223031012
/
DAMASK_EICMD
mirror of https://github.com/achalhp/DAMASK_EICMD.git
1
0
Fork 0
Code Issues Projects Releases Wiki Activity

Merge remote-tracking branch 'origin/development' into consistent-damage-parameter-names

This commit is contained in:
Martin Diehl 2022-04-15 10:32:36 +02:00
parent fb633798af 03b9a7679f
commit f9c43e9db7
11 changed files with 177 additions and 62 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
.github/workflows/Fortran.yml vendored
View File

@ -2,7 +2,7 @@ name: Grid and Mesh Solver
on: [push]
env:
PETSC_VERSION: '3.16.2'
PETSC_VERSION: '3.17.0'
HOMEBREW_NO_ANALYTICS: 'ON' # Make Homebrew installation a little quicker
HOMEBREW_NO_AUTO_UPDATE: 'ON'
HOMEBREW_NO_BOTTLE_SOURCE_FALLBACK: 'ON'

30
CMakeLists.txt
View File

@ -9,8 +9,10 @@ endif()
# Dummy project to determine compiler names and version
project(Prerequisites LANGUAGES)
set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig")
pkg_check_modules(PETSC REQUIRED PETSc>=3.12.0 PETSc<3.17.0)
set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}")
pkg_check_modules(PETSC_MIN REQUIRED PETSc>=3.12.0 QUIET) #CMake does not support version range
pkg_check_modules(PETSC REQUIRED PETSc<3.18.0)
pkg_get_variable(CMAKE_Fortran_COMPILER PETSc fcompiler)
pkg_get_variable(CMAKE_C_COMPILER PETSc ccompiler)
@ -25,6 +27,13 @@ else()
endif()
add_definitions("-D${DAMASK_SOLVER}")
# EXPERIMENTAL: This might help to detect HDF5 and FFTW3 in the future if PETSc is not aware of them
set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/externalpackages:$ENV{PKG_CONFIG_PATH}")
pkg_check_modules(HDF5 hdf5)
pkg_check_modules(FFTW3 fftw3)
pkg_check_modules(fYAML libfyaml)
pkg_check_modules(zlib zlib)
file(STRINGS ${PROJECT_SOURCE_DIR}/VERSION DAMASK_VERSION)
message("\nBuilding ${CMAKE_PROJECT_NAME} ${DAMASK_VERSION}\n")
@ -32,6 +41,9 @@ message("\nBuilding ${CMAKE_PROJECT_NAME} ${DAMASK_VERSION}\n")
add_definitions(-DPETSC)
add_definitions(-DDAMASKVERSION="${DAMASK_VERSION}")
add_definitions(-DCMAKE_SYSTEM="${CMAKE_SYSTEM}")
if(PETSC_VERSION VERSION_GREATER_EQUAL 3.17.0)
add_definitions("-DCHKERRQ=PetscCall")
endif()
if(CMAKE_BUILD_TYPE STREQUAL "")
set(CMAKE_BUILD_TYPE "RELEASE")
@ -104,8 +116,18 @@ if(CMAKE_BUILD_TYPE STREQUAL "DEBUG")
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} ${DEBUG_FLAGS}")
endif()
set(CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}} ${PETSC_INCLUDES} ${BUILDCMD_POST}")
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} <OBJECTS> -o <TARGET> <LINK_LIBRARIES> -L${PETSC_LIBRARY_DIRS} -lpetsc ${PETSC_EXTERNAL_LIB} -lz ${BUILDCMD_POST}")
set(CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}} ${PETSC_INCLUDES} ${BUILDCMD_POST}")
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} <OBJECTS> -o <TARGET> <LINK_LIBRARIES> -L${PETSC_LIBRARY_DIRS} -lpetsc ${PETSC_EXTERNAL_LIB} -lz")
if(fYAML_FOUND STREQUAL "1")
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} -L${fYAML_LIBRARY_DIRS} -l${fYAML_LIBRARIES}")
add_definitions(-DFYAML)
pkg_get_variable(fYAML_INCLUDE_DIR libfyaml includedir) # fYAML_INCLUDE_DIRS and fYAML_CFLAGS are not working
set(CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE} "${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE}} -I${fYAML_INCLUDE_DIR}")
endif()
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} ${BUILDCMD_POST}")
message("Fortran Compiler Flags:\n${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}}\n")
message("C Compiler Flags:\n${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE}}\n")

