Merge branch 'development' into geom-sort

.gitlab-ci.yml

@@ -20,12 +20,12 @@ stages:
 
 ###################################################################################################
 before_script:
-  - if [ $(awk "/$CI_PIPELINE_ID/{print NR}" $TESTROOT/GitLabCI.queue)x == 'x' ];
+  - if [ $(awk "/$CI_PIPELINE_ID/{print NR}" $LOCAL_HOME/GitLabCI.queue)x == 'x' ];
-      then echo $CI_PIPELINE_ID >> $TESTROOT/GitLabCI.queue;
+      then echo $CI_PIPELINE_ID >> $LOCAL_HOME/GitLabCI.queue;
     fi
-  - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $TESTROOT/GitLabCI.queue) != 1 ];
+  - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $LOCAL_HOME/GitLabCI.queue) != 1 ];
       do sleep 5m;
-      echo -e "Currently queued pipelines:\n$(cat $TESTROOT/GitLabCI.queue)\n";
+      echo -e "Currently queued pipelines:\n$(cat $LOCAL_HOME/GitLabCI.queue)\n";
     done
   - source $DAMASKROOT/env/DAMASK.sh
   - cd $DAMASKROOT/PRIVATE/testing
@@ -45,7 +45,8 @@ variables:
   # ===============================================================================================
   # Shortcut names
   # ===============================================================================================
-  DAMASKROOT: "$TESTROOT/GitLabCI_Pipeline_$CI_PIPELINE_ID/DAMASK"
+  DAMASKROOT: "$LOCAL_HOME/GitLabCI_Pipeline_$CI_PIPELINE_ID/DAMASK"
+  TESTROOT:   "$LOCAL_HOME/GitLabCI_Pipeline_$CI_PIPELINE_ID/tests"
 
   # ===============================================================================================
   # Names of module files to load
@@ -75,31 +76,25 @@ variables:
   MSC:                             "$MSC2019_1"
   IntelMarc:                       "$IntelCompiler17_8"
   HDF5Marc:                        "HDF5/1.10.5/Intel-17.8"
-  # ++++++++++++ Documentation ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-  Doxygen1_8_17:                   "Documentation/Doxygen/1.8.17"
-  # ------------ Defaults ----------------------------------------------
-  Doxygen:                         "$Doxygen1_8_17"
-
 
