvtu",fname,tsCtx->itstep);
    2194:   PetscSNPrintf(vtu_fname,sizeof(vtu_fname),"%s-%" PetscInt_FMT "-%" PetscInt_FMT ".vtu",fname,tsCtx->itstep,rank);
    2195:   PetscFOpen(comm,pvtu_fname,"w",&pvtu);
    2196:   PetscFPrintf(comm,pvtu,"<?xml version=\"1.0\"?>\n");
    2197:   PetscFPrintf(comm,pvtu,"<VTKFile type=\"PUnstructuredGrid\" version=\"0.1\" byte_order=\"%s\">\n",byte_order);
    2198:   PetscFPrintf(comm,pvtu," <PUnstructuredGrid GhostLevel=\"0\">\n");
    2199:   PetscFPrintf(comm,pvtu,"  <PPointData Scalars=\"Pressure\" Vectors=\"Velocity\">\n");
    2200:   PetscFPrintf(comm,pvtu,"   <PDataArray type=\"Float64\" Name=\"Pressure\" NumberOfComponents=\"1\" />\n");
    2201:   PetscFPrintf(comm,pvtu,"   <PDataArray type=\"Float64\" Name=\"Velocity\" NumberOfComponents=\"3\" />\n");
    2202:   PetscFPrintf(comm,pvtu,"  </PPointData>\n");
    2203:   PetscFPrintf(comm,pvtu,"  <PCellData>\n");
    2204:   PetscFPrintf(comm,pvtu,"   <PDataArray type=\"Int32\" Name=\"Rank\" NumberOfComponents=\"1\" />\n");
    2205:   PetscFPrintf(comm,pvtu,"  </PCellData>\n");
    2206:   PetscFPrintf(comm,pvtu,"  <PPoints>\n");
    2207:   PetscFPrintf(comm,pvtu,"   <PDataArray type=\"Float64\" Name=\"Position\" NumberOfComponents=\"3\" />\n");
    2208:   PetscFPrintf(comm,pvtu,"  </PPoints>\n");
    2209:   PetscFPrintf(comm,pvtu,"  <PCells>\n");
    2210:   PetscFPrintf(comm,pvtu,"   <PDataArray type=\"Int32\" Name=\"connectivity\" NumberOfComponents=\"1\" />\n");
    2211:   PetscFPrintf(comm,pvtu,"   <PDataArray type=\"Int32\" Name=\"offsets\"      NumberOfComponents=\"1\" />\n");
    2212:   PetscFPrintf(comm,pvtu,"   <PDataArray type=\"UInt8\" Name=\"types\"        NumberOfComponents=\"1\" />\n");
    2213:   PetscFPrintf(comm,pvtu,"  </PCells>\n");
    2214:   for (i=0; i<size; i++) {
    2215:     PetscFPrintf(comm,pvtu,"  <Piece Source=\"%s-%" PetscInt_FMT "-%" PetscInt_FMT ".vtu\" />\n",fname,tsCtx->itstep,i);
    2216:   }
    2217:   PetscFPrintf(comm,pvtu," </PUnstructuredGrid>\n");
    2218:   PetscFPrintf(comm,pvtu,"</VTKFile>\n");
    2219:   PetscFClose(comm,pvtu);

    2221:   Xloc = grid->qnodeLoc;
    2222:   VecScatterBegin(grid->scatter,grid->qnode,Xloc,INSERT_VALUES,SCATTER_FORWARD);
    2223:   VecScatterEnd(grid->scatter,grid->qnode,Xloc,INSERT_VALUES,SCATTER_FORWARD);
    2224:   VecGetBlockSize(Xloc,&bs);
    2226:   VecGetSize(Xloc,&nloc);
    2229:   VecCreateSeq(PETSC_COMM_SELF,nvertices,&Xploc);

    2231:   VecCreate(PETSC_COMM_SELF,&Xuloc);
    2232:   VecSetSizes(Xuloc,3*nvertices,3*nvertices);
    2233:   VecSetBlockSize(Xuloc,3);
    2234:   VecSetType(Xuloc,VECSEQ);

    2236:   VecGetArrayRead(Xloc,&x);
    2237:   VecGetArray(Xploc,&xp);
    2238:   VecGetArray(Xuloc,&xu);
    2239:   for (i=0; i<nvertices; i++) {
    2240:     xp[i]     = x[i*4+0];
    2241:     xu[i*3+0] = x[i*4+1];
    2242:     xu[i*3+1] = x[i*4+2];
    2243:     xu[i*3+2] = x[i*4+3];
    2244:   }
    2245:   VecRestoreArrayRead(Xloc,&x);

    2247:   InferLocalCellConnectivity(nvertices,nedgeLoc,eptr,&ncells,&conn);

