Actual source code: ex26f90.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
 18:     PetscInt,dimension(1)              :: fieldU = [0]
 19:     PetscInt,dimension(1)              :: fieldA = [2]
 20:     PetscInt,dimension(1)              :: 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
 74:     PetscPartitioner                    :: part

 76:     type(tVec)                          :: tmpVec
 77:     PetscReal                           :: norm
 78:     PetscReal                           :: time = 1.234_kPR

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

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

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

105:     ! Create the exodus result file

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

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

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

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

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

167:     PetscCallA(PetscObjectGetComm(dm,comm,ierr))
168:     PetscCallA(PetscSectionCreate(comm, section,ierr))
169:     PetscCallA(PetscSectionSetNumFields(section, 3_kPI,ierr))
170:     PetscCallA(PetscSectionSetFieldName(section, fieldU, 'U',ierr))
171:     PetscCallA(PetscSectionSetFieldName(section, fieldA, 'Alpha',ierr))
172:     PetscCallA(PetscSectionSetFieldName(section, fieldS, 'Sigma',ierr))
173:     PetscCallA(DMPlexGetChart(dm, pStart, pEnd,ierr))
174:     PetscCallA(PetscSectionSetChart(section, pStart, pEnd,ierr))

176:     allocate(pStartDepth(sdim+1))
177:     allocate(pEndDepth(sdim+1))
178:     do d = 1, sdim+1
179:         PetscCallA(DMPlexGetDepthStratum(dm, d-1, pStartDepth(d), pEndDepth(d),ierr))
180:     end do

182:     ! Vector field U, Scalar field Alpha, Tensor field Sigma
183:     PetscCallA(PetscSectionSetFieldComponents(section, fieldU, sdim,ierr));
184:     PetscCallA(PetscSectionSetFieldComponents(section, fieldA, 1_kPI,ierr));
185:     PetscCallA(PetscSectionSetFieldComponents(section, fieldS, sdim*(sdim+1)/2,ierr));

187:     ! Going through cell sets then cells, and setting up storage for the sections
188:     PetscCallA(DMGetLabelSize(dm, 'Cell Sets', numCS, ierr))
189:     PetscCallA(DMGetLabelIdIS(dm, 'Cell Sets', csIS, ierr))
190:     PetscCallA(ISGetIndicesF90(csIS, csID, ierr))
191:     do set = 1,numCS
192:         !!! This is pointless but will avoid a warning with gfortran and -Werror=maybe-uninitialized
193:         nullify(dofA)
194:         nullify(dofU)
195:         nullify(dofS)
196:         PetscCallA(DMGetStratumSize(dm, 'Cell Sets', csID(set), numCells,ierr))
197:         PetscCallA(DMGetStratumIS(dm, 'Cell Sets', csID(set), cellIS,ierr))
198:         if (numCells > 0) then
199:             select case(sdim)
200:             case(2)
201:                 dofs => dofS2D
202:             case(3)
203:                 dofs => dofS3D
204:             case default
205:                 write(IOBuffer,'("No layout for dimension ",I2)') sdim
206:                 SETERRA(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE,IOBuffer)
207:             end select ! sdim

