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DAMASK_EICMD
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Merge branch 'development' into table-out-of-place-only

This commit is contained in:
Martin Diehl 2020-09-14 08:06:44 +02:00
parent f6758ecc28 c6907bfa4b
commit b298962101
9 changed files with 453 additions and 88 deletions
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4
.gitlab-ci.yml
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@ -492,7 +492,7 @@ mergeIntoMaster:
removeData: removeData:
stage: clean stage: clean
before_script: before_script:
- echo 'Do nothing' - echo "Removing data and lock of pipeline $CI_PIPELINE_ID"
script: script:
- rm -rf $TESTROOT/GitLabCI_Pipeline_$CI_PIPELINE_ID - rm -rf $TESTROOT/GitLabCI_Pipeline_$CI_PIPELINE_ID
- sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue # in case pipeline was manually (web GUI) restarted and releaseLock was performed already - sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue # in case pipeline was manually (web GUI) restarted and releaseLock was performed already
@ -504,7 +504,7 @@ removeData:
removeLock: removeLock:
stage: releaseLock stage: releaseLock
before_script: before_script:
- echo 'Do nothing' - echo "Removing lock of pipeline $CI_PIPELINE_ID"
when: always when: always
script: sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue script: sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue
except: except:

2
PRIVATE

@ -1 +1 @@
Subproject commit 3bc60348981a68bc22a5ebaafe4173b7513ac264 Subproject commit 92ca3e83b6093c1af277cfc06a504e4bb09fe8bc

2
VERSION
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@ -1 +1 @@
v3.0.0-alpha-136-gc0ea8e3f v3.0.0-alpha-147-gf0806a9e

7
python/damask/_vtk.py
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@ -168,7 +168,7 @@ class VTK:
def _write(writer): def _write(writer):
"""Wrapper for parallel writing.""" """Wrapper for parallel writing."""
writer.Write() writer.Write()
def to_file(self,fname,parallel=True): def to_file(self,fname,parallel=True,compress=True):
""" """
Write to file. Write to file.
@ -192,7 +192,10 @@ class VTK:
if ext and ext != '.'+default_ext: if ext and ext != '.'+default_ext:
raise ValueError(f'Given extension {ext} does not match default .{default_ext}') raise ValueError(f'Given extension {ext} does not match default .{default_ext}')
writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext))) writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
writer.SetCompressorTypeToZLib() if compress:
writer.SetCompressorTypeToZLib()
else:
writer.SetCompressorTypeToNone()
writer.SetDataModeToBinary() writer.SetDataModeToBinary()
writer.SetInputData(self.vtk_data) writer.SetInputData(self.vtk_data)

2
src/IO.f90
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@ -585,6 +585,8 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
msg = 'incomplete information in grid mesh header' msg = 'incomplete information in grid mesh header'
case (843) case (843)
msg = 'microstructure count mismatch' msg = 'microstructure count mismatch'
case (844)
msg = 'invalid VTR file'
case (846) case (846)
msg = 'rotation for load case rotation ill-defined (R:RT != I)' msg = 'rotation for load case rotation ill-defined (R:RT != I)'
case (891) case (891)

136
src/base64.f90
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@ -16,7 +16,7 @@ module base64
public :: & public :: &
base64_init, & base64_init, &
base64_to_bytes, & base64_to_bytes, &
base64_nBase64, & base64_nChar, &
base64_nByte base64_nByte
contains contains
@ -37,14 +37,14 @@ end subroutine base64_init
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief Calculate number of Base64 characters required for storage of N bytes. !> @brief Calculate number of Base64 characters required for storage of N bytes.
