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DAMASK_EICMD
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Merge branch 'development' into Vectorize-Orientation

This commit is contained in:
Martin Diehl 2020-07-01 13:11:51 +02:00
parent e18a5b8a1b c33c5a18a8
commit a7e3dd5a56
55 changed files with 1060 additions and 1276 deletions
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15
.gitlab-ci.yml
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@ -192,21 +192,6 @@ Post_addGradient:
- master
- release
Post_ParaviewRelated:
stage: postprocessing
script: ParaviewRelated/test.py
except:
- master
- release
Post_OrientationConversion:
stage: postprocessing
script:
- OrientationConversion/test.py
except:
- master
- release
Post_OrientationAverageMisorientation:
stage: postprocessing
script:

2
PRIVATE

@ -1 +1 @@
Subproject commit a6109acd264c683fd335b1d1f69934fc4a4078e3
Subproject commit 073913bf152b3c48f358dfbea5145807c0f7690d

2
VERSION
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@ -1 +1 @@
v2.0.3-2654-g5c544a6e
v2.0.3-2717-g52aacf37

2
examples/ConfigFiles/Phase_DisloUCLA_Tungsten.config
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@ -27,7 +27,7 @@ SolidSolutionStrength 0.0 # Strength due to elements in solid solution
### Dislocation glide parameters ###
#per family
Nslip 12 0
Nslip 12
slipburgers 2.72e-10 # Burgers vector of slip system [m]
rhoedge0 1.0e12 # Initial edge dislocation density [m/m**3]
rhoedgedip0 1.0 # Initial edged dipole dislocation density [m/m**3]

56
installation/symlink_Processing.py
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@ -1,56 +1,30 @@
#!/usr/bin/env python3
# Makes postprocessing routines accessible from everywhere.
import os
import sys
from pathlib import Path
import damask
damaskEnv = damask.Environment()
baseDir = damaskEnv.relPath('processing/')
binDir = damaskEnv.relPath('bin/')
env = damask.Environment()
bin_dir = env.root_dir/Path('bin')
if not os.path.isdir(binDir):
os.mkdir(binDir)
if not bin_dir.exists():
bin_dir.mkdir()
#define ToDo list
processing_subDirs = ['pre',
'post',
]
sys.stdout.write('\nsymbolic linking...\n')
for sub_dir in ['pre','post']:
the_dir = env.root_dir/Path('processing')/Path(sub_dir)
for subDir in processing_subDirs:
theDir = os.path.abspath(os.path.join(baseDir,subDir))
sys.stdout.write('\n'+binDir+' ->\n'+theDir+damask.util.deemph(' ...')+'\n')
for theFile in os.listdir(theDir):
theName,theExt = os.path.splitext(theFile)
if theExt in ['.py']:
src = os.path.abspath(os.path.join(theDir,theFile))
sym_link = os.path.abspath(os.path.join(binDir,theName))
if os.path.lexists(sym_link):
os.remove(sym_link)
output = theName+damask.util.deemph(theExt)
else:
output = damask.util.emph(theName)+damask.util.deemph(theExt)
sys.stdout.write(damask.util.deemph('... ')+output+'\n')
os.symlink(src,sym_link)
for the_file in the_dir.glob('*.py'):
src = the_dir/the_file
dst = bin_dir/Path(the_file.with_suffix('').name)
if dst.is_file(): dst.unlink() # dst.unlink(True) for Python >3.8
dst.symlink_to(src)
sys.stdout.write('\npruning broken links...\n')
brokenLinks = 0
for filename in os.listdir(binDir):
path = os.path.join(binDir,filename)
if os.path.islink(path) and not os.path.exists(path):
sys.stdout.write(' '+damask.util.delete(path)+'\n')
os.remove(path)
brokenLinks += 1
sys.stdout.write(('none.' if brokenLinks == 0 else '')+'\n')
for filename in bin_dir.glob('*'):
if not filename.is_file():
filename.unlink

0
processing/post/addAPS34IDEstrainCoords.py → processing/legacy/addAPS34IDEstrainCoords.py
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0
processing/post/addCumulative.py → processing/legacy/addCumulative.py
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0
processing/post/addEhkl.py → processing/legacy/addEhkl.py
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0
processing/post/imageData.py → processing/legacy/imageData.py
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0
processing/post/imageDataDeformed.py → processing/legacy/imageDataDeformed.py
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0
processing/post/imageDataRGB.py → processing/legacy/imageDataRGB.py
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143
processing/post/binXY.py
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@ -1,143 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Produces a binned grid of two columns from an ASCIItable, i.e. a two-dimensional probability density map.
""", version = scriptID)
parser.add_option('-d','--data',
dest = 'data',
type = 'string', nargs = 2, metavar = 'string string',
help = 'column labels containing x and y ')
parser.add_option('-w','--weight',
dest = 'weight',
type = 'string', metavar = 'string',
help = 'column label containing weight of (x,y) point')
parser.add_option('-b','--bins',
dest = 'bins',
type = 'int', nargs = 2, metavar = 'int int',
help = 'number of bins in x and y direction [%default]')
parser.add_option('-t','--type',
dest = 'type',
type = 'string', nargs = 3, metavar = 'string string string',
help = 'type (linear/log) of x, y, and z axis [%default]')
parser.add_option('-x','--xrange',
dest = 'xrange',
type = 'float', nargs = 2, metavar = 'float float',
help = 'min max limits in x direction (optional)')
parser.add_option('-y','--yrange',
dest = 'yrange',
type = 'float', nargs = 2, metavar = 'float float',
help = 'min max limits in y direction (optional)')
parser.add_option('-z','--zrange',
dest = 'zrange',
type = 'float', nargs = 2, metavar = 'float float',
help = 'min max limits in z direction (optional)')
parser.add_option('-i','--invert',
dest = 'invert',
action = 'store_true',
help = 'invert probability density')
parser.add_option('-r','--rownormalize',
dest = 'normRow',
action = 'store_true',
help = 'normalize probability density in each row')
parser.add_option('-c','--colnormalize',
dest = 'normCol',
action = 'store_true',
help = 'normalize probability density in each column')
parser.set_defaults(bins = (10,10),
type = ('linear','linear','linear'),
xrange = (0.0,0.0),
yrange = (0.0,0.0),
zrange = (0.0,0.0),
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
minmax = np.array([options.xrange,options.yrange,options.zrange])
result = np.empty((options.bins[0],options.bins[1],3),'f')
if options.data is None: parser.error('no data columns specified.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
data = np.hstack((table.get(options.data[0]),table.get(options.data[1])))
for c in (0,1): # check data minmax for x and y (i = 0 and 1)
if (minmax[c] == 0.0).all(): minmax[c] = [data[:,c].min(),data[:,c].max()]
if options.type[c].lower() == 'log': # if log scale
data[:,c] = np.log(data[:,c]) # change x,y coordinates to log
minmax[c] = np.log(minmax[c]) # change minmax to log, too
delta = minmax[:,1]-minmax[:,0]
(grid,xedges,yedges) = np.histogram2d(data[:,0],data[:,1],
bins=options.bins,
range=minmax[:2],
weights=table.get(options.weight) if options.weight else None)
if options.normCol:
for x in range(options.bins[0]):
sum = np.sum(grid[x,:])
if sum > 0.0:
grid[x,:] /= sum
if options.normRow:
for y in range(options.bins[1]):
sum = np.sum(grid[:,y])
if sum > 0.0:
grid[:,y] /= sum
if (minmax[2] == 0.0).all(): minmax[2] = [grid.min(),grid.max()] # auto scale from data
if minmax[2,0] == minmax[2,1]:
minmax[2,0] -= 1.
minmax[2,1] += 1.
if (minmax[2] == 0.0).all(): # no data in grid?
damask.util.croak('no data found on grid...')
minmax[2,:] = np.array([0.0,1.0]) # making up arbitrary z minmax
if options.type[2].lower() == 'log':
grid = np.log(grid)
minmax[2] = np.log(minmax[2])
delta[2] = minmax[2,1]-minmax[2,0]
for x in range(options.bins[0]):
for y in range(options.bins[1]):
result[x,y,:] = [minmax[0,0]+delta[0]/options.bins[0]*(x+0.5),
minmax[1,0]+delta[1]/options.bins[1]*(y+0.5),
np.clip((grid[x,y]-minmax[2,0])/delta[2],0.0,1.0)]
for c in (0,1):
if options.type[c].lower() == 'log': result[:,:,c] = np.exp(result[:,:,c])
if options.invert: result[:,:,2] = 1.0 - result[:,:,2]
comments = scriptID + '\t' + ' '.join(sys.argv[1:])
shapes = {'bin_%s'%options.data[0]:(1,),'bin_%s'%options.data[1]:(1,),'z':(1,)}
table = damask.Table(result.reshape(options.bins[0]*options.bins[1],3),shapes,[comments])
if name:
outname = os.path.join(os.path.dirname(name),'binned-{}-{}_'.format(*options.data) +
('weighted-{}_'.format(options.weight) if options.weight else '') +
os.path.basename(name))
table.to_ASCII(outname)
else:
table.to_ASCII(sys.stdout)

65
processing/post/vtk_addData.py
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@ -1,65 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [ASCIItable(s)]',
description = 'Add scalars/vectors, tensors, and/or a RGB tuples from ASCIItable '
+ 'to existing VTK file (.vtr/.vtu/.vtp).',
version = scriptID)
parser.add_option( '--vtk',
dest = 'vtk',
type = 'string', metavar = 'string',
help = 'VTK file name')
parser.add_option('-d', '--data',
dest = 'data',
action = 'extend', metavar = '<string LIST>',
help = 'scalar/vector value(s) label(s)')
parser.add_option('-t', '--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'tensor (3x3) value label(s)')
parser.add_option('-c', '--color',
dest = 'color',
action = 'extend', metavar = '<string LIST>',
help = 'RGB color tuple label')
parser.set_defaults(data = [],
tensor = [],
color = [],
)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if not options.vtk:
parser.error('No VTK file specified.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
vtk = damask.VTK.from_file(options.vtk)
for data in options.data+options.tensor:
vtk.add(table.get(data),data)
for color in options.color:
vtk.add((table.get(color)*255).astype(np.uint8),color)
vtk.write(options.vtk)

45
processing/post/vtk_pointCloud.py
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@ -1,45 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Produce a VTK point cloud dataset based on coordinates given in an ASCIItable.
""", version = scriptID)
parser.add_option('-p',
'--pos', '--position',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.set_defaults(pos = 'pos',
)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
v = damask.VTK.from_polyData(table.get(options.pos))
if name:
v.write(os.path.splitext(name)[0])
else:
sys.stdout.write(v.__repr__())

58
processing/post/vtk_rectilinearGrid.py
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@ -1,58 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Create regular voxel grid from points in an ASCIItable.
""", version = scriptID)
parser.add_option('-m',
'--mode',
dest = 'mode',
metavar='string',
type = 'choice', choices = ['cell','point'],
help = 'cell-centered or point-centered coordinates')
parser.add_option('-p',
'--pos', '--position',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.set_defaults(mode = 'cell',
pos = 'pos',
)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
if options.mode == 'cell':
grid, size, origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
elif options.mode == 'point':
grid, size, origin = damask.grid_filters.node_coord0_gridSizeOrigin(table.get(options.pos))
v = damask.VTK.from_rectilinearGrid(grid,size,origin)
if name:
v.write('{}_{}({})'.format(os.path.splitext(name)[0],options.pos,options.mode))
else:
sys.stdout.write(v.__repr__())

