separating functionality for more flexibility
This commit is contained in:
Martin Diehl
parent
efa30d1f3a
commit
7ee440c1b1
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@ -440,7 +440,7 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
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case (155)
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msg = 'material index out of bounds'
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case (180)
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msg = 'missing/invalid material definition via State Variable 2'
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msg = 'missing/invalid material definition'
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case (190)
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msg = 'unknown element type:'
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case (191)
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224
src/VTK.f90
224
src/VTK.f90
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@ -11,24 +11,117 @@ module VTK
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implicit none
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private
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public :: VTK_readVTI
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public :: &
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VTK_readVTIdataset_int, &
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VTK_readVTI_cellsSizeOrigin
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contains
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!--------------------------------------------------------------------------------------------------
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!> @brief Parse vtk image data (.vti)
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!> @brief Read integer dataset from a VTK image data (*.vti) file.
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!> @details https://vtk.org/Wiki/VTK_XML_Formats
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!--------------------------------------------------------------------------------------------------
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subroutine VTK_readVTI(cells,geomSize,origin,material, &
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fileContent)
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function VTK_readVTIdataset_int(fileContent,label) result(dataset)
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character(len=*), intent(in) :: &
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label, &
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fileContent
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integer, dimension(:), allocatable :: &
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dataset
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character(len=:), allocatable :: dataType, headerType, base64_str
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logical :: compressed
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call VTK_readVTIdataset_raw(base64_str,dataType,headerType,compressed, &
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fileContent,label)
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dataset = as_Int(base64_str,headerType,compressed,dataType)
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if (.not. allocated(dataset)) call IO_error(error_ID = 844, ext_msg='dataset "'//label//'" not found')
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end function VTK_readVTIdataset_int
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!--------------------------------------------------------------------------------------------------
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!> @brief Read dataset as raw data (base64 string) from a VTK image data (*.vti) file.
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!> @details https://vtk.org/Wiki/VTK_XML_Formats
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!--------------------------------------------------------------------------------------------------
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subroutine VTK_readVTIdataset_raw(base64_str,dataType,headerType,compressed, &
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fileContent,label)
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character(len=*), intent(in) :: &
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label, &
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fileContent
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character(len=:), allocatable, intent(out) :: dataType, headerType, base64_str
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logical, intent(out) :: compressed
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logical :: inFile,inImage,gotCellData
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integer(pI64) :: &
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startPos, endPos, &
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s
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inFile = .false.
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inImage = .false.
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startPos = 1_pI64
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outer: do while (startPos < len(fileContent,kind=pI64))
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endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
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if (endPos < startPos) endPos = len(fileContent,kind=pI64) ! end of file without new line
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if (.not. inFile) then
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if (index(fileContent(startPos:endPos),'<VTKFile',kind=pI64) /= 0_pI64) then
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inFile = .true.
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if (.not. fileFormatOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format')
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headerType = merge('UInt64','UInt32',getXMLValue(fileContent(startPos:endPos),'header_type')=='UInt64')
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compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor'
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end if
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else
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if (.not. inImage) then
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if (index(fileContent(startPos:endPos),'<ImageData',kind=pI64) /= 0_pI64) then
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inImage = .true.
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end if
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else
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if (index(fileContent(startPos:endPos),'<CellData',kind=pI64) /= 0_pI64) then
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do while (index(fileContent(startPos:endPos),'</CellData>',kind=pI64) == 0_pI64)
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if (index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64 .and. &
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getXMLValue(fileContent(startPos:endPos),'Name') == label ) then
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if (getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
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call IO_error(error_ID = 844, ext_msg='format ('//label//')')
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dataType = getXMLValue(fileContent(startPos:endPos),'type')
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startPos = endPos + 2_pI64
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endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
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s = startPos + verify(fileContent(startPos:endPos),IO_WHITESPACE,kind=pI64) -1_pI64 ! start (no leading whitespace)
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base64_str = fileContent(s:endPos)
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exit outer
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end if
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startPos = endPos + 2_pI64
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endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
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end do
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end if
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end if
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end if
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startPos = endPos + 2_pI64
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end do outer
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end subroutine VTK_readVTIdataset_raw
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!--------------------------------------------------------------------------------------------------
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!> @brief Read cells, size, and origin of an VTK image data (*.vti) file.
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!> @details https://vtk.org/Wiki/VTK_XML_Formats
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!--------------------------------------------------------------------------------------------------
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subroutine VTK_readVTI_cellsSizeOrigin(cells,geomSize,origin, &
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fileContent)
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integer, dimension(3), intent(out) :: &
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cells ! # of cells (across all processes!)
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real(pReal), dimension(3), intent(out) :: &
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geomSize, & ! physical size (across all processes!)
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geomSize, & ! size (across all processes!)
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origin ! origin (across all processes!)
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integer, dimension(:), intent(out), allocatable :: &
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material
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character(len=*), intent(in) :: &
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fileContent
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@ -42,14 +135,10 @@ subroutine VTK_readVTI(cells,geomSize,origin,material, &
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cells = -1
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geomSize = -1.0_pReal
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inFile = .false.
