From 8d44c551414165ccd157bf09dbfec54d5bfdf3ee Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sun, 3 Apr 2022 17:56:17 +0200
Subject: [PATCH 01/36] support for PETSc 3.17.0

DCHKERRQ has been replaced by PetscCall
---
 .github/workflows/Fortran.yml | 2 +-
 CMakeLists.txt                | 7 ++++++-
 src/DAMASK_interface.f90      | 2 +-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/Fortran.yml b/.github/workflows/Fortran.yml
index 5cc241e00..d93cdd27f 100644
--- a/.github/workflows/Fortran.yml
+++ b/.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'
diff --git a/CMakeLists.txt b/CMakeLists.txt
index b4c405319..e9d37f281 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -10,7 +10,9 @@ 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)
+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)
 
@@ -32,6 +34,9 @@ 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")
diff --git a/src/DAMASK_interface.f90 b/src/DAMASK_interface.f90
index e958c8a29..1a6bb3ee6 100644
--- a/src/DAMASK_interface.f90
+++ b/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

From 3bf52d832f6e7aa875ec5269684742198909dd43 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Sun, 3 Apr 2022 23:33:19 +0200
Subject: [PATCH 02/36] [skip ci] updated version information after successful
 test of v3.0.0-alpha6-187-gbf7da2c71

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 65787866a..04e0c3d12 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha6-184-g1f98b04d4
+v3.0.0-alpha6-187-gbf7da2c71

From 34cc66f1bfdaf2d9e7186ff85e752099049b4dc2 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Mon, 4 Apr 2022 08:14:48 +0200
Subject: [PATCH 03/36] use old interface for previous PETSc versions

---
 src/mesh/discretization_mesh.f90 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/mesh/discretization_mesh.f90 b/src/mesh/discretization_mesh.f90
index 9baff52fb..70ee28343 100644
--- a/src/mesh/discretization_mesh.f90
+++ b/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)

From 0376de4a1134df952d36fa591a33b6900420a5e1 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Mon, 4 Apr 2022 08:17:06 +0200
Subject: [PATCH 04/36] not needed

---
 src/VTI.f90 | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/VTI.f90 b/src/VTI.f90
index d8b8f7778..a5918137e 100644
--- a/src/VTI.f90
+++ b/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, &
-    s
+    startPos, endPos
 
 
   cells = -1

From 700f256b7cadb6985df00e91dae4a26ed3b00644 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Mon, 4 Apr 2022 13:04:27 +0200
Subject: [PATCH 05/36] [skip ci] updated version information after successful
 test of v3.0.0-alpha6-191-gf8d4e3cf5

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 04e0c3d12..b2ee5ef1f 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha6-187-gbf7da2c71
+v3.0.0-alpha6-191-gf8d4e3cf5

From 16f5a27e089077f242dbaca13f88c1215fcd7665 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 9 Apr 2022 21:10:15 +0200
Subject: [PATCH 06/36] detecting HDF5 and FFTW

some PETSc installations are not aware of them, so it might make sense
to become independent of PETSc. But PETSc-defined variables should take
precedence
---
 CMakeLists.txt | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e9d37f281..d535492dc 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -9,7 +9,7 @@ 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_MIN REQUIRED PETSc>=3.12.0 QUIET) #CMake does not support version range
 pkg_check_modules(PETSC REQUIRED PETSc<3.18.0)
 
@@ -27,6 +27,12 @@ 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:$ENV{PKG_CONFIG_PATH}")
+message($ENV{PKG_CONFIG_PATH})
+pkg_check_modules(HDF5 hdf5)
+pkg_check_modules(FFTW3 fftw3)
+
 file(STRINGS ${PROJECT_SOURCE_DIR}/VERSION DAMASK_VERSION)
 
 message("\nBuilding ${CMAKE_PROJECT_NAME} ${DAMASK_VERSION}\n")

From 8ebd234aafaf3c7cb49ddfb30d4379acdf406c03 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Sun, 10 Apr 2022 15:18:41 +0200
Subject: [PATCH 07/36] [skip ci] updated version information after successful
 test of v3.0.0-alpha6-194-ga4c396949

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index b2ee5ef1f..735877ed3 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha6-191-gf8d4e3cf5
+v3.0.0-alpha6-194-ga4c396949

From 58b67007a9ed6ea3790f7af1c4e703f2c66d9476 Mon Sep 17 00:00:00 2001
From: Nikhil Prabhu <nikhil.prabhu@kuleuven.be>
Date: Tue, 12 Apr 2022 12:02:00 +0200
Subject: [PATCH 08/36] fixed missing add_strain

---
 python/damask/_result.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/damask/_result.py b/python/damask/_result.py
index f3b649a30..9195d2dd1 100644
--- a/python/damask/_result.py
+++ b/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})

From affa7baa223c1ea0d98376cdcf959717c702a634 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Tue, 12 Apr 2022 21:02:09 +0200
Subject: [PATCH 09/36] search for libfyaml

no consequences so far
---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d535492dc..cad36e42c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -29,9 +29,9 @@ 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:$ENV{PKG_CONFIG_PATH}")
-message($ENV{PKG_CONFIG_PATH})
 pkg_check_modules(HDF5 hdf5)
 pkg_check_modules(FFTW3 fftw3)
+pkg_check_modules(fYAML libfyaml)
 
 file(STRINGS ${PROJECT_SOURCE_DIR}/VERSION DAMASK_VERSION)
 

From 4622380134ad2f438968ed6e487cb7301512cd8c Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Tue, 12 Apr 2022 23:19:28 +0200
Subject: [PATCH 10/36] [skip ci] updated version information after successful
 test of v3.0.0-alpha6-197-g39d79c23b

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 735877ed3..f71bd0cab 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha6-194-ga4c396949
+v3.0.0-alpha6-197-g39d79c23b

From 723252ef15e613d3a7f5706a50d6a5f6ba519710 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Tue, 12 Apr 2022 22:14:04 +0200
Subject: [PATCH 11/36] libfyaml backend

currently it simply converts the whole file content to flow mode.
The nice thing is: It can convert EVERYTHING to flow mode. libfyaml is
the only library that passes the whole YAML test suite
---
 CMakeLists.txt          | 10 ++++--
 src/C_routines.c        | 27 ++++++++++++++
 src/IO.f90              |  4 ++-
 src/YAML_parse.f90      | 75 ++++++++++++++++++++++++++++++++------
 src/system_routines.f90 | 80 ++++++++++++++++++++++-------------------
 5 files changed, 146 insertions(+), 50 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index cad36e42c..6994afc77 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -115,8 +115,14 @@ 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)
+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")
diff --git a/src/C_routines.c b/src/C_routines.c
index 3d62a87c2..c4ebb4d6b 100644
--- a/src/C_routines.c
+++ b/src/C_routines.c
@@ -9,6 +9,10 @@
 #include <sys/stat.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
diff --git a/src/IO.f90 b/src/IO.f90
index 493970824..240c9e992 100644
--- a/src/IO.f90
+++ b/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)
diff --git a/src/YAML_parse.f90 b/src/YAML_parse.f90
index 8a3264cff..e589758c9 100644
--- a/src/YAML_parse.f90
+++ b/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)
@@ -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
diff --git a/src/system_routines.f90 b/src/system_routines.f90
index 2eb0b7958..e0adf9dc0 100644
--- a/src/system_routines.f90
+++ b/src/system_routines.f90
@@ -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
 