25
processing/pre/mentat_pbcOnBoxMesh.py
View File

@ -6,7 +6,7 @@ import numpy as np
from optparse import OptionParser
import damask
sys.path.append(damask.solver.Marc().libraryPath())
sys.path.append(str(damask.solver.Marc().library_path))
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -197,14 +197,15 @@ def add_servoLinks(mfd_data,active=[True,True,True]): # directions on which to
if mfd_data[i]['uid'] == 1705: del mfd_data[i]
mfd_data.insert(i, links)
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Set up servo linking to achieve periodic boundary conditions for a regular hexahedral mesh.
Use *py_connection to operate on model presently opened in MSC.Mentat.
""", version = scriptID)
parser.add_option('-p', '--port',
@ -229,10 +230,7 @@ if remote and filenames != []:
if filenames == []: filenames = [None]
if remote:
try: import py_mentat
except:
damask.util.croak('no valid Mentat release found.')
sys.exit(-1)
import py_mentat
damask.util.report(scriptName, 'waiting to connect...')
filenames = [os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()) + '.mfd')]
@ -240,14 +238,14 @@ if remote:
py_mentat.py_connect('',options.port)
py_mentat.py_send('*set_save_formatted on')
py_mentat.py_send('*save_as_model "{}" yes'.format(filenames[0]))
py_mentat.py_get_int("nnodes()") # hopefully blocks until file is written
except:
damask.util.croak('failed. try setting Tools/Python/"Run as Separate Process" & "Initiate".')
sys.exit()
py_mentat.py_get_int("nnodes()")
except py_mentat.InputError as err:
damask.util.croak('{}. Try Tools/Python/"Run as Separate Process" & "Initiate".'.format(err))
sys.exit(-1)
damask.util.croak( 'connected...')
for name in filenames:
while remote and not os.path.exists(name): time.sleep(0.5) # wait for Mentat to write MFD file
while remote and not os.path.exists(name): time.sleep(0.5)
with open( name,'r') if name is not None else sys.stdin as fileIn:
damask.util.report(scriptName, name)
mfd = parseMFD(fileIn)
@ -257,5 +255,4 @@ for name in filenames:
fileOut.write(asMFD(mfd))
if remote:
try: py_mentat.py_send('*open_model "{}"'.format(filenames[0]))
except: damask.util.croak('lost connection on sending open command for "{}".'.format(filenames[0]))
py_mentat.py_send('*open_model "{}"'.format(filenames[0]))

2
processing/pre/mentat_spectralBox.py
View File

@ -9,7 +9,7 @@ import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
sys.path.append(damask.solver.Marc().libraryPath())
sys.path.append(str(damask.solver.Marc().library_path))
#-------------------------------------------------------------------------------------------------
def outMentat(cmd,locals):

4
python/damask/__init__.py
View File

@ -1,9 +1,9 @@
"""Tools for pre and post processing of DAMASK simulations."""
import os as _os
from pathlib import Path as _Path
import re as _re
name = 'damask'
with open(_os.path.join(_os.path.dirname(__file__),'VERSION')) as _f:
with open(_Path(__file__).parent/_Path('VERSION')) as _f:
version = _re.sub(r'^v','',_f.readline().strip())
# make classes directly accessible as damask.Class

4
python/damask/_asciitable.py
View File

@ -157,7 +157,7 @@ class ASCIItable():
def head_write(self,
header = True):
"""Write current header information (info + labels)."""
head = ['{}\theader'.format(len(self.info)+self.__IO__['labeled'])] if header else []
head = [f"{len(self.info)+self.__IO__['labeled']}\theader"] if header else []
head.append(self.info)
if self.__IO__['labeled']:
head.append('\t'.join(map(self._quote,self.tags)))
@ -209,7 +209,7 @@ class ASCIItable():
labelList.append(tags[id])
else:
label = tags[id][2:] # get label
while id < len(tags) and tags[id] == '{}_{}'.format(dim,label): # check successors
while id < len(tags) and tags[id] == f'{dim}_{label}': # check successors
id += 1 # next label...
dim += 1 # ...should be one higher dimension
labelList.append(label) # reached end --> store

24
python/damask/_colormaps.py
View File

@ -1,4 +1,5 @@
import numpy as np
from . import util
class Color:
"""Color representation in and conversion between different color-spaces."""
@ -450,7 +451,7 @@ class Colormap:
def rad_diff(a,b):
return abs(a[2]-b[2])
def adjust_hue(Msh_sat, Msh_unsat):
"""If saturation of one of the two colors is too less than the other, hue of the less."""
if Msh_sat[0] >= Msh_unsat[0]:
@ -502,7 +503,7 @@ class Colormap:
[RGB] colormap for use in paraview or gmsh, or as raw string, or array.
Arguments: name, format, steps, crop.
Format is one of (paraview, gmsh, raw, list).
Format is one of (paraview, gmsh, gom, raw, list).
Crop selects a (sub)range in [-1.0,1.0].
Generates sequential map if one limiting color is either white or black,
diverging map otherwise.
@ -511,23 +512,22 @@ class Colormap:
frac = 0.5*(np.array(crop) + 1.0) # rescale crop range to fractions
colors = [self.color(float(i)/(steps-1)*(frac[1]-frac[0])+frac[0]).express_as(model).color for i in range(steps)]
if format == 'paraview':
colormap = ['[\n {{\n "ColorSpace": "RGB", "Name": "{}", "DefaultMap": true,\n "RGBPoints" : ['.format(name)] \
+ [' {:4d},{:8.6f},{:8.6f},{:8.6f},'.format(i,color[0],color[1],color[2],) \
for i,color in enumerate(colors[:-1])] \
+ [' {:4d},{:8.6f},{:8.6f},{:8.6f} '.format(len(colors),colors[-1][0],colors[-1][1],colors[-1][2],)] \
colormap = [f'[\n {{\n "ColorSpace": "RGB", "Name": "{name}", "DefaultMap": true,\n "RGBPoints" : ['] \
+ [f' {i:4d},{color[0]:8.6f},{color[1]:8.6f},{color[2]:8.6f}{"," if i+1<len(colors) else ""}' \
for i,color in enumerate(colors)] \
+ [' ]\n }\n]']
elif format == 'gmsh':
colormap = ['View.ColorTable = {'] \
+ [',\n'.join(['{%s}'%(','.join([str(x*255.0) for x in color])) for color in colors])] \
+ [',\n'.join([','.join([str(x*255.0) for x in color]) for color in colors])] \
+ ['}']
elif format == 'gom':
colormap = ['1 1 ' + str(name)
+ ' 9 ' + str(name)
+ ' 0 1 0 3 0 0 -1 9 \\ 0 0 0 255 255 255 0 0 255 '
+ '30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 ' + str(len(colors))
+ ' '.join([' 0 %s 255 1'%(' '.join([str(int(x*255.0)) for x in color])) for color in reversed(colors)])]
colormap = [ f'1 1 {name}'
+ f' 9 {name}'
+ ' 0 1 0 3 0 0 -1 9 \\ 0 0 0 255 255 255 0 0 255 '
+ f'30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 {len(colors)}'
+ ' '.join([f' 0 {util.srepr((255*np.array(c)).astype(int)," ")} 255 1' for c in reversed(colors)])]
elif format == 'raw':
colormap = ['\t'.join(map(str,color)) for color in colors]

25
python/damask/_environment.py
View File

@ -1,11 +1,11 @@
import os
from pathlib import Path
import tkinter
class Environment:
def __init__(self):
"""Read and provide values of DAMASK configuration."""
self.options = self._get_options()
try:
tk = tkinter.Tk()
self.screen_width = tk.winfo_screenwidth()
@ -15,17 +15,8 @@ class Environment:
self.screen_width = 1024
self.screen_height = 768
def relPath(self,relative = '.'):
"""Return absolute path from path relative to DAMASK root."""
return os.path.join(self.rootDir(),relative)
def rootDir(self):
"""Return DAMASK root path."""
return os.path.normpath(os.path.join(os.path.realpath(__file__),'../../../'))
def _get_options(self):
@property
def options(self):
options = {}
for item in ['DAMASK_NUM_THREADS',
'MSC_ROOT',
@ -34,3 +25,13 @@ class Environment:
options[item] = os.environ[item] if item in os.environ else None
return options
@property
def root_dir(self):
"""Return DAMASK root path."""
return Path(__file__).parents[2]
# for compatibility
def rootDir(self):
return str(self.root_dir)