209:             ! Identify cell type based on closure size only. This works for Tri/Tet/Quad/Hex meshes
210:             ! It will not be enough to identify more exotic elements like pyramid or prisms...  */
211:             PetscCallA(ISGetIndicesF90(cellIS, cellID,ierr))
212:             nullify(closureA)
213:             PetscCallA(DMPlexGetTransitiveClosure(dm,cellID(1), PETSC_TRUE, closureA,ierr))
214:             select case(size(closureA)/2)
215:             case(7) ! Tri
216:                 if (order == 1) then
217:                     dofU => dofUP1Tri
218:                     dofA => dofAP1Tri
219:                 else
220:                     dofU => dofUP2Tri
221:                     dofA => dofAP2Tri
222:                 end if
223:             case(9) ! Quad
224:                 if (order == 1) then
225:                     dofU => dofUP1Quad
226:                     dofA => dofAP1Quad
227:                 else
228:                     dofU => dofUP2Quad
229:                     dofA => dofAP2Quad
230:                 end if
231:             case(15) ! Tet
232:                 if (order == 1) then
233:                     dofU => dofUP1Tet
234:                     dofA => dofAP1Tet
235:                 else
236:                     dofU => dofUP2Tet
237:                     dofA => dofAP2Tet
238:                 end if
239:             case(27) ! Hex
240:                 if (order == 1) then
241:                     dofU => dofUP1Hex
242:                     dofA => dofAP1Hex
243:                 else
244:                     dofU => dofUP2Hex
245:                     dofA => dofAP2Hex
246:                 end if
247:             case default
248:                 write(IOBuffer,'("Unknown element with closure size ",I2)') size(closureA)/2
249:                 SETERRA(PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP,IOBuffer)
250:             end select
251:             PetscCallA(DMPlexRestoreTransitiveClosure(dm, cellID(1), PETSC_TRUE,closureA,ierr))
252:             do cell = 1,numCells!
253:                 nullify(closure)
254:                 PetscCallA(DMPlexGetTransitiveClosure(dm, cellID(cell), PETSC_TRUE, closure,ierr))
255:                 do p = 1,size(closure),2
256:                     ! find the depth of p
257:                     do d = 1,sdim+1
258:                         if ((closure(p) >= pStartDepth(d)) .and. (closure(p) < pEndDepth(d))) then
259:                             PetscCallA(PetscSectionSetDof(section, closure(p), dofU(d)+dofA(d)+dofS(d),ierr))
260:                             PetscCallA(PetscSectionSetFieldDof(section, closure(p), fieldU, dofU(d),ierr))
261:                             PetscCallA(PetscSectionSetFieldDof(section, closure(p), fieldA, dofA(d),ierr))
262:                             PetscCallA(PetscSectionSetFieldDof(section, closure(p), fieldS, dofS(d),ierr))
263:                         end if ! closure(p)
264:                     end do ! d
265:                 end do ! p
266:                 PetscCallA(DMPlexRestoreTransitiveClosure(dm, cellID(cell), PETSC_TRUE, closure,ierr))
267:             end do ! cell
268:             PetscCallA(ISRestoreIndicesF90(cellIS, cellID,ierr))
269:             PetscCallA(ISDestroy(cellIS,ierr))
270:         end if ! numCells
271:     end do ! set
272:     PetscCallA(ISRestoreIndicesF90(csIS, csID,ierr))
273:     PetscCallA(ISDestroy(csIS,ierr))
274:     PetscCallA(PetscSectionSetUp(section,ierr))
275:     PetscCallA(DMSetLocalSection(dm, section,ierr))
276:     PetscCallA(PetscObjectViewFromOptions(section, PETSC_NULL_SECTION, '-dm_section_view',ierr))
277:     PetscCallA(PetscSectionDestroy(section,ierr))

279:     PetscCallA(DMSetUseNatural(dm,PETSC_TRUE,ierr))
280:     PetscCallA(DMPlexGetPartitioner(dm,part,ierr))
281:     PetscCallA(PetscPartitionerSetFromOptions(part,ierr))
282:     PetscCallA(DMPlexDistribute(dm,0_kPI,migrationSF,pdm,ierr))

284:     if (numProc > 1) then
285:         PetscCallA(DMPlexSetMigrationSF(pdm,migrationSF,ierr))
286:         PetscCallA(PetscSFDestroy(migrationSF,ierr))
287:     else
288:         pdm = dm
289:     end if
290:     PetscCallA(DMViewFromOptions(pdm,PETSC_NULL_OPTIONS,'-dm_view',ierr))

292:     ! Get DM and IS for each field of dm
293:     PetscCallA(DMCreateSubDM(pdm, 1_kPI, fieldU,  isU,  dmU,ierr))
294:     PetscCallA(DMCreateSubDM(pdm, 1_kPI, fieldA,  isA,  dmA,ierr))
295:     PetscCallA(DMCreateSubDM(pdm, 1_kPI, fieldS,  isS,  dmS,ierr))
296:     PetscCallA(DMCreateSubDM(pdm, 2_kPI, fieldUA, isUA, dmUA,ierr))