    2249:   PetscFOpen(PETSC_COMM_SELF,vtu_fname,"w",&vtu);
    2250:   PetscFPrintf(PETSC_COMM_SELF,vtu,"<?xml version=\"1.0\"?>\n");
    2251:   PetscFPrintf(PETSC_COMM_SELF,vtu,"<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"%s\">\n",byte_order);
    2252:   PetscFPrintf(PETSC_COMM_SELF,vtu," <UnstructuredGrid>\n");
    2253:   PetscFPrintf(PETSC_COMM_SELF,vtu,"  <Piece NumberOfPoints=\"%" PetscInt_FMT "\" NumberOfCells=\"%" PetscInt_FMT "\">\n",nvertices,ncells);

    2255:   /* Solution fields */
    2256:   PetscFPrintf(PETSC_COMM_SELF,vtu,"   <PointData Scalars=\"Pressure\" Vectors=\"Velocity\">\n");
    2257:   PetscFPrintf(PETSC_COMM_SELF,vtu,"    <DataArray type=\"Float64\" Name=\"Pressure\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%" PetscInt_FMT "\" />\n",boffset);
    2258:   boffset += nvertices*sizeof(PetscScalar) + sizeof(int);
    2259:   PetscFPrintf(PETSC_COMM_SELF,vtu,"    <DataArray type=\"Float64\" Name=\"Velocity\" NumberOfComponents=\"3\" format=\"appended\" offset=\"%" PetscInt_FMT "\" />\n",boffset);
    2260:   boffset += nvertices*3*sizeof(PetscScalar) + sizeof(int);
    2261:   PetscFPrintf(PETSC_COMM_SELF,vtu,"   </PointData>\n");
    2262:   PetscFPrintf(PETSC_COMM_SELF,vtu,"   <CellData>\n");
    2263:   PetscFPrintf(PETSC_COMM_SELF,vtu,"    <DataArray type=\"Int32\" Name=\"Rank\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%" PetscInt_FMT "\" />\n",boffset);
    2264:   boffset += ncells*sizeof(int) + sizeof(int);
    2265:   PetscFPrintf(PETSC_COMM_SELF,vtu,"   </CellData>\n");
    2266:   /* Coordinate positions */
    2267:   PetscFPrintf(PETSC_COMM_SELF,vtu,"   <Points>\n");
    2268:   PetscFPrintf(PETSC_COMM_SELF,vtu,"    <DataArray type=\"Float64\" Name=\"Position\" NumberOfComponents=\"3\" format=\"appended\" offset=\"%" PetscInt_FMT "\" />\n",boffset);
    2269:   boffset += nvertices*3*sizeof(double) + sizeof(int);
    2270:   PetscFPrintf(PETSC_COMM_SELF,vtu,"   </Points>\n");
    2271:   /* Cell connectivity */
    2272:   PetscFPrintf(PETSC_COMM_SELF,vtu,"   <Cells>\n");
    2273:   PetscFPrintf(PETSC_COMM_SELF,vtu,"    <DataArray type=\"Int32\" Name=\"connectivity\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%" PetscInt_FMT "\" />\n",boffset);
    2274:   boffset += ncells*4*sizeof(int) + sizeof(int);
    2275:   PetscFPrintf(PETSC_COMM_SELF,vtu,"    <DataArray type=\"Int32\" Name=\"offsets\"      NumberOfComponents=\"1\" format=\"appended\" offset=\"%" PetscInt_FMT "\" />\n",boffset);
    2276:   boffset += ncells*sizeof(int) + sizeof(int);
    2277:   PetscFPrintf(PETSC_COMM_SELF,vtu,"    <DataArray type=\"UInt8\" Name=\"types\"        NumberOfComponents=\"1\" format=\"appended\" offset=\"%" PetscInt_FMT "\" />\n",boffset);
    2278:   boffset += ncells*sizeof(unsigned char) + sizeof(int);
    2279:   PetscFPrintf(PETSC_COMM_SELF,vtu,"   </Cells>\n");
    2280:   PetscFPrintf(PETSC_COMM_SELF,vtu,"  </Piece>\n");
    2281:   PetscFPrintf(PETSC_COMM_SELF,vtu," </UnstructuredGrid>\n");
    2282:   PetscFPrintf(PETSC_COMM_SELF,vtu," <AppendedData encoding=\"%s\">\n",base64 ? "base64" : "raw");
    2283:   PetscFPrintf(PETSC_COMM_SELF,vtu,"_");

    2285:   /* Write pressure */
    2286:   PetscFWrite_FUN3D(PETSC_COMM_SELF,vtu,xp,nvertices,PETSC_SCALAR,base64);

    2288:   /* Write velocity */
    2289:   PetscFWrite_FUN3D(PETSC_COMM_SELF,vtu,xu,nvertices*3,PETSC_SCALAR,base64);

