From 4a627161d57b8acd47f5b04558ef92f4b36fcac1 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Fri, 16 Sep 2016 03:23:59 +0200
Subject: [PATCH 01/32] clarified fixed expression

---
 DAMASK_env.zsh                     | 99 +++++++++++++-----------------
 processing/pre/geom_grainGrowth.py |  7 +--
 2 files changed, 46 insertions(+), 60 deletions(-)

diff --git a/DAMASK_env.zsh b/DAMASK_env.zsh
index 3bbab82df..730993bf8 100644
--- a/DAMASK_env.zsh
+++ b/DAMASK_env.zsh
@@ -1,87 +1,74 @@
-# sets up an environment for DAMASK on zsh
-# usage:  source DAMASK_env.zsh
+# sets up an environment for DAMASK on bash
+# usage:  source DAMASK_env.sh
 
-DAMASK_ROOT=${0:a:h}
-
-# defining set() allows to source the same file for tcsh and zsh, with and without space around =
-set() {
-    export $1$2$3
- }
-source $DAMASK_ROOT/CONFIG
-unset -f set
-
-# add DAMASK_BIN if present but not yet in $PATH
-MATCH=`echo ":$PATH:" | grep $DAMASK_BIN:`
-if [[ ( "x$DAMASK_BIN" != "x" ) && ( "x$MATCH" = "x" ) ]]; then
-  export PATH=$DAMASK_BIN:$PATH
+if [ "$OSTYPE" = "linux-gnu" ] || [ "$OSTYPE" = 'linux' ]; then
+  DAMASK_ROOT=$(readlink -f "`dirname ${(%):-%N}`")
+else
+  print 'Not done yet'
 fi
 
+[[ -f $HOME/.damask/damask.conf ]] && source $HOME/.damask/damask.conf || source /etc/damask.conf
+
+# if DAMASK_BIN is present and not in $PATH, add it
+#if [[ [[ "x$DAMASK_BIN" != "x" ]] && ! `echo ":$PATH:" | grep $DAMASK_BIN:` ]]; then
+  export PATH=$DAMASK_BIN:$PATH
+#fi
+
 SOLVER=`which DAMASK_spectral 2>/dev/null`
+if [ "x$SOLVER" = "x" ]; then
+  export SOLVER='Not found!'
+fi
 PROCESSING=`which postResults 2>/dev/null`
-if [ "x$DAMASK_NUM_THREADS" = "x" ]; then
-  DAMASK_NUM_THREADS=1
+if [ "x$PROCESSING" = "x" ]; then
+  export PROCESSING='Not found!'
 fi
 
 # according to http://software.intel.com/en-us/forums/topic/501500
 # this seems to make sense for the stack size
-if [ "`which free 2>/dev/null`" != "free not found" ]; then
-  freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'`
-
-  # http://superuser.com/questions/220059/what-parameters-has-ulimit             
-  ulimit -s `expr $freeMem / $DAMASK_NUM_THREADS / 2` 2>/dev/null # maximum stack size (kB)
-  ulimit -d `expr $freeMem                       / 2` 2>/dev/null # maximum  heap size (kB)
-fi
-ulimit -v unlimited   2>/dev/null # maximum virtual memory size
+#FREE=`which free 2>/dev/null`
+#if [ "x$FREE" != "x" ]; then
+#  freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'`
+#  heap=`expr $freeMem / 2`
+#  stack=`expr $freeMem / 2`
+#
+#  # http://superuser.com/questions/220059/what-parameters-has-ulimit             
+#  ulimit -s $stack      2>/dev/null # maximum stack size (kB)
+#  ulimit -d $heap       2>/dev/null # maximum heap size (kB)
+#fi
+#ulimit -c 2000        2>/dev/null # core  file size (512-byte blocks)
+#ulimit -v unlimited   2>/dev/null # maximum virtual memory size
 ulimit -m unlimited   2>/dev/null # maximum physical memory size
 
 # disable output in case of scp
 if [ ! -z "$PS1" ]; then
   echo
-  echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK
-  echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
-  echo https://damask.mpie.de
+  echo Düsseldorf Advanced Materials Simulation Kit - DAMASK
+  echo Max-Planck-Institut für Eisenforschung, Düsseldorf
+  echo http://damask.mpie.de
   echo
-  echo "Using environment with ..."
+  echo Using environment with ...
   echo "DAMASK             $DAMASK_ROOT"
-  echo "Spectral Solver    $SOLVER" 
-  echo "Post Processing    $PROCESSING"
+  [[ "x$SOLVER"       != "x" ]] && echo "Spectral Solver    $SOLVER" 
+  [[ "x$PROCESSING"   != "x" ]] && echo "Post Processing    $PROCESSING"
   echo "Multithreading     DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
   if [ "x$PETSC_DIR"   != "x" ]; then
     echo "PETSc location     $PETSC_DIR"
-    [[ $(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR") == $PETSC_DIR ]] \
-    || echo "               ~~> "$(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR")
+    [[ `readlink -f $PETSC_DIR` == $PETSC_DIR ]] || echo "               ~~> "`readlink -f $PETSC_DIR`
   fi
-  [[ "x$PETSC_ARCH"  == "x" ]] \
-  || echo "PETSc architecture $PETSC_ARCH"
+  [[ "x$PETSC_ARCH"  != "x" ]] && echo "PETSc architecture $PETSC_ARCH"
   echo "MSC.Marc/Mentat    $MSC_ROOT"
   echo
-  echo -n "heap  size         "
-   [[ "$(ulimit -d)" == "unlimited" ]] \
-   && echo "unlimited" \
-   || echo $(python -c \
-          "import math; \
-           size=$(( 1024*$(ulimit -d) )); \
-           print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
-           ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
-  echo -n "stack size         "
-   [[ "$(ulimit -s)" == "unlimited" ]] \
-   && echo "unlimited" \
-   || echo $(python -c \
-          "import math; \
-           size=$(( 1024*$(ulimit -s) )); \
-           print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
-           ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
+  echo -n "heap  size/MiB     "; echo "`ulimit -d`/1024" | bc
+  echo -n "stack size/MiB     "; echo "`ulimit -s`/1024" | bc
 fi
 
 export DAMASK_NUM_THREADS
 export PYTHONPATH=$DAMASK_ROOT/lib:$PYTHONPATH
 
-for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN MATCH; do
+for var in BASE STAT SOLVER PROCESSING FREE; do
   unset "${var}"
 done
-for var in DAMASK MSC; do
+for var in DAMASK IMKL ACML LAPACK MSC FFTW HDF5; do
   unset "${var}_ROOT"
 done
-for var in ABAQUS MARC; do
-  unset "${var}_VERSION"
-done
+
diff --git a/processing/pre/geom_grainGrowth.py b/processing/pre/geom_grainGrowth.py
index 95c67fb28..ac7af9e85 100755
--- a/processing/pre/geom_grainGrowth.py
+++ b/processing/pre/geom_grainGrowth.py
@@ -99,16 +99,15 @@ for name in filenames:
 
 
   for smoothIter in xrange(options.N):
-    boundary = np.zeros(microstructure.shape)
+    interfaceEnergy = np.zeros(microstructure.shape)
     for i in (-1,0,1):
       for j in (-1,0,1):
         for k in (-1,0,1):
             # assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
-          boundary = np.maximum(boundary,
+          interfaceEnergy = np.maximum(interfaceEnergy,
                                           interfacialEnergy(microstructure,np.roll(np.roll(np.roll(
                                                             microstructure,i,axis=0), j,axis=1), k,axis=2)))
-    interfaceEnergy = boundary
-    
+
     # periodically extend interfacial energy array by half a grid size in positive and negative directions
     periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
                                                                    grid[1]/2:-grid[1]/2,

From b86d91e8a48d363525349673d687cbd3cf6f8329 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Fri, 11 Nov 2016 06:42:35 +0100
Subject: [PATCH 02/32] not used

---
 lib/damask/util.py | 25 +------------------------
 1 file changed, 1 insertion(+), 24 deletions(-)

diff --git a/lib/damask/util.py b/lib/damask/util.py
index 6cea7c54b..c8aba4a5a 100644
--- a/lib/damask/util.py
+++ b/lib/damask/util.py
@@ -101,29 +101,6 @@ def execute(cmd,
   if process.returncode != 0: raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
   return out,error
 
-
-# -----------------------------
-# Matlab like trigonometric functions that take and return angles in degrees.
-# -----------------------------
-for f in ['cos', 'sin', 'tan']:
-  exec('def %sd(deg): return (np.%s(np.deg2rad(deg)))'%(f,f))
-  exec('def a%sd(val): return (np.rad2deg(np.arc%s(val)))'%(f,f))
-
-
-# -----------------------------
-def gridLocation(idx,res):
-  return ( idx  % res[0], \
-         ( idx // res[0]) % res[1], \
-         ( idx // res[0] // res[1]) % res[2] )
-
-
-# -----------------------------
-def gridIndex(location,res):
-  return ( location[0] % res[0]                    + \
-         ( location[1] % res[1]) * res[0]          + \
-         ( location[2] % res[2]) * res[1] * res[0]   )
-
-
 # -----------------------------
 class extendableOption(Option):
   """
@@ -469,4 +446,4 @@ def curve_fit_bound(f, xdata, ydata, p0=None, sigma=None, bounds=None, **kw):
     else:
         pcov = np.inf
 
