Actual source code: ex62f90.F90

  1: program ex62f90
  2: #include "petsc/finclude/petsc.h"
  3:     use petsc
  4:     implicit none
  5: #include "exodusII.inc"

  7:     ! Get the Fortran kind associated with PetscInt and PetscReal so that we can use literal constants.
  8:     PetscInt                           :: dummyPetscInt
  9:     PetscReal                          :: dummyPetscreal
 10:     integer,parameter                  :: kPI = kind(dummyPetscInt)
 11:     integer,parameter                  :: kPR = kind(dummyPetscReal)

 13:     type(tDM)                          :: dm,dmU,dmA,dmS,dmUA,dmUA2,pDM
 14:     type(tDM),dimension(:),pointer     :: dmList
 15:     type(tVec)                         :: X,U,A,S,UA,UA2
 16:     type(tIS)                          :: isU,isA,isS,isUA
 17:     type(tPetscSection)                :: section, rootSection, leafSection
 18:     PetscInt                           :: fieldU = 0
 19:     PetscInt                           :: fieldA = 2
 20:     PetscInt                           :: fieldS = 1
 21:     PetscInt,dimension(2)              :: fieldUA = [0,2]
 22:     character(len=PETSC_MAX_PATH_LEN)  :: ifilename,ofilename,IOBuffer
 23:     integer                            :: exoid = -1
 24:     type(tIS)                          :: csIS
 25:     PetscInt,dimension(:),pointer      :: csID
 26:     PetscInt,dimension(:),pointer      :: pStartDepth,pEndDepth
 27:     PetscInt                           :: order = 1
 28:     PetscInt                           :: sdim,d,pStart,pEnd,p,numCS,set,i,j
 29:     PetscMPIInt                        :: rank,numProc
 30:     PetscBool                          :: flg
 31:     PetscErrorCode                     :: ierr
 32:     MPI_Comm                           :: comm
 33:     type(tPetscViewer)                 :: viewer

 35:     Character(len=MXSTLN)              :: sJunk
 36:     PetscInt                           :: numstep = 3, step
 37:     PetscInt                           :: numNodalVar,numZonalVar
 38:     character(len=MXSTLN)              :: nodalVarName(4)
 39:     character(len=MXSTLN)              :: zonalVarName(6)
 40:     logical,dimension(:,:),pointer     :: truthtable

 42:     type(tIS)                          :: cellIS
 43:     PetscInt,dimension(:),pointer      :: cellID
 44:     PetscInt                           :: numCells, cell, closureSize
 45:     PetscInt,dimension(:),pointer      :: closureA,closure

 47:     type(tPetscSection)                :: sectionUA,coordSection
 48:     type(tVec)                         :: UALoc,coord
 49:     PetscScalar,dimension(:),pointer   :: cval,xyz
 50:     PetscInt                           :: dofUA,offUA,c

 52:     ! dof layout ordered by increasing height in the DAG: cell, face, edge, vertex
 53:     PetscInt,dimension(3),target        :: dofS2D     = [0, 0, 3]
 54:     PetscInt,dimension(3),target        :: dofUP1Tri  = [2, 0, 0]
 55:     PetscInt,dimension(3),target        :: dofAP1Tri  = [1, 0, 0]
 56:     PetscInt,dimension(3),target        :: dofUP2Tri  = [2, 2, 0]
 57:     PetscInt,dimension(3),target        :: dofAP2Tri  = [1, 1, 0]
 58:     PetscInt,dimension(3),target        :: dofUP1Quad = [2, 0, 0]
 59:     PetscInt,dimension(3),target        :: dofAP1Quad = [1, 0, 0]
 60:     PetscInt,dimension(3),target        :: dofUP2Quad = [2, 2, 2]
 61:     PetscInt,dimension(3),target        :: dofAP2Quad = [1, 1, 1]
 62:     PetscInt,dimension(4),target        :: dofS3D     = [0, 0, 0, 6]
 63:     PetscInt,dimension(4),target        :: dofUP1Tet  = [3, 0, 0, 0]
 64:     PetscInt,dimension(4),target        :: dofAP1Tet  = [1, 0, 0, 0]
 65:     PetscInt,dimension(4),target        :: dofUP2Tet  = [3, 3, 0, 0]
 66:     PetscInt,dimension(4),target        :: dofAP2Tet  = [1, 1, 0, 0]
 67:     PetscInt,dimension(4),target        :: dofUP1Hex  = [3, 0, 0, 0]
 68:     PetscInt,dimension(4),target        :: dofAP1Hex  = [1, 0, 0, 0]
 69:     PetscInt,dimension(4),target        :: dofUP2Hex  = [3, 3, 3, 3]
 70:     PetscInt,dimension(4),target        :: dofAP2Hex  = [1, 1, 1, 1]
 71:     PetscInt,dimension(:),pointer       :: dofU,dofA,dofS