From c806885cb5309f90a85d184bd7f27ceb8c2b0087 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 13 Apr 2022 05:55:34 +0200
Subject: [PATCH 12/36] include libfyaml headers from non-standard locations

the CMake manual promises more than it holds.
Also adding some diagnostics+fixes for zlib, we still assume that it
exists (true on most systems, HDF5 also requires it normally)
see also https://stackoverflow.com/questions/21593
---
 CMakeLists.txt   | 5 +++++
 src/C_routines.c | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6994afc77..6b341dbbe 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -32,6 +32,7 @@ set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/externalpackages:$ENV
 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)
 
@@ -118,10 +119,14 @@ 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 ${PETSC_EXTERNAL_LIB} -lz")
+
 if(fYAML_FOUND STREQUAL "1")
     set(CMAKE_Fortran_LINK_EXECUTABLE "${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")
diff --git a/src/C_routines.c b/src/C_routines.c
index c4ebb4d6b..3a1db91a0 100644
--- a/src/C_routines.c
+++ b/src/C_routines.c
@@ -7,7 +7,7 @@
 #include <pwd.h>
 #include <sys/types.h>
 #include <sys/stat.h>
-#include "zlib.h"
+#include <zlib.h>
 
 #ifdef FYAML
 #include <libfyaml.h>

From 03b9a7679f4c9c34247f1458dc0f3e40fdf16c74 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Wed, 13 Apr 2022 18:17:32 +0200
Subject: [PATCH 13/36] [skip ci] updated version information after successful
 test of v3.0.0-alpha6-202-g87b5097ff

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index f71bd0cab..946c163c0 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha6-197-g39d79c23b
+v3.0.0-alpha6-202-g87b5097ff

From 00671f943bfe41e77f303238909e14b056dcfbad Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 13 Apr 2022 23:45:14 +0200
Subject: [PATCH 14/36] easier to understand

---
 src/YAML_types.f90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/YAML_types.f90 b/src/YAML_types.f90
index d7ca71cbb..c4dcc0a83 100644
--- a/src/YAML_types.f90
+++ b/src/YAML_types.f90
@@ -1348,8 +1348,8 @@ subroutine tList_append(self,node)
   type(tItem), pointer :: item
 
   if (.not. associated(self%first)) then
-    allocate(self%first)
-    item => self%first
+    allocate(item)
+    self%first => item
   else
     item => self%first
     do while (associated(item%next))

From ca0df3389a96c7d867c0e884128662a3ee9a4c37 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 14 Apr 2022 00:06:54 +0200
Subject: [PATCH 15/36] avoid long pointer transversal

---
 src/YAML_types.f90 | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/YAML_types.f90 b/src/YAML_types.f90
index c4dcc0a83..b32651905 100644
--- a/src/YAML_types.f90
+++ b/src/YAML_types.f90
@@ -119,7 +119,8 @@ module YAML_types
 
   type, extends(tNode), public :: tList
 
-    class(tItem), pointer  :: first => NULL()
+    class(tItem), pointer :: first => NULL(), &
+                             last => NULL()
 
     contains
     procedure :: asFormattedString => tList_asFormattedString
@@ -1350,13 +1351,11 @@ subroutine tList_append(self,node)
   if (.not. associated(self%first)) then
     allocate(item)
     self%first => item
+    self%last => item
   else
-    item => self%first
-    do while (associated(item%next))
-      item => item%next
-    enddo
-    allocate(item%next)
-    item => item%next
+    allocate(self%last%next)
+    item => self%last%next
+    self%last => item
   end if
 
   item%node => node

From 563d566a3f699af85a8fe558ebf7c724d4fd4756 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 14 Apr 2022 01:06:47 +0200
Subject: [PATCH 16/36] made two loops faster

the most annoying one is still slow.
---
 src/YAML_types.f90 |  2 +-
 src/material.f90   | 50 ++++++++++++++++++++++++++++++----------------
 2 files changed, 34 insertions(+), 18 deletions(-)

diff --git a/src/YAML_types.f90 b/src/YAML_types.f90
index b32651905..857b24bd0 100644
--- a/src/YAML_types.f90
+++ b/src/YAML_types.f90
@@ -145,7 +145,7 @@ module YAML_types
   end type tDict
 
 
-  type :: tItem
+  type, public :: tItem
     character(len=:), allocatable :: key
     class(tNode),     pointer     :: node => NULL()
     class(tItem),     pointer     :: next => NULL()
diff --git a/src/material.f90 b/src/material.f90
index 3ff280b0d..4d6bc361d 100644
--- a/src/material.f90
+++ b/src/material.f90
@@ -91,6 +91,7 @@ subroutine parse()
                            homogenizations, &
                            homogenization
 
+  class(tItem), pointer :: item
   integer, dimension(:), allocatable :: &
     counterPhase, &
     counterHomogenization
@@ -102,6 +103,7 @@ subroutine parse()
     co, ce, &
     ma
 
+
   materials       => config_material%get('material')
   phases          => config_material%get('phase')
   homogenizations => config_material%get('homogenization')
@@ -169,17 +171,23 @@ subroutine parse()
   allocate(material_O_0(materials%length))
   allocate(material_F_i_0(materials%length))
 
-  do ma = 1, materials%length
-    material     => materials%get(ma)
-    constituents => material%get('constituents')
-    allocate(material_O_0(ma)%data(constituents%length))
-    allocate(material_F_i_0(ma)%data(1:3,1:3,constituents%length))
-    do co = 1, constituents%length
-      constituent => constituents%get(co)
-      call material_O_0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4))
-      material_F_i_0(ma)%data(1:3,1:3,co) = constituent%get_as2dFloat('F_i',defaultVal=math_I3,requiredShape=[3,3])
-    enddo
- enddo
+  ! manual iteration for performance
+  select type(materials)
+    class is(tList)
+      item => materials%first
+      do ma = 1, materials%length
+        material => item%node
+        constituents => material%get('constituents')
+        allocate(material_O_0(ma)%data(constituents%length))
+        allocate(material_F_i_0(ma)%data(1:3,1:3,constituents%length))
+        do co = 1, constituents%length
+          constituent => constituents%get(co)
+          call material_O_0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4))
+          material_F_i_0(ma)%data(1:3,1:3,co) = constituent%get_as2dFloat('F_i',defaultVal=math_I3,requiredShape=[3,3])
+        end do
+        item => item%next
+      end do
+  end select
 
 end subroutine parse
 
@@ -195,17 +203,25 @@ subroutine sanityCheck(materials,homogenizations)
   class(tNode), pointer :: material, &
                            homogenization, &
                            constituents
+  class(tItem), pointer :: item
   integer :: m
 