93
python/damask/_geom.py
View File

@ -43,12 +43,12 @@ class Geom:
def __repr__(self):
"""Basic information on geometry definition."""
return util.srepr([
'grid a b c: {}'.format(' x '.join(map(str,self.get_grid ()))),
'size x y z: {}'.format(' x '.join(map(str,self.get_size ()))),
'origin x y z: {}'.format(' '.join(map(str,self.get_origin()))),
'homogenization: {}'.format(self.get_homogenization()),
'# microstructures: {}'.format(len(np.unique(self.microstructure))),
'max microstructure: {}'.format(np.nanmax(self.microstructure)),
f'grid a b c: {util.srepr(self.get_grid ()," x ")}',
f'size x y z: {util.srepr(self.get_size ()," x ")}',
f'origin x y z: {util.srepr(self.get_origin()," ")}',
f'homogenization: {self.get_homogenization()}',
f'# microstructures: {self.N_microstructure}',
f'max microstructure: {np.nanmax(self.microstructure)}',
])
@ -71,7 +71,7 @@ class Geom:
grid_old = self.get_grid()
size_old = self.get_size()
origin_old = self.get_origin()
unique_old = len(np.unique(self.microstructure))
unique_old = self.N_microstructure
max_old = np.nanmax(self.microstructure)
if size is not None and rescale:
@ -85,32 +85,32 @@ class Geom:
elif rescale:
self.set_size(self.get_grid()/grid_old*self.size)
message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))]
message = [f'grid a b c: {util.srepr(grid_old," x ")}']
if np.any(grid_old != self.get_grid()):
message[-1] = util.delete(message[-1])
message.append(util.emph('grid a b c: {}'.format(' x '.join(map(str,self.get_grid())))))
message.append(util.emph(f'grid a b c: {util.srepr(self.get_grid()," x ")}'))
message.append('size x y z: {}'.format(' x '.join(map(str,size_old))))
message.append(f'size x y z: {util.srepr(size_old," x ")}')
if np.any(size_old != self.get_size()):
message[-1] = util.delete(message[-1])
message.append(util.emph('size x y z: {}'.format(' x '.join(map(str,self.get_size())))))
message.append(util.emph(f'size x y z: {util.srepr(self.get_size()," x ")}'))
message.append('origin x y z: {}'.format(' '.join(map(str,origin_old))))
message.append(f'origin x y z: {util.srepr(origin_old," ")}')
if np.any(origin_old != self.get_origin()):
message[-1] = util.delete(message[-1])
message.append(util.emph('origin x y z: {}'.format(' '.join(map(str,self.get_origin())))))
message.append(util.emph(f'origin x y z: {util.srepr(self.get_origin()," ")}'))
message.append('homogenization: {}'.format(self.get_homogenization()))
message.append(f'homogenization: {self.get_homogenization()}')
message.append('# microstructures: {}'.format(unique_old))
if unique_old != len(np.unique(self.microstructure)):
message.append(f'# microstructures: {unique_old}')
if unique_old != self.N_microstructure:
message[-1] = util.delete(message[-1])
message.append(util.emph('# microstructures: {}'.format(len(np.unique(self.microstructure)))))
message.append(util.emph(f'# microstructures: {self.N_microstructure}'))
message.append('max microstructure: {}'.format(max_old))
message.append(f'max microstructure: {max_old}')
if max_old != np.nanmax(self.microstructure):
message[-1] = util.delete(message[-1])
message.append(util.emph('max microstructure: {}'.format(np.nanmax(self.microstructure))))
message.append(util.emph(f'max microstructure: {np.nanmax(self.microstructure)}'))
return util.return_message(message)
@ -154,9 +154,9 @@ class Geom:
"""
if microstructure is not None:
if len(microstructure.shape) != 3:
raise ValueError('Invalid microstructure shape {}'.format(microstructure.shape))
raise ValueError(f'Invalid microstructure shape {microstructure.shape}')
elif microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype))
raise TypeError(f'Invalid microstructue data type {microstructure.dtype}')
else:
self.microstructure = np.copy(microstructure)
@ -175,8 +175,8 @@ class Geom:
grid = np.asarray(self.microstructure.shape)
self.size = grid/np.max(grid)
else:
if len(size) != 3 or any(np.array(size)<=0):
raise ValueError('Invalid size {}'.format(size))
if len(size) != 3 or any(np.array(size) <= 0):
raise ValueError(f'Invalid size {size}')
else:
self.size = np.array(size)
@ -193,7 +193,7 @@ class Geom:
"""
if origin is not None:
if len(origin) != 3:
raise ValueError('Invalid origin {}'.format(origin))
raise ValueError(f'Invalid origin {origin}')
else:
self.origin = np.array(origin)
@ -210,7 +210,7 @@ class Geom:
"""
if homogenization is not None:
if not isinstance(homogenization,int) or homogenization < 1:
raise TypeError('Invalid homogenization {}'.format(homogenization))
raise TypeError(f'Invalid homogenization {homogenization}')
else:
self.homogenization = homogenization
@ -222,7 +222,7 @@ class Geom:
@property
def N_microstructure(self):
return len(np.unique(self.microstructure))
return np.unique(self.microstructure).size
def get_microstructure(self):
@ -257,11 +257,11 @@ class Geom:
def get_header(self):
"""Return the full header (grid, size, origin, homogenization, comments)."""
header = ['{} header'.format(len(self.comments)+4)] + self.comments
header = [f'{len(self.comments)+4} header'] + self.comments
header.append('grid a {} b {} c {}'.format(*self.get_grid()))
header.append('size x {} y {} z {}'.format(*self.get_size()))
header.append('origin x {} y {} z {}'.format(*self.get_origin()))
header.append('homogenization {}'.format(self.get_homogenization()))
header.append(f'homogenization {self.get_homogenization()}')
return header
@ -320,7 +320,7 @@ class Geom:
i += len(items)
if i != grid.prod():
raise TypeError('Invalid file: expected {} entries, found {}'.format(grid.prod(),i))
raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')
if not np.any(np.mod(microstructure,1) != 0.0): # no float present
microstructure = microstructure.astype('int')
@ -331,6 +331,7 @@ class Geom:
@staticmethod
def _find_closest_seed(seeds, weights, point):
return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
@staticmethod
def from_Laguerre_tessellation(grid,size,seeds,weights,periodic=True):
"""
@ -373,7 +374,7 @@ class Geom:
else:
microstructure = microstructure.reshape(grid)
#comments = 'geom.py:from_Laguerre_tessellation v{}'.format(version)
#ToDo: comments = 'geom.py:from_Laguerre_tessellation v{}'.format(version)
return Geom(microstructure+1,size,homogenization=1)
@ -398,7 +399,7 @@ class Geom:
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
devNull,microstructure = KDTree.query(coords)
#comments = 'geom.py:from_Voronoi_tessellation v{}'.format(version)
#ToDo: comments = 'geom.py:from_Voronoi_tessellation v{}'.format(version)
return Geom(microstructure.reshape(grid)+1,size,homogenization=1)
@ -418,7 +419,7 @@ class Geom:
grid = self.get_grid()
if pack is None:
plain = grid.prod()/np.unique(self.microstructure).size < 250
plain = grid.prod()/self.N_microstructure < 250
else:
plain = not pack
@ -448,11 +449,11 @@ class Geom:
if compressType is None:
f.write('\n'.join(self.get_header())+'\n')
elif compressType == '.':
f.write('{}\n'.format(former))
f.write(f'{former}\n')
elif compressType == 'to':
f.write('{} to {}\n'.format(start,former))
f.write(f'{start} to {former}\n')
elif compressType == 'of':
f.write('{} of {}\n'.format(reps,former))
f.write(f'{reps} of {former}\n')
compressType = '.'
start = current
@ -461,11 +462,11 @@ class Geom:
former = current
if compressType == '.':
f.write('{}\n'.format(former))
f.write(f'{former}\n')
elif compressType == 'to':
f.write('{} to {}\n'.format(start,former))
f.write(f'{start} to {former}\n')
elif compressType == 'of':
f.write('{} of {}\n'.format(reps,former))
f.write(f'{reps} of {former}\n')
def to_vtk(self,fname=None):
@ -511,7 +512,7 @@ class Geom:
if not all(isinstance(d, str) for d in directions):
raise TypeError('Directions are not of type str.')
elif not set(directions).issubset(valid):
raise ValueError('Invalid direction specified {}'.format(set(directions).difference(valid)))
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
limits = [None,None] if reflect else [-2,0]
ms = self.get_microstructure()
@ -523,7 +524,7 @@ class Geom:
if 'x' in directions:
ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
#self.add_comments('geom.py:mirror v{}'.format(version)
#ToDo: self.add_comments('geom.py:mirror v{}'.format(version)
return self.update(ms,rescale=True)
@ -537,7 +538,7 @@ class Geom:
number of grid points in x,y,z direction.
"""
#self.add_comments('geom.py:scale v{}'.format(version)
#ToDo: self.add_comments('geom.py:scale v{}'.format(version)
return self.update(
ndimage.interpolation.zoom(
self.microstructure,
@ -564,7 +565,7 @@ class Geom:
unique, inverse = np.unique(arr, return_inverse=True)
return unique[np.argmax(np.bincount(inverse))]
#self.add_comments('geom.py:clean v{}'.format(version)
#ToDo: self.add_comments('geom.py:clean v{}'.format(version)
return self.update(ndimage.filters.generic_filter(
self.microstructure,
mostFrequent,
@ -579,7 +580,7 @@ class Geom:
for i, oldID in enumerate(np.unique(self.microstructure)):
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
#self.add_comments('geom.py:renumber v{}'.format(version)
#ToDo: self.add_comments('geom.py:renumber v{}'.format(version)
return self.update(renumbered)
@ -614,7 +615,7 @@ class Geom:
origin = self.origin-(np.asarray(microstructure_in.shape)-self.grid)*.5 * self.size/self.grid
#self.add_comments('geom.py:rotate v{}'.format(version)
#ToDo: self.add_comments('geom.py:rotate v{}'.format(version)
return self.update(microstructure_in,origin=origin,rescale=True)
@ -646,7 +647,7 @@ class Geom:
canvas[l[0]:r[0],l[1]:r[1],l[2]:r[2]] = self.microstructure[L[0]:R[0],L[1]:R[1],L[2]:R[2]]
#self.add_comments('geom.py:canvas v{}'.format(version)
#ToDo: self.add_comments('geom.py:canvas v{}'.format(version)
return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)
@ -666,5 +667,5 @@ class Geom:
for from_ms,to_ms in zip(from_microstructure,to_microstructure):
substituted[self.microstructure==from_ms] = to_ms
#self.add_comments('geom.py:substitute v{}'.format(version)
#ToDo: self.add_comments('geom.py:substitute v{}'.format(version)
return self.update(substituted)

24
python/damask/_lattice.py
View File

@ -38,7 +38,7 @@ class Symmetry:
def __repr__(self):
"""Readable string."""
return '{}'.format(self.system)
return f'{self.system}'
def __eq__(self, other):
@ -82,9 +82,9 @@ class Symmetry:
@property
def symmetry_operations(self):
"""Symmetry operations as Quaternions."""
"""Symmetry operations as quaternions."""
if self.system == 'cubic':
symQuats = [
sym_quats = [
[ 1.0, 0.0, 0.0, 0.0 ],
[ 0.0, 1.0, 0.0, 0.0 ],
[ 0.0, 0.0, 1.0, 0.0 ],
@ -111,7 +111,7 @@ class Symmetry:
[-0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0, 0.0 ],
]
elif self.system == 'hexagonal':
symQuats = [
sym_quats = [
[ 1.0, 0.0, 0.0, 0.0 ],
[-0.5*np.sqrt(3), 0.0, 0.0, -0.5 ],
[ 0.5, 0.0, 0.0, 0.5*np.sqrt(3) ],
@ -126,7 +126,7 @@ class Symmetry:
[ 0.0, 0.5*np.sqrt(3), 0.5, 0.0 ],
]
elif self.system == 'tetragonal':
symQuats = [
sym_quats = [
[ 1.0, 0.0, 0.0, 0.0 ],
[ 0.0, 1.0, 0.0, 0.0 ],
[ 0.0, 0.0, 1.0, 0.0 ],
@ -137,17 +137,17 @@ class Symmetry:
[-0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
]
elif self.system == 'orthorhombic':
symQuats = [
sym_quats = [
[ 1.0,0.0,0.0,0.0 ],
[ 0.0,1.0,0.0,0.0 ],
[ 0.0,0.0,1.0,0.0 ],
[ 0.0,0.0,0.0,1.0 ],
]
else:
symQuats = [
sym_quats = [
[ 1.0,0.0,0.0,0.0 ],
]
return np.array(symQuats)
return np.array(sym_quats)
def in_FZ(self,rho):
@ -350,7 +350,7 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
def __repr__(self):
"""Report basic lattice information."""
return 'Bravais lattice {} ({} crystal system)'.format(self.lattice,self.symmetry)
return f'Bravais lattice {self.lattice} ({self.symmetry} crystal system)'
# Kurdjomov--Sachs orientation relationship for fcc <-> bcc transformation
@ -616,17 +616,17 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
try:
relationship = models[model]
except KeyError :
raise KeyError('Orientation relationship "{}" is unknown'.format(model))
raise KeyError(f'Orientation relationship "{model}" is unknown')
if self.lattice not in relationship['mapping']:
raise ValueError('Relationship "{}" not supported for lattice "{}"'.format(model,self.lattice))
raise ValueError(f'Relationship "{model}" not supported for lattice "{self.lattice}"')
r = {'lattice':Lattice((set(relationship['mapping'])-{self.lattice}).pop()), # target lattice
'rotations':[] }
myPlane_id = relationship['mapping'][self.lattice]
otherPlane_id = (myPlane_id+1)%2
myDir_id = myPlane_id +2
myDir_id = myPlane_id +2
otherDir_id = otherPlane_id +2
for miller in np.hstack((relationship['planes'],relationship['directions'])):

2
python/damask/_orientation.py
View File

@ -61,7 +61,7 @@ class Orientation: # ToDo: make subclass of lattice and Rotation?
if self.lattice.symmetry != other.lattice.symmetry:
raise NotImplementedError('disorientation between different symmetry classes not supported yet.')
mySymEqs = self.equivalent if SST else self.equivalent[0] # take all or only first sym operation
mySymEqs = self.equivalent if SST else self.equivalent[0] #ToDo: This is just me! # take all or only first sym operation
otherSymEqs = other.equivalent
for i,sA in enumerate(mySymEqs):