 73:     type(tPetscSF)                      :: migrationSF, natSF, natPointSF, natPointSFInv
 74:     PetscPartitioner                    :: part

 76:     type(tVec)                          :: tmpVec
 77:     PetscReal                           :: norm
 78:     PetscReal                           :: time = 1.234_kPR
 79:     PetscInt, pointer                   :: remoteOffsets(:)

 81:     PetscCallA(PetscInitialize(PETSC_NULL_CHARACTER,ierr))
 82:     if (ierr /= 0) then
 83:       print*,'Unable to initialize PETSc'
 84:       stop
 85:     endif

 87:     PetscCallA(MPI_Comm_rank(PETSC_COMM_WORLD,rank,ierr))
 88:     PetscCallA(MPI_Comm_size(PETSC_COMM_WORLD,numProc,ierr))
 89:     PetscCallA(PetscOptionsGetString(PETSC_NULL_OPTIONS,PETSC_NULL_CHARACTER,'-i',ifilename,flg,ierr))
 90:     PetscCheckA(flg,PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,'missing input file name -i ')
 91:     PetscCallA(PetscOptionsGetString(PETSC_NULL_OPTIONS,PETSC_NULL_CHARACTER,'-o',ofilename,flg,ierr))
 92:     PetscCheckA(flg,PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,'missing output file name -o ')
 93:     PetscCallA(PetscOptionsGetInt(PETSC_NULL_OPTIONS,PETSC_NULL_CHARACTER,'-order',order,flg,ierr))
 94:     if ((order > 2) .or. (order < 1)) then
 95:         write(IOBuffer,'("Unsupported polynomial order ", I2, " not in [1,2]")') order
 96:         stop
 97:     end if

 99:     ! Read the mesh in any supported format
100:     PetscCallA(DMPlexCreateFromFile(PETSC_COMM_WORLD, ifilename,PETSC_NULL_CHARACTER,PETSC_TRUE,dm,ierr))
101:     PetscCallA(DMPlexDistributeSetDefault(dm,PETSC_FALSE,ierr))
102:     PetscCallA(DMSetFromOptions(dm,ierr))
103:     PetscCallA(DMGetDimension(dm, sdim,ierr))
104:     PetscCallA(DMViewFromOptions(dm, PETSC_NULL_OBJECT,'-dm_view',ierr))

106:     ! Create the exodus result file

108:     ! enable exodus debugging information
109:     PetscCallA(exopts(EXVRBS+EXDEBG,ierr))
110:     ! Create the exodus file
111:     PetscCallA(PetscViewerExodusIIOpen(PETSC_COMM_WORLD,ofilename,FILE_MODE_WRITE,viewer,ierr))
112:     ! The long way would be
113:     !
114:     ! PetscCallA(PetscViewerCreate(PETSC_COMM_WORLD,viewer,ierr))
115:     ! PetscCallA(PetscViewerSetType(viewer,PETSCVIEWEREXODUSII,ierr))
116:     ! PetscCallA(PetscViewerFileSetMode(viewer,FILE_MODE_WRITE,ierr))
117:     ! PetscCallA(PetscViewerFileSetName(viewer,ofilename,ierr))

119:     ! set the mesh order
120:     PetscCallA(PetscViewerExodusIISetOrder(viewer,order,ierr))
121:     PetscCallA(PetscViewerView(viewer,PETSC_VIEWER_STDOUT_WORLD,ierr))
122:     !
123:     !    Notice how the exodus file is actually NOT open at this point (exoid is -1)
124:     !    Since we are overwriting the file (mode is FILE_MODE_WRITE), we are going to have to
125:     !    write the geometry (the DM), which can only be done on a brand new file.
126:     !

128:     ! Save the geometry to the file, erasing all previous content
129:     PetscCallA(DMView(dm,viewer,ierr))
130:     PetscCallA(PetscViewerView(viewer,PETSC_VIEWER_STDOUT_WORLD,ierr))
131:     !
132:     !    Note how the exodus file is now open
133:     !
134:     ! 'Format' the exodus result file, i.e. allocate space for nodal and zonal variables
135:     select case(sdim)
136:     case(2)
137:         numNodalVar = 3
138:         nodalVarName(1:numNodalVar) = ['U_x  ','U_y  ','Alpha']
139:         numZonalVar = 3
140:         zonalVarName(1:numZonalVar) = ['Sigma_11','Sigma_22','Sigma_12']
141:     case(3)
142:         numNodalVar = 4
143:         nodalVarName(1:numNodalVar) = ['U_x  ','U_y  ','U_z  ','Alpha']
144:         numZonalVar = 6
145:         zonalVarName(1:numZonalVar) = ['Sigma_11','Sigma_22','Sigma_33','Sigma_23','Sigma_13','Sigma_12']
146:     case default
147:         write(IOBuffer,'("No layout for dimension ",I2)') sdim
148:     end select
149:     PetscCallA(PetscViewerExodusIIGetId(viewer,exoid,ierr))
150:     PetscCallA(expvp(exoid, 'E', numZonalVar,ierr))
151:     PetscCallA(expvan(exoid, 'E', numZonalVar, zonalVarName,ierr))
152:     PetscCallA(expvp(exoid, 'N', numNodalVar,ierr))
153:     PetscCallA(expvan(exoid, 'N', numNodalVar, nodalVarName,ierr))
154:     PetscCallA(exinq(exoid, EX_INQ_ELEM_BLK,numCS,PETSC_NULL_REAL,sjunk,ierr))