+
   if (maxval(discretization_materialAt) > materials%length) &
     call IO_error(155,ext_msg='More materials requested than found in material.yaml')
 
-  do m = 1, materials%length
-    material => materials%get(m)
-    constituents   => material%get('constituents')
-    homogenization => homogenizations%get(material%get_asString('homogenization'))
-    if (constituents%length /= homogenization%get_asInt('N_constituents')) call IO_error(148)
-  end do
+  ! manual iteration for performance
+  select type(materials)
+    class is(tList)
+      item => materials%first
+      do m = 1, materials%length
+        material => materials%get(m)
+        constituents   => material%get('constituents')
+        homogenization => homogenizations%get(material%get_asString('homogenization'))
+        if (constituents%length /= homogenization%get_asInt('N_constituents')) call IO_error(148)
+        item => item%next
+      end do
+  end select
 
 end subroutine sanityCheck
 

From 3309360e4bf96ee32d156b825098b8e573cbea67 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 14 Apr 2022 07:19:56 +0200
Subject: [PATCH 17/36] avoit out of bounds access

---
 src/YAML_parse.f90 | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/YAML_parse.f90 b/src/YAML_parse.f90
index e589758c9..8013089e1 100644
--- a/src/YAML_parse.f90
+++ b/src/YAML_parse.f90
@@ -168,8 +168,11 @@ logical function quotedString(line)
 
   character(len=*), intent(in) :: line
 
+
   quotedString = .false.
 
+  if (len(line) == 0) return
+
   if (scan(line(:1),IO_QUOTES) == 1) then
     quotedString = .true.
     if(line(len(line):len(line)) /= line(:1)) call IO_error(710,ext_msg=line)

From b56176d670d22616ec512e7c0c11326849f8aaf1 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 14 Apr 2022 12:55:11 +0200
Subject: [PATCH 18/36] all YAML related initialization is constant (linear in
 number of points)

---
 src/material.f90 | 125 +++++++++++++++++++++--------------------------
 1 file changed, 56 insertions(+), 69 deletions(-)

diff --git a/src/material.f90 b/src/material.f90
index 4d6bc361d..40d178540 100644
--- a/src/material.f90
+++ b/src/material.f90
@@ -94,7 +94,10 @@ subroutine parse()
   class(tItem), pointer :: item
   integer, dimension(:), allocatable :: &
     counterPhase, &
-    counterHomogenization
+    counterHomogenization, &
+    temp_ho
+  integer, dimension(:,:), allocatable :: temp_ph
+  real(pReal), dimension(:,:), allocatable :: temp_v
 
   real(pReal) :: v
   integer :: &
@@ -108,8 +111,6 @@ subroutine parse()
   phases          => config_material%get('phase')
   homogenizations => config_material%get('homogenization')
 
-  call sanityCheck(materials, homogenizations)
-
 #if defined (__GFORTRAN__)
   material_name_phase          = getKeys(phases)
   material_name_homogenization = getKeys(homogenizations)
@@ -136,10 +137,56 @@ subroutine parse()
 
   allocate(material_v(homogenization_maxNconstituents,discretization_Ncells),source=0.0_pReal)
 
-  do el = 1, discretization_Nelems
-    material => materials%get(discretization_materialAt(el))
+  allocate(material_O_0(materials%length))
+  allocate(material_F_i_0(materials%length))
+
+  select type(materials)
+
+    class is(tList)
+
+      if (maxval(discretization_materialAt) > materials%length) &
+        call IO_error(155,ext_msg='More materials requested than found in material.yaml')
+
+      allocate(temp_ho(materials%length))
+      allocate(temp_ph(materials%length,homogenization_maxNconstituents),source=-1)
+      allocate(temp_v(materials%length,homogenization_maxNconstituents),source=0.0_pReal)
+
+      item => materials%first
+      do ma = 1, materials%length
+        material => item%node
+        temp_ho(ma) = homogenizations%getIndex(material%get_asString('homogenization'))
+        constituents => material%get('constituents')
+
+        homogenization => homogenizations%get(temp_ho(ma))
+        if (constituents%length /= homogenization%get_asInt('N_constituents')) call IO_error(148)
+
+        allocate(material_O_0(ma)%data(constituents%length))
+        allocate(material_F_i_0(ma)%data(1:3,1:3,constituents%length))
+
+        do co = 1, constituents%length
+          constituent => constituents%get(co)
+          temp_v(ma,co) = constituent%get_asFloat('v')
+          temp_ph(ma,co) = phases%getIndex(constituent%get_asString('phase'))
+
+          call material_O_0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4))
+          material_F_i_0(ma)%data(1:3,1:3,co) = constituent%get_as2dFloat('F_i',defaultVal=math_I3,requiredShape=[3,3])
+
+        end do
+        if (dNeq(sum(temp_v(ma,:)),1.0_pReal,1.e-9_pReal)) call IO_error(153,ext_msg='constituent')
+
+        item => item%next
+
+      end do
+
+  end select
+
+
+  ! build mappings
+  do el = 1, discretization_Nelems
+
+    ma = discretization_materialAt(el)
+    ho = temp_ho(ma)
 
-    ho = homogenizations%getIndex(material%get_asString('homogenization'))
     do ip = 1, discretization_nIPs
       ce = (el-1)*discretization_nIPs + ip
       material_homogenizationID(ce) = ho
@@ -147,13 +194,11 @@ subroutine parse()
       material_homogenizationEntry(ce) = counterHomogenization(ho)
     end do
 
-    constituents => material%get('constituents')
-    do co = 1, constituents%length
-      constituent => constituents%get(co)
+    do co = 1, size(temp_ph(ma,:)>0)
 
-      v = constituent%get_asFloat('v')
+      v = temp_v(ma,co)
+      ph = temp_ph(ma,co)
 
-      ph = phases%getIndex(constituent%get_asString('phase'))
       do ip = 1, discretization_nIPs
         ce = (el-1)*discretization_nIPs + ip
         material_phaseID(co,ce) = ph
@@ -163,68 +208,10 @@ subroutine parse()
       end do
 
     end do
-    if (dNeq(sum(material_v(1:constituents%length,ce)),1.0_pReal,1.e-9_pReal)) &
-      call IO_error(153,ext_msg='constituent')
-
   end do
 
