Merge branch 'development' into cmake

.gitignore

@@ -1,4 +1,4 @@
-code
+.noH5py
 *.pyc
 *.mod
 *.o
@@ -6,5 +6,4 @@ code
 *.bak
 *~
 bin
-PRIVATE
 build

.gitlab-ci.yml

@@ -0,0 +1,490 @@
+stages:
+  - prepareAll
+  - preprocessing
+  - postprocessing
+  - compileSpectralIntel
+  - compileSpectralGNU
+  - prepareSpectral
+  - spectral
+  - compileMarc2014
+  - compileMarc2014.2
+  - compileMarc2015
+  - compileMarc2016
+  - marc
+  - compileAbaqus2016
+  - compileAbaqus2017
+  - example
+  - updateMaster
+  - createDocumentation
+  - clean
+
+###################################################################################################
+before_script:
+  - source $DAMASKROOT/DAMASK_env.sh
+  - module purge
+  - cd $DAMASKROOT/PRIVATE/testing
+
+###################################################################################################
+variables:
+  #================================================================================================
+  # GitLab Settings
+  #================================================================================================
+  GIT_SUBMODULE_STRATEGY: none
+
+  #================================================================================================
+  # Shortcut names
+  #================================================================================================
+  DAMASKROOT:                      "$HOME/GitLabCI_Pipeline_$CI_PIPELINE_ID/DAMASK"
+
+  #================================================================================================
+  # Names of module files to load
+  #================================================================================================
+  # ++++++++++++ Compiler ++++++++++++++++++++++++++++++++++++++++++++++
+  IntelCompiler16_0:               "Compiler/Intel/16.0 Libraries/IMKL/2016"
+  IntelCompiler17_0:               "Compiler/Intel/17.0 Libraries/IMKL/2017"
+  GNUCompiler5_3:                  "Compiler/GNU/5.3"
+  # ------------ Defaults ----------------------------------------------
+  IntelCompiler:                   "$IntelCompiler17_0"
+  GNUCompiler:                     "$GNUCompiler5_3"
+  # ++++++++++++ MPI +++++++++++++++++++++++++++++++++++++++++++++++++++
+  MPICH3_2Intel17_0:               "MPI/Intel/17.0/MPICH/3.2"
+  MPICH3_2GNU5_3:                  "MPI/GNU/5.3/MPICH/3.2"
+  # ------------ Defaults ----------------------------------------------
+  MPICH_GNU:                       "$MPICH3_2GNU5_3"
+  MPICH_Intel:                     "$MPICH3_2Intel17_0"
+  # ++++++++++++ PETSc +++++++++++++++++++++++++++++++++++++++++++++++++
+  PETSc3_6_4MPICH3_2Intel17_0:     "Libraries/PETSc/3.6.4/Intel-17.0-MPICH-3.2"
+  PETSc3_7_5MPICH3_2Intel17_0:     "Libraries/PETSc/3.7.5/Intel-17.0-MPICH-3.2"
+  PETSc3_7_5MPICH3_2GNU5_3:        "Libraries/PETSc/3.7.5/GNU-5.3-MPICH-3.2"
+  # ------------ Defaults ----------------------------------------------
+  PETSc_MPICH_Intel:               "$PETSc3_7_5MPICH3_2Intel17_0"
+  PETSc_MPICH_GNU:                 "$PETSc3_7_5MPICH3_2GNU5_3"
+  # ++++++++++++ FEM +++++++++++++++++++++++++++++++++++++++++++++++++++
+  Abaqus2016:                      "FEM/Abaqus/2016"
+  Abaqus2017:                      "FEM/Abaqus/2017"
+  MSC2014:                         "FEM/MSC/2014"
+  MSC2014_2:                       "FEM/MSC/2014.2"
+  MSC2015:                         "FEM/MSC/2015"
+  MSC2016:                         "FEM/MSC/2016"
+  # ------------ Defaults ----------------------------------------------
+  Abaqus:                          "$Abaqus2017"
+  MSC:                             "$MSC2016"
+  # ++++++++++++ Documentation +++++++++++++++++++++++++++++++++++++++++
+  Doxygen1_8_13:                   "Documentation/Doxygen/1.8.13"
+  # ------------ Defaults ----------------------------------------------
+  Doxygen:                         "$Doxygen1_8_13"
+
+
+###################################################################################################
+checkout: 
+  stage: prepareAll
+  before_script: 
+    - echo $CI_PIPELINE_ID >> $HOME/GitLabCI.queue
+    - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $HOME/GitLabCI.queue) -ne 1 ];do sleep 5m; done
+  script:
+    - mkdir -p $DAMASKROOT
+    - git clone -q git@magit1.mpie.de:damask/DAMASK.git $DAMASKROOT
+    - cd $DAMASKROOT
+    - git checkout $CI_COMMIT_SHA
+    - git clone -q git@magit1.mpie.de:damask/PRIVATE.git
+    - source $DAMASKROOT/DAMASK_env.sh
+    - make install
+  except:
+    - master
+    - release
+
+###################################################################################################
+OrientationRelationship:
+  stage: preprocessing
+  script: OrientationRelationship/test.py
+  except:
+    - master
+    - release
+
+Pre_SeedGeneration:
+  stage: preprocessing
+  script: PreProcessing_SeedGeneration/test.py
+  except:
+    - master
+    - release
+
+Pre_GeomGeneration:
+  stage: preprocessing
+  script: PreProcessing_GeomGeneration/test.py
+  except:
+    - master
+    - release
+
+Pre_GeomModification:
+  stage: preprocessing
+  script: PreProcessing_GeomModification/test.py
+  except:
+    - master
+    - release
+
+Pre_General:
+  stage: preprocessing
+  script: PreProcessing/test.py
+  except:
+    - master
+    - release
+
+Spectral_geometryPacking:
+  stage: preprocessing
+  script: Spectral_geometryPacking/test.py
+  except:
+    - master
+    - release
+
+###################################################################################################
+Post_General:
+  stage: postprocessing
+  script: PostProcessing/test.py
+  except:
+    - master
+    - release
+
+Post_GeometryReconstruction:
+  stage: postprocessing
+  script: Spectral_geometryReconstruction/test.py
+  except:
+    - master
+    - release
+
+Post_addCurl:
+  stage: postprocessing
+  script: addCurl/test.py
+  except:
+    - master
+    - release
+
+Post_addDivergence:
+  stage: postprocessing
+  script: addDivergence/test.py
+  except:
+    - master
+    - release
+
+Post_addGradient:
+  stage: postprocessing
+  script: addGradient/test.py
+  except:
+    - master
+    - release
+
+Post_ParaviewRelated:
+  stage: postprocessing
+  script: ParaviewRelated/test.py
+  except:
+    - master
+    - release
+
+###################################################################################################
+Compile_Intel:
+  stage: compileSpectralIntel 
+  script:
+    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
+    - SpectralAll_compileIfort/test.py
+  except:
+    - master
+    - release
+
+###################################################################################################
+Compile_GNU:
+  stage: compileSpectralGNU
+  script:
+    - module load $GNUCompiler $MPICH_GNU $PETSc_MPICH_GNU
+    - SpectralAll_compileGfortran/test.py
+  except:
+    - master
+    - release
+
+###################################################################################################
+Compile_Intel_Prepare:
+  stage: prepareSpectral
+  script:
+    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
+    - make -C $DAMASKROOT clean spectral install tidy
+  except:
+    - master
+    - release
+ 
+###################################################################################################
+Spectral_PackedGeometry:
+  stage: spectral
+  script: Spectral_PackedGeometry/test.py
+  except:
+    - master
+    - release
+
+Spectral_parsingArguments:
+  stage: spectral
+  script: Spectral_parsingArguments/test.py
+  except:
+    - master
+    - release
+
+StateIntegration_compareVariants:
+  stage: spectral
+  script: StateIntegration_compareVariants/test.py
+  except:
+    - master
+    - release
+
+nonlocal_densityConservation:
+  stage: spectral
+  script: nonlocal_densityConservation/test.py
+  except:
+    - master
+    - release
+
+Spectral_ipNeighborhood:
+  stage: spectral
+  script: Spectral_ipNeighborhood/test.py
+  except:
+    - master
+    - release
+
+Nonlocal_Damage_DetectChanges:
+  stage: spectral
+  script: Nonlocal_Damage_DetectChanges/test.py
+  except:
+    - master
+    - release
+
+SpectralAll_restart:
+  stage: spectral
+  script: SpectralAll_restart/test.py
+  except:
+    - master
+    - release
+
+SpectralAll_parsingLoadCase:
+  stage: spectral
+  script: SpectralAll_parsingLoadCase/test.py
+  except:
+    - master
+    - release
+
+SpectralBasic_loadCaseRotation:
+  stage: spectral
+  script: SpectralBasic_loadCaseRotation/test.py
+  except:
+    - master
+    - release
+
+Spectral_MPI:
+  stage: spectral
+  script:
+    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
+    - Spectral_MPI/test.py
+  except:
+    - master
+    - release
+
+Plasticity_DetectChanges:
+  stage: spectral
+  script: Plasticity_DetectChanges/test.py
+  except:
+    - master
+    - release
+
+Homogenization:
+  stage: spectral
+  script: Homogenization/test.py
+  except:
+    - master
+    - release
+
+Phenopowerlaw_singleSlip:
+  stage: spectral
+  script: Phenopowerlaw_singleSlip/test.py
+  except:
+    - master
+    - release
+
+HybridIA:
+  stage: spectral
+  script: HybridIA/test.py
+  except:
+    - master
+    - release
+
+###################################################################################################
+Marc_compileIfort2014:
+  stage: compileMarc2014
+  script:
+    - module load $IntelCompiler16_0 $MSC2014
+    - Marc_compileIfort/test.py -m 2014
+  except:
+    - master
+    - release
+
+###################################################################################################
+Marc_compileIfort2014.2:
+  stage: compileMarc2014.2
+  script:
+    - module load $IntelCompiler16_0 $MSC2014_2
+    - Marc_compileIfort/test.py -m 2014.2
+  except:
+    - master
+    - release
+
+###################################################################################################
+Marc_compileIfort2015:
+  stage: compileMarc2015
+  script:
+    - module load $IntelCompiler16_0 $MSC2015
+    - Marc_compileIfort/test.py -m 2015
+  except:
+    - master
+    - release
+
+###################################################################################################
+Marc_compileIfort2016:
+  stage: compileMarc2016
+  script:
+    - module load $IntelCompiler16_0 $MSC2016
+    - Marc_compileIfort/test.py -m 2016
+  except:
+    - master
+    - release
+
+###################################################################################################
+Hex_elastic:
+  stage: marc
+  script:
+    - module load $IntelCompiler16_0 $MSC
+    - Hex_elastic/test.py
+  except:
+    - master
+    - release
+
+CubicFCC_elastic:
+  stage: marc
+  script:
+    - module load $IntelCompiler16_0 $MSC
+    - CubicFCC_elastic/test.py
+  except:
+    - master
+    - release
+
+CubicBCC_elastic:
+  stage: marc
+  script:
+    - module load $IntelCompiler16_0 $MSC
+    - CubicBCC_elastic/test.py
+  except:
+    - master
+    - release
+
+J2_plasticBehavior:
+  stage: marc
+  script:
+    - module load $IntelCompiler16_0 $MSC
+    - J2_plasticBehavior/test.py
+  except:
+    - master
+    - release
+
+###################################################################################################
+Abaqus_compile2016:
+  stage: compileAbaqus2016
+  script:
+    - module load $IntelCompiler16_0 $Abaqus2016
+    - Abaqus_compileIfort/test.py -a 2016
+  except:
+    - master
+    - release
+
+###################################################################################################
+Abaqus_compile2017:
+  stage: compileAbaqus2017
+  script:
+    - module load $IntelCompiler16_0 $Abaqus2017
+    - Abaqus_compileIfort/test.py -a 2017
+  except:
+    - master
+    - release
+
+###################################################################################################
+SpectralExample:
+  stage: example
+  script: SpectralAll_example/test.py
+  only:
+    - development
+
+AbaqusExample:
+  stage: example
+  script:
+    - module load $IntelCompiler16_0 $Abaqus
+    - Abaqus_example/test.py
+  only:
+    - development
+
+##################################################################################################
+mergeIntoMaster: 
+  stage: updateMaster
+  script:
+    - cd $DAMASKROOT
+    - export TESTEDREV=$(git describe)                                                              # might be detached from development branch
+    - echo $TESTEDREV > VERSION
+    - git commit VERSION -m "[skip ci] updated version information after successful test of $TESTEDREV"
+    - export UPDATEDREV=$(git describe)                                                             # tested state + 1 commit
+    - git checkout master
+    - git merge $UPDATEDREV
+    - git push origin master                                                                        # master is now tested version and has updated VERSION file
+    - git checkout development
+    - git pull
+    - git merge master -s ours                                                                      # only possible conflict is in VERSION file
+    - git push origin development                                                                   # development is unchanged (as master is based on it) but has updated VERSION file
+  only:
+    - development
+
+###################################################################################################
+AbaqusExp: 
+  stage: createDocumentation
+  script:
+    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
+    - $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT abaqus_exp
+  except:
+    - master
+    - release
+
+AbaqusStd: 
+  stage: createDocumentation
+  script:
+    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
+    - $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT abaqus_std
+  except:
+    - master
+    - release
+
+Marc: 
+  stage: createDocumentation
+  script:
+    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
+    - $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT marc
+  except:
+    - master
+    - release
+
+Spectral: 
+  stage: createDocumentation
+  script:
+    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
+    - $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT spectral
+  except:
+    - master
+    - release
+
+###################################################################################################
+removeLock: 
+  stage: clean
+  before_script: 
+    - echo 'Do nothing'
+  when: always
+  script: sed -i "/$CI_PIPELINE_ID/d" $HOME/GitLabCI.queue
+  except:
+    - master
+    - release

