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Jan 31, 2024
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Updates in Mesh_Class #419

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8 changes: 7 additions & 1 deletion src/submodules/AbstractMesh/src/AbstractMesh_Class@IOMethods.F90
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Expand Up @@ -245,7 +245,13 @@
& fieldname="physicalTag", myname=myname, modname=modname, check=.TRUE.)

CALL HDF5ReadVector(hdf5=hdf5, VALUE=obj%boundingEntity, group=dsetname, &
& fieldname="boundingEntity", myname=myname, modname=modname, check=.TRUE.)
& fieldname="boundingEntity", myname=myname, modname=modname, check=.FALSE.)

! If boundingEntity is not initiated then we initiate it with size=0
! Bounding entity will not be initiated for point type
IF (.NOT. ALLOCATED(obj%boundingEntity)) THEN
CALL Reallocate(obj%boundingEntity, 0)
END IF

IF (obj%showTime) THEN
CALL TypeCPUTime%SetEndTime()
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174 changes: 78 additions & 96 deletions src/submodules/DynamicMesh/src/DynamicMesh_Class@IOMethods.F90
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Expand Up @@ -43,125 +43,107 @@
& '[START] ')
#endif

CALL obj%DEALLOCATE()

dsetname = TRIM(group)
CALL AbstractMeshImport(obj=obj, hdf5=hdf5, group=group)
IF (obj%tElements .EQ. 0) RETURN
! obj%tElements is read in AbstractMeshImport

CALL HDF5ReadScalar(hdf5=hdf5, VALUE=xidim, group=dsetname, &
& fieldname="xidim", myname=myname, modname=modname, check=.TRUE.)

CALL HDF5ReadScalar(hdf5=hdf5, VALUE=elemType, group=dsetname, &
& fieldname="elemType", myname=myname, modname=modname, check=.TRUE.)

! INFO:
! obj%tElements is read in AbstractMeshImport
IF (obj%tElements .EQ. 0) RETURN

CALL HDF5ReadVector(hdf5=hdf5, VALUE=elemNumber, group=dsetname, &
& fieldname="elemNumber", myname=myname, modname=modname, check=.TRUE.)

CALL HDF5ReadMatrix(hdf5=hdf5, VALUE=connectivity, group=dsetname, &
& fieldname="connectivity", myname=myname, modname=modname, check=.TRUE.)

CALL HDF5ReadVector(hdf5=hdf5, VALUE=internalNptrs, group=dsetname, &
& fieldname="intNodeNumber", myname=myname, modname=modname, check=.TRUE.)

isok = (elemType .EQ. Point1) .OR. (elemType .EQ. 0)

IF (isok) RETURN

CALL obj%elementDataList%Initiate()
CALL obj%nodeDataBinaryTree%Initiate()
CALL obj%nodeDataList%Initiate()
CALL obj%elementDataBinaryTree%Initiate()

DO ii = 1, obj%tElements

elemdata_ptr => ElemData_Pointer()
CALL ElemDataSet(obj=elemdata_ptr, globalElemNum=elemNumber(ii), &
& localElemNum=ii, globalNodes=connectivity(:, ii))
CALL obj%elementDataList%Add(elemdata_ptr)
CALL obj%elementDataBinaryTree%Insert(elemdata_ptr)

DO jj = 1, SIZE(connectivity, 1)

nodedata_ptr => NodeData_Pointer()
CALL NodeDataSet(obj=nodedata_ptr, globalNodeNum=connectivity(jj, ii), &
& nodeType=TypeNode%boundary)
! TypeNode is defined in NodeData_Class
! The above step is unusual, but we know the position of
! internal nptrs, so later we will set the
! those nodes as INTERNAL_NODE, in this way we can
! identify the boundary nodes

tsize1 = obj%nodeDataBinaryTree%SIZE()
CALL obj%nodeDataBinaryTree%Insert(nodedata_ptr)
tsize2 = obj%nodeDataBinaryTree%SIZE()