-  allocate(material_O_0(materials%length))
-  allocate(material_F_i_0(materials%length))
-
-  ! manual iteration for performance
-  select type(materials)
-    class is(tList)
-      item => materials%first
-      do ma = 1, materials%length
-        material => item%node
-        constituents => material%get('constituents')
-        allocate(material_O_0(ma)%data(constituents%length))
-        allocate(material_F_i_0(ma)%data(1:3,1:3,constituents%length))
-        do co = 1, constituents%length
-          constituent => constituents%get(co)
-          call material_O_0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4))
-          material_F_i_0(ma)%data(1:3,1:3,co) = constituent%get_as2dFloat('F_i',defaultVal=math_I3,requiredShape=[3,3])
-        end do
-        item => item%next
-      end do
-  end select
-
 end subroutine parse
 
-
-!--------------------------------------------------------------------------------------------------
-!> @brief Check if material.yaml is consistent and contains sufficient # of materials
-!--------------------------------------------------------------------------------------------------
-subroutine sanityCheck(materials,homogenizations)
-
-  class(tNode), intent(in) :: materials, &
-                              homogenizations
-
-  class(tNode), pointer :: material, &
-                           homogenization, &
-                           constituents
-  class(tItem), pointer :: item
-  integer :: m
-
-
-  if (maxval(discretization_materialAt) > materials%length) &
-    call IO_error(155,ext_msg='More materials requested than found in material.yaml')
-
-  ! manual iteration for performance
-  select type(materials)
-    class is(tList)
-      item => materials%first
-      do m = 1, materials%length
-        material => materials%get(m)
-        constituents   => material%get('constituents')
-        homogenization => homogenizations%get(material%get_asString('homogenization'))
-        if (constituents%length /= homogenization%get_asInt('N_constituents')) call IO_error(148)
-        item => item%next
-      end do
-  end select
-
-end subroutine sanityCheck
-
 #if defined (__GFORTRAN__)
 !--------------------------------------------------------------------------------------------------
 !> @brief %keys() is broken on gfortran

From dbf5ee84cb997febff4a10949c1bfa352e751188 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 14 Apr 2022 20:14:08 +0200
Subject: [PATCH 19/36] better readable

---
 src/material.f90 | 37 ++++++++++++++++++++-----------------
 1 file changed, 20 insertions(+), 17 deletions(-)

diff --git a/src/material.f90 b/src/material.f90
index 40d178540..7264738e5 100644
--- a/src/material.f90
+++ b/src/material.f90
@@ -111,6 +111,10 @@ subroutine parse()
   phases          => config_material%get('phase')
   homogenizations => config_material%get('homogenization')
 
+
+  if (maxval(discretization_materialAt) > materials%length) &
+    call IO_error(155,ext_msg='More materials requested than found in material.yaml')
+
 #if defined (__GFORTRAN__)
   material_name_phase          = getKeys(phases)
   material_name_homogenization = getKeys(homogenizations)
@@ -126,31 +130,20 @@ subroutine parse()
   end do
   homogenization_maxNconstituents = maxval(homogenization_Nconstituents)
 
-  allocate(counterPhase(phases%length),source=0)
-  allocate(counterHomogenization(homogenizations%length),source=0)
-
-  allocate(material_homogenizationID(discretization_Ncells),source=0)
-  allocate(material_homogenizationEntry(discretization_Ncells),source=0)
-
-  allocate(material_phaseID(homogenization_maxNconstituents,discretization_Ncells),source=0)
-  allocate(material_phaseEntry(homogenization_maxNconstituents,discretization_Ncells),source=0)
-
   allocate(material_v(homogenization_maxNconstituents,discretization_Ncells),source=0.0_pReal)
 
   allocate(material_O_0(materials%length))
   allocate(material_F_i_0(materials%length))
 
+  allocate(temp_ho(materials%length))
+  allocate(temp_ph(materials%length,homogenization_maxNconstituents),source=-1)
+  allocate(temp_v(materials%length,homogenization_maxNconstituents),source=0.0_pReal)
+
+  ! parse YAML structure
   select type(materials)
 
     class is(tList)
 
-      if (maxval(discretization_materialAt) > materials%length) &
-        call IO_error(155,ext_msg='More materials requested than found in material.yaml')
-
-      allocate(temp_ho(materials%length))
-      allocate(temp_ph(materials%length,homogenization_maxNconstituents),source=-1)
-      allocate(temp_v(materials%length,homogenization_maxNconstituents),source=0.0_pReal)
-
       item => materials%first
       do ma = 1, materials%length
         material => item%node
@@ -175,12 +168,21 @@ subroutine parse()
         if (dNeq(sum(temp_v(ma,:)),1.0_pReal,1.e-9_pReal)) call IO_error(153,ext_msg='constituent')
 
         item => item%next
-
       end do
 
   end select
 
 
+  allocate(counterPhase(phases%length),source=0)
+  allocate(counterHomogenization(homogenizations%length),source=0)
+
+  allocate(material_homogenizationID(discretization_Ncells),source=0)
+  allocate(material_homogenizationEntry(discretization_Ncells),source=0)
+
+  allocate(material_phaseID(homogenization_maxNconstituents,discretization_Ncells),source=0)
+  allocate(material_phaseEntry(homogenization_maxNconstituents,discretization_Ncells),source=0)
+
+
   ! build mappings
   do el = 1, discretization_Nelems
 
@@ -212,6 +214,7 @@ subroutine parse()
 
 end subroutine parse
 
+
 #if defined (__GFORTRAN__)
 !--------------------------------------------------------------------------------------------------
 !> @brief %keys() is broken on gfortran

From f11b6f54e55420a75887d4d823c88a075dde2ae1 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 15 Apr 2022 15:35:09 +0200
Subject: [PATCH 20/36] markdown - as for PRIVATE

---
 README    | 13 -------------
 README.md | 15 +++++++++++++++
 2 files changed, 15 insertions(+), 13 deletions(-)
 delete mode 100644 README
 create mode 100644 README.md

diff --git a/README b/README
deleted file mode 100644
index 543de378f..000000000
--- a/README
+++ /dev/null
@@ -1,13 +0,0 @@
-DAMASK - The Düsseldorf Advanced Material Simulation Kit
-Visit damask.mpie.de for installation and usage instructions
-
-CONTACT INFORMATION
-
-Max-Planck-Institut für Eisenforschung GmbH
-Max-Planck-Str. 1
-40237 Düsseldorf
-Germany
-
-damask@mpie.de
-https://damask.mpie.de
-https://git.damask.mpie.de
diff --git a/README.md b/README.md
new file mode 100644
index 000000000..a2178e0ab
--- /dev/null
+++ b/README.md
@@ -0,0 +1,15 @@
+# DAMASK - The Düsseldorf Advanced Material Simulation Kit
+
+Visit [damask.mpie.de](https://damask.mpie.de) for installation and usage instructions
+
+## Contact Information
+
+Max-Planck-Institut für Eisenforschung GmbH
+Max-Planck-Str. 1
+40237 Düsseldorf
+Germany
+
+damask@mpie.de
+https://damask.mpie.de
+https://git.damask.mpie.de
+