156:     !    An exodusII truth table specifies which fields are saved at which time step
157:     !    It speeds up I/O but reserving space for fields in the file ahead of time.
158:     allocate(truthtable(numCS,numZonalVar))
159:     truthtable = .true.
160:     PetscCallA(expvtt(exoid, numCS, numZonalVar, truthtable, ierr))
161:     deallocate(truthtable)

163:     !   Writing time step information in the file. Note that this is currently broken in the exodus library for netcdf4 (HDF5-based) files */
164:     do step = 1,numstep
165:         PetscCallA(exptim(exoid,step,Real(step,kind=kPR),ierr))
166:     end do

168:     PetscCallA(DMSetUseNatural(dm, PETSC_TRUE, ierr))
169:     PetscCallA(DMPlexGetPartitioner(dm,part,ierr))
170:     PetscCallA(PetscPartitionerSetFromOptions(part,ierr))
171:     PetscCallA(DMPlexDistribute(dm,0_kPI,migrationSF,pdm,ierr))

173:     if (numProc > 1) then
174:         PetscCallA(DMPlexSetMigrationSF(pdm,migrationSF,ierr))
175:         PetscCallA(PetscSFDestroy(migrationSF,ierr))
176:     else
177:         pdm = dm
178:     end if
179:     PetscCallA(DMViewFromOptions(pdm,PETSC_NULL_OBJECT,'-dm_view',ierr))

181:     PetscCallA(PetscObjectGetComm(pdm,comm,ierr))
182:     PetscCallA(PetscSectionCreate(comm, section,ierr))
183:     PetscCallA(PetscSectionSetNumFields(section, 3_kPI,ierr))
184:     PetscCallA(PetscSectionSetFieldName(section, fieldU, 'U',ierr))
185:     PetscCallA(PetscSectionSetFieldName(section, fieldA, 'Alpha',ierr))
186:     PetscCallA(PetscSectionSetFieldName(section, fieldS, 'Sigma',ierr))
187:     PetscCallA(DMPlexGetChart(pdm, pStart, pEnd,ierr))
188:     PetscCallA(PetscSectionSetChart(section, pStart, pEnd,ierr))

190:     allocate(pStartDepth(sdim+1))
191:     allocate(pEndDepth(sdim+1))
192:     do d = 1, sdim+1
193:         PetscCallA(DMPlexGetDepthStratum(pdm, d-1, pStartDepth(d), pEndDepth(d),ierr))
194:     end do

196:     ! Vector field U, Scalar field Alpha, Tensor field Sigma
197:     PetscCallA(PetscSectionSetFieldComponents(section, fieldU, sdim,ierr));
198:     PetscCallA(PetscSectionSetFieldComponents(section, fieldA, 1_kPI,ierr));
199:     PetscCallA(PetscSectionSetFieldComponents(section, fieldS, sdim*(sdim+1)/2,ierr));

201:     ! Going through cell sets then cells, and setting up storage for the sections
202:     PetscCallA(DMGetLabelSize(pdm, 'Cell Sets', numCS, ierr))
203:     PetscCallA(DMGetLabelIdIS(pdm, 'Cell Sets', csIS, ierr))
204:     PetscCallA(ISGetIndices(csIS, csID, ierr))
205:     do set = 1,numCS
206:         PetscCallA(DMGetStratumSize(pdm, 'Cell Sets', csID(set), numCells,ierr))
207:         PetscCallA(DMGetStratumIS(pdm, 'Cell Sets', csID(set), cellIS,ierr))
208:         if (numCells > 0) then
209:             select case(sdim)
210:             case(2)
211:                 dofs => dofS2D
212:             case(3)
213:                 dofs => dofS3D
214:             case default
215:                 write(IOBuffer,'("No layout for dimension ",I2)') sdim
216:                 stop
217:             end select ! sdim