    2291:   /* Label cell rank, not a measure of computation because nothing is actually computed at cells.  This is written
    2292:    * primarily to aid in debugging. The partition for computation should label vertices. */
    2293:   PetscMalloc1(ncells,&cellrank);
    2294:   for (i=0; i<ncells; i++) cellrank[i] = rank;
    2295:   PetscFWrite_FUN3D(PETSC_COMM_SELF,vtu,cellrank,ncells,PETSC_INT,base64);
    2296:   PetscFree(cellrank);

    2298:   PetscFWrite_FUN3D(PETSC_COMM_SELF,vtu,grid->xyz,nvertices*3,PETSC_DOUBLE,base64);
    2299:   PetscFWrite_FUN3D(PETSC_COMM_SELF,vtu,conn,ncells*4,PETSC_INT,base64);
    2300:   PetscFree(conn);

    2302:   PetscMalloc1(ncells,&celloffset);
    2303:   for (i=0; i<ncells; i++) celloffset[i] = 4*(i+1);
    2304:   PetscFWrite_FUN3D(PETSC_COMM_SELF,vtu,celloffset,ncells,PETSC_INT,base64);
    2305:   PetscFree(celloffset);

    2307:   PetscMalloc1(ncells,&celltype);
    2308:   for (i=0; i<ncells; i++) celltype[i] = 10; /* VTK_TETRA */
    2309:   PetscFWrite_FUN3D(PETSC_COMM_SELF,vtu,celltype,ncells,PETSC_CHAR,base64);
    2310:   PetscFree(celltype);

    2312:   PetscFPrintf(PETSC_COMM_SELF,vtu,"\n </AppendedData>\n");
    2313:   PetscFPrintf(PETSC_COMM_SELF,vtu,"</VTKFile>\n");
    2314:   PetscFClose(PETSC_COMM_SELF,vtu);

    2316:   VecRestoreArray(Xploc,&xp);
    2317:   VecRestoreArray(Xuloc,&xu);
    2318:   VecDestroy(&Xploc);
    2319:   VecDestroy(&Xuloc);
    2320:   PetscFree(eptr);
    2321:   return 0;
    2322: }

    2324: /*---------------------------------------------------------------------*/
    2325: int SetPetscDS(GRID *grid,TstepCtx *tsCtx)
    2326: /*---------------------------------------------------------------------*/
    2327: {
    2328:   int                    ierr,i,j,bs;
    2329:   int                    nnodes,jstart,jend,nbrs_diag,nbrs_offd;
    2330:   int                    nnodesLoc,nvertices;
    2331:   int                    *val_diag,*val_offd,*svertices,*loc2pet;
    2332:   IS                     isglobal,islocal;
    2333:   ISLocalToGlobalMapping isl2g;
    2334:   PetscBool              flg;
    2335:   MPI_Comm               comm = PETSC_COMM_WORLD;

    2337:   nnodes    = grid->nnodes;
    2338:   nnodesLoc = grid->nnodesLoc;
    2339:   nvertices = grid->nvertices;
    2340:   loc2pet   = grid->loc2pet;
    2341:   bs        = 4;

    2343:   /* Set up the PETSc datastructures */

    2345:   VecCreate(comm,&grid->qnode);
    2346:   VecSetSizes(grid->qnode,bs*nnodesLoc,bs*nnodes);
    2347:   VecSetBlockSize(grid->qnode,bs);
    2348:   VecSetType(grid->qnode,VECMPI);

    2350:   VecDuplicate(grid->qnode,&grid->res);
    2351:   VecDuplicate(grid->qnode,&tsCtx->qold);
    2352:   VecDuplicate(grid->qnode,&tsCtx->func);

    2354:   VecCreate(MPI_COMM_SELF,&grid->qnodeLoc);
    2355:   VecSetSizes(grid->qnodeLoc,bs*nvertices,bs*nvertices);
    2356:   VecSetBlockSize(grid->qnodeLoc,bs);
    2357:   VecSetType(grid->qnodeLoc,VECSEQ);

    2359:   VecCreate(comm,&grid->grad);
    2360:   VecSetSizes(grid->grad,3*bs*nnodesLoc,3*bs*nnodes);
    2361:   VecSetBlockSize(grid->grad,3*bs);
    2362:   VecSetType(grid->grad,VECMPI);

    2364:   VecCreate(MPI_COMM_SELF,&grid->gradLoc);
    2365:   VecSetSizes(grid->gradLoc,3*bs*nvertices,3*bs*nvertices);
    2366:   VecSetBlockSize(grid->gradLoc,3*bs);
    2367:   VecSetType(grid->gradLoc,VECSEQ);