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
pure function base64_nBase64(nByte) pure function base64_nChar(nByte)
integer(pLongInt), intent(in) :: nByte integer(pI64), intent(in) :: nByte
integer(pLongInt) :: base64_nBase64 integer(pI64) :: base64_nChar
base64_nBase64 = 4_pLongInt * (nByte/3_pLongInt + merge(1_pLongInt,0_pLongInt,mod(nByte,3_pLongInt) /= 0_pLongInt)) base64_nChar = 4_pI64 * (nByte/3_pI64 + merge(1_pI64,0_pI64,mod(nByte,3_pI64) /= 0_pI64))
end function base64_nBase64 end function base64_nChar
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -52,10 +52,10 @@ end function base64_nBase64
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
pure function base64_nByte(nBase64) pure function base64_nByte(nBase64)
integer(pLongInt), intent(in) :: nBase64 integer(pI64), intent(in) :: nBase64
integer(pLongInt) :: base64_nByte integer(pI64) :: base64_nByte
base64_nByte = 3_pLongInt * (nBase64/4_pLongInt) base64_nByte = 3_pI64 * (nBase64/4_pI64)
end function base64_nByte end function base64_nByte
@ -66,36 +66,36 @@ end function base64_nByte
function base64_to_bytes(base64_str,s,e) result(bytes) function base64_to_bytes(base64_str,s,e) result(bytes)
character(len=*), intent(in) :: base64_str !< Base64 string representation character(len=*), intent(in) :: base64_str !< Base64 string representation
integer(pLongInt), intent(in), optional :: & integer(pI64), intent(in), optional :: &
s, & !< start (in bytes) s, & !< start (in bytes)
e !< end (in bytes) e !< end (in bytes)
integer(pLongInt) :: s_bytes, e_bytes, s_str, e_str integer(pI64) :: s_bytes, e_bytes, s_str, e_str
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
if(.not. valid_base64(base64_str)) call IO_error(114,ext_msg='invalid character') if(.not. validBase64(base64_str)) call IO_error(114,ext_msg='invalid character')
if(present(s)) then if(present(s)) then
if(s<1_pLongInt) call IO_error(114, ext_msg='s out of range') if(s<1_pI64) call IO_error(114, ext_msg='s out of range')
s_str = ((s-1_pLongInt)/3_pLongInt)*4_pLongInt + 1_pLongInt s_str = ((s-1_pI64)/3_pI64)*4_pI64 + 1_pI64
s_bytes = mod(s-1_pLongInt,3_pLongInt) + 1_pLongInt s_bytes = mod(s-1_pI64,3_pI64) + 1_pI64
else else
s_str = 1_pLongInt s_str = 1_pI64
s_bytes = 1_pLongInt s_bytes = 1_pI64
endif endif
if(present(e)) then if(present(e)) then
if(e>base64_nByte(len(base64_str,kind=pLongInt))) call IO_error(114, ext_msg='e out of range') if(e>base64_nByte(len(base64_str,kind=pI64))) call IO_error(114, ext_msg='e out of range')
e_str = ((e-1_pLongInt)/3_pLongInt)*4_pLongInt + 4_pLongInt e_str = ((e-1_pI64)/3_pI64)*4_pI64 + 4_pI64
e_bytes = e - base64_nByte(s_str) e_bytes = e - base64_nByte(s_str)
else else
e_str = len(base64_str,kind=pLongInt) e_str = len(base64_str,kind=pI64)
e_bytes = base64_nByte(len(base64_str,kind=pLongInt)) - base64_nByte(s_str) e_bytes = base64_nByte(len(base64_str,kind=pI64)) - base64_nByte(s_str)
if(base64_str(e_str-0_pLongInt:e_str-0_pLongInt) == '=') e_bytes = e_bytes - 1_pLongInt if(base64_str(e_str-0_pI64:e_str-0_pI64) == '=') e_bytes = e_bytes - 1_pI64
if(base64_str(e_str-1_pLongInt:e_str-1_pLongInt) == '=') e_bytes = e_bytes - 1_pLongInt if(base64_str(e_str-1_pI64:e_str-1_pI64) == '=') e_bytes = e_bytes - 1_pI64
endif endif
bytes = decode_base64(base64_str(s_str:e_str)) bytes = decodeBase64(base64_str(s_str:e_str))
bytes = bytes(s_bytes:e_bytes) bytes = bytes(s_bytes:e_bytes)
end function base64_to_bytes end function base64_to_bytes
@ -104,21 +104,21 @@ end function base64_to_bytes
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief Convert a Base64 ASCII string into its byte-wise binary representation. !> @brief Convert a Base64 ASCII string into its byte-wise binary representation.
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
pure function decode_base64(base64_str) result(bytes) pure function decodeBase64(base64_str) result(bytes)
character(len=*), intent(in) :: base64_str !< Base64 string representation character(len=*), intent(in) :: base64_str !< Base64 string representation
integer(C_SIGNED_CHAR), dimension(base64_nByte(len(base64_str,pLongInt))) :: bytes integer(C_SIGNED_CHAR), dimension(base64_nByte(len(base64_str,pI64))) :: bytes
integer(C_SIGNED_CHAR), dimension(0:3) :: charPos integer(C_SIGNED_CHAR), dimension(0:3) :: charPos
integer(pLongInt) :: c, b, p integer(pI64) :: c, b, p
c = 1_pLongInt c = 1_pI64
b = 1_pLongInt b = 1_pI64
do while(c < len(base64_str,kind=pLongInt)) do while(c < len(base64_str,kind=pI64))
do p=0_pLongInt,3_pLongInt do p=0_pI64,3_pI64
if(c+p<=len(base64_str,kind=pLongInt)) then if(c+p<=len(base64_str,kind=pI64)) then
charPos(p) = int(index(base64_encoding,base64_str(c+p:c+p))-1,C_SIGNED_CHAR) charPos(p) = int(index(base64_encoding,base64_str(c+p:c+p))-1,C_SIGNED_CHAR)
else else
charPos(p) = 0_C_SIGNED_CHAR charPos(p) = 0_C_SIGNED_CHAR
@ -131,31 +131,31 @@ pure function decode_base64(base64_str) result(bytes)
call mvbits(charPos(2),2,4,bytes(b+1),0) call mvbits(charPos(2),2,4,bytes(b+1),0)
call mvbits(charPos(2),0,2,bytes(b+2),6) call mvbits(charPos(2),0,2,bytes(b+2),6)
call mvbits(charPos(3),0,6,bytes(b+2),0) call mvbits(charPos(3),0,6,bytes(b+2),0)
b = b+3_pLongInt b = b+3_pI64
c = c+4_pLongInt c = c+4_pI64
enddo enddo
end function decode_base64 end function decodeBase64
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief Test for valid Base64 encoded string. !> @brief Test for valid Base64 encoded string.