From 5f49f38a018971454f4f319aed36ed81a12d1b6b Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 15 Apr 2022 15:40:24 +0200
Subject: [PATCH 21/36] nicely formatted readmes

---
 PRIVATE   |  2 +-
 README.md | 14 +++++++-------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/PRIVATE b/PRIVATE
index 459326e98..f6a94aeaa 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit 459326e9840c843ade72b04cf28e50889c9779f1
+Subproject commit f6a94aeaaa3a81347821e7a092d43dd04115f5f6
diff --git a/README.md b/README.md
index a2178e0ab..5b5edf677 100644
--- a/README.md
+++ b/README.md
@@ -4,12 +4,12 @@ Visit [damask.mpie.de](https://damask.mpie.de) for installation and usage instru
 
 ## Contact Information
 
-Max-Planck-Institut für Eisenforschung GmbH
-Max-Planck-Str. 1
-40237 Düsseldorf
-Germany
+Max-Planck-Institut für Eisenforschung GmbH  
+Max-Planck-Str. 1  
+40237 Düsseldorf  
+Germany  
 
-damask@mpie.de
-https://damask.mpie.de
-https://git.damask.mpie.de
+damask@mpie.de  
+https://damask.mpie.de  
+https://git.damask.mpie.de  
 

From 51582b80f8882fc9032d90980f94168bec01365e Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 15 Apr 2022 15:48:21 +0200
Subject: [PATCH 22/36] don't fail

windows is unreliable
---
 .github/workflows/Python.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/Python.yml b/.github/workflows/Python.yml
index ca74c0016..3b6bb0df4 100644
--- a/.github/workflows/Python.yml
+++ b/.github/workflows/Python.yml
@@ -11,6 +11,7 @@ jobs:
       matrix:
         python-version: ['3.8', '3.9'] #, '3.10']
         os: [ubuntu-latest, macos-latest, windows-latest]
+      fail-fast: false
 
     steps:
       - uses: actions/checkout@v2

From 5d99b152eec889030486252988723a3d39a56ee5 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Fri, 15 Apr 2022 21:23:03 +0200
Subject: [PATCH 23/36] [skip ci] updated version information after successful
 test of v3.0.0-alpha6-206-g51582b80f

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 946c163c0..7ce9e687d 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha6-202-g87b5097ff
+v3.0.0-alpha6-206-g51582b80f

From 3cc3229792c82ef496f5bf3c376452a61652584e Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 16 Apr 2022 16:19:33 +0200
Subject: [PATCH 24/36] string new line which is added by libfyaml

---
 src/YAML_parse.f90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/YAML_parse.f90 b/src/YAML_parse.f90
index 8013089e1..bfce06bc9 100644
--- a/src/YAML_parse.f90
+++ b/src/YAML_parse.f90
@@ -83,7 +83,7 @@ recursive function parse_flow(YAML_flow) result(node)
     s, &                                                                                            ! start position of dictionary or list
     d                                                                                               ! position of key: value separator (':')
 
-  flow_string = trim(adjustl(YAML_flow(:)))
+  flow_string = trim(adjustl(YAML_flow))
   if (len_trim(flow_string) == 0) then
     node => emptyDict
     return
@@ -201,7 +201,7 @@ function to_flow(mixed) result(flow)
   block
     character(len=strlen,kind=c_char), pointer :: s
     call c_f_pointer(str_ptr,s)
-    flow = s
+    flow = s(:len(s)-1)
   end block
 
   call free_C(str_ptr)

From 954a336d92c278227525ee174e25d196f7a328b2 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 16 Apr 2022 16:24:29 +0200
Subject: [PATCH 25/36] Fortran side does not support tags (i.e. 'type hints')

---
 src/C_routines.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/C_routines.c b/src/C_routines.c
index 3a1db91a0..a25fde688 100644
--- a/src/C_routines.c
+++ b/src/C_routines.c
@@ -88,7 +88,7 @@ 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;
+  enum fy_emitter_cfg_flags emit_flags = FYECF_MODE_FLOW_ONELINE | FYECF_STRIP_LABELS | FYECF_STRIP_TAGS |FYECF_STRIP_DOC;
 
   fyd = fy_document_build_from_string(NULL, mixed, -1);
   if (!fyd) {

From 808ef139aefc56a530a1bcf6451b8035acf5d3b4 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Mon, 18 Apr 2022 13:16:45 +0200
Subject: [PATCH 26/36] avoid code duplication by using assumed rank "(..)"

- lack of modern Fortran interface for HDF5 still requires branching to
  call the same code
- not sure how to handle the read function (assumed rank and intent(out)
  ) does not work together
---
 src/HDF5_utilities.f90 | 137 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 136 insertions(+), 1 deletion(-)

diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90
index 93de4053b..86807507b 100644
--- a/src/HDF5_utilities.f90
+++ b/src/HDF5_utilities.f90
@@ -48,6 +48,7 @@ module HDF5_utilities
 !> @details for parallel IO, all dimension except for the last need to match
 !--------------------------------------------------------------------------------------------------
   interface HDF5_write
+#if defined(__GFORTRAN__) && __GNUC__<11
     module procedure HDF5_write_real1
     module procedure HDF5_write_real2
     module procedure HDF5_write_real3
@@ -55,7 +56,6 @@ module HDF5_utilities
     module procedure HDF5_write_real5
     module procedure HDF5_write_real6
     module procedure HDF5_write_real7
-
     module procedure HDF5_write_int1
     module procedure HDF5_write_int2
     module procedure HDF5_write_int3
@@ -63,6 +63,10 @@ module HDF5_utilities
     module procedure HDF5_write_int5
     module procedure HDF5_write_int6
     module procedure HDF5_write_int7
+#else
+    module procedure HDF5_write_real
+    module procedure HDF5_write_int
+#endif
   end interface HDF5_write
 
