149c89c76SBlaise Bourdin #define PETSCDM_DLL 249c89c76SBlaise Bourdin #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 349c89c76SBlaise Bourdin 449c89c76SBlaise Bourdin #include <netcdf.h> 549c89c76SBlaise Bourdin #include <exodusII.h> 649c89c76SBlaise Bourdin 749c89c76SBlaise Bourdin #include <petsc/private/viewerimpl.h> 849c89c76SBlaise Bourdin #include <petsc/private/viewerexodusiiimpl.h> 949c89c76SBlaise Bourdin /*@C 1049c89c76SBlaise Bourdin PETSC_VIEWER_EXODUSII_ - Creates an `PETSCVIEWEREXODUSII` `PetscViewer` shared by all processors in a communicator. 1149c89c76SBlaise Bourdin 1249c89c76SBlaise Bourdin Collective; No Fortran Support 1349c89c76SBlaise Bourdin 1449c89c76SBlaise Bourdin Input Parameter: 1549c89c76SBlaise Bourdin . comm - the MPI communicator to share the `PETSCVIEWEREXODUSII` `PetscViewer` 1649c89c76SBlaise Bourdin 1749c89c76SBlaise Bourdin Level: intermediate 1849c89c76SBlaise Bourdin 1949c89c76SBlaise Bourdin Note: 2049c89c76SBlaise Bourdin Unlike almost all other PETSc routines, `PETSC_VIEWER_EXODUSII_()` does not return 2149c89c76SBlaise Bourdin an error code. The GLVIS PetscViewer is usually used in the form 22*b44f4de4SBarry Smith .vb 23*b44f4de4SBarry Smith XXXView(XXX object, PETSC_VIEWER_EXODUSII_(comm)); 24*b44f4de4SBarry Smith .ve 2549c89c76SBlaise Bourdin 2649c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewer`, `PetscViewerExodusIIOpen()`, `PetscViewerType`, `PetscViewerCreate()`, `PetscViewerDestroy()` 2749c89c76SBlaise Bourdin @*/ 2849c89c76SBlaise Bourdin PetscViewer PETSC_VIEWER_EXODUSII_(MPI_Comm comm) 2949c89c76SBlaise Bourdin { 3049c89c76SBlaise Bourdin PetscViewer viewer; 3149c89c76SBlaise Bourdin 3249c89c76SBlaise Bourdin PetscFunctionBegin; 3349c89c76SBlaise Bourdin PetscCallNull(PetscViewerExodusIIOpen(comm, "mesh.exo", FILE_MODE_WRITE, &viewer)); 3449c89c76SBlaise Bourdin PetscCallNull(PetscObjectRegisterDestroy((PetscObject)viewer)); 3549c89c76SBlaise Bourdin PetscFunctionReturn(viewer); 3649c89c76SBlaise Bourdin } 3749c89c76SBlaise Bourdin 3849c89c76SBlaise Bourdin static PetscErrorCode PetscViewerView_ExodusII(PetscViewer v, PetscViewer viewer) 3949c89c76SBlaise Bourdin { 4049c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)v->data; 4149c89c76SBlaise Bourdin 4249c89c76SBlaise Bourdin PetscFunctionBegin; 4349c89c76SBlaise Bourdin if (exo->filename) PetscCall(PetscViewerASCIIPrintf(viewer, "Filename: %s\n", exo->filename)); 440a5cf5d8SBlaise Bourdin if (exo->exoid) PetscCall(PetscViewerASCIIPrintf(viewer, "exoid: %" PetscExodusIIInt_FMT "\n", exo->exoid)); 4549c89c76SBlaise Bourdin if (exo->btype) PetscCall(PetscViewerASCIIPrintf(viewer, "IO Mode: %d\n", exo->btype)); 460a5cf5d8SBlaise Bourdin if (exo->order) PetscCall(PetscViewerASCIIPrintf(viewer, "Mesh order: %" PetscInt_FMT "\n", exo->order)); 470a5cf5d8SBlaise Bourdin PetscCall(PetscViewerASCIIPrintf(viewer, "Number of nodal variables: %" PetscExodusIIInt_FMT "\n", exo->numNodalVariables)); 4849c89c76SBlaise Bourdin for (int i = 0; i < exo->numNodalVariables; i++) PetscCall(PetscViewerASCIIPrintf(viewer, " %d: %s\n", i, exo->nodalVariableNames[i])); 490a5cf5d8SBlaise Bourdin PetscCall(PetscViewerASCIIPrintf(viewer, "Number of zonal variables: %" PetscExodusIIInt_FMT "\n", exo->numZonalVariables)); 5049c89c76SBlaise Bourdin for (int i = 0; i < exo->numZonalVariables; i++) PetscCall(PetscViewerASCIIPrintf(viewer, " %d: %s\n", i, exo->zonalVariableNames[i])); 5149c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 5249c89c76SBlaise Bourdin } 5349c89c76SBlaise Bourdin 5449c89c76SBlaise Bourdin static PetscErrorCode PetscViewerFlush_ExodusII(PetscViewer v) 5549c89c76SBlaise Bourdin { 5649c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)v->data; 5749c89c76SBlaise Bourdin 5849c89c76SBlaise Bourdin PetscFunctionBegin; 5949c89c76SBlaise Bourdin if (exo->exoid >= 0) PetscCallExternal(ex_update, exo->exoid); 6049c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 6149c89c76SBlaise Bourdin } 6249c89c76SBlaise Bourdin 63ce78bad3SBarry Smith static PetscErrorCode PetscViewerSetFromOptions_ExodusII(PetscViewer v, PetscOptionItems PetscOptionsObject) 6449c89c76SBlaise Bourdin { 6549c89c76SBlaise Bourdin PetscFunctionBegin; 6649c89c76SBlaise Bourdin PetscOptionsHeadBegin(PetscOptionsObject, "ExodusII PetscViewer Options"); 6749c89c76SBlaise Bourdin PetscOptionsHeadEnd(); 6849c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 6949c89c76SBlaise Bourdin } 7049c89c76SBlaise Bourdin 7149c89c76SBlaise Bourdin static PetscErrorCode PetscViewerDestroy_ExodusII(PetscViewer viewer) 7249c89c76SBlaise Bourdin { 7349c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 7449c89c76SBlaise Bourdin 7549c89c76SBlaise Bourdin PetscFunctionBegin; 7649c89c76SBlaise Bourdin if (exo->exoid >= 0) PetscCallExternal(ex_close, exo->exoid); 775341eb2eSStefano Zampini for (PetscInt i = 0; i < exo->numZonalVariables; i++) PetscCall(PetscFree(exo->zonalVariableNames[i])); 7849c89c76SBlaise Bourdin PetscCall(PetscFree(exo->zonalVariableNames)); 795341eb2eSStefano Zampini for (PetscInt i = 0; i < exo->numNodalVariables; i++) PetscCall(PetscFree(exo->nodalVariableNames[i])); 8049c89c76SBlaise Bourdin PetscCall(PetscFree(exo->nodalVariableNames)); 8149c89c76SBlaise Bourdin PetscCall(PetscFree(exo->filename)); 8249c89c76SBlaise Bourdin PetscCall(PetscFree(exo)); 8349c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileSetName_C", NULL)); 8449c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileGetName_C", NULL)); 8549c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileSetMode_C", NULL)); 8649c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileGetMode_C", NULL)); 8749c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerGetId_C", NULL)); 8849c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerGetOrder_C", NULL)); 8949c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerSetOrder_C", NULL)); 9049c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 9149c89c76SBlaise Bourdin } 9249c89c76SBlaise Bourdin 9349c89c76SBlaise Bourdin static PetscErrorCode PetscViewerFileSetName_ExodusII(PetscViewer viewer, const char name[]) 9449c89c76SBlaise Bourdin { 9549c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 9649c89c76SBlaise Bourdin PetscMPIInt rank; 970a5cf5d8SBlaise Bourdin PetscExodusIIInt CPU_word_size, IO_word_size, EXO_mode; 9849c89c76SBlaise Bourdin MPI_Info mpi_info = MPI_INFO_NULL; 990a5cf5d8SBlaise Bourdin PetscExodusIIFloat EXO_version; 10049c89c76SBlaise Bourdin 10149c89c76SBlaise Bourdin PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank)); 10249c89c76SBlaise Bourdin CPU_word_size = sizeof(PetscReal); 10349c89c76SBlaise Bourdin IO_word_size = sizeof(PetscReal); 10449c89c76SBlaise Bourdin 10549c89c76SBlaise Bourdin PetscFunctionBegin; 10649c89c76SBlaise Bourdin if (exo->exoid >= 0) { 10749c89c76SBlaise Bourdin PetscCallExternal(ex_close, exo->exoid); 10849c89c76SBlaise Bourdin exo->exoid = -1; 10949c89c76SBlaise Bourdin } 11049c89c76SBlaise Bourdin if (exo->filename) PetscCall(PetscFree(exo->filename)); 11149c89c76SBlaise Bourdin PetscCall(PetscStrallocpy(name, &exo->filename)); 11249c89c76SBlaise Bourdin switch (exo->btype) { 11349c89c76SBlaise Bourdin case FILE_MODE_READ: 11449c89c76SBlaise Bourdin EXO_mode = EX_READ; 11549c89c76SBlaise Bourdin break; 11649c89c76SBlaise Bourdin case FILE_MODE_APPEND: 11749c89c76SBlaise Bourdin case FILE_MODE_UPDATE: 11849c89c76SBlaise Bourdin case FILE_MODE_APPEND_UPDATE: 11949c89c76SBlaise Bourdin /* Will fail if the file does not already exist */ 12049c89c76SBlaise Bourdin EXO_mode = EX_WRITE; 12149c89c76SBlaise Bourdin break; 12249c89c76SBlaise Bourdin case FILE_MODE_WRITE: 12349c89c76SBlaise Bourdin /* 12449c89c76SBlaise Bourdin exodus only allows writing geometry upon file creation, so we will let DMView create the file. 12549c89c76SBlaise Bourdin */ 12649c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 12749c89c76SBlaise Bourdin break; 12849c89c76SBlaise Bourdin default: 12949c89c76SBlaise Bourdin SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()"); 13049c89c76SBlaise Bourdin } 13149c89c76SBlaise Bourdin #if defined(PETSC_USE_64BIT_INDICES) 13249c89c76SBlaise Bourdin EXO_mode += EX_ALL_INT64_API; 13349c89c76SBlaise Bourdin #endif 13449c89c76SBlaise Bourdin exo->exoid = ex_open_par(name, EXO_mode, &CPU_word_size, &IO_word_size, &EXO_version, PETSC_COMM_WORLD, mpi_info); 13549c89c76SBlaise Bourdin PetscCheck(exo->exoid >= 0, PETSC_COMM_SELF, PETSC_ERR_LIB, "ex_open_par failed for %s", name); 13649c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 13749c89c76SBlaise Bourdin } 13849c89c76SBlaise Bourdin 13949c89c76SBlaise Bourdin static PetscErrorCode PetscViewerFileGetName_ExodusII(PetscViewer viewer, const char *name[]) 14049c89c76SBlaise Bourdin { 14149c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 14249c89c76SBlaise Bourdin 14349c89c76SBlaise Bourdin PetscFunctionBegin; 14449c89c76SBlaise Bourdin *name = exo->filename; 14549c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 14649c89c76SBlaise Bourdin } 14749c89c76SBlaise Bourdin 14849c89c76SBlaise Bourdin static PetscErrorCode PetscViewerFileSetMode_ExodusII(PetscViewer viewer, PetscFileMode type) 14949c89c76SBlaise Bourdin { 15049c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 15149c89c76SBlaise Bourdin 15249c89c76SBlaise Bourdin PetscFunctionBegin; 15349c89c76SBlaise Bourdin exo->btype = type; 15449c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 15549c89c76SBlaise Bourdin } 15649c89c76SBlaise Bourdin 15749c89c76SBlaise Bourdin static PetscErrorCode PetscViewerFileGetMode_ExodusII(PetscViewer viewer, PetscFileMode *type) 15849c89c76SBlaise Bourdin { 15949c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 16049c89c76SBlaise Bourdin 16149c89c76SBlaise Bourdin PetscFunctionBegin; 16249c89c76SBlaise Bourdin *type = exo->btype; 16349c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 16449c89c76SBlaise Bourdin } 16549c89c76SBlaise Bourdin 1660a5cf5d8SBlaise Bourdin static PetscErrorCode PetscViewerExodusIIGetId_ExodusII(PetscViewer viewer, PetscExodusIIInt *exoid) 16749c89c76SBlaise Bourdin { 16849c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 16949c89c76SBlaise Bourdin 17049c89c76SBlaise Bourdin PetscFunctionBegin; 17149c89c76SBlaise Bourdin *exoid = exo->exoid; 17249c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 17349c89c76SBlaise Bourdin } 17449c89c76SBlaise Bourdin 1750a5cf5d8SBlaise Bourdin static PetscErrorCode PetscViewerExodusIIGetOrder_ExodusII(PetscViewer viewer, PetscInt *order) 17649c89c76SBlaise Bourdin { 17749c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 17849c89c76SBlaise Bourdin 17949c89c76SBlaise Bourdin PetscFunctionBegin; 18049c89c76SBlaise Bourdin *order = exo->order; 18149c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 18249c89c76SBlaise Bourdin } 18349c89c76SBlaise Bourdin 1840a5cf5d8SBlaise Bourdin static PetscErrorCode PetscViewerExodusIISetOrder_ExodusII(PetscViewer viewer, PetscInt order) 18549c89c76SBlaise Bourdin { 18649c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 18749c89c76SBlaise Bourdin 18849c89c76SBlaise Bourdin PetscFunctionBegin; 18949c89c76SBlaise Bourdin exo->order = order; 19049c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 19149c89c76SBlaise Bourdin } 19249c89c76SBlaise Bourdin 19349c89c76SBlaise Bourdin /*@ 19449c89c76SBlaise Bourdin PetscViewerExodusIISetZonalVariable - Sets the number of zonal variables in an exodusII file 19549c89c76SBlaise Bourdin 19649c89c76SBlaise Bourdin Collective; 19749c89c76SBlaise Bourdin 19849c89c76SBlaise Bourdin Input Parameters: 19949c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 20049c89c76SBlaise Bourdin - num - the number of zonal variables in the exodusII file 20149c89c76SBlaise Bourdin 20249c89c76SBlaise Bourdin Level: intermediate 20349c89c76SBlaise Bourdin 20449c89c76SBlaise Bourdin Notes: 20549c89c76SBlaise Bourdin The exodusII API does not allow changing the number of variables in a file so this function will return an error 20649c89c76SBlaise Bourdin if called twice, called on a read-only file, or called on file for which the number of variables has already been specified 20749c89c76SBlaise Bourdin 20849c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIIGetZonalVariable()` 20949c89c76SBlaise Bourdin @*/ 2100a5cf5d8SBlaise Bourdin PetscErrorCode PetscViewerExodusIISetZonalVariable(PetscViewer viewer, PetscExodusIIInt num) 21149c89c76SBlaise Bourdin { 21249c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 21349c89c76SBlaise Bourdin MPI_Comm comm; 2140a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid = -1; 21549c89c76SBlaise Bourdin 21649c89c76SBlaise Bourdin PetscFunctionBegin; 21749c89c76SBlaise Bourdin PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm)); 21849c89c76SBlaise Bourdin PetscCheck(exo->numZonalVariables == -1, comm, PETSC_ERR_SUP, "The number of zonal variables has already been set to %d and cannot be overwritten", exo->numZonalVariables); 21949c89c76SBlaise Bourdin PetscCheck((exo->btype != FILE_MODE_READ) && (exo->btype != FILE_MODE_UNDEFINED), comm, PETSC_ERR_FILE_WRITE, "Cannot set the number of variables because the file is not writable"); 22049c89c76SBlaise Bourdin 22149c89c76SBlaise Bourdin exo->numZonalVariables = num; 22249c89c76SBlaise Bourdin PetscCall(PetscMalloc1(num, &exo->zonalVariableNames)); 22349c89c76SBlaise Bourdin for (int i = 0; i < num; i++) { exo->zonalVariableNames[i] = NULL; } 22449c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 22549c89c76SBlaise Bourdin PetscCallExternal(ex_put_variable_param, exoid, EX_ELEM_BLOCK, num); 22649c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 22749c89c76SBlaise Bourdin } 22849c89c76SBlaise Bourdin 22949c89c76SBlaise Bourdin /*@ 23049c89c76SBlaise Bourdin PetscViewerExodusIISetNodalVariable - Sets the number of nodal variables in an exodusII file 23149c89c76SBlaise Bourdin 23249c89c76SBlaise Bourdin Collective; 23349c89c76SBlaise Bourdin 23449c89c76SBlaise Bourdin Input Parameters: 23549c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 23649c89c76SBlaise Bourdin - num - the number of nodal variables in the exodusII file 23749c89c76SBlaise Bourdin 23849c89c76SBlaise Bourdin Level: intermediate 23949c89c76SBlaise Bourdin 24049c89c76SBlaise Bourdin Notes: 24149c89c76SBlaise Bourdin The exodusII API does not allow changing the number of variables in a file so this function will return an error 24249c89c76SBlaise Bourdin if called twice, called on a read-only file, or called on file for which the number of variables has already been specified 24349c89c76SBlaise Bourdin 24449c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIIGetNodalVariable()` 24549c89c76SBlaise Bourdin @*/ 2460a5cf5d8SBlaise Bourdin PetscErrorCode PetscViewerExodusIISetNodalVariable(PetscViewer viewer, PetscExodusIIInt num) 24749c89c76SBlaise Bourdin { 24849c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 24949c89c76SBlaise Bourdin