2
python/damask/VERSION
View File

@ -1 +1 @@
v3.0.0-alpha6-184-g1f98b04d4
v3.0.0-alpha6-202-g87b5097ff

4
python/damask/_result.py
View File

@ -1151,14 +1151,14 @@ class Result:
>>> import damask
>>> r = damask.Result('my_file.hdf5')
>>> r.strain(t='U',m=0.5)
>>> r.add_strain(t='U',m=0.5)
Add the plastic Euler-Almansi strain based on the
plastic deformation gradient 'F_p':
>>> import damask
>>> r = damask.Result('my_file.hdf5')
>>> r.strain('F_p','V',-1)
>>> r.add_strain('F_p','V',-1)
"""
self._add_generic_pointwise(self._add_strain,{'F':F},{'t':t,'m':m})

29
src/C_routines.c
View File

@ -7,7 +7,11 @@
#include <pwd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "zlib.h"
#include <zlib.h>
#ifdef FYAML
#include <libfyaml.h>
#endif
#define PATHLEN 4096
#define STRLEN 256
@ -80,3 +84,26 @@ void inflate_c(const uLong *s_deflated, const uLong *s_inflated, const Byte defl
}
}
}
#ifdef FYAML
void to_flow_c(char **flow, int* length_flow, const char *mixed){
struct fy_document *fyd = NULL;
enum fy_emitter_cfg_flags emit_flags = FYECF_MODE_FLOW_ONELINE | FYECF_STRIP_LABELS | FYECF_STRIP_DOC;
fyd = fy_document_build_from_string(NULL, mixed, -1);
if (!fyd) {
*length_flow = -1;
return;
}
int err = fy_document_resolve(fyd);
if (err) {
*length_flow = -1;
return;
}
*flow = fy_emit_document_to_string(fyd,emit_flags);
*length_flow = strlen(*flow);
fy_document_destroy(fyd);
}
#endif

2
src/DAMASK_interface.f90
View File

@ -11,7 +11,7 @@
!--------------------------------------------------------------------------------------------------
#define PETSC_MAJOR 3
#define PETSC_MINOR_MIN 12
#define PETSC_MINOR_MAX 16
#define PETSC_MINOR_MAX 17
module DAMASK_interface
use, intrinsic :: ISO_fortran_env

4
src/IO.f90
View File

@ -483,7 +483,9 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
case (701)
msg = 'Incorrect indent/Null value not allowed'
case (702)
msg = 'Invalid use of flow yaml'
msg = 'Invalid use of flow YAML'
case (703)
msg = 'Invalid YAML'
case (704)
msg = 'Space expected after a colon for <key>: <value> pair'
case (705)

7
src/VTI.f90
View File

@ -81,7 +81,7 @@ subroutine VTI_readDataset_raw(base64_str,dataType,headerType,compressed, &
character(len=:), allocatable, intent(out) :: dataType, headerType, base64_str
logical, intent(out) :: compressed
logical :: inFile,inImage,gotCellData
logical :: inFile, inImage
integer(pI64) :: &
startPos, endPos, &
s
@ -152,10 +152,9 @@ subroutine VTI_readCellsSizeOrigin(cells,geomSize,origin, &
fileContent
character(len=:), allocatable :: dataType, headerType
logical :: inFile,inImage,gotCellData,compressed
logical :: inFile, inImage, compressed
integer(pI64) :: &
startPos, endPos, &
s
startPos, endPos
cells = -1