    2369: /* Create Scatter between the local and global vectors */
    2370: /* First create scatter for qnode */
    2371:   ISCreateStride(MPI_COMM_SELF,bs*nvertices,0,1,&islocal);
    2372: #if defined(INTERLACING)
    2373: #if defined(BLOCKING)
    2374:   ICALLOC(nvertices,&svertices);
    2375:   for (i=0; i < nvertices; i++) svertices[i] = loc2pet[i];
    2376:   ISCreateBlock(MPI_COMM_SELF,bs,nvertices,svertices,PETSC_COPY_VALUES,&isglobal);
    2377: #else
    2378:   ICALLOC(bs*nvertices,&svertices);
    2379:   for (i = 0; i < nvertices; i++)
    2380:     for (j = 0; j < bs; j++) svertices[j+bs*i] = j + bs*loc2pet[i];
    2381:   ISCreateGeneral(MPI_COMM_SELF,bs*nvertices,svertices,PETSC_COPY_VALUES,&isglobal);
    2382: #endif
    2383: #else
    2384:   ICALLOC(bs*nvertices,&svertices);
    2385:   for (j = 0; j < bs; j++)
    2386:     for (i = 0; i < nvertices; i++) svertices[j*nvertices+i] = j*nvertices + loc2pet[i];
    2387:   ISCreateGeneral(MPI_COMM_SELF,bs*nvertices,svertices,PETSC_COPY_VALUES,&isglobal);
    2388: #endif
    2389:   PetscFree(svertices);
    2390:   VecScatterCreate(grid->qnode,isglobal,grid->qnodeLoc,islocal,&grid->scatter);
    2391:   ISDestroy(&isglobal);
    2392:   ISDestroy(&islocal);

    2394: /* Now create scatter for gradient vector of qnode */
    2395:   ISCreateStride(MPI_COMM_SELF,3*bs*nvertices,0,1,&islocal);
    2396: #if defined(INTERLACING)
    2397: #if defined(BLOCKING)
    2398:   ICALLOC(nvertices,&svertices);
    2399:   for (i=0; i < nvertices; i++) svertices[i] = loc2pet[i];
    2400:   ISCreateBlock(MPI_COMM_SELF,3*bs,nvertices,svertices,PETSC_COPY_VALUES,&isglobal);
    2401: #else
    2402:   ICALLOC(3*bs*nvertices,&svertices);
    2403:   for (i = 0; i < nvertices; i++)
    2404:     for (j = 0; j < 3*bs; j++) svertices[j+3*bs*i] = j + 3*bs*loc2pet[i];
    2405:   ISCreateGeneral(MPI_COMM_SELF,3*bs*nvertices,svertices,PETSC_COPY_VALUES,&isglobal);
    2406: #endif
    2407: #else
    2408:   ICALLOC(3*bs*nvertices,&svertices);
    2409:   for (j = 0; j < 3*bs; j++)
    2410:     for (i = 0; i < nvertices; i++) svertices[j*nvertices+i] = j*nvertices + loc2pet[i];
    2411:   ISCreateGeneral(MPI_COMM_SELF,3*bs*nvertices,svertices,PETSC_COPY_VALUES,&isglobal);
    2412: #endif
    2413:   PetscFree(svertices);
    2414:   VecScatterCreate(grid->grad,isglobal,grid->gradLoc,islocal,&grid->gradScatter);
    2415:   ISDestroy(&isglobal);
    2416:   ISDestroy(&islocal);

    2418: /* Store the number of non-zeroes per row */
    2419: #if defined(INTERLACING)
    2420: #if defined(BLOCKING)
    2421:   ICALLOC(nnodesLoc,&val_diag);
    2422:   ICALLOC(nnodesLoc,&val_offd);
    2423:   for (i = 0; i < nnodesLoc; i++) {
    2424:     jstart    = grid->ia[i] - 1;
    2425:     jend      = grid->ia[i+1] - 1;
    2426:     nbrs_diag = 0;
    2427:     nbrs_offd = 0;
    2428:     for (j = jstart; j < jend; j++) {
    2429:       if ((grid->ja[j] >= rstart) && (grid->ja[j] < (rstart+nnodesLoc))) nbrs_diag++;
    2430:       else nbrs_offd++;
    2431:     }
    2432:     val_diag[i] = nbrs_diag;
    2433:     val_offd[i] = nbrs_offd;
    2434:   }
    2435:   MatCreateBAIJ(comm,bs,bs*nnodesLoc,bs*nnodesLoc,
    2436:                        bs*nnodes,bs*nnodes,PETSC_DEFAULT,val_diag,
    2437:                        PETSC_DEFAULT,val_offd,&grid->A);
    2438: #else
    2439:   ICALLOC(nnodesLoc*4,&val_diag);
    2440:   ICALLOC(nnodesLoc*4,&val_offd);
    2441:   for (i = 0; i < nnodesLoc; i++) {
    2442:     jstart    = grid->ia[i] - 1;
    2443:     jend      = grid->ia[i+1] - 1;
    2444:     nbrs_diag = 0;
    2445:     nbrs_offd = 0;
    2446:     for (j = jstart; j < jend; j++) {
    2447:       if ((grid->ja[j] >= rstart) && (grid->ja[j] < (rstart+nnodesLoc))) nbrs_diag++;
    2448:       else nbrs_offd++;
    2449:     }
    2450:     for (j = 0; j < 4; j++) {
    2451:       row           = 4*i + j;
    2452:       val_diag[row] = nbrs_diag*4;
    2453:       val_offd[row] = nbrs_offd*4;
    2454:     }
    2455:   }
    2456:   MatCreateAIJ(comm,bs*nnodesLoc,bs*nnodesLoc,
    2457:                       bs*nnodes,bs*nnodes,NULL,val_diag,
    2458:                       NULL,val_offd,&grid->A);
    2459: #endif
    2460:   PetscFree(val_diag);
    2461:   PetscFree(val_offd);