298:     !Create the exodus result file
299:     allocate(dmList(2))
300:     dmList(1) = dmU;
301:     dmList(2) = dmA;
302:     PetscCallA(DMCreateSuperDM(dmList,2_kPI,PETSC_NULL_IS,dmUA2,ierr))
303:     deallocate(dmList)

305:     PetscCallA(DMGetGlobalVector(pdm,   X,ierr))
306:     PetscCallA(DMGetGlobalVector(dmU,  U,ierr))
307:     PetscCallA(DMGetGlobalVector(dmA,  A,ierr))
308:     PetscCallA(DMGetGlobalVector(dmS,  S,ierr))
309:     PetscCallA(DMGetGlobalVector(dmUA, UA,ierr))
310:     PetscCallA(DMGetGlobalVector(dmUA2, UA2,ierr))

312:     PetscCallA(PetscObjectSetName(U,  'U',ierr))
313:     PetscCallA(PetscObjectSetName(A,  'Alpha',ierr))
314:     PetscCallA(PetscObjectSetName(S,  'Sigma',ierr))
315:     PetscCallA(PetscObjectSetName(UA, 'UAlpha',ierr))
316:     PetscCallA(PetscObjectSetName(UA2, 'UAlpha2',ierr))
317:     PetscCallA(VecSet(X, -111.0_kPR,ierr))

319:     ! 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 */
320:     PetscCallA(DMGetLocalSection(dmUA, sectionUA,ierr))
321:     PetscCallA(DMGetLocalVector(dmUA, UALoc,ierr))
322:     PetscCallA(VecGetArrayF90(UALoc, cval,ierr))
323:     PetscCallA(DMGetCoordinateSection(dmUA, coordSection,ierr))
324:     PetscCallA(DMGetCoordinatesLocal(dmUA, coord,ierr))
325:     PetscCallA(DMPlexGetChart(dmUA, pStart, pEnd,ierr))

327:     do p = pStart,pEnd-1
328:         PetscCallA(PetscSectionGetDof(sectionUA, p, dofUA,ierr))
329:         if (dofUA > 0) then
330:             PetscCallA(PetscSectionGetOffset(sectionUA, p, offUA,ierr))
331:             PetscCallA(DMPlexVecGetClosure(dmUA, coordSection, coord, p, xyz,ierr))
332:             closureSize = size(xyz)
333:             do i = 1,sdim
334:                 do j = 0, closureSize-1,sdim
335:                     cval(offUA+i) = cval(offUA+i) + xyz(j/sdim+i)
336:                 end do
337:                 cval(offUA+i) = cval(offUA+i) * sdim / closureSize;
338:                 cval(offUA+sdim+1) = cval(offUA+sdim+1) + cval(offUA+i)**2
339:             end do
340:             PetscCallA(DMPlexVecRestoreClosure(dmUA, coordSection, coord, p, xyz,ierr))
341:         end if
342:     end do

344:     PetscCallA(VecRestoreArrayF90(UALoc, cval,ierr))
345:     PetscCallA(DMLocalToGlobalBegin(dmUA, UALoc, INSERT_VALUES, UA,ierr))
346:     PetscCallA(DMLocalToGlobalEnd(dmUA, UALoc, INSERT_VALUES, UA,ierr))
347:     PetscCallA(DMRestoreLocalVector(dmUA, UALoc,ierr))

