Merge branch 'development' into 26_autodoc-2

.gitlab-ci.yml

@@ -7,9 +7,9 @@ stages:
   - compilePETScGNU
   - prepareSpectral
   - spectral
-  - compileMarc2018_1
+  - compileMarc
   - marc
-  - compileAbaqus2017
+  - compileAbaqus
   - example
   - performance
   - createPackage
@@ -51,39 +51,37 @@ variables:
   # Names of module files to load
   # ===============================================================================================
   # ++++++++++++ Compiler ++++++++++++++++++++++++++++++++++++++++++++++
-  IntelCompiler16_0:               "Compiler/Intel/16.0 Libraries/IMKL/2016"
+  IntelCompiler16_4:               "Compiler/Intel/16.4 Libraries/IMKL/2016"
-  IntelCompiler16_4:               "Compiler/Intel/16.4 Libraries/IMKL/2016-4"
+  IntelCompiler17_8:               "Compiler/Intel/17.8 Libraries/IMKL/2017"
-  IntelCompiler17_0:               "Compiler/Intel/17.0 Libraries/IMKL/2017"
+  IntelCompiler18_4:               "Compiler/Intel/18.4 Libraries/IMKL/2018"
-  IntelCompiler18_1:               "Compiler/Intel/18.1 Libraries/IMKL/2018"
+  GNUCompiler8_2:                  "Compiler/GNU/8.2"
-  GNUCompiler7_3:                  "Compiler/GNU/7.3"
   # ------------ Defaults ----------------------------------------------
-  IntelCompiler:                   "$IntelCompiler18_1"
+  IntelCompiler:                   "$IntelCompiler18_4"
-  GNUCompiler:                     "$GNUCompiler7_3"
+  GNUCompiler:                     "$GNUCompiler8_2"
   # ++++++++++++ MPI +++++++++++++++++++++++++++++++++++++++++++++++++++
-  MPICH3_2Intel18_1:               "MPI/Intel/18.1/MPICH/3.2.1"
+  IMPI2018Intel18_4:               "MPI/Intel/18.4/IntelMPI/2018"
-  MPICH3_2GNU7_3:                  "MPI/GNU/7.3/MPICH/3.2.1"
+  MPICH3_3GNU8_2:                  "MPI/GNU/8.2/MPICH/3.3"
   # ------------ Defaults ----------------------------------------------
-  MPICH_Intel:                     "$MPICH3_2Intel18_1"
+  MPICH_Intel:                     "$IMPI2018Intel18_4"
-  MPICH_GNU:                       "$MPICH3_2GNU7_3"
+  MPICH_GNU:                       "$MPICH3_3GNU8_2"
   # ++++++++++++ PETSc +++++++++++++++++++++++++++++++++++++++++++++++++
-  PETSc3_10_0MPICH3_2Intel18_1:    "Libraries/PETSc/3.10.0/Intel-18.1-MPICH-3.2.1"
+  PETSc3_10_3IMPI2018Intel18_4:    "Libraries/PETSc/3.10.3/Intel-18.4-IntelMPI-2018"
-  PETSc3_10_0MPICH3_2GNU7_3:       "Libraries/PETSc/3.10.0/GNU-7.3-MPICH-3.2.1"
+  PETSc3_10_3MPICH3_3GNU8_2:       "Libraries/PETSc/3.10.3/GNU-8.2-MPICH-3.3"
   # ------------ Defaults ----------------------------------------------
-  PETSc_MPICH_Intel:               "$PETSc3_10_0MPICH3_2Intel18_1"
+  PETSc_MPICH_Intel:               "$PETSc3_10_3IMPI2018Intel18_4"
-  PETSc_MPICH_GNU:                 "$PETSc3_10_0MPICH3_2GNU7_3"
+  PETSc_MPICH_GNU:                 "$PETSc3_10_3MPICH3_3GNU8_2"
   # ++++++++++++ FEM +++++++++++++++++++++++++++++++++++++++++++++++++++
-  Abaqus2017:                      "FEM/Abaqus/2017"
+  Abaqus2019:                      "FEM/Abaqus/2019"
   MSC2018_1:                       "FEM/MSC/2018.1"
-  MSC2017:                         "FEM/MSC/2017"
   # ------------ Defaults ----------------------------------------------
-  Abaqus:                          "$Abaqus2017"
+  Abaqus:                          "$Abaqus2019"
   MSC:                             "$MSC2018_1"
-  IntelMarc:                       "$IntelCompiler17_0"
+  IntelMarc:                       "$IntelCompiler17_8"
   IntelAbaqus:                     "$IntelCompiler16_4"
   # ++++++++++++ Documentation +++++++++++++++++++++++++++++++++++++++++
-  Doxygen1_8_13:                   "Documentation/Doxygen/1.8.13"
+  Doxygen1_8_15:                   "Documentation/Doxygen/1.8.15"
   # ------------ Defaults ----------------------------------------------
-  Doxygen:                         "$Doxygen1_8_13"
+  Doxygen:                         "$Doxygen1_8_15"
 