    2463: #else
    2465:   ICALLOC(nnodes*4,&val_diag);
    2466:   ICALLOC(nnodes*4,&val_offd);
    2467:   for (j = 0; j < 4; j++)
    2468:     for (i = 0; i < nnodes; i++) {
    2469:       int row;
    2470:       row           = i + j*nnodes;
    2471:       jstart        = grid->ia[i] - 1;
    2472:       jend          = grid->ia[i+1] - 1;
    2473:       nbrs_diag     = jend - jstart;
    2474:       val_diag[row] = nbrs_diag*4;
    2475:       val_offd[row] = 0;
    2476:     }
    2477:   /* MatCreateSeqAIJ(MPI_COMM_SELF,nnodes*4,nnodes*4,NULL,
    2478:                         val,&grid->A);*/
    2479:   MatCreateAIJ(comm,bs*nnodesLoc,bs*nnodesLoc,
    2480:                       bs*nnodes,bs*nnodes,NULL,val_diag,
    2481:                       NULL,val_offd,&grid->A);
    2482:   MatSetBlockSize(grid->A,bs);
    2483:   PetscFree(val_diag);
    2484:   PetscFree(val_offd);
    2485: #endif

    2487:   flg  = PETSC_FALSE;
    2488:   PetscOptionsGetBool(0,"-mem_use",&flg,NULL);
    2489:   if (flg) {
    2490:     PetscMemoryView(PETSC_VIEWER_STDOUT_WORLD,"Memory usage after allocating PETSc data structures\n");
    2491:   }

    2493: /* Set local to global mapping for setting the matrix elements in
    2494:    local ordering : first set row by row mapping
    2495: */
    2496:   ISLocalToGlobalMappingCreate(MPI_COMM_SELF,bs,nvertices,loc2pet,PETSC_COPY_VALUES,&isl2g);
    2497:   MatSetLocalToGlobalMapping(grid->A,isl2g,isl2g);
    2498:   ISLocalToGlobalMappingDestroy(&isl2g);
    2499:   return 0;
    2500: }

    2502: /*================================= CLINK ===================================*/
    2503: /*                                                                           */
    2504: /* Used in establishing the links between FORTRAN common blocks and C        */
    2505: /*                                                                           */
    2506: /*===========================================================================*/
    2507: EXTERN_C_BEGIN
    2508: void f77CLINK(CINFO *p1,CRUNGE *p2,CGMCOM *p3)
    2509: {
    2510:   c_info  = p1;
    2511:   c_runge = p2;
    2512:   c_gmcom = p3;
    2513: }
    2514: EXTERN_C_END

    2516: /*========================== SET_UP_GRID====================================*/
    2517: /*                                                                          */
    2518: /* Allocates the memory for the fine grid                                   */
    2519: /*                                                                          */
    2520: /*==========================================================================*/
    2521: int set_up_grid(GRID *grid)
    2522: {
    2523:   int nnodes,nedge;
    2524:   int nsface,nvface,nfface,nbface;
    2525:   int tnode,ierr;
    2526:   /*int vface,lnodes,nnz,ncell,kvisc,ilu0,nsrch,ileast,ifcn,valloc;*/
    2527:   /*int nsnode,nvnode,nfnode; */
    2528:   /*int mgzero=0;*/ /* Variable so we dont allocate memory for multigrid */
    2529:   /*int jalloc;*/  /* If jalloc=1 allocate space for dfp and dfm */
    2530:   /*
    2531:   * stuff to read in dave's grids
    2532:   */
    2533:   /*int nnbound,nvbound,nfbound,nnfacet,nvfacet,nffacet,ntte;*/
    2534:   /* end of stuff */

    2536:   nnodes = grid->nnodes;
    2537:   tnode  = grid->nnodes;
    2538:   nedge  = grid->nedge;
    2539:   nsface = grid->nsface;
    2540:   nvface = grid->nvface;
    2541:   nfface = grid->nfface;
    2542:   nbface = nsface + nvface + nfface;

