Merge branch 'polishing' into 'development'

A few small changes + a bugfix

See merge request damask/DAMASK!434

.gitlab-ci.yml

@@ -224,24 +224,12 @@ source_distribution:
     - master
     - release
 
-library_documentation:
-  stage: deploy
-  script:
-    - cd $DAMASKROOT/PRIVATE/documenting/sphinx
-    - make html
-  except:
-    - master
-    - release
-
 ##################################################################################################
 backup_runtime_measurement:
   stage: backup
   script:
     - cd $LOCAL_HOME/performance                                                                    # location of new runtime results
     - git commit -am"${CI_PIPELINE_ID}_${CI_COMMIT_SHA}"
-    - mkdir $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}
-    - mv $LOCAL_HOME/performance/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
-    - mv $LOCAL_HOME/performance/memory.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
   only:
     - development
 

PRIVATE

@@ -1 +1 @@
-Subproject commit 7276083d38816c4cfc336b7597aace3f447273dd
+Subproject commit 65c453c46d157f6448ab48829d059b1d641fde47

README

@@ -10,4 +10,4 @@ Germany
 
 damask@mpie.de
 https://damask.mpie.de
-https://magit1.mpie.de
+https://git.damask.mpie.de

cmake/Compiler-GNU.cmake

@@ -25,7 +25,7 @@ set (LINKER_FLAGS  "${LINKER_FLAGS},-undefined,dynamic_lookup" )
 
 #------------------------------------------------------------------------------------------------
 # Fine tuning compilation options
-set (COMPILE_FLAGS "${COMPILE_FLAGS} -xf95-cpp-input")
+set (COMPILE_FLAGS "${COMPILE_FLAGS} -cpp")
 # preprocessor
 
 set (COMPILE_FLAGS "${COMPILE_FLAGS} -fPIC -fPIE")

env/DAMASK.sh

@@ -60,7 +60,7 @@ if [ ! -z "$PS1" ]; then
   echo -n "heap  size         "
    [[ "$(ulimit -d)" == "unlimited" ]] \
    && echo "unlimited" \
-   || echo $(python -c \
+   || echo $(python3 -c \
           "import math; \
            size=$(( 1024*$(ulimit -d) )); \
            print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
@@ -68,7 +68,7 @@ if [ ! -z "$PS1" ]; then
   echo -n "stack size         "
    [[ "$(ulimit -s)" == "unlimited" ]] \
    && echo "unlimited" \
-   || echo $(python -c \
+   || echo $(python3 -c \
           "import math; \
            size=$(( 1024*$(ulimit -s) )); \
            print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \

env/DAMASK.zsh

@@ -50,7 +50,7 @@ if [ ! -z "$PS1" ]; then
   echo -n "heap  size         "
    [[ "$(ulimit -d)" == "unlimited" ]] \
    && echo "unlimited" \
-   || echo $(python -c \
+   || echo $(python3 -c \
           "import math; \
            size=$(( 1024*$(ulimit -d) )); \
            print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
@@ -58,7 +58,7 @@ if [ ! -z "$PS1" ]; then
   echo -n "stack size         "
    [[ "$(ulimit -s)" == "unlimited" ]] \
    && echo "unlimited" \
-   || echo $(python -c \
+   || echo $(python3 -c \
           "import math; \
            size=$(( 1024*$(ulimit -s) )); \
            print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \

python/damask/_rotation.py

@@ -1026,7 +1026,7 @@ class Rotation:
         N : int, optional
             Number of samples, defaults to 500.
         degrees : boolean, optional
-            sigma is given in degrees.
+            sigma is given in degrees. Defaults to True.
         rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
             A seed to initialize the BitGenerator. Defaults to None, i.e. unpredictable entropy
             will be pulled from the OS.
@@ -1055,10 +1055,10 @@ class Rotation:
 
         Parameters
         ----------
-        alpha : numpy.ndarray of size 2
+        alpha : numpy.ndarray of shape (2)
-            Polar coordinates (phi from x,theta from z) of fiber direction in crystal frame.
+            Polar coordinates (phi from x, theta from z) of fiber direction in crystal frame.
-        beta : numpy.ndarray of size 2
+        beta : numpy.ndarray of shape (2)
-            Polar coordinates (phi from x,theta from z) of fiber direction in sample frame.
+            Polar coordinates (phi from x, theta from z) of fiber direction in sample frame.
         sigma : float, optional
             Standard deviation of (Gaussian) misorientation distribution.
             Defaults to 0.

python/damask/util.py

@@ -18,7 +18,7 @@ from . import version
 __all__=[
          'srepr',
          'emph', 'deemph', 'warn', 'strikeout',
-         'execute', 'run',
+         'run', 
          'natural_sort',
          'show_progress',
          'scale_to_coprime',

python/setup.py

@@ -19,6 +19,7 @@ setuptools.setup(
     python_requires = '>=3.6',
     install_requires = [
         'pandas>=0.24',                                                                             # requires numpy
+        'numpy>=1.17',                                                                              # needed for default_rng
         'scipy>=1.2',
         'h5py>=2.9',                                                                                # requires numpy
         'vtk>=8.1',

src/grid/discretization_grid.f90

@@ -266,7 +266,8 @@ subroutine readVTI(grid,geomSize,origin,material, &
     integer :: i
 
 
-    if (getXMLValue(header,'Direction') /= '1 0 0 0 1 0 0 0 1') &
+    temp = getXMLValue(header,'Direction')
+    if (temp /= '1 0 0 0 1 0 0 0 1' .and. temp /= '') &                                             ! https://discourse.vtk.org/t/vti-specification/6526
       call IO_error(error_ID = 844, ext_msg = 'coordinate order')
 
     temp = getXMLValue(header,'WholeExtent')