1 2 #include <petsc.h> 3 #include <petscdm.h> 4 #include <petscdmda.h> 5 #include <petscdmswarm.h> 6 #include <petsc/private/dmswarmimpl.h> 7 #include "data_bucket.h" 8 9 PetscErrorCode private_PetscViewerCreate_XDMF(MPI_Comm comm,const char filename[],PetscViewer *v) 10 { 11 long int *bytes; 12 PetscContainer container; 13 PetscViewer viewer; 14 PetscErrorCode ierr; 15 16 PetscFunctionBegin; 17 ierr = PetscViewerCreate(comm,&viewer);CHKERRQ(ierr); 18 ierr = PetscViewerSetType(viewer,PETSCVIEWERASCII);CHKERRQ(ierr); 19 ierr = PetscViewerFileSetMode(viewer,FILE_MODE_WRITE);CHKERRQ(ierr); 20 ierr = PetscViewerFileSetName(viewer,filename);CHKERRQ(ierr); 21 22 ierr = PetscMalloc1(1,&bytes);CHKERRQ(ierr); 23 bytes[0] = 0; 24 ierr = PetscContainerCreate(comm,&container);CHKERRQ(ierr); 25 ierr = PetscContainerSetPointer(container,(void*)bytes);CHKERRQ(ierr); 26 ierr = PetscObjectCompose((PetscObject)viewer,"XDMFViewerContext",(PetscObject)container);CHKERRQ(ierr); 27 28 /* write xdmf header */ 29 PetscViewerASCIIPrintf(viewer,"<?xml version=\"1.0\" encoding=\"utf-8\"?>\n"); 30 PetscViewerASCIIPrintf(viewer,"<Xdmf xmlns:xi=\"http://www.w3.org/2001/XInclude\" Version=\"2.99\">\n"); 31 /* write xdmf domain */ 32 PetscViewerASCIIPushTab(viewer); 33 PetscViewerASCIIPrintf(viewer,"<Domain>\n"); 34 *v = viewer; 35 PetscFunctionReturn(0); 36 } 37 38 PetscErrorCode private_PetscViewerDestroy_XDMF(PetscViewer *v) 39 { 40 PetscViewer viewer; 41 DM dm = NULL; 42 long int *bytes; 43 PetscContainer container = NULL; 44 PetscErrorCode ierr; 45 46 PetscFunctionBegin; 47 if (!v) PetscFunctionReturn(0); 48 viewer = *v; 49 50 ierr = PetscObjectQuery((PetscObject)viewer,"DMSwarm",(PetscObject*)&dm);CHKERRQ(ierr); 51 if (dm) { 52 PetscViewerASCIIPrintf(viewer,"</Grid>\n"); 53 PetscViewerASCIIPopTab(viewer); 54 } 55 56 /* close xdmf header */ 57 PetscViewerASCIIPrintf(viewer,"</Domain>\n"); 58 PetscViewerASCIIPopTab(viewer); 59 PetscViewerASCIIPrintf(viewer,"</Xdmf>\n"); 60 61 ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr); 62 if (container) { 63 ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr); 64 ierr = PetscFree(bytes);CHKERRQ(ierr); 65 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 66 } 67 68 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 69 *v = NULL; 70 PetscFunctionReturn(0); 71 } 72 73 PetscErrorCode private_CreateDataFileNameXDMF(const char filename[],char dfilename[]) 74 { 75 char *ext; 76 PetscBool flg; 77 PetscErrorCode ierr; 78 79 PetscFunctionBegin; 80 ierr = PetscStrrchr(filename,'.',&ext);CHKERRQ(ierr); 81 ierr = PetscStrcmp("xmf",ext,&flg);CHKERRQ(ierr); 82 if (flg) { 83 size_t len; 84 char viewername_minus_ext[PETSC_MAX_PATH_LEN]; 85 86 ierr = PetscStrlen(filename,&len);CHKERRQ(ierr); 87 ierr = PetscSNPrintf(viewername_minus_ext,len-3,"%s",filename);CHKERRQ(ierr); 88 ierr = PetscSNPrintf(dfilename,PETSC_MAX_PATH_LEN-1,"%s_swarm_fields.pbin",viewername_minus_ext);CHKERRQ(ierr); 89 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"File extension must by .xmf"); 90 91 PetscFunctionReturn(0); 92 } 93 94 PetscErrorCode private_DMSwarmView_XDMF(DM dm,PetscViewer viewer) 95 { 96 PetscBool isswarm = PETSC_FALSE; 97 const char *viewername; 98 char datafile[PETSC_MAX_PATH_LEN]; 99 PetscViewer fviewer; 100 PetscInt k,ng,dim; 101 Vec dvec; 102 long int *bytes = NULL; 103 PetscContainer container = NULL; 104 const char *dmname; 105 PetscErrorCode ierr; 106 107 PetscFunctionBegin; 108 ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr); 109 if (container) { 110 ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr); 111 } else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext"); 112 113 ierr = PetscObjectTypeCompare((PetscObject)dm,DMSWARM,&isswarm);CHKERRQ(ierr); 114 if (!isswarm) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Only valid for DMSwarm"); 115 116 ierr = PetscObjectCompose((PetscObject)viewer,"DMSwarm",(PetscObject)dm);CHKERRQ(ierr); 117 118 PetscViewerASCIIPushTab(viewer); 119 ierr = PetscObjectGetName((PetscObject)dm,&dmname);CHKERRQ(ierr); 120 if (!dmname) { 121 ierr = DMGetOptionsPrefix(dm,&dmname);CHKERRQ(ierr); 122 } 123 if (!dmname) { 124 PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm\" GridType=\"Uniform\">\n"); 125 } else { 126 PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm[%s]\" GridType=\"Uniform\">\n",dmname); 127 } 128 129 /* create a sub-viewer for topology, geometry and all data fields */ 130 /* name is viewer.name + "_swarm_fields.pbin" */ 131 ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr); 132 ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr); 133 ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr); 134 ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr); 135 ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_WRITE);CHKERRQ(ierr); 136 137 ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr); 138 //ierr = PetscSNPrintf(datafile,PETSC_MAX_PATH_LEN-1,"%s_swarm_fields.pbin",viewername);CHKERRQ(ierr); 139 ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr); 140 ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr); 141 142 ierr = DMSwarmGetSize(dm,&ng);CHKERRQ(ierr); 143 144 /* write topology header */ 145 PetscViewerASCIIPushTab(viewer); 146 PetscViewerASCIIPrintf(viewer,"<Topology Dimensions=\"%D\" TopologyType=\"Mixed\">\n",ng); 147 PetscViewerASCIIPushTab(viewer); 148 PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Dimensions=\"%D\" Seek=\"%D\">\n",ng*3,bytes[0]); 149 PetscViewerASCIIPushTab(viewer); 150 PetscViewerASCIIPrintf(viewer,"%s\n",datafile); 151 PetscViewerASCIIPopTab(viewer); 152 PetscViewerASCIIPrintf(viewer,"</DataItem>\n"); 153 PetscViewerASCIIPopTab(viewer); 154 PetscViewerASCIIPrintf(viewer,"</Topology>\n"); 155 PetscViewerASCIIPopTab(viewer); 156 157 /* write topology data */ 158 for (k=0; k<ng; k++) { 159 PetscInt pvertex[3]; 160 161 pvertex[0] = 1; 162 pvertex[1] = 1; 163 pvertex[2] = k; 164 ierr = PetscViewerBinaryWrite(fviewer,pvertex,3,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr); 165 } 166 bytes[0] += sizeof(PetscInt) * ng * 3; 167 168 /* write geometry header */ 169 PetscViewerASCIIPushTab(viewer); 170 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 171 switch (dim) { 172 case 1: 173 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for 1D"); 174 break; 175 case 2: 176 PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XY\">\n"); 177 break; 178 case 3: 179 PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XYZ\">\n"); 180 break; 181 } 182 PetscViewerASCIIPushTab(viewer); 183 PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D %D\" Seek=\"%D\">\n",ng,dim,bytes[0]); 184 PetscViewerASCIIPushTab(viewer); 185 PetscViewerASCIIPrintf(viewer,"%s\n",datafile); 186 PetscViewerASCIIPopTab(viewer); 187 PetscViewerASCIIPrintf(viewer,"</DataItem>\n"); 188 PetscViewerASCIIPopTab(viewer); 189 PetscViewerASCIIPrintf(viewer,"</Geometry>\n"); 190 PetscViewerASCIIPopTab(viewer); 191 192 /* write geometry data */ 193 ierr = DMSwarmCreateGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr); 194 ierr = VecView(dvec,fviewer);CHKERRQ(ierr); 195 ierr = DMSwarmDestroyGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr); 196 bytes[0] += sizeof(PetscReal) * ng * dim; 197 198 ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr); 199 200 PetscFunctionReturn(0); 201 } 202 203 PetscErrorCode private_VecView_Swarm_XDMF(Vec x,PetscViewer viewer) 204 { 205 long int *bytes = NULL; 206 PetscContainer container = NULL; 207 const char *viewername; 208 char datafile[PETSC_MAX_PATH_LEN]; 209 PetscViewer fviewer; 210 PetscInt N,bs; 211 const char *vecname; 212 char fieldname[PETSC_MAX_PATH_LEN]; 213 PetscErrorCode ierr; 214 215 PetscFunctionBegin; 216 ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr); 217 if (container) { 218 ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr); 219 } else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext"); 220 221 ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr); 222 //ierr = PetscSNPrintf(datafile,PETSC_MAX_PATH_LEN-1,"%s_swarm_fields.pbin",viewername);CHKERRQ(ierr); 223 ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr); 224 225 /* re-open a sub-viewer for all data fields */ 226 /* name is viewer.name + "_swarm_fields.pbin" */ 227 ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr); 228 ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr); 229 ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr); 230 ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr); 231 ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_APPEND);CHKERRQ(ierr); 232 ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr); 233 234 ierr = VecGetSize(x,&N);CHKERRQ(ierr); 235 ierr = VecGetBlockSize(x,&bs);CHKERRQ(ierr); 236 N = N/bs; 237 ierr = PetscObjectGetName((PetscObject)x,&vecname);CHKERRQ(ierr); 238 if (!vecname) { 239 ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"swarmfield_%D",((PetscObject)x)->tag);CHKERRQ(ierr); 240 } else { 241 ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"%s",vecname);CHKERRQ(ierr); 242 } 243 244 /* write data header */ 245 PetscViewerASCIIPushTab(viewer); 246 PetscViewerASCIIPrintf(viewer,"<Attribute Center=\"Node\" Name=\"%s\" Type=\"None\">\n",fieldname); 247 PetscViewerASCIIPushTab(viewer); 248 if (bs == 1) { 249 PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D\" Seek=\"%D\">\n",N,bytes[0]); 250 } else { 251 PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D %D\" Seek=\"%D\">\n",N,bs,bytes[0]); 252 } 253 PetscViewerASCIIPushTab(viewer); 254 PetscViewerASCIIPrintf(viewer,"%s\n",datafile); 255 PetscViewerASCIIPopTab(viewer); 256 PetscViewerASCIIPrintf(viewer,"</DataItem>\n"); 257 PetscViewerASCIIPopTab(viewer); 258 PetscViewerASCIIPrintf(viewer,"</Attribute>\n"); 259 PetscViewerASCIIPopTab(viewer); 260 261 /* write data */ 262 ierr = VecView(x,fviewer);CHKERRQ(ierr); 263 bytes[0] += sizeof(PetscReal) * N * bs; 264 265 ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr); 266 267 PetscFunctionReturn(0); 268 } 269 270 PETSC_EXTERN PetscErrorCode DMSwarmViewFieldsXDMF(DM dm,const char filename[],PetscInt nfields,const char *field_name_list[]) 271 { 272 PetscErrorCode ierr; 273 Vec dvec; 274 PetscInt f; 275 PetscViewer viewer; 276 277 PetscFunctionBegin; 278 ierr = private_PetscViewerCreate_XDMF(PetscObjectComm((PetscObject)dm),filename,&viewer);CHKERRQ(ierr); 279 ierr = private_DMSwarmView_XDMF(dm,viewer);CHKERRQ(ierr); 280 for (f=0; f<nfields; f++) { 281 ierr = DMSwarmCreateGlobalVectorFromField(dm,field_name_list[f],&dvec);CHKERRQ(ierr); 282 ierr = PetscObjectSetName((PetscObject)dvec,field_name_list[f]);CHKERRQ(ierr); 283 ierr = private_VecView_Swarm_XDMF(dvec,viewer);CHKERRQ(ierr); 284 ierr = DMSwarmDestroyGlobalVectorFromField(dm,field_name_list[f],&dvec);CHKERRQ(ierr); 285 } 286 ierr = private_PetscViewerDestroy_XDMF(&viewer);CHKERRQ(ierr); 287 PetscFunctionReturn(0); 288 } 289 290 PETSC_EXTERN PetscErrorCode DMSwarmViewXDMF(DM dm,const char filename[]) 291 { 292 DM_Swarm *swarm = (DM_Swarm*)dm->data; 293 PetscErrorCode ierr; 294 Vec dvec; 295 PetscInt f; 296 PetscViewer viewer; 297 298 PetscFunctionBegin; 299 ierr = private_PetscViewerCreate_XDMF(PetscObjectComm((PetscObject)dm),filename,&viewer);CHKERRQ(ierr); 300 ierr = private_DMSwarmView_XDMF(dm,viewer);CHKERRQ(ierr); 301 for (f=4; f<swarm->db->nfields; f++) { /* only examine user defined fields - the first 4 are internally created by DMSwarmPIC */ 302 DataField field; 303 304 /* query field type - accept all those of type PETSC_DOUBLE */ 305 field = swarm->db->field[f]; 306 if (field->petsc_type != PETSC_DOUBLE) continue; 307 308 ierr = DMSwarmCreateGlobalVectorFromField(dm,field->name,&dvec);CHKERRQ(ierr); 309 ierr = PetscObjectSetName((PetscObject)dvec,field->name);CHKERRQ(ierr); 310 ierr = private_VecView_Swarm_XDMF(dvec,viewer);CHKERRQ(ierr); 311 ierr = DMSwarmDestroyGlobalVectorFromField(dm,field->name,&dvec);CHKERRQ(ierr); 312 } 313 ierr = private_PetscViewerDestroy_XDMF(&viewer);CHKERRQ(ierr); 314 PetscFunctionReturn(0); 315 } 316