75
src/YAML_parse.f90
View File

@ -8,6 +8,9 @@ module YAML_parse
use prec
use IO
use YAML_types
#ifdef FYAML
use system_routines
#endif
implicit none
private
@ -16,14 +19,34 @@ module YAML_parse
YAML_parse_init, &
YAML_parse_str
#ifdef FYAML
interface
subroutine to_flow_C(flow,length_flow,mixed) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR, C_PTR
type(C_PTR), intent(out) :: flow
integer(C_INT), intent(out) :: length_flow
character(kind=C_CHAR), dimension(*), intent(in) :: mixed
end subroutine to_flow_C
end interface
#endif
contains
!--------------------------------------------------------------------------------------------------
!> @brief Do sanity checks.
!--------------------------------------------------------------------------------------------------
subroutine YAML_parse_init
subroutine YAML_parse_init()
call selfTest
print'(/,1x,a)', '<<<+- YAML_parse init -+>>>'
#ifdef FYAML
print'(/,1x,a)', 'libfyaml powered'
#else
call selfTest()
#endif
end subroutine YAML_parse_init
@ -155,8 +178,37 @@ logical function quotedString(line)
end function quotedString
#ifdef FYAML
!--------------------------------------------------------------------------------------------------
! @brief Returns Indentation.
! @brief Convert all block style YAML parts to flow style.
!--------------------------------------------------------------------------------------------------
function to_flow(mixed) result(flow)
character(len=*), intent(in) :: mixed
character(:,C_CHAR), allocatable :: flow
type(C_PTR) :: str_ptr
integer(C_INT) :: strlen
call to_flow_C(str_ptr,strlen,f_c_string(mixed))
if (strlen < 1) call IO_error(703,ext_msg='libyfaml')
allocate(character(len=strlen,kind=c_char) :: flow)
block
character(len=strlen,kind=c_char), pointer :: s
call c_f_pointer(str_ptr,s)
flow = s
end block
call free_C(str_ptr)
end function to_flow
#else
!--------------------------------------------------------------------------------------------------
! @brief Determine Indentation.
! @details It determines the indentation level for a given block/line.
! In cases for nested lists, an offset is added to determine the indent of the item block (skip
! leading dashes)
@ -280,7 +332,7 @@ subroutine skip_empty_lines(blck,s_blck)
enddo
end subroutine skip_empty_lines
!--------------------------------------------------------------------------------------------------
! @brief skip file header
@ -303,7 +355,7 @@ subroutine skip_file_header(blck,s_blck)
call IO_error(708,ext_msg = line)
end if
end if
end subroutine skip_file_header
@ -371,7 +423,7 @@ subroutine list_item_inline(blck,s_blck,inline,offset)
character(len=:), allocatable :: line
integer :: indent,indent_next
indent = indentDepth(blck(s_blck:),offset)
line = IO_rmComment(blck(s_blck:s_blck + index(blck(s_blck:),IO_EOL) - 2))
inline = line(indent-offset+3:)
@ -385,7 +437,7 @@ subroutine list_item_inline(blck,s_blck,inline,offset)
indent_next = indentDepth(blck(s_blck:))
enddo
if(scan(inline,",") > 0) inline = '"'//inline//'"'
if(scan(inline,",") > 0) inline = '"'//inline//'"'
end subroutine list_item_inline
@ -737,7 +789,7 @@ end subroutine
!--------------------------------------------------------------------------------------------------
! @brief convert all block style YAML parts to flow style
! @brief Convert all block style YAML parts to flow style.
!--------------------------------------------------------------------------------------------------
function to_flow(blck)
@ -749,7 +801,7 @@ function to_flow(blck)
s_flow, & !< start position in flow
offset, & !< counts leading '- ' in nested lists
end_line
allocate(character(len=len(blck)*2)::to_flow)
s_flow = 1
s_blck = 1
@ -876,7 +928,7 @@ subroutine selfTest
character(len=*), parameter :: flow = &
'{a: ["b", {c: "d"}, "e"]}'
if( .not. to_flow(flow_multi) == flow) error stop 'to_flow'
end block multi_line_flow1
@ -889,7 +941,7 @@ subroutine selfTest
"[c,"//IO_EOL//&
"d"//IO_EOL//&
"e, f]}"//IO_EOL
character(len=*), parameter :: flow = &
"[{a: {b: [c, d e, f]}}]"
@ -921,5 +973,6 @@ subroutine selfTest
end block basic_mixed
end subroutine selfTest
#endif
end module YAML_parse