!> @details Input string must be properly padded. !> @details Input string must be properly padded.
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
pure logical function valid_base64(base64_str) pure logical function validBase64(base64_str)
character(len=*), intent(in) :: base64_str !< Base64 string representation character(len=*), intent(in) :: base64_str !< Base64 string representation
integer(pLongInt) :: l integer(pI64) :: l
l = len(base64_str,pLongInt) l = len(base64_str,pI64)
valid_base64 = .true. validBase64 = .true.
if(mod(l,4_pLongInt)/=0_pLongInt .or. l < 4_pInt) valid_base64 = .false. if(mod(l,4_pI64)/=0_pI64 .or. l < 4_pInt) validBase64 = .false.
if(verify(base64_str(:l-2_pLongInt),base64_encoding, kind=pLongInt) /= 0_pLongInt) valid_base64 = .false. if(verify(base64_str(:l-2_pI64),base64_encoding, kind=pI64) /= 0_pI64) validBase64 = .false.
if(verify(base64_str(l-1_pLongInt:),base64_encoding//'=',kind=pLongInt) /= 0_pLongInt) valid_base64 = .false. if(verify(base64_str(l-1_pI64:),base64_encoding//'=',kind=pI64) /= 0_pI64) validBase64 = .false.
end function valid_base64 end function validBase64
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -167,58 +167,58 @@ subroutine selfTest
character(len=*), parameter :: zero_to_three = 'AAECAw==' character(len=*), parameter :: zero_to_three = 'AAECAw=='
! https://en.wikipedia.org/wiki/Base64#Output_padding ! https://en.wikipedia.org/wiki/Base64#Output_padding
if(base64_nBase64(20_pLongInt) /= 28_pLongInt) call IO_error(0,ext_msg='base64_nBase64/20/28') if(base64_nChar(20_pI64) /= 28_pI64) call IO_error(0,ext_msg='base64_nChar/20/28')
if(base64_nBase64(19_pLongInt) /= 28_pLongInt) call IO_error(0,ext_msg='base64_nBase64/19/28') if(base64_nChar(19_pI64) /= 28_pI64) call IO_error(0,ext_msg='base64_nChar/19/28')
if(base64_nBase64(18_pLongInt) /= 24_pLongInt) call IO_error(0,ext_msg='base64_nBase64/18/24') if(base64_nChar(18_pI64) /= 24_pI64) call IO_error(0,ext_msg='base64_nChar/18/24')
if(base64_nBase64(17_pLongInt) /= 24_pLongInt) call IO_error(0,ext_msg='base64_nBase64/17/24') if(base64_nChar(17_pI64) /= 24_pI64) call IO_error(0,ext_msg='base64_nChar/17/24')
if(base64_nBase64(16_pLongInt) /= 24_pLongInt) call IO_error(0,ext_msg='base64_nBase64/16/24') if(base64_nChar(16_pI64) /= 24_pI64) call IO_error(0,ext_msg='base64_nChar/16/24')
if(base64_nByte(4_pLongInt) /= 3_pLongInt) call IO_error(0,ext_msg='base64_nByte/4/3') if(base64_nByte(4_pI64) /= 3_pI64) call IO_error(0,ext_msg='base64_nByte/4/3')
if(base64_nByte(8_pLongInt) /= 6_pLongInt) call IO_error(0,ext_msg='base64_nByte/8/6') if(base64_nByte(8_pI64) /= 6_pI64) call IO_error(0,ext_msg='base64_nByte/8/6')
bytes = base64_to_bytes(zero_to_three) bytes = base64_to_bytes(zero_to_three)
if(any(bytes /= int([0,1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 4) call IO_error(0,ext_msg='base64_to_bytes//') if(any(bytes /= int([0,1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 4) call IO_error(0,ext_msg='base64_to_bytes//')
bytes = base64_to_bytes(zero_to_three,e=1_pLongInt) bytes = base64_to_bytes(zero_to_three,e=1_pI64)
if(any(bytes /= int([0],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes//1') if(any(bytes /= int([0],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes//1')
bytes = base64_to_bytes(zero_to_three,e=2_pLongInt) bytes = base64_to_bytes(zero_to_three,e=2_pI64)
if(any(bytes /= int([0,1],C_SIGNED_CHAR)) .or. size(bytes) /= 2) call IO_error(0,ext_msg='base64_to_bytes//2') if(any(bytes /= int([0,1],C_SIGNED_CHAR)) .or. size(bytes) /= 2) call IO_error(0,ext_msg='base64_to_bytes//2')
bytes = base64_to_bytes(zero_to_three,e=3_pLongInt) bytes = base64_to_bytes(zero_to_three,e=3_pI64)
if(any(bytes /= int([0,1,2],C_SIGNED_CHAR)) .or. size(bytes) /= 3) call IO_error(0,ext_msg='base64_to_bytes//3') if(any(bytes /= int([0,1,2],C_SIGNED_CHAR)) .or. size(bytes) /= 3) call IO_error(0,ext_msg='base64_to_bytes//3')
bytes = base64_to_bytes(zero_to_three,e=4_pLongInt) bytes = base64_to_bytes(zero_to_three,e=4_pI64)