CONFIG

@@ -5,7 +5,7 @@ set DAMASK_BIN            = ${DAMASK_ROOT}/bin
 
 set DAMASK_NUM_THREADS    = 4
 
-set MSC_ROOT              = /opt/MSC
+set MSC_ROOT              = /opt/msc
-set MARC_VERSION          = 2015
+set MARC_VERSION          = 2016
 
-set ABAQUS_VERSION        = 6.14-5
+set ABAQUS_VERSION        = 2017

DAMASK_env.sh

@@ -25,11 +25,11 @@ if [[ "x$DAMASK_BIN" != "x" && ! $(echo ":$PATH:" | grep $DAMASK_BIN:) ]]; then
   export PATH=$DAMASK_BIN:$PATH
 fi
 
-SOLVER=$(which DAMASK_spectral 2>/dev/null)
+SOLVER=$(which DAMASK_spectral || true 2>/dev/null)
 if [ "x$SOLVER" == "x" ]; then
   SOLVER='Not found!'
 fi
-PROCESSING=$(which postResults 2>/dev/null)
+PROCESSING=$(which postResults || true 2>/dev/null)
 if [ "x$PROCESSING" == "x" ]; then
   PROCESSING='Not found!'
 fi
@@ -39,12 +39,15 @@ fi
 
 # according to http://software.intel.com/en-us/forums/topic/501500
 # this seems to make sense for the stack size
-FREE=$(which free 2>/dev/null)
+FREE=$(type -p free 2>/dev/null)
 if [ "x$FREE" != "x" ]; then
   freeMem=$(free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}')
   # http://superuser.com/questions/220059/what-parameters-has-ulimit             
-  ulimit -d $(expr $freeMem                       / 2)  2>/dev/null # maximum  heap size (kB)
+  ulimit -d unlimited 2>/dev/null \
-  ulimit -s $(expr $freeMem / $DAMASK_NUM_THREADS / 2)  2>/dev/null # maximum stack size (kB)
+  || ulimit -d $(expr $freeMem                       / 2)  2>/dev/null # maximum  heap size (kB)
+  ulimit -s unlimited 2>/dev/null \
+  || echo "cannot unlimit stack..." \
+  && ulimit -s $(expr $freeMem / $DAMASK_NUM_THREADS / 2)  2>/dev/null # maximum stack size (kB)
 fi
 ulimit -v unlimited   2>/dev/null # maximum virtual memory size
 ulimit -m unlimited   2>/dev/null # maximum physical memory size

DAMASK_env.zsh

@@ -19,8 +19,8 @@ if [[ ( "x$DAMASK_BIN" != "x" ) && ( "x$MATCH" = "x" ) ]]; then
   export PATH=$DAMASK_BIN:$PATH
 fi
 
-SOLVER=`which DAMASK_spectral 2>/dev/null`
+SOLVER=`which DAMASK_spectral || True 2>/dev/null`
-PROCESSING=`which postResults 2>/dev/null`
+PROCESSING=`which postResults || True 2>/dev/null`
 if [ "x$DAMASK_NUM_THREADS" = "x" ]; then
   DAMASK_NUM_THREADS=1
 fi

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2011-16 Max-Planck-Institut für Eisenforschung GmbH
+Copyright 2011-17 Max-Planck-Institut für Eisenforschung GmbH
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by

VERSION

@@ -1 +1 @@
-v2.0.1-357-g38471c1
+v2.0.1-414-g81d0752

examples/ConfigFiles/Phase_Dislotwin_TWIP-Steel-FeMnC.config

@@ -50,7 +50,7 @@ interactionSlipSlip 0.122 0.122 0.625 0.07 0.137 0.122 # Interaction coefficient
 