 
 ###################################################################################################
@@ -158,6 +156,13 @@ Post_AverageDown:
     - master
     - release
 
+Post_ASCIItable:
+  stage: postprocessing
+  script: ASCIItable/test.py
+  except:
+    - master
+    - release
+
 Post_General:
   stage: postprocessing
   script: PostProcessing/test.py
@@ -383,9 +388,9 @@ TextureComponents:
 
 ###################################################################################################
 Marc_compileIfort2018_1:
-  stage: compileMarc2018_1
+  stage: compileMarc
   script:
-    - module load $IntelCompiler17_0 $MSC2018_1
+    - module load $IntelMarc $MSC
     - Marc_compileIfort/test.py -m 2018.1
   except:
     - master
@@ -430,11 +435,11 @@ J2_plasticBehavior:
     - release
 
 ###################################################################################################
-Abaqus_compile2017:
+Abaqus_compile:
-  stage: compileAbaqus2017
+  stage: compileAbaqus
   script:
-    - module load $IntelCompiler16_4 $Abaqus2017
+    - module load $IntelAbaqus $Abaqus
-    - Abaqus_compileIfort/test.py -a 2017
+    - Abaqus_compileIfort/test.py
   except:
     - master
     - release

CONFIG

@@ -8,6 +8,6 @@ set DAMASK_NUM_THREADS    = 4
 set MSC_ROOT              = /opt/msc
 set MARC_VERSION          = 2018.1
 
-set ABAQUS_VERSION        = 2017
+set ABAQUS_VERSION        = 2019
 
 set DAMASK_HDF5           = OFF

PRIVATE

@@ -1 +1 @@
-Subproject commit 30434a528f69d77eef1be91e8a2f2fc5e0f85054
+Subproject commit 18ba1ba6a5e9ba446dc9311acf2acf2781614db1

README

@@ -10,3 +10,4 @@ Germany
 
 Email: DAMASK@mpie.de
 https://damask.mpie.de
+https://magit1.mpie.de

processing/post/addCumulative.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys

processing/post/addDerivative.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys

processing/post/addLinked.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys
@@ -21,7 +21,7 @@ Add data of selected column(s) from (first) row of linked ASCIItable that shares
 parser.add_option('--link',
                   dest = 'link', nargs = 2,
                   type = 'string', metavar = 'string string',
-                  help = 'column labels containing linked values')
+                  help = 'column labels of table and linked table containing linking values')
 parser.add_option('-l','--label',
                   dest = 'label',
                   action = 'extend', metavar = '<string LIST>',
@@ -105,7 +105,8 @@ for name in filenames:
   outputAlive = True
   while outputAlive and table.data_read():                                                          # read next data line of ASCII table
     try:
-      table.data_append(data[np.argwhere(np.all((map(float,table.data[myLink:myLink+myLinkDim]) - index)==0,axis=1))[0]])  # add data of first matching line
+      table.data_append(data[np.argwhere(np.all((list(map(float,table.data[myLink:myLink+myLinkDim])) - index)==0,
+                                                 axis=1))[0]])                                      # add data of first matching line
     except IndexError:
       table.data_append(np.nan*np.ones_like(data[0]))                                               # or add NaNs
     outputAlive = table.data_write()                                                                # output processed line

processing/post/addTable.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys

processing/post/blowUp.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys

processing/post/vtk_addGridData.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,vtk

processing/post/vtk_addPointcloudData.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,vtk

processing/post/vtk_addRectilinearGridData.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,vtk

processing/post/vtk_pointcloud.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys,vtk

processing/post/vtk_rectilinearGrid.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys,vtk

processing/pre/geom_grainGrowth.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys,math
@@ -49,7 +49,7 @@ parser.set_defaults(d = 1,
 
 (options, filenames) = parser.parse_args()
 
-options.immutable = map(int,options.immutable)
+options.immutable = list(map(int,options.immutable))
 
 getInterfaceEnergy = lambda A,B: np.float32((A*B != 0)*(A != B)*1.0)                               # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
 struc = ndimage.generate_binary_structure(3,1)                                                     # 3D von Neumann neighborhood
@@ -70,9 +70,9 @@ for name in filenames:
   table.head_read()
   info,extra_header = table.head_getGeom()
   