if(any(bytes /= int([0,1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 4) call IO_error(0,ext_msg='base64_to_bytes//4') if(any(bytes /= int([0,1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 4) call IO_error(0,ext_msg='base64_to_bytes//4')
bytes = base64_to_bytes(zero_to_three,s=1_pLongInt) bytes = base64_to_bytes(zero_to_three,s=1_pI64)
if(any(bytes /= int([0,1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 4) call IO_error(0,ext_msg='base64_to_bytes/1/') if(any(bytes /= int([0,1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 4) call IO_error(0,ext_msg='base64_to_bytes/1/')
bytes = base64_to_bytes(zero_to_three,s=2_pLongInt) bytes = base64_to_bytes(zero_to_three,s=2_pI64)
if(any(bytes /= int([1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 3) call IO_error(0,ext_msg='base64_to_bytes/2/') if(any(bytes /= int([1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 3) call IO_error(0,ext_msg='base64_to_bytes/2/')
bytes = base64_to_bytes(zero_to_three,s=3_pLongInt) bytes = base64_to_bytes(zero_to_three,s=3_pI64)
if(any(bytes /= int([2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 2) call IO_error(0,ext_msg='base64_to_bytes/3/') if(any(bytes /= int([2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 2) call IO_error(0,ext_msg='base64_to_bytes/3/')
bytes = base64_to_bytes(zero_to_three,s=4_pLongInt) bytes = base64_to_bytes(zero_to_three,s=4_pI64)
if(any(bytes /= int([3],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes/4/') if(any(bytes /= int([3],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes/4/')
bytes = base64_to_bytes(zero_to_three,s=1_pLongInt,e=1_pLongInt) bytes = base64_to_bytes(zero_to_three,s=1_pI64,e=1_pI64)
if(any(bytes /= int([0],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes/1/1') if(any(bytes /= int([0],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes/1/1')
bytes = base64_to_bytes(zero_to_three,s=2_pLongInt,e=2_pLongInt) bytes = base64_to_bytes(zero_to_three,s=2_pI64,e=2_pI64)
if(any(bytes /= int([1],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes/2/2') if(any(bytes /= int([1],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes/2/2')
bytes = base64_to_bytes(zero_to_three,s=3_pLongInt,e=3_pLongInt) bytes = base64_to_bytes(zero_to_three,s=3_pI64,e=3_pI64)
if(any(bytes /= int([2],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes/3/3') if(any(bytes /= int([2],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes/3/3')
bytes = base64_to_bytes(zero_to_three,s=4_pLongInt,e=4_pLongInt) bytes = base64_to_bytes(zero_to_three,s=4_pI64,e=4_pI64)
if(any(bytes /= int([3],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes/4/4') if(any(bytes /= int([3],C_SIGNED_CHAR)) .or. size(bytes) /= 1) call IO_error(0,ext_msg='base64_to_bytes/4/4')
bytes = base64_to_bytes(zero_to_three,s=1_pLongInt,e=2_pLongInt) bytes = base64_to_bytes(zero_to_three,s=1_pI64,e=2_pI64)
if(any(bytes /= int([0,1],C_SIGNED_CHAR)) .or. size(bytes) /= 2) call IO_error(0,ext_msg='base64_to_bytes/1/2') if(any(bytes /= int([0,1],C_SIGNED_CHAR)) .or. size(bytes) /= 2) call IO_error(0,ext_msg='base64_to_bytes/1/2')
bytes = base64_to_bytes(zero_to_three,s=2_pLongInt,e=3_pLongInt) bytes = base64_to_bytes(zero_to_three,s=2_pI64,e=3_pI64)
if(any(bytes /= int([1,2],C_SIGNED_CHAR)) .or. size(bytes) /= 2) call IO_error(0,ext_msg='base64_to_bytes/2/3') if(any(bytes /= int([1,2],C_SIGNED_CHAR)) .or. size(bytes) /= 2) call IO_error(0,ext_msg='base64_to_bytes/2/3')
bytes = base64_to_bytes(zero_to_three,s=3_pLongInt,e=4_pLongInt) bytes = base64_to_bytes(zero_to_three,s=3_pI64,e=4_pI64)
if(any(bytes /= int([2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 2) call IO_error(0,ext_msg='base64_to_bytes/3/4') if(any(bytes /= int([2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 2) call IO_error(0,ext_msg='base64_to_bytes/3/4')
bytes = base64_to_bytes(zero_to_three,s=1_pLongInt,e=3_pLongInt) bytes = base64_to_bytes(zero_to_three,s=1_pI64,e=3_pI64)
