Merge branch 'vtr-as-input' into Fortran-simplifications
This commit is contained in:
Martin Diehl
commit
f266def906
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@ -499,7 +499,7 @@ mergeIntoMaster:
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removeData:
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stage: clean
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before_script:
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- echo 'Do nothing'
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||||
- echo "Removing data and lock of pipeline $CI_PIPELINE_ID"
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script:
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||||
- rm -rf $TESTROOT/GitLabCI_Pipeline_$CI_PIPELINE_ID
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- sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue # in case pipeline was manually (web GUI) restarted and releaseLock was performed already
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@ -511,7 +511,7 @@ removeData:
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|||
removeLock:
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stage: releaseLock
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before_script:
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- echo 'Do nothing'
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||||
- echo "Removing lock of pipeline $CI_PIPELINE_ID"
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when: always
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script: sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue
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except:
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@ -146,10 +146,10 @@ end subroutine discretization_grid_init
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subroutine readGeom(grid,geomSize,origin,microstructure)
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integer, dimension(3), intent(out) :: &
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grid ! grid (for all processes!)
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grid ! grid (across all processes!)
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real(pReal), dimension(3), intent(out) :: &
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geomSize, & ! size (for all processes!)
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origin ! origin (for 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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microstructure
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@ -195,7 +195,7 @@ subroutine readGeom(grid,geomSize,origin,microstructure)
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endif
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!--------------------------------------------------------------------------------------------------
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! read and interprete header
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! read and interpret header
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origin = 0.0_pReal
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l = 0
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do while (l < headerLength .and. startPos < len(rawData))
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@ -307,15 +307,15 @@ end subroutine readGeom
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subroutine readVTR(grid,geomSize,origin,microstructure)
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integer, dimension(3), intent(out) :: &
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grid ! grid (for all processes!)
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grid ! grid (across all processes!)
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real(pReal), dimension(3), intent(out) :: &
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geomSize, & ! size (for all processes!)
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origin ! origin (for 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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microstructure
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character(len=:), allocatable :: fileContent, data_type, header_type
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logical :: inFile,inGrid,readCoordinates,readCellData,compressed
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character(len=:), allocatable :: fileContent, dataType, headerType
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logical :: inFile,inGrid,gotCoordinates,gotCellData,compressed
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integer :: fileUnit, myStat, coord
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integer(pI64) :: &
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fileLength, & !< length of the geom file (in characters)
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@ -337,11 +337,11 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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inFile = .false.
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inGrid = .false.
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readCoordinates = .false.
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readCelldata = .false.
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gotCoordinates = .false.
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gotCelldata = .false.
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!--------------------------------------------------------------------------------------------------
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! interprete XML file
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! interpret XML file
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startPos = 1_pI64
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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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@ -350,19 +350,16 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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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. fileOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format')
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header_type = merge('UInt64','UInt32',getXMLValue(fileContent(startPos:endPos),'header_type')=='UInt64')
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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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endif
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else
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if(.not. inGrid) then
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if(index(fileContent(startPos:endPos),'<RectilinearGrid',kind=pI64) /= 0_pI64) then
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inGrid = .true.
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grid = getGrid(fileContent(startPos:endPos))
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endif
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if(index(fileContent(startPos:endPos),'<RectilinearGrid',kind=pI64) /= 0_pI64) inGrid = .true.
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else
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if(index(fileContent(startPos:endPos),'<CellData>',kind=pI64) /= 0_pI64) then
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readCellData = .true.
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gotCellData = .true.
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startPos = endPos + 2_pI64
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do while (index(fileContent(startPos:endPos),'</CellData>',kind=pI64) == 0_pI64)
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endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
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@ -371,18 +368,18 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
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call IO_error(error_ID = 844, ext_msg='format (materialpoint)')
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data_type = getXMLValue(fileContent(startPos:endPos),'type')
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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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microstructure = as_Int(fileContent(s:endPos),header_type,compressed,data_type)
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microstructure = as_Int(fileContent(s:endPos),headerType,compressed,dataType)
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exit
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endif
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startPos = endPos + 2_pI64
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enddo
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elseif(index(fileContent(startPos:endPos),'<Coordinates>',kind=pI64) /= 0_pI64) then
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readCoordinates = .true.
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gotCoordinates = .true.