IF (tsize1 .EQ. tsize2) THEN
CALL NodeData_Deallocate(nodedata_ptr)
! NOTE:
!! We have not added nodedata_ptr,
!! We know this because tsize1 == tsize2so
!! so we should remove this memory
!! this step is necessary for avoiding the memory leak
DEALLOCATE (nodedata_ptr)
ELSE
CALL obj%nodeDataList%Add(nodedata_ptr)
END IF

END DO
! DO ii = 1, obj%tElements

END DO
! elemdata_ptr => obj%elementData(ii)

CALL obj%nodeDataBinaryTree%SetID()
!! This method will set the local node number in the binarytree

CALL obj%elementDataBinaryTree%SetID()
!! This method will set the local element number in the binarytree

obj%tNodes = obj%nodeDataBinaryTree%SIZE()
!! This method returns the total number of nodes in mesh
! CALL ElemDataSet(obj=elemdata_ptr, globalElemNum=elemNumber(ii), &
! & localElemNum=ii, globalNodes=connectivity(:, ii))
!
! CALL obj%elementDataList%Add(elemdata_ptr)
! CALL obj%elementDataBinaryTree%Insert(elemdata_ptr)

nodedata_ptr => obj%nodeDataBinaryTree%GetMinPointer()
obj%minNptrs = nodedata_ptr%globalNodeNum
! DO jj = 1, SIZE(connectivity, 1)
!
! nodedata_ptr => NodeData_Pointer()
! CALL NodeDataSet(obj=nodedata_ptr, globalNodeNum=connectivity(jj, ii), &
! & nodeType=TypeNode%boundary)
! ! TypeNode is defined in NodeData_Class
! ! The above step is unusual, but we know the position of
! ! internal nptrs, so later we will set the
! ! those nodes as INTERNAL_NODE, in this way we can
! ! identify the boundary nodes
!
! tsize1 = obj%nodeDataBinaryTree%SIZE()
! CALL obj%nodeDataBinaryTree%Insert(nodedata_ptr)
! tsize2 = obj%nodeDataBinaryTree%SIZE()
!
! IF (tsize1 .EQ. tsize2) THEN
! CALL NodeData_Deallocate(nodedata_ptr)
! ! NOTE:
! !! We have not added nodedata_ptr,
! !! We know this because tsize1 == tsize2so
! !! so we should remove this memory
! !! this step is necessary for avoiding the memory leak
! DEALLOCATE (nodedata_ptr)
! ELSE
! CALL obj%nodeDataList%Add(nodedata_ptr)
! END IF
!
! END DO

nodedata_ptr => obj%nodeDataBinaryTree%GetMaxPointer()
obj%maxNptrs = nodedata_ptr%globalNodeNum
! END DO

nodedata_ptr => NULL()
CALL Reallocate(obj%local_Nptrs, obj%maxNptrs)

DO CONCURRENT(ii=1:obj%tElements)
obj%local_Nptrs(connectivity(:, ii)) = connectivity(:, ii)
END DO

! TODO: Parallel
DO ii = 1, obj%maxNptrs
IF (obj%local_Nptrs(ii) .NE. 0) THEN
nodedata%globalNodeNum = ii
nodedata_ptr => obj%nodeDataBinaryTree%GetValuePointer(VALUE=nodedata)
obj%local_Nptrs(ii) = nodedata_ptr%localNodeNum
END IF
END DO