-  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(map(str,info['grid']))),
+  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(list(map(str,info['grid'])))),
-                     'size     x y z:  {}'.format(' x '.join(map(str,info['size']))),
+                     'size     x y z:  {}'.format(' x '.join(list(map(str,info['size'])))),
-                     'origin   x y z:  {}'.format(' : '.join(map(str,info['origin']))),
+                     'origin   x y z:  {}'.format(' : '.join(list(map(str,info['origin'])))),
                      'homogenization:  {}'.format(info['homogenization']),
                      'microstructures: {}'.format(info['microstructures']),
                     ])
@@ -102,9 +102,9 @@ for name in filenames:
     gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d),dtype=np.float32) \
             /np.power(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(info['grid'] == 1))/2.,dtype=np.float32)
           
-    gauss[:,:,:grid[2]/2:-1] = gauss[:,:,1:(grid[2]+1)/2]     # trying to cope with uneven (odd) grid size
+    gauss[:,:,:grid[2]//2:-1] = gauss[:,:,1:(grid[2]+1)//2]     # trying to cope with uneven (odd) grid size
-    gauss[:,:grid[1]/2:-1,:] = gauss[:,1:(grid[1]+1)/2,:]
+    gauss[:,:grid[1]//2:-1,:] = gauss[:,1:(grid[1]+1)//2,:]
-    gauss[:grid[0]/2:-1,:,:] = gauss[1:(grid[0]+1)/2,:,:]
+    gauss[:grid[0]//2:-1,:,:] = gauss[1:(grid[0]+1)//2,:,:]
     gauss = np.fft.rfftn(gauss).astype(np.complex64)
 
   for smoothIter in range(options.N):
@@ -119,9 +119,9 @@ for name in filenames:
                                                           microstructure,i,axis=0), j,axis=1), k,axis=2)))
 
     # 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,
+    periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
-                                                                grid[1]/2:-grid[1]/2,
+                                                                grid[1]//2:-grid[1]//2,
-                                                                grid[2]/2:-grid[2]/2]
+                                                                grid[2]//2:-grid[2]//2]
 
     # transform bulk volume (i.e. where interfacial energy remained zero), store index of closest boundary voxel
     index = ndimage.morphology.distance_transform_edt(periodic_interfaceEnergy == 0.,                                            
@@ -148,15 +148,15 @@ for name in filenames:
                          ndimage.morphology.binary_dilation(interfaceEnergy > 0.,
                                                             structure = struc,
                                                             iterations = int(round(options.d*2.))-1),# fat boundary
-                         periodic_bulkEnergy[grid[0]/2:-grid[0]/2,                                 # retain filled energy on fat boundary...
+                         periodic_bulkEnergy[grid[0]//2:-grid[0]//2,                                 # retain filled energy on fat boundary...
-                                             grid[1]/2:-grid[1]/2,
+                                             grid[1]//2:-grid[1]//2,
-                                             grid[2]/2:-grid[2]/2],                                # ...and zero everywhere else
+                                             grid[2]//2:-grid[2]//2],                                # ...and zero everywhere else
                          0.)).astype(np.complex64) *
                          gauss).astype(np.float32)
 
-      periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
+      periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
-                                                                grid[1]/2:-grid[1]/2,
+                                                                grid[1]//2:-grid[1]//2,
-                                                                grid[2]/2:-grid[2]/2]              # periodically extend the smoothed bulk energy
+                                                                grid[2]//2:-grid[2]//2]              # periodically extend the smoothed bulk energy
 
 
     # transform voxels close to interface region
@@ -164,15 +164,15 @@ for name in filenames:
                                                       return_distances = False,
                                                       return_indices = True)                       # want index of closest bulk grain
 
-    periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]/2:-grid[0]/2,
+    periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]//2:-grid[0]//2,
-                                                              grid[1]/2:-grid[1]/2,
+                                                              grid[1]//2:-grid[1]//2,
-                                                              grid[2]/2:-grid[2]/2]                # periodically extend the microstructure
+                                                              grid[2]//2:-grid[2]//2]                # periodically extend the microstructure
 
     microstructure = periodic_microstructure[index[0],
                                              index[1],
-                                             index[2]].reshape(2*grid)[grid[0]/2:-grid[0]/2,
+                                             index[2]].reshape(2*grid)[grid[0]//2:-grid[0]//2,
-                                                                       grid[1]/2:-grid[1]/2,
+                                                                       grid[1]//2:-grid[1]//2,
-                                                                       grid[2]/2:-grid[2]/2]       # extent grains into interface region
+                                                                       grid[2]//2:-grid[2]//2]       # extent grains into interface region
 
     # replace immutable microstructures with closest mutable ones
     index = ndimage.morphology.distance_transform_edt(np.in1d(microstructure,options.immutable).reshape(grid),
@@ -236,3 +236,4 @@ for name in filenames:
 # --- output finalization --------------------------------------------------------------------------
 
   table.close()     
+  

processing/pre/geom_toTable.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys
@@ -48,11 +48,11 @@ for name in filenames:
   table.head_read()
   info,extra_header = table.head_getGeom()
   