MPI_Comm comm; 2500a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid = -1; 25149c89c76SBlaise Bourdin 25249c89c76SBlaise Bourdin PetscFunctionBegin; 25349c89c76SBlaise Bourdin PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm)); 25449c89c76SBlaise Bourdin PetscCheck(exo->numNodalVariables == -1, comm, PETSC_ERR_SUP, "The number of nodal variables has already been set to %d and cannot be overwritten", exo->numNodalVariables); 25549c89c76SBlaise Bourdin PetscCheck((exo->btype != FILE_MODE_READ) && (exo->btype != FILE_MODE_UNDEFINED), comm, PETSC_ERR_FILE_WRITE, "Cannot set the number of variables because the file is not writable"); 25649c89c76SBlaise Bourdin 25749c89c76SBlaise Bourdin exo->numNodalVariables = num; 25849c89c76SBlaise Bourdin PetscCall(PetscMalloc1(num, &exo->nodalVariableNames)); 25949c89c76SBlaise Bourdin for (int i = 0; i < num; i++) { exo->nodalVariableNames[i] = NULL; } 26049c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 26149c89c76SBlaise Bourdin PetscCallExternal(ex_put_variable_param, exoid, EX_NODAL, num); 26249c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 26349c89c76SBlaise Bourdin } 26449c89c76SBlaise Bourdin 26549c89c76SBlaise Bourdin /*@ 26649c89c76SBlaise Bourdin PetscViewerExodusIIGetZonalVariable - Gets the number of zonal variables in an exodusII file 26749c89c76SBlaise Bourdin 26849c89c76SBlaise Bourdin Collective 26949c89c76SBlaise Bourdin 27049c89c76SBlaise Bourdin Input Parameters: 27149c89c76SBlaise Bourdin . viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 27249c89c76SBlaise Bourdin 273ce78bad3SBarry Smith Output Parameter: 27449c89c76SBlaise Bourdin . num - the number variables in the exodusII file 27549c89c76SBlaise Bourdin 27649c89c76SBlaise Bourdin Level: intermediate 27749c89c76SBlaise Bourdin 27849c89c76SBlaise Bourdin Notes: 27949c89c76SBlaise Bourdin The number of variables in the exodusII file is cached in the viewer 28049c89c76SBlaise Bourdin 28149c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIIsetZonalVariable()` 28249c89c76SBlaise Bourdin @*/ 2830a5cf5d8SBlaise Bourdin PetscErrorCode PetscViewerExodusIIGetZonalVariable(PetscViewer viewer, PetscExodusIIInt *num) 28449c89c76SBlaise Bourdin { 28549c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 28649c89c76SBlaise Bourdin MPI_Comm comm; 2870a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid = -1; 28849c89c76SBlaise Bourdin 28949c89c76SBlaise Bourdin PetscFunctionBegin; 29049c89c76SBlaise Bourdin if (exo->numZonalVariables > -1) { 29149c89c76SBlaise Bourdin *num = exo->numZonalVariables; 29249c89c76SBlaise Bourdin } else { 29349c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 29449c89c76SBlaise Bourdin PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm)); 29549c89c76SBlaise Bourdin PetscCheck(exoid > 0, comm, PETSC_ERR_FILE_OPEN, "Exodus file is not open"); 29649c89c76SBlaise Bourdin PetscCallExternal(ex_get_variable_param, exoid, EX_ELEM_BLOCK, num); 29749c89c76SBlaise Bourdin exo->numZonalVariables = *num; 29849c89c76SBlaise Bourdin PetscCall(PetscMalloc1(*num, &exo->zonalVariableNames)); 29949c89c76SBlaise Bourdin for (int i = 0; i < *num; i++) { exo->zonalVariableNames[i] = NULL; } 30049c89c76SBlaise Bourdin } 30149c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 30249c89c76SBlaise Bourdin } 30349c89c76SBlaise Bourdin 30449c89c76SBlaise Bourdin /*@ 30549c89c76SBlaise Bourdin PetscViewerExodusIIGetNodalVariable - Gets the number of nodal variables in an exodusII file 30649c89c76SBlaise Bourdin 30749c89c76SBlaise Bourdin Collective 30849c89c76SBlaise Bourdin 30949c89c76SBlaise Bourdin Input Parameters: 31049c89c76SBlaise Bourdin . viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 31149c89c76SBlaise Bourdin 312ce78bad3SBarry Smith Output Parameter: 31349c89c76SBlaise Bourdin . num - the number variables in the exodusII file 31449c89c76SBlaise Bourdin 31549c89c76SBlaise Bourdin Level: intermediate 31649c89c76SBlaise Bourdin 31749c89c76SBlaise Bourdin Notes: 31849c89c76SBlaise Bourdin This function gets the number of nodal variables and saves it in the address of num. 31949c89c76SBlaise Bourdin 32049c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIISetNodalVariable()` 32149c89c76SBlaise Bourdin @*/ 3220a5cf5d8SBlaise Bourdin PetscErrorCode PetscViewerExodusIIGetNodalVariable(PetscViewer viewer, PetscExodusIIInt *num) 32349c89c76SBlaise Bourdin { 32449c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 32549c89c76SBlaise Bourdin MPI_Comm comm; 3260a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid = -1; 32749c89c76SBlaise Bourdin 32849c89c76SBlaise Bourdin PetscFunctionBegin; 32949c89c76SBlaise Bourdin if (exo->numNodalVariables > -1) { 33049c89c76SBlaise Bourdin *num = exo->numNodalVariables; 33149c89c76SBlaise Bourdin } else { 33249c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 33349c89c76SBlaise Bourdin PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm)); 33449c89c76SBlaise Bourdin PetscCheck(exoid > 0, comm, PETSC_ERR_FILE_OPEN, "Exodus file is not open"); 33549c89c76SBlaise Bourdin PetscCallExternal(ex_get_variable_param, exoid, EX_NODAL, num); 33649c89c76SBlaise Bourdin exo->numNodalVariables = *num; 33749c89c76SBlaise Bourdin PetscCall(PetscMalloc1(*num, &exo->nodalVariableNames)); 33849c89c76SBlaise Bourdin for (int i = 0; i < *num; i++) { exo->nodalVariableNames[i] = NULL; } 33949c89c76SBlaise Bourdin } 34049c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 34149c89c76SBlaise Bourdin } 34249c89c76SBlaise Bourdin 34349c89c76SBlaise Bourdin /*@ 34449c89c76SBlaise Bourdin PetscViewerExodusIISetZonalVariableName - Sets the name of a zonal variable. 34549c89c76SBlaise Bourdin 34649c89c76SBlaise Bourdin Collective; 34749c89c76SBlaise Bourdin 34849c89c76SBlaise Bourdin Input Parameters: 34949c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 35049c89c76SBlaise Bourdin . idx - the index for which you want to save the name 35149c89c76SBlaise Bourdin - name - string containing the name characters 35249c89c76SBlaise Bourdin 35349c89c76SBlaise Bourdin Level: intermediate 35449c89c76SBlaise Bourdin 35549c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIIGetZonalVariableName()` 35649c89c76SBlaise Bourdin @*/ 3570a5cf5d8SBlaise Bourdin PetscErrorCode PetscViewerExodusIISetZonalVariableName(PetscViewer viewer, PetscExodusIIInt idx, const char name[]) 35849c89c76SBlaise Bourdin { 35949c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 36049c89c76SBlaise Bourdin 36149c89c76SBlaise Bourdin PetscFunctionBegin; 36249c89c76SBlaise Bourdin PetscCheck((idx >= 0) && (idx < exo->numZonalVariables), PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Variable index out of range. Was PetscViewerExodusIISetZonalVariable called?"); 36349c89c76SBlaise Bourdin PetscCall(PetscStrallocpy(name, (char **)&exo->zonalVariableNames[idx])); 36449c89c76SBlaise Bourdin PetscCallExternal(ex_put_variable_name, exo->exoid, EX_ELEM_BLOCK, idx + 1, name); 36549c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 36649c89c76SBlaise Bourdin } 36749c89c76SBlaise Bourdin 36849c89c76SBlaise Bourdin /*@ 36949c89c76SBlaise Bourdin PetscViewerExodusIISetNodalVariableName - Sets the name of a nodal variable. 37049c89c76SBlaise Bourdin 37149c89c76SBlaise Bourdin Collective; 37249c89c76SBlaise Bourdin 37349c89c76SBlaise Bourdin Input Parameters: 37449c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 37549c89c76SBlaise Bourdin . idx - the index for which you want to save the name 37649c89c76SBlaise Bourdin - name - string containing the name characters 37749c89c76SBlaise Bourdin 37849c89c76SBlaise Bourdin Level: intermediate 37949c89c76SBlaise Bourdin 38049c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIIGetNodalVariableName()` 38149c89c76SBlaise Bourdin @*/ 3820a5cf5d8SBlaise Bourdin PetscErrorCode PetscViewerExodusIISetNodalVariableName(PetscViewer viewer, PetscExodusIIInt idx, const char name[]) 38349c89c76SBlaise Bourdin { 38449c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 38549c89c76SBlaise Bourdin 38649c89c76SBlaise Bourdin PetscFunctionBegin; 38749c89c76SBlaise Bourdin PetscCheck((idx >= 0) && (idx < exo->numNodalVariables), PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Variable index out of range. Was PetscViewerExodusIISetNodalVariable called?"); 38849c89c76SBlaise Bourdin PetscCall(PetscStrallocpy(name, (char **)&exo->nodalVariableNames[idx])); 38949c89c76SBlaise Bourdin PetscCallExternal(ex_put_variable_name, exo->exoid, EX_NODAL, idx + 1, name); 39049c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 39149c89c76SBlaise Bourdin } 39249c89c76SBlaise Bourdin 39349c89c76SBlaise Bourdin /*@ 39449c89c76SBlaise Bourdin PetscViewerExodusIIGetZonalVariableName - Gets the name of a zonal variable. 39549c89c76SBlaise Bourdin 39649c89c76SBlaise Bourdin Collective; 39749c89c76SBlaise Bourdin 39849c89c76SBlaise Bourdin Input Parameters: 39949c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 40049c89c76SBlaise Bourdin - idx - the index for which you want to get the name 40149c89c76SBlaise Bourdin 40249c89c76SBlaise Bourdin Output Parameter: 40349c89c76SBlaise Bourdin . name - pointer to the string containing the name characters 40449c89c76SBlaise Bourdin 40549c89c76SBlaise Bourdin Level: intermediate 40649c89c76SBlaise Bourdin 40749c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIISetZonalVariableName()` 40849c89c76SBlaise Bourdin @*/ 4090a5cf5d8SBlaise Bourdin PetscErrorCode PetscViewerExodusIIGetZonalVariableName(PetscViewer viewer, PetscExodusIIInt idx, const char *name[]) 41049c89c76SBlaise Bourdin { 41149c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 4120a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid = -1; 41349c89c76SBlaise Bourdin char tmpName[MAX_NAME_LENGTH + 1]; 41449c89c76SBlaise Bourdin 41549c89c76SBlaise Bourdin PetscFunctionBegin; 41649c89c76SBlaise Bourdin PetscCheck(idx >= 0 && idx < exo->numZonalVariables, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Variable index out of range. Was PetscViewerExodusIISetZonalVariable called?"); 41749c89c76SBlaise Bourdin if (!exo->zonalVariableNames[idx]) { 41849c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 41949c89c76SBlaise Bourdin PetscCallExternal(ex_get_variable_name, exoid, EX_ELEM_BLOCK, idx + 1, tmpName); 42049c89c76SBlaise Bourdin PetscCall(PetscStrallocpy(tmpName, (char **)&exo->zonalVariableNames[idx])); 42149c89c76SBlaise Bourdin } 42249c89c76SBlaise Bourdin *name = exo->zonalVariableNames[idx]; 42349c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 42449c89c76SBlaise Bourdin } 42549c89c76SBlaise Bourdin 42649c89c76SBlaise Bourdin /*@ 42749c89c76SBlaise Bourdin PetscViewerExodusIIGetNodalVariableName - Gets the name of a nodal variable. 42849c89c76SBlaise Bourdin 42949c89c76SBlaise Bourdin Collective; 43049c89c76SBlaise Bourdin 43149c89c76SBlaise Bourdin Input Parameters: 43249c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 43349c89c76SBlaise Bourdin - idx - the index for which you want to save the name 43449c89c76SBlaise Bourdin 43549c89c76SBlaise Bourdin Output Parameter: 43649c89c76SBlaise Bourdin . name - string array containing name characters 43749c89c76SBlaise Bourdin 43849c89c76SBlaise Bourdin Level: intermediate 43949c89c76SBlaise Bourdin 44049c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIISetNodalVariableName()` 44149c89c76SBlaise Bourdin @*/ 4420a5cf5d8SBlaise Bourdin PetscErrorCode PetscViewerExodusIIGetNodalVariableName(PetscViewer viewer, PetscExodusIIInt idx, const char *name[]) 44349c89c76SBlaise Bourdin { 44449c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 4450a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid = -1; 44649c89c76SBlaise Bourdin char tmpName[MAX_NAME_LENGTH + 1]; 44749c89c76SBlaise Bourdin 44849c89c76SBlaise Bourdin PetscFunctionBegin; 44949c89c76SBlaise Bourdin PetscCheck((idx >= 0) && (idx < exo->numNodalVariables), PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Variable index out of range. Was PetscViewerExodusIISetNodalVariable called?"); 45049c89c76SBlaise Bourdin if (!exo->nodalVariableNames[idx]) { 45149c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 45249c89c76SBlaise Bourdin PetscCallExternal(ex_get_variable_name, exoid, EX_NODAL, idx + 1, tmpName); 45349c89c76SBlaise Bourdin PetscCall(PetscStrallocpy(tmpName, (char **)&exo->nodalVariableNames[idx])); 45449c89c76SBlaise Bourdin } 45549c89c76SBlaise Bourdin *name = exo->nodalVariableNames[idx]; 45649c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 45749c89c76SBlaise Bourdin } 45849c89c76SBlaise Bourdin 45949c89c76SBlaise Bourdin /*@C 46049c89c76SBlaise Bourdin PetscViewerExodusIISetZonalVariableNames - Sets the names of all nodal variables 46149c89c76SBlaise Bourdin 46249c89c76SBlaise Bourdin Collective; No Fortran Support 46349c89c76SBlaise Bourdin 46449c89c76SBlaise Bourdin Input Parameters: 46549c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 466ce78bad3SBarry Smith - names - an array of string names to be set, the strings are copied into the `PetscViewer` 46749c89c76SBlaise Bourdin 46849c89c76SBlaise Bourdin Level: intermediate 46949c89c76SBlaise Bourdin 47049c89c76SBlaise Bourdin Notes: 47149c89c76SBlaise Bourdin This function allows users to set multiple zonal variable names at a time. 47249c89c76SBlaise Bourdin 47349c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIIGetZonalVariableNames()` 47449c89c76SBlaise Bourdin @*/ 475ce78bad3SBarry Smith PetscErrorCode PetscViewerExodusIISetZonalVariableNames(PetscViewer viewer, const char *const names[]) 47649c89c76SBlaise Bourdin { 4770a5cf5d8SBlaise Bourdin PetscExodusIIInt numNames; 4780a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid = -1; 47949c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 48049c89c76SBlaise Bourdin 48149c89c76SBlaise Bourdin PetscFunctionBegin; 48249c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetZonalVariable(viewer, &numNames)); 48349c89c76SBlaise Bourdin PetscCheck(numNames >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of zonal variables not set. Was PetscViewerExodusIISetZonalVariable called?"); 48449c89c76SBlaise Bourdin 48549c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 48649c89c76SBlaise Bourdin for (int i = 0; i < numNames; i++) { 48749c89c76SBlaise Bourdin PetscCall(PetscStrallocpy(names[i], &exo->zonalVariableNames[i])); 48849c89c76SBlaise Bourdin PetscCallExternal(ex_put_variable_name, exoid, EX_ELEM_BLOCK, i + 1, names[i]); 48949c89c76SBlaise Bourdin } 49049c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 49149c89c76SBlaise Bourdin } 49249c89c76SBlaise Bourdin 49349c89c76SBlaise Bourdin /*@C 49449c89c76SBlaise Bourdin PetscViewerExodusIISetNodalVariableNames - Sets the names of all nodal variables. 