 ### Shearband parameters ###
 shearbandresistance 180e6
-shearbandvelocity   1e-4            # set to zero to turn shear banding of
+shearbandvelocity   0e-4            # set to zero to turn shear banding of
 QedgePerSbSystem    3.7e-19         # Activation energy for shear banding [J]
 p_shearband         1.0             # p-exponent in glide velocity
 q_shearband         1.0             # q-exponent in glide velocity

examples/ConfigFiles/Phase_None_Orthorombic.config

@@ -12,4 +12,4 @@ c13                     60.41e9
 c23                     60.41e9
 c44                     28.34e9
 c55                     28.34e9
-c66                     28.34e9
+c66                     28.34e9

examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Ferrite.config

@@ -18,8 +18,5 @@ tau0_slip                95.e6  97.e6           # per family, optimization long
 tausat_slip             222.e6 412.7e6          # per family, optimization long simplex 109
 h0_slipslip             1000.0e6
 interaction_slipslip    1 1 1.4 1.4 1.4 1.4
-interaction_sliptwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twinslip    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twintwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 w0_slip                 2.0
 (output) totalshear

examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.config

@@ -18,8 +18,5 @@ tau0_slip               405.8e6  456.7e6        # per family
 tausat_slip             872.9e6  971.2e6        # per family
 h0_slipslip             563.0e9
 interaction_slipslip    1 1 1.4 1.4 1.4 1.4
-interaction_sliptwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twinslip    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twintwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 w0_slip                 2.0
 (output) totalshear

examples/ConfigFiles/Phase_Phenopowerlaw_Gold.config

@@ -35,18 +35,7 @@ tausat_slip             53.00e6                # per family
 a_slip                  1.0
 gdot0_twin              0.001
 n_twin                  20
-tau0_twin               0                     # per family
-s_pr                    0                     # push-up factor for slip saturation due to twinning
-twin_b                  0
-twin_c                  0
-twin_d                  0
-twin_e                  0
 h0_slipslip             75e6
-h0_twinslip             0
-h0_twintwin             0
 interaction_slipslip    1 1 1.4 1.4 1.4 1.4
-interaction_sliptwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twinslip    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twintwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
 atol_resistance         1
 

examples/ConfigFiles/Phase_Phenopowerlaw_multiField.config

@@ -29,18 +29,8 @@ a_slip                  2.25
 gdot0_twin              0.001
 n_twin                  20
 tau0_twin               31e6                # per family
-s_pr                    0                     # push-up factor for slip saturation due to twinning
-twin_b                  0
-twin_c                  0
-twin_d                  0
-twin_e                  0
 h0_slipslip             75e6
-h0_twinslip             0
-h0_twintwin             0
 interaction_slipslip    1 1 1.4 1.4 1.4 1.4
-interaction_sliptwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twinslip    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twintwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
 atol_resistance         1
 
 (stiffness_degradation) damage

examples/ConfigFiles/Source_Damage_IsoBrittle.config

@@ -2,4 +2,4 @@
 isobrittle_criticalStrainEnergy 1400000.0
 isobrittle_atol                 0.01
 isobrittle_N                    1.0
-(output) isoBrittle_DrivingForce
+(output) isoBrittle_DrivingForce

examples/ConfigFiles/Texture_Gauss_001.config

@@ -1,2 +1,2 @@
 [001]
-(gauss)		phi1	0.000	Phi	0.000	phi2	0.000	scatter	0.000	fraction	1.000
+(gauss)		phi1	0.000	Phi	0.000	phi2	0.000	scatter	0.000	fraction	1.000

examples/ConfigFiles/Texture_Gauss_101.config

@@ -1,2 +1,2 @@
 [101]
-(gauss)		phi1	0.000	Phi	45.000	phi2	90.000	scatter	0.000	fraction	1.000
+(gauss)		phi1	0.000	Phi	45.000	phi2	90.000	scatter	0.000	fraction	1.000

examples/ConfigFiles/Texture_Gauss_111.config

@@ -1,2 +1,2 @@
 [111]
-(gauss)		phi1	0.000	Phi	54.7356	phi2	45.000	scatter	0.000	fraction	1.000
+(gauss)		phi1	0.000	Phi	54.7356	phi2	45.000	scatter	0.000	fraction	1.000

examples/ConfigFiles/Texture_Gauss_123.config

@@ -1,2 +1,2 @@
 [123]
-(gauss)		phi1	209.805	Phi	29.206	phi2	63.435	scatter	0.000	fraction	1.000
+(gauss)		phi1	209.805	Phi	29.206	phi2	63.435	scatter	0.000	fraction	1.000

examples/ConfigFiles/Texture_RandomSingleCrystals.config

@@ -1,2 +1,2 @@
 [RandomSingleCrystals]
-(random) scatter 0.000 fraction 1.000
+(random) scatter 0.000 fraction 1.000

examples/MSC.Marc/material.config

@@ -2,7 +2,7 @@
 <homogenization>
 #-------------------#
 
-{../../code/config/Homogenization_None_Dummy.config}
+{../ConfigFiles/Homogenization_None_Dummy.config}
 
 #-------------------#
 <microstructure>
@@ -524,12 +524,12 @@ crystallite	1
 <crystallite>
 #-------------------#
 
-{../../code/config/Crystallite_All.config}
+{../ConfigFiles/Crystallite_All.config}
 
 #-------------------#
 <phase>
 #-------------------#
 
-{../../code/config/Phase_Phenopowerlaw_Aluminum.config}
+{../ConfigFiles/Phase_Phenopowerlaw_Aluminum.config}
 
-{../../code/config/Phase_J2_AluminumIsotropic.config}
+{../ConfigFiles/Phase_Isotropic_AluminumIsotropic.config}

examples/SpectralMethod/material.config

@@ -52,22 +52,8 @@ n_slip                  20
 tau0_slip                 31e6 # per family
 tausat_slip               63e6 # per family
 a_slip                  2.25
-gdot0_twin              0.001
-n_twin                  20
-tau0_twin                 31e6 # per family
-s_pr                    0                        # push-up factor for slip saturation due to twinning
-twin_b                  0
-twin_c                  0
-twin_d                  0
-twin_e                  0
 h0_slipslip             75e6
-h0_sliptwin             0
-h0_twinslip             0
-h0_twintwin             0
 interaction_slipslip    1 1 1.4 1.4 1.4 1.4
-interaction_sliptwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twinslip    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twintwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
 atol_resistance         1
 
 

installation/mods_Abaqus/abaqus_v6.env

@@ -31,7 +31,7 @@ fortCmd = "ifort"
 # -integer-size 32 -DINT=4     assume size of integer to be 4 bytes, matches our definition of pInt
 
 compile_fortran = (fortCmd + " -c -fPIC -auto -shared-intel " + 
-                   "-I%I -I../lib -free -O1 -fpp -openmp " +
+                   "-I%I -free -O1 -fpp -openmp " +
                    "-ftz -diag-disable 5268 " +
                    "-implicitnone -assume byterecl -stand f08 -standard-semantics " +
                    "-real-size 64 -integer-size 32 -DFLOAT=8 -DINT=4 " +
@@ -58,4 +58,4 @@ ask_delete=OFF
 
 # Remove the temporary names from the namespace
 del fortCmd
-
+del DAMASKVERSION

installation/mods_Abaqus/abaqus_v6_serial.env

@@ -31,7 +31,7 @@ fortCmd = "ifort"
 # -integer-size 32 -DINT=4     assume size of integer to be 4 bytes, matches our definition of pInt
 
 compile_fortran = (fortCmd + " -c -fPIC -auto -shared-intel " + 
-                   "-I%I -I../lib -free -O1 -fpp " +
+                   "-I%I -free -O1 -fpp " +
                    "-ftz -diag-disable 5268 " +
                    "-implicitnone -assume byterecl -stand f08 -standard-semantics " +
                    "-real-size 64 -integer-size 32 -DFLOAT=8 -DINT=4 " +
@@ -58,4 +58,4 @@ ask_delete=OFF
 
 # Remove the temporary names from the namespace
 del fortCmd
-
+del DAMASKVERSION

installation/mods_MarcMentat/apply_DAMASK_modifications.sh

@@ -25,6 +25,7 @@ do
   if [ -z "$VERSION" ]; then
     VERSION=${DEFAULT_VERSION}
   fi
+  [[ -d "$SCRIPTLOCATION/$VERSION" ]] || echo -e "$VERSION not supported..!\n"
 done
 echo "MSC version: $VERSION"
 
@@ -35,6 +36,7 @@ do
   if [ -z "$INSTALLDIR" ]; then
     INSTALLDIR=${DEFAULT_DIR}
   fi
+  [[ -d "$INSTALLDIR" ]] || echo -e "$INSTALLDIR not found..!\n"
 done
 
 INSTALLDIR=${INSTALLDIR%/}               # remove trailing slash

installation/patch/README.md

@@ -13,5 +13,3 @@ patch -p1 < installation/patch/nameOfPatch
 
   * **fwbw_derivative** switches the default spatial derivative from continuous to forward/backward difference.  
     This generally reduces spurious oscillations in the result as the spatial accuracy of the derivative is then compatible with the underlying solution grid.
-  * **petsc3.7** adapts to API changes introduced between PETSc 3.6.x and 3.7.x for setting PETSc options.  
-    Use this patch if your system runs PETSc 3.7.x.