-    return (popt, pcov, infodict, errmsg, ier) if return_full else (popt, pcov)
\ No newline at end of file
+    return (popt, pcov, infodict, errmsg, ier) if return_full else (popt, pcov)

From f6669a4a81938a7be0c5cca3b23be64d4ebcd788 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Fri, 5 May 2017 17:20:22 +0200
Subject: [PATCH 03/32] less verbose compilation

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 891d4b5f2..0ba67963e 100644
--- a/Makefile
+++ b/Makefile
@@ -7,7 +7,7 @@ all: spectral FEM marc processing
 
 .PHONY: spectral
 spectral: build/spectral
-	@(cd build/spectral;make --no-print-directory -ws all install VERBOSE=1;)
+	@(cd build/spectral;make --no-print-directory -ws all install;)
 
 .PHONY: FEM
 FEM: build/FEM

From 05bd760bc7a9d0a9c79d0d1de2439167a58c2ca1 Mon Sep 17 00:00:00 2001
From: Philip Eisenlohr <eisenlohr@egr.msu.edu>
Date: Fri, 5 May 2017 11:49:15 -0400
Subject: [PATCH 04/32] removed debug message that broke stack unlimiting

---
 DAMASK_env.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/DAMASK_env.sh b/DAMASK_env.sh
index 0ae3a2abf..264ae9c94 100644
--- a/DAMASK_env.sh
+++ b/DAMASK_env.sh
@@ -46,8 +46,7 @@ if [ "x$FREE" != "x" ]; then
   ulimit -d unlimited 2>/dev/null \
   || 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)
+  || 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

From 91ec0f1454e048edfff820863332a00f9e00f71d Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Fri, 5 May 2017 21:43:45 +0200
Subject: [PATCH 05/32] [skip ci] updated version information after successful
 test of v2.0.1-691-gf6669a4

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

diff --git a/VERSION b/VERSION
index b69932daf..66fa2ba89 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-684-gb7a138e
+v2.0.1-691-gf6669a4

From 153f49fd1c6325224af45e0ad4d789c9a929694b Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Sat, 6 May 2017 02:10:02 +0200
Subject: [PATCH 06/32] [skip ci] updated version information after successful
 test of v2.0.1-692-g05bd760

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

diff --git a/VERSION b/VERSION
index b69932daf..9135e0cbb 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-684-gb7a138e
+v2.0.1-692-g05bd760

From 742d01765ee98f118b2262dfb2e3ee5d34915ca0 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Mon, 8 May 2017 23:52:07 +0200
Subject: [PATCH 07/32] now also running runtime test

---
 .gitlab-ci.yml | 48 +++++++++++++++++++++++++++++++-----------------
 1 file changed, 31 insertions(+), 17 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f472d2bb8..a40a90ec9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -14,6 +14,7 @@ stages:
   - compileAbaqus2016
   - compileAbaqus2017
   - example
+  - performance
   - createDocumentation
   - updateMaster
   - clean
@@ -425,25 +426,19 @@ AbaqusExample:
   only:
     - development
 
-##################################################################################################
-mergeIntoMaster: 
-  stage: updateMaster
+###################################################################################################
+SpectralRuntime:
+  stage: performance
   script:
+    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
     - 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 -s recursive -X ours                                                    # conflicts occur only for inconsistent state
-    - git push origin master                                                                        # master is now tested version and has updated VERSION file
-    - git checkout development
-    - git pull
-    - git merge master -s recursive -X ours -m "[skip ci] Merge branch 'master' into development"   # 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
-
+    - make clean spectral processing OPTIMIZATION=AGGRESSIVE
+    - cd $DAMASKROOT/PRIVATE/testing
+    - SpectralAll_runtime/test.py
+  except:
+    - master
+    - release
+ 
 ###################################################################################################
 AbaqusExp: 
   stage: createDocumentation
@@ -481,6 +476,25 @@ Spectral:
     - master
     - release
 
+##################################################################################################
+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 -s recursive -X ours                                                    # conflicts occur only for inconsistent state
+    - git push origin master                                                                        # master is now tested version and has updated VERSION file
+    - git checkout development
+    - git pull
+    - git merge master -s recursive -X ours -m "[skip ci] Merge branch 'master' into development"   # 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
+
 ###################################################################################################
 removeLock: 
   stage: clean

From eb7ef4d4eaa0bf90e94c9d8c343b9444cf4a1c1b Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Tue, 9 May 2017 13:50:21 +0200
Subject: [PATCH 08/32] runtime test now active

---
 PRIVATE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PRIVATE b/PRIVATE
index 02c172417..38c5d829e 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit 02c172417e5f170b8b00b1f4c4b65b7b7aeb310b
+Subproject commit 38c5d829ee336afec8335ead1d7a509e073f2d03

From 9ffdf81e30c38be47493b55a476690fd60a4c2e8 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Tue, 9 May 2017 20:13:08 +0200
Subject: [PATCH 09/32] [skip ci] updated version information after successful
 test of v2.0.1-700-geb7ef4d

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

diff --git a/VERSION b/VERSION
index 66fa2ba89..7f7d75b9a 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-691-gf6669a4
+v2.0.1-700-geb7ef4d

From 25865d4b54dd893fb96765d317dbb786441a1350 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Wed, 10 May 2017 07:40:26 +0200
Subject: [PATCH 10/32] using asinh (defined in F2008) instead of equivalent
 formulation using log

---
 src/plastic_isotropic.f90 | 17 ++++++-----------
 1 file changed, 6 insertions(+), 11 deletions(-)

diff --git a/src/plastic_isotropic.f90 b/src/plastic_isotropic.f90
index 5e3722e6a..a82b9c820 100644
--- a/src/plastic_isotropic.f90
+++ b/src/plastic_isotropic.f90
@@ -568,18 +568,13 @@ subroutine plastic_isotropic_dotState(Tstar_v,ipc,ip,el)
    if (dEq0(param(instance)%tausat_SinhFitA)) then
      saturation = param(instance)%tausat
    else
-     saturation = (  param(instance)%tausat &
-                   + ( log(  ( gamma_dot / param(instance)%tausat_SinhFitA&
-                               )**(1.0_pReal / param(instance)%tausat_SinhFitD)&
-                            + sqrt(  ( gamma_dot / param(instance)%tausat_SinhFitA &
-                                      )**(2.0_pReal / param(instance)%tausat_SinhFitD) &
-                                   + 1.0_pReal ) &
-                            ) & ! asinh(K) = ln(K + sqrt(K^2 +1))
+     saturation = param(instance)%tausat &
+                + asinh( (gamma_dot / param(instance)%tausat_SinhFitA&
+                         )**(1.0_pReal / param(instance)%tausat_SinhFitD)&
                        )**(1.0_pReal / param(instance)%tausat_SinhFitC) &
-                   / (  param(instance)%tausat_SinhFitB &
-                      * (gamma_dot / param(instance)%gdot0)**(1.0_pReal / param(instance)%n) &
-                      ) &
-                   )
+                   / ( param(instance)%tausat_SinhFitB &
+                       * (gamma_dot / param(instance)%gdot0)**(1.0_pReal / param(instance)%n) &
+                     )
    endif
    hardening = ( param(instance)%h0 + param(instance)%h0_slopeLnRate * log(gamma_dot) ) &
                * abs( 1.0_pReal - state(instance)%flowstress(of)/saturation )**param(instance)%a &

From 7e15885efdedf79e45100849c8a54e3d4a70fc37 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Thu, 11 May 2017 07:10:55 +0200
Subject: [PATCH 11/32] incorporating Yannicks changes

---
 PRIVATE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PRIVATE b/PRIVATE
index 38c5d829e..bc2d351db 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit 38c5d829ee336afec8335ead1d7a509e073f2d03
+Subproject commit bc2d351db9d0fdc08b879c63f2667af34a6aab8b

From 6d4bb38f11c5e122011a129391f06d16d711bbdf Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Thu, 11 May 2017 20:34:13 +0200
Subject: [PATCH 12/32] [skip ci] updated version information after successful
 test of v2.0.1-703-g7e15885

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

diff --git a/VERSION b/VERSION
index 7f7d75b9a..76e549d1d 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-700-geb7ef4d
+v2.0.1-703-g7e15885

From 5f90230dbd183c29ade98ac3180a4eb3756a7834 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Thu, 11 May 2017 21:02:10 +0200
Subject: [PATCH 13/32] last one cleans (for manual start after one stage
 failed)

---
 .gitlab-ci.yml | 13 +++++++------
 PRIVATE        |  2 +-
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a40a90ec9..3aa2bfb20 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,8 +21,8 @@ stages:
 