49549c89c76SBlaise Bourdin 49649c89c76SBlaise Bourdin Collective; No Fortran Support 49749c89c76SBlaise Bourdin 49849c89c76SBlaise Bourdin Input Parameters: 49949c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 500ce78bad3SBarry Smith - names - an array of string names to be set, the strings are copied into the `PetscViewer` 50149c89c76SBlaise Bourdin 50249c89c76SBlaise Bourdin Level: intermediate 50349c89c76SBlaise Bourdin 50449c89c76SBlaise Bourdin Notes: 50549c89c76SBlaise Bourdin This function allows users to set multiple nodal variable names at a time. 50649c89c76SBlaise Bourdin 50749c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIIGetNodalVariableNames()` 50849c89c76SBlaise Bourdin @*/ 509ce78bad3SBarry Smith PetscErrorCode PetscViewerExodusIISetNodalVariableNames(PetscViewer viewer, const char *const names[]) 51049c89c76SBlaise Bourdin { 5110a5cf5d8SBlaise Bourdin PetscExodusIIInt numNames; 5120a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid = -1; 51349c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 51449c89c76SBlaise Bourdin 51549c89c76SBlaise Bourdin PetscFunctionBegin; 51649c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetNodalVariable(viewer, &numNames)); 51749c89c76SBlaise Bourdin PetscCheck(numNames >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of nodal variables not set. Was PetscViewerExodusIISetNodalVariable called?"); 51849c89c76SBlaise Bourdin 51949c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 52049c89c76SBlaise Bourdin for (int i = 0; i < numNames; i++) { 52149c89c76SBlaise Bourdin PetscCall(PetscStrallocpy(names[i], &exo->nodalVariableNames[i])); 52249c89c76SBlaise Bourdin PetscCallExternal(ex_put_variable_name, exoid, EX_NODAL, i + 1, names[i]); 52349c89c76SBlaise Bourdin } 52449c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 52549c89c76SBlaise Bourdin } 52649c89c76SBlaise Bourdin 52749c89c76SBlaise Bourdin /*@C 52849c89c76SBlaise Bourdin PetscViewerExodusIIGetZonalVariableNames - Gets the names of all zonal variables. 52949c89c76SBlaise Bourdin 53049c89c76SBlaise Bourdin Collective; No Fortran Support 53149c89c76SBlaise Bourdin 53249c89c76SBlaise Bourdin Input Parameters: 53349c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 53449c89c76SBlaise Bourdin - numVars - the number of zonal variable names to retrieve 53549c89c76SBlaise Bourdin 536ce78bad3SBarry Smith Output Parameter: 537ce78bad3SBarry Smith . varNames - returns an array of char pointers where the zonal variable names are 53849c89c76SBlaise Bourdin 53949c89c76SBlaise Bourdin Level: intermediate 54049c89c76SBlaise Bourdin 54149c89c76SBlaise Bourdin Notes: 54249c89c76SBlaise Bourdin This function returns a borrowed pointer which should not be freed. 54349c89c76SBlaise Bourdin 54449c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIISetZonalVariableNames()` 54549c89c76SBlaise Bourdin @*/ 546ce78bad3SBarry Smith PetscErrorCode PetscViewerExodusIIGetZonalVariableNames(PetscViewer viewer, PetscExodusIIInt *numVars, const char *const *varNames[]) 54749c89c76SBlaise Bourdin { 54849c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 5490a5cf5d8SBlaise Bourdin PetscExodusIIInt idx; 55049c89c76SBlaise Bourdin char tmpName[MAX_NAME_LENGTH + 1]; 5510a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid = -1; 55249c89c76SBlaise Bourdin 55349c89c76SBlaise Bourdin PetscFunctionBegin; 55449c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetZonalVariable(viewer, numVars)); 55549c89c76SBlaise Bourdin /* 55649c89c76SBlaise Bourdin Cache variable names if necessary 55749c89c76SBlaise Bourdin */ 55849c89c76SBlaise Bourdin for (idx = 0; idx < *numVars; idx++) { 55949c89c76SBlaise Bourdin if (!exo->zonalVariableNames[idx]) { 56049c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 56149c89c76SBlaise Bourdin PetscCallExternal(ex_get_variable_name, exoid, EX_ELEM_BLOCK, idx + 1, tmpName); 56249c89c76SBlaise Bourdin PetscCall(PetscStrallocpy(tmpName, (char **)&exo->zonalVariableNames[idx])); 56349c89c76SBlaise Bourdin } 56449c89c76SBlaise Bourdin } 565ce78bad3SBarry Smith *varNames = (const char *const *)exo->zonalVariableNames; 56649c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 56749c89c76SBlaise Bourdin } 56849c89c76SBlaise Bourdin 56949c89c76SBlaise Bourdin /*@C 57049c89c76SBlaise Bourdin PetscViewerExodusIIGetNodalVariableNames - Gets the names of all nodal variables. 57149c89c76SBlaise Bourdin 57249c89c76SBlaise Bourdin Collective; No Fortran Support 57349c89c76SBlaise Bourdin 57449c89c76SBlaise Bourdin Input Parameters: 57549c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 57649c89c76SBlaise Bourdin - numVars - the number of nodal variable names to retrieve 57749c89c76SBlaise Bourdin 578ce78bad3SBarry Smith Output Parameter: 579ce78bad3SBarry Smith . varNames - returns an array of char pointers where the nodal variable names are 58049c89c76SBlaise Bourdin 58149c89c76SBlaise Bourdin Level: intermediate 58249c89c76SBlaise Bourdin 58349c89c76SBlaise Bourdin Notes: 58449c89c76SBlaise Bourdin This function returns a borrowed pointer which should not be freed. 58549c89c76SBlaise Bourdin 58649c89c76SBlaise Bourdin .seealso: `PETSCVIEWEREXODUSII`, `PetscViewer`, `PetscViewerCreate()`, `PetscViewerDestroy()`, `PetscViewerExodusIIOpen()`, `PetscViewerSetType()`, `PetscViewerType`, `PetscViewerExodusIISetNodalVariableNames()` 58749c89c76SBlaise Bourdin @*/ 588ce78bad3SBarry Smith PetscErrorCode PetscViewerExodusIIGetNodalVariableNames(PetscViewer viewer, PetscExodusIIInt *numVars, const char *const *varNames[]) 58949c89c76SBlaise Bourdin { 59049c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 5910a5cf5d8SBlaise Bourdin PetscExodusIIInt idx; 59249c89c76SBlaise Bourdin char tmpName[MAX_NAME_LENGTH + 1]; 5930a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid = -1; 59449c89c76SBlaise Bourdin 59549c89c76SBlaise Bourdin PetscFunctionBegin; 59649c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetNodalVariable(viewer, numVars)); 59749c89c76SBlaise Bourdin /* 59849c89c76SBlaise Bourdin Cache variable names if necessary 59949c89c76SBlaise Bourdin */ 60049c89c76SBlaise Bourdin for (idx = 0; idx < *numVars; idx++) { 60149c89c76SBlaise Bourdin if (!exo->nodalVariableNames[idx]) { 60249c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 60349c89c76SBlaise Bourdin PetscCallExternal(ex_get_variable_name, exoid, EX_NODAL, idx + 1, tmpName); 60449c89c76SBlaise Bourdin PetscCall(PetscStrallocpy(tmpName, (char **)&exo->nodalVariableNames[idx])); 60549c89c76SBlaise Bourdin } 60649c89c76SBlaise Bourdin } 607ce78bad3SBarry Smith *varNames = (const char *const *)exo->nodalVariableNames; 60849c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 60949c89c76SBlaise Bourdin } 61049c89c76SBlaise Bourdin 61149c89c76SBlaise Bourdin /*MC 61249c89c76SBlaise Bourdin PETSCVIEWEREXODUSII - A viewer that writes to an Exodus II file 61349c89c76SBlaise Bourdin 61449c89c76SBlaise Bourdin Level: beginner 61549c89c76SBlaise Bourdin 61649c89c76SBlaise Bourdin .seealso: `PetscViewerExodusIIOpen()`, `PetscViewerCreate()`, `PETSCVIEWERBINARY`, `PETSCVIEWERHDF5`, `DMView()`, 61749c89c76SBlaise Bourdin `PetscViewerFileSetName()`, `PetscViewerFileSetMode()`, `PetscViewerFormat`, `PetscViewerType`, `PetscViewerSetType()` 61849c89c76SBlaise Bourdin M*/ 61949c89c76SBlaise Bourdin PETSC_EXTERN PetscErrorCode PetscViewerCreate_ExodusII(PetscViewer v) 62049c89c76SBlaise Bourdin { 62149c89c76SBlaise Bourdin PetscViewer_ExodusII *exo; 62249c89c76SBlaise Bourdin 62349c89c76SBlaise Bourdin PetscFunctionBegin; 62449c89c76SBlaise Bourdin PetscCall(PetscNew(&exo)); 62549c89c76SBlaise Bourdin 62649c89c76SBlaise Bourdin v->data = (void *)exo; 62749c89c76SBlaise Bourdin v->ops->destroy = PetscViewerDestroy_ExodusII; 62849c89c76SBlaise Bourdin v->ops->setfromoptions = PetscViewerSetFromOptions_ExodusII; 62949c89c76SBlaise Bourdin v->ops->view = PetscViewerView_ExodusII; 63049c89c76SBlaise Bourdin v->ops->flush = PetscViewerFlush_ExodusII; 63149c89c76SBlaise Bourdin exo->btype = FILE_MODE_UNDEFINED; 63249c89c76SBlaise Bourdin exo->filename = 0; 63349c89c76SBlaise Bourdin exo->exoid = -1; 63449c89c76SBlaise Bourdin exo->numNodalVariables = -1; 63549c89c76SBlaise Bourdin exo->numZonalVariables = -1; 63649c89c76SBlaise Bourdin exo->nodalVariableNames = NULL; 63749c89c76SBlaise Bourdin exo->zonalVariableNames = NULL; 63849c89c76SBlaise Bourdin 63949c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileSetName_C", PetscViewerFileSetName_ExodusII)); 64049c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileGetName_C", PetscViewerFileGetName_ExodusII)); 64149c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileSetMode_C", PetscViewerFileSetMode_ExodusII)); 64249c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileGetMode_C", PetscViewerFileGetMode_ExodusII)); 64349c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerGetId_C", PetscViewerExodusIIGetId_ExodusII)); 64449c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerSetOrder_C", PetscViewerExodusIISetOrder_ExodusII)); 64549c89c76SBlaise Bourdin PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerGetOrder_C", PetscViewerExodusIIGetOrder_ExodusII)); 64649c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 64749c89c76SBlaise Bourdin } 64849c89c76SBlaise Bourdin 64949c89c76SBlaise Bourdin /*@ 65049c89c76SBlaise Bourdin PetscViewerExodusIIGetNodalVariableIndex - return the location of a nodal variable in an exodusII file given its name 65149c89c76SBlaise Bourdin 65249c89c76SBlaise Bourdin Collective 65349c89c76SBlaise Bourdin 65449c89c76SBlaise Bourdin Input Parameters: 65549c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 65649c89c76SBlaise Bourdin - name - the name of the result 65749c89c76SBlaise Bourdin 65849c89c76SBlaise Bourdin Output Parameter: 65949c89c76SBlaise Bourdin . varIndex - the location of the variable in the exodus file or -1 if the variable is not found 66049c89c76SBlaise Bourdin 66149c89c76SBlaise Bourdin Level: beginner 66249c89c76SBlaise Bourdin 66349c89c76SBlaise Bourdin Notes: 66449c89c76SBlaise Bourdin The exodus variable index is obtained by comparing the name argument to the 66549c89c76SBlaise Bourdin names of zonal variables declared in the exodus file. For instance if name is "V" 66649c89c76SBlaise Bourdin the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11" 66749c89c76SBlaise Bourdin amongst all variables of type obj_type. 66849c89c76SBlaise Bourdin 66949c89c76SBlaise Bourdin .seealso: `PetscViewerExodusIISetNodalVariable()`, `PetscViewerExodusIIGetNodalVariable()`, `PetscViewerExodusIISetNodalVariableName()`, `PetscViewerExodusIISetNodalVariableNames()`, `PetscViewerExodusIIGetNodalVariableName()`, `PetscViewerExodusIIGetNodalVariableNames()` 67049c89c76SBlaise Bourdin @*/ 6710a5cf5d8SBlaise Bourdin PetscErrorCode PetscViewerExodusIIGetNodalVariableIndex(PetscViewer viewer, const char name[], PetscExodusIIInt *varIndex) 67249c89c76SBlaise Bourdin { 6730a5cf5d8SBlaise Bourdin PetscExodusIIInt num_vars = 0, i, j; 67449c89c76SBlaise Bourdin char ext_name[MAX_STR_LENGTH + 1]; 675ce78bad3SBarry Smith const char *const *var_names; 67649c89c76SBlaise Bourdin const int num_suffix = 5; 67749c89c76SBlaise Bourdin char *suffix[5]; 67849c89c76SBlaise Bourdin PetscBool flg; 67949c89c76SBlaise Bourdin 68049c89c76SBlaise Bourdin PetscFunctionBegin; 68149c89c76SBlaise Bourdin suffix[0] = (char *)""; 68249c89c76SBlaise Bourdin suffix[1] = (char *)"_X"; 68349c89c76SBlaise Bourdin suffix[2] = (char *)"_XX"; 68449c89c76SBlaise Bourdin suffix[3] = (char *)"_1"; 68549c89c76SBlaise Bourdin suffix[4] = (char *)"_11"; 68649c89c76SBlaise Bourdin *varIndex = -1; 68749c89c76SBlaise Bourdin 68849c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetNodalVariableNames(viewer, &num_vars, &var_names)); 68949c89c76SBlaise Bourdin for (i = 0; i < num_vars; ++i) { 69049c89c76SBlaise Bourdin for (j = 0; j < num_suffix; ++j) { 69149c89c76SBlaise Bourdin PetscCall(PetscStrncpy(ext_name, name, MAX_STR_LENGTH)); 69249c89c76SBlaise Bourdin PetscCall(PetscStrlcat(ext_name, suffix[j], MAX_STR_LENGTH)); 69349c89c76SBlaise Bourdin PetscCall(PetscStrcasecmp(ext_name, var_names[i], &flg)); 69449c89c76SBlaise Bourdin if (flg) *varIndex = i; 69549c89c76SBlaise Bourdin } 69649c89c76SBlaise Bourdin if (flg) break; 69749c89c76SBlaise Bourdin } 69849c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 69949c89c76SBlaise Bourdin } 70049c89c76SBlaise Bourdin 70149c89c76SBlaise Bourdin /*@ 70249c89c76SBlaise Bourdin PetscViewerExodusIIGetZonalVariableIndex - return the location of a zonal variable in an exodusII file given its name 70349c89c76SBlaise Bourdin 70449c89c76SBlaise Bourdin Collective 70549c89c76SBlaise Bourdin 70649c89c76SBlaise Bourdin Input Parameters: 70749c89c76SBlaise Bourdin + viewer - a `PetscViewer` of type `PETSCVIEWEREXODUSII` 70849c89c76SBlaise Bourdin - name - the name of the result 70949c89c76SBlaise Bourdin 71049c89c76SBlaise Bourdin Output Parameter: 71149c89c76SBlaise Bourdin . varIndex - the location of the variable in the exodus file or -1 if the variable is not found 71249c89c76SBlaise Bourdin 71349c89c76SBlaise Bourdin Level: beginner 71449c89c76SBlaise Bourdin 71549c89c76SBlaise Bourdin Notes: 71649c89c76SBlaise Bourdin The exodus variable index is obtained by comparing the name argument to the 71749c89c76SBlaise Bourdin names of zonal variables declared in the exodus file. For instance if name is "V" 71849c89c76SBlaise Bourdin the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11" 71949c89c76SBlaise Bourdin amongst all variables of type obj_type. 72049c89c76SBlaise Bourdin 72149c89c76SBlaise Bourdin .seealso: `PetscViewerExodusIISetNodalVariable()`, `PetscViewerExodusIIGetNodalVariable()`, `PetscViewerExodusIISetNodalVariableName()`, `PetscViewerExodusIISetNodalVariableNames()`, `PetscViewerExodusIIGetNodalVariableName()`, `PetscViewerExodusIIGetNodalVariableNames()` 72249c89c76SBlaise Bourdin @*/ 72349c89c76SBlaise Bourdin PetscErrorCode PetscViewerExodusIIGetZonalVariableIndex(PetscViewer viewer, const char name[], int *varIndex) 72449c89c76SBlaise Bourdin { 7250a5cf5d8SBlaise Bourdin PetscExodusIIInt num_vars = 0, i, j; 72649c89c76SBlaise Bourdin char ext_name[MAX_STR_LENGTH + 1]; 727ce78bad3SBarry Smith const char *const *var_names; 72849c89c76SBlaise Bourdin const int num_suffix = 5; 72949c89c76SBlaise Bourdin char *suffix[5]; 73049c89c76SBlaise Bourdin PetscBool flg; 73149c89c76SBlaise Bourdin 73249c89c76SBlaise Bourdin PetscFunctionBegin; 73349c89c76SBlaise Bourdin suffix[0] = (char *)""; 73449c89c76SBlaise Bourdin suffix[1] = (char *)"_X"; 73549c89c76SBlaise Bourdin suffix[2] = (char *)"_XX"; 73649c89c76SBlaise Bourdin suffix[3] = (char *)"_1"; 73749c89c76SBlaise Bourdin suffix[4] = (char *)"_11"; 73849c89c76SBlaise Bourdin *varIndex = -1; 73949c89c76SBlaise Bourdin 74049c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetZonalVariableNames(viewer, &num_vars, &var_names)); 74149c89c76SBlaise Bourdin for (i = 0; i < num_vars; ++i) { 74249c89c76SBlaise Bourdin for (j = 0; j < num_suffix; ++j) { 74349c89c76SBlaise Bourdin PetscCall(PetscStrncpy(ext_name, name, MAX_STR_LENGTH)); 74449c89c76SBlaise Bourdin PetscCall(PetscStrlcat(ext_name, suffix[j], MAX_STR_LENGTH)); 