349:     !Update X
350:     PetscCallA(VecISCopy(X, isUA, SCATTER_FORWARD, UA,ierr))
351:     ! Restrict to U and Alpha
352:     PetscCallA(VecISCopy(X, isU, SCATTER_REVERSE, U,ierr))
353:     PetscCallA(VecISCopy(X, isA, SCATTER_REVERSE, A,ierr))
354:     PetscCallA(VecViewFromOptions(UA, PETSC_NULL_OPTIONS, '-ua_vec_view',ierr))
355:     PetscCallA(VecViewFromOptions(U, PETSC_NULL_OPTIONS, '-u_vec_view',ierr))
356:     PetscCallA(VecViewFromOptions(A, PETSC_NULL_OPTIONS, '-a_vec_view',ierr))
357:     ! restrict to UA2
358:     PetscCallA(VecISCopy(X, isUA, SCATTER_REVERSE, UA2,ierr))
359:     PetscCallA(VecViewFromOptions(UA2, PETSC_NULL_OPTIONS, '-ua2_vec_view',ierr))

361:     ! Getting Natural Vec
362:     PetscCallA(DMSetOutputSequenceNumber(dmU, 0_kPI, time, ierr))
363:     PetscCallA(DMSetOutputSequenceNumber(dmA, 0_kPI, time, ierr))

365:     PetscCallA(VecView(U, viewer,ierr))
366:     PetscCallA(VecView(A, viewer,ierr))

368:     !Saving U and Alpha in one shot.
369:     !For this, we need to cheat and change the Vec's name
370:     !Note that in the end we write variables one component at a time,
371:     !so that there is no real value in doing this
372:     PetscCallA(DMSetOutputSequenceNumber(dmUA,1_kPI,time,ierr))
373:     PetscCallA(DMGetGlobalVector(dmUA, tmpVec,ierr))
374:     PetscCallA(VecCopy(UA, tmpVec,ierr))
375:     PetscCallA(PetscObjectSetName(tmpVec, 'U',ierr))
376:     PetscCallA(VecView(tmpVec, viewer,ierr))

378:     ! Reading nodal variables in Exodus file
379:     PetscCallA(VecSet(tmpVec, -1000.0_kPR,ierr))
380:     PetscCallA(VecLoad(tmpVec, viewer,ierr))
381:     PetscCallA(VecAXPY(UA, -1.0_kPR, tmpVec,ierr))
382:     PetscCallA(VecNorm(UA, NORM_INFINITY, norm,ierr))
383:     if (norm > PETSC_SQRT_MACHINE_EPSILON) then
384:         write(IOBuffer,'("UAlpha ||Vin - Vout|| = ",ES12.5)') norm
385:     end if
386:     PetscCallA(DMRestoreGlobalVector(dmUA, tmpVec,ierr))

388:     ! same thing with the UA2 Vec obtained from the superDM
389:     PetscCallA(DMGetGlobalVector(dmUA2, tmpVec,ierr))
390:     PetscCallA(VecCopy(UA2, tmpVec,ierr))
391:     PetscCallA(PetscObjectSetName(tmpVec, 'U',ierr))
392:     PetscCallA(DMSetOutputSequenceNumber(dmUA2,2_kPI,time,ierr))
393:     PetscCallA(VecView(tmpVec, viewer,ierr))

395:     ! Reading nodal variables in Exodus file
396:     PetscCallA(VecSet(tmpVec, -1000.0_kPR,ierr))
397:     PetscCallA(VecLoad(tmpVec,viewer,ierr))
398:     PetscCallA(VecAXPY(UA2, -1.0_kPR, tmpVec,ierr))
399:     PetscCallA(VecNorm(UA2, NORM_INFINITY, norm,ierr))
400:     if (norm > PETSC_SQRT_MACHINE_EPSILON) then
401:         write(IOBuffer,'("UAlpha2 ||Vin - Vout|| = ",ES12.5)') norm
402:     end if
403:     PetscCallA(DMRestoreGlobalVector(dmUA2, tmpVec,ierr))

405:     ! Building and saving Sigma
406:     !   We set sigma_0 = rank (to see partitioning)
407:     !          sigma_1 = cell set ID
408:     !          sigma_2 = x_coordinate of the cell center of mass
409:     PetscCallA(DMGetCoordinateSection(dmS, coordSection,ierr))
410:     PetscCallA(DMGetCoordinatesLocal(dmS, coord,ierr))
411:     PetscCallA(DMGetLabelIdIS(dmS, 'Cell Sets', csIS,ierr))
412:     PetscCallA(DMGetLabelSize(dmS, 'Cell Sets',numCS,ierr))
413:     PetscCallA(ISGetIndicesF90(csIS, csID,ierr))