128
python/damask/_result.py
View File

@ -6,6 +6,7 @@ import os
import datetime
import xml.etree.ElementTree as ET
import xml.dom.minidom
from pathlib import Path
from functools import partial
import h5py
@ -50,8 +51,7 @@ class Result:
self.version_minor = f.attrs['DADF5-minor']
if self.version_major != 0 or not 2 <= self.version_minor <= 6:
raise TypeError('Unsupported DADF5 version {}.{} '.format(self.version_major,
self.version_minor))
raise TypeError(f'Unsupported DADF5 version {self.version_major}.{self.version_minor}')
self.structured = 'grid' in f['geometry'].attrs.keys()
@ -89,7 +89,7 @@ class Result:
'con_physics': self.con_physics, 'mat_physics': self.mat_physics
}
self.fname = os.path.abspath(fname)
self.fname = Path(fname).absolute()
self._allow_modification = False
@ -107,7 +107,7 @@ class Result:
self.pick('increments',all_selected_increments)
in_between = '' if len(all_selected_increments) < 3 else \
''.join(['\n{}\n ...\n'.format(inc) for inc in all_selected_increments[1:-2]])
''.join([f'\n{inc}\n ...\n' for inc in all_selected_increments[1:-2]])
return util.srepr(first + in_between + last)
@ -137,7 +137,7 @@ class Result:
if what == 'increments':
choice = [c if isinstance(c,str) and c.startswith('inc') else
'inc{}'.format(c) for c in choice]
f'inc{c}' for c in choice]
elif what == 'times':
what = 'increments'
if choice == ['*']:
@ -412,21 +412,19 @@ class Result:
message = ''
with h5py.File(self.fname,'r') as f:
for i in self.iterate('increments'):
message += '\n{} ({}s)\n'.format(i,self.times[self.increments.index(i)])
message += f'\n{i} ({self.times[self.increments.index(i)]}s)\n'
for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
for oo in self.iterate(o):
message += ' {}\n'.format(oo)
message += f' {oo}\n'
for pp in self.iterate(p):
message += ' {}\n'.format(pp)
message += f' {pp}\n'
group = '/'.join([i,o[:-1],oo,pp]) # o[:-1]: plural/singular issue
for d in f[group].keys():
try:
dataset = f['/'.join([group,d])]
unit = f" / {dataset.attrs['Unit'].decode()}" if 'Unit' in dataset.attrs else ''
description = dataset.attrs['Description'].decode()
if 'Unit' in dataset.attrs:
message += ' {} / ({}): {}\n'.format(d,dataset.attrs['Unit'].decode(),description)
else:
message += ' {}: {}\n'.format(d,description)
message += f' {d}{unit}: {description}\n'
except KeyError:
pass
return message
@ -528,10 +526,10 @@ class Result:
def _add_absolute(x):
return {
'data': np.abs(x['data']),
'label': '|{}|'.format(x['label']),
'label': f'|{x["label"]}|',
'meta': {
'Unit': x['meta']['Unit'],
'Description': 'Absolute value of {} ({})'.format(x['label'],x['meta']['Description']),
'Description': f"Absolute value of {x['label']} ({x['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -552,14 +550,14 @@ class Result:
def _add_calculation(**kwargs):
formula = kwargs['formula']
for d in re.findall(r'#(.*?)#',formula):
formula = formula.replace('#{}#'.format(d),"kwargs['{}']['data']".format(d))
formula = formula.replace(f'#{d}#',f"kwargs['{d}']['data']")
return {
'data': eval(formula),
'label': kwargs['label'],
'meta': {
'Unit': kwargs['unit'],
'Description': '{} (formula: {})'.format(kwargs['description'],kwargs['formula']),
'Description': f"{kwargs['description']} (formula: {kwargs['formula']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -596,8 +594,9 @@ class Result:
'label': 'sigma',
'meta': {
'Unit': P['meta']['Unit'],
'Description': 'Cauchy stress calculated from {} ({}) and {} ({})'\
.format(P['label'],P['meta']['Description'],F['label'],F['meta']['Description']),
'Description': "Cauchy stress calculated "
f"from {P['label']} ({P['meta']['Description']})"
f" and {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -620,10 +619,10 @@ class Result:
def _add_determinant(T):
return {
'data': np.linalg.det(T['data']),
'label': 'det({})'.format(T['label']),
'label': f"det({T['label']})",
'meta': {
'Unit': T['meta']['Unit'],
'Description': 'Determinant of tensor {} ({})'.format(T['label'],T['meta']['Description']),
'Description': f"Determinant of tensor {T['label']} ({T['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -644,10 +643,10 @@ class Result:
def _add_deviator(T):
return {
'data': mechanics.deviatoric_part(T['data']),
'label': 's_{}'.format(T['label']),
'label': f"s_{T['label']}",
'meta': {
'Unit': T['meta']['Unit'],
'Description': 'Deviator of tensor {} ({})'.format(T['label'],T['meta']['Description']),
'Description': f"Deviator of tensor {T['label']} ({T['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -675,10 +674,10 @@ class Result:
return {
'data': mechanics.eigenvalues(T_sym['data'])[:,p],
'label': 'lambda_{}({})'.format(eigenvalue,T_sym['label']),
'label': f"lambda_{eigenvalue}({T_sym['label']})",
'meta' : {
'Unit': T_sym['meta']['Unit'],
'Description': '{} eigenvalue of {} ({})'.format(label,T_sym['label'],T_sym['meta']['Description']),
'Description': f"{label} eigenvalue of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -708,14 +707,14 @@ class Result:
print('p',eigenvalue)
return {
'data': mechanics.eigenvectors(T_sym['data'])[:,p],
'label': 'v_{}({})'.format(eigenvalue,T_sym['label']),
'label': f"v_{eigenvalue}({T_sym['label']})",
'meta' : {
'Unit': '1',
'Description': 'Eigenvector corresponding to {} eigenvalue of {} ({})'\
.format(label,T_sym['label'],T_sym['meta']['Description']),
'Description': f"Eigenvector corresponding to {label} eigenvalue"
f" of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
}
def add_eigenvector(self,T_sym,eigenvalue='max'):
"""
Add eigenvector of symmetric tensor.
@ -768,10 +767,10 @@ class Result:
def _add_maximum_shear(T_sym):
return {
'data': mechanics.maximum_shear(T_sym['data']),
'label': 'max_shear({})'.format(T_sym['label']),
'label': f"max_shear({T_sym['label']})",
'meta': {
'Unit': T_sym['meta']['Unit'],
'Description': 'Maximum shear component of {} ({})'.format(T_sym['label'],T_sym['meta']['Description']),
'Description': f"Maximum shear component of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -794,11 +793,11 @@ class Result:
'stress'
return {
'data': mechanics.Mises_strain(T_sym['data']) if t=='strain' else mechanics.Mises_stress(T_sym['data']),
'label': '{}_vM'.format(T_sym['label']),
'data': (mechanics.Mises_strain if t=='strain' else mechanics.Mises_stress)(T_sym['data']),
'label': f"{T_sym['label']}_vM",
'meta': {
'Unit': T_sym['meta']['Unit'],
'Description': 'Mises equivalent {} of {} ({})'.format(t,T_sym['label'],T_sym['meta']['Description']),
'Description': f"Mises equivalent {t} of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -831,10 +830,10 @@ class Result:
return {
'data': np.linalg.norm(x['data'],ord=o,axis=axis,keepdims=True),
'label': '|{}|_{}'.format(x['label'],o),
'label': f"|{x['label']}|_{o}",
'meta': {
'Unit': x['meta']['Unit'],
'Description': '{}-norm of {} {} ({})'.format(o,t,x['label'],x['meta']['Description']),
'Description': f"{o}-norm of {t} {x['label']} ({x['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -860,19 +859,20 @@ class Result:
'label': 'S',
'meta': {
'Unit': P['meta']['Unit'],
'Description': '2. Piola-Kirchhoff stress calculated from {} ({}) and {} ({})'\
.format(P['label'],P['meta']['Description'],F['label'],F['meta']['Description']),
'Description': "2. Piola-Kirchhoff stress calculated "
f"from {P['label']} ({P['meta']['Description']})"
f" and {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
def add_PK2(self,P='P',F='F'):
"""
Add second Piola-Kirchhoff calculated from first Piola-Kirchhoff stress and deformation gradient.
Add second Piola-Kirchhoff stress calculated from first Piola-Kirchhoff stress and deformation gradient.
Parameters
----------
P : str, optional
Label first Piola-Kirchhoff stress dataset. Defaults to ‘P’.
Label of first Piola-Kirchhoff stress dataset. Defaults to ‘P’.
F : str, optional
Label of deformation gradient dataset. Defaults to ‘F’.
@ -922,10 +922,10 @@ class Result:
def _add_rotational_part(F):
return {
'data': mechanics.rotational_part(F['data']),
'label': 'R({})'.format(F['label']),
'label': f"R({F['label']})",
'meta': {
'Unit': F['meta']['Unit'],
'Description': 'Rotational part of {} ({})'.format(F['label'],F['meta']['Description']),
'Description': f"Rotational part of {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -946,10 +946,10 @@ class Result:
def _add_spherical(T):
return {
'data': mechanics.spherical_part(T['data']),
'label': 'p_{}'.format(T['label']),
'label': f"p_{T['label']}",
'meta': {
'Unit': T['meta']['Unit'],
'Description': 'Spherical component of tensor {} ({})'.format(T['label'],T['meta']['Description']),
'Description': f"Spherical component of tensor {T['label']} ({T['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -970,10 +970,10 @@ class Result:
def _add_strain_tensor(F,t,m):
return {
'data': mechanics.strain_tensor(F['data'],t,m),
'label': 'epsilon_{}^{}({})'.format(t,m,F['label']),
'label': f"epsilon_{t}^{m}({F['label']})",
'meta': {
'Unit': F['meta']['Unit'],
'Description': 'Strain tensor of {} ({})'.format(F['label'],F['meta']['Description']),
'Description': f"Strain tensor of {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
}
}
@ -1000,11 +1000,11 @@ class Result:
@staticmethod
def _add_stretch_tensor(F,t):
return {
'data': mechanics.left_stretch(F['data']) if t == 'V' else mechanics.right_stretch(F['data']),
'label': '{}({})'.format(t,F['label']),
'data': (mechanics.left_stretch if t.upper() == 'V' else mechanics.right_stretch)(F['data']),
'label': f"{t}({F['label']})",
'meta': {
'Unit': F['meta']['Unit'],
'Description': '{} stretch tensor of {} ({})'.format('Left' if t == 'V' else 'Right',
'Description': '{} stretch tensor of {} ({})'.format('Left' if t.upper() == 'V' else 'Right',
F['label'],F['meta']['Description']),
'Creator': inspect.stack()[0][3][1:]
}
@ -1040,7 +1040,7 @@ class Result:
r = func(**datasets_in,**args)
return [group,r]
except Exception as err:
print('Error during calculation: {}.'.format(err))
print(f'Error during calculation: {err}.')
return None
@ -1051,14 +1051,17 @@ class Result:
Parameters
----------
func : function
Callback function that calculates a new dataset from one or more datasets per HDF5 group.
Callback function that calculates a new dataset from one or
more datasets per HDF5 group.
datasets : dictionary
Details of the datasets to be used: label (in HDF5 file) and arg (argument to which the data is parsed in func).
Details of the datasets to be used: label (in HDF5 file) and
arg (argument to which the data is parsed in func).
args : dictionary, optional
Arguments parsed to func.
"""
pool = multiprocessing.Pool(int(Environment().options['DAMASK_NUM_THREADS']))
num_threads = Environment().options['DAMASK_NUM_THREADS']
pool = multiprocessing.Pool(int(num_threads) if num_threads is not None else None)
lock = multiprocessing.Manager().Lock()
groups = self.groups_with_datasets(datasets.values())
@ -1082,11 +1085,11 @@ class Result:
for l,v in result[1]['meta'].items():
dataset.attrs[l]=v.encode()
creator = 'damask.Result.{} v{}'.format(dataset.attrs['Creator'].decode(),version)
creator = f"damask.Result.{dataset.attrs['Creator'].decode()} v{version}"
dataset.attrs['Creator'] = creator.encode()
except (OSError,RuntimeError) as err:
print('Could not add dataset: {}.'.format(err))
print(f'Could not add dataset: {err}.')
lock.release()
pool.close()
@ -1119,7 +1122,7 @@ class Result:
time_data = ET.SubElement(time, 'DataItem')
time_data.attrib={'Format': 'XML',
'NumberType': 'Float',
'Dimensions': '{}'.format(len(self.times))}
'Dimensions': f'{len(self.times)}'}
time_data.text = ' '.join(map(str,self.times))
attributes = []
@ -1160,7 +1163,7 @@ class Result:
data_items[-1].attrib={'Format': 'HDF',
'Precision': '8',
'Dimensions': '{} {} {} 3'.format(*(self.grid+1))}
data_items[-1].text='{}:/{}/geometry/u_n'.format(os.path.split(self.fname)[1],inc)
data_items[-1].text=f'{os.path.split(self.fname)[1]}:/{inc}/geometry/u_n'
for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
for oo in getattr(self,o):
@ -1175,17 +1178,17 @@ class Result:
if (shape not in [(1,), (3,), (3,3)]) or dtype != np.float64: continue
attributes.append(ET.SubElement(grid, 'Attribute'))
attributes[-1].attrib={'Name': '{}'.format(name.split('/',2)[2]),
attributes[-1].attrib={'Name': name.split('/',2)[2],
'Center': 'Cell',
'AttributeType': 'Tensor'}
data_items.append(ET.SubElement(attributes[-1], 'DataItem'))
data_items[-1].attrib={'Format': 'HDF',
'NumberType': 'Float',
'Precision': '{}'.format(prec),
'Precision': f'{prec}',
'Dimensions': '{} {} {} {}'.format(*self.grid,np.prod(shape))}
data_items[-1].text='{}:{}'.format(os.path.split(self.fname)[1],name)
data_items[-1].text=f'{os.path.split(self.fname)[1]}:{name}'
with open(os.path.splitext(self.fname)[0]+'.xdmf','w') as f:
with open(self.fname.with_suffix('.xdmf').name,'w') as f:
f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
@ -1261,7 +1264,4 @@ class Result:
u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p'))
v.add(u,'u')
file_out = '{}_inc{}'.format(os.path.splitext(os.path.basename(self.fname))[0],
inc[3:].zfill(N_digits))
v.write(file_out)
v.write(f'{self.fname.stem}_inc{inc[3:].zfill(N_digits)}')

