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:     if (.not. flg) then
 90:         SETERRA(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"missing input file name -i <input file name>")
 91:     end if
 92:     PetscCallA(PetscOptionsGetString(PETSC_NULL_OPTIONS,PETSC_NULL_CHARACTER,"-o",ofilename,flg,ierr))
 93:     if (.not. flg) then
 94:         SETERRA(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"missing output file name -o <output file name>")
 95:     end if
 96:     PetscCallA(PetscOptionsGetInt(PETSC_NULL_OPTIONS,PETSC_NULL_CHARACTER,"-order",order,flg,ierr))
 97:     if ((order > 2) .or. (order < 1)) then
 98:         write(IOBuffer,'("Unsupported polynomial order ", I2, " not in [1,2]")') order
 99:         SETERRA(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,IOBuffer)
100:     end if

102:     ! Read the mesh in any supported format
103:     PetscCallA(DMPlexCreateFromFile(PETSC_COMM_WORLD, ifilename,PETSC_NULL_CHARACTER,PETSC_TRUE,dm,ierr))
104:     DMPlexDistributeSetDefault(dm,PETSC_FALSE,ierr);
105:     DMSetFromOptions(dm,ierr);
106:     PetscCallA(DMGetDimension(dm, sdim,ierr))
107:     DMViewFromOptions(dm, PETSC_NULL_OPTIONS,"-dm_view",ierr);

109:     ! Create the exodus result file

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

122:     ! set the mesh order
123:     PetscCallA(PetscViewerExodusIISetOrder(viewer,order,ierr))
124:     PetscCallA(PetscViewerView(viewer,PETSC_VIEWER_STDOUT_WORLD,ierr))
125:     !
126:     !    Notice how the exodus file is actually NOT open at this point (exoid is -1)
127:     !    Since we are overwriting the file (mode is FILE_MODE_WRITE), we are going to have to
128:     !    write the geometry (the DM), which can only be done on a brand new file.
129:     !

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

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

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

171:     PetscCallA(PetscObjectGetComm(dm,comm,ierr))
172:     PetscCallA(PetscSectionCreate(comm, section,ierr))
173:     PetscCallA(PetscSectionSetNumFields(section, 3_kPI,ierr))
174:     PetscCallA(PetscSectionSetFieldName(section, fieldU, "U",ierr))
175:     PetscCallA(PetscSectionSetFieldName(section, fieldA, "Alpha",ierr))
176:     PetscCallA(PetscSectionSetFieldName(section, fieldS, "Sigma",ierr))
177:     PetscCallA(DMPlexGetChart(dm, pStart, pEnd,ierr))
178:     PetscCallA(PetscSectionSetChart(section, pStart, pEnd,ierr))

180:     allocate(pStartDepth(sdim+1))
181:     allocate(pEndDepth(sdim+1))
182:     do d = 1, sdim+1
183:         PetscCallA(DMPlexGetDepthStratum(dm, d-1, pStartDepth(d), pEndDepth(d),ierr))
184:     end do

186:     ! Vector field U, Scalar field Alpha, Tensor field Sigma
187:     PetscSectionSetFieldComponents(section, fieldU, sdim,ierr);
188:     PetscSectionSetFieldComponents(section, fieldA, 1_kPI,ierr);
189:     PetscSectionSetFieldComponents(section, fieldS, sdim*(sdim+1)/2,ierr);

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

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

283:     PetscCallA(DMSetUseNatural(dm,PETSC_TRUE,ierr))
284:     PetscCallA(DMPlexGetPartitioner(dm,part,ierr))
285:     PetscCallA(PetscPartitionerSetFromOptions(part,ierr))
286:     PetscCallA(DMPlexDistribute(dm,0_kPI,migrationSF,pdm,ierr))

288:     if (numProc > 1) then
289:         PetscCallA(DMPlexSetMigrationSF(pdm,migrationSF,ierr))
290:         PetscCallA(PetscSFDestroy(migrationSF,ierr))
291:     else
292:         pdm = dm
293:     end if
294:     PetscCallA(DMViewFromOptions(pdm,PETSC_NULL_OPTIONS,"-dm_view",ierr))

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

302:     !Create the exodus result file
303:     allocate(dmList(2))
304:     dmList(1) = dmU;
305:     dmList(2) = dmA;
306:     PetscCallA(DMCreateSuperDM(dmList,2_kPI,PETSC_NULL_IS,dmUA2,ierr))
307:     deallocate(dmList)

309:     PetscCallA(DMGetGlobalVector(pdm,   X,ierr))
310:     PetscCallA(DMGetGlobalVector(dmU,  U,ierr))
311:     PetscCallA(DMGetGlobalVector(dmA,  A,ierr))
312:     PetscCallA(DMGetGlobalVector(dmS,  S,ierr))
313:     PetscCallA(DMGetGlobalVector(dmUA, UA,ierr))
314:     PetscCallA(DMGetGlobalVector(dmUA2, UA2,ierr))

316:     PetscCallA(PetscObjectSetName(U,  "U",ierr))
317:     PetscCallA(PetscObjectSetName(A,  "Alpha",ierr))
318:     PetscCallA(PetscObjectSetName(S,  "Sigma",ierr))
319:     PetscCallA(PetscObjectSetName(UA, "UAlpha",ierr))
320:     PetscCallA(PetscObjectSetName(UA2, "UAlpha2",ierr))
321:     PetscCallA(VecSet(X, -111.0_kPR,ierr))

