Actual source code: swarmpic_view.c

      1: #include <petscdm.h>
      2: #include <petscdmda.h>
      3: #include <petscdmswarm.h>
      4: #include <petsc/private/dmswarmimpl.h>
      5: #include "../src/dm/impls/swarm/data_bucket.h"

      7: PetscErrorCode private_PetscViewerCreate_XDMF(MPI_Comm comm,const char filename[],PetscViewer *v)
      8: {
      9:   long int       *bytes;
     10:   PetscContainer container;
     11:   PetscViewer    viewer;

     15:   PetscViewerCreate(comm,&viewer);
     16:   PetscViewerSetType(viewer,PETSCVIEWERASCII);
     17:   PetscViewerFileSetMode(viewer,FILE_MODE_WRITE);
     18:   PetscViewerFileSetName(viewer,filename);

     20:   PetscMalloc1(1,&bytes);
     21:   bytes[0] = 0;
     22:   PetscContainerCreate(comm,&container);
     23:   PetscContainerSetPointer(container,(void*)bytes);
     24:   PetscObjectCompose((PetscObject)viewer,"XDMFViewerContext",(PetscObject)container);

     26:   /* write xdmf header */
     27:   PetscViewerASCIIPrintf(viewer,"<?xml version=\"1.0\" encoding=\"utf-8\"?>\n");
     28:   PetscViewerASCIIPrintf(viewer,"<Xdmf xmlns:xi=\"http://www.w3.org/2001/XInclude/\" Version=\"2.99\">\n");
     29:   /* write xdmf domain */
     30:   PetscViewerASCIIPushTab(viewer);
     31:   PetscViewerASCIIPrintf(viewer,"<Domain>\n");
     32:   *v = viewer;
     33:   return(0);
     34: }

     36: PetscErrorCode private_PetscViewerDestroy_XDMF(PetscViewer *v)
     37: {
     38:   PetscViewer    viewer;
     39:   DM             dm = NULL;
     40:   long int       *bytes;
     41:   PetscContainer container = NULL;

     45:   if (!v) return(0);
     46:   viewer = *v;

     48:   PetscObjectQuery((PetscObject)viewer,"DMSwarm",(PetscObject*)&dm);
     49:   if (dm) {
     50:     PetscViewerASCIIPrintf(viewer,"</Grid>\n");
     51:     PetscViewerASCIIPopTab(viewer);
     52:   }

     54:   /* close xdmf header */
     55:   PetscViewerASCIIPrintf(viewer,"</Domain>\n");
     56:   PetscViewerASCIIPopTab(viewer);
     57:   PetscViewerASCIIPrintf(viewer,"</Xdmf>\n");

     59:   PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);
     60:   if (container) {
     61:     PetscContainerGetPointer(container,(void**)&bytes);
     62:     PetscFree(bytes);
     63:     PetscContainerDestroy(&container);
     64:   }

     66:   PetscViewerDestroy(&viewer);
     67:   *v = NULL;
     68:   return(0);
     69: }

     71: PetscErrorCode private_CreateDataFileNameXDMF(const char filename[],char dfilename[])
     72: {
     73:   char           *ext;
     74:   PetscBool      flg;

     78:   PetscStrrchr(filename,'.',&ext);
     79:   PetscStrcmp("xmf",ext,&flg);
     80:   if (flg) {
     81:     size_t len;
     82:     char    viewername_minus_ext[PETSC_MAX_PATH_LEN];

     84:     PetscStrlen(filename,&len);
     85:     PetscStrncpy(viewername_minus_ext,filename,len-2);
     86:     PetscSNPrintf(dfilename,PETSC_MAX_PATH_LEN-1,"%s_swarm_fields.pbin",viewername_minus_ext);
     87:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"File extension must by .xmf");