74549c89c76SBlaise Bourdin PetscCall(PetscStrcasecmp(ext_name, var_names[i], &flg)); 74649c89c76SBlaise Bourdin if (flg) *varIndex = i; 74749c89c76SBlaise Bourdin } 74849c89c76SBlaise Bourdin if (flg) break; 74949c89c76SBlaise Bourdin } 75049c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 75149c89c76SBlaise Bourdin } 75249c89c76SBlaise Bourdin 75349c89c76SBlaise Bourdin PetscErrorCode DMView_PlexExodusII(DM dm, PetscViewer viewer) 75449c89c76SBlaise Bourdin { 75549c89c76SBlaise Bourdin enum ElemType { 75649c89c76SBlaise Bourdin SEGMENT, 75749c89c76SBlaise Bourdin TRI, 75849c89c76SBlaise Bourdin QUAD, 75949c89c76SBlaise Bourdin TET, 76049c89c76SBlaise Bourdin HEX 76149c89c76SBlaise Bourdin }; 76249c89c76SBlaise Bourdin MPI_Comm comm; 7630a5cf5d8SBlaise Bourdin PetscInt degree; /* the order of the mesh */ 76449c89c76SBlaise Bourdin /* Connectivity Variables */ 76549c89c76SBlaise Bourdin PetscInt cellsNotInConnectivity; 76649c89c76SBlaise Bourdin /* Cell Sets */ 76749c89c76SBlaise Bourdin DMLabel csLabel; 76849c89c76SBlaise Bourdin IS csIS; 76949c89c76SBlaise Bourdin const PetscInt *csIdx; 77049c89c76SBlaise Bourdin PetscInt num_cs, cs; 77149c89c76SBlaise Bourdin enum ElemType *type; 77249c89c76SBlaise Bourdin PetscBool hasLabel; 77349c89c76SBlaise Bourdin /* Coordinate Variables */ 77449c89c76SBlaise Bourdin DM cdm; 77549c89c76SBlaise Bourdin PetscSection coordSection; 77649c89c76SBlaise Bourdin Vec coord; 77749c89c76SBlaise Bourdin PetscInt **nodes; 77849c89c76SBlaise Bourdin PetscInt depth, d, dim, skipCells = 0; 77949c89c76SBlaise Bourdin PetscInt pStart, pEnd, p, cStart, cEnd, numCells, vStart, vEnd, numVertices, eStart, eEnd, numEdges, fStart, fEnd, numFaces, numNodes; 78049c89c76SBlaise Bourdin PetscInt num_vs, num_fs; 78149c89c76SBlaise Bourdin PetscMPIInt rank, size; 78249c89c76SBlaise Bourdin const char *dmName; 78349c89c76SBlaise Bourdin PetscInt nodesLineP1[4] = {2, 0, 0, 0}; 78449c89c76SBlaise Bourdin PetscInt nodesLineP2[4] = {2, 0, 0, 1}; 78549c89c76SBlaise Bourdin PetscInt nodesTriP1[4] = {3, 0, 0, 0}; 78649c89c76SBlaise Bourdin PetscInt nodesTriP2[4] = {3, 3, 0, 0}; 78749c89c76SBlaise Bourdin PetscInt nodesQuadP1[4] = {4, 0, 0, 0}; 78849c89c76SBlaise Bourdin PetscInt nodesQuadP2[4] = {4, 4, 0, 1}; 78949c89c76SBlaise Bourdin PetscInt nodesTetP1[4] = {4, 0, 0, 0}; 79049c89c76SBlaise Bourdin PetscInt nodesTetP2[4] = {4, 6, 0, 0}; 79149c89c76SBlaise Bourdin PetscInt nodesHexP1[4] = {8, 0, 0, 0}; 79249c89c76SBlaise Bourdin PetscInt nodesHexP2[4] = {8, 12, 6, 1}; 7930a5cf5d8SBlaise Bourdin PetscExodusIIInt CPU_word_size, IO_word_size, EXO_mode; 7940a5cf5d8SBlaise Bourdin PetscExodusIIFloat EXO_version; 79549c89c76SBlaise Bourdin 79649c89c76SBlaise Bourdin PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *)viewer->data; 79749c89c76SBlaise Bourdin 79849c89c76SBlaise Bourdin PetscFunctionBegin; 79949c89c76SBlaise Bourdin PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 80049c89c76SBlaise Bourdin PetscCallMPI(MPI_Comm_rank(comm, &rank)); 80149c89c76SBlaise Bourdin PetscCallMPI(MPI_Comm_size(comm, &size)); 80249c89c76SBlaise Bourdin 80349c89c76SBlaise Bourdin /* 80449c89c76SBlaise Bourdin Creating coordSection is a collective operation so we do it somewhat out of sequence 80549c89c76SBlaise Bourdin */ 80649c89c76SBlaise Bourdin PetscCall(PetscSectionCreate(comm, &coordSection)); 80749c89c76SBlaise Bourdin PetscCall(DMGetCoordinatesLocalSetUp(dm)); 80849c89c76SBlaise Bourdin /* 80949c89c76SBlaise Bourdin Check that all points are on rank 0 since we don't know how to save distributed DM in exodus format 81049c89c76SBlaise Bourdin */ 81149c89c76SBlaise Bourdin PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 81249c89c76SBlaise Bourdin PetscCall(DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd)); 81349c89c76SBlaise Bourdin PetscCall(DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd)); 81449c89c76SBlaise Bourdin PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 81549c89c76SBlaise Bourdin numCells = cEnd - cStart; 81649c89c76SBlaise Bourdin numEdges = eEnd - eStart; 81749c89c76SBlaise Bourdin numVertices = vEnd - vStart; 81849c89c76SBlaise Bourdin PetscCheck(!(rank && (numCells || numEdges || numVertices)), PETSC_COMM_SELF, PETSC_ERR_SUP, "Writing distributed DM in exodusII format not supported"); 81949c89c76SBlaise Bourdin if (rank == 0) { 82049c89c76SBlaise Bourdin switch (exo->btype) { 82149c89c76SBlaise Bourdin case FILE_MODE_READ: 82249c89c76SBlaise Bourdin case FILE_MODE_APPEND: 82349c89c76SBlaise Bourdin case FILE_MODE_UPDATE: 82449c89c76SBlaise Bourdin case FILE_MODE_APPEND_UPDATE: 82549c89c76SBlaise Bourdin /* exodusII does not allow writing geometry to an existing file */ 82649c89c76SBlaise Bourdin SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "cannot add geometry to existing file %s", exo->filename); 82749c89c76SBlaise Bourdin case FILE_MODE_WRITE: 82849c89c76SBlaise Bourdin /* Create an empty file if one already exists*/ 82949c89c76SBlaise Bourdin EXO_mode = EX_CLOBBER; 83049c89c76SBlaise Bourdin #if defined(PETSC_USE_64BIT_INDICES) 83149c89c76SBlaise Bourdin EXO_mode += EX_ALL_INT64_API; 83249c89c76SBlaise Bourdin #endif 83349c89c76SBlaise Bourdin CPU_word_size = sizeof(PetscReal); 83449c89c76SBlaise Bourdin IO_word_size = sizeof(PetscReal); 83549c89c76SBlaise Bourdin exo->exoid = ex_create(exo->filename, EXO_mode, &CPU_word_size, &IO_word_size); 83649c89c76SBlaise Bourdin PetscCheck(exo->exoid >= 0, PETSC_COMM_SELF, PETSC_ERR_LIB, "ex_create failed for %s", exo->filename); 83749c89c76SBlaise Bourdin 83849c89c76SBlaise Bourdin break; 83949c89c76SBlaise Bourdin default: 84049c89c76SBlaise Bourdin SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()"); 84149c89c76SBlaise Bourdin } 84249c89c76SBlaise Bourdin 84349c89c76SBlaise Bourdin /* --- Get DM info --- */ 84449c89c76SBlaise Bourdin PetscCall(PetscObjectGetName((PetscObject)dm, &dmName)); 84549c89c76SBlaise Bourdin PetscCall(DMPlexGetDepth(dm, &depth)); 84649c89c76SBlaise Bourdin PetscCall(DMGetDimension(dm, &dim)); 84749c89c76SBlaise Bourdin PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 84849c89c76SBlaise Bourdin if (depth == 3) { 84949c89c76SBlaise Bourdin numFaces = fEnd - fStart; 85049c89c76SBlaise Bourdin } else { 85149c89c76SBlaise Bourdin numFaces = 0; 85249c89c76SBlaise Bourdin } 85349c89c76SBlaise Bourdin PetscCall(DMGetLabelSize(dm, "Cell Sets", &num_cs)); 85449c89c76SBlaise Bourdin PetscCall(DMGetLabelSize(dm, "Vertex Sets", &num_vs)); 85549c89c76SBlaise Bourdin PetscCall(DMGetLabelSize(dm, "Face Sets", &num_fs)); 85649c89c76SBlaise Bourdin PetscCall(DMGetCoordinatesLocal(dm, &coord)); 85749c89c76SBlaise Bourdin PetscCall(DMGetCoordinateDM(dm, &cdm)); 85849c89c76SBlaise Bourdin if (num_cs > 0) { 85949c89c76SBlaise Bourdin PetscCall(DMGetLabel(dm, "Cell Sets", &csLabel)); 86049c89c76SBlaise Bourdin PetscCall(DMLabelGetValueIS(csLabel, &csIS)); 86149c89c76SBlaise Bourdin PetscCall(ISGetIndices(csIS, &csIdx)); 86249c89c76SBlaise Bourdin } 86349c89c76SBlaise Bourdin PetscCall(PetscMalloc1(num_cs, &nodes)); 86449c89c76SBlaise Bourdin /* Set element type for each block and compute total number of nodes */ 86549c89c76SBlaise Bourdin PetscCall(PetscMalloc1(num_cs, &type)); 86649c89c76SBlaise Bourdin numNodes = numVertices; 86749c89c76SBlaise Bourdin 86849c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetOrder(viewer, °ree)); 86949c89c76SBlaise Bourdin if (degree == 2) numNodes += numEdges; 87049c89c76SBlaise Bourdin cellsNotInConnectivity = numCells; 87149c89c76SBlaise Bourdin for (cs = 0; cs < num_cs; ++cs) { 87249c89c76SBlaise Bourdin IS stratumIS; 87349c89c76SBlaise Bourdin const PetscInt *cells; 87449c89c76SBlaise Bourdin PetscScalar *xyz = NULL; 87549c89c76SBlaise Bourdin PetscInt csSize, closureSize; 87649c89c76SBlaise Bourdin 87749c89c76SBlaise Bourdin PetscCall(DMLabelGetStratumIS(csLabel, csIdx[cs], &stratumIS)); 87849c89c76SBlaise Bourdin PetscCall(ISGetIndices(stratumIS, &cells)); 87949c89c76SBlaise Bourdin PetscCall(ISGetSize(stratumIS, &csSize)); 88049c89c76SBlaise Bourdin PetscCall(DMPlexVecGetClosure(cdm, NULL, coord, cells[0], &closureSize, &xyz)); 88149c89c76SBlaise Bourdin switch (dim) { 88249c89c76SBlaise Bourdin case 1: 88349c89c76SBlaise Bourdin if (closureSize == 2 * dim) { 88449c89c76SBlaise Bourdin type[cs] = SEGMENT; 88549c89c76SBlaise Bourdin } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of vertices %" PetscInt_FMT " in dimension %" PetscInt_FMT " has no ExodusII type", closureSize / dim, dim); 886fac68d15SPierre Jolivet break; 88749c89c76SBlaise Bourdin case 2: 88849c89c76SBlaise Bourdin if (closureSize == 3 * dim) { 88949c89c76SBlaise Bourdin type[cs] = TRI; 89049c89c76SBlaise Bourdin } else if (closureSize == 4 * dim) { 89149c89c76SBlaise Bourdin type[cs] = QUAD; 89249c89c76SBlaise Bourdin } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of vertices %" PetscInt_FMT " in dimension %" PetscInt_FMT " has no ExodusII type", closureSize / dim, dim); 89349c89c76SBlaise Bourdin break; 89449c89c76SBlaise Bourdin case 3: 89549c89c76SBlaise Bourdin if (closureSize == 4 * dim) { 89649c89c76SBlaise Bourdin type[cs] = TET; 89749c89c76SBlaise Bourdin } else if (closureSize == 8 * dim) { 89849c89c76SBlaise Bourdin type[cs] = HEX; 89949c89c76SBlaise Bourdin } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of vertices %" PetscInt_FMT " in dimension %" PetscInt_FMT " has no ExodusII type", closureSize / dim, dim); 90049c89c76SBlaise Bourdin break; 90149c89c76SBlaise Bourdin default: 90249c89c76SBlaise Bourdin SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %" PetscInt_FMT " not handled by ExodusII viewer", dim); 90349c89c76SBlaise Bourdin } 90449c89c76SBlaise Bourdin if ((degree == 2) && (type[cs] == SEGMENT)) numNodes += csSize; 90549c89c76SBlaise Bourdin if ((degree == 2) && (type[cs] == QUAD)) numNodes += csSize; 90649c89c76SBlaise Bourdin if ((degree == 2) && (type[cs] == HEX)) { 90749c89c76SBlaise Bourdin numNodes += csSize; 90849c89c76SBlaise Bourdin numNodes += numFaces; 90949c89c76SBlaise Bourdin } 91049c89c76SBlaise Bourdin PetscCall(DMPlexVecRestoreClosure(cdm, NULL, coord, cells[0], &closureSize, &xyz)); 91149c89c76SBlaise Bourdin /* Set nodes and Element type */ 91249c89c76SBlaise Bourdin if (type[cs] == SEGMENT) { 91349c89c76SBlaise Bourdin if (degree == 1) nodes[cs] = nodesLineP1; 91449c89c76SBlaise Bourdin else if (degree == 2) nodes[cs] = nodesLineP2; 91549c89c76SBlaise Bourdin } else if (type[cs] == TRI) { 91649c89c76SBlaise Bourdin if (degree == 1) nodes[cs] = nodesTriP1; 91749c89c76SBlaise Bourdin else if (degree == 2) nodes[cs] = nodesTriP2; 91849c89c76SBlaise Bourdin } else if (type[cs] == QUAD) { 91949c89c76SBlaise Bourdin if (degree == 1) nodes[cs] = nodesQuadP1; 92049c89c76SBlaise Bourdin else if (degree == 2) nodes[cs] = nodesQuadP2; 92149c89c76SBlaise Bourdin } else if (type[cs] == TET) { 92249c89c76SBlaise Bourdin if (degree == 1) nodes[cs] = nodesTetP1; 92349c89c76SBlaise Bourdin else if (degree == 2) nodes[cs] = nodesTetP2; 92449c89c76SBlaise Bourdin } else if (type[cs] == HEX) { 92549c89c76SBlaise Bourdin if (degree == 1) nodes[cs] = nodesHexP1; 92649c89c76SBlaise Bourdin else if (degree == 2) nodes[cs] = nodesHexP2; 92749c89c76SBlaise Bourdin } 92849c89c76SBlaise Bourdin /* Compute the number of cells not in the connectivity table */ 92949c89c76SBlaise Bourdin cellsNotInConnectivity -= nodes[cs][3] * csSize; 93049c89c76SBlaise Bourdin 93149c89c76SBlaise Bourdin PetscCall(ISRestoreIndices(stratumIS, &cells)); 93249c89c76SBlaise Bourdin PetscCall(ISDestroy(&stratumIS)); 93349c89c76SBlaise Bourdin } 93449c89c76SBlaise Bourdin if (num_cs) PetscCallExternal(ex_put_init, exo->exoid, dmName, dim, numNodes, numCells, num_cs, num_vs, num_fs); 93549c89c76SBlaise Bourdin /* --- Connectivity --- */ 93649c89c76SBlaise Bourdin for (cs = 0; cs < num_cs; ++cs) { 93749c89c76SBlaise Bourdin IS stratumIS; 93849c89c76SBlaise Bourdin const PetscInt *cells; 93949c89c76SBlaise Bourdin PetscInt *connect, off = 0; 94049c89c76SBlaise Bourdin PetscInt edgesInClosure = 0, facesInClosure = 0, verticesInClosure = 0; 94149c89c76SBlaise Bourdin PetscInt csSize, c, connectSize, closureSize; 94249c89c76SBlaise Bourdin char *elem_type = NULL; 94349c89c76SBlaise Bourdin char elem_type_bar2[] = "BAR2", elem_type_bar3[] = "BAR3"; 94449c89c76SBlaise Bourdin char elem_type_tri3[] = "TRI3", elem_type_quad4[] = "QUAD4"; 94549c89c76SBlaise Bourdin char elem_type_tri6[] = "TRI6", elem_type_quad9[] = "QUAD9"; 94649c89c76SBlaise Bourdin char elem_type_tet4[] = "TET4", elem_type_hex8[] = "HEX8"; 94749c89c76SBlaise Bourdin char elem_type_tet10[] = "TET10", elem_type_hex27[] = "HEX27"; 94849c89c76SBlaise Bourdin 94949c89c76SBlaise Bourdin PetscCall(DMLabelGetStratumIS(csLabel, csIdx[cs], &stratumIS)); 95049c89c76SBlaise Bourdin PetscCall(ISGetIndices(stratumIS, &cells)); 95149c89c76SBlaise Bourdin PetscCall(ISGetSize(stratumIS, &csSize)); 95249c89c76SBlaise Bourdin /* Set Element type */ 95349c89c76SBlaise Bourdin if (type[cs] == SEGMENT) { 95449c89c76SBlaise Bourdin if (degree == 1) elem_type = elem_type_bar2; 95549c89c76SBlaise Bourdin else if (degree == 2) elem_type = elem_type_bar3; 95649c89c76SBlaise Bourdin } else if (type[cs] == TRI) { 95749c89c76SBlaise Bourdin if (degree == 1) elem_type = elem_type_tri3; 95849c89c76SBlaise Bourdin else if (degree == 2) elem_type = elem_type_tri6; 95949c89c76SBlaise Bourdin } else if (type[cs] == QUAD) { 96049c89c76SBlaise Bourdin if (degree == 1) elem_type = elem_type_quad4; 96149c89c76SBlaise Bourdin else if (degree == 2) elem_type = elem_type_quad9; 96249c89c76SBlaise Bourdin } else if (type[cs] == TET) { 96349c89c76SBlaise Bourdin if (degree == 1) elem_type = elem_type_tet4; 96449c89c76SBlaise Bourdin else if (degree == 2) elem_type = elem_type_tet10; 96549c89c76SBlaise Bourdin } else if (type[cs] == HEX) { 96649c89c76SBlaise Bourdin if (degree == 1) elem_type = elem_type_hex8; 96749c89c76SBlaise Bourdin else if (degree == 2) elem_type = elem_type_hex27; 96849c89c76SBlaise Bourdin } 96949c89c76SBlaise Bourdin connectSize = nodes[cs][0] + nodes[cs][1] + nodes[cs][2] + nodes[cs][3]; 97049c89c76SBlaise Bourdin PetscCall(PetscMalloc1(PetscMax(27, connectSize) * csSize, &connect)); 97149c89c76SBlaise Bourdin PetscCallExternal(ex_put_block, exo->exoid, EX_ELEM_BLOCK, csIdx[cs], elem_type, csSize, connectSize, 0, 0, 1); 97249c89c76SBlaise Bourdin /* Find number of vertices, edges, and faces in the closure */ 97349c89c76SBlaise Bourdin verticesInClosure = nodes[cs][0]; 97449c89c76SBlaise Bourdin if (depth > 1) { 97549c89c76SBlaise Bourdin if (dim == 2) { 97649c89c76SBlaise Bourdin PetscCall(DMPlexGetConeSize(dm, cells[0], &edgesInClosure)); 97749c89c76SBlaise Bourdin } else if (dim == 3) { 97849c89c76SBlaise Bourdin PetscInt *closure = NULL; 97949c89c76SBlaise Bourdin 98049c89c76SBlaise Bourdin PetscCall(DMPlexGetConeSize(dm, cells[0], &facesInClosure)); 98149c89c76SBlaise Bourdin