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DAMASK_EICMD
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polishing 

- unified style (CamelCase)
- more sanity checks
- simplified determination of grid
This commit is contained in:
Martin Diehl 2020-09-13 06:58:34 +02:00
parent 81063046c4
commit e2ded43636
1 changed files with 78 additions and 90 deletions
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158
src/grid/discretization_grid.f90
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@ -313,7 +313,7 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
integer, dimension(:), intent(out), allocatable :: & integer, dimension(:), intent(out), allocatable :: &
microstructure microstructure
character(len=:), allocatable :: fileContent, data_type, header_type character(len=:), allocatable :: fileContent, dataType, headerType
logical :: inFile,inGrid,readCoordinates,readCellData,compressed logical :: inFile,inGrid,readCoordinates,readCellData,compressed
integer :: fileUnit, myStat, coord integer :: fileUnit, myStat, coord
integer(pI64) :: & integer(pI64) :: &
@ -350,15 +350,12 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
if(index(fileContent(startPos:endPos),'<VTKFile',kind=pI64) /= 0_pI64) then if(index(fileContent(startPos:endPos),'<VTKFile',kind=pI64) /= 0_pI64) then
inFile = .true. inFile = .true.
if(.not. fileOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format') if(.not. fileOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format')
header_type = merge('UInt64','UInt32',getXMLValue(fileContent(startPos:endPos),'header_type')=='UInt64') headerType = merge('UInt64','UInt32',getXMLValue(fileContent(startPos:endPos),'header_type')=='UInt64')
compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor' compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor'
endif endif
else else
if(.not. inGrid) then if(.not. inGrid) then
if(index(fileContent(startPos:endPos),'<RectilinearGrid',kind=pI64) /= 0_pI64) then if(index(fileContent(startPos:endPos),'<RectilinearGrid',kind=pI64) /= 0_pI64) inGrid = .true.
inGrid = .true.
grid = getGrid(fileContent(startPos:endPos))
endif
else else
if(index(fileContent(startPos:endPos),'<CellData>',kind=pI64) /= 0_pI64) then if(index(fileContent(startPos:endPos),'<CellData>',kind=pI64) /= 0_pI64) then
readCellData = .true. readCellData = .true.
@ -370,12 +367,12 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') & if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
call IO_error(error_ID = 844, ext_msg='format (materialpoint)') call IO_error(error_ID = 844, ext_msg='format (materialpoint)')
data_type = getXMLValue(fileContent(startPos:endPos),'type') dataType = getXMLValue(fileContent(startPos:endPos),'type')
startPos = endPos + 2_pI64 startPos = endPos + 2_pI64
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64 endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
s = startPos + verify(fileContent(startPos:endPos),IO_WHITESPACE,kind=pI64) -1_pI64 ! start (no leading whitespace) s = startPos + verify(fileContent(startPos:endPos),IO_WHITESPACE,kind=pI64) -1_pI64 ! start (no leading whitespace)
microstructure = as_Int(fileContent(s:endPos),header_type,compressed,data_type) microstructure = as_Int(fileContent(s:endPos),headerType,compressed,dataType)
exit exit
endif endif
startPos = endPos + 2_pI64 startPos = endPos + 2_pI64
@ -391,7 +388,7 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') & if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
call IO_error(error_ID = 844, ext_msg='format (coordinates)') call IO_error(error_ID = 844, ext_msg='format (coordinates)')
data_type = getXMLValue(fileContent(startPos:endPos),'type') dataType = getXMLValue(fileContent(startPos:endPos),'type')
startPos = endPos + 2_pI64 startPos = endPos + 2_pI64
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64 endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
@ -399,7 +396,7 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
coord = coord + 1 coord = coord + 1
call origin_and_size(fileContent(s:endPos),header_type,compressed,data_type,coord) call gridSizeOrigin(fileContent(s:endPos),headerType,compressed,dataType,coord)
endif endif
if(index(fileContent(startPos:endPos),'</Coordinates>',kind=pI64) /= 0_pI64) exit if(index(fileContent(startPos:endPos),'</Coordinates>',kind=pI64) /= 0_pI64) exit
startPos = endPos + 2_pI64 startPos = endPos + 2_pI64
@ -423,18 +420,23 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