     89:   return(0);
     90: }

     92: PetscErrorCode private_DMSwarmView_XDMF(DM dm,PetscViewer viewer)
     93: {
     94:   PetscBool      isswarm = PETSC_FALSE;
     95:   const char     *viewername;
     96:   char           datafile[PETSC_MAX_PATH_LEN];
     97:   char           *datafilename;
     98:   PetscViewer    fviewer;
     99:   PetscInt       k,ng,dim;
    100:   Vec            dvec;
    101:   long int       *bytes = NULL;
    102:   PetscContainer container = NULL;
    103:   const char     *dmname;

    107:   PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);
    108:   if (container) {
    109:     PetscContainerGetPointer(container,(void**)&bytes);
    110:   } else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext");

    112:   PetscObjectTypeCompare((PetscObject)dm,DMSWARM,&isswarm);
    113:   if (!isswarm) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Only valid for DMSwarm");

    115:   PetscObjectCompose((PetscObject)viewer,"DMSwarm",(PetscObject)dm);

    117:   PetscViewerASCIIPushTab(viewer);
    118:   PetscObjectGetName((PetscObject)dm,&dmname);
    119:   if (!dmname) {
    120:     DMGetOptionsPrefix(dm,&dmname);
    121:   }
    122:   if (!dmname) {
    123:     PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm\" GridType=\"Uniform\">\n");
    124:   } else {
    125:     PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm[%s]\" GridType=\"Uniform\">\n",dmname);
    126:   }

    128:   /* create a sub-viewer for topology, geometry and all data fields */
    129:   /* name is viewer.name + "_swarm_fields.pbin" */
    130:   PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);
    131:   PetscViewerSetType(fviewer,PETSCVIEWERBINARY);
    132:   PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);
    133:   PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);
    134:   PetscViewerFileSetMode(fviewer,FILE_MODE_WRITE);

    136:   PetscViewerFileGetName(viewer,&viewername);
    137:   private_CreateDataFileNameXDMF(viewername,datafile);
    138:   PetscViewerFileSetName(fviewer,datafile);
    139:   PetscStrrchr(datafile,'/',&datafilename);

    141:   DMSwarmGetSize(dm,&ng);

    143:   /* write topology header */
    144:   PetscViewerASCIIPushTab(viewer);
    145:   PetscViewerASCIIPrintf(viewer,"<Topology Dimensions=\"%D\" TopologyType=\"Mixed\">\n",ng);
    146:   PetscViewerASCIIPushTab(viewer);
    147:   PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Dimensions=\"%D\" Seek=\"%D\">\n",ng*3,bytes[0]);
    148:   PetscViewerASCIIPushTab(viewer);
    149:   PetscViewerASCIIPrintf(viewer,"%s\n",datafilename);
    150:   PetscViewerASCIIPopTab(viewer);
    151:   PetscViewerASCIIPrintf(viewer,"</DataItem>\n");
    152:   PetscViewerASCIIPopTab(viewer);
    153:   PetscViewerASCIIPrintf(viewer,"</Topology>\n");
    154:   PetscViewerASCIIPopTab(viewer);

    156:   /* write topology data */
    157:   for (k=0; k<ng; k++) {
    158:     PetscInt pvertex[3];

    160:     pvertex[0] = 1;
    161:     pvertex[1] = 1;
    162:     pvertex[2] = k;
    163:     PetscViewerBinaryWrite(fviewer,pvertex,3,PETSC_INT);
    164:   }
    165:   bytes[0] += sizeof(PetscInt) * ng * 3;

    167:   /* write geometry header */
    168:   PetscViewerASCIIPushTab(viewer);
    169:   DMGetDimension(dm,&dim);
    170:   switch (dim) {
    171:     case 1:
    172:       SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for 1D");
    173:     case 2:
    174:       PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XY\">\n");
    175:       break;
    176:     case 3:
    177:       PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XYZ\">\n");
    178:       break;
    179:   }
    180:   PetscViewerASCIIPushTab(viewer);
    181:   PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D %D\" Seek=\"%D\">\n",ng,dim,bytes[0]);
    182:   PetscViewerASCIIPushTab(viewer);
    183:   PetscViewerASCIIPrintf(viewer,"%s\n",datafilename);
    184:   PetscViewerASCIIPopTab(viewer);
    185:   PetscViewerASCIIPrintf(viewer,"</DataItem>\n");
    186:   PetscViewerASCIIPopTab(viewer);
    187:   PetscViewerASCIIPrintf(viewer,"</Geometry>\n");
    188:   PetscViewerASCIIPopTab(viewer);