! TODO: Parallel
DO ii = 1, SIZE(internalNptrs)
! jj = internalNptrs(ii)
! CALL NodeDataSet(obj=nodedata, globalNodeNum=jj)
nodedata%globalNodeNum = internalNptrs(ii)
nodedata_ptr => obj%nodeDataBinaryTree%GetValuePointer(VALUE=nodedata)
nodedata_ptr%nodeType = TypeNode%internal
! CALL NodeDataSet(obj=nodedata_ptr, nodeType=TypeNode%internal)
END DO
! CALL obj%nodeDataBinaryTree%SetID()
! !! This method will set the local node number in the binarytree
!
! CALL obj%elementDataBinaryTree%SetID()
! !! This method will set the local element number in the binarytree
!
! obj%tNodes = obj%nodeDataBinaryTree%SIZE()
! !! This method returns the total number of nodes in mesh
!
! nodedata_ptr => obj%nodeDataBinaryTree%GetMinPointer()
! obj%minNptrs = nodedata_ptr%globalNodeNum
!
! nodedata_ptr => obj%nodeDataBinaryTree%GetMaxPointer()
! obj%maxNptrs = nodedata_ptr%globalNodeNum
!
! nodedata_ptr => NULL()
! CALL Reallocate(obj%local_Nptrs, obj%maxNptrs)
!
! DO CONCURRENT(ii=1:obj%tElements)
! obj%local_Nptrs(connectivity(:, ii)) = connectivity(:, ii)
! END DO
!
! ! TODO: Parallel
! DO ii = 1, obj%maxNptrs
! IF (obj%local_Nptrs(ii) .NE. 0) THEN
! nodedata%globalNodeNum = ii
! nodedata_ptr => obj%nodeDataBinaryTree%GetValuePointer(VALUE=nodedata)
! obj%local_Nptrs(ii) = nodedata_ptr%localNodeNum
! END IF
! END DO
!
! ! TODO: Parallel
! DO ii = 1, SIZE(internalNptrs)
! ! jj = internalNptrs(ii)
! ! CALL NodeDataSet(obj=nodedata, globalNodeNum=jj)
! nodedata%globalNodeNum = internalNptrs(ii)
! nodedata_ptr => obj%nodeDataBinaryTree%GetValuePointer(VALUE=nodedata)
! nodedata_ptr%nodeType = TypeNode%internal
! ! CALL NodeDataSet(obj=nodedata_ptr, nodeType=TypeNode%internal)
! END DO

nodedata_ptr => NULL()

IF (ALLOCATED(elemNumber)) DEALLOCATE (elemNumber)
IF (ALLOCATED(connectivity)) DEALLOCATE (connectivity)
IF (ALLOCATED(internalNptrs)) DEALLOCATE (internalNptrs)

#ifdef DEBUG_VER
CALL e%RaiseInformation(modName//'::'//myName//' - '// &
& '[END] ')
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91 changes: 5 additions & 86 deletions src/submodules/Mesh/src/Mesh_Class@IOMethods.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -51,19 +51,14 @@

MODULE PROCEDURE obj_Import
CHARACTER(*), PARAMETER :: myName = "obj_Import()"
INTEGER(I4B), ALLOCATABLE :: connectivity(:, :), elemNumber(:), &
& internalNptrs(:)
CHARACTER(:), ALLOCATABLE :: dsetname
INTEGER(I4B) :: ii, dummy, jj
LOGICAL(LGT) :: isok, abool
LOGICAL(LGT) :: isok

#ifdef DEBUG_VER
CALL e%RaiseInformation(modName//'::'//myName//' - '// &
& '[START] ')
#endif

CALL obj%DEALLOCATE()

dsetname = TRIM(group)
CALL AbstractMeshImport(obj=obj, hdf5=hdf5, group=group)

Expand All @@ -73,90 +68,14 @@
CALL HDF5ReadScalar(hdf5=hdf5, VALUE=obj%elemType, group=dsetname, &
& fieldname="elemType", myname=myname, modname=modname, check=.TRUE.)

IF (obj%tElements .NE. 0) THEN
ALLOCATE (obj%elementData(obj%tElements))
END IF

CALL HDF5ReadVector(hdf5=hdf5, VALUE=elemNumber, group=dsetname, &
& fieldname="elemNumber", myname=myname, modname=modname, check=.TRUE.)