 !--------------------------------------------------------------------------------------------------
@@ -1210,6 +1214,7 @@ subroutine HDF5_read_int7(dataset,loc_id,datasetName,parallel)
 
 end subroutine HDF5_read_int7
 
+#if defined(__GFORTRAN__) && __GNUC__<11
 
 !--------------------------------------------------------------------------------------------------
 !> @brief write dataset of type real with 1 dimension
@@ -1499,6 +1504,71 @@ subroutine HDF5_write_real7(dataset,loc_id,datasetName,parallel)
 
 end subroutine HDF5_write_real7
 
+#else
+
+!--------------------------------------------------------------------------------------------------
+!> @brief write dataset of type real with 1-7 dimension
+!--------------------------------------------------------------------------------------------------
+subroutine HDF5_write_real(dataset,loc_id,datasetName,parallel)
+
+  real(pReal),      intent(in), dimension(..) :: dataset                                            !< data written to file
+  integer(HID_T),   intent(in)  :: loc_id                                                           !< file or group handle
+  character(len=*), intent(in)  :: datasetName                                                      !< name of the dataset in the file
+  logical, intent(in), optional :: parallel                                                         !< dataset is distributed over multiple processes
+
+
+  integer :: hdferr
+  integer(HID_T)   :: dset_id, filespace_id, memspace_id, plist_id
+  integer(HSIZE_T), dimension(rank(dataset)) :: &
+    myStart, &
+    myShape, &                                                                                      !< shape of the dataset (this process)
+    totalShape                                                                                      !< shape of the dataset (all processes)
+
+!---------------------------------------------------------------------------------------------------
+! determine shape of dataset
+  myShape = int(shape(dataset),HSIZE_T)
+  if (any(myShape(1:size(myShape)-1) == 0)) return                                                  !< empty dataset (last dimension can be empty)
+
+  if (present(parallel)) then
+    call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
+                          myStart, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
+  else
+    call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
+                          myStart, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
+  end if
+
+  if (product(totalShape) /= 0) then
+    select rank(dataset)
+      rank (1)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
+                        file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank (2)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
+                        file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank (3)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
+                        file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank (4)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
+                        file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank (5)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
+                        file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank (6)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
+                        file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank (7)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
+                        file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+    end select
+    if(hdferr < 0) error stop 'HDF5 error'
+  end if
+
+  call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
+
+end subroutine HDF5_write_real
+#endif
+
 
 !--------------------------------------------------------------------------------------------------
 !> @brief Write dataset of type string (scalar).
@@ -1561,6 +1631,7 @@ subroutine HDF5_write_str(dataset,loc_id,datasetName)
 
 end subroutine HDF5_write_str
 
+#if defined(__GFORTRAN__) && __GNUC__<11
 
 !--------------------------------------------------------------------------------------------------
 !> @brief write dataset of type integer with 1 dimension
@@ -1849,6 +1920,70 @@ subroutine HDF5_write_int7(dataset,loc_id,datasetName,parallel)
 
 end subroutine HDF5_write_int7
 
+#else
+
+!--------------------------------------------------------------------------------------------------
+!> @brief write dataset of type integer with 1-7 dimension
+!--------------------------------------------------------------------------------------------------
+subroutine HDF5_write_int(dataset,loc_id,datasetName,parallel)
+
+  integer,          intent(in), dimension(..) :: dataset                                            !< data written to file
+  integer(HID_T),   intent(in)  :: loc_id                                                           !< file or group handle
+  character(len=*), intent(in)  :: datasetName                                                      !< name of the dataset in the file
+  logical, intent(in), optional :: parallel                                                         !< dataset is distributed over multiple processes
+
+
+  integer :: hdferr
+  integer(HID_T)   :: dset_id, filespace_id, memspace_id, plist_id
+  integer(HSIZE_T), dimension(rank(dataset)) :: &
+    myStart, &
+    myShape, &                                                                                      !< shape of the dataset (this process)
+    totalShape                                                                                      !< shape of the dataset (all processes)
+
+!---------------------------------------------------------------------------------------------------
+! determine shape of dataset
+  myShape = int(shape(dataset),HSIZE_T)
+  if (any(myShape(1:size(myShape)-1) == 0)) return                                                  !< empty dataset (last dimension can be empty)
+
+  if (present(parallel)) then
+    call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
+                          myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
+  else
+    call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
+                          myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
+  end if
+
+  if (product(totalShape) /= 0) then
+    select rank(dataset)
+      rank(1)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
+                       file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank(2)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
+                       file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank(3)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
+                       file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank(4)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
+                       file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank(5)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
+                       file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank(6)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
+                       file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+      rank(7)
+        call H5Dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
+                       file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
+    end select
+    if(hdferr < 0) error stop 'HDF5 error'
+  end if
+
+  call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
+
+end subroutine HDF5_write_int
+#endif
 
 !--------------------------------------------------------------------------------------------------
 !> @brief initialize HDF5 handles, determines global shape and start for parallel read

From b796ccb04a3b2e3e0ffac0f74f31d8c5b2ff1553 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Mon, 18 Apr 2022 13:18:14 +0200
Subject: [PATCH 27/36] DAMASK requires gfortran >= 9

---
 src/rotations.f90 | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/src/rotations.f90 b/src/rotations.f90
index 53f1fe976..7aa81fcab 100644
--- a/src/rotations.f90
+++ b/src/rotations.f90
@@ -658,11 +658,7 @@ function om2ax(om) result(ax)
   else
     call dgeev('N','V',3,om_,3,Wr,Wi,devNull,3,VR,3,work,size(work,1),ierr)
     if (ierr /= 0) error stop 'LAPACK error'
-#if defined(__GFORTRAN__) &&  __GNUC__<9
-    i = maxloc(merge(1,0,cEq(cmplx(Wr,Wi,pReal),cmplx(1.0_pReal,0.0_pReal,pReal),tol=1.0e-14_pReal)),dim=1)
-#else
     i = findloc(cEq(cmplx(Wr,Wi,pReal),cmplx(1.0_pReal,0.0_pReal,pReal),tol=1.0e-14_pReal),.true.,dim=1) !find eigenvalue (1,0)
-#endif
     if (i == 0) error stop 'om2ax conversion failed'
     ax(1:3) = VR(1:3,i)
     where (                dNeq0([om(2,3)-om(3,2), om(3,1)-om(1,3), om(1,2)-om(2,1)])) &
@@ -1427,10 +1423,6 @@ subroutine selfTest()
 
   do i = 1, 20
 
-#if defined(__GFORTRAN__) && __GNUC__<9
-    if(i<7) cycle
-#endif
-
     if(i==1) then
       qu = om2qu(math_I3)
     elseif(i==2) then

From 4a93dbec117cbb0092ddc8f33e1a5cbe00097d2b Mon Sep 17 00:00:00 2001
From: Philip Eisenlohr <eisenlohr@egr.msu.edu>
Date: Tue, 19 Apr 2022 13:11:40 -0400
Subject: [PATCH 28/36] more descriptive variable names

---
 src/material.f90 | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/src/material.f90 b/src/material.f90
index 7264738e5..2258c40a1 100644
--- a/src/material.f90
+++ b/src/material.f90
@@ -95,9 +95,9 @@ subroutine parse()
   integer, dimension(:), allocatable :: &
     counterPhase, &
     counterHomogenization, &
-    temp_ho
-  integer, dimension(:,:), allocatable :: temp_ph
-  real(pReal), dimension(:,:), allocatable :: temp_v
+    ho_of
+  integer, dimension(:,:), allocatable :: ph_of
+  real(pReal), dimension(:,:), allocatable :: v_of
 
   real(pReal) :: v
   integer :: &
@@ -135,9 +135,9 @@ subroutine parse()
   allocate(material_O_0(materials%length))
   allocate(material_F_i_0(materials%length))
 