283
python/damask/_rotation.py
View File

@ -20,8 +20,8 @@ class Rotation:
when viewing from the end point of the rotation axis towards the origin.
- rotations will be interpreted in the passive sense.
- Euler angle triplets are implemented using the Bunge convention,
with the angular ranges as [0, 2π],[0, π],[0, 2π].
- the rotation angle ω is limited to the interval [0, π].
with the angular ranges as [0,2π], [0,π], [0,2π].
- the rotation angle ω is limited to the interval [0,π].
- the real part of a quaternion is positive, Re(q) > 0
- P = -1 (as default).
@ -49,7 +49,8 @@ class Rotation:
Parameters
----------
quaternion : numpy.ndarray, optional
Unit quaternion that follows the conventions. Use .from_quaternion to perform a sanity check.
Unit quaternion in positive real hemisphere.
Use .from_quaternion to perform a sanity check.
"""
if quaternion.shape[-1] != 4:
@ -76,7 +77,7 @@ class Rotation:
return 'Quaternions:\n'+str(self.quaternion) # ToDo: could be nicer ...
return '\n'.join([
'Quaternion: (real={:.3f}, imag=<{:+.3f}, {:+.3f}, {:+.3f}>)'.format(*(self.quaternion)),
'Matrix:\n{}'.format(self.as_matrix()),
'Matrix:\n{}'.format(np.round(self.as_matrix(),8)),
'Bunge Eulers / deg: ({:3.2f}, {:3.2f}, {:3.2f})'.format(*self.as_Eulers(degrees=True)),
])
@ -116,7 +117,7 @@ class Rotation:
p_o = other.quaternion[...,1:]
q = (q_m*q_o - np.einsum('...i,...i',p_m,p_o).reshape(self.shape+(1,)))
p = q_m*p_o + q_o*p_m + _P * np.cross(p_m,p_o)
return self.__class__(np.block([q,p])).standardize()
return self.__class__(np.block([q,p]))._standardize()
elif isinstance(other,np.ndarray):
if self.shape + (3,) == other.shape:
@ -139,28 +140,26 @@ class Rotation:
else:
raise ValueError('Can only rotate vectors, 2nd order tensors, and 4th order tensors')
else:
raise TypeError('Cannot rotate {}'.format(type(other)))
def inverse(self):
"""In-place inverse rotation/backward rotation."""
self.quaternion[...,1:] *= -1
return self
#@property
def inversed(self):
"""Inverse rotation/backward rotation."""
return self.copy().inverse()
raise TypeError(f'Cannot rotate {type(other)}')
def standardize(self):
"""In-place quaternion representation with positive real part."""
def _standardize(self):
"""Standardize (ensure positive real hemisphere)."""
self.quaternion[self.quaternion[...,0] < 0.0] *= -1
return self
#@property
def standardized(self):
"""Quaternion representation with positive real part."""
return self.copy().standardize()
def inverse(self):
"""In-place inverse rotation (backward rotation)."""
self.quaternion[...,1:] *= -1
return self
def __invert__(self):
"""Inverse rotation (backward rotation)."""
return self.copy().inverse()
def inversed(self):
"""Inverse rotation (backward rotation)."""
return ~ self
def misorientation(self,other):
@ -173,7 +172,7 @@ class Rotation:
Rotation to which the misorientation is computed.
"""
return other*self.inversed()
return other@~self
def broadcast_to(self,shape):
@ -188,7 +187,7 @@ class Rotation:
return self.__class__(q)
def average(self,other):
def average(self,other): #ToDo: discuss calling for vectors
"""
Calculate the average rotation.
@ -208,25 +207,31 @@ class Rotation:
def as_quaternion(self):
"""
Unit quaternion [q, p_1, p_2, p_3].
Represent as unit quaternion.
Parameters
----------
quaternion : bool, optional
return quaternion as DAMASK object.
Returns
-------
q : numpy.ndarray of shape (...,4)
Unit quaternion in positive real hemisphere: (q_0, q_1, q_2, q_3), |q|=1, q_0 ≥ 0.
"""
return self.quaternion
return self.quaternion.copy()
def as_Eulers(self,
degrees = False):
"""
Bunge-Euler angles: (φ_1, ϕ, φ_2).
Represent as Bunge-Euler angles.
Parameters
----------
degrees : bool, optional
return angles in degrees.
Return angles in degrees.
Returns
-------
phi : numpy.ndarray of shape (...,3)
Bunge-Euler angles: (φ_1, ϕ, φ_2), φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π]
unless degrees == True: φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360]
"""
eu = Rotation._qu2eu(self.quaternion)
@ -237,14 +242,21 @@ class Rotation:
degrees = False,
pair = False):
"""
Axis angle representation [n_1, n_2, n_3, ω] unless pair == True: ([n_1, n_2, n_3], ω).
Represent as axis angle pair.
Parameters
----------
degrees : bool, optional
return rotation angle in degrees.
Return rotation angle in degrees. Defaults to False.
pair : bool, optional
return tuple of axis and angle.
Return tuple of axis and angle. Defaults to False.
Returns
-------
axis_angle : numpy.ndarray of shape (...,4) unless pair == True:
tuple containing numpy.ndarray of shapes (...,3) and (...)
Axis angle pair: (n_1, n_2, n_3, ω), |n| = 1 and ω ∈ [0,π]
unless degrees = True: ω ∈ [0,180].
"""
ax = Rotation._qu2ax(self.quaternion)
@ -252,30 +264,60 @@ class Rotation:
return (ax[...,:3],ax[...,3]) if pair else ax
def as_matrix(self):
"""Rotation matrix."""
"""
Represent as rotation matrix.
Returns
-------
R : numpy.ndarray of shape (...,3,3)
Rotation matrix R, det(R) = 1, R.T∙R=I.
"""
return Rotation._qu2om(self.quaternion)
def as_Rodrigues(self,
vector = False):
"""
Rodrigues-Frank vector representation [n_1, n_2, n_3, tan(ω/2)] unless vector == True: [n_1, n_2, n_3] * tan(ω/2).
Represent as Rodrigues-Frank vector with separated axis and angle argument.
Parameters
----------
vector : bool, optional
return as actual Rodrigues--Frank vector, i.e. rotation axis scaled by tan(ω/2).
Return as actual Rodrigues-Frank vector, i.e. axis
and angle argument are not separated.
Returns
-------
rho : numpy.ndarray of shape (...,4) unless vector == True:
numpy.ndarray of shape (...,3)
Rodrigues-Frank vector: [n_1, n_2, n_3, tan(ω/2)], |n| = 1 and ω ∈ [0,π].
"""
ro = Rotation._qu2ro(self.quaternion)
with np.errstate(invalid='ignore'):
return ro[...,:3]*ro[...,3:] if vector else ro
return ro[...,:3]*ro[...,3:4] if vector else ro
def as_homochoric(self):
"""Homochoric vector: (h_1, h_2, h_3)."""
"""
Represent as homochoric vector.
Returns
-------
h : numpy.ndarray of shape (...,3)
Homochoric vector: (h_1, h_2, h_3), |h| < 1/2*π^(2/3).
"""
return Rotation._qu2ho(self.quaternion)
def as_cubochoric(self):
"""Cubochoric vector: (c_1, c_2, c_3)."""
"""
Represent as cubochoric vector.
Returns
-------
c : numpy.ndarray of shape (...,3)
Cubochoric vector: (c_1, c_2, c_3), max(c_i) < 1/2*π^(2/3).
"""
return Rotation._qu2cu(self.quaternion)
@property
@ -296,18 +338,34 @@ class Rotation:
# Static constructors. The input data needs to follow the conventions, options allow to
# relax the conventions.
@staticmethod
def from_quaternion(quaternion,
def from_quaternion(q,
accept_homomorph = False,
P = -1,
acceptHomomorph = None):
acceptHomomorph = None): # old name (for compatibility)
"""
Initialize from quaternion.
Parameters
----------
q : numpy.ndarray of shape (...,4)
Unit quaternion in positive real hemisphere: (q_0, q_1, q_2, q_3),
|q|=1, q_0 ≥ 0.
accept_homomorph : boolean, optional
Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere).
Defaults to False.
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
if acceptHomomorph is not None:
accept_homomorph = acceptHomomorph
qu = np.array(quaternion,dtype=float)
accept_homomorph = acceptHomomorph # for compatibility
qu = np.array(q,dtype=float)
if qu.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if P > 0: qu[...,1:4] *= -1 # convert from P=1 to P=-1
if P == 1: qu[...,1:4] *= -1
if accept_homomorph:
qu[qu[...,0] < 0.0] *= -1
else:
@ -319,10 +377,21 @@ class Rotation:
return Rotation(qu)
@staticmethod
def from_Eulers(eulers,
def from_Eulers(phi,
degrees = False):
"""
Initialize from Bunge-Euler angles.
eu = np.array(eulers,dtype=float)
Parameters
----------
phi : numpy.ndarray of shape (...,3)
Bunge-Euler angles: (φ_1, ϕ, φ_2), φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π]
unless degrees == True: φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360].
degrees : boolean, optional
Bunge-Euler angles are given in degrees. Defaults to False.
"""
eu = np.array(phi,dtype=float)
if eu.shape[:-2:-1] != (3,):
raise ValueError('Invalid shape.')
@ -337,12 +406,29 @@ class Rotation:
degrees = False,
normalise = False,
P = -1):
"""
Initialize from Axis angle pair.
Parameters
----------
axis_angle : numpy.ndarray of shape (...,4)
Axis angle pair: [n_1, n_2, n_3, ω], |n| = 1 and ω ∈ [0,π]
unless degrees = True: ω ∈ [0,180].
degrees : boolean, optional
Angle ω is given in degrees. Defaults to False.
normalize: boolean, optional
Allow |n| ≠ 1. Defaults to False.
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
ax = np.array(axis_angle,dtype=float)
if ax.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if P > 0: ax[...,0:3] *= -1 # convert from P=1 to P=-1
if P == 1: ax[...,0:3] *= -1
if degrees: ax[..., 3] = np.radians(ax[...,3])
if normalise: ax[...,0:3] /= np.linalg.norm(ax[...,0:3],axis=-1)
if np.any(ax[...,3] < 0.0) or np.any(ax[...,3] > np.pi):
@ -356,7 +442,19 @@ class Rotation:
def from_basis(basis,
orthonormal = True,
reciprocal = False):
"""
Initialize from lattice basis vectors.
Parameters
----------
basis : numpy.ndarray of shape (...,3,3)
Three lattice basis vectors in three dimensions.
orthonormal : boolean, optional
Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True.
reciprocal : boolean, optional
Basis vectors are given in reciprocal (instead of real) space. Defaults to False.
"""
om = np.array(basis,dtype=float)
if om.shape[:-3:-1] != (3,3):
raise ValueError('Invalid shape.')
@ -377,20 +475,43 @@ class Rotation:
return Rotation(Rotation._om2qu(om))
@staticmethod
def from_matrix(om):
def from_matrix(R):
"""
Initialize from rotation matrix.
return Rotation.from_basis(om)
Parameters
----------
R : numpy.ndarray of shape (...,3,3)
Rotation matrix: det(R) = 1, R.T∙R=I.
"""
return Rotation.from_basis(R)
@staticmethod
def from_Rodrigues(rodrigues,
def from_Rodrigues(rho,
normalise = False,
P = -1):
"""
Initialize from Rodrigues-Frank vector.
ro = np.array(rodrigues,dtype=float)
Parameters
----------
rho : numpy.ndarray of shape (...,4)
Rodrigues-Frank vector (angle separated from axis).
(n_1, n_2, n_3, tan(ω/2)), |n| = 1 and ω ∈ [0,π].
normalize : boolean, optional
Allow |n| ≠ 1. Defaults to False.
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
ro = np.array(rho,dtype=float)
if ro.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if P > 0: ro[...,0:3] *= -1 # convert from P=1 to P=-1
if P == 1: ro[...,0:3] *= -1
if normalise: ro[...,0:3] /= np.linalg.norm(ro[...,0:3],axis=-1)
if np.any(ro[...,3] < 0.0):
raise ValueError('Rodrigues vector rotation angle not positive.')
@ -400,14 +521,26 @@ class Rotation:
return Rotation(Rotation._ro2qu(ro))
@staticmethod
def from_homochoric(homochoric,
def from_homochoric(h,
P = -1):
"""
Initialize from homochoric vector.
ho = np.array(homochoric,dtype=float)
Parameters
----------
h : numpy.ndarray of shape (...,3)
Homochoric vector: (h_1, h_2, h_3), |h| < (3/4*π)^(1/3).
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
ho = np.array(h,dtype=float)
if ho.shape[:-2:-1] != (3,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if P > 0: ho *= -1 # convert from P=1 to P=-1
if P == 1: ho *= -1
if np.any(np.linalg.norm(ho,axis=-1) >_R1+1e-9):
raise ValueError('Homochoric coordinate outside of the sphere.')
@ -415,18 +548,30 @@ class Rotation:
return Rotation(Rotation._ho2qu(ho))
@staticmethod
def from_cubochoric(cubochoric,
P = -1):
def from_cubochoric(c,
P = -1):
"""
Initialize from cubochoric vector.
cu = np.array(cubochoric,dtype=float)
Parameters
----------
c : numpy.ndarray of shape (...,3)
Cubochoric vector: (c_1, c_2, c_3), max(c_i) < 1/2*π^(2/3).
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
cu = np.array(c,dtype=float)
if cu.shape[:-2:-1] != (3,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if np.abs(np.max(cu))>np.pi**(2./3.) * 0.5+1e-9:
raise ValueError('Cubochoric coordinate outside of the cube: {} {} {}.'.format(*cu))
if np.abs(np.max(cu)) > np.pi**(2./3.) * 0.5+1e-9:
raise ValueError('Cubochoric coordinate outside of the cube.')
ho = Rotation._cu2ho(cu)
if P > 0: ho *= -1 # convert from P=1 to P=-1
if P == 1: ho *= -1
return Rotation(Rotation._ho2qu(ho))
@ -479,7 +624,7 @@ class Rotation:
np.cos(2.0*np.pi*r[...,1])*B,
np.sin(2.0*np.pi*r[...,0])*A],axis=-1)
return Rotation(q.reshape(r.shape[:-1]+(4,)) if shape is not None else q).standardize()
return Rotation(q.reshape(r.shape[:-1]+(4,)) if shape is not None else q)._standardize()
# for compatibility (old names do not follow convention)
@ -493,7 +638,7 @@ class Rotation:
####################################################################################################
# Code below available according to the following conditions on https://github.com/MarDiehl/3Drotations
####################################################################################################
# Copyright (c) 2017-2019, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
# Copyright (c) 2017-2020, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
# Copyright (c) 2013-2014, Marc De Graef/Carnegie Mellon University
# All rights reserved.
#
@ -552,7 +697,7 @@ class Rotation:
np.zeros(qu.shape[:-1]+(2,))]),
np.where(np.abs(q03_s) < 1.0e-8,
np.block([np.arctan2( 2.0*qu[...,1:2]*qu[...,2:3],qu[...,1:2]**2-qu[...,2:3]**2),
np.broadcast_to(np.pi,qu.shape[:-1]+(1,)),
np.broadcast_to(np.pi,qu[...,0:1].shape),
np.zeros(qu.shape[:-1]+(1,))]),
np.block([np.arctan2((-_P*q02+q13)*chi, (-_P*q01-q23)*chi),
np.arctan2( 2.0*chi, q03_s-q12_s ),
@ -575,7 +720,7 @@ class Rotation:
s = np.sign(qu[...,0:1])/np.sqrt(qu[...,1:2]**2+qu[...,2:3]**2+qu[...,3:4]**2)
omega = 2.0 * np.arccos(np.clip(qu[...,0:1],-1.0,1.0))
ax = np.where(np.broadcast_to(qu[...,0:1] < 1.0e-8,qu.shape),
np.block([qu[...,1:4],np.broadcast_to(np.pi,qu.shape[:-1]+(1,))]),
np.block([qu[...,1:4],np.broadcast_to(np.pi,qu[...,0:1].shape)]),
np.block([qu[...,1:4]*s,omega]))
ax[np.isclose(qu[...,0],1.,rtol=0.0)] = [0.0, 0.0, 1.0, 0.0]
return ax
@ -586,7 +731,7 @@ class Rotation:
with np.errstate(invalid='ignore',divide='ignore'):
s = np.linalg.norm(qu[...,1:4],axis=-1,keepdims=True)
ro = np.where(np.broadcast_to(np.abs(qu[...,0:1]) < 1.0e-12,qu.shape),
np.block([qu[...,1:2], qu[...,2:3], qu[...,3:4], np.broadcast_to(np.inf,qu.shape[:-1]+(1,))]),
np.block([qu[...,1:2], qu[...,2:3], qu[...,3:4], np.broadcast_to(np.inf,qu[...,0:1].shape)]),
np.block([qu[...,1:2]/s,qu[...,2:3]/s,qu[...,3:4]/s,
np.tan(np.arccos(np.clip(qu[...,0:1],-1.0,1.0)))
])