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startPos = endPos + 2_pI64
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coord = 0
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@ -392,7 +389,7 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
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call IO_error(error_ID = 844, ext_msg='format (coordinates)')
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data_type = getXMLValue(fileContent(startPos:endPos),'type')
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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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@ -400,7 +397,7 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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coord = coord + 1
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call origin_and_size(fileContent(s:endPos),header_type,compressed,data_type,coord)
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call gridSizeOrigin(fileContent(s:endPos),headerType,compressed,dataType,coord)
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endif
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if(index(fileContent(startPos:endPos),'</Coordinates>',kind=pI64) /= 0_pI64) exit
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startPos = endPos + 2_pI64
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@ -409,7 +406,7 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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endif
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endif
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if(readCellData .and. readCoordinates) exit
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if(gotCellData .and. gotCoordinates) exit
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startPos = endPos + 2_pI64
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end do
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@ -424,19 +421,23 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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!------------------------------------------------------------------------------------------------
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!> @brief determine size and origin from coordinates
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!------------------------------------------------------------------------------------------------
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!ToDo: check for regular spacing
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subroutine origin_and_size(base64_str,header_type,compressed,data_type,direction)
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subroutine gridSizeOrigin(base64_str,headerType,compressed,dataType,direction)
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string of 1D coordinates
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header_type, & ! header type (UInt32 or Uint64)
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data_type ! data type (Int32, Int64, Float32, Float64)
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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, intent(in) :: direction ! direction (1=x,2=y,3=z)
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real(pReal), dimension(:), allocatable :: coords
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real(pReal), dimension(:), allocatable :: coords,delta
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coords = as_pReal(base64_str,header_type,compressed,data_type)
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coords = as_pReal(base64_str,headerType,compressed,dataType)
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delta = coords(2:) - coords(:size(coords)-1)
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if(any(delta<0.0_pReal) .or. dNeq(maxval(delta),minval(delta))) &
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call IO_error(error_ID = 844, ext_msg = 'grid spacing')
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grid(direction) = size(coords)-1
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origin(direction) = coords(1)
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geomSize(direction) = coords(size(coords)) - coords(1)
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@ -446,26 +447,26 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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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,header_type,compressed,data_type)
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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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header_type, & ! header type (UInt32 or Uint64)
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data_type ! data type (Int32, Int64, Float32, Float64)
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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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select case(data_type)
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select case(dataType)
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case('Int32')
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as_Int = int(bytes_to_C_INT32_T(asBytes(base64_str,header_type,compressed)))
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as_Int = int(bytes_to_C_INT32_T(asBytes(base64_str,headerType,compressed)))
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case('Int64')
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as_Int = int(bytes_to_C_INT64_T(asBytes(base64_str,header_type,compressed)))
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as_Int = int(bytes_to_C_INT64_T(asBytes(base64_str,headerType,compressed)))
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case('Float32')
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as_Int = int(bytes_to_C_FLOAT (asBytes(base64_str,header_type,compressed)))
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as_Int = int(bytes_to_C_FLOAT (asBytes(base64_str,headerType,compressed)))
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case('Float64')
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as_Int = int(bytes_to_C_DOUBLE (asBytes(base64_str,header_type,compressed)))
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as_Int = int(bytes_to_C_DOUBLE (asBytes(base64_str,headerType,compressed)))
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case default
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allocate(as_Int(0))
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call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
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end select
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end function as_Int
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@ -474,26 +475,26 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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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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function as_pReal(base64_str,header_type,compressed,data_type)