219:             ! Identify cell type based on closure size only. This works for Tri/Tet/Quad/Hex meshes
220:             ! It will not be enough to identify more exotic elements like pyramid or prisms...  */
221:             PetscCallA(ISGetIndices(cellIS, cellID,ierr))
222:             nullify(closureA)
223:             PetscCallA(DMPlexGetTransitiveClosure(pdm,cellID(1), PETSC_TRUE, PETSC_NULL_INTEGER,closureA,ierr))
224:             select case(size(closureA)/2)
225:             case(7) ! Tri
226:                 if (order == 1) then
227:                     dofU => dofUP1Tri
228:                     dofA => dofAP1Tri
229:                 else
230:                     dofU => dofUP2Tri
231:                     dofA => dofAP2Tri
232:                 end if
233:             case(9) ! Quad
234:                 if (order == 1) then
235:                     dofU => dofUP1Quad
236:                     dofA => dofAP1Quad
237:                 else
238:                     dofU => dofUP2Quad
239:                     dofA => dofAP2Quad
240:                 end if
241:             case(15) ! Tet
242:                 if (order == 1) then
243:                     dofU => dofUP1Tet
244:                     dofA => dofAP1Tet
245:                 else
246:                     dofU => dofUP2Tet
247:                     dofA => dofAP2Tet
248:                 end if
249:             case(27) ! Hex
250:                 if (order == 1) then
251:                     dofU => dofUP1Hex
252:                     dofA => dofAP1Hex
253:                 else
254:                     dofU => dofUP2Hex
255:                     dofA => dofAP2Hex
256:                 end if
257:             case default
258:                 write(IOBuffer,'("Unknown element with closure size ",I2)') size(closureA)/2
259:                 stop
260:             end select
261:             PetscCallA(DMPlexRestoreTransitiveClosure(pdm, cellID(1), PETSC_TRUE, PETSC_NULL_INTEGER, closureA,ierr))
262:             do cell = 1,numCells!
263:                 nullify(closure)
264:                 PetscCallA(DMPlexGetTransitiveClosure(pdm, cellID(cell), PETSC_TRUE, PETSC_NULL_INTEGER, closure,ierr))
265:                 do p = 1,size(closure),2
266:                     ! find the depth of p
267:                     do d = 1,sdim+1
268:                         if ((closure(p) >= pStartDepth(d)) .and. (closure(p) < pEndDepth(d))) then
269:                             PetscCallA(PetscSectionSetDof(section, closure(p), dofU(d)+dofA(d)+dofS(d),ierr))
270:                             PetscCallA(PetscSectionSetFieldDof(section, closure(p), fieldU, dofU(d),ierr))
271:                             PetscCallA(PetscSectionSetFieldDof(section, closure(p), fieldA, dofA(d),ierr))
272:                             PetscCallA(PetscSectionSetFieldDof(section, closure(p), fieldS, dofS(d),ierr))
273:                         end if ! closure(p)
274:                     end do ! d
275:                 end do ! p
276:                 PetscCallA(DMPlexRestoreTransitiveClosure(pdm, cellID(cell), PETSC_TRUE, PETSC_NULL_INTEGER, closure,ierr))
277:             end do ! cell
278:             PetscCallA(ISRestoreIndices(cellIS, cellID,ierr))
279:             PetscCallA(ISDestroy(cellIS,ierr))
280:         end if ! numCells
281:     end do ! set
282:     PetscCallA(ISRestoreIndices(csIS, csID,ierr))
283:     PetscCallA(ISDestroy(csIS,ierr))
284:     PetscCallA(PetscSectionSetUp(section,ierr))
285:     PetscCallA(DMSetLocalSection(pdm, section,ierr))
286:     PetscCallA(PetscObjectViewFromOptions(section, PETSC_NULL_OBJECT, '-dm_section_view',ierr))
287:     PetscCallA(PetscSectionDestroy(section,ierr))

289:     ! Creating section on the sequential DM + creating the GlobalToNatural SF
290:     if (numProc > 1) then
291:         PetscCallA(DMPlexGetMigrationSF(pdm, natPointSF, ierr))
292:         PetscCallA(DMGetLocalSection(pdm, rootSection, ierr))
293:         PetscCallA(PetscSFCreateInverseSF(natPointSF, natPointSFInv, ierr))
294:         PetscCallA(PetscSectionCreate(PETSC_COMM_WORLD, leafSection, ierr))
295:         PetscCallA(PetscSFDistributeSection(natPointSFInv, rootSection, remoteOffsets, leafSection, ierr))
296:         PetscCallA(PetscSFDestroyRemoteOffsets(remoteOffsets, ierr))
297:         PetscCallA(DMSetLocalSection(dm, leafSection, ierr))
298:         PetscCallA(DMPlexCreateGlobalToNaturalSF(pdm, leafSection, natPointSF, natSF, ierr))
299:         PetscCallA(PetscSFDestroy(natPointSFInv, ierr))
300:         PetscCallA(PetscSectionDestroy(leafSection,ierr))
301:         PetscCallA(DMSetNaturalSF(pdm, natSF, ierr))
302:         PetscCallA(PetscObjectDereference(natSF, ierr))
303:     end if