installation/patch/petsc3.7

@@ -1,22 +0,0 @@
-diff --git a/code/spectral_utilities.f90 b/code/spectral_utilities.f90
-index 34eb0ea..a33c7a9 100644
---- a/code/spectral_utilities.f90
-+++ b/code/spectral_utilities.f90
-@@ -227,12 +227,13 @@ subroutine utilities_init()
-                 trim(PETScDebug), &
-                 ' add more using the PETSc_Options keyword in numerics.config '; flush(6)
- 
-- call PetscOptionsClear(ierr); CHKERRQ(ierr)
-- if(debugPETSc) call PetscOptionsInsertString(trim(PETSCDEBUG),ierr)
-+ call PetscOptionsClear(PETSC_NULL_OBJECT,ierr)
-  CHKERRQ(ierr)
-- call PetscOptionsInsertString(trim(petsc_defaultOptions),ierr)
-+ if(debugPETSc) call PetscOptionsInsertString(PETSC_NULL_OBJECT,trim(PETSCDEBUG),ierr)
-  CHKERRQ(ierr)
-- call PetscOptionsInsertString(trim(petsc_options),ierr)
-+ call PetscOptionsInsertString(PETSC_NULL_OBJECT,trim(petsc_defaultOptions),ierr)
-+ CHKERRQ(ierr)
-+ call PetscOptionsInsertString(PETSC_NULL_OBJECT,trim(petsc_options),ierr)
-  CHKERRQ(ierr)
- 
-  grid1Red = grid(1)/2_pInt + 1_pInt

lib/damask/__init__.py

@@ -1,7 +1,13 @@
 # -*- coding: UTF-8 no BOM -*-
 
 """Main aggregator"""
-import os
+import os,sys,time
+
+h5py_flag = os.path.join(os.path.dirname(__file__),'../../.noH5py')
+h5py_grace = 7200                         # only complain once every 7200 sec (2 hours)
+h5py_msg = "h5py module not found."
+
+now = time.time()
 
 with open(os.path.join(os.path.dirname(__file__),'../../VERSION')) as f:
   version = f.readline()[:-1]
@@ -9,9 +15,18 @@ with open(os.path.join(os.path.dirname(__file__),'../../VERSION')) as f:
 from .environment import Environment      # noqa
 from .asciitable  import ASCIItable       # noqa
 try:
-  from .h5table     import H5Table        # noqa
+  from .h5table   import H5Table          # noqa
+  if os.path.exists(h5py_flag): os.remove(h5py_flag)  # delete flagging file on success
 except ImportError:
-  print("h5py module not found")
+  if os.path.exists(h5py_flag):
+    if now - os.path.getmtime(h5py_flag) > h5py_grace: # complain (again) every so-and-so often
+      sys.stderr.write(h5py_msg+'\n')
+      with open(h5py_flag, 'a'):
+        os.utime(h5py_flag,(now,now))     # update flag modification time to "now"
+  else:
+    open(h5py_flag, 'a').close()          # create flagging file
+    sys.stderr.write(h5py_msg+'\n')       # complain for the first time
+    
 from .config      import Material         # noqa
 from .colormaps   import Colormap, Color  # noqa
 from .orientation import Quaternion, Rodrigues, Symmetry, Orientation # noqa

lib/damask/environment.py

@@ -33,7 +33,7 @@ class Environment():
                       'explicit':5}
     if Nneeded == -1: Nneeded = licensesNeeded[software]
     try:
-      cmd = """ ssh mulicense2 "/Stat_Flexlm | grep 'Users of %s: ' | cut -d' ' -f7,13" """%software
+      cmd = """ ssh mulicense2 "/lm-status | grep 'Users of %s: ' | cut -d' ' -f7,13" """%software
       process = subprocess.Popen(shlex.split(cmd),stdout = subprocess.PIPE,stderr = subprocess.PIPE)
       licenses = list(map(int, process.stdout.readline().split()))
       try:

lib/damask/test/test.py

@@ -203,58 +203,63 @@ class Test():
         shutil.copy2(source,target)
       except:
         logging.critical('error copying {} to {}'.format(source,target))
+        raise
 
 
   def copy_Reference2Current(self,sourcefiles=[],targetfiles=[]):
 
     if len(targetfiles) == 0: targetfiles = sourcefiles
-    for i,file in enumerate(sourcefiles):
+    for i,f in enumerate(sourcefiles):
       try:
-        shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
+        shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
       except:
-        logging.critical('Reference2Current: Unable to copy file "{}"'.format(file))
+        logging.critical('Reference2Current: Unable to copy file "{}"'.format(f))
+        raise
 
 
   def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
 
     source=os.path.normpath(os.path.join(self.dirBase,'../../..',sourceDir))
     if len(targetfiles) == 0: targetfiles = sourcefiles
-    for i,file in enumerate(sourcefiles):
+    for i,f in enumerate(sourcefiles):
       try:
-        shutil.copy2(os.path.join(source,file),self.fileInCurrent(targetfiles[i]))
+        shutil.copy2(os.path.join(source,f),self.fileInCurrent(targetfiles[i]))
       except:
-        logging.error(os.path.join(source,file))
+        logging.error(os.path.join(source,f))
-        logging.critical('Base2Current: Unable to copy file "{}"'.format(file))
+        logging.critical('Base2Current: Unable to copy file "{}"'.format(f))
+        raise
 
 
   def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]):
 
     if len(targetfiles) == 0: targetfiles = sourcefiles
-    for i,file in enumerate(sourcefiles):
+    for i,f in enumerate(sourcefiles):
       try:
-        shutil.copy2(self.fileInCurrent(file),self.fileInReference(targetfiles[i]))
+        shutil.copy2(self.fileInCurrent(f),self.fileInReference(targetfiles[i]))
       except:
-        logging.critical('Current2Reference: Unable to copy file "{}"'.format(file))
+        logging.critical('Current2Reference: Unable to copy file "{}"'.format(f))
+        raise
 
 
   def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]):
 
     if len(targetfiles) == 0: targetfiles = sourcefiles
-    for i,file in enumerate(sourcefiles):
+    for i,f in enumerate(sourcefiles):
       try:
-        shutil.copy2(self.fileInProof(file),self.fileInCurrent(targetfiles[i]))
+        shutil.copy2(self.fileInProof(f),self.fileInCurrent(targetfiles[i]))
       except:
-        logging.critical('Proof2Current: Unable to copy file "{}"'.format(file))
+        logging.critical('Proof2Current: Unable to copy file "{}"'.format(f))
+        raise
 
 
   def copy_Current2Current(self,sourcefiles=[],targetfiles=[]):
 
-    for i,file in enumerate(sourcefiles):
+    for i,f in enumerate(sourcefiles):
       try:
-        shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
+        shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
       except:
-        logging.critical('Current2Current: Unable to copy file "{}"'.format(file))
+        logging.critical('Current2Current: Unable to copy file "{}"'.format(f))
-
+        raise
 
   def execute_inCurrentDir(self,cmd,streamIn=None):
 

processing/post/postResults.py

@@ -851,7 +851,7 @@ for opt in ['nodalScalar','elemScalar','elemTensor','homogenizationResult','crys
 
 if options.info:
   if options.filetype == 'marc':
-    print('\n\nMentat release {}'.format(damask.solver.Marc().version('../../')))
+    print('\n\nMentat release {}'.format(damask.solver.Marc().version()))
   if options.filetype == 'spectral':
     print('\n\n{}'.format(p))
 

processing/pre/geom_addPrimitive.py

@@ -9,8 +9,6 @@ import damask
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
-oversampling = 2.
-
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
@@ -33,40 +31,49 @@ Depending on the sign of the dimension parameters, these objects can be boxes, c
 
 """, version = scriptID)
 
-parser.add_option('-c', '--center',     dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3),
+parser.add_option('-c', '--center',     dest='center', type='float', nargs = 3, metavar=' '.join(['float']*3),
                   help='a,b,c origin of primitive %default')
-parser.add_option('-d', '--dimension',  dest='dimension', type='int', nargs = 3, metavar=' '.join(['int']*3),
+parser.add_option('-d', '--dimension',  dest='dimension', type='float', nargs = 3, metavar=' '.join(['float']*3),
                   help='a,b,c extension of hexahedral box; negative values are diameters')
+parser.add_option('-e', '--exponent',  dest='exponent', type='float', nargs = 3, metavar=' '.join(['float']*3),
+                  help='i,j,k exponents for axes - 2 gives a sphere (x^2 + y^2 + z^2 < 1), 1 makes \
+octahedron (|x| + |y| + |z| < 1).  Large values produce boxes, 0 - 1 is concave. ')
 parser.add_option('-f', '--fill',       dest='fill', type='int', metavar = 'int',
                   help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]')
 parser.add_option('-q', '--quaternion', dest='quaternion', type='float', nargs = 4, metavar=' '.join(['float']*4),
                   help = 'rotation of primitive as quaternion')
 parser.add_option('-a', '--angleaxis',  dest='angleaxis', nargs = 4, metavar=' '.join(['float']*4),
-                  help = 'rotation of primitive as angle and axis')
+                  help = 'angle,x,y,z clockwise rotation of primitive about axis by angle')
 parser.add_option(     '--degrees',     dest='degrees', action='store_true',
                   help = 'angle is given in degrees [%default]')
-
+parser.add_option(     '--nonperiodic', dest='periodic', action='store_false',
-parser.set_defaults(center = [0,0,0],
+                  help = 'wrap around edges [%default]')
+parser.add_option(     '--voxelspace',  dest='voxelspace', action='store_true',
+                  help = '-c and -d are given in (0 to grid) coordinates instead of (origin to origin+size) \
+coordinates [%default]')
+parser.set_defaults(center = (.0,.0,.0),
                     fill = 0,
-                    quaternion = [],
-                    angleaxis = [],
                     degrees = False,
+                    exponent = (1e10,1e10,1e10), # box shape by default
+                    periodic = True,
+                    voxelspace = False
                    )
 