-  allocate(temp_ho(materials%length))
-  allocate(temp_ph(materials%length,homogenization_maxNconstituents),source=-1)
-  allocate(temp_v(materials%length,homogenization_maxNconstituents),source=0.0_pReal)
+  allocate(ho_of(materials%length))
+  allocate(ph_of(materials%length,homogenization_maxNconstituents),source=-1)
+  allocate( v_of(materials%length,homogenization_maxNconstituents),source=0.0_pReal)
 
   ! parse YAML structure
   select type(materials)
@@ -147,10 +147,10 @@ subroutine parse()
       item => materials%first
       do ma = 1, materials%length
         material => item%node
-        temp_ho(ma) = homogenizations%getIndex(material%get_asString('homogenization'))
+        ho_of(ma) = homogenizations%getIndex(material%get_asString('homogenization'))
         constituents => material%get('constituents')
 
-        homogenization => homogenizations%get(temp_ho(ma))
+        homogenization => homogenizations%get(ho_of(ma))
         if (constituents%length /= homogenization%get_asInt('N_constituents')) call IO_error(148)
 
         allocate(material_O_0(ma)%data(constituents%length))
@@ -158,14 +158,14 @@ subroutine parse()
 
         do co = 1, constituents%length
           constituent => constituents%get(co)
-          temp_v(ma,co) = constituent%get_asFloat('v')
-          temp_ph(ma,co) = phases%getIndex(constituent%get_asString('phase'))
+           v_of(ma,co) = constituent%get_asFloat('v')
+          ph_of(ma,co) = phases%getIndex(constituent%get_asString('phase'))
 
           call material_O_0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4))
           material_F_i_0(ma)%data(1:3,1:3,co) = constituent%get_as2dFloat('F_i',defaultVal=math_I3,requiredShape=[3,3])
 
         end do
-        if (dNeq(sum(temp_v(ma,:)),1.0_pReal,1.e-9_pReal)) call IO_error(153,ext_msg='constituent')
+        if (dNeq(sum(v_of(ma,:)),1.0_pReal,1.e-9_pReal)) call IO_error(153,ext_msg='constituent')
 
         item => item%next
       end do
@@ -187,7 +187,7 @@ subroutine parse()
   do el = 1, discretization_Nelems
 
     ma = discretization_materialAt(el)
-    ho = temp_ho(ma)
+    ho = ho_of(ma)
 
     do ip = 1, discretization_nIPs
       ce = (el-1)*discretization_nIPs + ip
@@ -196,10 +196,10 @@ subroutine parse()
       material_homogenizationEntry(ce) = counterHomogenization(ho)
     end do
 
-    do co = 1, size(temp_ph(ma,:)>0)
+    do co = 1, size(ph_of(ma,:)>0)
 
-      v = temp_v(ma,co)
-      ph = temp_ph(ma,co)
+      v  =  v_of(ma,co)
+      ph = ph_of(ma,co)
 
       do ip = 1, discretization_nIPs
         ce = (el-1)*discretization_nIPs + ip

From 9e2fcfc9df47b1fb3fdb2a89fdcb5c8c540f3e81 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Wed, 20 Apr 2022 05:24:57 +0200
Subject: [PATCH 29/36] [skip ci] updated version information after successful
 test of v3.0.0-alpha6-210-ge8c1f8453

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 7ce9e687d..c2c4f8316 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha6-206-g51582b80f
+v3.0.0-alpha6-210-ge8c1f8453

From df3f4d9480524dc84a815f3149354d2c235fd0f5 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 20 Apr 2022 07:00:02 +0200
Subject: [PATCH 30/36] testing forward/backward FFT

---
 src/grid/spectral_utilities.f90 | 39 ++++++++++++++++++++++++++++++++-
 src/prec.f90                    |  6 ++---
 2 files changed, 41 insertions(+), 4 deletions(-)

diff --git a/src/grid/spectral_utilities.f90 b/src/grid/spectral_utilities.f90
index 525f68d7e..3f7c32668 100644
--- a/src/grid/spectral_utilities.f90
+++ b/src/grid/spectral_utilities.f90
@@ -142,7 +142,7 @@ contains
 !> level chosen.
 !> Initializes FFTW.
 !--------------------------------------------------------------------------------------------------
-subroutine spectral_utilities_init
+subroutine spectral_utilities_init()
 
   PetscErrorCode :: err_PETSc
   integer        :: i, j, k, &
@@ -1146,4 +1146,41 @@ subroutine utilities_saveReferenceStiffness
 
 end subroutine utilities_saveReferenceStiffness
 
+
+!--------------------------------------------------------------------------------------------------
+!> @brief Check correctness of forward-backward transform.
+!--------------------------------------------------------------------------------------------------
+subroutine selfTest()
+
+  real(pReal), allocatable, dimension(:,:,:,:,:) :: tensorField_real_
+  real(pReal), allocatable, dimension(:,:,:,:) :: vectorField_real_
+  real(pReal), allocatable, dimension(:,:,:) :: scalarField_real_
+
+
+  call random_number(tensorField_real)
+  tensorField_real(1:3,1:3,cells(1)+1:cells1Red*2,:,:) = 0.0_pReal
+  tensorField_real_ = tensorField_real
+  call utilities_FFTtensorForward()
+  call utilities_FFTtensorBackward()
+  tensorField_real(1:3,1:3,cells(1)+1:cells1Red*2,:,:) = 0.0_pReal
+  if (maxval(abs(tensorField_real_ - tensorField_real))>1.0e-15_pReal) error stop 'tensorField'
+
+  call random_number(vectorField_real)
+  vectorField_real(1:3,cells(1)+1:cells1Red*2,:,:) = 0.0_pReal
+  vectorField_real_ = vectorField_real
+  call utilities_FFTvectorForward()
+  call utilities_FFTvectorBackward()
+  vectorField_real(1:3,cells(1)+1:cells1Red*2,:,:) = 0.0_pReal
+  if (maxval(abs(vectorField_real_ - vectorField_real))>1.0e-15_pReal) error stop 'vectorField'
+
+  call random_number(scalarField_real)
+  scalarField_real(cells(1)+1:cells1Red*2,:,:) = 0.0_pReal
+  scalarField_real_ = scalarField_real
+  call utilities_FFTscalarForward()
+  call utilities_FFTscalarBackward()
+  scalarField_real(cells(1)+1:cells1Red*2,:,:) = 0.0_pReal
+  if (maxval(abs(scalarField_real_ - scalarField_real))>1.0e-15_pReal) error stop 'scalarField'
+
+end subroutine selfTest
+
 end module spectral_utilities
diff --git a/src/prec.f90 b/src/prec.f90
index d0753790e..73563d4f2 100644
--- a/src/prec.f90
+++ b/src/prec.f90
@@ -48,7 +48,7 @@ contains
 !--------------------------------------------------------------------------------------------------
 !> @brief Report precision and do self test.
 !--------------------------------------------------------------------------------------------------
-subroutine prec_init
+subroutine prec_init()
 
   print'(/,1x,a)', '<<<+-  prec init  -+>>>'
 