305:     ! Get DM and IS for each field of dm
306:     PetscCallA(DMCreateSubDM(pdm, 1_kPI, [fieldU],  isU,  dmU,ierr))
307:     PetscCallA(DMCreateSubDM(pdm, 1_kPI, [fieldA],  isA,  dmA,ierr))
308:     PetscCallA(DMCreateSubDM(pdm, 1_kPI, [fieldS],  isS,  dmS,ierr))
309:     PetscCallA(DMCreateSubDM(pdm, 2_kPI, fieldUA, isUA, dmUA,ierr))

311:     !Create the exodus result file
312:     allocate(dmList(2))
313:     dmList(1) = dmU;
314:     dmList(2) = dmA;
315:     PetscCallA(DMCreateSuperDM(dmList,2_kPI,PETSC_NULL_IS_POINTER,dmUA2,ierr))
316:     deallocate(dmList)

318:     PetscCallA(DMGetGlobalVector(pdm,   X,ierr))
319:     PetscCallA(DMGetGlobalVector(dmU,  U,ierr))
320:     PetscCallA(DMGetGlobalVector(dmA,  A,ierr))
321:     PetscCallA(DMGetGlobalVector(dmS,  S,ierr))
322:     PetscCallA(DMGetGlobalVector(dmUA, UA,ierr))
323:     PetscCallA(DMGetGlobalVector(dmUA2, UA2,ierr))

325:     PetscCallA(PetscObjectSetName(U,  'U',ierr))
326:     PetscCallA(PetscObjectSetName(A,  'Alpha',ierr))
327:     PetscCallA(PetscObjectSetName(S,  'Sigma',ierr))
328:     PetscCallA(PetscObjectSetName(UA, 'UAlpha',ierr))
329:     PetscCallA(PetscObjectSetName(UA2, 'UAlpha2',ierr))
330:     PetscCallA(VecSet(X, -111.0_kPR,ierr))

332:     ! Setting u to [x,y,z]  and alpha to x^2+y^2+z^2 by writing in UAlpha then restricting to U and Alpha */
333:     PetscCallA(DMGetLocalSection(dmUA, sectionUA,ierr))
334:     PetscCallA(DMGetLocalVector(dmUA, UALoc,ierr))
335:     PetscCallA(VecGetArray(UALoc, cval,ierr))
336:     PetscCallA(DMGetCoordinateSection(dmUA, coordSection,ierr))
337:     PetscCallA(DMGetCoordinatesLocal(dmUA, coord,ierr))
338:     PetscCallA(DMPlexGetChart(dmUA, pStart, pEnd,ierr))

340:     do p = pStart,pEnd-1
341:         PetscCallA(PetscSectionGetDof(sectionUA, p, dofUA,ierr))
342:         if (dofUA > 0) then
343:             PetscCallA(PetscSectionGetOffset(sectionUA, p, offUA,ierr))
344:             PetscCallA(DMPlexVecGetClosure(dmUA, coordSection, coord, p, PETSC_NULL_INTEGER, xyz,ierr))
345:             closureSize = size(xyz)
346:             do i = 1,sdim
347:                 do j = 0, closureSize-1,sdim
348:                     cval(offUA+i) = cval(offUA+i) + xyz(j/sdim+i)
349:                 end do
350:                 cval(offUA+i) = cval(offUA+i) * sdim / closureSize;
351:                 cval(offUA+sdim+1) = cval(offUA+sdim+1) + cval(offUA+i)**2
352:             end do
353:             PetscCallA(DMPlexVecRestoreClosure(dmUA, coordSection, coord, p, PETSC_NULL_INTEGER, xyz,ierr))
354:         end if
355:     end do

357:     PetscCallA(VecRestoreArray(UALoc, cval,ierr))
358:     PetscCallA(DMLocalToGlobalBegin(dmUA, UALoc, INSERT_VALUES, UA,ierr))
359:     PetscCallA(DMLocalToGlobalEnd(dmUA, UALoc, INSERT_VALUES, UA,ierr))
360:     PetscCallA(DMRestoreLocalVector(dmUA, UALoc,ierr))