 ###################################################################################################
 checkout:
   stage: prepareAll
   before_script:
-    - echo $CI_PIPELINE_ID >> $TESTROOT/GitLabCI.queue
+    - echo $CI_PIPELINE_ID >> $LOCAL_HOME/GitLabCI.queue
-    - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $TESTROOT/GitLabCI.queue) != 1 ];
+    - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $LOCAL_HOME/GitLabCI.queue) != 1 ];
         do sleep 5m;
-        echo -e "Currently queued pipelines:\n$(cat $TESTROOT/GitLabCI.queue)\n";
+        echo -e "Currently queued pipelines:\n$(cat $LOCAL_HOME/GitLabCI.queue)\n";
       done
   script:
     - mkdir -p $DAMASKROOT
+    - mkdir -p $TESTROOT
     - cd $DAMASKROOT
-    - if [ -d DAMASK ]; then rm -rf DAMASK; fi                                                      # there might be some leftovers from a failed clone
     - git clone -q git@magit1.mpie.de:damask/DAMASK.git .
     - git checkout $CI_COMMIT_SHA
     - git submodule update --init
     - source env/DAMASK.sh
     - make processing
-    - mkdir /tmp/$CI_PIPELINE_ID
   except:
     - master
     - release
@@ -109,7 +104,7 @@ Pytest_python:
   stage: python
   script:
     - cd $DAMASKROOT/python
-    - pytest --basetemp=/tmp/${CI_PIPELINE_ID}/python
+    - pytest --basetemp=${TESTROOT}/python -v
   except:
     - master
     - release
@@ -195,7 +190,7 @@ grid_mech_compile_Intel:
     - cp -r grid_mech_compile grid_mech_compile_Intel
     - grid_mech_compile_Intel/test.py
     - cd pytest
-    - pytest -k 'compile and grid' --basetemp=/tmp/${CI_PIPELINE_ID}/compile_grid_Intel
+    - pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_Intel
   except:
     - master
     - release
@@ -207,7 +202,7 @@ Compile_FEM_Intel:
     - cp -r FEM_compile FEM_compile_Intel
     - FEM_compile_Intel/test.py
     - cd pytest
-    - pytest -k 'compile and mesh' --basetemp=/tmp/${CI_PIPELINE_ID}/compile_mesh_Intel
+    - pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_Intel
   except:
     - master
     - release
@@ -219,7 +214,7 @@ grid_mech_compile_GNU:
     - cp -r grid_mech_compile grid_mech_compile_GNU
     - grid_mech_compile_GNU/test.py
     - cd pytest
-    - pytest -k 'compile and grid' --basetemp=/tmp/${CI_PIPELINE_ID}/compile_grid_GNU
+    - pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_GNU
   except:
     - master
     - release
@@ -231,7 +226,7 @@ Compile_FEM_GNU:
     - cp -r FEM_compile FEM_compile_GNU
     - FEM_compile_GNU/test.py
     - cd pytest
-    - pytest -k 'compile and mesh' --basetemp=/tmp/${CI_PIPELINE_ID}/compile_mesh_GNU
+    - pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_GNU
   except:
     - master
     - release
@@ -253,7 +248,7 @@ Pytest_grid:
   script:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
     - cd pytest
-    - pytest -m 'not compile' --basetemp=/tmp/${CI_PIPELINE_ID}/fortran
+    - pytest -k 'not compile' --basetemp=${TESTROOT}/fortran -v
   except:
     - master
     - release
@@ -314,9 +309,8 @@ Marc_compileIfort:
   stage: compileMarc
   script:
     - module load $IntelMarc $HDF5Marc $MSC
-    - Marc_compileIfort/test.py
     - cd pytest
-    - pytest -k 'compile and Marc'
+    - pytest -k 'compile and Marc' --basetemp=${TESTROOT}/compile_Marc
   except:
     - master
     - release
@@ -382,10 +376,10 @@ SpectralRuntime:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
     - cd $DAMASKROOT
     - make clean grid processing OPTIMIZATION=AGGRESSIVE
-    - cd $TESTROOT/performance                                                                      # location of old results
+    - cd $LOCAL_HOME/performance                                                                    # location of old results
     - git checkout .                                                                                # undo any changes (i.e. run time data from non-development branch)
     - cd $DAMASKROOT/PRIVATE/testing
-    - SpectralAll_runtime/test.py -d $TESTROOT/performance
+    - SpectralAll_runtime/test.py -d $LOCAL_HOME/performance
   except:
     - master
     - release
@@ -401,20 +395,10 @@ createTar:
     - release
 
 ###################################################################################################
-Marc:
+Python:
   stage: createDocumentation
   script:
-    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
+    - echo 'tbd one matesting1'
-    - $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT marc
-  except:
-    - master
-    - release
-
-GridSolver:
-  stage: createDocumentation
-  script:
-    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
-    - $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT grid
   except:
     - master
     - release
@@ -423,11 +407,11 @@ GridSolver:
 backupData:
   stage: saveDocumentation
   script:
-    - cd $TESTROOT/performance                                                                      # location of new runtime results
+    - 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 $TESTROOT/performance/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - mv $LOCAL_HOME/performance/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
-    - mv $TESTROOT/performance/memory.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - mv $LOCAL_HOME/performance/memory.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
     - mv $DAMASKROOT/PRIVATE/documenting/DAMASK_* $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
   only:
     - development
@@ -457,8 +441,8 @@ removeData:
   before_script:
     - echo "Removing data and lock of pipeline $CI_PIPELINE_ID"
   script:
-    - rm -rf $TESTROOT/GitLabCI_Pipeline_$CI_PIPELINE_ID
+    - rm -rf $LOCAL_HOME/GitLabCI_Pipeline_$CI_PIPELINE_ID
-    - sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue                                          # in case pipeline was manually (web GUI) restarted and releaseLock was performed already
+    - sed -i "/$CI_PIPELINE_ID/d" $LOCAL_HOME/GitLabCI.queue                                        # in case pipeline was manually (web GUI) restarted and releaseLock was performed already
   except:
     - master
     - release
@@ -469,7 +453,7 @@ removeLock:
   before_script:
     - echo "Removing lock of pipeline $CI_PIPELINE_ID"
   when: always
-  script: sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue
+  script: sed -i "/$CI_PIPELINE_ID/d" $LOCAL_HOME/GitLabCI.queue
   except:
     - master
     - release

