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DAMASK_EICMD
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Merge branch 'vtr-as-input' into Fortran-simplifications

This commit is contained in:
Martin Diehl 2020-09-13 19:34:48 +02:00
parent bb6b91e857 507910ffcd
commit f266def906
2 changed files with 107 additions and 119 deletions
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4
.gitlab-ci.yml
View File

@ -499,7 +499,7 @@ mergeIntoMaster:
removeData:
stage: clean
before_script:
- echo 'Do nothing'
- echo "Removing data and lock of pipeline $CI_PIPELINE_ID"
script:
- rm -rf $TESTROOT/GitLabCI_Pipeline_$CI_PIPELINE_ID
- sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue # in case pipeline was manually (web GUI) restarted and releaseLock was performed already
@ -511,7 +511,7 @@ removeData:
removeLock:
stage: releaseLock
before_script:
- echo 'Do nothing'
- echo "Removing lock of pipeline $CI_PIPELINE_ID"
when: always
script: sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue
except:

222
src/grid/discretization_grid.f90
View File

@ -146,10 +146,10 @@ end subroutine discretization_grid_init
subroutine readGeom(grid,geomSize,origin,microstructure)
integer, dimension(3), intent(out) :: &
grid ! grid (for all processes!)
grid ! grid (across all processes!)
real(pReal), dimension(3), intent(out) :: &
geomSize, & ! size (for all processes!)
origin ! origin (for all processes!)
geomSize, & ! size (across all processes!)
origin ! origin (across all processes!)
integer, dimension(:), intent(out), allocatable :: &
microstructure
@ -195,7 +195,7 @@ subroutine readGeom(grid,geomSize,origin,microstructure)
endif
!--------------------------------------------------------------------------------------------------
! read and interprete header
! read and interpret header
origin = 0.0_pReal
l = 0
do while (l < headerLength .and. startPos < len(rawData))
@ -307,15 +307,15 @@ end subroutine readGeom
subroutine readVTR(grid,geomSize,origin,microstructure)
integer, dimension(3), intent(out) :: &
grid ! grid (for all processes!)
grid ! grid (across all processes!)
real(pReal), dimension(3), intent(out) :: &
geomSize, & ! size (for all processes!)
origin ! origin (for all processes!)
geomSize, & ! size (across all processes!)
origin ! origin (across all processes!)
integer, dimension(:), intent(out), allocatable :: &
microstructure
character(len=:), allocatable :: fileContent, data_type, header_type
logical :: inFile,inGrid,readCoordinates,readCellData,compressed
character(len=:), allocatable :: fileContent, dataType, headerType
logical :: inFile,inGrid,gotCoordinates,gotCellData,compressed
integer :: fileUnit, myStat, coord
integer(pI64) :: &
fileLength, & !< length of the geom file (in characters)
@ -335,13 +335,13 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
read(fileUnit) fileContent
close(fileUnit)
inFile = .false.
inGrid = .false.
readCoordinates = .false.
readCelldata = .false.
inFile = .false.
inGrid = .false.
gotCoordinates = .false.
gotCelldata = .false.
!--------------------------------------------------------------------------------------------------
! interprete XML file
! interpret XML file
startPos = 1_pI64
do while (startPos < len(fileContent,kind=pI64))
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
@ -350,19 +350,16 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
if(.not. inFile) then
if(index(fileContent(startPos:endPos),'<VTKFile',kind=pI64) /= 0_pI64) then
inFile = .true.
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')
if(.not. fileFormatOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format')
headerType = merge('UInt64','UInt32',getXMLValue(fileContent(startPos:endPos),'header_type')=='UInt64')
compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor'
endif
else
if(.not. inGrid) then
if(index(fileContent(startPos:endPos),'<RectilinearGrid',kind=pI64) /= 0_pI64) then
inGrid = .true.
grid = getGrid(fileContent(startPos:endPos))
endif
if(index(fileContent(startPos:endPos),'<RectilinearGrid',kind=pI64) /= 0_pI64) inGrid = .true.
else
if(index(fileContent(startPos:endPos),'<CellData>',kind=pI64) /= 0_pI64) then
readCellData = .true.
gotCellData = .true.
startPos = endPos + 2_pI64
do while (index(fileContent(startPos:endPos),'</CellData>',kind=pI64) == 0_pI64)
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
@ -371,18 +368,18 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
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
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)
microstructure = as_Int(fileContent(s:endPos),header_type,compressed,data_type)
microstructure = as_Int(fileContent(s:endPos),headerType,compressed,dataType)
exit
endif
startPos = endPos + 2_pI64
enddo
elseif(index(fileContent(startPos:endPos),'<Coordinates>',kind=pI64) /= 0_pI64) then
readCoordinates = .true.
gotCoordinates = .true.
startPos = endPos + 2_pI64
coord = 0
@ -392,7 +389,7 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
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
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
@ -400,7 +397,7 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