415:     do set = 1, numCS
416:         PetscCallA(DMGetStratumIS(dmS, 'Cell Sets', csID(set), cellIS,ierr))
417:         PetscCallA(ISGetIndicesF90(cellIS, cellID,ierr))
418:         PetscCallA(ISGetSize(cellIS, numCells,ierr))
419:         do cell = 1,numCells
420:             PetscCallA(DMPlexVecGetClosure(dmS, PETSC_NULL_SECTION, S, cellID(cell), cval,ierr))
421:             PetscCallA(DMPlexVecGetClosure(dmS, coordSection, coord, cellID(cell), xyz,ierr))
422:             cval(1) = rank
423:             cval(2) = csID(set)
424:             cval(3) = 0.0_kPR
425:             do c = 1, size(xyz),sdim
426:                 cval(3) = cval(3) + xyz(c)
427:             end do
428:             cval(3) = cval(3) * sdim / size(xyz)
429:             PetscCallA(DMPlexVecSetClosure(dmS, PETSC_NULL_SECTION, S, cellID(cell), cval, INSERT_ALL_VALUES,ierr))
430:             PetscCallA(DMPlexVecRestoreClosure(dmS, PETSC_NULL_SECTION, S, cellID(cell), cval,ierr))
431:             PetscCallA(DMPlexVecRestoreClosure(dmS, coordSection, coord, cellID(cell), xyz,ierr))
432:         end do
433:         PetscCallA(ISRestoreIndicesF90(cellIS, cellID,ierr))
434:         PetscCallA(ISDestroy(cellIS,ierr))
435:     end do
436:     PetscCallA(ISRestoreIndicesF90(csIS, csID,ierr))
437:     PetscCallA(ISDestroy(csIS,ierr))
438:     PetscCallA(VecViewFromOptions(S, PETSC_NULL_OPTIONS, '-s_vec_view',ierr))

440:     ! Writing zonal variables in Exodus file
441:     PetscCallA(DMSetOutputSequenceNumber(dmS,0_kPI,time,ierr))
442:     PetscCallA(VecView(S,viewer,ierr))

444:     ! Reading zonal variables in Exodus file */
445:     PetscCallA(DMGetGlobalVector(dmS, tmpVec,ierr))
446:     PetscCallA(VecSet(tmpVec, -1000.0_kPR,ierr))
447:     PetscCallA(PetscObjectSetName(tmpVec, 'Sigma',ierr))
448:     PetscCallA(VecLoad(tmpVec,viewer,ierr))
449:     PetscCallA(VecAXPY(S, -1.0_kPR, tmpVec,ierr))
450:     PetscCallA(VecNorm(S, NORM_INFINITY,norm,ierr))
451:     if (norm > PETSC_SQRT_MACHINE_EPSILON) then
452:        write(IOBuffer,'("Sigma ||Vin - Vout|| = ",ES12.5)') norm
453:     end if
454:     PetscCallA(DMRestoreGlobalVector(dmS, tmpVec,ierr))

456:     PetscCallA(DMRestoreGlobalVector(dmUA2, UA2,ierr))
457:     PetscCallA(DMRestoreGlobalVector(dmUA, UA,ierr))
458:     PetscCallA(DMRestoreGlobalVector(dmS,  S,ierr))
459:     PetscCallA(DMRestoreGlobalVector(dmA,  A,ierr))
460:     PetscCallA(DMRestoreGlobalVector(dmU,  U,ierr))
461:     PetscCallA(DMRestoreGlobalVector(pdm,   X,ierr))
462:     PetscCallA(DMDestroy(dmU,ierr))
463:     PetscCallA(ISDestroy(isU,ierr))
464:     PetscCallA(DMDestroy(dmA,ierr))
465:     PetscCallA(ISDestroy(isA,ierr))
466:     PetscCallA(DMDestroy(dmS,ierr))
467:     PetscCallA(ISDestroy(isS,ierr))
468:     PetscCallA(DMDestroy(dmUA,ierr))
469:     PetscCallA(ISDestroy(isUA,ierr))
470:     PetscCallA(DMDestroy(dmUA2,ierr))
471:     PetscCallA(DMDestroy(pdm,ierr))
472:     if (numProc > 1) then
473:         PetscCallA(DMDestroy(dm,ierr))
474:     end if