PRIVATE

@@ -1 +1 @@
-Subproject commit fb8647f77aeb52098605f0fd7fe95764e6d26027
+Subproject commit e2301f7d12ff0ae12218d9b58e33a814eb5431c9

VERSION

@@ -1 +1 @@
-v3.0.0-alpha-609-g657d7b06b
+v3.0.0-alpha-633-g086b215d9

env/DAMASK.csh

@@ -51,4 +51,4 @@ else
   setenv PYTHONPATH $DAMASK_ROOT/python:$PYTHONPATH
 endif
 setenv MSC_ROOT
-setenv MARC_VERSION
+setenv MSC_VERSION

examples/SpectralMethod/Polycrystal/material.yaml

@@ -110,7 +110,7 @@ phase:
   Aluminum:
     elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
     generic:
-      output: [F, P, Fe, Fp, Lp, O]
+      output: [F, P, F_e, F_p, L_p, O]
     lattice: fcc
     plasticity:
       N_sl: [12]

installation/mods_MarcMentat/apply_DAMASK_modifications.py

@@ -7,15 +7,15 @@ from pathlib import Path
 
 import damask
 
-marc_version = float(damask.environment.options['MSC_VERSION'])
+msc_version = float(damask.environment.options['MSC_VERSION'])
-if int(marc_version) == marc_version:
+if int(msc_version) == msc_version:
-    marc_version = int(marc_version)
+    msc_version = int(msc_version)
 msc_root     = Path(damask.environment.options['MSC_ROOT'])
 damask_root  = damask.environment.root_dir
 
 parser = argparse.ArgumentParser(
      description='Apply DAMASK modification to MSC.Marc/Mentat',
-     epilog = f'MSC_ROOT={msc_root} and MSC_VERSION={marc_version} (from {damask_root}/env/CONFIG)')
+     epilog = f'MSC_ROOT={msc_root} and MSC_VERSION={msc_version} (from {damask_root}/env/CONFIG)')
 parser.add_argument('--editor', dest='editor', metavar='string', default='vi',
                     help='Name of the editor for MSC.Mentat (executable)')
 
@@ -24,7 +24,7 @@ def copy_and_replace(in_file,dst):
     with open(in_file) as f:
         content = f.read()
     content = content.replace('%INSTALLDIR%',str(msc_root))
-    content = content.replace('%VERSION%',str(marc_version))
+    content = content.replace('%VERSION%',str(msc_version))
     content = content.replace('%EDITOR%', parser.parse_args().editor)
     with open(dst/Path(in_file).name,'w') as f:
         f.write(content)
@@ -32,36 +32,36 @@ def copy_and_replace(in_file,dst):
 
 print('adapting Marc tools...\n')
 
-src = damask_root/f'installation/mods_MarcMentat/{marc_version}/Marc_tools'
+src = damask_root/f'installation/mods_MarcMentat/{msc_version}/Marc_tools'
-dst = msc_root/f'marc{marc_version}/tools'
+dst = msc_root/f'marc{msc_version}/tools'
 for in_file in glob.glob(str(src/'*damask*')) + [str(src/'include_linux64')]:
     copy_and_replace(in_file,dst)
 
 
 print('adapting Mentat scripts and menus...\n')
 
-src = damask_root/f'installation/mods_MarcMentat/{marc_version}/Mentat_bin'
+src = damask_root/f'installation/mods_MarcMentat/{msc_version}/Mentat_bin'
-dst = msc_root/f'mentat{marc_version}/bin'
+dst = msc_root/f'mentat{msc_version}/bin'
 for in_file in glob.glob(str(src/'*[!.original]')):
     copy_and_replace(in_file,dst)
 
-src = damask_root/f'installation/mods_MarcMentat/{marc_version}/Mentat_menus'
+src = damask_root/f'installation/mods_MarcMentat/{msc_version}/Mentat_menus'
-dst = msc_root/f'mentat{marc_version}/menus'
+dst = msc_root/f'mentat{msc_version}/menus'
 for in_file in glob.glob(str(src/'job_run.ms')):
     copy_and_replace(in_file,dst)
 
 
 print('compiling Mentat menu binaries...')
 