362:     !Update X
363:     PetscCallA(VecISCopy(X, isUA, SCATTER_FORWARD, UA,ierr))
364:     ! Restrict to U and Alpha
365:     PetscCallA(VecISCopy(X, isU, SCATTER_REVERSE, U,ierr))
366:     PetscCallA(VecISCopy(X, isA, SCATTER_REVERSE, A,ierr))
367:     PetscCallA(VecViewFromOptions(UA, PETSC_NULL_OBJECT, '-ua_vec_view',ierr))
368:     PetscCallA(VecViewFromOptions(U, PETSC_NULL_OBJECT, '-u_vec_view',ierr))
369:     PetscCallA(VecViewFromOptions(A, PETSC_NULL_OBJECT, '-a_vec_view',ierr))
370:     ! restrict to UA2
371:     PetscCallA(VecISCopy(X, isUA, SCATTER_REVERSE, UA2,ierr))
372:     PetscCallA(VecViewFromOptions(UA2, PETSC_NULL_OBJECT, '-ua2_vec_view',ierr))

374:     ! Getting Natural Vec
375:     PetscCallA(DMSetOutputSequenceNumber(dmU, 0_kPI, time, ierr))
376:     PetscCallA(DMSetOutputSequenceNumber(dmA, 0_kPI, time, ierr))

378:     PetscCallA(VecView(U, viewer,ierr))
379:     PetscCallA(VecView(A, viewer,ierr))

381:     ! Saving U and Alpha in one shot.
382:     ! For this, we need to cheat and change the Vec's name
383:     ! Note that in the end we write variables one component at a time,
384:     ! so that there is no real value in doing this
385:     PetscCallA(DMSetOutputSequenceNumber(dmUA,1_kPI,time,ierr))
386:     PetscCallA(DMGetGlobalVector(dmUA, tmpVec,ierr))
387:     PetscCallA(VecCopy(UA, tmpVec,ierr))
388:     PetscCallA(PetscObjectSetName(tmpVec, 'U',ierr))
389:     PetscCallA(VecView(tmpVec, viewer,ierr))

391:     ! Reading nodal variables in Exodus file
392:     PetscCallA(VecSet(tmpVec, -1000.0_kPR,ierr))
393:     PetscCallA(VecLoad(tmpVec, viewer,ierr))
394:     PetscCallA(VecAXPY(UA, -1.0_kPR, tmpVec,ierr))
395:     PetscCallA(VecNorm(UA, NORM_INFINITY, norm,ierr))
396:     if (norm > PETSC_SQRT_MACHINE_EPSILON) then
397:         write(IOBuffer,'("UAlpha ||Vin - Vout|| = ",ES12.5)') norm
398:     end if
399:     PetscCallA(DMRestoreGlobalVector(dmUA, tmpVec,ierr))

401:     ! same thing with the UA2 Vec obtained from the superDM
402:     PetscCallA(DMGetGlobalVector(dmUA2, tmpVec,ierr))
403:     PetscCallA(VecCopy(UA2, tmpVec,ierr))
404:     PetscCallA(PetscObjectSetName(tmpVec, 'U',ierr))
405:     PetscCallA(DMSetOutputSequenceNumber(dmUA2,2_kPI,time,ierr))
406:     PetscCallA(VecView(tmpVec, viewer,ierr))

408:     ! Reading nodal variables in Exodus file
409:     PetscCallA(VecSet(tmpVec, -1000.0_kPR,ierr))
410:     PetscCallA(VecLoad(tmpVec,viewer,ierr))
411:     PetscCallA(VecAXPY(UA2, -1.0_kPR, tmpVec,ierr))
412:     PetscCallA(VecNorm(UA2, NORM_INFINITY, norm,ierr))
413:     if (norm > PETSC_SQRT_MACHINE_EPSILON) then
414:         write(IOBuffer,'("UAlpha2 ||Vin - Vout|| = ",ES12.5)') norm
415:     end if
416:     PetscCallA(DMRestoreGlobalVector(dmUA2, tmpVec,ierr))

418:     ! Building and saving Sigma
419:     !   We set sigma_0 = rank (to see partitioning)
420:     !          sigma_1 = cell set ID
421:     !          sigma_2 = x_coordinate of the cell center of mass
422:     PetscCallA(DMGetCoordinateSection(dmS, coordSection,ierr))
423:     PetscCallA(DMGetCoordinatesLocal(dmS, coord,ierr))
424:     PetscCallA(DMGetLabelIdIS(dmS, 'Cell Sets', csIS,ierr))
425:     PetscCallA(DMGetLabelSize(dmS, 'Cell Sets',numCS,ierr))
426:     PetscCallA(ISGetIndices(csIS, csID,ierr))