 (options, filenames) = parser.parse_args()
-
+if options.dimension is None:
-if options.angleaxis != []:
+  parser.error('no dimension specified.')   
+if options.angleaxis is not None:
   options.angleaxis = map(float,options.angleaxis)
   rotation = damask.Quaternion().fromAngleAxis(np.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0],
-                                               options.angleaxis[1:4]).conjugated()
+                                               options.angleaxis[1:4])
-elif options.quaternion != []:
+elif options.quaternion is not None:
   options.quaternion = map(float,options.quaternion)
-  rotation = damask.Quaternion(options.quaternion).conjugated()
+  rotation = damask.Quaternion(options.quaternion)
 else:
-  rotation = damask.Quaternion().conjugated()
+  rotation = damask.Quaternion()
 
 options.center = np.array(options.center)
-invRotation = rotation.conjugated()                                                             # rotation of gridpos into primitive coordinate system
+options.dimension = np.array(options.dimension)
 
 # --- loop over input files -------------------------------------------------------------------------
 if filenames == []: filenames = [None]
@@ -108,33 +115,92 @@ for name in filenames:
              'microstructures': 0,
             }
 
-
   if options.fill == 0:
     options.fill = microstructure.max()+1
-
+  
+  # If we have a negative dimension, make it an ellipsoid for backwards compatibility
+  options.exponent = np.where(np.array(options.dimension) > 0, options.exponent, 2)
   microstructure = microstructure.reshape(info['grid'],order='F')
+  
+  # coordinates given in real space (default) vs voxel space
+  if not options.voxelspace:
+    options.center    += info['origin']
+    options.center    *= np.array(info['grid']) / np.array(info['size'])
+    options.dimension *= np.array(info['grid']) / np.array(info['size'])
 
-  if options.dimension is not None:
+  size = microstructure.shape  
-    mask = (np.array(options.dimension) < 0).astype(float)                                       # zero where positive dimension, otherwise one
-    dim = abs(np.array(options.dimension))                                                       # dimensions of primitive body
-    pos = np.zeros(3,dtype='float')
-#    hiresPrimitive = np.zeros((2*dim[0],2*dim[1],2*dim[2],3))                                   # primitive discretized at twice the grid resolution
-    for     i,pos[0] in enumerate(np.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)):
-      for   j,pos[1] in enumerate(np.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)):
-        for k,pos[2] in enumerate(np.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)):
-          gridpos = np.floor(rotation*pos)                                                       # rotate and lock into spacial grid
-          primPos = invRotation*gridpos                                                             # rotate back to primitive coordinate system
-          if np.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \
-             np.all(abs((1.-mask)*primPos/dim) <= 0.5):                                          # inside ellipsoid and inside box
-             microstructure[int((gridpos[0]+options.center[0])%info['grid'][0]),
-                            int((gridpos[1]+options.center[1])%info['grid'][1]),
-                            int((gridpos[2]+options.center[2])%info['grid'][2])] = options.fill          # assign microstructure index
 
+  # change to coordinate space where the primitive is the unit sphere/cube/etc
+  if options.periodic: # use padding to achieve periodicity
+    (X, Y, Z) = np.meshgrid(np.arange(-size[0]/2, (3*size[0])/2, dtype=np.float32), # 50% padding on each side 
+                            np.arange(-size[1]/2, (3*size[1])/2, dtype=np.float32), 
+                            np.arange(-size[2]/2, (3*size[2])/2, dtype=np.float32),
+                            indexing='ij')
+    # Padding handling
+    X = np.roll(np.roll(np.roll(X,
+            -size[0]/2, axis=0), 
+            -size[1]/2, axis=1), 
+            -size[2]/2, axis=2)
+    Y = np.roll(np.roll(np.roll(Y,
+            -size[0]/2, axis=0), 
+            -size[1]/2, axis=1), 
+            -size[2]/2, axis=2)
+    Z = np.roll(np.roll(np.roll(Z,
+            -size[0]/2, axis=0), 
+            -size[1]/2, axis=1), 
+            -size[2]/2, axis=2)
+  else: # nonperiodic, much lighter on resources
+    # change to coordinate space where the primitive is the unit sphere/cube/etc
+    (X, Y, Z) = np.meshgrid(np.arange(0, size[0], dtype=np.float32), 
+                            np.arange(0, size[1], dtype=np.float32), 
+                            np.arange(0, size[2], dtype=np.float32),
+                            indexing='ij')
+    
+  # first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel
+  X -= options.center[0] - 0.5
+  Y -= options.center[1] - 0.5
+  Z -= options.center[2] - 0.5
+  # and then by applying the quaternion
+  # this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
+  (X, Y, Z) = rotation * (X, Y, Z)
+  # and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line)
+  X /= options.dimension[0] * 0.5
+  Y /= options.dimension[1] * 0.5
+  Z /= options.dimension[2] * 0.5
+    
+
+ # High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine
+  old_settings = np.seterr()
+  np.seterr(over='ignore', under='ignore')
+  
+  if options.periodic: # use padding to achieve periodicity
+    inside = np.zeros(size, dtype=bool)
+    for i in range(2):
+      for j in range(2):
+        for k in range(2):
+          inside = inside | ( # Most of this is handling the padding
+                np.abs(X[size[0] * i : size[0] * (i+1),
+                         size[1] * j : size[1] * (j+1),
+                         size[2] * k : size[2] * (k+1)])**options.exponent[0] +
+                np.abs(Y[size[0] * i : size[0] * (i+1),
+                         size[1] * j : size[1] * (j+1),
+                         size[2] * k : size[2] * (k+1)])**options.exponent[1] +
+                np.abs(Z[size[0] * i : size[0] * (i+1),
+                         size[1] * j : size[1] * (j+1),
+                         size[2] * k : size[2] * (k+1)])**options.exponent[2] < 1)
+    
+    microstructure = np.where(inside, options.fill, microstructure)   
+
+  else: # nonperiodic, much lighter on resources
+    microstructure = np.where(np.abs(X)**options.exponent[0] +
+                              np.abs(Y)**options.exponent[1] +
+                              np.abs(Z)**options.exponent[2] < 1, options.fill, microstructure)
+
+  np.seterr(**old_settings) # Reset warnings to old state
   newInfo['microstructures'] = microstructure.max()
 
-
 # --- report ---------------------------------------------------------------------------------------
-  if (    newInfo['microstructures'] != info['microstructures']):
+  if (newInfo['microstructures'] != info['microstructures']):
     damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
 
 

processing/pre/mentat_pbcOnBoxMesh.py

@@ -153,34 +153,31 @@ parser.add_option("-p", "--port", type="int", dest="port", metavar='int',
                                   help="Mentat connection port [%default]")
 parser.add_option("-v", "--verbose", action="store_true", dest="verbose",
                                   help="write Mentat command stream also to stdout [%default]")
-parser.set_defaults(port = 40007)
+parser.set_defaults(port = 40007,
-parser.set_defaults(verbose = False)
+                    verbose = False)
 
 (options, args) = parser.parse_args()
 
-if options.verbose:
-  file={'croak':sys.stderr}
-else:
-  file={'croak':sys.stdout}
-
 try:
   import py_mentat
 except:
-  file['croak'].write('error: no valid Mentat release found')
+  damask.util.croak('error: no valid Mentat release found')
   sys.exit(-1)
 
 outputLocals = {}
 
-file['croak'].write('\033[1m'+scriptName+'\033[0m\n\n')
+damask.util.report(scriptName,'waiting to connect...')
-file['croak'].write( 'waiting to connect...\n')
+
 try:
   py_mentat.py_connect('',options.port)
-# prevent redrawing in Mentat, should be much faster. Since py_connect has no return value, try this to determine if failed or not
+# prevent redrawing in Mentat, should be much faster.
+# Since py_connect has no return value, try this to determine if failed or not
   output(['*draw_manual'],outputLocals,'Mentat')
 except:
-  file['croak'].write('Could not connect. Set Tools/Python/"Run as Separate Process" & "Initiate"...\n')
+  damask.util.croak('Could not connect. Set Tools/Python/"Run as Separate Process" & "Initiate"...')
   sys.exit()
-file['croak'].write( 'connected...\n')
+
+damask.util.croak('connected...')
 
 output(['*remove_all_servos',
         '*sweep_all',
@@ -190,6 +187,10 @@ output(['*remove_all_servos',
 
 cmds = servoLink()
 output(cmds,outputLocals,'Mentat')
+
+output(['*draw_automatic',
+        ],outputLocals,'Mentat')     # script depends on consecutive numbering of nodes
+
 py_mentat.py_disconnect()
 
 if options.verbose:

processing/pre/mentat_spectralBox.py

@@ -247,6 +247,7 @@ for name in filenames:
     '*identify_sets',
     '*show_model',
     '*redraw',
+    '*draw_automatic',
   ]
   
   outputLocals = {}

src/DAMASK_marc.f90

@@ -1,5 +1,5 @@
-#define QUOTE(x) #x                                                                                 
+#define QUOTE(x) #x
-#define PASTE(x,y) x ## y  
+#define PASTE(x,y) x ## y
 
 #ifndef INT
 #define INT 4
@@ -35,7 +35,7 @@
 !> @details   - creeps: timinc
 !--------------------------------------------------------------------------------------------------
 module DAMASK_interface
- 
+
  implicit none
  character(len=4), parameter :: InputFileExtension = '.dat'
  character(len=4), parameter :: LogFileExtension = '.log'
@@ -57,18 +57,18 @@ subroutine DAMASK_interface_init
  write(6,'(/,a)')              ' Version: '//DAMASKVERSION
  write(6,'(a,2(i2.2,a),i4.4)') ' Date:    ',dateAndTime(3),'/',&
                                             dateAndTime(2),'/',&
-                                            dateAndTime(1) 
+                                            dateAndTime(1)
  write(6,'(a,2(i2.2,a),i2.2)') ' Time:    ',dateAndTime(5),':',&
                                             dateAndTime(6),':',&
-                                            dateAndTime(7)  
+                                            dateAndTime(7)
  write(6,'(/,a)') ' <<<+-  DAMASK_interface init  -+>>>'
-#include "compilation_info.f90"  
+#include "compilation_info.f90"
 
 end subroutine DAMASK_interface_init
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief returns the current workingDir 
+!> @brief returns the current workingDir
 !--------------------------------------------------------------------------------------------------
 function getSolverWorkingDirectoryName()
 