-  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
+  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(list(map(str,info['grid'])))),
-                     'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
+                     'size     x y z:  {}'.format(' x '.join(list(map(str,info['size'])))),
-                     'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
+                     'origin   x y z:  {}'.format(' : '.join(list(map(str,info['origin'])))),
-                     'homogenization:  %i'%info['homogenization'],
+                     'homogenization:  {}'.format(info['homogenization']),
-                     'microstructures: %i'%info['microstructures'],
+                     'microstructures: {}'.format(info['microstructures']),
                     ])
 
   errors = []

processing/pre/seeds_fromDistribution.py

@@ -1,10 +1,11 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import threading,time,os,sys,random
 import numpy as np
 from optparse import OptionParser
-from cStringIO import StringIO
+from io import StringIO
+import binascii
 import damask
 
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
@@ -96,7 +97,7 @@ class myThread (threading.Thread):
       perturbedGeomVFile = StringIO()
       perturbedSeedsVFile.reset()
       perturbedGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
-                     ' -g '+' '.join(map(str, options.grid)),streamIn=perturbedSeedsVFile)[0])
+                     ' -g '+' '.join(list(map(str, options.grid))),streamIn=perturbedSeedsVFile)[0])
       perturbedGeomVFile.reset()
 
 #--- evaluate current seeds file ----------------------------------------------------------------------
@@ -214,7 +215,7 @@ options = parser.parse_args()[0]
 damask.util.report(scriptName,options.seedFile)
 
 if options.randomSeed is None:
-  options.randomSeed = int(os.urandom(4).encode('hex'), 16)
+  options.randomSeed = int(binascii.hexlify(os.urandom(4)),16)
 damask.util.croak(options.randomSeed)
 delta = (options.scale/options.grid[0],options.scale/options.grid[1],options.scale/options.grid[2])
 baseFile=os.path.splitext(os.path.basename(options.seedFile))[0]
@@ -240,17 +241,17 @@ if os.path.isfile(os.path.splitext(options.seedFile)[0]+'.seeds'):
     for line in initialSeedFile: bestSeedsVFile.write(line)
 else:
   bestSeedsVFile.write(damask.util.execute('seeds_fromRandom'+\
-                                ' -g '+' '.join(map(str, options.grid))+\
+                                ' -g '+' '.join(list(map(str, options.grid)))+\
                                 ' -r {:d}'.format(options.randomSeed)+\
                                 ' -N '+str(nMicrostructures))[0])
 bestSeedsUpdate = time.time()
 
 # ----------- tessellate initial seed file to get and evaluate geom file
-bestSeedsVFile.reset()
+bestSeedsVFile.seek(0)
 initialGeomVFile = StringIO()
 initialGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
-                               ' -g '+' '.join(map(str, options.grid)),bestSeedsVFile)[0])
+                               ' -g '+' '.join(list(map(str, options.grid))),bestSeedsVFile)[0])
-initialGeomVFile.reset()
+initialGeomVFile.seek(0)
 initialGeomTable = damask.ASCIItable(initialGeomVFile,None,labeled=False,readonly=True)
 initialGeomTable.head_read()
 info,devNull =  initialGeomTable.head_getGeom()

python/damask/solver/abaqus.py

@@ -2,7 +2,7 @@
 
 from .solver import Solver
 import damask
-import subprocess,re
+import subprocess
 
 class Abaqus(Solver):
 
@@ -15,14 +15,13 @@ class Abaqus(Solver):
 
   def return_run_command(self,model):
     env=damask.Environment()
-    shortVersion = re.sub('[\.,-]', '',self.version)
     try:
-      cmd='abq'+shortVersion
+      cmd='abq'+self.version
-      subprocess.check_output(['abq'+shortVersion,'information=release'])
+      subprocess.check_output([cmd,'information=release'])
     except OSError:                                                                                 # link to abqXXX not existing
       cmd='abaqus'
       process = subprocess.Popen(['abaqus','information=release'],stdout = subprocess.PIPE,stderr = subprocess.PIPE)
-      detectedVersion = process.stdout.readlines()[1].split()[1]
+      detectedVersion = process.stdout.readlines()[1].split()[1].decode('utf-8')
       if self.version != detectedVersion:
-        raise Exception('found Abaqus version %s, but requested %s'%(detectedVersion,self.version))
+        raise Exception('found Abaqus version {}, but requested {}'.format(detectedVersion,self.version))
-    return '%s -job %s -user %s/src/DAMASK_abaqus interactive'%(cmd,model,env.rootDir())
+    return '{} -job {} -user {}/src/DAMASK_abaqus interactive'.format(cmd,model,env.rootDir())