    190:   /* write geometry data */
    191:   DMSwarmCreateGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);
    192:   VecView(dvec,fviewer);
    193:   DMSwarmDestroyGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);
    194:   bytes[0] += sizeof(PetscReal) * ng * dim;

    196:   PetscViewerDestroy(&fviewer);

    198:   return(0);
    199: }

    201: PetscErrorCode private_VecView_Swarm_XDMF(Vec x,PetscViewer viewer)
    202: {
    203:   long int       *bytes = NULL;
    204:   PetscContainer container = NULL;
    205:   const char     *viewername;
    206:   char           datafile[PETSC_MAX_PATH_LEN];
    207:   char           *datafilename;
    208:   PetscViewer    fviewer;
    209:   PetscInt       N,bs;
    210:   const char     *vecname;
    211:   char           fieldname[PETSC_MAX_PATH_LEN];

    215:   PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);
    216:   if (container) {
    217:     PetscContainerGetPointer(container,(void**)&bytes);
    218:   } else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext");

    220:   PetscViewerFileGetName(viewer,&viewername);
    221:   private_CreateDataFileNameXDMF(viewername,datafile);

    223:   /* re-open a sub-viewer for all data fields */
    224:   /* name is viewer.name + "_swarm_fields.pbin" */
    225:   PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);
    226:   PetscViewerSetType(fviewer,PETSCVIEWERBINARY);
    227:   PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);
    228:   PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);
    229:   PetscViewerFileSetMode(fviewer,FILE_MODE_APPEND);
    230:   PetscViewerFileSetName(fviewer,datafile);
    231:   PetscStrrchr(datafile,'/',&datafilename);

    233:   VecGetSize(x,&N);
    234:   VecGetBlockSize(x,&bs);
    235:   N = N/bs;
    236:   PetscObjectGetName((PetscObject)x,&vecname);
    237:   if (!vecname) {
    238:     PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"swarmfield_%D",((PetscObject)x)->tag);
    239:   } else {
    240:     PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"%s",vecname);
    241:   }

    243:   /* write data header */
    244:   PetscViewerASCIIPushTab(viewer);
    245:   PetscViewerASCIIPrintf(viewer,"<Attribute Center=\"Node\" Name=\"%s\" Type=\"None\">\n",fieldname);
    246:   PetscViewerASCIIPushTab(viewer);
    247:   if (bs == 1) {
    248:     PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D\" Seek=\"%D\">\n",N,bytes[0]);
    249:   } else {
    250:     PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D %D\" Seek=\"%D\">\n",N,bs,bytes[0]);
    251:   }
    252:   PetscViewerASCIIPushTab(viewer);
    253:   PetscViewerASCIIPrintf(viewer,"%s\n",datafilename);
    254:   PetscViewerASCIIPopTab(viewer);
    255:   PetscViewerASCIIPrintf(viewer,"</DataItem>\n");
    256:   PetscViewerASCIIPopTab(viewer);
    257:   PetscViewerASCIIPrintf(viewer,"</Attribute>\n");
    258:   PetscViewerASCIIPopTab(viewer);

    260:   /* write data */
    261:   VecView(x,fviewer);
    262:   bytes[0] += sizeof(PetscReal) * N * bs;

    264:   PetscViewerDestroy(&fviewer);

    266:   return(0);
    267: }

    269: PetscErrorCode private_ISView_Swarm_XDMF(IS is,PetscViewer viewer)
    270: {
    271:   long int       *bytes = NULL;
    272:   PetscContainer container = NULL;
    273:   const char     *viewername;
    274:   char           datafile[PETSC_MAX_PATH_LEN];
    275:   char           *datafilename;
    276:   PetscViewer    fviewer;
    277:   PetscInt       N,bs;
    278:   const char     *vecname;
    279:   char           fieldname[PETSC_MAX_PATH_LEN];