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inImage = .false.
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gotCelldata = .false.
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!--------------------------------------------------------------------------------------------------
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! parse XML file
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inFile = .false.
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inImage = .false.
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startPos = 1_pI64
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do while (startPos < len(fileContent,kind=pI64))
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outer: do while (startPos < len(fileContent,kind=pI64))
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endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
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if (endPos < startPos) endPos = len(fileContent,kind=pI64) ! end of file without new line
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@ -65,49 +154,24 @@ subroutine VTK_readVTI(cells,geomSize,origin,material, &
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if (index(fileContent(startPos:endPos),'<ImageData',kind=pI64) /= 0_pI64) then
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inImage = .true.
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call cellsSizeOrigin(cells,geomSize,origin,fileContent(startPos:endPos))
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end if
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else
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if (index(fileContent(startPos:endPos),'<CellData',kind=pI64) /= 0_pI64) then
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gotCellData = .true.
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do while (index(fileContent(startPos:endPos),'</CellData>',kind=pI64) == 0_pI64)
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if (index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64 .and. &
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getXMLValue(fileContent(startPos:endPos),'Name') == 'material' ) then
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if (getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
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call IO_error(error_ID = 844, ext_msg='format (material)')
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dataType = getXMLValue(fileContent(startPos:endPos),'type')
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startPos = endPos + 2_pI64
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endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
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s = startPos + verify(fileContent(startPos:endPos),IO_WHITESPACE,kind=pI64) -1_pI64 ! start (no leading whitespace)
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material = as_Int(fileContent(s:endPos),headerType,compressed,dataType)
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exit
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end if
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startPos = endPos + 2_pI64
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endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
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end do
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exit outer
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end if
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end if
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end if
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if (gotCellData) exit
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startPos = endPos + 2_pI64
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end do
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end do outer
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if (.not. allocated(material)) call IO_error(error_ID = 844, ext_msg='material data not found')
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if (size(material) /= product(cells)) call IO_error(error_ID = 844, ext_msg='size(material)')
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if (any(geomSize<=0)) call IO_error(error_ID = 844, ext_msg='size')
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if (any(cells<1)) call IO_error(error_ID = 844, ext_msg='cells')
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material = material + 1
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if (any(material<1)) call IO_error(error_ID = 844, ext_msg='material ID < 0')
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end subroutine VTK_readVTI
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end subroutine VTK_readVTI_cellsSizeOrigin
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!------------------------------------------------------------------------------------------------
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!> @brief determine size and origin from coordinates
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!------------------------------------------------------------------------------------------------
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!--------------------------------------------------------------------------------------------------
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!> @brief Determine size and origin from coordinates.
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!--------------------------------------------------------------------------------------------------
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subroutine cellsSizeOrigin(c,s,o,header)
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integer, dimension(3), intent(out) :: c
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@ -120,7 +184,7 @@ subroutine cellsSizeOrigin(c,s,o,header)
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temp = getXMLValue(header,'Direction')
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if (temp /= '1 0 0 0 1 0 0 0 1' .and. temp /= '') & ! https://discourse.vtk.org/t/vti-specification/6526
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if (temp /= '1 0 0 0 1 0 0 0 1' .and. temp /= '') & ! https://discourse.vtk.org/t/vti-specification/6526
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call IO_error(error_ID = 844, ext_msg = 'coordinate order')
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temp = getXMLValue(header,'WholeExtent')
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@ -138,15 +202,15 @@ subroutine cellsSizeOrigin(c,s,o,header)
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end subroutine
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!------------------------------------------------------------------------------------------------
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!> @brief Interpret Base64 string in vtk XML file as integer of default kind
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!------------------------------------------------------------------------------------------------
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!--------------------------------------------------------------------------------------------------
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!> @brief Interpret Base64 string in vtk XML file as integer of default kind.
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!--------------------------------------------------------------------------------------------------
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function as_Int(base64_str,headerType,compressed,dataType)
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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headerType, & ! header type (UInt32 or Uint64)
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dataType ! data type (Int32, Int64, Float32, Float64)
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logical, intent(in) :: compressed ! indicate whether data is zlib compressed
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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headerType, & ! header type (UInt32 or Uint64)
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dataType ! data type (Int32, Int64, Float32, Float64)
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logical, intent(in) :: compressed ! indicate whether data is zlib compressed
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integer, dimension(:), allocatable :: as_Int
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@ -167,15 +231,15 @@ function as_Int(base64_str,headerType,compressed,dataType)
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end function as_Int
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!------------------------------------------------------------------------------------------------
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!> @brief Interpret Base64 string in vtk XML file as integer of pReal kind
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!------------------------------------------------------------------------------------------------
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!--------------------------------------------------------------------------------------------------
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!> @brief Interpret Base64 string in vtk XML file as real of kind pReal.