!------------------------------------------------------------------------------------------------ !------------------------------------------------------------------------------------------------
!> @brief determine size and origin from coordinates !> @brief determine size and origin from coordinates
!------------------------------------------------------------------------------------------------ !------------------------------------------------------------------------------------------------
!ToDo: check for regular spacing subroutine gridSizeOrigin(base64_str,headerType,compressed,dataType,direction)
subroutine origin_and_size(base64_str,header_type,compressed,data_type,direction)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string of 1D coordinates character(len=*), intent(in) :: base64_str, & ! base64 encoded string of 1D coordinates
header_type, & ! header type (UInt32 or Uint64) headerType, & ! header type (UInt32 or Uint64)
data_type ! data type (Int32, Int64, Float32, Float64) dataType ! data type (Int32, Int64, Float32, Float64)
logical, intent(in) :: compressed ! indicate whether data is zlib compressed logical, intent(in) :: compressed ! indicate whether data is zlib compressed
integer, intent(in) :: direction ! direction (1=x,2=y,3=z) integer, intent(in) :: direction ! direction (1=x,2=y,3=z)
real(pReal), dimension(:), allocatable :: coords real(pReal), dimension(:), allocatable :: coords,delta
coords = as_pReal(base64_str,header_type,compressed,data_type) coords = as_pReal(base64_str,headerType,compressed,dataType)
delta = coords(2:) - coords(:size(coords)-1)
if(any(delta<0.0_pReal) .or. dNeq(maxval(delta),minval(delta))) &
call IO_error(error_ID = 844, ext_msg = 'grid spacing')
grid(direction) = size(coords)-1
origin(direction) = coords(1) origin(direction) = coords(1)
geomSize(direction) = coords(size(coords)) - coords(1) geomSize(direction) = coords(size(coords)) - coords(1)
@ -444,26 +446,26 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
!------------------------------------------------------------------------------------------------ !------------------------------------------------------------------------------------------------
!> @brief Interpret Base64 string in vtk XML file as integer of default kind !> @brief Interpret Base64 string in vtk XML file as integer of default kind
!------------------------------------------------------------------------------------------------ !------------------------------------------------------------------------------------------------
function as_Int(base64_str,header_type,compressed,data_type) function as_Int(base64_str,headerType,compressed,dataType)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string character(len=*), intent(in) :: base64_str, & ! base64 encoded string
header_type, & ! header type (UInt32 or Uint64) headerType, & ! header type (UInt32 or Uint64)
data_type ! data type (Int32, Int64, Float32, Float64) dataType ! data type (Int32, Int64, Float32, Float64)
logical, intent(in) :: compressed ! indicate whether data is zlib compressed logical, intent(in) :: compressed ! indicate whether data is zlib compressed
integer, dimension(:), allocatable :: as_Int integer, dimension(:), allocatable :: as_Int
select case(data_type) select case(dataType)
case('Int32') case('Int32')
as_Int = int(bytes_to_C_INT32_T(asBytes(base64_str,header_type,compressed))) as_Int = int(bytes_to_C_INT32_T(asBytes(base64_str,headerType,compressed)))
case('Int64') case('Int64')
as_Int = int(bytes_to_C_INT64_T(asBytes(base64_str,header_type,compressed))) as_Int = int(bytes_to_C_INT64_T(asBytes(base64_str,headerType,compressed)))
case('Float32') case('Float32')
as_Int = int(bytes_to_C_FLOAT (asBytes(base64_str,header_type,compressed))) as_Int = int(bytes_to_C_FLOAT (asBytes(base64_str,headerType,compressed)))
case('Float64') case('Float64')
as_Int = int(bytes_to_C_DOUBLE (asBytes(base64_str,header_type,compressed))) as_Int = int(bytes_to_C_DOUBLE (asBytes(base64_str,headerType,compressed)))
case default case default
call IO_error(844_pInt,ext_msg='unknown data type: '//trim(data_type)) call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
end select end select
end function as_Int end function as_Int
@ -472,26 +474,26 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
!------------------------------------------------------------------------------------------------ !------------------------------------------------------------------------------------------------
!> @brief Interpret Base64 string in vtk XML file as integer of pReal kind !> @brief Interpret Base64 string in vtk XML file as integer of pReal kind