428:     do set = 1, numCS
429:         PetscCallA(DMGetStratumIS(dmS, 'Cell Sets', csID(set), cellIS,ierr))
430:         PetscCallA(ISGetIndices(cellIS, cellID,ierr))
431:         PetscCallA(ISGetSize(cellIS, numCells,ierr))
432:         do cell = 1,numCells
433:             PetscCallA(DMPlexVecGetClosure(dmS, PETSC_NULL_SECTION, S, cellID(cell), PETSC_NULL_INTEGER, cval,ierr))
434:             PetscCallA(DMPlexVecGetClosure(dmS, coordSection, coord, cellID(cell), PETSC_NULL_INTEGER, xyz,ierr))
435:             cval(1) = rank
436:             cval(2) = csID(set)
437:             cval(3) = 0.0_kPR
438:             do c = 1, size(xyz),sdim
439:                 cval(3) = cval(3) + xyz(c)
440:             end do
441:             cval(3) = cval(3) * sdim / size(xyz)
442:             PetscCallA(DMPlexVecSetClosure(dmS, PETSC_NULL_SECTION, S, cellID(cell), cval, INSERT_ALL_VALUES,ierr))
443:             PetscCallA(DMPlexVecRestoreClosure(dmS, PETSC_NULL_SECTION, S, cellID(cell), PETSC_NULL_INTEGER, cval,ierr))
444:             PetscCallA(DMPlexVecRestoreClosure(dmS, coordSection, coord, cellID(cell), PETSC_NULL_INTEGER, xyz,ierr))
445:         end do
446:         PetscCallA(ISRestoreIndices(cellIS, cellID,ierr))
447:         PetscCallA(ISDestroy(cellIS,ierr))
448:     end do
449:     PetscCallA(ISRestoreIndices(csIS, csID,ierr))
450:     PetscCallA(ISDestroy(csIS,ierr))
451:     PetscCallA(VecViewFromOptions(S, PETSC_NULL_OBJECT, '-s_vec_view',ierr))

453:     ! Writing zonal variables in Exodus file
454:     PetscCallA(DMSetOutputSequenceNumber(dmS,0_kPI,time,ierr))
455:     PetscCallA(VecView(S,viewer,ierr))

457:     ! Reading zonal variables in Exodus file */
458:     PetscCallA(DMGetGlobalVector(dmS, tmpVec,ierr))
459:     PetscCallA(VecSet(tmpVec, -1000.0_kPR,ierr))
460:     PetscCallA(PetscObjectSetName(tmpVec, 'Sigma',ierr))
461:     PetscCallA(VecLoad(tmpVec,viewer,ierr))
462:     PetscCallA(VecAXPY(S, -1.0_kPR, tmpVec,ierr))
463:     PetscCallA(VecNorm(S, NORM_INFINITY,norm,ierr))
464:     if (norm > PETSC_SQRT_MACHINE_EPSILON) then
465:        write(IOBuffer,'("Sigma ||Vin - Vout|| = ",ES12.5)') norm
466:     end if
467:     PetscCallA(DMRestoreGlobalVector(dmS, tmpVec,ierr))

469:     PetscCallA(DMRestoreGlobalVector(dmUA2, UA2,ierr))
470:     PetscCallA(DMRestoreGlobalVector(dmUA, UA,ierr))
471:     PetscCallA(DMRestoreGlobalVector(dmS,  S,ierr))
472:     PetscCallA(DMRestoreGlobalVector(dmA,  A,ierr))
473:     PetscCallA(DMRestoreGlobalVector(dmU,  U,ierr))
474:     PetscCallA(DMRestoreGlobalVector(pdm,   X,ierr))
475:     PetscCallA(DMDestroy(dmU,ierr))
476:     PetscCallA(ISDestroy(isU,ierr))
477:     PetscCallA(DMDestroy(dmA,ierr))
478:     PetscCallA(ISDestroy(isA,ierr))
479:     PetscCallA(DMDestroy(dmS,ierr))
480:     PetscCallA(ISDestroy(isS,ierr))
481:     PetscCallA(DMDestroy(dmUA,ierr))
482:     PetscCallA(ISDestroy(isUA,ierr))
483:     PetscCallA(DMDestroy(dmUA2,ierr))
484:     PetscCallA(DMDestroy(pdm,ierr))
485:     if (numProc > 1) then
486:         PetscCallA(DMDestroy(dm,ierr))
487:     end if

489:     deallocate(pStartDepth)
490:     deallocate(pEndDepth)

492:     PetscCallA(PetscViewerDestroy(viewer,ierr))
493:     PetscCallA(PetscFinalize(ierr))
494: end program ex62f90