@@ -185,7 +185,7 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
 !$ include "omp_lib.h"                                                                              ! the openMP function library
  integer(pInt),                         intent(in) :: &                                             ! according to MSC.Marc 2012 Manual D
    ngens, &                                                                                         !< size of stress-strain law
-   nn, &                                                                                            !< integration point number 
+   nn, &                                                                                            !< integration point number
    ndi, &                                                                                           !< number of direct components
    nshear, &                                                                                        !< number of shear components
    ncrd, &                                                                                          !< number of coordinates
@@ -199,7 +199,7 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
  integer(pInt), dimension(2),           intent(in) :: &                                             ! according to MSC.Marc 2012 Manual D
    m, &                                                                                             !< (1) user element number, (2) internal element number
    matus, &                                                                                         !< (1) user material identification number, (2) internal material identification number
-   kcus, &                                                                                          !< (1) layer number, (2) internal layer number 
+   kcus, &                                                                                          !< (1) layer number, (2) internal layer number
    lclass                                                                                           !< (1) element class, (2) 0: displacement, 1: low order Herrmann, 2: high order Herrmann
  real(pReal),   dimension(*),           intent(in) :: &                                             ! has dimension(1) according to MSC.Marc 2012 Manual D, but according to example hypela2.f dimension(*)
    e, &                                                                                             !< total elastic strain
@@ -244,13 +244,13 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
 
  if (iand(debug_level(debug_MARC),debug_LEVELBASIC) /= 0_pInt) then
    write(6,'(a,/,i8,i8,i2)') ' MSC.MARC information on shape of element(2), IP:', m, nn
-   write(6,'(a,2(i1))')      ' Jacobian:                      ', ngens,ngens 
+   write(6,'(a,2(i1))')      ' Jacobian:                      ', ngens,ngens
-   write(6,'(a,i1)')         ' Direct stress:                 ', ndi  
+   write(6,'(a,i1)')         ' Direct stress:                 ', ndi
-   write(6,'(a,i1)')         ' Shear stress:                  ', nshear  
+   write(6,'(a,i1)')         ' Shear stress:                  ', nshear
    write(6,'(a,i2)')         ' DoF:                           ', ndeg
    write(6,'(a,i2)')         ' Coordinates:                   ', ncrd
-   write(6,'(a,i12)')        ' Nodes:                         ', nnode 
+   write(6,'(a,i12)')        ' Nodes:                         ', nnode
-   write(6,'(a,i1)')         ' Deformation gradient:          ', itel 
+   write(6,'(a,i1)')         ' Deformation gradient:          ', itel
    write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') ' Deformation gradient at t=n:', &
                                  math_transpose33(ffn)
    write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') ' Deformation gradient at t=n+1:', &
@@ -310,7 +310,7 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
      !$OMP END CRITICAL (write2out)
    endif                                                                                            ! convergence treatment end
 
-   
+
    if (usePingPong) then
      calcMode(nn,cp_en) = .not. calcMode(nn,cp_en)                                                  ! ping pong (calc <--> collect)
      if (calcMode(nn,cp_en)) then                                                                   ! now --- CALC ---
@@ -339,7 +339,7 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
          mesh_node(1:ndeg,CPnodeID) = mesh_node0(1:ndeg,CPnodeID) + numerics_unitlength * dispt(1:ndeg,node)
        enddo
      endif
-   
+
    else                                                                                             ! --- PLAIN MODE ---
      computationMode = CPFEM_CALCRESULTS                                                            ! always calc
      if (lastLovl /= lovl) then
@@ -378,12 +378,39 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
  s(1:ndi+nshear) = stress(1:ndi+nshear)*invnrmMandel(1:ndi+nshear)
  g = 0.0_pReal
  if(symmetricSolver) d = 0.5_pReal*(d+transpose(d))
- 
+
  !$ call omp_set_num_threads(defaultNumThreadsInt)                                                  ! reset number of threads to stored default value
 
 end subroutine hypela2
 
 
+!--------------------------------------------------------------------------------------------------
+!> @brief calculate internal heat generated due to inelastic energy dissipation
+!--------------------------------------------------------------------------------------------------
+subroutine flux(f,ts,n,time)
+ use prec, only: &
+   pReal, &
+   pInt
+ use thermal_conduction, only: &
+   thermal_conduction_getSourceAndItsTangent
+ use mesh, only: &
+   mesh_FEasCP
+
+ implicit none
+ real(pReal),   dimension(6),           intent(in) :: &
+   ts
+ integer(pInt), dimension(10),          intent(in) :: &
+   n
+ real(pReal),                           intent(in) :: &
+   time
+ real(pReal),   dimension(2),           intent(out) :: &
+   f
+
+ call thermal_conduction_getSourceAndItsTangent(f(1), f(2), ts(3), n(3),mesh_FEasCP('elem',n(1)))
+
+ end subroutine flux
+
+
 !--------------------------------------------------------------------------------------------------
 !> @brief sets user defined output variables for Marc
 !> @details select a variable contour plotting (user subroutine).
@@ -399,7 +426,7 @@ subroutine plotv(v,s,sp,etot,eplas,ecreep,t,m,nn,layer,ndi,nshear,jpltcd)
  use homogenization, only: &
    materialpoint_results,&
    materialpoint_sizeResults
- 
+
  implicit none
  integer(pInt),               intent(in) :: &
    m, &                                                                                             !< element number
@@ -411,7 +438,7 @@ subroutine plotv(v,s,sp,etot,eplas,ecreep,t,m,nn,layer,ndi,nshear,jpltcd)
  real(pReal),   dimension(*), intent(in) :: &
    s, &                                                                                             !< stress array
    sp, &                                                                                            !< stresses in preferred direction
-   etot, &                                                                                          !< total strain (generalized) 
+   etot, &                                                                                          !< total strain (generalized)
    eplas, &                                                                                         !< total plastic strain
    ecreep, &                                                                                        !< total creep strain
    t                                                                                                !< current temperature

src/IO.f90

@@ -878,7 +878,7 @@ function IO_spotTagInPart(fileUnit,part,tag,Nsections)
 
  IO_spotTagInPart = .false.                                                                         ! assume to nowhere spot tag
  section = 0_pInt
- line =''
+ line = ''
 
  rewind(fileUnit)
  do while (trim(line) /= IO_EOF .and. IO_lc(IO_getTag(line,'<','>')) /= part)                       ! search for part
@@ -1669,33 +1669,33 @@ subroutine IO_error(error_ID,el,ip,g,ext_msg)
  end select
  
  !$OMP CRITICAL (write2out)
- write(6,'(/,a)')      ' +--------------------------------------------------------+'
+ write(0,'(/,a)')      ' +--------------------------------------------------------+'
- write(6,'(a)')        ' +                         error                          +'
+ write(0,'(a)')        ' +                         error                          +'
- write(6,'(a,i3,a)')   ' +                         ',error_ID,'                            +'
+ write(0,'(a,i3,a)')   ' +                         ',error_ID,'                            +'
- write(6,'(a)')        ' +                                                        +'
+ write(0,'(a)')        ' +                                                        +'
  write(formatString,'(a,i6.6,a,i6.6,a)') '(1x,a2,a',max(1,len(trim(msg))),',',&
                                                     max(1,60-len(trim(msg))-5),'x,a)'
- write(6,formatString) '+ ', trim(msg),'+'
+ write(0,formatString) '+ ', trim(msg),'+'
  if (present(ext_msg)) then
    write(formatString,'(a,i6.6,a,i6.6,a)') '(1x,a2,a',max(1,len(trim(ext_msg))),',',&
                                                       max(1,60-len(trim(ext_msg))-5),'x,a)'
-   write(6,formatString) '+ ', trim(ext_msg),'+'
+   write(0,formatString) '+ ', trim(ext_msg),'+'
  endif
  if (present(el)) then
    if (present(ip)) then
      if (present(g)) then
-       write(6,'(a13,1x,i9,1x,a2,1x,i2,1x,a5,1x,i4,18x,a1)') ' + at element',el,'IP',ip,'grain',g,'+'
+       write(0,'(a13,1x,i9,1x,a2,1x,i2,1x,a5,1x,i4,18x,a1)') ' + at element',el,'IP',ip,'grain',g,'+'
      else
-       write(6,'(a13,1x,i9,1x,a2,1x,i2,29x,a1)') ' + at element',el,'IP',ip,'+'
+       write(0,'(a13,1x,i9,1x,a2,1x,i2,29x,a1)') ' + at element',el,'IP',ip,'+'
      endif
    else
-     write(6,'(a13,1x,i9,35x,a1)') ' + at element',el,'+'
+     write(0,'(a13,1x,i9,35x,a1)') ' + at element',el,'+'
    endif
  elseif (present(ip)) then                                                                          ! now having the meaning of "instance"
-   write(6,'(a15,1x,i9,33x,a1)') ' + for instance',ip,'+'
+   write(0,'(a15,1x,i9,33x,a1)') ' + for instance',ip,'+'
  endif
- write(6,'(a)')      ' +--------------------------------------------------------+'
+ write(0,'(a)')      ' +--------------------------------------------------------+'
- flush(6)
+ flush(0)
  call quit(9000_pInt+error_ID)
  !$OMP END CRITICAL (write2out)
 

src/lattice.f90

@@ -1283,11 +1283,9 @@ subroutine lattice_init
    a_fcc, &                                                                                         !< lattice parameter a for fcc austenite
    a_bcc                                                                                            !< lattice paramater a for bcc martensite
 