!------------------------------------------------------------------------------------------------ !------------------------------------------------------------------------------------------------
function as_pReal(base64_str,header_type,compressed,data_type) function as_pReal(base64_str,headerType,compressed,dataType)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string character(len=*), intent(in) :: base64_str, & ! base64 encoded string
header_type, & ! header type (UInt32 or Uint64) headerType, & ! header type (UInt32 or Uint64)
data_type ! data type (Int32, Int64, Float32, Float64) dataType ! data type (Int32, Int64, Float32, Float64)
logical, intent(in) :: compressed ! indicate whether data is zlib compressed logical, intent(in) :: compressed ! indicate whether data is zlib compressed
real(pReal), dimension(:), allocatable :: as_pReal real(pReal), dimension(:), allocatable :: as_pReal
select case(data_type) select case(dataType)
case('Int32') case('Int32')
as_pReal = real(bytes_to_C_INT32_T(asBytes(base64_str,header_type,compressed)),pReal) as_pReal = real(bytes_to_C_INT32_T(asBytes(base64_str,headerType,compressed)),pReal)
case('Int64') case('Int64')
as_pReal = real(bytes_to_C_INT64_T(asBytes(base64_str,header_type,compressed)),pReal) as_pReal = real(bytes_to_C_INT64_T(asBytes(base64_str,headerType,compressed)),pReal)
case('Float32') case('Float32')
as_pReal = real(bytes_to_C_FLOAT (asBytes(base64_str,header_type,compressed)),pReal) as_pReal = real(bytes_to_C_FLOAT (asBytes(base64_str,headerType,compressed)),pReal)
case('Float64') case('Float64')
as_pReal = real(bytes_to_C_DOUBLE (asBytes(base64_str,header_type,compressed)),pReal) as_pReal = real(bytes_to_C_DOUBLE (asBytes(base64_str,headerType,compressed)),pReal)
case default case default
call IO_error(844_pInt,ext_msg='unknown data type: '//trim(data_type)) call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
end select end select
end function as_pReal end function as_pReal
@ -500,18 +502,18 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
!------------------------------------------------------------------------------------------------ !------------------------------------------------------------------------------------------------
!> @brief Interpret Base64 string in vtk XML file as bytes !> @brief Interpret Base64 string in vtk XML file as bytes
!------------------------------------------------------------------------------------------------ !------------------------------------------------------------------------------------------------
function asBytes(base64_str,header_type,compressed) result(bytes) function asBytes(base64_str,headerType,compressed) result(bytes)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string character(len=*), intent(in) :: base64_str, & ! base64 encoded string
header_type ! header type (UInt32 or Uint64) headerType ! header type (UInt32 or Uint64)
logical, intent(in) :: compressed ! indicate whether data is zlib compressed logical, intent(in) :: compressed ! indicate whether data is zlib compressed
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
if(compressed) then if(compressed) then
bytes = asBytes_compressed(base64_str,header_type) bytes = asBytes_compressed(base64_str,headerType)
else else
bytes = asBytes_uncompressed(base64_str,header_type) bytes = asBytes_uncompressed(base64_str,headerType)
endif endif
end function asBytes end function asBytes
@ -525,36 +527,36 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
! #p-size = Size of last partial block (zero if it not needed) ! #p-size = Size of last partial block (zero if it not needed)
! #c-size-i = Size in bytes of block i after compression ! #c-size-i = Size in bytes of block i after compression
!------------------------------------------------------------------------------------------------ !------------------------------------------------------------------------------------------------
function asBytes_compressed(base64_str,header_type) result(bytes) function asBytes_compressed(base64_str,headerType) result(bytes)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string character(len=*), intent(in) :: base64_str, & ! base64 encoded string
header_type ! header type (UInt32 or Uint64) headerType ! header type (UInt32 or Uint64)
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes, bytes_inflated integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes, bytes_inflated
integer(pI64), dimension(:), allocatable :: temp, size_inflated, size_deflated 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 if (headerType == 'UInt32') then