    283:   PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);
    284:   if (container) {
    285:     PetscContainerGetPointer(container,(void**)&bytes);
    286:   } else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext");

    288:   PetscViewerFileGetName(viewer,&viewername);
    289:   private_CreateDataFileNameXDMF(viewername,datafile);

    291:   /* re-open a sub-viewer for all data fields */
    292:   /* name is viewer.name + "_swarm_fields.pbin" */
    293:   PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);
    294:   PetscViewerSetType(fviewer,PETSCVIEWERBINARY);
    295:   PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);
    296:   PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);
    297:   PetscViewerFileSetMode(fviewer,FILE_MODE_APPEND);
    298:   PetscViewerFileSetName(fviewer,datafile);
    299:   PetscStrrchr(datafile,'/',&datafilename);

    301:   ISGetSize(is,&N);
    302:   ISGetBlockSize(is,&bs);
    303:   N = N/bs;
    304:   PetscObjectGetName((PetscObject)is,&vecname);
    305:   if (!vecname) {
    306:     PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"swarmfield_%D",((PetscObject)is)->tag);
    307:   } else {
    308:     PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"%s",vecname);
    309:   }

    311:   /* write data header */
    312:   PetscViewerASCIIPushTab(viewer);
    313:   PetscViewerASCIIPrintf(viewer,"<Attribute Center=\"Node\" Name=\"%s\" Type=\"None\">\n",fieldname);
    314:   PetscViewerASCIIPushTab(viewer);
    315:   if (bs == 1) {
    316:     PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Precision=\"4\" Dimensions=\"%D\" Seek=\"%D\">\n",N,bytes[0]);
    317:   } else {
    318:     PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Precision=\"4\" Dimensions=\"%D %D\" Seek=\"%D\">\n",N,bs,bytes[0]);
    319:   }
    320:   PetscViewerASCIIPushTab(viewer);
    321:   PetscViewerASCIIPrintf(viewer,"%s\n",datafilename);
    322:   PetscViewerASCIIPopTab(viewer);
    323:   PetscViewerASCIIPrintf(viewer,"</DataItem>\n");
    324:   PetscViewerASCIIPopTab(viewer);
    325:   PetscViewerASCIIPrintf(viewer,"</Attribute>\n");
    326:   PetscViewerASCIIPopTab(viewer);

    328:   /* write data */
    329:   ISView(is,fviewer);
    330:   bytes[0] += sizeof(PetscInt) * N * bs;

    332:   PetscViewerDestroy(&fviewer);

    334:   return(0);
    335: }

    337: /*@C
    338:    DMSwarmViewFieldsXDMF - Write a selection of DMSwarm fields to an XDMF3 file

    340:    Collective on dm

    342:    Input parameters:
    343: +  dm - the DMSwarm
    344: .  filename - the file name of the XDMF file (must have the extension .xmf)
    345: .  nfields - the number of fields to write into the XDMF file
    346: -  field_name_list - array of length nfields containing the textual name of fields to write

    348:    Level: beginner

    350:    Notes:
    351:    Only fields registered with data type PETSC_DOUBLE or PETSC_INT can be written into the file

    353: .seealso: DMSwarmViewXDMF()
    354: @*/
    355: PETSC_EXTERN PetscErrorCode DMSwarmViewFieldsXDMF(DM dm,const char filename[],PetscInt nfields,const char *field_name_list[])
    356: {
    358:   Vec            dvec;
    359:   PetscInt       f,N;
    360:   PetscViewer    viewer;

    363:   private_PetscViewerCreate_XDMF(PetscObjectComm((PetscObject)dm),filename,&viewer);
    364:   private_DMSwarmView_XDMF(dm,viewer);
    365:   DMSwarmGetLocalSize(dm,&N);
    366:   for (f=0; f<nfields; f++) {
    367:     void          *data;
    368:     PetscDataType type;

