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

.github/workflows/Fortran.yml

@@ -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'

CMakeLists.txt

@@ -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")
+set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}")
-pkg_check_modules(PETSC REQUIRED PETSc>=3.12.0 PETSc<3.17.0)
+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")
@@ -105,7 +117,17 @@ if(CMAKE_BUILD_TYPE STREQUAL "DEBUG")
 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 ${BUILDCMD_POST}")
+
+set(CMAKE_Fortran_LINK_EXECUTABLE "${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")

python/damask/VERSION

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

python/damask/_result.py

@@ -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})

src/C_routines.c

@@ -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

src/DAMASK_interface.f90

@@ -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

src/IO.f90

@@ -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)

src/VTI.f90

@@ -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, &
+    startPos, endPos
-    s
 
 
   cells = -1

src/YAML_parse.f90

@@ -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)
@@ -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)
 
@@ -921,5 +973,6 @@ subroutine selfTest
   end block basic_mixed
 
 end subroutine selfTest
+#endif
 
 end module YAML_parse

src/mesh/discretization_mesh.f90

@@ -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)

src/system_routines.f90

@@ -17,7 +17,9 @@ module system_routines
     getUserName, &
     signalterm_C, &
     signalusr1_C, &
-    signalusr2_C
+    signalusr2_C, &
+    f_c_string, &
+    free_C
 
 
   interface
@@ -71,6 +73,12 @@ module system_routines
       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
+
+
   end interface
 
 contains