-executable = str(msc_root/f'mentat{marc_version}/bin/mentat')
+executable = str(msc_root/f'mentat{msc_version}/bin/mentat')
-menu_file  = str(msc_root/f'mentat{marc_version}/menus/linux64/main.msb')
+menu_file  = str(msc_root/f'mentat{msc_version}/menus/linux64/main.msb')
 os.system(f'xvfb-run {executable} -compile {menu_file}')
 
 
 print('setting file access rights...\n')
 
-for pattern in [msc_root/f'marc{marc_version}/tools/*damask*',
+for pattern in [msc_root/f'marc{msc_version}/tools/*damask*',
-                msc_root/f'mentat{marc_version}/bin/submit?',
+                msc_root/f'mentat{msc_version}/bin/submit?',
-                msc_root/f'mentat{marc_version}/bin/kill?']:
+                msc_root/f'mentat{msc_version}/bin/kill?']:
     for f in glob.glob(str(pattern)):
         os.chmod(f,0o755)

processing/post/permuteData.py

@@ -1,61 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-import sys
-from io import StringIO
-from optparse import OptionParser
-
-import numpy as np
-
-import damask
-
-
-scriptName = os.path.splitext(os.path.basename(__file__))[0]
-scriptID   = ' '.join([scriptName,damask.version])
-
-
-# --------------------------------------------------------------------
-#                                MAIN
-# --------------------------------------------------------------------
-
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
-Permute all values in given column(s).
-
-""", version = scriptID)
-
-parser.add_option('-l','--label',
-                  dest = 'label',
-                  action = 'extend', metavar = '<string LIST>',
-                  help  ='column(s) to permute')
-parser.add_option('-u', '--unique',
-                  dest = 'unique',
-                  action = 'store_true',
-                  help = 'shuffle unique values as group')
-parser.add_option('-r', '--rnd',
-                  dest = 'randomSeed',
-                  type = 'int', metavar = 'int',
-                  help = 'seed of random number generator [%default]')
-
-parser.set_defaults(label = [],
-                    unique = False,
-                    randomSeed = None,
-                   )
-
-(options,filenames) = parser.parse_args()
-if filenames == []: filenames = [None]
-
-for name in filenames:
-    damask.util.report(scriptName,name)
-
-    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
-
-    randomSeed = int(os.urandom(4).hex(), 16) if options.randomSeed is None else options.randomSeed # random seed per file
-    rng = np.random.default_rng(randomSeed)
-
-    for label in options.label:
-        data = table.get(label)
-        uniques,inverse  = np.unique(data,return_inverse=True,axis=0) if options.unique else (data,np.arange(len(data)))
-        rng.shuffle(uniques)
-        table = table.set(label,uniques[inverse], scriptID+' '+' '.join(sys.argv[1:]))
-
-    table.save((sys.stdout if name is None else name), legacy=True)

processing/pre/geom_fromTable.py

@@ -1,57 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-import sys
-from optparse import OptionParser
-
-import damask
-
-
-scriptName = os.path.splitext(os.path.basename(__file__))[0]
-scriptID   = ' '.join([scriptName,damask.version])
-
-
-# --------------------------------------------------------------------
-#                                MAIN
-# --------------------------------------------------------------------
-
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
-Converts ASCII table. Input can be microstructure or orientation (as quaternion). For the latter,
-phase information can be given additionally.
-
-""", version = scriptID)
-
-parser.add_option('--coordinates',
-                  dest = 'pos',
-                  type = 'string', metavar = 'string',
-                  help = 'coordinates label (%default)')
-parser.add_option('--phase',
-                  dest = 'phase',
-                  type = 'string', metavar = 'string',
-                  help = 'phase label')
-parser.add_option('--microstructure',
-                  dest = 'microstructure',
-                  type = 'string', metavar = 'string',
-                  help = 'microstructure label')
-parser.add_option('-q', '--quaternion',
-                  dest = 'quaternion',
-                  type = 'string', metavar='string',
-                  help = 'quaternion label')
-
-parser.set_defaults(pos= 'pos')
-
-(options,filenames) = parser.parse_args()
-if filenames == []: filenames = [None]
-
-for name in filenames:
-    damask.util.report(scriptName,name)
-
-    labels = []
-    for l in [options.quaternion,options.phase,options.microstructure]:
-        if l is not None: labels.append(l)
-
-    t = damask.Table.load(name)
-    geom = damask.Geom.from_table(t,options.pos,labels)
-    damask.util.croak(geom)
-
-    geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom')