 ###################################################################################################
 before_script:
-  - if [ $(awk "/$CI_PIPELINE_ID/{print NR}" $HOME/GitLabCI.queue)x == 'x' ]; then echo $CI_PIPELINE_ID >> $HOME/GitLabCI.queue; fi
-  - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $HOME/GitLabCI.queue) -ne 1 ];do sleep 5m; done
+  - if [ $(awk "/$CI_PIPELINE_ID/{print NR}" $TESTROOT/GitLabCI.queue)x == 'x' ]; then echo $CI_PIPELINE_ID >> $TESTROOT/GitLabCI.queue; fi
+  - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $TESTROOT/GitLabCI.queue) -ne 1 ];do sleep 5m; done
   - source $DAMASKROOT/DAMASK_env.sh
   - cd $DAMASKROOT/PRIVATE/testing
 
@@ -36,7 +36,7 @@ variables:
   #================================================================================================
   # Shortcut names
   #================================================================================================
-  DAMASKROOT:                      "$HOME/GitLabCI_Pipeline_$CI_PIPELINE_ID/DAMASK"
+  DAMASKROOT:                      "$TESTROOT/GitLabCI_Pipeline_$CI_PIPELINE_ID/DAMASK"
 
   #================================================================================================
   # Names of module files to load
@@ -82,8 +82,8 @@ variables:
 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
+    - echo $CI_PIPELINE_ID >> $TESTROOT/GitLabCI.queue
+    - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $TESTROOT/GitLabCI.queue) -ne 1 ];do sleep 5m; done
   script:
     - mkdir -p $DAMASKROOT
     - cd $DAMASKROOT
@@ -492,6 +492,7 @@ mergeIntoMaster:
     - git pull
     - git merge master -s recursive -X ours -m "[skip ci] Merge branch 'master' into development"   # only possible conflict is in VERSION file
     - git push origin development                                                                   # development is unchanged (as master is based on it) but has updated VERSION file
+    - sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue
   only:
     - development
 
@@ -501,7 +502,7 @@ removeLock:
   before_script: 
     - echo 'Do nothing'
   when: always
-  script: sed -i "/$CI_PIPELINE_ID/d" $HOME/GitLabCI.queue
+  script: sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue
   except:
     - master
     - release
diff --git a/PRIVATE b/PRIVATE
index bc2d351db..3ba3671e3 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit bc2d351db9d0fdc08b879c63f2667af34a6aab8b
+Subproject commit 3ba3671e3d0ec9ac1dcc6a5521822b4828574581

From 464fafa736471e400a054c3f2afa1b49ee295d12 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Fri, 12 May 2017 08:07:50 +0200
Subject: [PATCH 14/32] [skip ci] updated version information after successful
 test of v2.0.1-705-g5f90230

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

diff --git a/VERSION b/VERSION
index 76e549d1d..239d87251 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-703-g7e15885
+v2.0.1-705-g5f90230

From c7632dcf427ad8a3703d4d48fb4291f55561d2bb Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Fri, 12 May 2017 09:39:33 +0200
Subject: [PATCH 15/32] storing documentation and results of runtime tests

---
 .gitlab-ci.yml | 33 ++++++++++++++++++++++++++++++---
 PRIVATE        |  2 +-
 2 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3aa2bfb20..b523aaf34 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,8 +16,10 @@ stages:
   - example
   - performance
   - createDocumentation
+  - saveDocumentation
   - updateMaster
   - clean
+  - releaseLock
 
 ###################################################################################################
 before_script:
@@ -92,6 +94,7 @@ checkout:
     - git submodule update --init
     - source DAMASK_env.sh
     - make processing
+    - mkdir $BACKUP/$CI_COMMIT_SHA
   except:
     - master
     - release
@@ -434,7 +437,7 @@ SpectralRuntime:
     - cd $DAMASKROOT
     - make clean spectral processing OPTIMIZATION=AGGRESSIVE
     - cd $DAMASKROOT/PRIVATE/testing
-    - SpectralAll_runtime/test.py
+    - SpectralAll_runtime/test.py -d $TESTROOT
   except:
     - master
     - release
@@ -476,6 +479,19 @@ Spectral:
     - master
     - release
 
+##################################################################################################
+mergeIntoMaster: 
+  stage: saveDocumentation
+  script:
+    - cp $TESTROOT/time.txt $BACKUP/$CI_COMMIT_SHA
+    - mv $TESTROOT/time.png $BACKUP/$CI_COMMIT_SHA
+    - cp $TESTROOT/time.txt $BACKUP/$CI_COMMIT_SHA
+    - mv $TESTROOT/time.png $BACKUP/$CI_COMMIT_SHA
+    - mv $DAMASKROOT/PRIVATE/documenting/DAMASK_* $BACKUP/$CI_COMMIT_SHA/
+  except:
+    - master
+    - release
+
 ##################################################################################################
 mergeIntoMaster: 
   stage: updateMaster
@@ -492,13 +508,24 @@ mergeIntoMaster:
     - git pull
     - git merge master -s recursive -X ours -m "[skip ci] Merge branch 'master' into development"   # 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
-    - sed -i "/$CI_PIPELINE_ID/d" $TESTROOT/GitLabCI.queue
   only:
     - development
 
 ###################################################################################################
-removeLock: 
+removeData: 
   stage: clean
+  before_script: 
+    - echo 'Do nothing'
+  script:
+    - rm -rf $TESTROOT/GitLabCI_Pipeline_$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
+  except:
+    - master
+    - release
+
+###################################################################################################
+removeLock: 
+  stage: releaseLock
   before_script: 
     - echo 'Do nothing'
   when: always
diff --git a/PRIVATE b/PRIVATE
index 3ba3671e3..a629ee95c 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit 3ba3671e3d0ec9ac1dcc6a5521822b4828574581
+Subproject commit a629ee95c53924f2da16e8981855f9abcc1d50f7

From 393e7d58878dfdd04c14195c849f4428d2f30c90 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Fri, 12 May 2017 18:28:28 +0200
Subject: [PATCH 16/32] [skip ci] updated version information after successful
 test of v2.0.1-707-gc7632dc

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

diff --git a/VERSION b/VERSION
index 239d87251..a452662a1 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-705-g5f90230
+v2.0.1-707-gc7632dc

From 1dfe6972652ab8b671ec8fb4821903d623d72c22 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Sat, 13 May 2017 03:02:19 +0200
Subject: [PATCH 17/32] [skip ci] updated version information after successful
 test of v2.0.1-715-g5d58752

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

diff --git a/VERSION b/VERSION
index a452662a1..0b350382b 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-707-gc7632dc
+v2.0.1-715-g5d58752

From 4437f7900033c574201944c519b8683453ba66b7 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Sat, 13 May 2017 16:27:11 +0200
Subject: [PATCH 18/32] wrong name cause 'backup' stage not to run

---
 .gitlab-ci.yml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b523aaf34..2701edcc0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -94,7 +94,6 @@ checkout:
     - git submodule update --init
     - source DAMASK_env.sh
     - make processing
-    - mkdir $BACKUP/$CI_COMMIT_SHA
   except:
     - master
     - release
@@ -480,14 +479,15 @@ Spectral:
     - release
 
 ##################################################################################################
-mergeIntoMaster: 
+backupData: 
   stage: saveDocumentation
   script:
-    - cp $TESTROOT/time.txt $BACKUP/$CI_COMMIT_SHA
-    - mv $TESTROOT/time.png $BACKUP/$CI_COMMIT_SHA
-    - cp $TESTROOT/time.txt $BACKUP/$CI_COMMIT_SHA
-    - mv $TESTROOT/time.png $BACKUP/$CI_COMMIT_SHA
-    - mv $DAMASKROOT/PRIVATE/documenting/DAMASK_* $BACKUP/$CI_COMMIT_SHA/
+    - mkdir $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}
+    - cp $TESTROOT/time.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - mv $TESTROOT/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - cp $TESTROOT/time.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - mv $TESTROOT/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - mv $DAMASKROOT/PRIVATE/documenting/DAMASK_* $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
   except:
     - master
     - release
@@ -512,9 +512,9 @@ mergeIntoMaster:
     - development
 
 ###################################################################################################
-removeData: 
+removeData:
   stage: clean
-  before_script: 
+  before_script:
     - echo 'Do nothing'
   script:
     - rm -rf $TESTROOT/GitLabCI_Pipeline_$CI_PIPELINE_ID

From eeed5c76417a14fe3431135c13f0b6d6be2d2050 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Sat, 13 May 2017 22:03:55 +0200
Subject: [PATCH 19/32] tried to adjust to Cereceda IJP paper