4
src/mesh/discretization_mesh.f90
View File

@ -100,7 +100,11 @@ subroutine discretization_mesh_init(restart)
debug_element = config_debug%get_asInt('element',defaultVal=1)
debug_ip = config_debug%get_asInt('integrationpoint',defaultVal=1)
#if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>16)
call DMPlexCreateFromFile(PETSC_COMM_WORLD,interface_geomFile,'n/a',PETSC_TRUE,globalMesh,err_PETSc)
#else
call DMPlexCreateFromFile(PETSC_COMM_WORLD,interface_geomFile,PETSC_TRUE,globalMesh,err_PETSc)
#endif
CHKERRQ(err_PETSc)
call DMGetDimension(globalMesh,dimPlex,err_PETSc)
CHKERRQ(err_PETSc)

80
src/system_routines.f90
View File

@ -17,59 +17,67 @@ module system_routines
getUserName, &
signalterm_C, &
signalusr1_C, &
signalusr2_C
signalusr2_C, &
f_c_string, &
free_C
interface
function setCWD_C(cwd) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
function setCWD_C(cwd) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
integer(C_INT) :: setCWD_C
character(kind=C_CHAR), dimension(*), intent(in) :: cwd
end function setCWD_C
integer(C_INT) :: setCWD_C
character(kind=C_CHAR), dimension(*), intent(in) :: cwd
end function setCWD_C
subroutine getCWD_C(cwd, stat) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
use prec
subroutine getCWD_C(cwd, stat) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
use prec
character(kind=C_CHAR), dimension(pPathLen+1), intent(out) :: cwd ! NULL-terminated array
integer(C_INT), intent(out) :: stat
end subroutine getCWD_C
character(kind=C_CHAR), dimension(pPathLen+1), intent(out) :: cwd ! NULL-terminated array
integer(C_INT), intent(out) :: stat
end subroutine getCWD_C
subroutine getHostName_C(hostname, stat) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
use prec
subroutine getHostName_C(hostname, stat) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
use prec
character(kind=C_CHAR), dimension(pStringLen+1), intent(out) :: hostname ! NULL-terminated array
integer(C_INT), intent(out) :: stat
end subroutine getHostName_C
character(kind=C_CHAR), dimension(pStringLen+1), intent(out) :: hostname ! NULL-terminated array
integer(C_INT), intent(out) :: stat
end subroutine getHostName_C
subroutine getUserName_C(username, stat) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
use prec
subroutine getUserName_C(username, stat) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
use prec
character(kind=C_CHAR), dimension(pStringLen+1), intent(out) :: username ! NULL-terminated array
integer(C_INT), intent(out) :: stat
end subroutine getUserName_C
character(kind=C_CHAR), dimension(pStringLen+1), intent(out) :: username ! NULL-terminated array
integer(C_INT), intent(out) :: stat
end subroutine getUserName_C
subroutine signalterm_C(handler) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_FUNPTR
subroutine signalterm_C(handler) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_FUNPTR
type(C_FUNPTR), intent(in), value :: handler
end subroutine signalterm_C
type(C_FUNPTR), intent(in), value :: handler
end subroutine signalterm_C
subroutine signalusr1_C(handler) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_FUNPTR
subroutine signalusr1_C(handler) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_FUNPTR
type(C_FUNPTR), intent(in), value :: handler
end subroutine signalusr1_C
type(C_FUNPTR), intent(in), value :: handler
end subroutine signalusr1_C
subroutine signalusr2_C(handler) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_FUNPTR
subroutine signalusr2_C(handler) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_FUNPTR
type(C_FUNPTR), intent(in), value :: handler
end subroutine signalusr2_C
subroutine free_C(ptr) bind(C,name='free')
import c_ptr
type(c_ptr), value :: ptr
end subroutine free_C
type(C_FUNPTR), intent(in), value :: handler
end subroutine signalusr2_C
end interface