    2544:   /*ncell  = grid->ncell;
    2545:   vface  = grid->nedge;
    2546:   lnodes = grid->nnodes;
    2547:   nsnode = grid->nsnode;
    2548:   nvnode = grid->nvnode;
    2549:   nfnode = grid->nfnode;
    2550:   nsrch  = c_gmcom->nsrch;
    2551:   ilu0   = c_gmcom->ilu0;
    2552:   ileast = grid->ileast;
    2553:   ifcn   = c_gmcom->ifcn;
    2554:   jalloc = 0;
    2555:   kvisc  = grid->jvisc;*/

    2557:   /* if (ilu0 >=1 && ifcn == 1) jalloc=0;*/

    2559:   /*
    2560:   * stuff to read in dave's grids
    2561:   */
    2562:   /*nnbound = grid->nnbound;
    2563:   nvbound = grid->nvbound;
    2564:   nfbound = grid->nfbound;
    2565:   nnfacet = grid->nnfacet;
    2566:   nvfacet = grid->nvfacet;
    2567:   nffacet = grid->nffacet;
    2568:   ntte    = grid->ntte;*/
    2569:   /* end of stuff */

    2571:   /* if (!ileast) lnodes = 1;
    2572:     printf("In set_up_grid->jvisc = %d\n",grid->jvisc);

    2574:   if (grid->jvisc != 2 && grid->jvisc != 4 && grid->jvisc != 6)vface = 1;
    2575:   printf(" vface = %d \n",vface);
    2576:   if (grid->jvisc < 3) tnode = 1;
    2577:   valloc = 1;
    2578:   if (grid->jvisc ==  0)valloc = 0;*/

    2580:   /*PetscPrintf(PETSC_COMM_WORLD," nsnode= %d nvnode= %d nfnode= %d\n",nsnode,nvnode,nfnode);*/
    2581:   /*PetscPrintf(PETSC_COMM_WORLD," nsface= %d nvface= %d nfface= %d\n",nsface,nvface,nfface);
    2582:   PetscPrintf(PETSC_COMM_WORLD," nbface= %d\n",nbface);*/
    2583:   /* Now allocate memory for the other grid arrays */
    2584:   /* ICALLOC(nedge*2,  &grid->eptr); */
    2585:   ICALLOC(nsface,   &grid->isface);
    2586:   ICALLOC(nvface,   &grid->ivface);
    2587:   ICALLOC(nfface,   &grid->ifface);
    2588:   /* ICALLOC(nsnode,   &grid->isnode);
    2589:     ICALLOC(nvnode,   &grid->ivnode);
    2590:     ICALLOC(nfnode,   &grid->ifnode);*/
    2591:   /*ICALLOC(nnodes,   &grid->clist);
    2592:   ICALLOC(nnodes,   &grid->iupdate);
    2593:   ICALLOC(nsface*2, &grid->sface);
    2594:   ICALLOC(nvface*2, &grid->vface);
    2595:   ICALLOC(nfface*2, &grid->fface);
    2596:   ICALLOC(lnodes,   &grid->icount);*/