35
python/damask/_table.py
View File

@ -4,6 +4,7 @@ import pandas as pd
import numpy as np
from . import version
from . import util
class Table:
"""Store spreadsheet-like data."""
@ -24,7 +25,7 @@ class Table:
"""
self.comments = [] if comments is None else [c for c in comments]
self.data = pd.DataFrame(data=data)
self.shapes = shapes
self.shapes = { k:(v,) if isinstance(v,(np.int,int)) else v for k,v in shapes.items() }
self._label_condensed()
@ -33,7 +34,7 @@ class Table:
labels = []
for label,shape in self.shapes.items():
size = int(np.prod(shape))
labels += ['{}{}'.format('' if size == 1 else '{}_'.format(i+1),label) for i in range(size)]
labels += [('' if size == 1 else f'{i+1}_')+label for i in range(size)]
self.data.columns = labels
@ -47,8 +48,7 @@ class Table:
def _add_comment(self,label,shape,info):
if info is not None:
c = '{}{}: {}'.format(label,' '+str(shape) if np.prod(shape,dtype=int) > 1 else '',info)
self.comments.append(c)
self.comments.append(f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}')
@staticmethod
@ -126,8 +126,6 @@ class Table:
Filename or file for reading.
"""
shapes = {'eu':(3,), 'pos':(2,),
'IQ':(1,), 'CI':(1,), 'ID':(1,), 'intensity':(1,), 'fit':(1,)}
try:
f = open(fname)
except TypeError:
@ -136,7 +134,7 @@ class Table:
content = f.readlines()
comments = ['table.py:from_ang v {}'.format(version)]
comments = [f'table.py:from_ang v{version}']
for line in content:
if line.startswith('#'):
comments.append(line.strip())
@ -144,8 +142,11 @@ class Table:
break
data = np.loadtxt(content)
for c in range(data.shape[1]-10):
shapes['n/a_{}'.format(c+1)] = (1,)
shapes = {'eu':3, 'pos':2, 'IQ':1, 'CI':1, 'ID':1, 'intensity':1, 'fit':1}
remainder = data.shape[1]-sum(shapes.values())
if remainder > 0: # 3.8 can do: if (remainder := data.shape[1]-sum(shapes.values())) > 0
shapes['unknown'] = remainder
return Table(data,shapes,comments)
@ -234,7 +235,6 @@ class Table:
"""
self.data.drop(columns=label,inplace=True)
del self.shapes[label]
@ -251,8 +251,7 @@ class Table:
"""
self.data.rename(columns={label_old:label_new},inplace=True)
c = '{} => {}{}'.format(label_old,label_new,'' if info is None else ': {}'.format(info))
self.comments.append(c)
self.comments.append(f'{label_old} => {label_new}'+('' if info is None else f': {info}'))
self.shapes = {(label if label != label_old else label_new):self.shapes[label] for label in self.shapes}
@ -271,7 +270,7 @@ class Table:
self._label_flat()
self.data.sort_values(labels,axis=0,inplace=True,ascending=ascending)
self._label_condensed()
self.comments.append('sorted by [{}]'.format(', '.join(labels)))
self.comments.append(f'sorted by [{", ".join(labels)}]')
def append(self,other):
@ -328,18 +327,18 @@ class Table:
labels = []
for l in [x for x in self.data.columns if not (x in seen or seen.add(x))]:
if self.shapes[l] == (1,):
labels.append('{}'.format(l))
labels.append(f'{l}')
elif len(self.shapes[l]) == 1:
labels += ['{}_{}'.format(i+1,l) \
labels += [f'{i+1}_{l}' \
for i in range(self.shapes[l][0])]
else:
labels += ['{}:{}_{}'.format('x'.join([str(d) for d in self.shapes[l]]),i+1,l) \
labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
for i in range(np.prod(self.shapes[l]))]
if new_style:
header = ['# {}'.format(comment) for comment in self.comments]
header = [f'# {comment}' for comment in self.comments]
else:
header = ['{} header'.format(len(self.comments)+1)] \
header = [f'{len(self.comments)+1} header'] \
+ self.comments \
try:

78
python/damask/_test.py
View File

@ -53,7 +53,7 @@ class Test:
self.dirBase = os.path.dirname(os.path.realpath(sys.modules[self.__class__.__module__].__file__))
self.parser = OptionParser(option_class=damask.extendableOption,
description = '{} (Test class version: {})'.format(self.description,damask.version),
description = f'{self.description} (Test class version: {damask.version})',
usage = './test.py [options]')
self.parser.add_option("-k", "--keep",
action = "store_true",
@ -93,7 +93,7 @@ class Test:
for variant,object in enumerate(self.variants):
name = self.variantName(variant)
if self.options.show:
logging.critical('{}: {}'.format(variant+1,name))
logging.critical(f'{variant+1}: {name}')
elif self.options.select is not None \
and not (name in self.options.select or str(variant+1) in self.options.select):
pass
@ -106,12 +106,12 @@ class Test:
self.postprocess(variant)
if self.options.update:
if self.update(variant) != 0: logging.critical('update for "{}" failed.'.format(name))
if self.update(variant) != 0: logging.critical(f'update for "{name}" failed.')
elif not (self.options.accept or self.compare(variant)): # no update, do comparison
return variant+1 # return culprit
except Exception as e:
logging.critical('exception during variant execution: "{}"'.format(str(e)))
logging.critical(f'exception during variant execution: "{e}"')
return variant+1 # return culprit
return 0
@ -124,13 +124,13 @@ class Test:
try:
shutil.rmtree(self.dirCurrent())
except FileNotFoundError:
logging.warning('removal of directory "{}" not possible...'.format(self.dirCurrent()))
logging.warning(f'removal of directory "{self.dirCurrent()}" not possible...')
try:
os.mkdir(self.dirCurrent())
return True
except FileExistsError:
logging.critical('creation of directory "{}" failed.'.format(self.dirCurrent()))
logging.critical(f'creation of directory "{self.dirCurrent()}" failed.')
return False
def prepareAll(self):
@ -211,7 +211,7 @@ class Test:
try:
shutil.copy2(source,target)
except FileNotFoundError:
logging.critical('error copying {} to {}'.format(source,target))
logging.critical(f'error copying {source} to {target}')
raise FileNotFoundError
@ -222,7 +222,7 @@ class Test:
try:
shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
except FileNotFoundError:
logging.critical('Reference2Current: Unable to copy file "{}"'.format(f))
logging.critical(f'Reference2Current: Unable to copy file "{f}"')
raise FileNotFoundError
@ -235,7 +235,7 @@ class Test:
shutil.copy2(os.path.join(source,f),self.fileInCurrent(targetfiles[i]))
except FileNotFoundError:
logging.error(os.path.join(source,f))
logging.critical('Base2Current: Unable to copy file "{}"'.format(f))
logging.critical(f'Base2Current: Unable to copy file "{f}"')
raise FileNotFoundError
@ -246,7 +246,7 @@ class Test:
try:
shutil.copy2(self.fileInCurrent(f),self.fileInReference(targetfiles[i]))
except FileNotFoundError:
logging.critical('Current2Reference: Unable to copy file "{}"'.format(f))
logging.critical(f'Current2Reference: Unable to copy file "{f}"')
raise FileNotFoundError
@ -257,7 +257,7 @@ class Test:
try:
shutil.copy2(self.fileInProof(f),self.fileInCurrent(targetfiles[i]))
except FileNotFoundError:
logging.critical('Proof2Current: Unable to copy file "{}"'.format(f))
logging.critical(f'Proof2Current: Unable to copy file "{f}"')
raise FileNotFoundError
@ -267,7 +267,7 @@ class Test:
try:
shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
except FileNotFoundError:
logging.critical('Current2Current: Unable to copy file "{}"'.format(f))
logging.critical(f'Current2Current: Unable to copy file "{f}"')
raise FileNotFoundError
@ -302,9 +302,7 @@ class Test:
max_loc=np.argmax(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
refArrayNonZero = refArrayNonZero[curArray.nonzero()]
curArray = curArray[curArray.nonzero()]
print(' ********\n * maximum relative error {} between {} and {}\n ********'.format(max_err,
refArrayNonZero[max_loc],
curArray[max_loc]))
print(f' ********\n * maximum relative error {max_err} between {refArrayNonZero[max_loc]} and {curArray[max_loc]}\n ********')
return max_err
else:
raise Exception('mismatch in array size to compare')
@ -350,7 +348,7 @@ class Test:
for i in range(dataLength):
if headings0[i]['shape'] != headings1[i]['shape']:
raise Exception('shape mismatch between {} and {} '.format(headings0[i]['label'],headings1[i]['label']))
raise Exception(f"shape mismatch between {headings0[i]['label']} and {headings1[i]['label']}")
shape[i] = headings0[i]['shape']
for j in range(np.shape(shape[i])[0]):
length[i] *= shape[i][j]
@ -358,9 +356,7 @@ class Test:
for j in range(np.shape(normShape[i])[0]):
normLength[i] *= normShape[i][j]
else:
raise Exception('trying to compare {} with {} normed by {} data sets'.format(len(headings0),
len(headings1),
len(normHeadings)))
raise Exception(f'trying to compare {len(headings0)} with {len(headings1)} normed by {len(normHeadings)} data sets')
table0 = damask.ASCIItable(name=file0,readonly=True)
table0.head_read()
@ -372,11 +368,11 @@ class Test:
key1 = ('1_' if length[i]>1 else '') + headings1[i]['label']
normKey = ('1_' if normLength[i]>1 else '') + normHeadings[i]['label']
if key0 not in table0.labels(raw = True):
raise Exception('column "{}" not found in first table...\n'.format(key0))
raise Exception(f'column "{key0}" not found in first table...')
elif key1 not in table1.labels(raw = True):
raise Exception('column "{}" not found in second table...\n'.format(key1))
raise Exception(f'column "{key1}" not found in second table...')
elif normKey not in table0.labels(raw = True):
raise Exception('column "{}" not found in first table...\n'.format(normKey))
raise Exception(f'column "{normKey}" not found in first table...')
else:
column[0][i] = table0.label_index(key0)
column[1][i] = table1.label_index(key1)
@ -404,9 +400,9 @@ class Test:
norm[i] = [1.0 for j in range(line0-len(skipLines))]
absTol[i] = True
if perLine:
logging.warning('At least one norm of "{}" in first table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
logging.warning(f"At least one norm of \"{headings0[i]['label']}\" in first table is 0.0, using absolute tolerance")
else:
logging.warning('Maximum norm of "{}" in first table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
logging.warning(f"Maximum norm of \"{headings0[i]['label']}\" in first table is 0.0, using absolute tolerance")
line1 = 0
while table1.data_read(): # read next data line of ASCII table
@ -418,18 +414,14 @@ class Test:
norm[i][line1-len(skipLines)])
line1 +=1
if (line0 != line1): raise Exception('found {} lines in first table but {} in second table'.format(line0,line1))
if (line0 != line1): raise Exception(f'found {line0} lines in first table but {line1} in second table')
logging.info(' ********')
for i in range(dataLength):
if absTol[i]:
logging.info(' * maximum absolute error {} between {} and {}'.format(maxError[i],
headings0[i]['label'],
headings1[i]['label']))
logging.info(f" * maximum absolute error {maxError[i]} between {headings0[i]['label']} and {headings1[i]['label']}")
else:
logging.info(' * maximum relative error {} between {} and {}'.format(maxError[i],
headings0[i]['label'],
headings1[i]['label']))
logging.info(f" * maximum relative error {maxError[i]} between {headings0[i]['label']} and {headings1[i]['label']}")
logging.info(' ********')
return maxError
@ -480,8 +472,8 @@ class Test:
normedDelta = np.where(normBy>preFilter,delta/normBy,0.0)
mean = np.amax(np.abs(np.mean(normedDelta,0)))
std = np.amax(np.std(normedDelta,0))
logging.info('mean: {:f}'.format(mean))
logging.info('std: {:f}'.format(std))
logging.info(f'mean: {mean:f}')
logging.info(f'std: {std:f}')
return (mean<meanTol) & (std < stdTol)
@ -521,7 +513,7 @@ class Test:
for i,(table,labels) in enumerate(zip(tables,columns)):
if np.any(dimensions != [np.prod(table.shapes[c]) for c in labels]): # check data object consistency
logging.critical('Table {} differs in data layout.'.format(files[i]))
logging.critical(f'Table {files[i]} differs in data layout.')
return False
data.append(np.hstack(list(table.get(label) for label in labels)).astype(np.float)) # store
@ -537,19 +529,19 @@ class Test:
for i in range(len(data)):
data[i] /= maximum # normalize each table
logging.info('shape of data {}: {}'.format(i,data[i].shape))
logging.info(f'shape of data {i}: {data[i].shape}')
if debug:
violators = np.absolute(data[0]-data[1]) > atol + rtol*np.absolute(data[1])
logging.info('shape of violators: {}'.format(violators.shape))
logging.info(f'shape of violators: {violators.shape}')
for j,culprits in enumerate(violators):
goodguys = np.logical_not(culprits)
if culprits.any():
logging.info('{} has {}'.format(j,np.sum(culprits)))
logging.info('deviation: {}'.format(np.absolute(data[0][j]-data[1][j])[culprits]))
logging.info('data : {}'.format(np.absolute(data[1][j])[culprits]))
logging.info('deviation: {}'.format(np.absolute(data[0][j]-data[1][j])[goodguys]))
logging.info('data : {}'.format(np.absolute(data[1][j])[goodguys]))
logging.info(f'{j} has {np.sum(culprits)}')
logging.info(f'deviation: {np.absolute(data[0][j]-data[1][j])[culprits]}')
logging.info(f'data : {np.absolute(data[1][j])[culprits]}')
logging.info(f'deviation: {np.absolute(data[0][j]-data[1][j])[goodguys]}')
logging.info(f'data : {np.absolute(data[1][j])[goodguys]}')
allclose = True # start optimistic
for i in range(1,len(data)):
@ -588,12 +580,12 @@ class Test:
if culprit == 0:
count = len(self.variants) if self.options.select is None else len(self.options.select)
msg = 'Test passed.' if count == 1 else 'All {} tests passed.'.format(count)
msg = 'Test passed.' if count == 1 else f'All {count} tests passed.'
elif culprit == -1:
msg = 'Warning: could not start test...'
ret = 0
else:
msg = 'Test "{}" failed.'.format(self.variantName(culprit-1))
msg = f'Test "{self.variantName(culprit-1)}" failed.'
logging.critical('\n'.join(['*'*40,msg,'*'*40]) + '\n')
return ret

36
python/damask/_vtk.py
View File

@ -1,4 +1,4 @@
import os
from pathlib import Path
import pandas as pd
import numpy as np
@ -51,9 +51,11 @@ class VTK:
"""
geom = vtk.vtkRectilinearGrid()
geom.SetDimensions(*(grid+1))
geom.SetXCoordinates(np_to_vtk(np.linspace(origin[0],origin[0]+size[0],grid[0]+1),deep=True))
geom.SetYCoordinates(np_to_vtk(np.linspace(origin[1],origin[1]+size[1],grid[1]+1),deep=True))
geom.SetZCoordinates(np_to_vtk(np.linspace(origin[2],origin[2]+size[2],grid[2]+1),deep=True))
coord = [np_to_vtk(np.linspace(origin[i],origin[i]+size[i],grid[i]+1),deep=True) for i in [0,1,2]]
[coord[i].SetName(n) for i,n in enumerate(['x','y','z'])]
geom.SetXCoordinates(coord[0])
geom.SetYCoordinates(coord[1])
geom.SetZCoordinates(coord[2])
return VTK(geom)
@ -85,7 +87,7 @@ class VTK:
geom = vtk.vtkUnstructuredGrid()
geom.SetPoints(vtk_nodes)
geom.SetCells(eval('vtk.VTK_{}'.format(cell_type.split('_',1)[-1].upper())),cells)
geom.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
return VTK(geom)
@ -119,17 +121,17 @@ class VTK:
Parameters
----------
fname : str
fname : str or pathlib.Path
Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk.
dataset_type : str, optional
Name of the vtk.vtkDataSet subclass when opening an .vtk file. Valid types are vtkRectilinearGrid,
vtkUnstructuredGrid, and vtkPolyData.
"""
ext = os.path.splitext(fname)[1]
if ext == '.vtk':
ext = Path(fname).suffix
if ext == '.vtk' or dataset_type:
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(fname)
reader.SetFileName(str(fname))
reader.Update()
if dataset_type is None:
raise TypeError('Dataset type for *.vtk file not given.')
@ -140,7 +142,7 @@ class VTK:
elif dataset_type.lower().endswith('polydata'):
geom = reader.GetPolyDataOutput()
else:
raise TypeError('Unknown dataset type for vtk file {}'.format(dataset_type))
raise TypeError(f'Unknown dataset type {dataset_type} for vtk file')
else:
if ext == '.vtr':
reader = vtk.vtkXMLRectilinearGridReader()
@ -149,9 +151,9 @@ class VTK:
elif ext == '.vtp':
reader = vtk.vtkXMLPolyDataReader()
else:
raise TypeError('Unknown file extension {}'.format(ext))
raise TypeError(f'Unknown file extension {ext}')
reader.SetFileName(fname)
reader.SetFileName(str(fname))
reader.Update()
geom = reader.GetOutput()
@ -164,7 +166,7 @@ class VTK:
Parameters
----------
fname : str
fname : str or pathlib.Path
Filename for writing.
"""
@ -176,10 +178,10 @@ class VTK:
writer = vtk.vtkXMLPolyDataWriter()
default_ext = writer.GetDefaultFileExtension()
name, ext = os.path.splitext(fname)
ext = Path(fname).suffix
if ext and ext != '.'+default_ext:
raise ValueError('Given extension {} is not .{}'.format(ext,default_ext))
writer.SetFileName('{}.{}'.format(name,default_ext))
raise ValueError(f'Given extension {ext} does not match default .{default_ext}')
writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
writer.SetCompressorTypeToZLib()
writer.SetDataModeToBinary()
writer.SetInputData(self.geom)
@ -214,7 +216,7 @@ class VTK:
def __repr__(self):
"""ASCII representation of the VTK data."""
writer = vtk.vtkDataSetWriter()
writer.SetHeader('# DAMASK.VTK v{}'.format(version))
writer.SetHeader(f'# DAMASK.VTK v{version}')
writer.WriteToOutputStringOn()
writer.SetInputData(self.geom)
writer.Write()