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
if(index(fileContent(startPos:endPos),'</Coordinates>',kind=pI64) /= 0_pI64) exit
startPos = endPos + 2_pI64
@ -409,7 +406,7 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
endif
endif
if(readCellData .and. readCoordinates) exit
if(gotCellData .and. gotCoordinates) exit
startPos = endPos + 2_pI64
end do
@ -424,20 +421,24 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
!------------------------------------------------------------------------------------------------
!> @brief determine size and origin from coordinates
!------------------------------------------------------------------------------------------------
!ToDo: check for regular spacing
subroutine origin_and_size(base64_str,header_type,compressed,data_type,direction)
subroutine gridSizeOrigin(base64_str,headerType,compressed,dataType,direction)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string of 1D coordinates
header_type, & ! header type (UInt32 or Uint64)
data_type ! data type (Int32, Int64, Float32, Float64)
headerType, & ! header type (UInt32 or Uint64)
dataType ! data type (Int32, Int64, Float32, Float64)
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
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)
origin(direction) = coords(1)
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)
geomSize(direction) = coords(size(coords)) - coords(1)
end subroutine
@ -446,26 +447,26 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
!------------------------------------------------------------------------------------------------
!> @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
header_type, & ! header type (UInt32 or Uint64)
data_type ! data type (Int32, Int64, Float32, Float64)
headerType, & ! header type (UInt32 or Uint64)
dataType ! data type (Int32, Int64, Float32, Float64)
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
integer, dimension(:), allocatable :: as_Int
select case(data_type)
select case(dataType)
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')
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')
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')
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
allocate(as_Int(0))
call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
end select
end function as_Int
@ -474,26 +475,26 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
!------------------------------------------------------------------------------------------------
!> @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
header_type, & ! header type (UInt32 or Uint64)
data_type ! data type (Int32, Int64, Float32, Float64)
headerType, & ! header type (UInt32 or Uint64)
dataType ! data type (Int32, Int64, Float32, Float64)
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
real(pReal), dimension(:), allocatable :: as_pReal
select case(data_type)
select case(dataType)
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')
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')
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')
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
allocate(as_pReal(0))
call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
end select
end function as_pReal
@ -502,18 +503,18 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
!------------------------------------------------------------------------------------------------
!> @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
header_type ! header type (UInt32 or Uint64)
headerType ! header type (UInt32 or Uint64)
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
if(compressed) then
bytes = asBytes_compressed(base64_str,header_type)
bytes = asBytes_compressed(base64_str,headerType)
else
bytes = asBytes_uncompressed(base64_str,header_type)
bytes = asBytes_uncompressed(base64_str,headerType)
endif
end function asBytes
@ -527,38 +528,39 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
! #p-size = Size of last partial block (zero if it not needed)
! #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
header_type ! header type (UInt32 or Uint64)
headerType ! header type (UInt32 or Uint64)
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
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
if (headerType == 'UInt32') then
temp = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(:base64_nChar(4_pI64)))),pI64)
N_blocks = int(temp(1),pI64)
header_len = 4_pI64 * (3_pI64 + N_blocks)
temp = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(:base64_nChar(header_len)))),pI64)
elseif(header_type == 'UInt64') then
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)
e = s + index(line(s:),q) - 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
e = s + index(line(s:),merge("'",'"',line(s-1:s-1)=="'")) - 1
#endif
getXMLValue = line(s:e-1)
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. &
getXMLValue(line,'byte_order') == 'LittleEndian' .and. &
getXMLValue(line,'compressor') /= 'vtkLZ4DataCompressor' .and. &
getXMLValue(line,'compressor') /= 'vtkLZMADataCompressor'
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