CALL HDF5ReadMatrix(hdf5=hdf5, VALUE=connectivity, group=dsetname, &
& fieldname="connectivity", myname=myname, modname=modname, check=.TRUE.)

CALL HDF5ReadVector(hdf5=hdf5, VALUE=internalNptrs, group=dsetname, &
& fieldname="intNodeNumber", myname=myname, modname=modname, check=.TRUE.)

DO CONCURRENT(ii=1:obj%tElements)
obj%elementData(ii)%globalElemNum = elemNumber(ii)
obj%elementData(ii)%localElemNum = ii
END DO

isok = (obj%elemType .EQ. Point1) .OR. (obj%elemType .EQ. 0)

IF (isok) THEN
obj%tNodes = 1
ALLOCATE (obj%nodeData(obj%tNodes))
obj%nodeData(1)%localNodeNum = 1
obj%nodeData(1)%globalNodeNum = internalNptrs(1)
obj%nodeData(1)%nodeType = INTERNAL_NODE

IF (ALLOCATED(elemNumber)) DEALLOCATE (elemNumber)
IF (ALLOCATED(connectivity)) DEALLOCATE (connectivity)
IF (ALLOCATED(internalNptrs)) DEALLOCATE (internalNptrs)

#ifdef DEBUG_VER
CALL e%RaiseInformation(modName//'::'//myName//' - '// &
& '[END] ')
#endif

RETURN
END IF

obj%maxNptrs = MAXVAL(connectivity)
obj%minNptrs = MINVAL(connectivity)
CALL Reallocate(obj%local_Nptrs, obj%maxNptrs)
obj%refelem => ReferenceElement_Pointer(xidim=obj%xidim, &
& nsd=obj%nsd, elemType=obj%elemType, ipType=Equidistance)

DO CONCURRENT(ii=1:obj%tElements)
obj%elementData(ii)%globalNodes = connectivity(:, ii)
obj%local_Nptrs(connectivity(:, ii)) = connectivity(:, ii)
END DO

obj%tNodes = COUNT(obj%local_Nptrs .NE. 0)
ALLOCATE (obj%nodeData(obj%tNodes))
dummy = 0

DO ii = 1, obj%maxNptrs
IF (obj%local_Nptrs(ii) .NE. 0) THEN
dummy = dummy + 1
obj%nodeData(dummy)%globalNodeNum = obj%local_Nptrs(ii)
obj%nodeData(dummy)%localNodeNum = dummy
obj%nodeData(dummy)%nodeType = BOUNDARY_NODE
! The above step is unusual, but we know the position of
! internal nptrs, so later we will set the
! those nodes as INTERNAL_NODE, in this way we can
! identify the boundary nodes
obj%local_Nptrs(ii) = dummy
END IF
END DO

DO ii = 1, SIZE(internalNptrs)
jj = obj%GetLocalNodeNumber(internalNptrs(ii))
obj%nodeData(jj)%globalNodeNum = internalNptrs(ii)
obj%nodeData(jj)%nodeType = INTERNAL_NODE
END DO

isok = obj%tElements .GT. 0
abool = obj%xidim .GT. 0
isok = obj%xidim .GT. 0
IF (isok) THEN
obj%refelem => ReferenceElement_Pointer(xidim=obj%xidim, &
& nsd=obj%nsd, elemType=obj%elemType, ipType=Equidistance)
IF (abool) obj%facetElements = FacetElements(obj%refelem)
obj%facetElements = FacetElements(obj%refelem)
END IF

IF (ALLOCATED(elemNumber)) DEALLOCATE (elemNumber)
IF (ALLOCATED(connectivity)) DEALLOCATE (connectivity)
IF (ALLOCATED(internalNptrs)) DEALLOCATE (internalNptrs)

#ifdef DEBUG_VER
CALL e%RaiseInformation(modName//'::'//myName//' - '// &
& '[END] ')
Expand Down