1 #include <petscdm.h> 2 #include <petscdmda.h> 3 #include <petscdmswarm.h> 4 #include <petsc/private/dmswarmimpl.h> 5 #include "data_bucket.h" 6 7 PetscErrorCode private_PetscViewerCreate_XDMF(MPI_Comm comm,const char filename[],PetscViewer *v) 8 { 9 long int *bytes; 10 PetscContainer container; 11 PetscViewer viewer; 12 PetscErrorCode ierr; 13 14 PetscFunctionBegin; 15 ierr = PetscViewerCreate(comm,&viewer);CHKERRQ(ierr); 16 ierr = PetscViewerSetType(viewer,PETSCVIEWERASCII);CHKERRQ(ierr); 17 ierr = PetscViewerFileSetMode(viewer,FILE_MODE_WRITE);CHKERRQ(ierr); 18 ierr = PetscViewerFileSetName(viewer,filename);CHKERRQ(ierr); 19 20 ierr = PetscMalloc1(1,&bytes);CHKERRQ(ierr); 21 bytes[0] = 0; 22 ierr = PetscContainerCreate(comm,&container);CHKERRQ(ierr); 23 ierr = PetscContainerSetPointer(container,(void*)bytes);CHKERRQ(ierr); 24 ierr = PetscObjectCompose((PetscObject)viewer,"XDMFViewerContext",(PetscObject)container);CHKERRQ(ierr); 25 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 PetscFunctionReturn(0); 34 } 35 36 PetscErrorCode private_PetscViewerDestroy_XDMF(PetscViewer *v) 37 { 38 PetscViewer viewer; 39 DM dm = NULL; 40 long int *bytes; 41 PetscContainer container = NULL; 42 PetscErrorCode ierr; 43 44 PetscFunctionBegin; 45 if (!v) PetscFunctionReturn(0); 46 viewer = *v; 47 48 ierr = PetscObjectQuery((PetscObject)viewer,"DMSwarm",(PetscObject*)&dm);CHKERRQ(ierr); 49 if (dm) { 50 PetscViewerASCIIPrintf(viewer,"</Grid>\n"); 51 PetscViewerASCIIPopTab(viewer); 52 } 53 54 /* close xdmf header */ 55 PetscViewerASCIIPrintf(viewer,"</Domain>\n"); 56 PetscViewerASCIIPopTab(viewer); 57 PetscViewerASCIIPrintf(viewer,"</Xdmf>\n"); 58 59 ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr); 60 if (container) { 61 ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr); 62 ierr = PetscFree(bytes);CHKERRQ(ierr); 63 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 64 } 65 66 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 67 *v = NULL; 68 PetscFunctionReturn(0); 69 } 70 71 PetscErrorCode private_CreateDataFileNameXDMF(const char filename[],char dfilename[]) 72 { 73 char *ext; 74 PetscBool flg; 75 PetscErrorCode ierr; 76 77 PetscFunctionBegin; 78 ierr = PetscStrrchr(filename,'.',&ext);CHKERRQ(ierr); 79 ierr = PetscStrcmp("xmf",ext,&flg);CHKERRQ(ierr); 80 if (flg) { 81 size_t len; 82 char viewername_minus_ext[PETSC_MAX_PATH_LEN]; 83 84 ierr = PetscStrlen(filename,&len);CHKERRQ(ierr); 85 ierr = PetscSNPrintf(viewername_minus_ext,len-3,"%s",filename);CHKERRQ(ierr); 86 ierr = PetscSNPrintf(dfilename,PETSC_MAX_PATH_LEN-1,"%s_swarm_fields.pbin",viewername_minus_ext);CHKERRQ(ierr); 87 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"File extension must by .xmf"); 88 89 PetscFunctionReturn(0); 90 } 91 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 PetscViewer fviewer; 98 PetscInt k,ng,dim; 99 Vec dvec; 100 long int *bytes = NULL; 101 PetscContainer container = NULL; 102 const char *dmname; 103 PetscErrorCode ierr; 104 105 PetscFunctionBegin; 106 ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr); 107 if (container) { 108 ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr); 109 } else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext"); 110 111 ierr = PetscObjectTypeCompare((PetscObject)dm,DMSWARM,&isswarm);CHKERRQ(ierr); 112 if (!isswarm) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Only valid for DMSwarm"); 113 114 ierr = PetscObjectCompose((PetscObject)viewer,"DMSwarm",(PetscObject)dm);CHKERRQ(ierr); 115 116 PetscViewerASCIIPushTab(viewer); 117 ierr = PetscObjectGetName((PetscObject)dm,&dmname);CHKERRQ(ierr); 118 if (!dmname) { 119 ierr = DMGetOptionsPrefix(dm,&dmname);CHKERRQ(ierr); 120 } 121 if (!dmname) { 122 PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm\" GridType=\"Uniform\">\n"); 123 } else { 124 PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm[%s]\" GridType=\"Uniform\">\n",dmname); 125 } 126 127 /* create a sub-viewer for topology, geometry and all data fields */ 128 /* name is viewer.name + "_swarm_fields.pbin" */ 129 ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr); 130 ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr); 131 ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr); 132 ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr); 133 ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_WRITE);CHKERRQ(ierr); 134 135 ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr); 136 ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr); 137 ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr); 138 139 ierr = DMSwarmGetSize(dm,&ng);CHKERRQ(ierr); 140 141 /* write topology header */ 142 PetscViewerASCIIPushTab(viewer); 143 PetscViewerASCIIPrintf(viewer,"<Topology Dimensions=\"%D\" TopologyType=\"Mixed\">\n",ng); 144 PetscViewerASCIIPushTab(viewer); 145 PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Dimensions=\"%D\" Seek=\"%D\">\n",ng*3,bytes[0]); 146 PetscViewerASCIIPushTab(viewer); 147 PetscViewerASCIIPrintf(viewer,"%s\n",datafile); 148 PetscViewerASCIIPopTab(viewer); 149 PetscViewerASCIIPrintf(viewer,"</DataItem>\n"); 150 PetscViewerASCIIPopTab(viewer); 151 PetscViewerASCIIPrintf(viewer,"</Topology>\n"); 152 PetscViewerASCIIPopTab(viewer); 153 154 /* write topology data */ 155 for (k=0; k<ng; k++) { 156 PetscInt pvertex[3]; 157 158 pvertex[0] = 1; 159 pvertex[1] = 1; 160 pvertex[2] = k; 161 ierr = PetscViewerBinaryWrite(fviewer,pvertex,3,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr); 162 } 163 bytes[0] += sizeof(PetscInt) * ng * 3; 164 165 /* write geometry header */ 166 PetscViewerASCIIPushTab(viewer); 167 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 168 switch (dim) { 169 case 1: 170 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for 1D"); 171 break; 172 case 2: 173 PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XY\">\n"); 174 break; 175 case 3: 176 PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XYZ\">\n"); 177 break; 178 } 179 PetscViewerASCIIPushTab(viewer); 180 PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D %D\" Seek=\"%D\">\n",ng,dim,bytes[0]); 181 PetscViewerASCIIPushTab(viewer); 182 PetscViewerASCIIPrintf(viewer,"%s\n",datafile); 183 PetscViewerASCIIPopTab(viewer); 184 PetscViewerASCIIPrintf(viewer,"</DataItem>\n"); 185 PetscViewerASCIIPopTab(viewer); 186 PetscViewerASCIIPrintf(viewer,"</Geometry>\n"); 187 PetscViewerASCIIPopTab(viewer); 188 189 /* write geometry data */ 190 ierr = DMSwarmCreateGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr); 191 ierr = VecView(dvec,fviewer);CHKERRQ(ierr); 192 ierr = DMSwarmDestroyGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr); 193 bytes[0] += sizeof(PetscReal) * ng * dim; 194 195 ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr); 196 197 PetscFunctionReturn(0); 198 } 199 200 PetscErrorCode private_VecView_Swarm_XDMF(Vec x,PetscViewer viewer) 201 { 202 long int *bytes = NULL; 203 PetscContainer container = NULL; 204 const char *viewername; 205 char datafile[PETSC_MAX_PATH_LEN]; 206 PetscViewer fviewer; 207 PetscInt N,bs; 208 const char *vecname; 209 char fieldname[PETSC_MAX_PATH_LEN]; 210 PetscErrorCode ierr; 211 212 PetscFunctionBegin; 213 ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr); 214 if (container) { 215 ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr); 216 } else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext"); 217 218 ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr); 219 ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr); 220 221 /* re-open a sub-viewer for all data fields */ 222 /* name is viewer.name + "_swarm_fields.pbin" */ 223 ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr); 224 ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr); 225 ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr); 226 ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr); 227 ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_APPEND);CHKERRQ(ierr); 228 ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr); 229 230 ierr = VecGetSize(x,&N);CHKERRQ(ierr); 231 ierr = VecGetBlockSize(x,&bs);CHKERRQ(ierr); 232 N = N/bs; 233 ierr = PetscObjectGetName((PetscObject)x,&vecname);CHKERRQ(ierr); 234 if (!vecname) { 235 ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"swarmfield_%D",((PetscObject)x)->tag);CHKERRQ(ierr); 236 } else { 237 ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"%s",vecname);CHKERRQ(ierr); 238 } 239 240 /* write data header */ 241 PetscViewerASCIIPushTab(viewer); 242 PetscViewerASCIIPrintf(viewer,"<Attribute Center=\"Node\" Name=\"%s\" Type=\"None\">\n",fieldname); 243 PetscViewerASCIIPushTab(viewer); 244 if (bs == 1) { 245 PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D\" Seek=\"%D\">\n",N,bytes[0]); 246 } else { 247 PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D %D\" Seek=\"%D\">\n",N,bs,bytes[0]); 248 } 249 PetscViewerASCIIPushTab(viewer); 250 PetscViewerASCIIPrintf(viewer,"%s\n",datafile); 251 PetscViewerASCIIPopTab(viewer); 252 PetscViewerASCIIPrintf(viewer,"</DataItem>\n"); 253 PetscViewerASCIIPopTab(viewer); 254 PetscViewerASCIIPrintf(viewer,"</Attribute>\n"); 255 PetscViewerASCIIPopTab(viewer); 256 257 /* write data */ 258 ierr = VecView(x,fviewer);CHKERRQ(ierr); 259 bytes[0] += sizeof(PetscReal) * N * bs; 260 261 ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr); 262 263 PetscFunctionReturn(0); 264 } 265 266 /*@C 267 DMSwarmViewFieldsXDMF - Write a selection of DMSwarm fields to an XDMF3 file 268 269 Collective on DM 270 271 Input parameters: 272 + dm - the DMSwarm 273 . filename - the file name of the XDMF file (must have the extension .xmf) 274 . nfields - the number of fields to write into the XDMF file 275 - field_name_list - array of length nfields containing the textual name of fields to write 276 277 Level: beginner 278 279 Notes: 280 Only fields registered with data type PETSC_REAL can be written into the file 281 282 .seealso: DMSwarmViewXDMF() 283 @*/ 284 PETSC_EXTERN PetscErrorCode DMSwarmViewFieldsXDMF(DM dm,const char filename[],PetscInt nfields,const char *field_name_list[]) 285 { 286 PetscErrorCode ierr; 287 Vec dvec; 288 PetscInt f; 289 PetscViewer viewer; 290 291 PetscFunctionBegin; 292 ierr = private_PetscViewerCreate_XDMF(PetscObjectComm((PetscObject)dm),filename,&viewer);CHKERRQ(ierr); 293 ierr = private_DMSwarmView_XDMF(dm,viewer);CHKERRQ(ierr); 294 for (f=0; f<nfields; f++) { 295 ierr = DMSwarmCreateGlobalVectorFromField(dm,field_name_list[f],&dvec);CHKERRQ(ierr); 296 ierr = PetscObjectSetName((PetscObject)dvec,field_name_list[f]);CHKERRQ(ierr); 297 ierr = private_VecView_Swarm_XDMF(dvec,viewer);CHKERRQ(ierr); 298 ierr = DMSwarmDestroyGlobalVectorFromField(dm,field_name_list[f],&dvec);CHKERRQ(ierr); 299 } 300 ierr = private_PetscViewerDestroy_XDMF(&viewer);CHKERRQ(ierr); 301 PetscFunctionReturn(0); 302 } 303 304 /*@C 305 DMSwarmViewXDMF - Write DMSwarm fields to an XDMF3 file 306 307 Collective on DM 308 309 Input parameters: 310 + dm - the DMSwarm 311 - filename - the file name of the XDMF file (must have the extension .xmf) 312 313 Level: beginner 314 315 Notes: 316 Only fields registered with data type PETSC_REAL will be written into the file 317 318 .seealso: DMSwarmViewFieldsXDMF() 319 @*/ 320 PETSC_EXTERN PetscErrorCode DMSwarmViewXDMF(DM dm,const char filename[]) 321 { 322 DM_Swarm *swarm = (DM_Swarm*)dm->data; 323 PetscErrorCode ierr; 324 Vec dvec; 325 PetscInt f; 326 PetscViewer viewer; 327 328 PetscFunctionBegin; 329 ierr = private_PetscViewerCreate_XDMF(PetscObjectComm((PetscObject)dm),filename,&viewer);CHKERRQ(ierr); 330 ierr = private_DMSwarmView_XDMF(dm,viewer);CHKERRQ(ierr); 331 for (f=4; f<swarm->db->nfields; f++) { /* only examine user defined fields - the first 4 are internally created by DMSwarmPIC */ 332 DataField field; 333 334 /* query field type - accept all those of type PETSC_DOUBLE */ 335 field = swarm->db->field[f]; 336 if (field->petsc_type != PETSC_DOUBLE) continue; 337 338 ierr = DMSwarmCreateGlobalVectorFromField(dm,field->name,&dvec);CHKERRQ(ierr); 339 ierr = PetscObjectSetName((PetscObject)dvec,field->name);CHKERRQ(ierr); 340 ierr = private_VecView_Swarm_XDMF(dvec,viewer);CHKERRQ(ierr); 341 ierr = DMSwarmDestroyGlobalVectorFromField(dm,field->name,&dvec);CHKERRQ(ierr); 342 } 343 ierr = private_PetscViewerDestroy_XDMF(&viewer);CHKERRQ(ierr); 344 PetscFunctionReturn(0); 345 } 346