FCALLOC(nnodes, &grid->y);
FCALLOC(nnodes, &grid->z);
FCALLOC(nnodes, &grid->area);*/
/*
* FCALLOC(nnodes*4, &grid->gradx);
* FCALLOC(nnodes*4, &grid->grady);
* FCALLOC(nnodes*4, &grid->gradz);
* FCALLOC(nnodes, &grid->cdt);
*/
/*
* FCALLOC(nnodes*4, &grid->qnode);
* FCALLOC(nnodes*4, &grid->dq);
* FCALLOC(nnodes*4, &grid->res);
* FCALLOC(jalloc*nnodes*4*4,&grid->A);
* FCALLOC(nnodes*4, &grid->B);
* FCALLOC(jalloc*nedge*4*4,&grid->dfp);
* FCALLOC(jalloc*nedge*4*4,&grid->dfm);
*/
FCALLOC(nsnode, &grid->syn);
FCALLOC(nsnode, &grid->szn);
FCALLOC(nsnode, &grid->sa);
FCALLOC(nvnode, &grid->vxn);
FCALLOC(nvnode, &grid->vyn);
FCALLOC(nvnode, &grid->vzn);
FCALLOC(nvnode, &grid->va);
FCALLOC(nfnode, &grid->fxn);
FCALLOC(nfnode, &grid->fyn);
FCALLOC(nfnode, &grid->fzn);
FCALLOC(nfnode, &grid->fa);
FCALLOC(nedge, &grid->xn);
FCALLOC(nedge, &grid->yn);
FCALLOC(nedge, &grid->zn);
FCALLOC(nedge, &grid->rl);*/
line2633">2633: FCALLOC(nbface*15,&grid-&
line2634">2634: FCALLOC(nbface*15,&grid-&
line2635">2635: FCALLOC(nbface*15,&grid-&
/*
* FCALLOC(nnodes*4, &grid->phi);
* FCALLOC(nnodes, &grid->r11);
* FCALLOC(nnodes, &grid->r12);
* FCALLOC(nnodes, &grid->r13);
* FCALLOC(nnodes, &grid->r22);
* FCALLOC(nnodes, &grid->r23);
* FCALLOC(nnodes, &grid->r33);
*/
/*
* Allocate memory for viscous length scale if turbulent
*/
line2648">2648: if (grid->jvisc >
line2649">2649: FCALLOC(tnode, &grid->
line2650">2650: FCALLOC(nnodes, &grid->t
line2651">2651: FCALLOC(nnodes, &grid->
line2652">2652: FCALLOC(tnode, &grid->tu
line2653">2653: FCALLOC(nedge, &grid->
line2654">2654: FCALLOC(nedge, &grid->
line2655">2655:
/*
* Allocate memory for MG transfer
*/
/*
ICALLOC(mgzero*nsface, &grid->isford);
ICALLOC(mgzero*nvface, &grid->ivford);
ICALLOC(mgzero*nfface, &grid->ifford);
ICALLOC(mgzero*nnodes, &grid->nflag);
ICALLOC(mgzero*nnodes, &grid->nnext);
ICALLOC(mgzero*nnodes, &grid->nneigh);
ICALLOC(mgzero*ncell, &grid->ctag);
ICALLOC(mgzero*ncell, &grid->csearch);
ICALLOC(valloc*ncell*4, &grid->c2n);
ICALLOC(valloc*ncell*6, &grid->c2e);
grid->c2c = (int*)grid->dfp;
ICALLOC(ncell*4, &grid->c2c);
ICALLOC(nnodes, &grid->cenc);
if (grid->iup == 1) {
ICALLOC(mgzero*nnodes*3, &grid->icoefup);
FCALLOC(mgzero*nnodes*3, &grid->rcoefup);
}
if (grid->idown == 1) {
ICALLOC(mgzero*nnodes*3, &grid->icoefdn);
FCALLOC(mgzero*nnodes*3, &grid->rcoefdn);
}
FCALLOC(nnodes*4, &grid->ff);
FCALLOC(tnode, &grid->turbff);
*/
/*
* If using GMRES (nsrch>0) allocate memory
*/
/* NoEq = 0;
if (nsrch > 0)NoEq = 4*nnodes;
if (nsrch < 0)NoEq = nnodes;
FCALLOC(NoEq, &grid->AP);
FCALLOC(NoEq, &grid->Xgm);
FCALLOC(NoEq, &grid->temr);
FCALLOC((abs(nsrch)+1)*NoEq,&grid->Fgm);
*/
/*
* stuff to read in dave's grids
*/
/*
ICALLOC(nnbound, &grid->ncolorn);
ICALLOC(nnbound*100,&grid->countn);
ICALLOC(nvbound, &grid->ncolorv);
ICALLOC(nvbound*100,&grid->countv);
ICALLOC(nfbound, &grid->ncolorf);
ICALLOC(nfbound*100,&grid->countf);
*/
/*ICALLOC(nnbound, &grid->nntet);
ICALLOC(nnbound, &grid->nnpts);
ICALLOC(nvbound, &grid->nvtet);
ICALLOC(nvbound, &grid->nvpts);
ICALLOC(nfbound, &grid->nftet);
ICALLOC(nfbound, &grid->nfpts);
ICALLOC(nnfacet*4,&grid->f2ntn);
ICALLOC(nvfacet*4,&grid->f2ntv);
ICALLOC(nffacet*4,&grid->f2ntf);*/
line2715">2715: return line2716">2716
/*========================== WRITE_FINE_GRID ================================*/
/* */
/* Write memory locations and other information for the fine grid */
/* */
/*===========================================================================*/
line2723">2723: int write_fine_grid(GRID *grid) line2724">2724
line2725">2725: FILE *
/* open file for output */
/* call the output frame.out */
line2731">2731: fprintf(output,"information for fine grid\n" line2732">2732: fprintf(output,"\n" line2733">2733: fprintf(output," address of fine grid = %p\n",(void*
line2735">2735: fprintf(output,"grid.nnodes = %d\n",grid->n