if(any(bytes /= int([0,1,2],C_SIGNED_CHAR)) .or. size(bytes) /= 3) call IO_error(0,ext_msg='base64_to_bytes/1/3') if(any(bytes /= int([0,1,2],C_SIGNED_CHAR)) .or. size(bytes) /= 3) call IO_error(0,ext_msg='base64_to_bytes/1/3')
bytes = base64_to_bytes(zero_to_three,s=2_pLongInt,e=4_pLongInt) bytes = base64_to_bytes(zero_to_three,s=2_pI64,e=4_pI64)
if(any(bytes /= int([1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 3) call IO_error(0,ext_msg='base64_to_bytes/2/4') if(any(bytes /= int([1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 3) call IO_error(0,ext_msg='base64_to_bytes/2/4')
bytes = base64_to_bytes(zero_to_three,s=1_pLongInt,e=4_pLongInt) bytes = base64_to_bytes(zero_to_three,s=1_pI64,e=4_pI64)
if(any(bytes /= int([0,1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 4) call IO_error(0,ext_msg='base64_to_bytes/1/4') if(any(bytes /= int([0,1,2,3],C_SIGNED_CHAR)) .or. size(bytes) /= 4) call IO_error(0,ext_msg='base64_to_bytes/1/4')
end subroutine selfTest end subroutine selfTest

371
src/grid/discretization_grid.f90
View File

@ -10,6 +10,8 @@ module discretization_grid
use prec use prec
use system_routines use system_routines
use base64
use zlib
use DAMASK_interface use DAMASK_interface
use IO use IO
use config use config
@ -64,7 +66,11 @@ subroutine discretization_grid_init(restart)
write(6,'(/,a)') ' <<<+- discretization_grid init -+>>>'; flush(6) write(6,'(/,a)') ' <<<+- discretization_grid init -+>>>'; flush(6)
call readGeom(grid,geomSize,origin,microstructureAt) if(index(geometryFile,'.vtr') /= 0) then
call readVTR(grid,geomSize,origin,microstructureAt)
else
call readGeom(grid,geomSize,origin,microstructureAt)
endif
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! grid solver specific quantities ! grid solver specific quantities
@ -139,10 +145,10 @@ end subroutine discretization_grid_init
subroutine readGeom(grid,geomSize,origin,microstructure) subroutine readGeom(grid,geomSize,origin,microstructure)
integer, dimension(3), intent(out) :: & integer, dimension(3), intent(out) :: &
grid ! grid (for all processes!) grid ! grid (across all processes!)
real(pReal), dimension(3), intent(out) :: & real(pReal), dimension(3), intent(out) :: &
geomSize, & ! size (for all processes!) geomSize, & ! size (across all processes!)
origin ! origin (for all processes!) origin ! origin (across all processes!)
integer, dimension(:), intent(out), allocatable :: & integer, dimension(:), intent(out), allocatable :: &
microstructure microstructure
@ -150,7 +156,6 @@ subroutine readGeom(grid,geomSize,origin,microstructure)
character(len=65536) :: line character(len=65536) :: line
integer, allocatable, dimension(:) :: chunkPos integer, allocatable, dimension(:) :: chunkPos
integer :: & integer :: &
h =- 1, &
headerLength = -1, & !< length of header (in lines) headerLength = -1, & !< length of header (in lines)
fileLength, & !< length of the geom file (in characters) fileLength, & !< length of the geom file (in characters)
fileUnit, & fileUnit, &
@ -189,7 +194,7 @@ subroutine readGeom(grid,geomSize,origin,microstructure)
endif endif
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! read and interprete header ! read and interpret header
origin = 0.0_pReal origin = 0.0_pReal
l = 0 l = 0
do while (l < headerLength .and. startPos < len(rawData)) do while (l < headerLength .and. startPos < len(rawData))
@ -294,6 +299,360 @@ subroutine readGeom(grid,geomSize,origin,microstructure)
end subroutine readGeom end subroutine readGeom
!--------------------------------------------------------------------------------------------------
!> @brief Parse vtk rectilinear grid (.vtr)
!> @details https://vtk.org/Wiki/VTK_XML_Formats
!--------------------------------------------------------------------------------------------------
subroutine readVTR(grid,geomSize,origin,microstructure)
integer, dimension(3), intent(out) :: &
grid ! grid (across all processes!)