- mainProcess: if (worldrank == 0) then
+ write(6,'(/,a)') ' <<<+-  lattice init  -+>>>'
-   write(6,'(/,a)') ' <<<+-  lattice init  -+>>>'
+ write(6,'(a15,a)')   ' Current time: ',IO_timeStamp()
-   write(6,'(a15,a)')   ' Current time: ',IO_timeStamp()
 #include "compilation_info.f90"
- endif mainProcess
 
 !--------------------------------------------------------------------------------------------------
 ! consistency checks (required since ifort 15.0 does not support sum/maxval in parameter definition)
@@ -1718,7 +1716,7 @@ subroutine lattice_initializeStructure(myPhase,CoverA,CoverA_trans,a_fcc,a_bcc)
          lattice_trans_C66(1:6,1:6,myPhase) = math_Mandel3333to66(lattice_trans_C3333(1:3,1:3,1:3,1:3,myPhase))
          do i = 1_pInt, 6_pInt
            if (abs(lattice_trans_C66(i,i,myPhase))<tol_math_check) &
-           call IO_error(135_pInt,el=i,ip=myPhase,ext_msg='matrix diagonal "el"ement of phase "ip"')
+           call IO_error(135_pInt,el=i,ip=myPhase,ext_msg='matrix diagonal "el"ement of phase "ip" in fcc-->bcc transformation')
          enddo
        case (LATTICE_hex_ID)
          c11bar = (lattice_C66(1,1,myPhase) + lattice_C66(1,2,myPhase) + 2.0_pReal*lattice_C66(4,4,myPhase))/2.0_pReal
@@ -1751,7 +1749,7 @@ subroutine lattice_initializeStructure(myPhase,CoverA,CoverA_trans,a_fcc,a_bcc)
          lattice_trans_C66(1:6,1:6,myPhase) = math_Mandel3333to66(lattice_trans_C3333(1:3,1:3,1:3,1:3,myPhase))
          do i = 1_pInt, 6_pInt
            if (abs(lattice_trans_C66(i,i,myPhase))<tol_math_check) &
-           call IO_error(135_pInt,el=i,ip=myPhase,ext_msg='matrix diagonal "el"ement of phase "ip"')
+           call IO_error(135_pInt,el=i,ip=myPhase,ext_msg='matrix diagonal "el"ement of phase "ip" in fcc-->hex transformation')
          enddo
      end select
  end select

src/material.f90

@@ -619,7 +619,7 @@ subroutine material_parseHomogenization(fileUnit,myPart)
      chunkPos = IO_stringPos(line)
      tag = IO_lc(IO_stringValue(line,chunkPos,1_pInt))                                             ! extract key
      select case(tag)
-       case ('type')
+       case ('type','mech','mechanical')
          select case (IO_lc(IO_stringValue(line,chunkPos,2_pInt)))
            case(HOMOGENIZATION_NONE_label)
              homogenization_type(section) = HOMOGENIZATION_NONE_ID
@@ -758,7 +758,7 @@ subroutine material_parseMicrostructure(fileUnit,myPart)
  allocate(microstructure_elemhomo(Nsections),             source=.false.)
 
  if(any(mesh_element(4,1:mesh_NcpElems) > Nsections)) &
-  call IO_error(155_pInt,ext_msg='Microstructure in geometry > Sections in material.config')
+  call IO_error(155_pInt,ext_msg='More microstructures in geometry than sections in material.config')
 
  forall (e = 1_pInt:mesh_NcpElems) microstructure_active(mesh_element(4,e)) = .true.                ! current microstructure used in model? Elementwise view, maximum N operations for N elements
 
@@ -801,7 +801,7 @@ subroutine material_parseMicrostructure(fileUnit,myPart)
          microstructure_crystallite(section) = IO_intValue(line,chunkPos,2_pInt)
        case ('(constituent)')
          constituent = constituent + 1_pInt
-         do i=2_pInt,6_pInt,2_pInt
+         do i = 2_pInt,6_pInt,2_pInt
            tag = IO_lc(IO_stringValue(line,chunkPos,i))
            select case (tag)
              case('phase')
@@ -816,6 +816,11 @@ subroutine material_parseMicrostructure(fileUnit,myPart)
    endif
  enddo
 
+ !sanity check
+do section = 1_pInt, Nsections
+  if (sum(microstructure_fraction(:,section)) /= 1.0_pReal) &
+    call IO_error(153_pInt,ext_msg=microstructure_name(section))
+enddo
 end subroutine material_parseMicrostructure
 
 

src/math.f90

@@ -1180,6 +1180,9 @@ end function math_Voigt66to3333
 
 !--------------------------------------------------------------------------------------------------
 !> @brief random quaternion
+! http://math.stackexchange.com/questions/131336/uniform-random-quaternion-in-a-restricted-angle-range
+! K. Shoemake. Uniform random rotations. In D. Kirk, editor, Graphics Gems III, pages 124-132. 
+! Academic, New York, 1992.
 !--------------------------------------------------------------------------------------------------
 function math_qRand()
 

src/mesh.f90

@@ -472,9 +472,8 @@ contains
 !! Order and routines strongly depend on type of solver
 !--------------------------------------------------------------------------------------------------
 subroutine mesh_init(ip,el)
- use, intrinsic :: iso_c_binding
- use DAMASK_interface
  use, intrinsic :: iso_fortran_env                                                                  ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment)
+ use DAMASK_interface
  use IO, only: &
 #ifdef Abaqus
    IO_abaqus_hasNoPart, &

src/numerics.f90

@@ -694,9 +694,9 @@ subroutine numerics_init
                    .not. memory_efficient) call IO_error(error_ID = 847_pInt)
  if (err_stress_tolrel <= 0.0_pReal)       call IO_error(301_pInt,ext_msg='err_stress_tolRel')
  if (err_stress_tolabs <= 0.0_pReal)       call IO_error(301_pInt,ext_msg='err_stress_tolAbs')
- if (err_div_tolRel <= 0.0_pReal)          call IO_error(301_pInt,ext_msg='err_div_tolRel')
+ if (err_div_tolRel < 0.0_pReal)           call IO_error(301_pInt,ext_msg='err_div_tolRel')
  if (err_div_tolAbs <= 0.0_pReal)          call IO_error(301_pInt,ext_msg='err_div_tolAbs')
- if (err_curl_tolRel <= 0.0_pReal)         call IO_error(301_pInt,ext_msg='err_curl_tolRel')
+ if (err_curl_tolRel < 0.0_pReal)          call IO_error(301_pInt,ext_msg='err_curl_tolRel')
  if (err_curl_tolAbs <= 0.0_pReal)         call IO_error(301_pInt,ext_msg='err_curl_tolAbs')
  if (polarAlpha <= 0.0_pReal .or. &
      polarAlpha >  2.0_pReal)              call IO_error(301_pInt,ext_msg='polarAlpha')

src/spectral_interface.f90

@@ -20,7 +20,6 @@ module DAMASK_interface
    geometryFile = '', &                                                                             !< parameter given for geometry file
    loadCaseFile = ''                                                                                !< parameter given for load case file
  character(len=1024), private           :: workingDirectory                                         !< accessed by getSolverWorkingDirectoryName for compatibility reasons
- character,           private,parameter :: pathSep = '/'
 
  public :: &
    getSolverWorkingDirectoryName, &
@@ -95,6 +94,14 @@ subroutine DAMASK_interface_init()
      write(output_unit,'(a)') ' STDOUT != 6'
      call quit(1_pInt)
    endif
+   if (error_unit /= 0) then
+     write(output_unit,'(a)') ' STDERR != 0'
+     call quit(1_pInt)
+   endif
+   if (PETSC_VERSION_MAJOR /= 3 .or. PETSC_VERSION_MINOR /= 7) then
+     write(6,'(a,2(i1.1,a))') 'PETSc ',PETSC_VERSION_MAJOR,'.',PETSC_VERSION_MINOR,'.x not supported'
+     call quit(1_pInt)
+   endif
  else mainProcess
    close(6)                                                                                         ! disable output for non-master processes (open 6 to rank specific file for debug)
    open(6,file='/dev/null',status='replace')                                                        ! close(6) alone will leave some temp files in cwd
@@ -164,7 +171,7 @@ subroutine DAMASK_interface_init()
        write(6,'(a)')  ' Help:'
        write(6,'(/,a)')'   --help'
        write(6,'(a,/)')'        Prints this message and exits'
-       call quit(0_pInt)                                                                        ! normal Termination
+       call quit(0_pInt)                                                                            ! normal Termination
      case ('-l', '--load', '--loadcase')
        loadcaseArg = IIO_stringValue(commandLine,chunkPos,i+1_pInt)
      case ('-g', '--geom', '--geometry')
@@ -190,7 +197,6 @@ subroutine DAMASK_interface_init()
  error = getHostName(hostName)
  write(6,'(a,a)')      ' Host name:             ', trim(hostName)
  write(6,'(a,a)')      ' User name:             ', trim(userName)
- write(6,'(a,a)')      ' Path separator:        ', pathSep
  write(6,'(a,a)')      ' Command line call:     ', trim(commandLine)
  if (len(trim(workingDirArg))>0) &
    write(6,'(a,a)')    ' Working dir argument:  ', trim(workingDirArg)
@@ -225,22 +231,22 @@ character(len=1024) function storeWorkingDirectory(workingDirectoryArg,geometryA
  external                      :: quit
 