line2736">2736: fprintf(output,"grid.ncell = %d\n",grid->
line2737">2737: fprintf(output,"grid.nedge = %d\n",grid->
line2738">2738: fprintf(output,"grid.nsface = %d\n",grid->n
line2739">2739: fprintf(output,"grid.nvface = %d\n",grid->n
line2740">2740: fprintf(output,"grid.nfface = %d\n",grid->n
line2741">2741: fprintf(output,"grid.nsnode = %d\n",grid->n
line2742">2742: fprintf(output,"grid.nvnode = %d\n",grid->n
line2743">2743: fprintf(output,"grid.nfnode = %d\n",grid->n
/*
fprintf(output,"grid.eptr = %p\n",grid->eptr);
fprintf(output,"grid.isface = %p\n",grid->isface);
fprintf(output,"grid.ivface = %p\n",grid->ivface);
fprintf(output,"grid.ifface = %p\n",grid->ifface);
fprintf(output,"grid.isnode = %p\n",grid->isnode);
fprintf(output,"grid.ivnode = %p\n",grid->ivnode);
fprintf(output,"grid.ifnode = %p\n",grid->ifnode);
fprintf(output,"grid.c2n = %p\n",grid->c2n);
fprintf(output,"grid.c2e = %p\n",grid->c2e);
fprintf(output,"grid.xyz = %p\n",grid->xyz);
*/
/*fprintf(output,"grid.y = %p\n",grid->xyz);
fprintf(output,"grid.z = %p\n",grid->z);*/
/*
fprintf(output,"grid.area = %p\n",grid->area);
fprintf(output,"grid.qnode = %p\n",grid->qnode);
*/
/*
fprintf(output,"grid.gradx = %p\n",grid->gradx);
fprintf(output,"grid.grady = %p\n",grid->grady);
fprintf(output,"grid.gradz = %p\n",grid->gradz);
*/
/*
fprintf(output,"grid.cdt = %p\n",grid->cdt);
fprintf(output,"grid.sxn = %p\n",grid->sxn);
fprintf(output,"grid.syn = %p\n",grid->syn);
fprintf(output,"grid.szn = %p\n",grid->szn);
fprintf(output,"grid.vxn = %p\n",grid->vxn);
fprintf(output,"grid.vyn = %p\n",grid->vyn);
fprintf(output,"grid.vzn = %p\n",grid->vzn);
fprintf(output,"grid.fxn = %p\n",grid->fxn);
fprintf(output,"grid.fyn = %p\n",grid->fyn);
fprintf(output,"grid.fzn = %p\n",grid->fzn);
fprintf(output,"grid.xyzn = %p\n",grid->xyzn);
*/
/*fprintf(output,"grid.yn = %p\n",grid->yn);
fprintf(output,"grid.zn = %p\n",grid->zn);
fprintf(output,"grid.rl = %p\n",grid->rl);*/
line2783">2783: fclose(o
line2784">2784: return line2785">2785
line2787">2787: #if defined(_OPENMP) && defined(HAVE_EDGE_COLORING)
line2788">2788: int EdgeColoring(int nnodes,int nedge,int *e2n,int *eperm,int *ncle,int *counte) line2789">2789
line2790">2790: int ncolore = *nc
line2791">2791: int iedg = 0,ib = 0,ie = nedge,ta
line2792">2792: int i
line2793">2793: in
line2794">2794: ICALLOC(nnodes,&am
line2795">2795: while (ib <
line2796">2796: for (i = 0; i < nnodes; i++) tag[
line2797">2797: counte[ncolor
line2798">2798: for (i = ib; i < ie;
line2799">2799: n1 =
line2800">2800: n2 = e2n[i+
line2801">2801: tagcount = tag[n1]+t
/* If tagcount = 0 then this edge belongs in this color */
line2803">2803: if (!tagc
line2804">2804: tag[n1]
line2805">2805: tag[n2]
line2806">2806: e2n[i] = e2n
line2807">2807: e2n[i+nedge] = e2n[iedg+
line2808">2808: e2n[iedg]
line2809">2809: e2n[iedg+nedge
line2810">2810: n1 = ep
line2811">2811: eperm[i] = eperm
line2812">2812: eperm[iedg]
line2813">2813:
line2814">2814: counte[ncolor
line2815">2815:
line2816">2816: line2817">2817: ib
line2818">2818: nco
line2819">2819:
line2820">2820: *ncle = n
line2821">2821: return line2822">2822
line2823">2823: #endif
line2824">2824: #if defined(PARCH_IRIX64) && defined(USE_HW_COUNTERS)
line2825">2825: int EventCountersBegin(int *gen_start,PetscScalar *time_start_counters) line2826">2826
line2828">2828: PetscTime(&time_start_cou
line2829">2829: return line2830">2830
line2832">2832: int EventCountersEnd(int gen_start,PetscScalar time_start_counters) line2833">2833
line2834">2834: int gen_rea
line2835">2835: PetscScalar time_read_co
line2836">2836: long long _counter0,_co
line2839">2839: PetscTime(&&time_read_cou
line2841">2841: counter0 += _co
line2842">2842: counter1 += _co
line2843">2843: time_counters += time_read_counters-time_start_co
line2844">2844: return line2845">2845
line2846">2846: #endif