real(pReal), dimension(3), intent(out) :: &
geomSize, & ! size (across all processes!)
origin ! origin (across all processes!)
integer, dimension(:), intent(out), allocatable :: &
microstructure
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)
startPos, endPos, &
s
grid = -1
geomSize = -1.0_pReal
!--------------------------------------------------------------------------------------------------
! read raw data as stream
inquire(file = trim(geometryFile), size=fileLength)
open(newunit=fileUnit, file=trim(geometryFile), access='stream',&
status='old', position='rewind', action='read',iostat=myStat)
if(myStat /= 0) call IO_error(100,ext_msg=trim(geometryFile))
allocate(character(len=fileLength)::fileContent)
read(fileUnit) fileContent
close(fileUnit)
inFile = .false.
inGrid = .false.
gotCoordinates = .false.
gotCelldata = .false.
!--------------------------------------------------------------------------------------------------
! interpret XML file
startPos = 1_pI64
do while (startPos < len(fileContent,kind=pI64))
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
if (endPos < startPos) endPos = len(fileContent,kind=pI64) ! end of file without new line
if(.not. inFile) then
if(index(fileContent(startPos:endPos),'<VTKFile',kind=pI64) /= 0_pI64) then
inFile = .true.
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) inGrid = .true.
else
if(index(fileContent(startPos:endPos),'<CellData>',kind=pI64) /= 0_pI64) then
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
if(index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64 .and. &
getXMLValue(fileContent(startPos:endPos),'Name') == 'materialpoint' ) then
if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
call IO_error(error_ID = 844, ext_msg='format (materialpoint)')
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),headerType,compressed,dataType)
exit
endif
startPos = endPos + 2_pI64
enddo
elseif(index(fileContent(startPos:endPos),'<Coordinates>',kind=pI64) /= 0_pI64) then
gotCoordinates = .true.
startPos = endPos + 2_pI64
coord = 0
do while (startPos<fileLength)
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
if(index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64) then
if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
call IO_error(error_ID = 844, ext_msg='format (coordinates)')
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)
coord = coord + 1
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
enddo
endif
endif
endif
if(gotCellData .and. gotCoordinates) exit
startPos = endPos + 2_pI64
end do
if(.not. allocated(microstructure)) call IO_error(error_ID = 844, ext_msg='materialpoint not found')
if(size(microstructure) /= product(grid)) call IO_error(error_ID = 844, ext_msg='size(materialpoint)')
if(any(geomSize<=0)) call IO_error(error_ID = 844, ext_msg='size')
if(any(grid<1)) call IO_error(error_ID = 844, ext_msg='grid')
contains
!------------------------------------------------------------------------------------------------
!> @brief determine size and origin from coordinates
!------------------------------------------------------------------------------------------------
subroutine gridSizeOrigin(base64_str,headerType,compressed,dataType,direction)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string of 1D coordinates
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,delta
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)
geomSize(direction) = coords(size(coords)) - coords(1)
end subroutine
!------------------------------------------------------------------------------------------------
!> @brief Interpret Base64 string in vtk XML file as integer of default kind
!------------------------------------------------------------------------------------------------
function as_Int(base64_str,headerType,compressed,dataType)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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(dataType)
case('Int32')
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,headerType,compressed)))
case('Float32')
as_Int = int(bytes_to_C_FLOAT (asBytes(base64_str,headerType,compressed)))
case('Float64')
as_Int = int(bytes_to_C_DOUBLE (asBytes(base64_str,headerType,compressed)))
case default
call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
end select
end function as_Int
!------------------------------------------------------------------------------------------------
!> @brief Interpret Base64 string in vtk XML file as integer of pReal kind
!------------------------------------------------------------------------------------------------
function as_pReal(base64_str,headerType,compressed,dataType)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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(dataType)
case('Int32')
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,headerType,compressed)),pReal)
case('Float32')
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,headerType,compressed)),pReal)
case default
call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
end select
end function as_pReal
!------------------------------------------------------------------------------------------------
!> @brief Interpret Base64 string in vtk XML file as bytes
!------------------------------------------------------------------------------------------------
function asBytes(base64_str,headerType,compressed) result(bytes)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
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,headerType)
else
bytes = asBytes_uncompressed(base64_str,headerType)
endif
end function asBytes
!------------------------------------------------------------------------------------------------
!> @brief Interpret compressed Base64 string in vtk XML file as bytes
!> @details A compressed Base64 string consists of a header block and a data block
! [#blocks/#u-size/#p-size/#c-size-1/#c-size-2/.../#c-size-#blocks][DATA-1/DATA-2...]