  wdGiven: if (len(workingDirectoryArg)>0) then
-   absolutePath: if (workingDirectoryArg(1:1) == pathSep) then
+   absolutePath: if (workingDirectoryArg(1:1) == '/') then
      storeWorkingDirectory = workingDirectoryArg
    else absolutePath
      error = getCWD(cwd)
      if (error) call quit(1_pInt)
-     storeWorkingDirectory = trim(cwd)//pathSep//workingDirectoryArg
+     storeWorkingDirectory = trim(cwd)//'/'//workingDirectoryArg
    endif absolutePath
-   if (storeWorkingDirectory(len(trim(storeWorkingDirectory)):len(trim(storeWorkingDirectory))) /= pathSep) &
+   if (storeWorkingDirectory(len(trim(storeWorkingDirectory)):len(trim(storeWorkingDirectory))) /= '/') &
-     storeWorkingDirectory = trim(storeWorkingDirectory)//pathSep                                   ! if path seperator is not given, append it
+     storeWorkingDirectory = trim(storeWorkingDirectory)//'/'                                       ! if path seperator is not given, append it
  else wdGiven
-   if (geometryArg(1:1) == pathSep) then                                                            ! absolute path given as command line argument
+   if (geometryArg(1:1) == '/') then                                                                ! absolute path given as command line argument
-     storeWorkingDirectory = geometryArg(1:scan(geometryArg,pathSep,back=.true.))
+     storeWorkingDirectory = geometryArg(1:scan(geometryArg,'/',back=.true.))
    else
      error = getCWD(cwd)                                                                            ! relative path given as command line argument
      if (error) call quit(1_pInt)
-     storeWorkingDirectory = trim(cwd)//pathSep//geometryArg(1:scan(geometryArg,pathSep,back=.true.))
+     storeWorkingDirectory = trim(cwd)//'/'//geometryArg(1:scan(geometryArg,'/',back=.true.))
    endif
  endif wdGiven
 
@@ -277,13 +283,13 @@ character(len=1024) function getSolverJobName()
 
  tempString = geometryFile
  posExt = scan(tempString,'.',back=.true.)
- posSep = scan(tempString,pathSep,back=.true.)
+ posSep = scan(tempString,'/',back=.true.)
 
  getSolverJobName = tempString(posSep+1:posExt-1)
 
  tempString = loadCaseFile
  posExt = scan(tempString,'.',back=.true.)
- posSep = scan(tempString,pathSep,back=.true.)
+ posSep = scan(tempString,'/',back=.true.)
 
  getSolverJobName = trim(getSolverJobName)//'_'//tempString(posSep+1:posExt-1)
 
@@ -308,13 +314,13 @@ character(len=1024) function getGeometryFile(geometryParameter)
 
  getGeometryFile = geometryParameter
  posExt = scan(getGeometryFile,'.',back=.true.)
- posSep = scan(getGeometryFile,pathSep,back=.true.)
+ posSep = scan(getGeometryFile,'/',back=.true.)
 
  if (posExt <= posSep) getGeometryFile = trim(getGeometryFile)//('.geom')                           ! no extension present
- if (scan(getGeometryFile,pathSep) /= 1) then                                                       ! relative path given as command line argument
+ if (scan(getGeometryFile,'/') /= 1) then                                                           ! relative path given as command line argument
    error = getcwd(cwd)
    if (error) call quit(1_pInt)
-   getGeometryFile = rectifyPath(trim(cwd)//pathSep//getGeometryFile)
+   getGeometryFile = rectifyPath(trim(cwd)//'/'//getGeometryFile)
  else
    getGeometryFile = rectifyPath(getGeometryFile)
  endif
@@ -342,13 +348,13 @@ character(len=1024) function getLoadCaseFile(loadCaseParameter)
 
  getLoadCaseFile = loadcaseParameter
  posExt = scan(getLoadCaseFile,'.',back=.true.)
- posSep = scan(getLoadCaseFile,pathSep,back=.true.)
+ posSep = scan(getLoadCaseFile,'/',back=.true.)
 
  if (posExt <= posSep) getLoadCaseFile = trim(getLoadCaseFile)//('.load')                           ! no extension present
- if (scan(getLoadCaseFile,pathSep) /= 1) then                                                       ! relative path given as command line argument
+ if (scan(getLoadCaseFile,'/') /= 1) then                                                           ! relative path given as command line argument
    error = getcwd(cwd)
    if (error) call quit(1_pInt)
-   getLoadCaseFile = rectifyPath(trim(cwd)//pathSep//getLoadCaseFile)
+   getLoadCaseFile = rectifyPath(trim(cwd)//'/'//getLoadCaseFile)
  else
    getLoadCaseFile = rectifyPath(getLoadCaseFile)
  endif
@@ -373,26 +379,26 @@ function rectifyPath(path)
  l = len_trim(path)
  rectifyPath = path
  do i = l,3,-1
-   if (rectifyPath(i-2:i) == pathSep//'.'//pathSep) &
+   if (rectifyPath(i-2:i) == '/'//'.'//'/') &
      rectifyPath(i-1:l) = rectifyPath(i+1:l)//'  '
  enddo
 
 !--------------------------------------------------------------------------------------------------
 ! remove ../ and corresponding directory from rectifyPath
  l = len_trim(rectifyPath)
- i = index(rectifyPath(i:l),'..'//pathSep)
+ i = index(rectifyPath(i:l),'..'//'/')
  j = 0
  do while (i > j)
-    j = scan(rectifyPath(1:i-2),pathSep,back=.true.)
+    j = scan(rectifyPath(1:i-2),'/',back=.true.)
     rectifyPath(j+1:l) = rectifyPath(i+3:l)//repeat(' ',2+i-j)
-    if (rectifyPath(j+1:j+1) == pathSep) then                                                       !search for '//' that appear in case of XXX/../../XXX
+    if (rectifyPath(j+1:j+1) == '/') then                                                           !search for '//' that appear in case of XXX/../../XXX
       k = len_trim(rectifyPath)
       rectifyPath(j+1:k-1) = rectifyPath(j+2:k)
       rectifyPath(k:k) = ' '
     endif
-    i = j+index(rectifyPath(j+1:l),'..'//pathSep)
+    i = j+index(rectifyPath(j+1:l),'..'//'/')
  enddo
- if(len_trim(rectifyPath) == 0) rectifyPath = pathSep
+ if(len_trim(rectifyPath) == 0) rectifyPath = '/'
 
 end function rectifyPath
 
@@ -411,12 +417,12 @@ character(len=1024) function makeRelativePath(a,b)
 
  do i = 1, min(1024,len_trim(a),len_trim(b))
    if (a(i:i) /= b(i:i)) exit
-   if (a(i:i) == pathSep) posLastCommonSlash = i
+   if (a(i:i) == '/') posLastCommonSlash = i
  enddo
  do i = posLastCommonSlash+1,len_trim(a)
-   if (a(i:i) == pathSep) remainingSlashes = remainingSlashes + 1
+   if (a(i:i) == '/') remainingSlashes = remainingSlashes + 1
  enddo
- makeRelativePath = repeat('..'//pathSep,remainingSlashes)//b(posLastCommonSlash+1:len_trim(b))
+ makeRelativePath = repeat('..'//'/',remainingSlashes)//b(posLastCommonSlash+1:len_trim(b))
 
 end function makeRelativePath
 

src/spectral_utilities.f90

@@ -227,12 +227,13 @@ subroutine utilities_init()
                 trim(PETScDebug), &
                 ' add more using the PETSc_Options keyword in numerics.config '; flush(6)
 
- call PetscOptionsClear(ierr); CHKERRQ(ierr)
+ call PetscOptionsClear(PETSC_NULL_OBJECT,ierr)
- if(debugPETSc) call PetscOptionsInsertString(trim(PETSCDEBUG),ierr)
  CHKERRQ(ierr)
- call PetscOptionsInsertString(trim(petsc_defaultOptions),ierr)
+ if(debugPETSc) call PetscOptionsInsertString(PETSC_NULL_OBJECT,trim(PETSCDEBUG),ierr)
  CHKERRQ(ierr)
- call PetscOptionsInsertString(trim(petsc_options),ierr)
+ call PetscOptionsInsertString(PETSC_NULL_OBJECT,trim(petsc_defaultOptions),ierr)
+ CHKERRQ(ierr)
+ call PetscOptionsInsertString(PETSC_NULL_OBJECT,trim(petsc_options),ierr)
  CHKERRQ(ierr)
 
  grid1Red = grid(1)/2_pInt + 1_pInt