223031012
/
DAMASK_EICMD
mirror of https://github.com/achalhp/DAMASK_EICMD.git
1
0
Fork 0
Code Issues Projects Releases Wiki Activity

added ASCIItable tests to CI pipelining

This commit is contained in:
Philip Eisenlohr 2019-02-14 18:24:09 -05:00
parent 1adffb0deb
commit 742d58cfce
6 changed files with 45 additions and 36 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
.gitlab-ci.yml
View File

@ -156,6 +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

2
PRIVATE

@ -1 +1 @@
Subproject commit c6db7cee2d9349e2d463f5ef6284446007fc7915
Subproject commit 3d12562fbfb3a57dbb3777ac045a12376b3400e8

6
processing/post/addLinked.py
View File

@ -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 +105,7 @@ 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
View File

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

47
processing/pre/geom_grainGrowth.py
View File

@ -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()

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()