PetscCall(DMPlexGetTransitiveClosure(dm, cells[0], PETSC_TRUE, &closureSize, &closure)); 98249c89c76SBlaise Bourdin edgesInClosure = closureSize - facesInClosure - 1 - verticesInClosure; 98349c89c76SBlaise Bourdin PetscCall(DMPlexRestoreTransitiveClosure(dm, cells[0], PETSC_TRUE, &closureSize, &closure)); 98449c89c76SBlaise Bourdin } 98549c89c76SBlaise Bourdin } 98649c89c76SBlaise Bourdin /* Get connectivity for each cell */ 98749c89c76SBlaise Bourdin for (c = 0; c < csSize; ++c) { 98849c89c76SBlaise Bourdin PetscInt *closure = NULL; 98949c89c76SBlaise Bourdin PetscInt temp, i; 99049c89c76SBlaise Bourdin 99149c89c76SBlaise Bourdin PetscCall(DMPlexGetTransitiveClosure(dm, cells[c], PETSC_TRUE, &closureSize, &closure)); 99249c89c76SBlaise Bourdin for (i = 0; i < connectSize; ++i) { 99349c89c76SBlaise Bourdin if (i < nodes[cs][0]) { /* Vertices */ 99449c89c76SBlaise Bourdin connect[i + off] = closure[(i + edgesInClosure + facesInClosure + 1) * 2] + 1; 99549c89c76SBlaise Bourdin connect[i + off] -= cellsNotInConnectivity; 99649c89c76SBlaise Bourdin } else if (i < nodes[cs][0] + nodes[cs][1]) { /* Edges */ 99749c89c76SBlaise Bourdin connect[i + off] = closure[(i - verticesInClosure + facesInClosure + 1) * 2] + 1; 99849c89c76SBlaise Bourdin if (nodes[cs][2] == 0) connect[i + off] -= numFaces; 99949c89c76SBlaise Bourdin connect[i + off] -= cellsNotInConnectivity; 100049c89c76SBlaise Bourdin } else if (i < nodes[cs][0] + nodes[cs][1] + nodes[cs][3]) { /* Cells */ 100149c89c76SBlaise Bourdin connect[i + off] = closure[0] + 1; 100249c89c76SBlaise Bourdin connect[i + off] -= skipCells; 100349c89c76SBlaise Bourdin } else if (i < nodes[cs][0] + nodes[cs][1] + nodes[cs][3] + nodes[cs][2]) { /* Faces */ 100449c89c76SBlaise Bourdin connect[i + off] = closure[(i - edgesInClosure - verticesInClosure) * 2] + 1; 100549c89c76SBlaise Bourdin connect[i + off] -= cellsNotInConnectivity; 100649c89c76SBlaise Bourdin } else { 100749c89c76SBlaise Bourdin connect[i + off] = -1; 100849c89c76SBlaise Bourdin } 100949c89c76SBlaise Bourdin } 101049c89c76SBlaise Bourdin /* Tetrahedra are inverted */ 101149c89c76SBlaise Bourdin if (type[cs] == TET) { 101249c89c76SBlaise Bourdin temp = connect[0 + off]; 101349c89c76SBlaise Bourdin connect[0 + off] = connect[1 + off]; 101449c89c76SBlaise Bourdin connect[1 + off] = temp; 101549c89c76SBlaise Bourdin if (degree == 2) { 101649c89c76SBlaise Bourdin temp = connect[5 + off]; 101749c89c76SBlaise Bourdin connect[5 + off] = connect[6 + off]; 101849c89c76SBlaise Bourdin connect[6 + off] = temp; 101949c89c76SBlaise Bourdin temp = connect[7 + off]; 102049c89c76SBlaise Bourdin connect[7 + off] = connect[8 + off]; 102149c89c76SBlaise Bourdin connect[8 + off] = temp; 102249c89c76SBlaise Bourdin } 102349c89c76SBlaise Bourdin } 102449c89c76SBlaise Bourdin /* Hexahedra are inverted */ 102549c89c76SBlaise Bourdin if (type[cs] == HEX) { 102649c89c76SBlaise Bourdin temp = connect[1 + off]; 102749c89c76SBlaise Bourdin connect[1 + off] = connect[3 + off]; 102849c89c76SBlaise Bourdin connect[3 + off] = temp; 102949c89c76SBlaise Bourdin if (degree == 2) { 103049c89c76SBlaise Bourdin temp = connect[8 + off]; 103149c89c76SBlaise Bourdin connect[8 + off] = connect[11 + off]; 103249c89c76SBlaise Bourdin connect[11 + off] = temp; 103349c89c76SBlaise Bourdin temp = connect[9 + off]; 103449c89c76SBlaise Bourdin connect[9 + off] = connect[10 + off]; 103549c89c76SBlaise Bourdin connect[10 + off] = temp; 103649c89c76SBlaise Bourdin temp = connect[16 + off]; 103749c89c76SBlaise Bourdin connect[16 + off] = connect[17 + off]; 103849c89c76SBlaise Bourdin connect[17 + off] = temp; 103949c89c76SBlaise Bourdin temp = connect[18 + off]; 104049c89c76SBlaise Bourdin connect[18 + off] = connect[19 + off]; 104149c89c76SBlaise Bourdin connect[19 + off] = temp; 104249c89c76SBlaise Bourdin 104349c89c76SBlaise Bourdin temp = connect[12 + off]; 104449c89c76SBlaise Bourdin connect[12 + off] = connect[16 + off]; 104549c89c76SBlaise Bourdin connect[16 + off] = temp; 104649c89c76SBlaise Bourdin temp = connect[13 + off]; 104749c89c76SBlaise Bourdin connect[13 + off] = connect[17 + off]; 104849c89c76SBlaise Bourdin connect[17 + off] = temp; 104949c89c76SBlaise Bourdin temp = connect[14 + off]; 105049c89c76SBlaise Bourdin connect[14 + off] = connect[18 + off]; 105149c89c76SBlaise Bourdin connect[18 + off] = temp; 105249c89c76SBlaise Bourdin temp = connect[15 + off]; 105349c89c76SBlaise Bourdin connect[15 + off] = connect[19 + off]; 105449c89c76SBlaise Bourdin connect[19 + off] = temp; 105549c89c76SBlaise Bourdin 105649c89c76SBlaise Bourdin temp = connect[23 + off]; 105749c89c76SBlaise Bourdin connect[23 + off] = connect[26 + off]; 105849c89c76SBlaise Bourdin connect[26 + off] = temp; 105949c89c76SBlaise Bourdin temp = connect[24 + off]; 106049c89c76SBlaise Bourdin connect[24 + off] = connect[25 + off]; 106149c89c76SBlaise Bourdin connect[25 + off] = temp; 106249c89c76SBlaise Bourdin temp = connect[25 + off]; 106349c89c76SBlaise Bourdin connect[25 + off] = connect[26 + off]; 106449c89c76SBlaise Bourdin connect[26 + off] = temp; 106549c89c76SBlaise Bourdin } 106649c89c76SBlaise Bourdin } 106749c89c76SBlaise Bourdin off += connectSize; 106849c89c76SBlaise Bourdin PetscCall(DMPlexRestoreTransitiveClosure(dm, cells[c], PETSC_TRUE, &closureSize, &closure)); 106949c89c76SBlaise Bourdin } 107049c89c76SBlaise Bourdin PetscCallExternal(ex_put_conn, exo->exoid, EX_ELEM_BLOCK, csIdx[cs], connect, 0, 0); 107149c89c76SBlaise Bourdin skipCells += (nodes[cs][3] == 0) * csSize; 107249c89c76SBlaise Bourdin PetscCall(PetscFree(connect)); 107349c89c76SBlaise Bourdin PetscCall(ISRestoreIndices(stratumIS, &cells)); 107449c89c76SBlaise Bourdin PetscCall(ISDestroy(&stratumIS)); 107549c89c76SBlaise Bourdin } 107649c89c76SBlaise Bourdin PetscCall(PetscFree(type)); 107749c89c76SBlaise Bourdin /* --- Coordinates --- */ 107849c89c76SBlaise Bourdin PetscCall(PetscSectionSetChart(coordSection, pStart, pEnd)); 107949c89c76SBlaise Bourdin if (num_cs) { 108049c89c76SBlaise Bourdin for (d = 0; d < depth; ++d) { 108149c89c76SBlaise Bourdin PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd)); 108249c89c76SBlaise Bourdin for (p = pStart; p < pEnd; ++p) PetscCall(PetscSectionSetDof(coordSection, p, nodes[0][d] > 0)); 108349c89c76SBlaise Bourdin } 108449c89c76SBlaise Bourdin } 108549c89c76SBlaise Bourdin for (cs = 0; cs < num_cs; ++cs) { 108649c89c76SBlaise Bourdin IS stratumIS; 108749c89c76SBlaise Bourdin const PetscInt *cells; 108849c89c76SBlaise Bourdin PetscInt csSize, c; 108949c89c76SBlaise Bourdin 109049c89c76SBlaise Bourdin PetscCall(DMLabelGetStratumIS(csLabel, csIdx[cs], &stratumIS)); 109149c89c76SBlaise Bourdin PetscCall(ISGetIndices(stratumIS, &cells)); 109249c89c76SBlaise Bourdin PetscCall(ISGetSize(stratumIS, &csSize)); 109349c89c76SBlaise Bourdin for (c = 0; c < csSize; ++c) PetscCall(PetscSectionSetDof(coordSection, cells[c], nodes[cs][3] > 0)); 109449c89c76SBlaise Bourdin PetscCall(ISRestoreIndices(stratumIS, &cells)); 109549c89c76SBlaise Bourdin PetscCall(ISDestroy(&stratumIS)); 109649c89c76SBlaise Bourdin } 109749c89c76SBlaise Bourdin if (num_cs) { 109849c89c76SBlaise Bourdin PetscCall(ISRestoreIndices(csIS, &csIdx)); 109949c89c76SBlaise Bourdin PetscCall(ISDestroy(&csIS)); 110049c89c76SBlaise Bourdin } 110149c89c76SBlaise Bourdin PetscCall(PetscFree(nodes)); 110249c89c76SBlaise Bourdin PetscCall(PetscSectionSetUp(coordSection)); 110349c89c76SBlaise Bourdin if (numNodes) { 110449c89c76SBlaise Bourdin const char *coordNames[3] = {"x", "y", "z"}; 110549c89c76SBlaise Bourdin PetscScalar *closure, *cval; 110649c89c76SBlaise Bourdin PetscReal *coords; 110749c89c76SBlaise Bourdin PetscInt hasDof, n = 0; 110849c89c76SBlaise Bourdin 110949c89c76SBlaise Bourdin /* There can't be more than 24 values in the closure of a point for the coord coordSection */ 111049c89c76SBlaise Bourdin PetscCall(PetscCalloc3(numNodes * 3, &coords, dim, &cval, 24, &closure)); 111149c89c76SBlaise Bourdin PetscCall(DMGetCoordinatesLocalNoncollective(dm, &coord)); 111249c89c76SBlaise Bourdin PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 111349c89c76SBlaise Bourdin for (p = pStart; p < pEnd; ++p) { 111449c89c76SBlaise Bourdin PetscCall(PetscSectionGetDof(coordSection, p, &hasDof)); 111549c89c76SBlaise Bourdin if (hasDof) { 111649c89c76SBlaise Bourdin PetscInt closureSize = 24, j; 111749c89c76SBlaise Bourdin 111849c89c76SBlaise Bourdin PetscCall(DMPlexVecGetClosure(cdm, NULL, coord, p, &closureSize, &closure)); 111949c89c76SBlaise Bourdin for (d = 0; d < dim; ++d) { 112049c89c76SBlaise Bourdin cval[d] = 0.0; 112149c89c76SBlaise Bourdin for (j = 0; j < closureSize / dim; j++) cval[d] += closure[j * dim + d]; 112249c89c76SBlaise Bourdin coords[d * numNodes + n] = PetscRealPart(cval[d]) * dim / closureSize; 112349c89c76SBlaise Bourdin } 112449c89c76SBlaise Bourdin ++n; 112549c89c76SBlaise Bourdin } 112649c89c76SBlaise Bourdin } 112749c89c76SBlaise Bourdin PetscCallExternal(ex_put_coord, exo->exoid, &coords[0 * numNodes], &coords[1 * numNodes], &coords[2 * numNodes]); 112849c89c76SBlaise Bourdin PetscCall(PetscFree3(coords, cval, closure)); 112949c89c76SBlaise Bourdin PetscCallExternal(ex_put_coord_names, exo->exoid, (char **)coordNames); 113049c89c76SBlaise Bourdin } 113149c89c76SBlaise Bourdin 113249c89c76SBlaise Bourdin /* --- Node Sets/Vertex Sets --- */ 113349c89c76SBlaise Bourdin PetscCall(DMHasLabel(dm, "Vertex Sets", &hasLabel)); 113449c89c76SBlaise Bourdin if (hasLabel) { 113549c89c76SBlaise Bourdin PetscInt i, vs, vsSize; 113649c89c76SBlaise Bourdin const PetscInt *vsIdx, *vertices; 113749c89c76SBlaise Bourdin PetscInt *nodeList; 113849c89c76SBlaise Bourdin IS vsIS, stratumIS; 113949c89c76SBlaise Bourdin DMLabel vsLabel; 114049c89c76SBlaise Bourdin PetscCall(DMGetLabel(dm, "Vertex Sets", &vsLabel)); 114149c89c76SBlaise Bourdin PetscCall(DMLabelGetValueIS(vsLabel, &vsIS)); 114249c89c76SBlaise Bourdin PetscCall(ISGetIndices(vsIS, &vsIdx)); 114349c89c76SBlaise Bourdin for (vs = 0; vs < num_vs; ++vs) { 114449c89c76SBlaise Bourdin PetscCall(DMLabelGetStratumIS(vsLabel, vsIdx[vs], &stratumIS)); 114549c89c76SBlaise Bourdin PetscCall(ISGetIndices(stratumIS, &vertices)); 114649c89c76SBlaise Bourdin PetscCall(ISGetSize(stratumIS, &vsSize)); 114749c89c76SBlaise Bourdin PetscCall(PetscMalloc1(vsSize, &nodeList)); 114849c89c76SBlaise Bourdin for (i = 0; i < vsSize; ++i) nodeList[i] = vertices[i] - skipCells + 1; 114949c89c76SBlaise Bourdin PetscCallExternal(ex_put_set_param, exo->exoid, EX_NODE_SET, vsIdx[vs], vsSize, 0); 115049c89c76SBlaise Bourdin PetscCallExternal(ex_put_set, exo->exoid, EX_NODE_SET, vsIdx[vs], nodeList, NULL); 115149c89c76SBlaise Bourdin PetscCall(ISRestoreIndices(stratumIS, &vertices)); 115249c89c76SBlaise Bourdin PetscCall(ISDestroy(&stratumIS)); 115349c89c76SBlaise Bourdin PetscCall(PetscFree(nodeList)); 115449c89c76SBlaise Bourdin } 115549c89c76SBlaise Bourdin PetscCall(ISRestoreIndices(vsIS, &vsIdx)); 115649c89c76SBlaise Bourdin PetscCall(ISDestroy(&vsIS)); 115749c89c76SBlaise Bourdin } 115849c89c76SBlaise Bourdin /* --- Side Sets/Face Sets --- */ 115949c89c76SBlaise Bourdin PetscCall(DMHasLabel(dm, "Face Sets", &hasLabel)); 116049c89c76SBlaise Bourdin if (hasLabel) { 116149c89c76SBlaise Bourdin PetscInt i, j, fs, fsSize; 116249c89c76SBlaise Bourdin const PetscInt *fsIdx, *faces; 116349c89c76SBlaise Bourdin IS fsIS, stratumIS; 116449c89c76SBlaise Bourdin DMLabel fsLabel; 116549c89c76SBlaise Bourdin PetscInt numPoints, *points; 116649c89c76SBlaise Bourdin PetscInt elem_list_size = 0; 116749c89c76SBlaise Bourdin PetscInt *elem_list, *elem_ind, *side_list; 116849c89c76SBlaise Bourdin 116949c89c76SBlaise Bourdin PetscCall(DMGetLabel(dm, "Face Sets", &fsLabel)); 117049c89c76SBlaise Bourdin /* Compute size of Node List and Element List */ 117149c89c76SBlaise Bourdin PetscCall(DMLabelGetValueIS(fsLabel, &fsIS)); 117249c89c76SBlaise Bourdin PetscCall(ISGetIndices(fsIS, &fsIdx)); 117349c89c76SBlaise Bourdin for (fs = 0; fs < num_fs; ++fs) { 117449c89c76SBlaise Bourdin PetscCall(DMLabelGetStratumIS(fsLabel, fsIdx[fs], &stratumIS)); 117549c89c76SBlaise Bourdin PetscCall(ISGetSize(stratumIS, &fsSize)); 117649c89c76SBlaise Bourdin elem_list_size += fsSize; 117749c89c76SBlaise Bourdin PetscCall(ISDestroy(&stratumIS)); 117849c89c76SBlaise Bourdin } 117949c89c76SBlaise Bourdin if (num_fs) { 118049c89c76SBlaise Bourdin PetscCall(PetscMalloc3(num_fs, &elem_ind, elem_list_size, &elem_list, elem_list_size, &side_list)); 118149c89c76SBlaise Bourdin elem_ind[0] = 0; 118249c89c76SBlaise Bourdin for (fs = 0; fs < num_fs; ++fs) { 118349c89c76SBlaise Bourdin PetscCall(DMLabelGetStratumIS(fsLabel, fsIdx[fs], &stratumIS)); 118449c89c76SBlaise Bourdin PetscCall(ISGetIndices(stratumIS, &faces)); 118549c89c76SBlaise Bourdin PetscCall(ISGetSize(stratumIS, &fsSize)); 118649c89c76SBlaise Bourdin /* Set Parameters */ 118749c89c76SBlaise Bourdin PetscCallExternal(ex_put_set_param, exo->exoid, EX_SIDE_SET, fsIdx[fs], fsSize, 0); 118849c89c76SBlaise Bourdin /* Indices */ 118949c89c76SBlaise Bourdin if (fs < num_fs - 1) elem_ind[fs + 1] = elem_ind[fs] + fsSize; 119049c89c76SBlaise Bourdin 119149c89c76SBlaise Bourdin for (i = 0; i < fsSize; ++i) { 119249c89c76SBlaise Bourdin /* Element List */ 119349c89c76SBlaise Bourdin points = NULL; 119449c89c76SBlaise Bourdin PetscCall(DMPlexGetTransitiveClosure(dm, faces[i], PETSC_FALSE, &numPoints, &points)); 119549c89c76SBlaise Bourdin elem_list[elem_ind[fs] + i] = points[2] + 1; 119649c89c76SBlaise Bourdin PetscCall(DMPlexRestoreTransitiveClosure(dm, faces[i], PETSC_FALSE, &numPoints, &points)); 119749c89c76SBlaise Bourdin 119849c89c76SBlaise Bourdin /* Side List */ 119949c89c76SBlaise Bourdin points = NULL; 120049c89c76SBlaise Bourdin PetscCall(DMPlexGetTransitiveClosure(dm, elem_list[elem_ind[fs] + i] - 1, PETSC_TRUE, &numPoints, &points)); 120149c89c76SBlaise Bourdin for (j = 1; j < numPoints; ++j) { 120249c89c76SBlaise Bourdin if (points[j * 2] == faces[i]) break; 120349c89c76SBlaise Bourdin } 120449c89c76SBlaise Bourdin /* Convert HEX sides */ 120549c89c76SBlaise Bourdin if (numPoints == 27) { 120649c89c76SBlaise Bourdin if (j == 1) { 120749c89c76SBlaise Bourdin j = 5; 120849c89c76SBlaise Bourdin } else if (j == 2) { 120949c89c76SBlaise Bourdin j = 6; 121049c89c76SBlaise Bourdin } else if (j == 3) { 121149c89c76SBlaise Bourdin j = 1; 121249c89c76SBlaise Bourdin } else if (j == 4) { 121349c89c76SBlaise Bourdin j = 3; 121449c89c76SBlaise Bourdin } else if (j == 5) { 121549c89c76SBlaise Bourdin j = 2; 121649c89c76SBlaise Bourdin } else if (j == 6) { 121749c89c76SBlaise Bourdin j = 4; 121849c89c76SBlaise Bourdin } 121949c89c76SBlaise Bourdin } 122049c89c76SBlaise Bourdin /* Convert TET sides */ 122149c89c76SBlaise Bourdin if (numPoints == 15) { 122249c89c76SBlaise Bourdin --j; 122349c89c76SBlaise Bourdin if (j == 0) j = 4; 122449c89c76SBlaise Bourdin } 122549c89c76SBlaise Bourdin side_list[elem_ind[fs] + i] = j; 122649c89c76SBlaise Bourdin PetscCall(DMPlexRestoreTransitiveClosure(dm, elem_list[elem_ind[fs] + i] - 1, PETSC_TRUE, &numPoints, &points)); 122749c89c76SBlaise Bourdin } 122849c89c76SBlaise Bourdin PetscCall(ISRestoreIndices(stratumIS, &faces)); 122949c89c76SBlaise Bourdin PetscCall(ISDestroy(&stratumIS)); 123049c89c76SBlaise Bourdin } 123149c89c76SBlaise Bourdin PetscCall(ISRestoreIndices(fsIS, &fsIdx)); 123249c89c76SBlaise Bourdin PetscCall(ISDestroy(&fsIS)); 123349c89c76SBlaise Bourdin 123449c89c76SBlaise Bourdin /* Put side sets */ 123549c89c76SBlaise Bourdin for (fs = 0; fs < num_fs; ++fs) PetscCallExternal(ex_put_set, exo->exoid, EX_SIDE_SET, fsIdx[fs], &elem_list[elem_ind[fs]], &side_list[elem_ind[fs]]); 123649c89c76SBlaise Bourdin PetscCall(PetscFree3(elem_ind, elem_list, side_list)); 123749c89c76SBlaise Bourdin } 123849c89c76SBlaise Bourdin } 123949c89c76SBlaise Bourdin /* 124049c89c76SBlaise Bourdin close the exodus file 124149c89c76SBlaise Bourdin */ 124249c89c76SBlaise Bourdin ex_close(exo->exoid); 124349c89c76SBlaise Bourdin exo->exoid = -1; 124449c89c76SBlaise Bourdin } 124549c89c76SBlaise Bourdin PetscCall(PetscSectionDestroy(&coordSection)); 124649c89c76SBlaise Bourdin 124749c89c76SBlaise Bourdin /* 124849c89c76SBlaise Bourdin reopen the file in parallel 124949c89c76SBlaise Bourdin */ 125049c89c76SBlaise Bourdin EXO_mode = EX_WRITE; 125149c89c76SBlaise Bourdin #if defined(PETSC_USE_64BIT_INDICES) 125249c89c76SBlaise Bourdin EXO_mode += EX_ALL_INT64_API; 125349c89c76SBlaise Bourdin #endif 125449c89c76SBlaise Bourdin CPU_word_size = sizeof(PetscReal); 125549c89c76SBlaise Bourdin IO_word_size = sizeof(PetscReal); 125649c89c76SBlaise Bourdin exo->exoid = ex_open_par(exo->filename, EXO_mode, &CPU_word_size, &IO_word_size, &EXO_version, comm, MPI_INFO_NULL); 125749c89c76SBlaise Bourdin PetscCheck(exo->exoid >= 0, PETSC_COMM_SELF, PETSC_ERR_LIB, "ex_open_par failed for %s", exo->filename); 125849c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 125949c89c76SBlaise Bourdin } 126049c89c76SBlaise Bourdin 12610a5cf5d8SBlaise Bourdin static PetscErrorCode VecViewPlex_ExodusII_Nodal_Internal(Vec v, PetscExodusIIInt exoid, PetscExodusIIInt step, PetscExodusIIInt offset); 12620a5cf5d8SBlaise Bourdin static PetscErrorCode VecViewPlex_ExodusII_Zonal_Internal(Vec v, PetscExodusIIInt exoid, PetscExodusIIInt step, PetscExodusIIInt offset); 12630a5cf5d8SBlaise Bourdin static PetscErrorCode VecLoadPlex_ExodusII_Nodal_Internal(Vec v, PetscExodusIIInt exoid, PetscExodusIIInt step, PetscExodusIIInt offset); 12640a5cf5d8SBlaise Bourdin static PetscErrorCode VecLoadPlex_ExodusII_Zonal_Internal(Vec v, PetscExodusIIInt exoid, PetscExodusIIInt step, PetscExodusIIInt offset); 126549c89c76SBlaise Bourdin 126649c89c76SBlaise Bourdin PetscErrorCode VecView_PlexExodusII_Internal(Vec v, PetscViewer viewer) 126749c89c76SBlaise Bourdin { 126849c89c76SBlaise Bourdin DM dm; 126949c89c76SBlaise Bourdin MPI_Comm comm; 127049c89c76SBlaise Bourdin PetscMPIInt rank; 127149c89c76SBlaise Bourdin 12720a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid, offsetN = -1, offsetZ = -1; 127349c89c76SBlaise Bourdin const char *vecname; 127449c89c76SBlaise Bourdin PetscInt step; 127549c89c76SBlaise Bourdin 127649c89c76SBlaise Bourdin PetscFunctionBegin; 127749c89c76SBlaise Bourdin PetscCall(PetscObjectGetComm((PetscObject)v, &comm)); 127849c89c76SBlaise Bourdin PetscCallMPI(MPI_Comm_rank(comm, &rank)); 127949c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 128049c89c76SBlaise Bourdin PetscCall(VecGetDM(v, &dm)); 128149c89c76SBlaise Bourdin PetscCall(PetscObjectGetName((PetscObject)v, &vecname)); 128249c89c76SBlaise Bourdin 128349c89c76SBlaise Bourdin PetscCall(DMGetOutputSequenceNumber(dm, &step, NULL)); 128449c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetNodalVariableIndex(viewer, vecname, &offsetN)); 128549c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetZonalVariableIndex(viewer, vecname, &offsetZ)); 128649c89c76SBlaise Bourdin PetscCheck(!(offsetN >= 0 && offsetZ >= 0), comm, PETSC_ERR_FILE_UNEXPECTED, "Found both nodal and zonal variable %s in exodus file. ", vecname); 128749c89c76SBlaise Bourdin if (offsetN >= 0) { 12880a5cf5d8SBlaise Bourdin PetscCall(VecViewPlex_ExodusII_Nodal_Internal(v, exoid, (PetscExodusIIInt)step + 1, offsetN + 1)); 128949c89c76SBlaise Bourdin } else if (offsetZ >= 0) { 12900a5cf5d8SBlaise Bourdin PetscCall(VecViewPlex_ExodusII_Zonal_Internal(v, exoid, (PetscExodusIIInt)step + 1, offsetZ + 1)); 129149c89c76SBlaise Bourdin } else SETERRQ(comm, PETSC_ERR_FILE_UNEXPECTED, "Could not find nodal or zonal variable %s in exodus file. ", vecname); 129249c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 129349c89c76SBlaise Bourdin } 129449c89c76SBlaise Bourdin 129549c89c76SBlaise Bourdin PetscErrorCode VecLoad_PlexExodusII_Internal(Vec v, PetscViewer viewer) 129649c89c76SBlaise Bourdin { 129749c89c76SBlaise Bourdin DM dm; 129849c89c76SBlaise Bourdin MPI_Comm comm; 129949c89c76SBlaise Bourdin PetscMPIInt rank; 130049c89c76SBlaise Bourdin 13010a5cf5d8SBlaise Bourdin PetscExodusIIInt exoid, offsetN = 0, offsetZ = 0; 130249c89c76SBlaise Bourdin const char *vecname; 130349c89c76SBlaise Bourdin PetscInt step; 130449c89c76SBlaise Bourdin 130549c89c76SBlaise Bourdin PetscFunctionBegin; 130649c89c76SBlaise Bourdin PetscCall(PetscObjectGetComm((PetscObject)v, &comm)); 130749c89c76SBlaise Bourdin PetscCallMPI(MPI_Comm_rank(comm, &rank)); 130849c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetId(viewer, &exoid)); 130949c89c76SBlaise Bourdin PetscCall(VecGetDM(v, &dm)); 131049c89c76SBlaise Bourdin PetscCall(PetscObjectGetName((PetscObject)v, &vecname)); 131149c89c76SBlaise Bourdin 131249c89c76SBlaise Bourdin PetscCall(DMGetOutputSequenceNumber(dm, &step, NULL)); 131349c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetNodalVariableIndex(viewer, vecname, &offsetN)); 131449c89c76SBlaise Bourdin PetscCall(PetscViewerExodusIIGetZonalVariableIndex(viewer, vecname, &offsetZ)); 131549c89c76SBlaise Bourdin PetscCheck(!(offsetN >= 0 && offsetZ >= 0), comm, PETSC_ERR_FILE_UNEXPECTED, "Found both nodal and zonal variable %s in exodus file. ", vecname); 13160a5cf5d8SBlaise Bourdin if (offsetN >= 0) PetscCall(VecLoadPlex_ExodusII_Nodal_Internal(v, exoid, (PetscExodusIIInt)step + 1, offsetN + 1)); 13170a5cf5d8SBlaise Bourdin else if (offsetZ >= 0) PetscCall(VecLoadPlex_ExodusII_Zonal_Internal(v, exoid, (PetscExodusIIInt)step + 1, offsetZ + 1)); 131849c89c76SBlaise Bourdin else SETERRQ(comm, PETSC_ERR_FILE_UNEXPECTED, "Could not find nodal or zonal variable %s in exodus file. ", vecname); 131949c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 132049c89c76SBlaise Bourdin } 132149c89c76SBlaise Bourdin 13220a5cf5d8SBlaise Bourdin static PetscErrorCode VecViewPlex_ExodusII_Nodal_Internal(Vec v, PetscExodusIIInt exoid, PetscExodusIIInt step, PetscExodusIIInt offset) 132349c89c76SBlaise Bourdin { 132449c89c76SBlaise Bourdin MPI_Comm comm; 132549c89c76SBlaise Bourdin PetscMPIInt size; 132649c89c76SBlaise Bourdin DM dm; 132749c89c76SBlaise Bourdin Vec vNatural, vComp; 132849c89c76SBlaise Bourdin const PetscScalar *varray; 132949c89c76SBlaise Bourdin PetscInt xs, xe, bs; 133049c89c76SBlaise Bourdin PetscBool useNatural; 133149c89c76SBlaise Bourdin 133249c89c76SBlaise Bourdin PetscFunctionBegin; 133349c89c76SBlaise Bourdin PetscCall(PetscObjectGetComm((PetscObject)v, &comm)); 133449c89c76SBlaise Bourdin PetscCallMPI(MPI_Comm_size(comm, &size)); 133549c89c76SBlaise Bourdin PetscCall(VecGetDM(v, &dm)); 133649c89c76SBlaise Bourdin PetscCall(DMGetUseNatural(dm, &useNatural)); 133749c89c76SBlaise Bourdin useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE; 133849c89c76SBlaise Bourdin if (useNatural) { 133949c89c76SBlaise Bourdin PetscCall(DMPlexCreateNaturalVector(dm, &vNatural)); 134049c89c76SBlaise Bourdin PetscCall(DMPlexGlobalToNaturalBegin(dm, v, vNatural)); 134149c89c76SBlaise Bourdin PetscCall(DMPlexGlobalToNaturalEnd(dm, v, vNatural)); 134249c89c76SBlaise Bourdin } else { 134349c89c76SBlaise Bourdin vNatural = v; 134449c89c76SBlaise Bourdin } 134549c89c76SBlaise Bourdin 134649c89c76SBlaise Bourdin /* Write local chunk of the result in the exodus file 134749c89c76SBlaise Bourdin exodus stores each component of a vector-valued field as a separate variable. 134849c89c76SBlaise Bourdin We assume that they are stored sequentially */ 134949c89c76SBlaise Bourdin PetscCall(VecGetOwnershipRange(vNatural, &xs, &xe)); 135049c89c76SBlaise Bourdin PetscCall(VecGetBlockSize(vNatural, &bs)); 135149c89c76SBlaise Bourdin if (bs == 1) { 135249c89c76SBlaise Bourdin PetscCall(VecGetArrayRead(vNatural, &varray)); 135349c89c76SBlaise Bourdin PetscCallExternal(ex_put_partial_var, exoid, step, EX_NODAL, offset, 1, xs + 1, xe - xs, varray); 135449c89c76SBlaise Bourdin PetscCall(VecRestoreArrayRead(vNatural, &varray)); 135549c89c76SBlaise Bourdin } else { 135649c89c76SBlaise Bourdin IS compIS; 135749c89c76SBlaise Bourdin PetscInt c; 135849c89c76SBlaise Bourdin 135949c89c76SBlaise Bourdin PetscCall(ISCreateStride(comm, (xe - xs) / bs, xs, bs, &compIS)); 136049c89c76SBlaise Bourdin for (c = 0; c < bs; ++c) { 136149c89c76SBlaise Bourdin PetscCall(ISStrideSetStride(compIS, (xe - xs) / bs, xs + c, bs)); 136249c89c76SBlaise Bourdin PetscCall(VecGetSubVector(vNatural, compIS, &vComp)); 136349c89c76SBlaise Bourdin PetscCall(VecGetArrayRead(vComp, &varray)); 136449c89c76SBlaise Bourdin PetscCallExternal(ex_put_partial_var, exoid, step, EX_NODAL, offset + c, 1, xs / bs + 1, (xe - xs) / bs, varray); 136549c89c76SBlaise Bourdin PetscCall(VecRestoreArrayRead(vComp, &varray)); 136649c89c76SBlaise Bourdin PetscCall(VecRestoreSubVector(vNatural, compIS, &vComp)); 136749c89c76SBlaise Bourdin } 136849c89c76SBlaise Bourdin PetscCall(ISDestroy(&compIS)); 136949c89c76SBlaise Bourdin } 137049c89c76SBlaise Bourdin if (useNatural) PetscCall(VecDestroy(&vNatural)); 137149c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 137249c89c76SBlaise Bourdin } 137349c89c76SBlaise Bourdin 13740a5cf5d8SBlaise Bourdin static PetscErrorCode VecLoadPlex_ExodusII_Nodal_Internal(Vec v, PetscExodusIIInt exoid, PetscExodusIIInt step, PetscExodusIIInt offset) 137549c89c76SBlaise Bourdin { 137649c89c76SBlaise Bourdin MPI_Comm comm; 137749c89c76SBlaise Bourdin PetscMPIInt size; 137849c89c76SBlaise Bourdin DM dm; 137949c89c76SBlaise Bourdin Vec vNatural, vComp; 138049c89c76SBlaise Bourdin PetscScalar *varray; 138149c89c76SBlaise Bourdin PetscInt xs, xe, bs; 138249c89c76SBlaise Bourdin PetscBool useNatural; 138349c89c76SBlaise Bourdin 138449c89c76SBlaise Bourdin PetscFunctionBegin; 138549c89c76SBlaise Bourdin PetscCall(PetscObjectGetComm((PetscObject)v, &comm)); 138649c89c76SBlaise Bourdin PetscCallMPI(MPI_Comm_size(comm, &size)); 138749c89c76SBlaise Bourdin PetscCall(VecGetDM(v, &dm)); 138849c89c76SBlaise Bourdin PetscCall(DMGetUseNatural(dm, &useNatural)); 138949c89c76SBlaise Bourdin useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE; 139049c89c76SBlaise Bourdin if (useNatural) PetscCall(DMPlexCreateNaturalVector(dm, &vNatural)); 139149c89c76SBlaise Bourdin else vNatural = v; 139249c89c76SBlaise Bourdin 139349c89c76SBlaise Bourdin /* Read local chunk from the file */ 139449c89c76SBlaise Bourdin PetscCall(VecGetOwnershipRange(vNatural, &xs, &xe)); 139549c89c76SBlaise Bourdin PetscCall(VecGetBlockSize(vNatural, &bs)); 139649c89c76SBlaise Bourdin if (bs == 1) { 139749c89c76SBlaise Bourdin PetscCall(VecGetArray(vNatural, &varray)); 139849c89c76SBlaise Bourdin PetscCallExternal(ex_get_partial_var, exoid, step, EX_NODAL, offset, 1, xs + 1, xe - xs, varray); 139949c89c76SBlaise Bourdin PetscCall(VecRestoreArray(vNatural, &varray)); 140049c89c76SBlaise Bourdin } else { 140149c89c76SBlaise Bourdin IS compIS; 140249c89c76SBlaise Bourdin PetscInt c; 140349c89c76SBlaise Bourdin 140449c89c76SBlaise Bourdin PetscCall(ISCreateStride(comm, (xe - xs) / bs, xs, bs, &compIS)); 140549c89c76SBlaise Bourdin for (c = 0; c < bs; ++c) { 140649c89c76SBlaise Bourdin PetscCall(ISStrideSetStride(compIS, (xe - xs) / bs, xs + c, bs)); 140749c89c76SBlaise Bourdin PetscCall(VecGetSubVector(vNatural, compIS, &vComp)); 140849c89c76SBlaise Bourdin PetscCall(VecGetArray(vComp, &varray)); 140949c89c76SBlaise Bourdin PetscCallExternal(ex_get_partial_var, exoid, step, EX_NODAL, offset + c, 1, xs / bs + 1, (xe - xs) / bs, varray); 141049c89c76SBlaise Bourdin PetscCall(VecRestoreArray(vComp, &varray)); 141149c89c76SBlaise Bourdin PetscCall(VecRestoreSubVector(vNatural, compIS, &vComp)); 141249c89c76SBlaise Bourdin } 141349c89c76SBlaise Bourdin PetscCall(ISDestroy(&compIS)); 141449c89c76SBlaise Bourdin } 141549c89c76SBlaise Bourdin if (useNatural) { 141649c89c76SBlaise Bourdin PetscCall(DMPlexNaturalToGlobalBegin(dm, vNatural, v)); 141749c89c76SBlaise Bourdin PetscCall(DMPlexNaturalToGlobalEnd(dm, vNatural, v)); 141849c89c76SBlaise Bourdin PetscCall(VecDestroy(&vNatural)); 141949c89c76SBlaise Bourdin } 142049c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 142149c89c76SBlaise Bourdin } 142249c89c76SBlaise Bourdin 14230a5cf5d8SBlaise Bourdin static PetscErrorCode VecViewPlex_ExodusII_Zonal_Internal(Vec v, PetscExodusIIInt exoid, PetscExodusIIInt step, PetscExodusIIInt offset) 142449c89c76SBlaise Bourdin { 142549c89c76SBlaise Bourdin MPI_Comm comm; 142649c89c76SBlaise Bourdin PetscMPIInt size; 142749c89c76SBlaise Bourdin DM dm; 142849c89c76SBlaise Bourdin Vec vNatural, vComp; 142949c89c76SBlaise Bourdin const PetscScalar *varray; 143049c89c76SBlaise Bourdin PetscInt xs, xe, bs; 143149c89c76SBlaise Bourdin PetscBool useNatural; 143249c89c76SBlaise Bourdin IS compIS; 143349c89c76SBlaise Bourdin PetscInt *csSize, *csID; 14340a5cf5d8SBlaise Bourdin PetscExodusIIInt numCS, set, csxs = 0; 143549c89c76SBlaise Bourdin 143649c89c76SBlaise Bourdin PetscFunctionBegin; 143749c89c76SBlaise Bourdin PetscCall(PetscObjectGetComm((PetscObject)v, &comm)); 143849c89c76SBlaise Bourdin PetscCallMPI(MPI_Comm_size(comm, &size)); 143949c89c76SBlaise Bourdin PetscCall(VecGetDM(v, &dm)); 144049c89c76SBlaise Bourdin PetscCall(DMGetUseNatural(dm, &useNatural)); 144149c89c76SBlaise Bourdin useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE; 144249c89c76SBlaise Bourdin if (useNatural) { 144349c89c76SBlaise Bourdin PetscCall(DMPlexCreateNaturalVector(dm, &vNatural)); 144449c89c76SBlaise Bourdin PetscCall(DMPlexGlobalToNaturalBegin(dm, v, vNatural)); 144549c89c76SBlaise Bourdin PetscCall(DMPlexGlobalToNaturalEnd(dm, v, vNatural)); 144649c89c76SBlaise Bourdin } else { 144749c89c76SBlaise Bourdin vNatural = v; 144849c89c76SBlaise Bourdin } 144949c89c76SBlaise Bourdin 145049c89c76SBlaise Bourdin /* Write local chunk of the result in the exodus file 145149c89c76SBlaise Bourdin exodus stores each component of a vector-valued field as a separate variable. 