python/damask/_geom.py

@@ -266,13 +266,9 @@ class Geom:
 
         labels_ = [labels] if isinstance(labels,str) else labels
         unique,unique_inverse = np.unique(np.hstack([table.get(l) for l in labels_]),return_inverse=True,axis=0)
-        if len(unique) == grid.prod():
+
-            ma = np.arange(grid.prod())
+        ma = np.arange(grid.prod()) if len(unique) == grid.prod() else \
-        else:
+             np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
-            from_ma = pd.unique(unique_inverse)
-            sort_idx = np.argsort(from_ma)
-            idx = np.searchsorted(from_ma,unique_inverse,sorter = sort_idx)
-            ma = np.arange(from_ma.size)[sort_idx][idx]
 
         return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','from_table'))
 

python/damask/solver/_marc.py

@@ -1,6 +1,7 @@
 import subprocess
 import shlex
-import string
+import re
+import io
 from pathlib import Path
 
 from .. import environment
@@ -27,7 +28,10 @@ class Marc:
         path_MSC = environment.options['MSC_ROOT']
         path_lib = Path(f'{path_MSC}/mentat{self.version}/shlib/linux64')
 
-        return path_lib if path_lib.is_dir() else None
+        if not path_lib.is_dir():
+            raise FileNotFoundError(f'library path "{path_lib}" not found')
+
+        return path_lib
 
 
     @property
@@ -36,10 +40,12 @@ class Marc:
         path_MSC   = environment.options['MSC_ROOT']
         path_tools = Path(f'{path_MSC}/marc{self.version}/tools')
 
-        return path_tools if path_tools.is_dir() else None
+        if not path_tools.is_dir():
+            raise FileNotFoundError(f'tools path "{path_tools}" not found')
+
+        return path_tools
 
 
-#--------------------------
     def submit_job(self,
                    model,
                    job          = 'job1',
@@ -48,38 +54,37 @@ class Marc:
                    optimization = '',
                   ):
 
-
         usersub = environment.root_dir/'src/DAMASK_marc'
         usersub = usersub.parent/(usersub.name + ('.f90' if compile else '.marc'))
         if not usersub.is_file():
-            raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),usersub))
+            raise FileNotFoundError(f'subroutine ({"source" if compile else "binary"}) "{usersub}" not found')
 
         # Define options [see Marc Installation and Operation Guide, pp 23]
         script = f'run_damask_{optimization}mp'
 
-        cmd = str(self.tools_path/Path(script)) + \
+        cmd = str(self.tools_path/script) + \
-              ' -jid ' + model + '_' + job + \
+              ' -jid ' + model+'_'+job + \
-              ' -nprocd 1  -autorst 0 -ci n  -cr n  -dcoup 0 -b no -v no'
+              ' -nprocd 1 -autorst 0 -ci n -cr n -dcoup 0 -b no -v no'
-
+        cmd += ' -u ' + str(usersub) + ' -save y' if compile else \
-        if compile: cmd += ' -u ' + str(usersub) + ' -save y'
+               ' -prog ' + str(usersub.with_suffix(''))
-        else:       cmd += ' -prog ' + str(usersub.with_suffix(''))
-
-        print('job submission {} compilation: {}'.format(('with' if compile else 'without'),usersub))
-        if logfile: log = open(logfile, 'w')
         print(cmd)
-        process = subprocess.Popen(shlex.split(cmd),stdout = log,stderr = subprocess.STDOUT)
-        log.close()
-        process.wait()
 
-#--------------------------
+        if logfile is not None:
-    def exit_number_from_outFile(self,outFile=None):
+            try:
-        exitnumber = -1
+                f = open(logfile,'w+')
-        with open(outFile,'r') as fid_out:
+            except TypeError:
-            for line in fid_out:
+                f = logfile
-                if (string.find(line,'tress iteration') != -1):
+        else:
-                    print(line)
+            f = io.StringIO()
-                elif (string.find(line,'Exit number')   != -1):
-                    substr = line[string.find(line,'Exit number'):len(line)]
-                    exitnumber = int(substr[12:16])
 