@@ -60,7 +60,7 @@ subroutine prec_init
   print'(  a,e10.3)', '   epsilon value:      ',PREAL_EPSILON
   print'(  a,i3)',    '   decimal precision:  ',precision(0.0_pReal)
 
-  call selfTest
+  call selfTest()
 
 end subroutine prec_init
 
@@ -245,7 +245,7 @@ end function prec_bytesToC_INT64_T
 !--------------------------------------------------------------------------------------------------
 !> @brief Check correctness of some prec functions.
 !--------------------------------------------------------------------------------------------------
-subroutine selfTest
+subroutine selfTest()
 
   integer, allocatable, dimension(:) :: realloc_lhs_test
   real(pReal),   dimension(1) :: f

From d6f2b99199a770512634544f018d1ed451b0d75d Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Wed, 20 Apr 2022 10:02:55 +0200
Subject: [PATCH 31/36] [skip ci] updated version information after successful
 test of v3.0.0-alpha6-221-gdff78154a

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index c2c4f8316..b96558745 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha6-210-ge8c1f8453
+v3.0.0-alpha6-221-gdff78154a

From d916c7c6b19da5c83af152d81571a42e872845b2 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 21 Apr 2022 17:32:30 +0200
Subject: [PATCH 32/36] small polishing

---
 PRIVATE                | 2 +-
 python/damask/_grid.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/PRIVATE b/PRIVATE
index f6a94aeaa..e3d9c0cc3 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit f6a94aeaaa3a81347821e7a092d43dd04115f5f6
+Subproject commit e3d9c0cc3ffa1435003f934a0f0e6c7d969a022a
diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 6dc9879ce..d4a7ea02f 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -292,7 +292,7 @@ class Grid:
         >>> import damask
         >>> N_grains = 20
         >>> cells = (32,32,32)
-        >>> damask.util.run(f'neper -T -n {N_grains} -tesrsize {cells[0]}:{cells[1]}:{cells[2]} -periodicity "all" -format "vtk"')
+        >>> damask.util.run(f'neper -T -n {N_grains} -tesrsize {cells[0]}:{cells[1]}:{cells[2]} -periodicity all -format vtk')
         >>> damask.Grid.load_Neper(f'n{N_grains}-id1.vtk')
         cells:  32 × 32 × 32
         size:   1.0 × 1.0 × 1.0 m³

From 8e668a565ec500007adabccf06fdad5d4afbf5a1 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Thu, 21 Apr 2022 21:58:03 +0200
Subject: [PATCH 33/36] [skip ci] updated version information after successful
 test of v3.0.0-alpha6-223-gd916c7c6b

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index b96558745..f5c5e0426 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha6-221-gdff78154a
+v3.0.0-alpha6-223-gd916c7c6b

From 745f5348cd0bc4c816cfb694cc9c1b7bac9f5302 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 22 Apr 2022 00:01:54 +0200
Subject: [PATCH 34/36] running new tests

---
 src/grid/spectral_utilities.f90 | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/grid/spectral_utilities.f90 b/src/grid/spectral_utilities.f90
index 3f7c32668..8e7da7647 100644
--- a/src/grid/spectral_utilities.f90
+++ b/src/grid/spectral_utilities.f90
@@ -350,6 +350,8 @@ subroutine spectral_utilities_init()
     allocate (gamma_hat(3,3,3,3,cells1Red,cells(2),cells3), source = cmplx(0.0_pReal,0.0_pReal,pReal))
   endif
 
+  call selfTest()
+
 end subroutine spectral_utilities_init
 
 

From 690b2e9c21c2dbcaf8725666a7c6fe51cba116ff Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 22 Apr 2022 07:18:53 +0200
Subject: [PATCH 35/36] tolerances were to strict for certain operations

---
 src/grid/spectral_utilities.f90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/grid/spectral_utilities.f90 b/src/grid/spectral_utilities.f90
index 8e7da7647..4375ec860 100644
--- a/src/grid/spectral_utilities.f90
+++ b/src/grid/spectral_utilities.f90
@@ -1165,7 +1165,7 @@ subroutine selfTest()
   call utilities_FFTtensorForward()
   call utilities_FFTtensorBackward()
   tensorField_real(1:3,1:3,cells(1)+1:cells1Red*2,:,:) = 0.0_pReal
-  if (maxval(abs(tensorField_real_ - tensorField_real))>1.0e-15_pReal) error stop 'tensorField'
+  if (maxval(abs(tensorField_real_ - tensorField_real))>5.0e-15_pReal) error stop 'tensorField'
 
   call random_number(vectorField_real)
   vectorField_real(1:3,cells(1)+1:cells1Red*2,:,:) = 0.0_pReal
@@ -1173,7 +1173,7 @@ subroutine selfTest()
   call utilities_FFTvectorForward()
   call utilities_FFTvectorBackward()
   vectorField_real(1:3,cells(1)+1:cells1Red*2,:,:) = 0.0_pReal
-  if (maxval(abs(vectorField_real_ - vectorField_real))>1.0e-15_pReal) error stop 'vectorField'
+  if (maxval(abs(vectorField_real_ - vectorField_real))>5.0e-15_pReal) error stop 'vectorField'
 
   call random_number(scalarField_real)
   scalarField_real(cells(1)+1:cells1Red*2,:,:) = 0.0_pReal
@@ -1181,7 +1181,7 @@ subroutine selfTest()
   call utilities_FFTscalarForward()
   call utilities_FFTscalarBackward()
   scalarField_real(cells(1)+1:cells1Red*2,:,:) = 0.0_pReal
-  if (maxval(abs(scalarField_real_ - scalarField_real))>1.0e-15_pReal) error stop 'scalarField'
+  if (maxval(abs(scalarField_real_ - scalarField_real))>5.0e-15_pReal) error stop 'scalarField'
 
 end subroutine selfTest
 

From 5d12ef5b9f0c59ec9203c32b1c6f5c2b70ffdfba Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Fri, 22 Apr 2022 18:07:42 +0200
Subject: [PATCH 36/36] [skip ci] updated version information after successful
 test of v3.0.0-alpha6-228-g758ad6072

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index f5c5e0426..f8dcddc79 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha6-223-gd916c7c6b
+v3.0.0-alpha6-228-g758ad6072