145249c89c76SBlaise Bourdin We assume that they are stored sequentially 145349c89c76SBlaise Bourdin Zonal variables are accessed one element block at a time, so we loop through the cell sets, 145449c89c76SBlaise Bourdin but once the vector has been reordered to natural size, we cannot use the label information 145549c89c76SBlaise Bourdin to figure out what to save where. */ 14568a1c49cdSMatthew G. Knepley numCS = (PetscExodusIIInt)ex_inquire_int(exoid, EX_INQ_ELEM_BLK); // This is an int64_t 145749c89c76SBlaise Bourdin PetscCall(PetscMalloc2(numCS, &csID, numCS, &csSize)); 145849c89c76SBlaise Bourdin PetscCallExternal(ex_get_ids, exoid, EX_ELEM_BLOCK, csID); 145949c89c76SBlaise Bourdin for (set = 0; set < numCS; ++set) { 146049c89c76SBlaise Bourdin ex_block block; 146149c89c76SBlaise Bourdin 146249c89c76SBlaise Bourdin block.id = csID[set]; 146349c89c76SBlaise Bourdin block.type = EX_ELEM_BLOCK; 146449c89c76SBlaise Bourdin PetscCallExternal(ex_get_block_param, exoid, &block); 146562e4c2b1SMatthew G. Knepley PetscCall(PetscIntCast(block.num_entry, &csSize[set])); // This is an int64_t 146649c89c76SBlaise Bourdin } 146749c89c76SBlaise Bourdin PetscCall(VecGetOwnershipRange(vNatural, &xs, &xe)); 146849c89c76SBlaise Bourdin PetscCall(VecGetBlockSize(vNatural, &bs)); 146949c89c76SBlaise Bourdin if (bs > 1) PetscCall(ISCreateStride(comm, (xe - xs) / bs, xs, bs, &compIS)); 147049c89c76SBlaise Bourdin for (set = 0; set < numCS; set++) { 147149c89c76SBlaise Bourdin PetscInt csLocalSize, c; 147249c89c76SBlaise Bourdin 147349c89c76SBlaise Bourdin /* range of indices for set setID[set]: csxs:csxs + csSize[set]-1 147449c89c76SBlaise Bourdin local slice of zonal values: xs/bs,xm/bs-1 147549c89c76SBlaise Bourdin intersection: max(xs/bs,csxs),min(xm/bs-1,csxs + csSize[set]-1) */ 147649c89c76SBlaise Bourdin csLocalSize = PetscMax(0, PetscMin(xe / bs, csxs + csSize[set]) - PetscMax(xs / bs, csxs)); 147749c89c76SBlaise Bourdin if (bs == 1) { 147849c89c76SBlaise Bourdin PetscCall(VecGetArrayRead(vNatural, &varray)); 147949c89c76SBlaise Bourdin PetscCallExternal(ex_put_partial_var, exoid, step, EX_ELEM_BLOCK, offset, csID[set], PetscMax(xs - csxs, 0) + 1, csLocalSize, &varray[PetscMax(0, csxs - xs)]); 148049c89c76SBlaise Bourdin PetscCall(VecRestoreArrayRead(vNatural, &varray)); 148149c89c76SBlaise Bourdin } else { 148249c89c76SBlaise Bourdin for (c = 0; c < bs; ++c) { 148349c89c76SBlaise Bourdin PetscCall(ISStrideSetStride(compIS, (xe - xs) / bs, xs + c, bs)); 148449c89c76SBlaise Bourdin PetscCall(VecGetSubVector(vNatural, compIS, &vComp)); 148549c89c76SBlaise Bourdin PetscCall(VecGetArrayRead(vComp, &varray)); 148649c89c76SBlaise Bourdin PetscCallExternal(ex_put_partial_var, exoid, step, EX_ELEM_BLOCK, offset + c, csID[set], PetscMax(xs / bs - csxs, 0) + 1, csLocalSize, &varray[PetscMax(0, csxs - xs / bs)]); 148749c89c76SBlaise Bourdin PetscCall(VecRestoreArrayRead(vComp, &varray)); 148849c89c76SBlaise Bourdin PetscCall(VecRestoreSubVector(vNatural, compIS, &vComp)); 148949c89c76SBlaise Bourdin } 149049c89c76SBlaise Bourdin } 149149c89c76SBlaise Bourdin csxs += csSize[set]; 149249c89c76SBlaise Bourdin } 149349c89c76SBlaise Bourdin PetscCall(PetscFree2(csID, csSize)); 149449c89c76SBlaise Bourdin if (bs > 1) PetscCall(ISDestroy(&compIS)); 149549c89c76SBlaise Bourdin if (useNatural) PetscCall(VecDestroy(&vNatural)); 149649c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 149749c89c76SBlaise Bourdin } 149849c89c76SBlaise Bourdin 14990a5cf5d8SBlaise Bourdin static PetscErrorCode VecLoadPlex_ExodusII_Zonal_Internal(Vec v, PetscExodusIIInt exoid, PetscExodusIIInt step, PetscExodusIIInt offset) 150049c89c76SBlaise Bourdin { 150149c89c76SBlaise Bourdin MPI_Comm comm; 150249c89c76SBlaise Bourdin PetscMPIInt size; 150349c89c76SBlaise Bourdin DM dm; 150449c89c76SBlaise Bourdin Vec vNatural, vComp; 150549c89c76SBlaise Bourdin PetscScalar *varray; 150649c89c76SBlaise Bourdin PetscInt xs, xe, bs; 150749c89c76SBlaise Bourdin PetscBool useNatural; 150849c89c76SBlaise Bourdin IS compIS; 150949c89c76SBlaise Bourdin PetscInt *csSize, *csID; 15100a5cf5d8SBlaise Bourdin PetscExodusIIInt numCS, set, csxs = 0; 151149c89c76SBlaise Bourdin 151249c89c76SBlaise Bourdin PetscFunctionBegin; 151349c89c76SBlaise Bourdin PetscCall(PetscObjectGetComm((PetscObject)v, &comm)); 151449c89c76SBlaise Bourdin PetscCallMPI(MPI_Comm_size(comm, &size)); 151549c89c76SBlaise Bourdin PetscCall(VecGetDM(v, &dm)); 151649c89c76SBlaise Bourdin PetscCall(DMGetUseNatural(dm, &useNatural)); 151749c89c76SBlaise Bourdin useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE; 151849c89c76SBlaise Bourdin if (useNatural) PetscCall(DMPlexCreateNaturalVector(dm, &vNatural)); 151949c89c76SBlaise Bourdin else vNatural = v; 152049c89c76SBlaise Bourdin 152149c89c76SBlaise Bourdin /* Read local chunk of the result in the exodus file 152249c89c76SBlaise Bourdin exodus stores each component of a vector-valued field as a separate variable. 152349c89c76SBlaise Bourdin We assume that they are stored sequentially 152449c89c76SBlaise Bourdin Zonal variables are accessed one element block at a time, so we loop through the cell sets, 152549c89c76SBlaise Bourdin but once the vector has been reordered to natural size, we cannot use the label information 152649c89c76SBlaise Bourdin to figure out what to save where. */ 15278a1c49cdSMatthew G. Knepley numCS = (PetscExodusIIInt)ex_inquire_int(exoid, EX_INQ_ELEM_BLK); // This is an int64_t 152849c89c76SBlaise Bourdin PetscCall(PetscMalloc2(numCS, &csID, numCS, &csSize)); 152949c89c76SBlaise Bourdin PetscCallExternal(ex_get_ids, exoid, EX_ELEM_BLOCK, csID); 153049c89c76SBlaise Bourdin for (set = 0; set < numCS; ++set) { 153149c89c76SBlaise Bourdin ex_block block; 153249c89c76SBlaise Bourdin 153349c89c76SBlaise Bourdin block.id = csID[set]; 153449c89c76SBlaise Bourdin block.type = EX_ELEM_BLOCK; 153549c89c76SBlaise Bourdin PetscCallExternal(ex_get_block_param, exoid, &block); 153662e4c2b1SMatthew G. Knepley PetscCall(PetscIntCast(block.num_entry, &csSize[set])); // This is an int64_t 153749c89c76SBlaise Bourdin } 153849c89c76SBlaise Bourdin PetscCall(VecGetOwnershipRange(vNatural, &xs, &xe)); 153949c89c76SBlaise Bourdin PetscCall(VecGetBlockSize(vNatural, &bs)); 154049c89c76SBlaise Bourdin if (bs > 1) PetscCall(ISCreateStride(comm, (xe - xs) / bs, xs, bs, &compIS)); 154149c89c76SBlaise Bourdin for (set = 0; set < numCS; ++set) { 154249c89c76SBlaise Bourdin PetscInt csLocalSize, c; 154349c89c76SBlaise Bourdin 154449c89c76SBlaise Bourdin /* range of indices for set setID[set]: csxs:csxs + csSize[set]-1 154549c89c76SBlaise Bourdin local slice of zonal values: xs/bs,xm/bs-1 154649c89c76SBlaise Bourdin intersection: max(xs/bs,csxs),min(xm/bs-1,csxs + csSize[set]-1) */ 154749c89c76SBlaise Bourdin csLocalSize = PetscMax(0, PetscMin(xe / bs, csxs + csSize[set]) - PetscMax(xs / bs, csxs)); 154849c89c76SBlaise Bourdin if (bs == 1) { 154949c89c76SBlaise Bourdin PetscCall(VecGetArray(vNatural, &varray)); 155049c89c76SBlaise Bourdin PetscCallExternal(ex_get_partial_var, exoid, step, EX_ELEM_BLOCK, offset, csID[set], PetscMax(xs - csxs, 0) + 1, csLocalSize, &varray[PetscMax(0, csxs - xs)]); 155149c89c76SBlaise Bourdin PetscCall(VecRestoreArray(vNatural, &varray)); 155249c89c76SBlaise Bourdin } else { 155349c89c76SBlaise Bourdin for (c = 0; c < bs; ++c) { 155449c89c76SBlaise Bourdin PetscCall(ISStrideSetStride(compIS, (xe - xs) / bs, xs + c, bs)); 155549c89c76SBlaise Bourdin PetscCall(VecGetSubVector(vNatural, compIS, &vComp)); 155649c89c76SBlaise Bourdin PetscCall(VecGetArray(vComp, &varray)); 155749c89c76SBlaise Bourdin PetscCallExternal(ex_get_partial_var, exoid, step, EX_ELEM_BLOCK, offset + c, csID[set], PetscMax(xs / bs - csxs, 0) + 1, csLocalSize, &varray[PetscMax(0, csxs - xs / bs)]); 155849c89c76SBlaise Bourdin PetscCall(VecRestoreArray(vComp, &varray)); 155949c89c76SBlaise Bourdin PetscCall(VecRestoreSubVector(vNatural, compIS, &vComp)); 156049c89c76SBlaise Bourdin } 156149c89c76SBlaise Bourdin } 156249c89c76SBlaise Bourdin csxs += csSize[set]; 156349c89c76SBlaise Bourdin } 156449c89c76SBlaise Bourdin PetscCall(PetscFree2(csID, csSize)); 156549c89c76SBlaise Bourdin if (bs > 1) PetscCall(ISDestroy(&compIS)); 156649c89c76SBlaise Bourdin if (useNatural) { 156749c89c76SBlaise Bourdin PetscCall(DMPlexNaturalToGlobalBegin(dm, vNatural, v)); 156849c89c76SBlaise Bourdin PetscCall(DMPlexNaturalToGlobalEnd(dm, vNatural, v)); 156949c89c76SBlaise Bourdin PetscCall(VecDestroy(&vNatural)); 157049c89c76SBlaise Bourdin } 157149c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 157249c89c76SBlaise Bourdin } 157349c89c76SBlaise Bourdin 157449c89c76SBlaise Bourdin static PetscErrorCode ExodusGetCellType_Internal(const char *elem_type, DMPolytopeType *ct) 157549c89c76SBlaise Bourdin { 157649c89c76SBlaise Bourdin PetscBool flg; 157749c89c76SBlaise Bourdin 157849c89c76SBlaise Bourdin PetscFunctionBegin; 157949c89c76SBlaise Bourdin *ct = DM_POLYTOPE_UNKNOWN; 158049c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "BAR2", &flg)); 158149c89c76SBlaise Bourdin if (flg) { 158249c89c76SBlaise Bourdin *ct = DM_POLYTOPE_SEGMENT; 158349c89c76SBlaise Bourdin goto done; 158449c89c76SBlaise Bourdin } 158549c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "BAR3", &flg)); 158649c89c76SBlaise Bourdin if (flg) { 158749c89c76SBlaise Bourdin *ct = DM_POLYTOPE_SEGMENT; 158849c89c76SBlaise Bourdin goto done; 158949c89c76SBlaise Bourdin } 159049c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "TRI", &flg)); 159149c89c76SBlaise Bourdin if (flg) { 159249c89c76SBlaise Bourdin *ct = DM_POLYTOPE_TRIANGLE; 159349c89c76SBlaise Bourdin goto done; 159449c89c76SBlaise Bourdin } 159549c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "TRI3", &flg)); 159649c89c76SBlaise Bourdin if (flg) { 159749c89c76SBlaise Bourdin *ct = DM_POLYTOPE_TRIANGLE; 159849c89c76SBlaise Bourdin goto done; 159949c89c76SBlaise Bourdin } 160049c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "QUAD", &flg)); 160149c89c76SBlaise Bourdin if (flg) { 160249c89c76SBlaise Bourdin *ct = DM_POLYTOPE_QUADRILATERAL; 160349c89c76SBlaise Bourdin goto done; 160449c89c76SBlaise Bourdin } 160549c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "QUAD4", &flg)); 160649c89c76SBlaise Bourdin if (flg) { 160749c89c76SBlaise Bourdin *ct = DM_POLYTOPE_QUADRILATERAL; 160849c89c76SBlaise Bourdin goto done; 160949c89c76SBlaise Bourdin } 161049c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "SHELL4", &flg)); 161149c89c76SBlaise Bourdin if (flg) { 161249c89c76SBlaise Bourdin *ct = DM_POLYTOPE_QUADRILATERAL; 161349c89c76SBlaise Bourdin goto done; 161449c89c76SBlaise Bourdin } 161549c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "TETRA", &flg)); 161649c89c76SBlaise Bourdin if (flg) { 161749c89c76SBlaise Bourdin *ct = DM_POLYTOPE_TETRAHEDRON; 161849c89c76SBlaise Bourdin goto done; 161949c89c76SBlaise Bourdin } 162049c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "TET4", &flg)); 162149c89c76SBlaise Bourdin if (flg) { 162249c89c76SBlaise Bourdin *ct = DM_POLYTOPE_TETRAHEDRON; 162349c89c76SBlaise Bourdin goto done; 162449c89c76SBlaise Bourdin } 162549c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "WEDGE", &flg)); 162649c89c76SBlaise Bourdin if (flg) { 162749c89c76SBlaise Bourdin *ct = DM_POLYTOPE_TRI_PRISM; 162849c89c76SBlaise Bourdin goto done; 162949c89c76SBlaise Bourdin } 163049c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "HEX", &flg)); 163149c89c76SBlaise Bourdin if (flg) { 163249c89c76SBlaise Bourdin *ct = DM_POLYTOPE_HEXAHEDRON; 163349c89c76SBlaise Bourdin goto done; 163449c89c76SBlaise Bourdin } 163549c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "HEX8", &flg)); 163649c89c76SBlaise Bourdin if (flg) { 163749c89c76SBlaise Bourdin *ct = DM_POLYTOPE_HEXAHEDRON; 163849c89c76SBlaise Bourdin goto done; 163949c89c76SBlaise Bourdin } 164049c89c76SBlaise Bourdin PetscCall(PetscStrcmp(elem_type, "HEXAHEDRON", &flg)); 164149c89c76SBlaise Bourdin if (flg) { 164249c89c76SBlaise Bourdin *ct = DM_POLYTOPE_HEXAHEDRON; 164349c89c76SBlaise Bourdin goto done; 164449c89c76SBlaise Bourdin } 164549c89c76SBlaise Bourdin SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unrecognized element type %s", elem_type); 164649c89c76SBlaise Bourdin done: 164749c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 164849c89c76SBlaise Bourdin } 164949c89c76SBlaise Bourdin 165049c89c76SBlaise Bourdin /*@ 165149c89c76SBlaise Bourdin DMPlexCreateExodus - Create a `DMPLEX` mesh from an ExodusII file ID. 165249c89c76SBlaise Bourdin 165349c89c76SBlaise Bourdin Collective 165449c89c76SBlaise Bourdin 165549c89c76SBlaise Bourdin Input Parameters: 165649c89c76SBlaise Bourdin + comm - The MPI communicator 165749c89c76SBlaise Bourdin . exoid - The ExodusII id associated with a exodus file and obtained using ex_open 165849c89c76SBlaise Bourdin - interpolate - Create faces and edges in the mesh 165949c89c76SBlaise Bourdin 166049c89c76SBlaise Bourdin Output Parameter: 166149c89c76SBlaise Bourdin . dm - The `DM` object representing the mesh 166249c89c76SBlaise Bourdin 166349c89c76SBlaise Bourdin Level: beginner 166449c89c76SBlaise Bourdin 166549c89c76SBlaise Bourdin .seealso: [](ch_unstructured), `DM`, `PETSCVIEWEREXODUSII`, `DMPLEX`, `DMCreate()` 166649c89c76SBlaise Bourdin @*/ 16670a5cf5d8SBlaise Bourdin PetscErrorCode DMPlexCreateExodus(MPI_Comm comm, PetscExodusIIInt exoid, PetscBool interpolate, DM *dm) 166849c89c76SBlaise Bourdin { 166949c89c76SBlaise Bourdin PetscMPIInt num_proc, rank; 167049c89c76SBlaise Bourdin DMLabel cellSets = NULL, faceSets = NULL, vertSets = NULL; 167149c89c76SBlaise Bourdin PetscSection coordSection; 167249c89c76SBlaise Bourdin Vec coordinates; 167349c89c76SBlaise Bourdin PetscScalar *coords; 167449c89c76SBlaise Bourdin PetscInt coordSize, v; 167549c89c76SBlaise Bourdin /* Read from ex_get_init() */ 167649c89c76SBlaise Bourdin char title[PETSC_MAX_PATH_LEN + 1]; 167749c89c76SBlaise Bourdin int dim = 0, dimEmbed = 0, numVertices = 0, numCells = 0; 167849c89c76SBlaise Bourdin int num_cs = 0, num_vs = 0, num_fs = 0; 167949c89c76SBlaise Bourdin 168049c89c76SBlaise Bourdin PetscFunctionBegin; 168149c89c76SBlaise Bourdin PetscCallMPI(MPI_Comm_rank(comm, &rank)); 168249c89c76SBlaise Bourdin PetscCallMPI(MPI_Comm_size(comm, &num_proc)); 168349c89c76SBlaise Bourdin PetscCall(DMCreate(comm, dm)); 168449c89c76SBlaise Bourdin PetscCall(DMSetType(*dm, DMPLEX)); 168549c89c76SBlaise Bourdin /* Open EXODUS II file and read basic information on rank 0, then broadcast to all processors */ 168649c89c76SBlaise Bourdin if (rank == 0) { 168749c89c76SBlaise Bourdin PetscCall(PetscMemzero(title, PETSC_MAX_PATH_LEN + 1)); 168849c89c76SBlaise Bourdin PetscCallExternal(ex_get_init, exoid, title, &dimEmbed, &numVertices, &numCells, &num_cs, &num_vs, &num_fs); 168949c89c76SBlaise Bourdin PetscCheck(num_cs, PETSC_COMM_SELF, PETSC_ERR_SUP, "Exodus file does not contain any cell set"); 169049c89c76SBlaise Bourdin } 169149c89c76SBlaise Bourdin PetscCallMPI(MPI_Bcast(title, PETSC_MAX_PATH_LEN + 1, MPI_CHAR, 0, comm)); 169249c89c76SBlaise Bourdin PetscCallMPI(MPI_Bcast(&dim, 1, MPI_INT, 0, comm)); 169349c89c76SBlaise Bourdin PetscCall(PetscObjectSetName((PetscObject)*dm, title)); 169449c89c76SBlaise Bourdin PetscCall(DMPlexSetChart(*dm, 