-        return exitnumber
+        proc = subprocess.Popen(shlex.split(cmd),stdout=f,stderr=subprocess.STDOUT)
+        proc.wait()
+        f.seek(0)
+
+        try:
+            v = int(re.search('Exit number ([0-9]+)',''.join(f.readlines())).group(1))
+        except (AttributeError,ValueError):
+            raise RuntimeError('Marc simulation failed (unknown return value)')
+
+        if v != 3004:
+            raise RuntimeError(f'Marc simulation failed ({v})')

python/damask/util.py

@@ -169,6 +169,7 @@ def scale_to_coprime(v):
 
     def lcm(a, b):
         """Least common multiple."""
+        # Python 3.9 provides math.lcm, see https://stackoverflow.com/questions/51716916.
         return a * b // np.gcd(a, b)
 
     m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(np.int)

src/crystallite.f90

@@ -749,23 +749,23 @@ subroutine crystallite_results
           selected_tensors = select_tensors(crystallite_partitionedF,p)
           call results_writeDataset(group,selected_tensors,output_constituent(p)%label(o),&
                                    'deformation gradient','1')
-        case('Fe')
+        case('F_e')
           selected_tensors = select_tensors(crystallite_Fe,p)
           call results_writeDataset(group,selected_tensors,output_constituent(p)%label(o),&
                                    'elastic deformation gradient','1')
-        case('Fp')
+        case('F_p')
           selected_tensors = select_tensors(crystallite_Fp,p)
           call results_writeDataset(group,selected_tensors,output_constituent(p)%label(o),&
                                    'plastic deformation gradient','1')
-        case('Fi')
+        case('F_i')
           selected_tensors = select_tensors(crystallite_Fi,p)
           call results_writeDataset(group,selected_tensors,output_constituent(p)%label(o),&
                                    'inelastic deformation gradient','1')
-        case('Lp')
+        case('L_p')
           selected_tensors = select_tensors(crystallite_Lp,p)
           call results_writeDataset(group,selected_tensors,output_constituent(p)%label(o),&
                                    'plastic velocity gradient','1/s')
-        case('Li')
+        case('L_i')
           selected_tensors = select_tensors(crystallite_Li,p)
           call results_writeDataset(group,selected_tensors,output_constituent(p)%label(o),&
                                    'inelastic velocity gradient','1/s')
@@ -1547,11 +1547,11 @@ subroutine crystallite_restartWrite
   fileHandle = HDF5_openFile(fileName,'a')
 
   call HDF5_write(fileHandle,crystallite_partitionedF,'F')
-  call HDF5_write(fileHandle,crystallite_Fp,        'Fp')
+  call HDF5_write(fileHandle,crystallite_Fp,        'F_p')
-  call HDF5_write(fileHandle,crystallite_Fi,        'Fi')
+  call HDF5_write(fileHandle,crystallite_Fi,        'F_i')
-  call HDF5_write(fileHandle,crystallite_Lp,        'Lp')
+  call HDF5_write(fileHandle,crystallite_Lp,        'L_p')
-  call HDF5_write(fileHandle,crystallite_Li,        'Li')
+  call HDF5_write(fileHandle,crystallite_Li,        'L_i')
-  call HDF5_write(fileHandle,crystallite_S,         'S')
+  call HDF5_write(fileHandle,crystallite_S,           'S')
 
   groupHandle = HDF5_addGroup(fileHandle,'constituent')
   do i = 1,size(material_name_phase)
@@ -1588,10 +1588,10 @@ subroutine crystallite_restartRead
   fileHandle = HDF5_openFile(fileName)
 
   call HDF5_read(fileHandle,crystallite_F0, 'F')
-  call HDF5_read(fileHandle,crystallite_Fp0,'Fp')
+  call HDF5_read(fileHandle,crystallite_Fp0,'F_p')
-  call HDF5_read(fileHandle,crystallite_Fi0,'Fi')
+  call HDF5_read(fileHandle,crystallite_Fi0,'F_i')
-  call HDF5_read(fileHandle,crystallite_Lp0,'Lp')
+  call HDF5_read(fileHandle,crystallite_Lp0,'L_p')
-  call HDF5_read(fileHandle,crystallite_Li0,'Li')
+  call HDF5_read(fileHandle,crystallite_Li0,'L_i')
   call HDF5_read(fileHandle,crystallite_S0, 'S')
 
   groupHandle = HDF5_openGroup(fileHandle,'constituent')