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!--------------------------------------------------------------------------------------------------
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function as_pReal(base64_str,headerType,compressed,dataType)
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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headerType, & ! header type (UInt32 or Uint64)
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dataType ! data type (Int32, Int64, Float32, Float64)
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logical, intent(in) :: compressed ! indicate whether data is zlib compressed
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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headerType, & ! header type (UInt32 or Uint64)
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dataType ! data type (Int32, Int64, Float32, Float64)
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logical, intent(in) :: compressed ! indicate whether data is zlib compressed
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real(pReal), dimension(:), allocatable :: as_pReal
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@ -196,14 +260,14 @@ function as_pReal(base64_str,headerType,compressed,dataType)
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end function as_pReal
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!------------------------------------------------------------------------------------------------
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!> @brief Interpret Base64 string in vtk XML file as bytes
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!------------------------------------------------------------------------------------------------
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!--------------------------------------------------------------------------------------------------
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!> @brief Interpret Base64 string in vtk XML file as bytes.
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!--------------------------------------------------------------------------------------------------
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function asBytes(base64_str,headerType,compressed) result(bytes)
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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headerType ! header type (UInt32 or Uint64)
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logical, intent(in) :: compressed ! indicate whether data is zlib compressed
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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headerType ! header type (UInt32 or Uint64)
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logical, intent(in) :: compressed ! indicate whether data is zlib compressed
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integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
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@ -217,19 +281,19 @@ function asBytes(base64_str,headerType,compressed) result(bytes)
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end function asBytes
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!------------------------------------------------------------------------------------------------
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!> @brief Interpret compressed Base64 string in vtk XML file as bytes
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!--------------------------------------------------------------------------------------------------
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!> @brief Interpret compressed Base64 string in vtk XML file as bytes.
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!> @details A compressed Base64 string consists of a header block and a data block
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! [#blocks/#u-size/#p-size/#c-size-1/#c-size-2/.../#c-size-#blocks][DATA-1/DATA-2...]
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! #blocks = Number of blocks
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! #u-size = Block size before compression
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! #p-size = Size of last partial block (zero if it not needed)
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! #c-size-i = Size in bytes of block i after compression
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!------------------------------------------------------------------------------------------------
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!--------------------------------------------------------------------------------------------------
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function asBytes_compressed(base64_str,headerType) result(bytes)
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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headerType ! header type (UInt32 or Uint64)
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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headerType ! header type (UInt32 or Uint64)
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integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
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integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes_inflated
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@ -265,15 +329,15 @@ function asBytes_compressed(base64_str,headerType) result(bytes)
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end function asBytes_compressed
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!------------------------------------------------------------------------------------------------
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!> @brief Interprete uncompressed Base64 string in vtk XML file as bytes
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!--------------------------------------------------------------------------------------------------
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!> @brief Interprete uncompressed Base64 string in vtk XML file as bytes.
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!> @details An uncompressed Base64 string consists of N headers blocks and a N data blocks
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![#bytes-1/DATA-1][#bytes-2/DATA-2]...
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!------------------------------------------------------------------------------------------------
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!--------------------------------------------------------------------------------------------------
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function asBytes_uncompressed(base64_str,headerType) result(bytes)
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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headerType ! header type (UInt32 or Uint64)
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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headerType ! header type (UInt32 or Uint64)
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integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
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integer(pI64) :: s
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@ -300,9 +364,9 @@ function asBytes_uncompressed(base64_str,headerType) result(bytes)
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end function asBytes_uncompressed
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!------------------------------------------------------------------------------------------------
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!--------------------------------------------------------------------------------------------------
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!> @brief Get XML string value for given key.
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!------------------------------------------------------------------------------------------------
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!--------------------------------------------------------------------------------------------------
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pure function getXMLValue(line,key)
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character(len=*), intent(in) :: line, key
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@ -337,9 +401,9 @@ pure function getXMLValue(line,key)
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end function
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!------------------------------------------------------------------------------------------------
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!--------------------------------------------------------------------------------------------------
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!> @brief Check for supported file format variants.
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!------------------------------------------------------------------------------------------------
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!--------------------------------------------------------------------------------------------------
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pure function fileFormatOk(line)
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character(len=*),intent(in) :: line
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@ -76,7 +76,12 @@ subroutine discretization_grid_init(restart)
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if (worldrank == 0) then
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fileContent = IO_read(interface_geomFile)
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call VTK_readVTI(cells,geomSize,origin,materialAt_global,fileContent)
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call VTK_readVTI_cellsSizeOrigin(cells,geomSize,origin,fileContent)
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materialAt_global = VTK_readVTIdataset_int(fileContent,'material') + 1
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if (any(materialAt_global < 1)) &
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call IO_error(180,ext_msg='material ID < 1')
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if (size(materialAt_global) /= product(cells)) &
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call IO_error(180,ext_msg='mismatch of material IDs and # cells')
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fname = interface_geomFile
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if (scan(fname,'/') /= 0) fname = fname(scan(fname,'/',.true.)+1:)
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call results_openJobFile(parallel=.false.)
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