0, numCells + numVertices)); 169549c89c76SBlaise Bourdin /* We do not want this label automatically computed, instead we compute it here */ 169649c89c76SBlaise Bourdin PetscCall(DMCreateLabel(*dm, "celltype")); 169749c89c76SBlaise Bourdin 169849c89c76SBlaise Bourdin /* Read cell sets information */ 169949c89c76SBlaise Bourdin if (rank == 0) { 170049c89c76SBlaise Bourdin PetscInt *cone; 170149c89c76SBlaise Bourdin int c, cs, ncs, c_loc, v, v_loc; 170249c89c76SBlaise Bourdin /* Read from ex_get_elem_blk_ids() */ 170349c89c76SBlaise Bourdin int *cs_id, *cs_order; 170449c89c76SBlaise Bourdin /* Read from ex_get_elem_block() */ 170549c89c76SBlaise Bourdin char buffer[PETSC_MAX_PATH_LEN + 1]; 170649c89c76SBlaise Bourdin int num_cell_in_set, num_vertex_per_cell, num_hybrid, num_attr; 170749c89c76SBlaise Bourdin /* Read from ex_get_elem_conn() */ 170849c89c76SBlaise Bourdin int *cs_connect; 170949c89c76SBlaise Bourdin 171049c89c76SBlaise Bourdin /* Get cell sets IDs */ 171149c89c76SBlaise Bourdin PetscCall(PetscMalloc2(num_cs, &cs_id, num_cs, &cs_order)); 171249c89c76SBlaise Bourdin PetscCallExternal(ex_get_ids, exoid, EX_ELEM_BLOCK, cs_id); 171349c89c76SBlaise Bourdin /* Read the cell set connectivity table and build mesh topology 171449c89c76SBlaise Bourdin EXO standard requires that cells in cell sets be numbered sequentially and be pairwise disjoint. */ 171549c89c76SBlaise Bourdin /* Check for a hybrid mesh */ 171649c89c76SBlaise Bourdin for (cs = 0, num_hybrid = 0; cs < num_cs; ++cs) { 171749c89c76SBlaise Bourdin DMPolytopeType ct; 171849c89c76SBlaise Bourdin char elem_type[PETSC_MAX_PATH_LEN]; 171949c89c76SBlaise Bourdin 172049c89c76SBlaise Bourdin PetscCall(PetscArrayzero(elem_type, sizeof(elem_type))); 172149c89c76SBlaise Bourdin PetscCallExternal(ex_get_elem_type, exoid, cs_id[cs], elem_type); 172249c89c76SBlaise Bourdin PetscCall(ExodusGetCellType_Internal(elem_type, &ct)); 172349c89c76SBlaise Bourdin dim = PetscMax(dim, DMPolytopeTypeGetDim(ct)); 172449c89c76SBlaise Bourdin PetscCallExternal(ex_get_block, exoid, EX_ELEM_BLOCK, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, 0, 0, &num_attr); 172549c89c76SBlaise Bourdin switch (ct) { 172649c89c76SBlaise Bourdin case DM_POLYTOPE_TRI_PRISM: 172749c89c76SBlaise Bourdin cs_order[cs] = cs; 172849c89c76SBlaise Bourdin ++num_hybrid; 172949c89c76SBlaise Bourdin break; 173049c89c76SBlaise Bourdin default: 173149c89c76SBlaise Bourdin for (c = cs; c > cs - num_hybrid; --c) cs_order[c] = cs_order[c - 1]; 173249c89c76SBlaise Bourdin cs_order[cs - num_hybrid] = cs; 173349c89c76SBlaise Bourdin } 173449c89c76SBlaise Bourdin } 173549c89c76SBlaise Bourdin /* First set sizes */ 173649c89c76SBlaise Bourdin for (ncs = 0, c = 0; ncs < num_cs; ++ncs) { 173749c89c76SBlaise Bourdin DMPolytopeType ct; 173849c89c76SBlaise Bourdin char elem_type[PETSC_MAX_PATH_LEN]; 173949c89c76SBlaise Bourdin const PetscInt cs = cs_order[ncs]; 174049c89c76SBlaise Bourdin 174149c89c76SBlaise Bourdin PetscCall(PetscArrayzero(elem_type, sizeof(elem_type))); 174249c89c76SBlaise Bourdin PetscCallExternal(ex_get_elem_type, exoid, cs_id[cs], elem_type); 174349c89c76SBlaise Bourdin PetscCall(ExodusGetCellType_Internal(elem_type, &ct)); 174449c89c76SBlaise Bourdin PetscCallExternal(ex_get_block, exoid, EX_ELEM_BLOCK, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, 0, 0, &num_attr); 174549c89c76SBlaise Bourdin for (c_loc = 0; c_loc < num_cell_in_set; ++c_loc, ++c) { 174649c89c76SBlaise Bourdin PetscCall(DMPlexSetConeSize(*dm, c, num_vertex_per_cell)); 174749c89c76SBlaise Bourdin PetscCall(DMPlexSetCellType(*dm, c, ct)); 174849c89c76SBlaise Bourdin } 174949c89c76SBlaise Bourdin } 175049c89c76SBlaise Bourdin for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT)); 175149c89c76SBlaise Bourdin PetscCall(DMSetUp(*dm)); 175249c89c76SBlaise Bourdin for (ncs = 0, c = 0; ncs < num_cs; ++ncs) { 175349c89c76SBlaise Bourdin const PetscInt cs = cs_order[ncs]; 175449c89c76SBlaise Bourdin PetscCallExternal(ex_get_block, exoid, EX_ELEM_BLOCK, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, 0, 0, &num_attr); 175549c89c76SBlaise Bourdin PetscCall(PetscMalloc2(num_vertex_per_cell * num_cell_in_set, &cs_connect, num_vertex_per_cell, &cone)); 175649c89c76SBlaise Bourdin PetscCallExternal(ex_get_conn, exoid, EX_ELEM_BLOCK, cs_id[cs], cs_connect, NULL, NULL); 175749c89c76SBlaise Bourdin /* EXO uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */ 175849c89c76SBlaise Bourdin for (c_loc = 0, v = 0; c_loc < num_cell_in_set; ++c_loc, ++c) { 175949c89c76SBlaise Bourdin DMPolytopeType ct; 176049c89c76SBlaise Bourdin 176149c89c76SBlaise Bourdin for (v_loc = 0; v_loc < num_vertex_per_cell; ++v_loc, ++v) cone[v_loc] = cs_connect[v] + numCells - 1; 176249c89c76SBlaise Bourdin PetscCall(DMPlexGetCellType(*dm, c, &ct)); 176349c89c76SBlaise Bourdin PetscCall(DMPlexInvertCell(ct, cone)); 176449c89c76SBlaise Bourdin PetscCall(DMPlexSetCone(*dm, c, cone)); 176549c89c76SBlaise Bourdin PetscCall(DMSetLabelValue_Fast(*dm, &cellSets, "Cell Sets", c, cs_id[cs])); 176649c89c76SBlaise Bourdin } 176749c89c76SBlaise Bourdin PetscCall(PetscFree2(cs_connect, cone)); 176849c89c76SBlaise Bourdin } 176949c89c76SBlaise Bourdin PetscCall(PetscFree2(cs_id, cs_order)); 177049c89c76SBlaise Bourdin } 177149c89c76SBlaise Bourdin { 177249c89c76SBlaise Bourdin PetscInt ints[] = {dim, dimEmbed}; 177349c89c76SBlaise Bourdin 177449c89c76SBlaise Bourdin PetscCallMPI(MPI_Bcast(ints, 2, MPIU_INT, 0, comm)); 177549c89c76SBlaise Bourdin PetscCall(DMSetDimension(*dm, ints[0])); 177649c89c76SBlaise Bourdin PetscCall(DMSetCoordinateDim(*dm, ints[1])); 177749c89c76SBlaise Bourdin dim = ints[0]; 177849c89c76SBlaise Bourdin dimEmbed = ints[1]; 177949c89c76SBlaise Bourdin } 178049c89c76SBlaise Bourdin PetscCall(DMPlexSymmetrize(*dm)); 178149c89c76SBlaise Bourdin PetscCall(DMPlexStratify(*dm)); 178249c89c76SBlaise Bourdin if (interpolate) { 178349c89c76SBlaise Bourdin DM idm; 178449c89c76SBlaise Bourdin 178549c89c76SBlaise Bourdin PetscCall(DMPlexInterpolate(*dm, &idm)); 178649c89c76SBlaise Bourdin PetscCall(DMDestroy(dm)); 178749c89c76SBlaise Bourdin *dm = idm; 178849c89c76SBlaise Bourdin } 178949c89c76SBlaise Bourdin 179049c89c76SBlaise Bourdin /* Create vertex set label */ 179149c89c76SBlaise Bourdin if (rank == 0 && (num_vs > 0)) { 179249c89c76SBlaise Bourdin int vs, v; 179349c89c76SBlaise Bourdin /* Read from ex_get_node_set_ids() */ 179449c89c76SBlaise Bourdin int *vs_id; 179549c89c76SBlaise Bourdin /* Read from ex_get_node_set_param() */ 179649c89c76SBlaise Bourdin int num_vertex_in_set; 179749c89c76SBlaise Bourdin /* Read from ex_get_node_set() */ 179849c89c76SBlaise Bourdin int *vs_vertex_list; 179949c89c76SBlaise Bourdin 180049c89c76SBlaise Bourdin /* Get vertex set ids */ 180149c89c76SBlaise Bourdin PetscCall(PetscMalloc1(num_vs, &vs_id)); 180249c89c76SBlaise Bourdin PetscCallExternal(ex_get_ids, exoid, EX_NODE_SET, vs_id); 180349c89c76SBlaise Bourdin for (vs = 0; vs < num_vs; ++vs) { 180449c89c76SBlaise Bourdin PetscCallExternal(ex_get_set_param, exoid, EX_NODE_SET, vs_id[vs], &num_vertex_in_set, NULL); 180549c89c76SBlaise Bourdin PetscCall(PetscMalloc1(num_vertex_in_set, &vs_vertex_list)); 180649c89c76SBlaise Bourdin PetscCallExternal(ex_get_set, exoid, EX_NODE_SET, vs_id[vs], vs_vertex_list, NULL); 180749c89c76SBlaise Bourdin for (v = 0; v < num_vertex_in_set; ++v) PetscCall(DMSetLabelValue_Fast(*dm, &vertSets, "Vertex Sets", vs_vertex_list[v] + numCells - 1, vs_id[vs])); 180849c89c76SBlaise Bourdin PetscCall(PetscFree(vs_vertex_list)); 180949c89c76SBlaise Bourdin } 181049c89c76SBlaise Bourdin PetscCall(PetscFree(vs_id)); 181149c89c76SBlaise Bourdin } 181249c89c76SBlaise Bourdin /* Read coordinates */ 181349c89c76SBlaise Bourdin PetscCall(DMGetCoordinateSection(*dm, &coordSection)); 181449c89c76SBlaise Bourdin PetscCall(PetscSectionSetNumFields(coordSection, 1)); 181549c89c76SBlaise Bourdin PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dimEmbed)); 181649c89c76SBlaise Bourdin PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); 181749c89c76SBlaise Bourdin for (v = numCells; v < numCells + numVertices; ++v) { 181849c89c76SBlaise Bourdin PetscCall(PetscSectionSetDof(coordSection, v, dimEmbed)); 181949c89c76SBlaise Bourdin PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed)); 182049c89c76SBlaise Bourdin } 182149c89c76SBlaise Bourdin PetscCall(PetscSectionSetUp(coordSection)); 182249c89c76SBlaise Bourdin PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 182349c89c76SBlaise Bourdin PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 182449c89c76SBlaise Bourdin PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 182549c89c76SBlaise Bourdin PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 182649c89c76SBlaise Bourdin PetscCall(VecSetBlockSize(coordinates, dimEmbed)); 182749c89c76SBlaise Bourdin PetscCall(VecSetType(coordinates, VECSTANDARD)); 182849c89c76SBlaise Bourdin PetscCall(VecGetArray(coordinates, &coords)); 182949c89c76SBlaise Bourdin if (rank == 0) { 183049c89c76SBlaise Bourdin PetscReal *x, *y, *z; 183149c89c76SBlaise Bourdin 183249c89c76SBlaise Bourdin PetscCall(PetscMalloc3(numVertices, &x, numVertices, &y, numVertices, &z)); 183349c89c76SBlaise Bourdin PetscCallExternal(ex_get_coord, exoid, x, y, z); 183449c89c76SBlaise Bourdin if (dimEmbed > 0) { 183549c89c76SBlaise Bourdin for (v = 0; v < numVertices; ++v) coords[v * dimEmbed + 0] = x[v]; 183649c89c76SBlaise Bourdin } 183749c89c76SBlaise Bourdin if (dimEmbed > 1) { 183849c89c76SBlaise Bourdin for (v = 0; v < numVertices; ++v) coords[v * dimEmbed + 1] = y[v]; 183949c89c76SBlaise Bourdin } 184049c89c76SBlaise Bourdin if (dimEmbed > 2) { 184149c89c76SBlaise Bourdin for (v = 0; v < numVertices; ++v) coords[v * dimEmbed + 2] = z[v]; 184249c89c76SBlaise Bourdin } 184349c89c76SBlaise Bourdin PetscCall(PetscFree3(x, y, z)); 184449c89c76SBlaise Bourdin } 184549c89c76SBlaise Bourdin PetscCall(VecRestoreArray(coordinates, &coords)); 184649c89c76SBlaise Bourdin PetscCall(DMSetCoordinatesLocal(*dm, coordinates)); 184749c89c76SBlaise Bourdin PetscCall(VecDestroy(&coordinates)); 184849c89c76SBlaise Bourdin 184949c89c76SBlaise Bourdin /* Create side set label */ 185049c89c76SBlaise Bourdin if (rank == 0 && interpolate && (num_fs > 0)) { 185149c89c76SBlaise Bourdin int fs, f, voff; 185249c89c76SBlaise Bourdin /* Read from ex_get_side_set_ids() */ 185349c89c76SBlaise Bourdin int *fs_id; 185449c89c76SBlaise Bourdin /* Read from ex_get_side_set_param() */ 185549c89c76SBlaise Bourdin int num_side_in_set; 185649c89c76SBlaise Bourdin /* Read from ex_get_side_set_node_list() */ 185749c89c76SBlaise Bourdin int *fs_vertex_count_list, *fs_vertex_list, *fs_side_list; 185849c89c76SBlaise Bourdin /* Read side set labels */ 185949c89c76SBlaise Bourdin char fs_name[MAX_STR_LENGTH + 1]; 186049c89c76SBlaise Bourdin size_t fs_name_len; 186149c89c76SBlaise Bourdin 186249c89c76SBlaise Bourdin /* Get side set ids */ 186349c89c76SBlaise Bourdin PetscCall(PetscMalloc1(num_fs, &fs_id)); 186449c89c76SBlaise Bourdin PetscCallExternal(ex_get_ids, exoid, EX_SIDE_SET, fs_id); 186549c89c76SBlaise Bourdin // Ids 1 and 2 are reserved by ExodusII for indicating things in 3D 186649c89c76SBlaise Bourdin for (fs = 0; fs < num_fs; ++fs) { 186749c89c76SBlaise Bourdin PetscCallExternal(ex_get_set_param, exoid, EX_SIDE_SET, fs_id[fs], &num_side_in_set, NULL); 186849c89c76SBlaise Bourdin PetscCall(PetscMalloc3(num_side_in_set, &fs_vertex_count_list, num_side_in_set * 4, &fs_vertex_list, num_side_in_set, &fs_side_list)); 186949c89c76SBlaise Bourdin PetscCallExternal(ex_get_side_set_node_list, exoid, fs_id[fs], fs_vertex_count_list, fs_vertex_list); 187049c89c76SBlaise Bourdin PetscCallExternal(ex_get_set, exoid, EX_SIDE_SET, fs_id[fs], NULL, fs_side_list); 187149c89c76SBlaise Bourdin 187249c89c76SBlaise Bourdin /* Get the specific name associated with this side set ID. */ 187349c89c76SBlaise Bourdin int fs_name_err = ex_get_name(exoid, EX_SIDE_SET, fs_id[fs], fs_name); 187449c89c76SBlaise Bourdin if (!fs_name_err) { 187549c89c76SBlaise Bourdin PetscCall(PetscStrlen(fs_name, &fs_name_len)); 187649c89c76SBlaise Bourdin if (fs_name_len == 0) PetscCall(PetscStrncpy(fs_name, "Face Sets", MAX_STR_LENGTH)); 187749c89c76SBlaise Bourdin } 187849c89c76SBlaise Bourdin for (f = 0, voff = 0; f < num_side_in_set; ++f) { 187949c89c76SBlaise Bourdin const PetscInt *faces = NULL; 188049c89c76SBlaise Bourdin PetscInt faceSize = fs_vertex_count_list[f], numFaces; 188149c89c76SBlaise Bourdin PetscInt faceVertices[4], v; 188249c89c76SBlaise Bourdin 188349c89c76SBlaise Bourdin PetscCheck(faceSize <= 4, comm, PETSC_ERR_ARG_WRONG, "ExodusII side cannot have %" PetscInt_FMT " > 4 vertices", faceSize); 188449c89c76SBlaise Bourdin for (v = 0; v < faceSize; ++v, ++voff) faceVertices[v] = fs_vertex_list[voff] + numCells - 1; 188549c89c76SBlaise Bourdin PetscCall(DMPlexGetFullJoin(*dm, faceSize, faceVertices, &numFaces, &faces)); 188649c89c76SBlaise Bourdin PetscCheck(numFaces == 1, comm, PETSC_ERR_ARG_WRONG, "Invalid ExodusII side %d in set %d maps to %" PetscInt_FMT " faces", f, fs, numFaces); 188749c89c76SBlaise Bourdin PetscCheck(dim == 1 || faces[0] >= numCells + numVertices, comm, PETSC_ERR_ARG_WRONG, "Invalid ExodusII side %d in set %d maps to point %" PetscInt_FMT " which is not a face", f, fs, faces[0]); 188849c89c76SBlaise Bourdin PetscCall(DMSetLabelValue_Fast(*dm, &faceSets, "Face Sets", faces[0], fs_id[fs])); 188949c89c76SBlaise Bourdin /* Only add the label if one has been detected for this side set. */ 189049c89c76SBlaise Bourdin if (!fs_name_err) PetscCall(DMSetLabelValue(*dm, fs_name, faces[0], fs_id[fs])); 189149c89c76SBlaise Bourdin PetscCall(DMPlexRestoreJoin(*dm, faceSize, faceVertices, &numFaces, &faces)); 189249c89c76SBlaise Bourdin } 189349c89c76SBlaise Bourdin PetscCall(PetscFree3(fs_vertex_count_list, fs_vertex_list, fs_side_list)); 189449c89c76SBlaise Bourdin } 189549c89c76SBlaise Bourdin PetscCall(PetscFree(fs_id)); 189649c89c76SBlaise Bourdin } 189749c89c76SBlaise Bourdin 189849c89c76SBlaise Bourdin { /* Create Cell/Face/Vertex Sets labels at all processes */ 189949c89c76SBlaise Bourdin enum { 190049c89c76SBlaise Bourdin n = 3 190149c89c76SBlaise Bourdin }; 190249c89c76SBlaise Bourdin PetscBool flag[n]; 190349c89c76SBlaise Bourdin 190449c89c76SBlaise Bourdin flag[0] = cellSets ? PETSC_TRUE : PETSC_FALSE; 190549c89c76SBlaise Bourdin flag[1] = faceSets ? PETSC_TRUE : PETSC_FALSE; 190649c89c76SBlaise Bourdin flag[2] = vertSets ? PETSC_TRUE : PETSC_FALSE; 190749c89c76SBlaise Bourdin PetscCallMPI(MPI_Bcast(flag, n, MPIU_BOOL, 0, comm)); 190849c89c76SBlaise Bourdin if (flag[0]) PetscCall(DMCreateLabel(*dm, "Cell Sets")); 190949c89c76SBlaise Bourdin if (flag[1]) PetscCall(DMCreateLabel(*dm, "Face Sets")); 191049c89c76SBlaise Bourdin if (flag[2]) PetscCall(DMCreateLabel(*dm, "Vertex Sets")); 191149c89c76SBlaise Bourdin } 191249c89c76SBlaise Bourdin PetscFunctionReturn(PETSC_SUCCESS); 191349c89c76SBlaise Bourdin } 1914