! #blocks = Number of blocks
! #u-size = Block size before compression
! #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,headerType) result(bytes)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
headerType ! header type (UInt32 or Uint64)
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes, bytes_inflated
integer(pI64), dimension(:), allocatable :: temp, size_inflated, size_deflated
integer(pI64) :: headerLen, nBlock, b,s,e
if (headerType == 'UInt32') then
temp = int(bytes_to_C_INT32_T(base64_to_bytes(base64_str(:base64_nChar(4_pI64)))),pI64)
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)
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(nBlock),source=temp(2))
size_inflated(nBlock) = merge(temp(3),temp(2),temp(3)/=0_pI64)
size_deflated = temp(4:)
bytes_inflated = base64_to_bytes(base64_str(base64_nChar(headerLen)+1_pI64:))
allocate(bytes(0))
e = 0_pI64
do b = 1, nBlock
s = e + 1_pI64
e = s + size_deflated(b) - 1_pI64
bytes = [bytes,zlib_inflate(bytes_inflated(s:e),size_inflated(b))]
enddo
end function asBytes_compressed
!------------------------------------------------------------------------------------------------
!> @brief Interprete uncompressed Base64 string in vtk XML file as bytes
!> @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,headerType) result(bytes)
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
headerType ! header type (UInt32 or Uint64)
integer(pI64) :: s
integer(pI64), dimension(1) :: nByte
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
allocate(bytes(0))
s=0_pI64
if (headerType == 'UInt32') then
do while(s+base64_nChar(4_pI64)<(len(base64_str,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+nByte(1))),5_pI64)]
s = s + base64_nChar(4_pI64+nByte(1))
enddo
elseif(headerType == 'UInt64') then
do while(s+base64_nChar(8_pI64)<(len(base64_str,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+nByte(1))),9_pI64)]
s = s + base64_nChar(8_pI64+nByte(1))
enddo
endif
end function asBytes_uncompressed
!------------------------------------------------------------------------------------------------
!> @brief Get XML string value for given key
!------------------------------------------------------------------------------------------------
pure function getXMLValue(line,key)
character(len=*), intent(in) :: line, key
character(len=:), allocatable :: getXMLValue
integer :: s,e
#ifdef __INTEL_COMPILER
character :: q
#endif
s = index(line," "//key,back=.true.)
if(s==0) then
getXMLValue = ''
else
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 = 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 check for supported file format
!------------------------------------------------------------------------------------------------
pure function fileFormatOk(line)
character(len=*),intent(in) :: line
logical :: fileFormatOk
fileFormatOk = getXMLValue(line,'type') == 'RectilinearGrid' .and. &
getXMLValue(line,'byte_order') == 'LittleEndian' .and. &
getXMLValue(line,'compressor') /= 'vtkLZ4DataCompressor' .and. &
getXMLValue(line,'compressor') /= 'vtkLZMADataCompressor'
end function fileFormatOk
end subroutine readVTR
!--------------------------------------------------------------------------------------------------- !---------------------------------------------------------------------------------------------------
!> @brief Calculate undeformed position of IPs/cell centers (pretend to be an element) !> @brief Calculate undeformed position of IPs/cell centers (pretend to be an element)
!--------------------------------------------------------------------------------------------------- !---------------------------------------------------------------------------------------------------

15
src/prec.f90
View File

@ -15,12 +15,13 @@ module prec
! https://software.intel.com/en-us/blogs/2017/03/27/doctor-fortran-in-it-takes-all-kinds ! https://software.intel.com/en-us/blogs/2017/03/27/doctor-fortran-in-it-takes-all-kinds
integer, parameter :: pReal = IEEE_selected_real_kind(15,307) !< number with 15 significant digits, up to 1e+-307 (typically 64 bit) integer, parameter :: pReal = IEEE_selected_real_kind(15,307) !< number with 15 significant digits, up to 1e+-307 (typically 64 bit)
integer, parameter :: pI32 = selected_int_kind(9) !< number with at least up to +-1e9 (typically 32 bit)