496: ! /*TEST
497: !
498: ! build:
499: !   requires: exodusii pnetcdf !complex
500: !   # 2D seq
501: ! test:
502: !   suffix: 0
503: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareT-large.exo -o FourSquareT-large_out.exo -dm_view -petscpartitioner_type simple -order 1
504: !   #TODO: bug in PetscCallA(to NetCDF failed to complete invalid type definition in file id 65536 NetCDF: One or more variable sizes violate format constraints
505: ! test:
506: !   suffix: 1
507: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareQ-large.exo -o FourSquareQ-large_out.exo -dm_view -petscpartitioner_type simple -order 1
508: !
509: ! test:
510: !   suffix: 2
511: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareH-large.exo -o FourSquareH-large_out.exo -dm_view -petscpartitioner_type simple -order 1
512: !   #TODO: bug in PetscCallA(to NetCDF failed to complete invalid type definition in file id 65536 NetCDF: One or more variable sizes violate format constraints
513: ! test:
514: !   suffix: 3
515: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareT-large.exo -o FourSquareT-large_out.exo -dm_view -petscpartitioner_type simple -order 2
516: ! test:
517: !   suffix: 4
518: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareQ-large.exo -o FourSquareQ-large_out.exo -dm_view -petscpartitioner_type simple -order 2
519: ! test:
520: !   suffix: 5
521: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareH-large.exo -o FourSquareH-large_out.exo -dm_view -petscpartitioner_type simple -order 2
522: !   # 2D par
523: ! test:
524: !   suffix: 6
525: !   nsize: 2
526: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareT-large.exo -o FourSquareT-large_out.exo -dm_view -petscpartitioner_type simple -order 1
527: !   #TODO: bug in PetscCallA(to NetCDF failed to complete invalid type definition in file id 65536 NetCDF: One or more variable sizes violate format constraints
528: ! test:
529: !   suffix: 7
530: !   nsize: 2
531: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareQ-large.exo -o FourSquareQ-large_out.exo -dm_view -petscpartitioner_type simple -order 1
532: ! test:
533: !   suffix: 8
534: !   nsize: 2
535: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareH-large.exo -o FourSquareH-large_out.exo -dm_view -petscpartitioner_type simple -order 1
536: !   #TODO: bug in PetscCallA(to NetCDF failed to complete invalid type definition in file id 65536 NetCDF: invalid dimension ID or name
537: ! test:
538: !   suffix: 9
539: !   nsize: 2
540: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareT-large.exo -o FourSquareT-large_out.exo -dm_view -petscpartitioner_type simple -order 2
541: ! test:
542: !   suffix: 10
543: !   nsize: 2
544: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareQ-large.exo -o FourSquareQ-large_out.exo -dm_view -petscpartitioner_type simple -order 2
545: ! test:
546: !   # Something is now broken with parallel read/write for whatever shape H is
547: !   TODO: broken
548: !   suffix: 11
549: !   nsize: 2
550: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareH-large.exo -o FourSquareH-large_out.exo -dm_view -petscpartitioner_type simple -order 2
551: !   #3d seq
552: ! test:
553: !   suffix: 12
554: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickHex-large.exo -o FourBrickHex-large_out.exo -dm_view -petscpartitioner_type simple -order 1
555: ! test:
556: !   suffix: 13
557: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickTet-large.exo -o FourBrickTet-large_out.exo -dm_view -petscpartitioner_type simple -order 1
558: !   #TODO: bug in PetscCallA(to NetCDF failed to complete invalid type definition in file id 65536 NetCDF: One or more variable sizes violate format constraints
559: ! test:
560: !   suffix: 14
561: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickHex-large.exo -o FourBrickHex-large_out.exo -dm_view -petscpartitioner_type simple -order 2
562: ! test:
563: !   suffix: 15
564: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickTet-large.exo -o FourBrickTet-large_out.exo -dm_view -petscpartitioner_type simple -order 2
565: !   #TODO: bug in PetscCallA(to NetCDF failed to complete invalid type definition in file id 65536 NetCDF: One or more variable sizes violate format constraints
566: !   #3d par
567: ! test:
568: !   suffix: 16
569: !   nsize: 2
570: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickHex-large.exo -o FourBrickHex-large_out.exo -dm_view -petscpartitioner_type simple -order 1
571: ! test:
572: !   suffix: 17
573: !   nsize: 2
574: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickTet-large.exo -o FourBrickTet-large_out.exo -dm_view -petscpartitioner_type simple -order 1
575: !   #TODO: bug in PetscCallA(to NetCDF failed to complete invalid type definition in file id 65536 NetCDF: One or more variable sizes violate format constraints
576: ! test:
577: !   suffix: 18
578: !   nsize: 2
579: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickHex-large.exo -o FourBrickHex-large_out.exo -dm_view -petscpartitioner_type simple -order 2
580: ! test:
581: !   suffix: 19
582: !   nsize: 2
583: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickTet-large.exo -o FourBrickTet-large_out.exo -dm_view -petscpartitioner_type simple -order 2
584: !   #TODO: bug in PetscCallA(to NetCDF failed to complete invalid type definition in file id 65536 NetCDF: One or more variable sizes violate format constraints
585: !
586: ! TEST*/