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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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header_type, & ! header type (UInt32 or Uint64)
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data_type ! data type (Int32, Int64, Float32, Float64)
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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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select case(data_type)
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select case(dataType)
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case('Int32')
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as_pReal = real(bytes_to_C_INT32_T(asBytes(base64_str,header_type,compressed)),pReal)
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as_pReal = real(bytes_to_C_INT32_T(asBytes(base64_str,headerType,compressed)),pReal)
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case('Int64')
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as_pReal = real(bytes_to_C_INT64_T(asBytes(base64_str,header_type,compressed)),pReal)
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as_pReal = real(bytes_to_C_INT64_T(asBytes(base64_str,headerType,compressed)),pReal)
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case('Float32')
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as_pReal = real(bytes_to_C_FLOAT (asBytes(base64_str,header_type,compressed)),pReal)
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as_pReal = real(bytes_to_C_FLOAT (asBytes(base64_str,headerType,compressed)),pReal)
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case('Float64')
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as_pReal = real(bytes_to_C_DOUBLE (asBytes(base64_str,header_type,compressed)),pReal)
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as_pReal = real(bytes_to_C_DOUBLE (asBytes(base64_str,headerType,compressed)),pReal)
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case default
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allocate(as_pReal(0))
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call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
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end select
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end function as_pReal
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@ -502,18 +503,18 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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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,header_type,compressed) result(bytes)
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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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header_type ! header type (UInt32 or Uint64)
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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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if(compressed) then
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bytes = asBytes_compressed(base64_str,header_type)
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bytes = asBytes_compressed(base64_str,headerType)
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else
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bytes = asBytes_uncompressed(base64_str,header_type)
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bytes = asBytes_uncompressed(base64_str,headerType)
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endif
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end function asBytes
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@ -527,38 +528,39 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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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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function asBytes_compressed(base64_str,header_type) result(bytes)
|
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function asBytes_compressed(base64_str,headerType) result(bytes)
|
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|
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character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
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header_type ! header type (UInt32 or Uint64)
|
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headerType ! header type (UInt32 or Uint64)
|
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|
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integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
|
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integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes, bytes_inflated
|
||||
|
||||
integer(pI64), dimension(:), allocatable :: temp, size_inflated, size_deflated
|
||||
integer(pI64) :: header_len, N_blocks, b,s,e
|
||||
integer(pI64) :: headerLen, nBlock, b,s,e
|
||||
|
||||
if (header_type == 'UInt32') then
|
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if (headerType == 'UInt32') then
|
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temp = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(:base64_nChar(4_pI64)))),pI64)
|
||||
N_blocks = int(temp(1),pI64)
|
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header_len = 4_pI64 * (3_pI64 + N_blocks)
|
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temp = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(:base64_nChar(header_len)))),pI64)
|
||||
elseif(header_type == 'UInt64') then
|
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nBlock = int(temp(1),pI64)
|
||||
headerLen = 4_pI64 * (3_pI64 + nBlock)
|
||||
temp = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
|
||||
elseif(headerType == 'UInt64') then
|
||||
temp = int(bytes_to_C_INT64_T(base64_to_bytes(base64_str(:base64_nChar(8_pI64)))),pI64)
|
||||
N_blocks = int(temp(1),pI64)
|
||||
header_len = 8_pI64 * (3_pI64 + N_blocks)
|
||||
temp = int(bytes_to_C_INT64_T(base64_to_bytes(base64_str(:base64_nChar(header_len)))),pI64)
|
||||
nBlock = int(temp(1),pI64)
|
||||
headerLen = 8_pI64 * (3_pI64 + nBlock)
|
||||
temp = int(bytes_to_C_INT64_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
|
||||
endif
|
||||
|
||||
allocate(size_inflated(N_blocks),source=temp(2))
|
||||
size_inflated(N_blocks) = merge(temp(3),temp(2),temp(3)/=0_pI64)
|
||||
allocate(size_inflated(nBlock),source=temp(2))
|
||||
size_inflated(nBlock) = merge(temp(3),temp(2),temp(3)/=0_pI64)
|
||||
size_deflated = temp(4:)
|
||||
allocate(bytes(0))
|
||||
bytes_inflated = base64_to_bytes(base64_str(base64_nChar(headerLen)+1_pI64:))
|
||||
|
||||
allocate(bytes(0))
|
||||
e = 0_pI64
|
||||
do b = 1, N_blocks
|
||||
do b = 1, nBlock
|
||||
s = e + 1_pI64
|
||||
e = s + size_deflated(b) - 1_pI64
|
||||
bytes = [bytes,zlib_inflate(base64_to_bytes(base64_str(base64_nChar(header_len)+1:),s,e),size_inflated(b))]
|
||||
bytes = [bytes,zlib_inflate(bytes_inflated(s:e),size_inflated(b))]
|
||||
enddo
|
||||
|
||||
end function asBytes_compressed
|
||||
|
|
@ -569,29 +571,29 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
|
|||
!> @details An uncompressed Base64 string consists of N headers blocks and a N data blocks
|
||||
![#bytes-1/DATA-1][#bytes-2/DATA-2]...