323:     ! 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 */
324:     PetscCallA(DMGetLocalSection(dmUA, sectionUA,ierr))
325:     PetscCallA(DMGetLocalVector(dmUA, UALoc,ierr))
326:     PetscCallA(VecGetArrayF90(UALoc, cval,ierr))
327:     PetscCallA(DMGetCoordinateSection(dmUA, coordSection,ierr))
328:     PetscCallA(DMGetCoordinatesLocal(dmUA, coord,ierr))
329:     PetscCallA(DMPlexGetChart(dmUA, pStart, pEnd,ierr))

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

348:     PetscCallA(VecRestoreArrayF90(UALoc, cval,ierr))
349:     PetscCallA(DMLocalToGlobalBegin(dmUA, UALoc, INSERT_VALUES, UA,ierr))
350:     PetscCallA(DMLocalToGlobalEnd(dmUA, UALoc, INSERT_VALUES, UA,ierr))
351:     PetscCallA(DMRestoreLocalVector(dmUA, UALoc,ierr))

353:     !Update X
354:     PetscCallA(VecISCopy(X, isUA, SCATTER_FORWARD, UA,ierr))
355:     ! Restrict to U and Alpha
356:     PetscCallA(VecISCopy(X, isU, SCATTER_REVERSE, U,ierr))
357:     PetscCallA(VecISCopy(X, isA, SCATTER_REVERSE, A,ierr))
358:     PetscCallA(VecViewFromOptions(UA, PETSC_NULL_OPTIONS, "-ua_vec_view",ierr))
359:     PetscCallA(VecViewFromOptions(U, PETSC_NULL_OPTIONS, "-u_vec_view",ierr))
360:     PetscCallA(VecViewFromOptions(A, PETSC_NULL_OPTIONS, "-a_vec_view",ierr))
361:     ! restrict to UA2
362:     PetscCallA(VecISCopy(X, isUA, SCATTER_REVERSE, UA2,ierr))
363:     PetscCallA(VecViewFromOptions(UA2, PETSC_NULL_OPTIONS, "-ua2_vec_view",ierr))

365:     ! Getting Natural Vec
366:     PetscCallA(DMSetOutputSequenceNumber(dmU, 0_kPI, time, ierr))
367:     PetscCallA(DMSetOutputSequenceNumber(dmA, 0_kPI, time, ierr))

369:     PetscCallA(VecView(U, viewer,ierr))
370:     PetscCallA(VecView(A, viewer,ierr))

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

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

392:     ! same thing with the UA2 Vec obtained from the superDM
393:     PetscCallA(DMGetGlobalVector(dmUA2, tmpVec,ierr))
394:     PetscCallA(VecCopy(UA2, tmpVec,ierr))
395:     PetscCallA(PetscObjectSetName(tmpVec, "U",ierr))
396:     PetscCallA(DMSetOutputSequenceNumber(dmUA2,2_kPI,time,ierr))
397:     PetscCallA(VecView(tmpVec, viewer,ierr))

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

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

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

444:     ! Writing zonal variables in Exodus file
445:     PetscCallA(DMSetOutputSequenceNumber(dmS,0_kPI,time,ierr))
446:     PetscCallA(VecView(S,viewer,ierr))

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

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

480:     deallocate(pStartDepth)
481:     deallocate(pEndDepth)

483:     PetscCallA(PetscViewerDestroy(viewer,ierr))
484:     PetscCallA(PetscFinalize(ierr))
485: end program ex62f90

487: ! /*TEST
488: !
489: ! build:
490: !   requires: exodusii pnetcdf !complex
491: !   # 2D seq
492: ! test:
493: !   suffix: 0
494: !   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
495: !   #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
496: ! test:
497: !   suffix: 1
498: !   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
499: !
500: ! test:
501: !   suffix: 2
502: !   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
503: !   #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
504: ! test:
505: !   suffix: 3
506: !   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
507: ! test:
508: !   suffix: 4
509: !   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
510: ! test:
511: !   suffix: 5
512: !   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
513: !   # 2D par
514: ! test:
515: !   suffix: 6
516: !   nsize: 2
517: !   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
518: !   #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
519: ! test:
520: !   suffix: 7
521: !   nsize: 2
522: !   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
523: ! test:
524: !   suffix: 8
525: !   nsize: 2
526: !   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
527: !   #TODO: bug in PetscCallA(to NetCDF failed to complete invalid type definition in file id 65536 NetCDF: invalid dimension ID or name
528: ! test:
529: !   suffix: 9
530: !   nsize: 2
531: !   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
532: ! test:
533: !   suffix: 10
534: !   nsize: 2
535: !   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
536: ! test:
537: !   # Something is now broken with parallel read/write for wahtever shape H is
538: !   TODO: broken
539: !   suffix: 11
540: !   nsize: 2
541: !   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

543: !   #3d seq
544: ! test:
545: !   suffix: 12
546: !   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
547: ! test:
548: !   suffix: 13
549: !   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
550: !   #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
551: ! test:
552: !   suffix: 14
553: !   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
554: ! test:
555: !   suffix: 15
556: !   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
557: !   #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
558: !   #3d par
559: ! test:
560: !   suffix: 16
561: !   nsize: 2
562: !   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
563: ! test:
564: !   suffix: 17
565: !   nsize: 2
566: !   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
567: !   #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
568: ! test:
569: !   suffix: 18
570: !   nsize: 2
571: !   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
572: ! test:
573: !   suffix: 19
574: !   nsize: 2
575: !   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
576: !   #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

578: ! TEST*/