476:     deallocate(pStartDepth)
477:     deallocate(pEndDepth)

479:     PetscCallA(PetscViewerDestroy(viewer,ierr))
480:     PetscCallA(PetscFinalize(ierr))
481: end program ex62f90

483: ! /*TEST
484: !
485: ! build:
486: !   requires: exodusii pnetcdf !complex
487: !   # 2D seq
488: ! test:
489: !   suffix: 0
490: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareT-large.exo -o FourSquareT-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 1
491: !   #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
492: ! test:
493: !   suffix: 1
494: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareQ-large.exo -o FourSquareQ-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 1
495: !
496: ! test:
497: !   suffix: 2
498: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareH-large.exo -o FourSquareH-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 1
499: !   #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
500: ! test:
501: !   suffix: 3
502: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareT-large.exo -o FourSquareT-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 2
503: ! test:
504: !   suffix: 4
505: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareQ-large.exo -o FourSquareQ-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 2
506: ! test:
507: !   suffix: 5
508: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareH-large.exo -o FourSquareH-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 2
509: !   # 2D par
510: ! test:
511: !   suffix: 6
512: !   nsize: 2
513: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareT-large.exo -o FourSquareT-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 1
514: !   #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
515: ! test:
516: !   suffix: 7
517: !   nsize: 2
518: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareQ-large.exo -o FourSquareQ-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 1
519: ! test:
520: !   suffix: 8
521: !   nsize: 2
522: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareH-large.exo -o FourSquareH-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 1
523: !   #TODO: bug in PetscCallA(to NetCDF failed to complete invalid type definition in file id 65536 NetCDF: invalid dimension ID or name
524: ! test:
525: !   suffix: 9
526: !   nsize: 2
527: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareT-large.exo -o FourSquareT-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 2
528: ! test:
529: !   suffix: 10
530: !   nsize: 2
531: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareQ-large.exo -o FourSquareQ-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 2
532: ! test:
533: !   # Something is now broken with parallel read/write for whatever shape H is
534: !   TODO: broken
535: !   suffix: 11
536: !   nsize: 2
537: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourSquareH-large.exo -o FourSquareH-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 2

539: !   #3d seq
540: ! test:
541: !   suffix: 12
542: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickHex-large.exo -o FourBrickHex-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 1
543: ! test:
544: !   suffix: 13
545: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickTet-large.exo -o FourBrickTet-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 1
546: !   #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
547: ! test:
548: !   suffix: 14
549: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickHex-large.exo -o FourBrickHex-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 2
550: ! test:
551: !   suffix: 15
552: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickTet-large.exo -o FourBrickTet-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 2
553: !   #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
554: !   #3d par
555: ! test:
556: !   suffix: 16
557: !   nsize: 2
558: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickHex-large.exo -o FourBrickHex-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 1
559: ! test:
560: !   suffix: 17
561: !   nsize: 2
562: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickTet-large.exo -o FourBrickTet-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 1
563: !   #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
564: ! test:
565: !   suffix: 18
566: !   nsize: 2
567: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickHex-large.exo -o FourBrickHex-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 2
568: ! test:
569: !   suffix: 19
570: !   nsize: 2
571: !   args: -i ${wPETSC_DIR}/share/petsc/datafiles/meshes/FourBrickTet-large.exo -o FourBrickTet-large_out.exo -dm_view -dm_section_view -petscpartitioner_type simple -order 2
572: !   #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

574: ! TEST*/