---
 .../Phase_DisloUCLA_Tungsten.config           | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/examples/ConfigFiles/Phase_DisloUCLA_Tungsten.config b/examples/ConfigFiles/Phase_DisloUCLA_Tungsten.config
index 6d7dd6859..d69a4b82a 100644
--- a/examples/ConfigFiles/Phase_DisloUCLA_Tungsten.config
+++ b/examples/ConfigFiles/Phase_DisloUCLA_Tungsten.config
@@ -29,21 +29,20 @@ SolidSolutionStrength 0.0           # Strength due to elements in solid solution
 #per family
 Nslip               12  0        
 slipburgers         2.72e-10                # Burgers vector of slip system [m]
-rhoedge0            1.0e12                  # Initial edge dislocation density [m/m**3] 1.0e12
+rhoedge0            1.0e12                  # Initial edge dislocation density [m/m**3]
 rhoedgedip0         1.0                     # Initial edged dipole dislocation density [m/m**3]
-Qedge               2.725e-19               # Activation energy for dislocation glide [J]
-v0                  3693.4                  # Initial glide velocity [m/s] 1.0e-4 (kmC 3693.4 ; 755.59)
+Qedge               2.61154e-19             # Activation energy for dislocation glide [J], 1.63 eV
+v0                  1                       # Initial glide velocity [m/s]
 p_slip              0.86                    # p-exponent in glide velocity
 q_slip              1.69                    # q-exponent in glide velocity
 tau_peierls         2.03e9                  # peierls stress [Pa]
 
 #mobility law
-kink_height	    2.567e-10                   # kink height sqrt(6)/3*lattice_parameter [m]	    
-omega		    9.1e11	                        # attemp frequency (from kMC paper) [s^(-1)]	    
+kink_height	    2.567e-10                   # kink height sqrt(6)/3*lattice_parameter [m]
+omega		        9.1e11	                    # attemp frequency (from kMC paper) [s^(-1)]
 kink_width	    29.95e-10                   # kink pair width ~ 11 b (kMC paper) [m]
-dislolength	    78.0e-10	                  # dislocation length (ideally lambda) [m] initial value 25b
-friction_coeff      8.3e-5                  # friction coeff. B (kMC)  [Pa*s]  
-#
+dislolength	    78e-10	                    # dislocation length (ideally lambda) [m] initial value 11b
+friction_coeff  8.3e-5                      # friction coeff. B [Pa*s]
 
 #hardening
 dipoleformationfactor 0                     # to have hardening due to dipole formation off
@@ -52,5 +51,5 @@ D0                  4.0e-5                  # Vacancy diffusion prefactor [m**2/
 Qsd                 4.5e-19                 # Activation energy for climb [J]
 Catomicvolume       1.0                     # Adj. parameter controlling the atomic volume [in b]
 Cedgedipmindistance 1.0                     # Adj. parameter controlling the minimum dipole distance [in b]
-interaction_slipslip     0.0625 0.0625 0.72 0.05 0.09 0.06 # Queyreau 
-#nonschmid_coefficients   0 0.56 0.75 0 0 0 #??????????????
+interaction_slipslip     0.009 0.009 0.72 0.05 009 006
+nonschmid_coefficients   0.938 0.71 4.43 0.0 0.0 0.0

From 4bcc57add7ead54ad18f02d093baf9aad8d1fd1b Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Sun, 14 May 2017 08:48:54 +0200
Subject: [PATCH 20/32] typo, tried to copy time data again instead of memory
 data

---
 .gitlab-ci.yml | 4 ++--
 PRIVATE        | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2701edcc0..6eb527fbb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -485,8 +485,8 @@ backupData:
     - mkdir $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}
     - cp $TESTROOT/time.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
     - mv $TESTROOT/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
-    - cp $TESTROOT/time.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
-    - mv $TESTROOT/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - cp $TESTROOT/memory.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - mv $TESTROOT/memory.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
     - mv $DAMASKROOT/PRIVATE/documenting/DAMASK_* $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
   except:
     - master
diff --git a/PRIVATE b/PRIVATE
index a629ee95c..19a53f622 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit a629ee95c53924f2da16e8981855f9abcc1d50f7
+Subproject commit 19a53f6229603aeafb2466b58679a1cd04fc0142

From 4f3b0e4c34fb2503b9fda652d348884e010621a8 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Mon, 15 May 2017 06:45:53 +0200
Subject: [PATCH 21/32] symlinks should not be part of the repository

---
 src/DAMASK_marc2011.f90   | 1 -
 src/DAMASK_marc2012.f90   | 1 -
 src/DAMASK_marc2013.1.f90 | 1 -
 src/DAMASK_marc2013.f90   | 1 -
 src/DAMASK_marc2014.2.f90 | 1 -
 src/DAMASK_marc2014.f90   | 1 -
 src/DAMASK_marc2015.f90   | 1 -
 7 files changed, 7 deletions(-)
 delete mode 120000 src/DAMASK_marc2011.f90
 delete mode 120000 src/DAMASK_marc2012.f90
 delete mode 120000 src/DAMASK_marc2013.1.f90
 delete mode 120000 src/DAMASK_marc2013.f90
 delete mode 120000 src/DAMASK_marc2014.2.f90
 delete mode 120000 src/DAMASK_marc2014.f90
 delete mode 120000 src/DAMASK_marc2015.f90

diff --git a/src/DAMASK_marc2011.f90 b/src/DAMASK_marc2011.f90
deleted file mode 120000
index 2c5bec706..000000000
--- a/src/DAMASK_marc2011.f90
+++ /dev/null
@@ -1 +0,0 @@
-DAMASK_marc.f90
\ No newline at end of file
diff --git a/src/DAMASK_marc2012.f90 b/src/DAMASK_marc2012.f90
deleted file mode 120000
index 2c5bec706..000000000
--- a/src/DAMASK_marc2012.f90
+++ /dev/null
@@ -1 +0,0 @@
-DAMASK_marc.f90
\ No newline at end of file
diff --git a/src/DAMASK_marc2013.1.f90 b/src/DAMASK_marc2013.1.f90
deleted file mode 120000
index 2c5bec706..000000000
--- a/src/DAMASK_marc2013.1.f90
+++ /dev/null
@@ -1 +0,0 @@
-DAMASK_marc.f90
\ No newline at end of file
diff --git a/src/DAMASK_marc2013.f90 b/src/DAMASK_marc2013.f90
deleted file mode 120000
index 2c5bec706..000000000
--- a/src/DAMASK_marc2013.f90
+++ /dev/null
@@ -1 +0,0 @@
-DAMASK_marc.f90
\ No newline at end of file
diff --git a/src/DAMASK_marc2014.2.f90 b/src/DAMASK_marc2014.2.f90
deleted file mode 120000
index 2c5bec706..000000000
--- a/src/DAMASK_marc2014.2.f90
+++ /dev/null
@@ -1 +0,0 @@
-DAMASK_marc.f90
\ No newline at end of file
diff --git a/src/DAMASK_marc2014.f90 b/src/DAMASK_marc2014.f90
deleted file mode 120000
index 2c5bec706..000000000
--- a/src/DAMASK_marc2014.f90
+++ /dev/null
@@ -1 +0,0 @@
-DAMASK_marc.f90
\ No newline at end of file
diff --git a/src/DAMASK_marc2015.f90 b/src/DAMASK_marc2015.f90
deleted file mode 120000
index 2c5bec706..000000000
--- a/src/DAMASK_marc2015.f90
+++ /dev/null
@@ -1 +0,0 @@
-DAMASK_marc.f90
\ No newline at end of file

From 73040c91c56be53d2b9022310f8e5f8087cba9b5 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Mon, 15 May 2017 07:42:48 +0200
Subject: [PATCH 22/32] comparison was done twice

---
 lib/damask/test/test.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/damask/test/test.py b/lib/damask/test/test.py
index 1bb80a939..d67b31f72 100644
--- a/lib/damask/test/test.py
+++ b/lib/damask/test/test.py
@@ -99,7 +99,6 @@ class Test():
             self.run(variant)
 
           self.postprocess(variant)
-          self.compare(variant)
           
           if self.options.update:
             if self.update(variant) != 0: logging.critical('update for "{}" failed.'.format(name))

From 9724c95f58de5a8f6a82ef3843735871749bc25d Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Mon, 15 May 2017 15:23:16 +0200
Subject: [PATCH 23/32] [skip ci] updated version information after successful
 test of v2.0.1-719-g4f3b0e4

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

diff --git a/VERSION b/VERSION
index 0b350382b..e39f391eb 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-715-g5d58752
+v2.0.1-719-g4f3b0e4

From c813e98d22df5e742f5f85614b21e588c258b140 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Mon, 15 May 2017 17:40:49 +0200
Subject: [PATCH 24/32] clean root directory, symbolic links for transition
 compatibility

---
 DAMASK_env.csh     |  66 +----------------------------
 DAMASK_env.sh      | 103 +--------------------------------------------
 DAMASK_env.zsh     |  91 +--------------------------------------
 env/DAMASK_env.csh |  65 ++++++++++++++++++++++++++++
 env/DAMASK_env.sh  | 102 ++++++++++++++++++++++++++++++++++++++++++++
 env/DAMASK_env.zsh |  90 +++++++++++++++++++++++++++++++++++++++
 6 files changed, 260 insertions(+), 257 deletions(-)
 mode change 100644 => 120000 DAMASK_env.csh
 mode change 100644 => 120000 DAMASK_env.sh
 mode change 100644 => 120000 DAMASK_env.zsh
 create mode 100644 env/DAMASK_env.csh
 create mode 100644 env/DAMASK_env.sh
 create mode 100644 env/DAMASK_env.zsh

diff --git a/DAMASK_env.csh b/DAMASK_env.csh
deleted file mode 100644
index 81d4de421..000000000
--- a/DAMASK_env.csh
+++ /dev/null
@@ -1,65 +0,0 @@
-# sets up an environment for DAMASK on tcsh
-# usage:  source DAMASK_env.csh
-
-set CALLED=($_)
-set DIRNAME=`dirname $CALLED[2]`
-set DAMASK_ROOT=`python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" $DIRNAME`
-
-source $DAMASK_ROOT/CONFIG
-
-# if DAMASK_BIN is present and not in $PATH, add it
-if ( $?DAMASK_BIN) then
-  set MATCH=`echo :${PATH}: | grep ${DAMASK_BIN}:`
-  if ( "x$MATCH" == "x" ) then
-    set PATH=${DAMASK_BIN}:${PATH}
-  endif
-endif
-
-set SOLVER=`which DAMASK_spectral`                                                          
-set PROCESSING=`which postResults`                                                          
-if ( "x$DAMASK_NUM_THREADS" == "x" ) then                                                                  
-  set DAMASK_NUM_THREADS=1
-endif
-
-# according to http://software.intel.com/en-us/forums/topic/501500
-# this seems to make sense for the stack size
-if ( `which free` != "free: Command not found." ) then
-  set freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'`
-  set heap=` expr $freeMem                       / 2`
-  set stack=`expr $freeMem / $DAMASK_NUM_THREADS / 2`
-  # http://superuser.com/questions/220059/what-parameters-has-ulimit             
-  limit datasize  $heap  # maximum  heap size (kB)
-  limit stacksize $stack # maximum stack size (kB)
-endif
-if ( `limit | grep memoryuse` != "" ) then
-  limit memoryuse  unlimited  # maximum physical memory size
-endif
-if ( `limit | grep vmemoryuse` != "" ) then
-  limit vmemoryuse unlimited  # maximum virtual memory size
-endif
-
-# disable output in case of scp
-if ( $?prompt ) then
-  echo ''
-  echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK
-  echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
-  echo https://damask.mpie.de
-  echo
-  echo Using environment with ...
-  echo "DAMASK             $DAMASK_ROOT"
-  echo "Spectral Solver    $SOLVER" 
-  echo "Post Processing    $PROCESSING"
-  echo "Multithreading     DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
-  if ( $?PETSC_DIR) then
-    echo "PETSc location     $PETSC_DIR"
-  endif
-  if ( $?MSC_ROOT) then
-    echo "MSC.Marc/Mentat    $MSC_ROOT"
-  endif
-  echo
-  echo `limit datasize`
-  echo `limit stacksize`
-endif
-
-setenv DAMASK_NUM_THREADS $DAMASK_NUM_THREADS
-setenv PYTHONPATH $DAMASK_ROOT/lib:$PYTHONPATH
diff --git a/DAMASK_env.csh b/DAMASK_env.csh
new file mode 120000
index 000000000..4535015d8
--- /dev/null
+++ b/DAMASK_env.csh
@@ -0,0 +1 @@
+env/DAMASK_env.csh
\ No newline at end of file
diff --git a/DAMASK_env.sh b/DAMASK_env.sh
deleted file mode 100644
index 264ae9c94..000000000
--- a/DAMASK_env.sh
+++ /dev/null
@@ -1,102 +0,0 @@
-# sets up an environment for DAMASK on bash
-# usage:  source DAMASK_env.sh
-
-
-if [ "$OSTYPE" == "linux-gnu" ] || [ "$OSTYPE" == 'linux' ]; then
-  DAMASK_ROOT=$(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$(dirname $BASH_SOURCE)")
-else
-  [[ "${BASH_SOURCE::1}" == "/" ]] && BASE="" || BASE="$(pwd)/"
-  STAT=$(stat "$(dirname $BASE$BASH_SOURCE)")
-  DAMASK_ROOT=${STAT##* }
-fi
-
-# shorthand command to change to DAMASK_ROOT directory
-eval "function damask() { cd $DAMASK_ROOT; }"
-
-# defining set() allows to source the same file for tcsh and bash, with and without space around =
-set() {
-    export $1$2$3
- }
-source $DAMASK_ROOT/CONFIG
-unset -f set
-
-# add DAMASK_BIN if present but not yet in $PATH
-if [[ "x$DAMASK_BIN" != "x" && ! $(echo ":$PATH:" | grep $DAMASK_BIN:) ]]; then
-  export PATH=$DAMASK_BIN:$PATH
-fi
-
-SOLVER=$(which DAMASK_spectral || true 2>/dev/null)
-if [ "x$SOLVER" == "x" ]; then
-  SOLVER='Not found!'
-fi
-PROCESSING=$(which postResults || true 2>/dev/null)
-if [ "x$PROCESSING" == "x" ]; then
-  PROCESSING='Not found!'
-fi
-if [ "x$DAMASK_NUM_THREADS" == "x" ]; then
-  DAMASK_NUM_THREADS=1
-fi
-
-# according to http://software.intel.com/en-us/forums/topic/501500
-# this seems to make sense for the stack size
-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 unlimited 2>/dev/null \
-  || ulimit -d $(expr $freeMem                       / 2)  2>/dev/null # maximum  heap size (kB)
-  ulimit -s unlimited 2>/dev/null \
-  || ulimit -s $(expr $freeMem / $DAMASK_NUM_THREADS / 2)  2>/dev/null # maximum stack size (kB)
-fi
-ulimit -v unlimited   2>/dev/null # maximum virtual memory size
-ulimit -m unlimited   2>/dev/null # maximum physical memory size
-
-# disable output in case of scp
-if [ ! -z "$PS1" ]; then
-  echo
-  echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK
-  echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
-  echo https://damask.mpie.de
-  echo
-  echo Using environment with ...
-  echo "DAMASK             $DAMASK_ROOT"
-  echo "Spectral Solver    $SOLVER" 
-  echo "Post Processing    $PROCESSING"
-  echo "Multithreading     DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
-  if [ "x$PETSC_DIR"   != "x" ]; then
-    echo "PETSc location     $PETSC_DIR"
-    [[ $(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR") == $PETSC_DIR ]] \
-    || echo "               ~~> "$(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR")
-  fi
-  echo "MSC.Marc/Mentat    $MSC_ROOT"
-  echo
-  echo -n "heap  size         "
-   [[ "$(ulimit -d)" == "unlimited" ]] \
-   && echo "unlimited" \
-   || echo $(python -c \
-          "import math; \
-           size=$(( 1024*$(ulimit -d) )); \
-           print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
-           ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
-  echo -n "stack size         "
-   [[ "$(ulimit -s)" == "unlimited" ]] \
-   && echo "unlimited" \
-   || echo $(python -c \
-          "import math; \
-           size=$(( 1024*$(ulimit -s) )); \
-           print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
-           ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
-fi
-
-export DAMASK_NUM_THREADS
-export PYTHONPATH=$DAMASK_ROOT/lib:$PYTHONPATH
-
-for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN; do
-  unset "${var}"
-done
-for var in DAMASK MSC; do
-  unset "${var}_ROOT"
-done
-for var in ABAQUS MARC; do
-  unset "${var}_VERSION"
-done
diff --git a/DAMASK_env.sh b/DAMASK_env.sh
new file mode 120000
index 000000000..e49b7df7c
--- /dev/null
+++ b/DAMASK_env.sh
@@ -0,0 +1 @@
+env/DAMASK_env.sh
\ No newline at end of file
diff --git a/DAMASK_env.zsh b/DAMASK_env.zsh
deleted file mode 100644
index 9098352bf..000000000
--- a/DAMASK_env.zsh
+++ /dev/null
@@ -1,90 +0,0 @@
-# sets up an environment for DAMASK on zsh
-# usage:  source DAMASK_env.zsh
-
-DAMASK_ROOT=${0:a:h}
-
-# shorthand command to change to DAMASK_ROOT directory
-eval "function damask() { cd $DAMASK_ROOT; }"
-
-# defining set() allows to source the same file for tcsh and zsh, with and without space around =
-set() {
-    export $1$2$3
- }
-source $DAMASK_ROOT/CONFIG
-unset -f set
-
-# add DAMASK_BIN if present but not yet in $PATH
-MATCH=`echo ":$PATH:" | grep $DAMASK_BIN:`
-if [[ ( "x$DAMASK_BIN" != "x" ) && ( "x$MATCH" = "x" ) ]]; then
-  export PATH=$DAMASK_BIN:$PATH
-fi
-
-SOLVER=`which DAMASK_spectral || True 2>/dev/null`
-PROCESSING=`which postResults || True 2>/dev/null`
-if [ "x$DAMASK_NUM_THREADS" = "x" ]; then
-  DAMASK_NUM_THREADS=1
-fi
-
-# according to http://software.intel.com/en-us/forums/topic/501500
-# this seems to make sense for the stack size
-if [ "`which free 2>/dev/null`" != "free not found" ]; 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 -s `expr $freeMem / $DAMASK_NUM_THREADS / 2` 2>/dev/null # maximum stack size (kB)
-fi
-ulimit -v unlimited   2>/dev/null # maximum virtual memory size
-ulimit -m unlimited   2>/dev/null # maximum physical memory size
-
-# disable output in case of scp
-if [ ! -z "$PS1" ]; then
-  echo
-  echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK
-  echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
-  echo https://damask.mpie.de
-  echo
-  echo "Using environment with ..."
-  echo "DAMASK             $DAMASK_ROOT"
-  echo "Spectral Solver    $SOLVER" 
-  echo "Post Processing    $PROCESSING"
-  echo "Multithreading     DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
-  if [ "x$PETSC_DIR"   != "x" ]; then
-    echo "PETSc location     $PETSC_DIR"
-    [[ $(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR") == $PETSC_DIR ]] \
-    || echo "               ~~> "$(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR")
-  fi
-  [[ "x$PETSC_ARCH"  == "x" ]] \
-  || echo "PETSc architecture $PETSC_ARCH"
-  echo "MSC.Marc/Mentat    $MSC_ROOT"
-  echo
-  echo -n "heap  size         "
-   [[ "$(ulimit -d)" == "unlimited" ]] \
-   && echo "unlimited" \
-   || echo $(python -c \
-          "import math; \
-           size=$(( 1024*$(ulimit -d) )); \
-           print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
-           ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
-  echo -n "stack size         "
-   [[ "$(ulimit -s)" == "unlimited" ]] \
-   && echo "unlimited" \
-   || echo $(python -c \
-          "import math; \
-           size=$(( 1024*$(ulimit -s) )); \
-           print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
-           ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
-fi
-
-export DAMASK_NUM_THREADS
-export PYTHONPATH=$DAMASK_ROOT/lib:$PYTHONPATH
-
-for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN MATCH; do
-  unset "${var}"
-done
-for var in DAMASK MSC; do
-  unset "${var}_ROOT"
-done
-for var in ABAQUS MARC; do
-  unset "${var}_VERSION"
-done
diff --git a/DAMASK_env.zsh b/DAMASK_env.zsh
new file mode 120000
index 000000000..22da3bd4d
--- /dev/null
+++ b/DAMASK_env.zsh
@@ -0,0 +1 @@
+env/DAMASK_env.zsh
\ No newline at end of file
diff --git a/env/DAMASK_env.csh b/env/DAMASK_env.csh
new file mode 100644
index 000000000..81d4de421
--- /dev/null
+++ b/env/DAMASK_env.csh
@@ -0,0 +1,65 @@
+# sets up an environment for DAMASK on tcsh
+# usage:  source DAMASK_env.csh
+
+set CALLED=($_)
+set DIRNAME=`dirname $CALLED[2]`
+set DAMASK_ROOT=`python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" $DIRNAME`
+
+source $DAMASK_ROOT/CONFIG
+
+# if DAMASK_BIN is present and not in $PATH, add it
+if ( $?DAMASK_BIN) then
+  set MATCH=`echo :${PATH}: | grep ${DAMASK_BIN}:`
+  if ( "x$MATCH" == "x" ) then
+    set PATH=${DAMASK_BIN}:${PATH}
+  endif
+endif
+
+set SOLVER=`which DAMASK_spectral`                                                          
+set PROCESSING=`which postResults`                                                          
+if ( "x$DAMASK_NUM_THREADS" == "x" ) then                                                                  
+  set DAMASK_NUM_THREADS=1
+endif
+
+# according to http://software.intel.com/en-us/forums/topic/501500
+# this seems to make sense for the stack size
+if ( `which free` != "free: Command not found." ) then
+  set freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'`
+  set heap=` expr $freeMem                       / 2`
+  set stack=`expr $freeMem / $DAMASK_NUM_THREADS / 2`
+  # http://superuser.com/questions/220059/what-parameters-has-ulimit             
+  limit datasize  $heap  # maximum  heap size (kB)
+  limit stacksize $stack # maximum stack size (kB)
+endif
+if ( `limit | grep memoryuse` != "" ) then
+  limit memoryuse  unlimited  # maximum physical memory size
+endif
+if ( `limit | grep vmemoryuse` != "" ) then
+  limit vmemoryuse unlimited  # maximum virtual memory size
+endif
+
+# disable output in case of scp
+if ( $?prompt ) then
+  echo ''
+  echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK
+  echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
+  echo https://damask.mpie.de
+  echo
+  echo Using environment with ...
+  echo "DAMASK             $DAMASK_ROOT"
+  echo "Spectral Solver    $SOLVER" 
+  echo "Post Processing    $PROCESSING"
+  echo "Multithreading     DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
+  if ( $?PETSC_DIR) then
+    echo "PETSc location     $PETSC_DIR"
+  endif
+  if ( $?MSC_ROOT) then
+    echo "MSC.Marc/Mentat    $MSC_ROOT"
+  endif
+  echo
+  echo `limit datasize`
+  echo `limit stacksize`
+endif
+
+setenv DAMASK_NUM_THREADS $DAMASK_NUM_THREADS
+setenv PYTHONPATH $DAMASK_ROOT/lib:$PYTHONPATH
diff --git a/env/DAMASK_env.sh b/env/DAMASK_env.sh
new file mode 100644
index 000000000..264ae9c94
--- /dev/null
+++ b/env/DAMASK_env.sh
@@ -0,0 +1,102 @@
+# sets up an environment for DAMASK on bash
+# usage:  source DAMASK_env.sh
+
+
+if [ "$OSTYPE" == "linux-gnu" ] || [ "$OSTYPE" == 'linux' ]; then
+  DAMASK_ROOT=$(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$(dirname $BASH_SOURCE)")
+else
+  [[ "${BASH_SOURCE::1}" == "/" ]] && BASE="" || BASE="$(pwd)/"
+  STAT=$(stat "$(dirname $BASE$BASH_SOURCE)")
+  DAMASK_ROOT=${STAT##* }
+fi
+
+# shorthand command to change to DAMASK_ROOT directory
+eval "function damask() { cd $DAMASK_ROOT; }"
+
+# defining set() allows to source the same file for tcsh and bash, with and without space around =
+set() {
+    export $1$2$3
+ }
+source $DAMASK_ROOT/CONFIG
+unset -f set
+
+# add DAMASK_BIN if present but not yet in $PATH
+if [[ "x$DAMASK_BIN" != "x" && ! $(echo ":$PATH:" | grep $DAMASK_BIN:) ]]; then
+  export PATH=$DAMASK_BIN:$PATH
+fi
+
+SOLVER=$(which DAMASK_spectral || true 2>/dev/null)
+if [ "x$SOLVER" == "x" ]; then
+  SOLVER='Not found!'
+fi
+PROCESSING=$(which postResults || true 2>/dev/null)
+if [ "x$PROCESSING" == "x" ]; then
+  PROCESSING='Not found!'
+fi
+if [ "x$DAMASK_NUM_THREADS" == "x" ]; then
+  DAMASK_NUM_THREADS=1
+fi
+
+# according to http://software.intel.com/en-us/forums/topic/501500
+# this seems to make sense for the stack size
+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 unlimited 2>/dev/null \
+  || ulimit -d $(expr $freeMem                       / 2)  2>/dev/null # maximum  heap size (kB)
+  ulimit -s unlimited 2>/dev/null \
+  || ulimit -s $(expr $freeMem / $DAMASK_NUM_THREADS / 2)  2>/dev/null # maximum stack size (kB)
+fi
+ulimit -v unlimited   2>/dev/null # maximum virtual memory size
+ulimit -m unlimited   2>/dev/null # maximum physical memory size
+
+# disable output in case of scp
+if [ ! -z "$PS1" ]; then
+  echo
+  echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK
+  echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
+  echo https://damask.mpie.de
+  echo
+  echo Using environment with ...
+  echo "DAMASK             $DAMASK_ROOT"
+  echo "Spectral Solver    $SOLVER" 
+  echo "Post Processing    $PROCESSING"
+  echo "Multithreading     DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
+  if [ "x$PETSC_DIR"   != "x" ]; then
+    echo "PETSc location     $PETSC_DIR"
+    [[ $(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR") == $PETSC_DIR ]] \
+    || echo "               ~~> "$(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR")
+  fi
+  echo "MSC.Marc/Mentat    $MSC_ROOT"
+  echo
+  echo -n "heap  size         "
+   [[ "$(ulimit -d)" == "unlimited" ]] \
+   && echo "unlimited" \
+   || echo $(python -c \
+          "import math; \
+           size=$(( 1024*$(ulimit -d) )); \
+           print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
+           ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
+  echo -n "stack size         "
+   [[ "$(ulimit -s)" == "unlimited" ]] \
+   && echo "unlimited" \
+   || echo $(python -c \
+          "import math; \
+           size=$(( 1024*$(ulimit -s) )); \
+           print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
+           ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
+fi
+
+export DAMASK_NUM_THREADS
+export PYTHONPATH=$DAMASK_ROOT/lib:$PYTHONPATH
+
+for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN; do
+  unset "${var}"
+done
+for var in DAMASK MSC; do
+  unset "${var}_ROOT"
+done
+for var in ABAQUS MARC; do
+  unset "${var}_VERSION"
+done
diff --git a/env/DAMASK_env.zsh b/env/DAMASK_env.zsh
new file mode 100644
index 000000000..9098352bf
--- /dev/null
+++ b/env/DAMASK_env.zsh
@@ -0,0 +1,90 @@
+# sets up an environment for DAMASK on zsh
+# usage:  source DAMASK_env.zsh
+
+DAMASK_ROOT=${0:a:h}
+
+# shorthand command to change to DAMASK_ROOT directory
+eval "function damask() { cd $DAMASK_ROOT; }"
+
+# defining set() allows to source the same file for tcsh and zsh, with and without space around =
+set() {
+    export $1$2$3
+ }
+source $DAMASK_ROOT/CONFIG
+unset -f set
+
+# add DAMASK_BIN if present but not yet in $PATH
+MATCH=`echo ":$PATH:" | grep $DAMASK_BIN:`
+if [[ ( "x$DAMASK_BIN" != "x" ) && ( "x$MATCH" = "x" ) ]]; then
+  export PATH=$DAMASK_BIN:$PATH
+fi
+
+SOLVER=`which DAMASK_spectral || True 2>/dev/null`
+PROCESSING=`which postResults || True 2>/dev/null`
+if [ "x$DAMASK_NUM_THREADS" = "x" ]; then
+  DAMASK_NUM_THREADS=1
+fi
+
+# according to http://software.intel.com/en-us/forums/topic/501500
+# this seems to make sense for the stack size
+if [ "`which free 2>/dev/null`" != "free not found" ]; 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 -s `expr $freeMem / $DAMASK_NUM_THREADS / 2` 2>/dev/null # maximum stack size (kB)
+fi
+ulimit -v unlimited   2>/dev/null # maximum virtual memory size
+ulimit -m unlimited   2>/dev/null # maximum physical memory size
+
+# disable output in case of scp
+if [ ! -z "$PS1" ]; then
+  echo
+  echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK
+  echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
+  echo https://damask.mpie.de
+  echo
+  echo "Using environment with ..."
+  echo "DAMASK             $DAMASK_ROOT"
+  echo "Spectral Solver    $SOLVER" 
+  echo "Post Processing    $PROCESSING"
+  echo "Multithreading     DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
+  if [ "x$PETSC_DIR"   != "x" ]; then
+    echo "PETSc location     $PETSC_DIR"
+    [[ $(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR") == $PETSC_DIR ]] \
+    || echo "               ~~> "$(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR")
+  fi
+  [[ "x$PETSC_ARCH"  == "x" ]] \
+  || echo "PETSc architecture $PETSC_ARCH"
+  echo "MSC.Marc/Mentat    $MSC_ROOT"
+  echo
+  echo -n "heap  size         "
+   [[ "$(ulimit -d)" == "unlimited" ]] \
+   && echo "unlimited" \
+   || echo $(python -c \
+          "import math; \
+           size=$(( 1024*$(ulimit -d) )); \
+           print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
+           ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
+  echo -n "stack size         "
+   [[ "$(ulimit -s)" == "unlimited" ]] \
+   && echo "unlimited" \
+   || echo $(python -c \
+          "import math; \
+           size=$(( 1024*$(ulimit -s) )); \
+           print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
+           ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
+fi
+
+export DAMASK_NUM_THREADS
+export PYTHONPATH=$DAMASK_ROOT/lib:$PYTHONPATH
+
+for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN MATCH; do
+  unset "${var}"
+done
+for var in DAMASK MSC; do
+  unset "${var}_ROOT"
+done
+for var in ABAQUS MARC; do
+  unset "${var}_VERSION"
+done

From 1f1a1826a131e85a44306c79333d10c856494cc9 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Mon, 15 May 2017 21:53:25 +0200
Subject: [PATCH 25/32] string length was wrong, IO_warning now also with new
 style

---
 src/IO.f90 | 93 ++++++++++++++++++++++++------------------------------
 1 file changed, 42 insertions(+), 51 deletions(-)

diff --git a/src/IO.f90 b/src/IO.f90
index 452bc0588..3d80feefa 100644
--- a/src/IO.f90
+++ b/src/IO.f90
@@ -14,10 +14,11 @@ module IO
  private
  character(len=5), parameter, public :: &
    IO_EOF = '#EOF#'                                                                                 !< end of file string
- character(len=168), parameter, private :: &
-   IO_divider = '───────────────────'//&
+ character(len=207), parameter, private :: &
+   IO_DIVIDER = '───────────────────'//&
                 '───────────────────'//&
-                '──────────────────'
+                '───────────────────'//&
+                '────────────'
  public :: &
    IO_init, &
    IO_read, &
@@ -1457,11 +1458,11 @@ end function IO_timeStamp
 !> @brief write error statements to standard out and terminate the Marc/spectral run with exit #9xxx
 !> in ABAQUS either time step is reduced or execution terminated
 !--------------------------------------------------------------------------------------------------
-subroutine IO_error(error_ID,el,ip,g,ext_msg)
+subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
 
  implicit none
  integer(pInt),              intent(in) :: error_ID
- integer(pInt),    optional, intent(in) :: el,ip,g
+ integer(pInt),    optional, intent(in) :: el,ip,g,instance
  character(len=*), optional, intent(in) :: ext_msg
  
  external                               :: quit
@@ -1672,34 +1673,28 @@ subroutine IO_error(error_ID,el,ip,g,ext_msg)
  end select
  
  !$OMP CRITICAL (write2out)
- write(0,'(/,a)')    ' ┌'//IO_divider//'┐'
- write(0,'(a)')      ' │                         error                          │'
- write(0,'(a)')      ' ├'//IO_divider//'┤'
- write(0,'(a,i3,a)') ' │                          ',error_ID,'                           │'
- write(0,'(a)')      ' │                                                        │'
+ write(0,'(/,a)')                ' ┌'//IO_DIVIDER//'┐'
+ write(0,'(a,24x,a,40x,a)')      ' │','error',                                             '│'
+ write(0,'(a,24x,i3,42x,a)')     ' │',error_ID,                                            '│'
+ write(0,'(a)')                  ' ├'//IO_DIVIDER//'┤'
  write(formatString,'(a,i6.6,a,i6.6,a)') '(1x,a4,a',max(1,len(trim(msg))),',',&
-                                                    max(1,60-len(trim(msg))-5),'x,a)'
- write(0,formatString) '│ ',trim(msg),'│'
+                                                    max(1,72-len(trim(msg))-4),'x,a)'
+ write(0,formatString)            '│ ',trim(msg),                                          '│'
  if (present(ext_msg)) then
    write(formatString,'(a,i6.6,a,i6.6,a)') '(1x,a4,a',max(1,len(trim(ext_msg))),',',&
-                                                      max(1,60-len(trim(ext_msg))-5),'x,a)'
-   write(0,formatString) '│ ',trim(ext_msg),'│'
+                                                      max(1,72-len(trim(ext_msg))-4),'x,a)'
+   write(0,formatString)          '│ ',trim(ext_msg),                                      '│'
  endif
- if (present(el)) then
-   if (present(ip)) then
-     if (present(g)) then
-       write(0,'(a13,1x,i9,1x,a2,1x,i2,1x,a5,1x,i4,18x,a1)') ' │ at element',el,'IP',ip,'grain',g,'│'
-     else
-       write(0,'(a13,1x,i9,1x,a2,1x,i2,29x,a1)') ' │ at element',el,'IP',ip,'│'
-     endif
-   else
-     write(0,'(a13,1x,i9,35x,a1)') ' │ at element',el,'│'
-   endif
- elseif (present(ip)) then                                                                          ! now having the meaning of "instance"
-   write(0,'(a14,1x,i9,34x,a1)') ' │ at instance',ip,'│'
- endif
- write(0,'(a)')      ' │                                                        │'
- write(0,'(a)')      ' └'//IO_divider//'┘'
+ if (present(el)) &
+   write(0,'(a19,1x,i9,44x,a3)') ' │ at element    ',el,                                   '│'
+ if (present(ip)) &
+   write(0,'(a19,1x,i9,44x,a3)') ' │ at IP         ',ip,                                   '│'
+ if (present(g)) &
+   write(0,'(a19,1x,i9,44x,a3)') ' │ at constituent',g,                                    '│'
+ if (present(instance)) &
+   write(0,'(a19,1x,i9,44x,a3)') ' │ at instance   ',instance,                             '│'
+ write(0,'(a,69x,a)')            ' │',                                                     '│'
+ write(0,'(a)')                  ' └'//IO_DIVIDER//'┘'
  flush(0)
  call quit(9000_pInt+error_ID)
  !$OMP END CRITICAL (write2out)
@@ -1766,30 +1761,26 @@ subroutine IO_warning(warning_ID,el,ip,g,ext_msg)
  end select
  
  !$OMP CRITICAL (write2out)
- write(6,'(/,a)')      ' +--------------------------------------------------------+'
- write(6,'(a)')        ' +                        warning                         +'
- write(6,'(a,i3,a)')   ' +                         ',warning_ID,'                            +'
- write(6,'(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(6,'(/,a)')                ' ┌'//IO_DIVIDER//'┐'
+ write(6,'(a,24x,a,38x,a)')      ' │','warning',                                           '│'
+ write(6,'(a,24x,i3,42x,a)')     ' │',warning_ID,                                          '│'
+ write(6,'(a)')                  ' ├'//IO_DIVIDER//'┤'
+ write(formatString,'(a,i6.6,a,i6.6,a)') '(1x,a4,a',max(1,len(trim(msg))),',',&
+                                                    max(1,72-len(trim(msg))-4),'x,a)'
+ write(6,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(formatString,'(a,i6.6,a,i6.6,a)') '(1x,a4,a',max(1,len(trim(ext_msg))),',',&
+                                                      max(1,72-len(trim(ext_msg))-4),'x,a)'
+   write(6,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,'+'
-     else
-       write(6,'(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,'+'
-   endif
- endif
- write(6,'(a)')      ' +--------------------------------------------------------+'
+ if (present(el)) &
+   write(6,'(a19,1x,i9,44x,a3)') ' │ at element    ',el,                                   '│'
+ if (present(ip)) &
+   write(6,'(a19,1x,i9,44x,a3)') ' │ at IP         ',ip,                                   '│'
+ if (present(g)) &
+   write(6,'(a19,1x,i9,44x,a3)') ' │ at constituent',g,                                    '│'
+ write(6,'(a,69x,a)')            ' │',                                                     '│'
+ write(6,'(a)')                  ' └'//IO_DIVIDER//'┘'
  flush(6)
  !$OMP END CRITICAL (write2out)
 

From 5118111ed9ee71eb9bbf2e6d8bda125700c31fb7 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Tue, 16 May 2017 00:29:10 +0200
Subject: [PATCH 26/32] [skip ci] updated version information after successful
 test of v2.0.1-722-g3633a03

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

diff --git a/VERSION b/VERSION
index e39f391eb..742dc6632 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-719-g4f3b0e4
+v2.0.1-722-g3633a03

From f9375f432582e058d1095477a179f5ccb81526b4 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Tue, 16 May 2017 03:16:27 +0200
Subject: [PATCH 27/32] backup runtime measurements and documentation only for
 development

---
 .gitlab-ci.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6eb527fbb..0084e70b5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -488,9 +488,8 @@ backupData:
     - cp $TESTROOT/memory.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
     - mv $TESTROOT/memory.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
     - mv $DAMASKROOT/PRIVATE/documenting/DAMASK_* $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
-  except:
-    - master
-    - release
+  only:
+    - development
 
 ##################################################################################################
 mergeIntoMaster: 

From 629a30b1a89e4c9a845c756a1be009a80afdca30 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Tue, 16 May 2017 06:28:46 +0200
Subject: [PATCH 28/32] saving runtime results only for development branch

---
 .gitlab-ci.yml | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0084e70b5..709655863 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -435,8 +435,10 @@ SpectralRuntime:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
     - cd $DAMASKROOT
     - make clean spectral processing OPTIMIZATION=AGGRESSIVE
+    - cd $TESTROOT/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
+    - SpectralAll_runtime/test.py -d $TESTROOT/performance
   except:
     - master
     - release
@@ -482,11 +484,13 @@ Spectral:
 backupData: 
   stage: saveDocumentation
   script:
+    - cd $TESTROOT/performance                                                                      # location of new runtime results
+    - git commit -am"${CI_PIPELINE_ID}_${CI_COMMIT_SHA}"
     - mkdir $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}
-    - cp $TESTROOT/time.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
-    - mv $TESTROOT/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
-    - cp $TESTROOT/memory.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
-    - mv $TESTROOT/memory.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - cp $TESTROOT/performance/time.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - mv $TESTROOT/performance/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - cp $TESTROOT/performance/memory.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - mv $TESTROOT/performance/memory.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
     - mv $DAMASKROOT/PRIVATE/documenting/DAMASK_* $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
   only:
     - development

From 7da8bc8d4a890053c3246d9327fe9dd8a7d28f24 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Tue, 16 May 2017 11:10:01 +0200
Subject: [PATCH 29/32] symlinks can be handled by Git, so we can store them
 and simplify the installation

---
 installation/mods_MarcMentat/apply_DAMASK_modifications.sh | 7 +------
 src/.gitignore                                             | 1 -
 src/DAMASK_marc2014.2.f90                                  | 1 +
 src/DAMASK_marc2014.f90                                    | 1 +
 src/DAMASK_marc2015.f90                                    | 1 +
 src/DAMASK_marc2016.f90                                    | 1 +
 6 files changed, 5 insertions(+), 7 deletions(-)
 create mode 120000 src/DAMASK_marc2014.2.f90
 create mode 120000 src/DAMASK_marc2014.f90
 create mode 120000 src/DAMASK_marc2015.f90
 create mode 120000 src/DAMASK_marc2016.f90

diff --git a/installation/mods_MarcMentat/apply_DAMASK_modifications.sh b/installation/mods_MarcMentat/apply_DAMASK_modifications.sh
index 761883de5..d1c1e37dd 100755
--- a/installation/mods_MarcMentat/apply_DAMASK_modifications.sh
+++ b/installation/mods_MarcMentat/apply_DAMASK_modifications.sh
@@ -129,7 +129,7 @@ for filename in marc$VERSION/tools/run_damask* \
   chmod 755 $INSTALLDIR/${filename}
 done
 
-#creating symlinks for run_damask_scripts in /usr/local/bin
+#creating symlinks for run_damask_scripts
 
 if [ -d "$BIN_DIR" ]; then
   echo ''
@@ -158,11 +158,6 @@ if [ -d "$BIN_DIR" ]; then
   esac
 fi
 
-# cloning user subroutine
-echo ''
-echo 'cloning $VERSION HYPELA2 user subroutine...'
-ln -s DAMASK_marc.f90 ${DAMASK_ROOT}/src/DAMASK_marc${VERSION}.f90
-
 # precompiling user subroutine
 echo ''
 echo 'precompiling $VERSION HYPELA2 user subroutine...'
diff --git a/src/.gitignore b/src/.gitignore
index c90e213cf..e9956554e 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -1,4 +1,3 @@
-DAMASK_marc*.f90
 Makefile
 cmake_install.cmake
 quit__genmod.f90
diff --git a/src/DAMASK_marc2014.2.f90 b/src/DAMASK_marc2014.2.f90
new file mode 120000
index 000000000..2c5bec706
--- /dev/null
+++ b/src/DAMASK_marc2014.2.f90
@@ -0,0 +1 @@
+DAMASK_marc.f90
\ No newline at end of file
diff --git a/src/DAMASK_marc2014.f90 b/src/DAMASK_marc2014.f90
new file mode 120000
index 000000000..2c5bec706
--- /dev/null
+++ b/src/DAMASK_marc2014.f90
@@ -0,0 +1 @@
+DAMASK_marc.f90
\ No newline at end of file
diff --git a/src/DAMASK_marc2015.f90 b/src/DAMASK_marc2015.f90
new file mode 120000
index 000000000..2c5bec706
--- /dev/null
+++ b/src/DAMASK_marc2015.f90
@@ -0,0 +1 @@
+DAMASK_marc.f90
\ No newline at end of file
diff --git a/src/DAMASK_marc2016.f90 b/src/DAMASK_marc2016.f90
new file mode 120000
index 000000000..2c5bec706
--- /dev/null
+++ b/src/DAMASK_marc2016.f90
@@ -0,0 +1 @@
+DAMASK_marc.f90
\ No newline at end of file

From ed59f3d7e0f2f47712d779ffa3cc1776a5344c2f Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Tue, 16 May 2017 11:55:11 +0200
Subject: [PATCH 30/32] [skip ci] updated version information after successful
 test of v2.0.1-728-g66efd90

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

diff --git a/VERSION b/VERSION
index 742dc6632..5a76f3ec4 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-722-g3633a03
+v2.0.1-728-g66efd90

From f52e62e6b9d5c67d62d6e6a19e9f8bb76b397c96 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Tue, 16 May 2017 20:39:45 +0200
Subject: [PATCH 31/32] [skip ci] updated version information after successful
 test of v2.0.1-734-g64fde94

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

diff --git a/VERSION b/VERSION
index 5a76f3ec4..8484dacfc 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-728-g66efd90
+v2.0.1-734-g64fde94

From 60b7870abea949456f8706f74c0a06586ff7647e Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Tue, 16 May 2017 23:00:49 +0200
Subject: [PATCH 32/32] [skip ci] updated version information after successful
 test of v2.0.1-735-gf52e62e

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

diff --git a/VERSION b/VERSION
index 8484dacfc..5dabd576c 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.0.1-734-g64fde94
+v2.0.1-735-gf52e62e