    370:     DMSwarmGetField(dm,field_name_list[f],NULL,&type,&data);
    371:     DMSwarmRestoreField(dm,field_name_list[f],NULL,&type,&data);

    373:     if (type == PETSC_DOUBLE) {
    374:       DMSwarmCreateGlobalVectorFromField(dm,field_name_list[f],&dvec);
    375:       PetscObjectSetName((PetscObject)dvec,field_name_list[f]);
    376:       private_VecView_Swarm_XDMF(dvec,viewer);
    377:       DMSwarmDestroyGlobalVectorFromField(dm,field_name_list[f],&dvec);
    378:     } else if (type == PETSC_INT) {
    379:       IS is;
    380:       const PetscInt *idx;

    382:       DMSwarmGetField(dm,field_name_list[f],NULL,&type,&data);
    383:       idx = (const PetscInt*)data;

    385:       ISCreateGeneral(PetscObjectComm((PetscObject)dm),N,idx,PETSC_USE_POINTER,&is);
    386:       PetscObjectSetName((PetscObject)is,field_name_list[f]);
    387:       private_ISView_Swarm_XDMF(is,viewer);
    388:       ISDestroy(&is);
    389:       DMSwarmRestoreField(dm,field_name_list[f],NULL,&type,&data);
    390:     } else SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Can only write PETSC_INT and PETSC_DOUBLE");

    392:   }
    393:   private_PetscViewerDestroy_XDMF(&viewer);
    394:   return(0);
    395: }

    397: /*@C
    398:    DMSwarmViewXDMF - Write DMSwarm fields to an XDMF3 file

    400:    Collective on dm

    402:    Input parameters:
    403: +  dm - the DMSwarm
    404: -  filename - the file name of the XDMF file (must have the extension .xmf)

    406:    Level: beginner

    408:    Notes:
    409:    Only fields user registered with data type PETSC_DOUBLE or PETSC_INT will be written into the file

    411: .seealso: DMSwarmViewFieldsXDMF()
    412: @*/
    413: PETSC_EXTERN PetscErrorCode DMSwarmViewXDMF(DM dm,const char filename[])
    414: {
    415:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;
    417:   Vec            dvec;
    418:   PetscInt       f;
    419:   PetscViewer    viewer;

    422:   private_PetscViewerCreate_XDMF(PetscObjectComm((PetscObject)dm),filename,&viewer);
    423:   private_DMSwarmView_XDMF(dm,viewer);
    424:   for (f=4; f<swarm->db->nfields; f++) { /* only examine user defined fields - the first 4 are internally created by DMSwarmPIC */
    425:     DMSwarmDataField field;

    427:     /* query field type - accept all those of type PETSC_DOUBLE */
    428:     field = swarm->db->field[f];
    429:     if (field->petsc_type == PETSC_DOUBLE) {
    430:       DMSwarmCreateGlobalVectorFromField(dm,field->name,&dvec);
    431:       PetscObjectSetName((PetscObject)dvec,field->name);
    432:       private_VecView_Swarm_XDMF(dvec,viewer);
    433:       DMSwarmDestroyGlobalVectorFromField(dm,field->name,&dvec);
    434:     } else if (field->petsc_type == PETSC_INT) {
    435:       IS             is;
    436:       PetscInt       N;
    437:       const PetscInt *idx;
    438:       void           *data;

    440:       DMSwarmGetLocalSize(dm,&N);
    441:       DMSwarmGetField(dm,field->name,NULL,NULL,&data);
    442:       idx = (const PetscInt*)data;

    444:       ISCreateGeneral(PetscObjectComm((PetscObject)dm),N,idx,PETSC_USE_POINTER,&is);
    445:       PetscObjectSetName((PetscObject)is,field->name);
    446:       private_ISView_Swarm_XDMF(is,viewer);
    447:       ISDestroy(&is);
    448:       DMSwarmRestoreField(dm,field->name,NULL,NULL,&data);
    449:     }
    450:   }
    451:   private_PetscViewerDestroy_XDMF(&viewer);
    452:   return(0);
    453: }