temp = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(:base64_nChar(4_pI64)))),pI64) temp = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(:base64_nChar(4_pI64)))),pI64)
N_blocks = int(temp(1),pI64) nBlock = int(temp(1),pI64)
header_len = 4_pI64 * (3_pI64 + N_blocks) headerLen = 4_pI64 * (3_pI64 + nBlock)
temp = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(:base64_nChar(header_len)))),pI64) temp = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
elseif(header_type == 'UInt64') then elseif(headerType == 'UInt64') then
temp = int(bytes_to_C_INT64_T(base64_to_bytes(base64_str(:base64_nChar(8_pI64)))),pI64) temp = int(bytes_to_C_INT64_T(base64_to_bytes(base64_str(:base64_nChar(8_pI64)))),pI64)
N_blocks = int(temp(1),pI64) nBlock = int(temp(1),pI64)
header_len = 8_pI64 * (3_pI64 + N_blocks) headerLen = 8_pI64 * (3_pI64 + nBlock)
temp = int(bytes_to_C_INT64_T(base64_to_bytes(base64_str(:base64_nChar(header_len)))),pI64) temp = int(bytes_to_C_INT64_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
endif endif
allocate(size_inflated(N_blocks),source=temp(2)) allocate(size_inflated(nBlock),source=temp(2))
size_inflated(N_blocks) = merge(temp(3),temp(2),temp(3)/=0_pI64) size_inflated(nBlock) = merge(temp(3),temp(2),temp(3)/=0_pI64)
size_deflated = temp(4:) size_deflated = temp(4:)
bytes_inflated = base64_to_bytes(base64_str(base64_nChar(header_len)+1_pI64:)) bytes_inflated = base64_to_bytes(base64_str(base64_nChar(headerLen)+1_pI64:))
allocate(bytes(0)) allocate(bytes(0))
e = 0_pI64 e = 0_pI64
do b = 1, N_blocks do b = 1, nBlock
s = e + 1_pI64 s = e + 1_pI64
e = s + size_deflated(b) - 1_pI64 e = s + size_deflated(b) - 1_pI64
bytes = [bytes,zlib_inflate(bytes_inflated(s:e),size_inflated(b))] bytes = [bytes,zlib_inflate(bytes_inflated(s:e),size_inflated(b))]
@ -568,29 +570,29 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
!> @details An uncompressed Base64 string consists of N headers blocks and a N data blocks !> @details An uncompressed Base64 string consists of N headers blocks and a N data blocks
![#bytes-1/DATA-1][#bytes-2/DATA-2]... ![#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 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) :: s
integer(pI64), dimension(1) :: N_bytes integer(pI64), dimension(1) :: nByte
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
allocate(bytes(0)) allocate(bytes(0))
s=0_pI64 s=0_pI64
if (header_type == 'UInt32') then if (headerType == 'UInt32') then
do while(s+base64_nChar(4_pI64)<(len(base64_str,pI64))) 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) 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+N_bytes(1))),5_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+N_bytes(1)) s = s + base64_nChar(4_pI64+nByte(1))
enddo enddo
elseif(header_type == 'UInt64') then elseif(headerType == 'UInt64') then
do while(s+base64_nChar(8_pI64)<(len(base64_str,pI64))) 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) 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+N_bytes(1))),9_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+N_bytes(1)) s = s + base64_nChar(8_pI64+nByte(1))
enddo enddo
endif endif
@ -599,7 +601,6 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
!------------------------------------------------------------------------------------------------ !------------------------------------------------------------------------------------------------
!> @brief Get XML string value for given key !> @brief Get XML string value for given key
!------------------------------------------------------------------------------------------------ !------------------------------------------------------------------------------------------------
! ToDo: check if "=" is between key and value
pure function getXMLValue(line,key) pure function getXMLValue(line,key)
character(len=*), intent(in) :: line, key character(len=*), intent(in) :: line, key
@ -615,7 +616,12 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
if(s==0) then if(s==0) then
getXMLValue = '' getXMLValue = ''
else 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 #ifdef __INTEL_COMPILER
q = line(s-1:s-1) q = line(s-1:s-1)
e = s + index(line(s:),q) - 1 e = s + index(line(s:),q) - 1
@ -624,6 +630,7 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
#endif #endif
getXMLValue = line(s:e-1) getXMLValue = line(s:e-1)
endif endif
endif
end function end function
@ -643,25 +650,6 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
end function fileOk 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 subroutine readVTR end subroutine readVTR