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DAMASK_EICMD
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Merge branch 'development' into 26_autodoc-2

This commit is contained in:
Martin Diehl 2019-02-15 20:47:14 +01:00
parent cced449dd3 d53d1224b8
commit 0cc4e582e4
18 changed files with 95 additions and 87 deletions
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63
.gitlab-ci.yml
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@ -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/2016-4"
IntelCompiler17_0: "Compiler/Intel/17.0 Libraries/IMKL/2017"
IntelCompiler18_1: "Compiler/Intel/18.1 Libraries/IMKL/2018"
GNUCompiler7_3: "Compiler/GNU/7.3"
IntelCompiler16_4: "Compiler/Intel/16.4 Libraries/IMKL/2016"
IntelCompiler17_8: "Compiler/Intel/17.8 Libraries/IMKL/2017"
IntelCompiler18_4: "Compiler/Intel/18.4 Libraries/IMKL/2018"
GNUCompiler8_2: "Compiler/GNU/8.2"
# ------------ Defaults ----------------------------------------------
IntelCompiler: "$IntelCompiler18_1"
GNUCompiler: "$GNUCompiler7_3"
IntelCompiler: "$IntelCompiler18_4"
GNUCompiler: "$GNUCompiler8_2"
# ++++++++++++ MPI +++++++++++++++++++++++++++++++++++++++++++++++++++
MPICH3_2Intel18_1: "MPI/Intel/18.1/MPICH/3.2.1"
MPICH3_2GNU7_3: "MPI/GNU/7.3/MPICH/3.2.1"
IMPI2018Intel18_4: "MPI/Intel/18.4/IntelMPI/2018"
MPICH3_3GNU8_2: "MPI/GNU/8.2/MPICH/3.3"
# ------------ Defaults ----------------------------------------------
MPICH_Intel: "$MPICH3_2Intel18_1"
MPICH_GNU: "$MPICH3_2GNU7_3"
MPICH_Intel: "$IMPI2018Intel18_4"
MPICH_GNU: "$MPICH3_3GNU8_2"
# ++++++++++++ PETSc +++++++++++++++++++++++++++++++++++++++++++++++++
PETSc3_10_0MPICH3_2Intel18_1: "Libraries/PETSc/3.10.0/Intel-18.1-MPICH-3.2.1"
PETSc3_10_0MPICH3_2GNU7_3: "Libraries/PETSc/3.10.0/GNU-7.3-MPICH-3.2.1"
PETSc3_10_3IMPI2018Intel18_4: "Libraries/PETSc/3.10.3/Intel-18.4-IntelMPI-2018"
PETSc3_10_3MPICH3_3GNU8_2: "Libraries/PETSc/3.10.3/GNU-8.2-MPICH-3.3"
# ------------ Defaults ----------------------------------------------
PETSc_MPICH_Intel: "$PETSc3_10_0MPICH3_2Intel18_1"
PETSc_MPICH_GNU: "$PETSc3_10_0MPICH3_2GNU7_3"
PETSc_MPICH_Intel: "$PETSc3_10_3IMPI2018Intel18_4"
PETSc_MPICH_GNU: "$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:
stage: compileAbaqus2017
Abaqus_compile:
stage: compileAbaqus
script:
- module load $IntelCompiler16_4 $Abaqus2017
- Abaqus_compileIfort/test.py -a 2017
- module load $IntelAbaqus $Abaqus
- Abaqus_compileIfort/test.py
except:
- master
- release

2
CONFIG
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@ -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

2
PRIVATE

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

1
README
View File

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

2
processing/post/addCumulative.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys

2
processing/post/addDerivative.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys

7
processing/post/addLinked.py
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@ -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

2
processing/post/addTable.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys

2
processing/post/blowUp.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys

2
processing/post/vtk_addGridData.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,vtk

2
processing/post/vtk_addPointcloudData.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,vtk

2
processing/post/vtk_addRectilinearGridData.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,vtk

2
processing/post/vtk_pointcloud.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,vtk

2
processing/post/vtk_rectilinearGrid.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,vtk

47
processing/pre/geom_grainGrowth.py
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@ -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']))),
'size x y z: {}'.format(' x '.join(map(str,info['size']))),
'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
damask.util.croak(['grid a b c: {}'.format(' x '.join(list(map(str,info['grid'])))),
'size x y z: {}'.format(' x '.join(list(map(str,info['size'])))),
'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[1]/2:-1,:] = gauss[:,1:(grid[1]+1)/2,:]
gauss[:grid[0]/2:-1,:,:] = gauss[1:(grid[0]+1)/2,:,:]
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[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,
grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2]
periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//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...
grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2], # ...and zero everywhere else
periodic_bulkEnergy[grid[0]//2:-grid[0]//2, # retain filled energy on fat boundary...
grid[1]//2:-grid[1]//2,
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,
grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2] # periodically extend the smoothed bulk energy
periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//2,
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,
grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2] # periodically extend the microstructure
periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//2,
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,
grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2] # extent grains into interface region
index[2]].reshape(2*grid)[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//2,
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()

12
processing/pre/geom_toTable.py
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@ -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']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
damask.util.croak(['grid a b c: {}'.format(' x '.join(list(map(str,info['grid'])))),
'size x y z: {}'.format(' x '.join(list(map(str,info['size'])))),
'origin x y z: {}'.format(' : '.join(list(map(str,info['origin'])))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(info['microstructures']),
])
errors = []

17
processing/pre/seeds_fromDistribution.py
View File

@ -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])
initialGeomVFile.reset()
' -g '+' '.join(list(map(str, options.grid))),bestSeedsVFile)[0])
initialGeomVFile.seek(0)
initialGeomTable = damask.ASCIItable(initialGeomVFile,None,labeled=False,readonly=True)
initialGeomTable.head_read()
info,devNull = initialGeomTable.head_getGeom()

13
python/damask/solver/abaqus.py
View File

@ -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
subprocess.check_output(['abq'+shortVersion,'information=release'])
cmd='abq'+self.version
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))
return '%s -job %s -user %s/src/DAMASK_abaqus interactive'%(cmd,model,env.rootDir())
raise Exception('found Abaqus version {}, but requested {}'.format(detectedVersion,self.version))
return '{} -job {} -user {}/src/DAMASK_abaqus interactive'.format(cmd,model,env.rootDir())