|
||||
!------------------------------------------------------------------------------------------------
|
||||
function asBytes_uncompressed(base64_str,header_type) result(bytes)
|
||||
function asBytes_uncompressed(base64_str,headerType) result(bytes)
|
||||
|
||||
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
||||
header_type ! header type (UInt32 or Uint64)
|
||||
headerType ! header type (UInt32 or Uint64)
|
||||
|
||||
integer(pI64) :: s
|
||||
integer(pI64), dimension(1) :: N_bytes
|
||||
integer(pI64), dimension(1) :: nByte
|
||||
|
||||
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
|
||||
allocate(bytes(0))
|
||||
|
||||
s=0_pI64
|
||||
if (header_type == 'UInt32') then
|
||||
if (headerType == 'UInt32') then
|
||||
do while(s+base64_nChar(4_pI64)<(len(base64_str,pI64)))
|
||||
N_bytes = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64)))),pI64)
|
||||
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64+N_bytes(1))),5_pI64)]
|
||||
s = s + base64_nChar(4_pI64+N_bytes(1))
|
||||
nByte = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64)))),pI64)
|
||||
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64+nByte(1))),5_pI64)]
|
||||
s = s + base64_nChar(4_pI64+nByte(1))
|
||||
enddo
|
||||
elseif(header_type == 'UInt64') then
|
||||
elseif(headerType == 'UInt64') then
|
||||
do while(s+base64_nChar(8_pI64)<(len(base64_str,pI64)))
|
||||
N_bytes = int(bytes_to_C_INT64_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64)))),pI64)
|
||||
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64+N_bytes(1))),9_pI64)]
|
||||
s = s + base64_nChar(8_pI64+N_bytes(1))
|
||||
nByte = int(bytes_to_C_INT64_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64)))),pI64)
|
||||
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64+nByte(1))),9_pI64)]
|
||||
s = s + base64_nChar(8_pI64+nByte(1))
|
||||
enddo
|
||||
endif
|
||||
|
||||
|
|
@ -600,7 +602,6 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
|
|||
!------------------------------------------------------------------------------------------------
|
||||
!> @brief Get XML string value for given key
|
||||
!------------------------------------------------------------------------------------------------
|
||||
! ToDo: check if "=" is between key and value
|
||||
pure function getXMLValue(line,key)
|
||||
|
||||
character(len=*), intent(in) :: line, key
|
||||
|
|
@ -616,52 +617,39 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
|
|||
if(s==0) then
|
||||
getXMLValue = ''
|
||||
else
|
||||
s = s + 1 + scan(line(s+1:),"'"//'"')
|
||||
e = s + 1 + scan(line(s+1:),"'"//'"')
|
||||
if(scan(line(s:e-2),'=') == 0) then
|
||||
getXMLValue = ''
|
||||
else
|
||||
s = e
|
||||
! https://community.intel.com/t5/Intel-Fortran-Compiler/ICE-for-merge-with-strings/m-p/1207204#M151657
|
||||
#ifdef __INTEL_COMPILER
|
||||
q = str(s-1:s-1)
|
||||
q = line(s-1:s-1)
|
||||
e = s + index(line(s:),q) - 1
|
||||
#else
|
||||
e = s + index(line(s:),merge("'",'"',line(s-1:s-1)=="'")) - 1
|
||||
#endif
|
||||
getXMLValue = line(s:e-1)
|
||||
endif
|
||||
endif
|
||||
|
||||
end function
|
||||
|
||||
|
||||
!------------------------------------------------------------------------------------------------
|
||||
!> @brief figure out if file format is understandable
|
||||
!> @brief check for supported file format
|
||||
!------------------------------------------------------------------------------------------------
|
||||
pure function fileOk(line)
|
||||
pure function fileFormatOk(line)
|
||||
|
||||
character(len=*),intent(in) :: line
|
||||
logical :: fileOk
|
||||
logical :: fileFormatOk
|
||||
|
||||
fileOk = getXMLValue(line,'type') == 'RectilinearGrid' .and. &
|
||||
fileFormatOk = getXMLValue(line,'type') == 'RectilinearGrid' .and. &
|
||||
getXMLValue(line,'byte_order') == 'LittleEndian' .and. &
|
||||
getXMLValue(line,'compressor') /= 'vtkLZ4DataCompressor' .and. &
|
||||
getXMLValue(line,'compressor') /= 'vtkLZMADataCompressor'
|
||||
|
||||
end function fileOk
|
||||
|
||||
|
||||
!------------------------------------------------------------------------------------------------
|
||||
!> @brief get grid information from '<RectilinearGrid WholeExtent="0 x 0 y 0 z">'
|
||||
!------------------------------------------------------------------------------------------------
|
||||
function getGrid(line)
|
||||
|
||||
character(len=*),intent(in) :: line
|
||||
|
||||
integer,dimension(3) :: getGrid
|
||||
|
||||
integer :: s,e,i
|
||||
|
||||
s=scan(line,'"'//"'",back=.False.)
|
||||
e=scan(line,'"'//"'",back=.True.)
|
||||
|
||||
getGrid = [(IO_intValue(line(s+1:e-1),IO_stringPos(line(s+1:e-1)),i*2),i=1,3)]
|
||||
|
||||
end function getGrid
|
||||
end function fileFormatOk
|
||||
|
||||
end subroutine readVTR
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue