Merge branch 'development' into PRIVATEasSubmodule

.gitlab-ci.yml

@@ -34,7 +34,7 @@ variables:
   #================================================================================================
   # Shortcut names
   #================================================================================================
-  DAMASKROOT:                      "$HOME/GitlabCI_Pipeline_$CI_PIPELINE_ID/DAMASK"
+  DAMASKROOT:                      "$HOME/GitLabCI_Pipeline_$CI_PIPELINE_ID/DAMASK"
 
   #================================================================================================
   # Names of module files to load
@@ -79,8 +79,8 @@ variables:
 checkout: 
   stage: prepareAll
   before_script: 
-    - while [ -e $HOME/GitLabCI.lock ]; do sleep 5m; done
-    - echo $CI_PIPELINE_ID > $HOME/GitLabCI.lock
+    - echo $CI_PIPELINE_ID >> $HOME/GitLabCI.queue
+    - while [ "$(awk '/$CI_PIPELINE_ID/{print NR}' GitLabCI.queue)" -ne 1 ];do sleep 5m; done
   script:
     - mkdir -p $DAMASKROOT
     - git clone -q --recurse-submodules git@magit1.mpie.de:damask/DAMASK.git $DAMASKROOT
@@ -435,6 +435,7 @@ mergeIntoMaster:
     - 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:
@@ -483,7 +484,7 @@ removeLock:
   before_script: 
     - echo 'Do nothing'
   when: always
-  script: if grep -q $CI_PIPELINE_ID $HOME/GitLabCI.lock; then; rm $HOME/GitLabCI.lock; fi
+  script: sed -i '/$CI_PIPELINE_ID/d' GitLabCI.queue
   except:
     - master
     - release

DAMASK_env.sh

@@ -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 -s $(expr $freeMem / $DAMASK_NUM_THREADS / 2)  2>/dev/null # maximum stack size (kB)
+  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)
 fi
 ulimit -v unlimited   2>/dev/null # maximum virtual memory size
 ulimit -m unlimited   2>/dev/null # maximum physical memory size

code/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

code/material.f90

@@ -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
 
 

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(verbose = False)
+parser.set_defaults(port = 40007,
+                    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')
-file['croak'].write( 'waiting to connect...\n')
+damask.util.report(scriptName,'waiting to connect...')
+
 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 = {}