integer, parameter :: pI64 = selected_int_kind(18) !< number with at least up to +-1e18 (typically 64 bit)
#if(INT==8) #if(INT==8)
integer, parameter :: pInt = selected_int_kind(18) !< number with at least up to +-1e18 (typically 64 bit) integer, parameter :: pInt = pI64
#else #else
integer, parameter :: pInt = selected_int_kind(9) !< number with at least up to +-1e9 (typically 32 bit) integer, parameter :: pInt = pI32
#endif #endif
integer, parameter :: pLongInt = selected_int_kind(18) !< number with at least up to +-1e18 (typically 64 bit)
integer, parameter :: pStringLen = 256 !< default string length integer, parameter :: pStringLen = 256 !< default string length
integer, parameter :: pPathLen = 4096 !< maximum length of a path name on linux integer, parameter :: pPathLen = 4096 !< maximum length of a path name on linux
@ -237,7 +238,7 @@ end function cNeq
pure function bytes_to_C_FLOAT(bytes) pure function bytes_to_C_FLOAT(bytes)
integer(C_SIGNED_CHAR), dimension(:), intent(in) :: bytes !< byte-wise representation of a C_FLOAT array integer(C_SIGNED_CHAR), dimension(:), intent(in) :: bytes !< byte-wise representation of a C_FLOAT array
real(C_FLOAT), dimension(size(bytes,kind=pLongInt)/(storage_size(0._C_FLOAT,pLongInt)/8_pLongInt)) :: & real(C_FLOAT), dimension(size(bytes,kind=pI64)/(storage_size(0._C_FLOAT,pI64)/8_pI64)) :: &
bytes_to_C_FLOAT bytes_to_C_FLOAT
bytes_to_C_FLOAT = transfer(bytes,bytes_to_C_FLOAT,size(bytes_to_C_FLOAT)) bytes_to_C_FLOAT = transfer(bytes,bytes_to_C_FLOAT,size(bytes_to_C_FLOAT))
@ -251,7 +252,7 @@ end function bytes_to_C_FLOAT
pure function bytes_to_C_DOUBLE(bytes) pure function bytes_to_C_DOUBLE(bytes)
integer(C_SIGNED_CHAR), dimension(:), intent(in) :: bytes !< byte-wise representation of a C_DOUBLE array integer(C_SIGNED_CHAR), dimension(:), intent(in) :: bytes !< byte-wise representation of a C_DOUBLE array
real(C_DOUBLE), dimension(size(bytes,kind=pLongInt)/(storage_size(0._C_DOUBLE,pLongInt)/8_pLongInt)) :: & real(C_DOUBLE), dimension(size(bytes,kind=pI64)/(storage_size(0._C_DOUBLE,pI64)/8_pI64)) :: &
bytes_to_C_DOUBLE bytes_to_C_DOUBLE
bytes_to_C_DOUBLE = transfer(bytes,bytes_to_C_DOUBLE,size(bytes_to_C_DOUBLE)) bytes_to_C_DOUBLE = transfer(bytes,bytes_to_C_DOUBLE,size(bytes_to_C_DOUBLE))
@ -265,7 +266,7 @@ end function bytes_to_C_DOUBLE
pure function bytes_to_C_INT32_T(bytes) pure function bytes_to_C_INT32_T(bytes)
integer(C_SIGNED_CHAR), dimension(:), intent(in) :: bytes !< byte-wise representation of a C_INT32_T array integer(C_SIGNED_CHAR), dimension(:), intent(in) :: bytes !< byte-wise representation of a C_INT32_T array
integer(C_INT32_T), dimension(size(bytes,kind=pLongInt)/(storage_size(0_C_INT32_T,pLongInt)/8_pLongInt)) :: & integer(C_INT32_T), dimension(size(bytes,kind=pI64)/(storage_size(0_C_INT32_T,pI64)/8_pI64)) :: &
bytes_to_C_INT32_T bytes_to_C_INT32_T
bytes_to_C_INT32_T = transfer(bytes,bytes_to_C_INT32_T,size(bytes_to_C_INT32_T)) bytes_to_C_INT32_T = transfer(bytes,bytes_to_C_INT32_T,size(bytes_to_C_INT32_T))
@ -279,7 +280,7 @@ end function bytes_to_C_INT32_T
pure function bytes_to_C_INT64_T(bytes) pure function bytes_to_C_INT64_T(bytes)
integer(C_SIGNED_CHAR), dimension(:), intent(in) :: bytes !< byte-wise representation of a C_INT64_T array integer(C_SIGNED_CHAR), dimension(:), intent(in) :: bytes !< byte-wise representation of a C_INT64_T array
integer(C_INT64_T), dimension(size(bytes,kind=pLongInt)/(storage_size(0_C_INT64_T,pLongInt)/8_pLongInt)) :: & integer(C_INT64_T), dimension(size(bytes,kind=pI64)/(storage_size(0_C_INT64_T,pI64)/8_pI64)) :: &
bytes_to_C_INT64_T bytes_to_C_INT64_T
bytes_to_C_INT64_T = transfer(bytes,bytes_to_C_INT64_T,size(bytes_to_C_INT64_T)) bytes_to_C_INT64_T = transfer(bytes,bytes_to_C_INT64_T,size(bytes_to_C_INT64_T))

2
src/zlib.f90
View File

@ -33,7 +33,7 @@ contains
function zlib_inflate(deflated,size_inflated) function zlib_inflate(deflated,size_inflated)
integer(C_SIGNED_CHAR), dimension(:), intent(in) :: deflated integer(C_SIGNED_CHAR), dimension(:), intent(in) :: deflated
integer(pLongInt), intent(in) :: size_inflated integer(pI64), intent(in) :: size_inflated
integer(C_SIGNED_CHAR), dimension(size_inflated) :: zlib_inflate integer(C_SIGNED_CHAR), dimension(size_inflated) :: zlib_inflate