91
python/damask/config/material.py
View File

@ -1,6 +1,7 @@
import re
import os
from damask import util
class Section():
def __init__(self,data = {'__order__':[]},part = ''):
@ -27,7 +28,7 @@ class Section():
if multiKey not in self.parameters: self.parameters[multiKey] = []
if multiKey not in self.parameters['__order__']: self.parameters['__order__'] += [multiKey]
self.parameters[multiKey] += [[item] for item in data] if isinstance(data, list) else [[data]]
def data(self):
return self.parameters
@ -42,27 +43,27 @@ class Crystallite(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <crystallite> section."""
Section.__init__(self,data)
class Phase(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <Phase> section."""
Section.__init__(self,data)
class Microstructure(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <microstructure> section."""
Section.__init__(self,data)
class Texture(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <texture> section."""
Section.__init__(self,data)
def add_component(self,theType,properties):
scatter = properties['scatter'] if 'scatter' in list(map(str.lower,list(properties.keys()))) else 0.0
fraction = properties['fraction'] if 'fraction' in list(map(str.lower,list(properties.keys()))) else 1.0
@ -81,45 +82,45 @@ class Texture(Section):
)
)
class Material():
"""Read, manipulate, and write material.config files."""
def __init__(self,verbose=True):
"""Generates ordered list of parts."""
self.parts = [
'homogenization',
'crystallite',
'phase',
'texture',
'microstructure',
'homogenization',
'crystallite',
'phase',
'texture',
'microstructure',
]
self.data = {\
'homogenization': {'__order__': []},
'microstructure': {'__order__': []},
'crystallite': {'__order__': []},
'phase': {'__order__': []},
'texture': {'__order__': []},
}
self.data = {
'homogenization': {'__order__': []},
'microstructure': {'__order__': []},
'crystallite': {'__order__': []},
'phase': {'__order__': []},
'texture': {'__order__': []},
}
self.verbose = verbose
def __repr__(self):
"""Returns current data structure in material.config format."""
me = []
for part in self.parts:
if self.verbose: print('processing <{}>'.format(part))
if self.verbose: print(f'processing <{part}>')
me += ['',
'#'*100,
'<{}>'.format(part),
f'<{part}>',
'#'*100,
]
for section in self.data[part]['__order__']:
me += ['[{}] {}'.format(section,'#'+'-'*max(0,96-len(section)))]
me += [f'[{section}] {"#"+"-"*max(0,96-len(section))}']
for key in self.data[part][section]['__order__']:
if key.startswith('(') and key.endswith(')'): # multiple (key)
me += ['{}\t{}'.format(key,' '.join(values)) for values in self.data[part][section][key]]
me += [f'{key}\t{" ".join(values)}' for values in self.data[part][section][key]]
else: # plain key
me += ['{}\t{}'.format(key,' '.join(map(str,self.data[part][section][key])))]
me += [f'{key}\t{util.srepr(self.data[part][section][key]," ")}']
return '\n'.join(me) + '\n'
def parse(self, part=None, sections=[], content=None):
@ -158,7 +159,7 @@ class Material():
self.data[part][name_section][items[0]].append(items[1:])
else: # plain key
self.data[part][name_section][items[0]] = items[1:]
def read(self,filename=None):
@ -174,20 +175,20 @@ class Material():
recursiveRead(match.group(1) if match.group(1).startswith('/') else
os.path.normpath(os.path.join(os.path.dirname(filename),match.group(1))))
return result
c = recursiveRead(filename)
for p in self.parts:
self.parse(part=p, content=c)
def write(self,filename='material.config', overwrite=False):
"""Write to material.config."""
i = 0
outname = filename
while os.path.exists(outname) and not overwrite:
i += 1
outname = '{}_{}'.format(filename,i)
outname = f'{filename}_{i}'
if self.verbose: print('Writing material data to {}'.format(outname))
if self.verbose: print(f'Writing material data to {outname}')
with open(outname,'w') as f:
f.write(str(self))
return outname
@ -196,11 +197,11 @@ class Material():
"""Add Update."""
part = part.lower()
section = section.lower()
if part not in self.parts: raise Exception('invalid part {}'.format(part))
if part not in self.parts: raise Exception(f'invalid part {part}')
if not isinstance(initialData, dict):
initialData = initialData.data()
if section not in self.data[part]: self.data[part]['__order__'] += [section]
if section in self.data[part] and merge:
for existing in self.data[part][section]['__order__']: # replace existing
@ -215,9 +216,9 @@ class Material():
self.data[part][section]['__order__'] += [new]
else:
self.data[part][section] = initialData
def add_microstructure(self, section='',
components={}, # dict of phase,texture, and fraction lists
@ -226,7 +227,7 @@ class Material():
microstructure = Microstructure()
# make keys lower case (http://stackoverflow.com/questions/764235/dictionary-to-lowercase-in-python)
components=dict((k.lower(), v) for k,v in components.items())
for key in ['phase','texture','fraction','crystallite']:
if isinstance(components[key], list):
for i, x in enumerate(components[key]):
@ -239,7 +240,7 @@ class Material():
components[key] = [components[key].lower()]
except AttributeError:
components[key] = [components[key]]
for (phase,texture,fraction,crystallite) in zip(components['phase'],components['texture'],
components['fraction'],components['crystallite']):
microstructure.add_multiKey('constituent','phase %i\ttexture %i\tfraction %g\ncrystallite %i'%(
@ -247,19 +248,19 @@ class Material():
self.data['texture']['__order__'].index(texture)+1,
fraction,
self.data['crystallite']['__order__'].index(crystallite)+1))
self.add_section('microstructure',section,microstructure)
def change_value(self, part=None,
section=None,
key=None,
def change_value(self, part=None,
section=None,
key=None,
value=None):
if not isinstance(value,list):
if not isinstance(value,list):
if not isinstance(value,str):
value = '%s'%value
value = [value]
newlen = len(value)
newlen = len(value)
oldval = self.data[part.lower()][section.lower()][key.lower()]
oldlen = len(oldval)
print('changing %s:%s:%s from %s to %s '%(part.lower(),section.lower(),key.lower(),oldval,value))

4
python/damask/grid_filters.py
View File

@ -233,7 +233,7 @@ def cell_coord0_gridSizeOrigin(coord0,ordered=True):
origin[_np.where(grid==1)] = 0.0
if grid.prod() != len(coord0):
raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
raise ValueError('Data count {len(coord0)} does not match grid {grid}.')
start = origin + delta*.5
end = origin - delta*.5 + size
@ -384,7 +384,7 @@ def node_coord0_gridSizeOrigin(coord0,ordered=True):
origin = mincorner
if (grid+1).prod() != len(coord0):
raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
raise ValueError('Data count {len(coord0)} does not match grid {grid}.')
atol = _np.max(size)*5e-2
if not (_np.allclose(coords[0],_np.linspace(mincorner[0],maxcorner[0],grid[0]+1),atol=atol) and \

42
python/damask/solver/_marc.py
View File

@ -1,7 +1,7 @@
import os
import subprocess
import shlex
import string
from pathlib import Path
from .._environment import Environment
@ -19,28 +19,24 @@ class Marc:
"""
self.solver = 'Marc'
try:
self.version = int(version)
except TypeError:
self.version = -1
self.version = version
#--------------------------
def libraryPath(self):
@property
def library_path(self):
path_MSC = Environment().options['MSC_ROOT']
path_lib = '{}/mentat{}/shlib/linux64'.format(path_MSC,self.version)
path_lib = Path(f'{path_MSC}/mentat{self.version}/shlib/linux64')
return path_lib if os.path.exists(path_lib) else ''
return path_lib if path_lib.is_dir() else None
#--------------------------
def toolsPath(self):
@property
def tools_path(self):
path_MSC = Environment().options['MSC_ROOT']
path_tools = '{}/marc{}/tools'.format(path_MSC,self.version)
path_tools = Path(f'{path_MSC}/marc{self.version}/tools')
return path_tools if os.path.exists(path_tools) else ''
return path_tools if path_tools.is_dir() else None
#--------------------------
@ -53,23 +49,23 @@ class Marc:
):
damaskEnv = Environment()
env = Environment()
user = os.path.join(damaskEnv.relPath('src'),'DAMASK_marc{}.{}'.format(self.version,'f90' if compile else 'marc'))
if not os.path.isfile(user):
raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),user))
usersub = env.root_dir/Path(f'src/DAMASK_marc{self.version}').with_suffix('.f90' if compile else '.marc')
if not usersub.is_file():
raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),usersub))
# Define options [see Marc Installation and Operation Guide, pp 23]
script = 'run_damask_{}mp'.format(optimization)
script = f'run_damask_{optimization}mp'
cmd = os.path.join(self.toolsPath(),script) + \
cmd = str(self.tools_path/Path(script)) + \
' -jid ' + model + '_' + job + \
' -nprocd 1 -autorst 0 -ci n -cr n -dcoup 0 -b no -v no'
if compile: cmd += ' -u ' + user + ' -save y'
else: cmd += ' -prog ' + os.path.splitext(user)[0]
if compile: cmd += ' -u ' + str(usersub) + ' -save y'
else: cmd += ' -prog ' + str(usersub.with_suffix(''))
print('job submission {} compilation: {}'.format('with' if compile else 'without',user))
print('job submission {} compilation: {}'.format(('with' if compile else 'without'),usersub))
if logfile: log = open(logfile, 'w')
print(cmd)
process = subprocess.Popen(shlex.split(cmd),stdout = log,stderr = subprocess.STDOUT)

44
python/damask/util.py
View File

@ -27,7 +27,7 @@ __all__=[
####################################################################################################
def srepr(arg,glue = '\n'):
r"""
Join arguments as individual lines.
Join arguments with glue string.
Parameters
----------
@ -93,7 +93,7 @@ def strikeout(what):
def execute(cmd,
streamIn = None,
stream_in = None,
wd = './',
env = None):
"""
@ -103,7 +103,7 @@ def execute(cmd,
----------
cmd : str
Command to be executed.
streanIn :, optional
stream_in : file object, optional
Input (via pipe) for executed process.
wd : str, optional
Working directory of process. Defaults to ./ .
@ -119,14 +119,14 @@ def execute(cmd,
stderr = subprocess.PIPE,
stdin = subprocess.PIPE,
env = myEnv)
out,error = [i for i in (process.communicate() if streamIn is None
else process.communicate(streamIn.read().encode('utf-8')))]
stdout, stderr = [i for i in (process.communicate() if stream_in is None
else process.communicate(stream_in.read().encode('utf-8')))]
os.chdir(initialPath)
out = out.decode('utf-8').replace('\x08','')
error = error.decode('utf-8').replace('\x08','')
stdout = stdout.decode('utf-8').replace('\x08','')
stderr = stderr.decode('utf-8').replace('\x08','')
if process.returncode != 0:
raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
return out,error
raise RuntimeError(f'{cmd} failed with returncode {process.returncode}')
return stdout, stderr
def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
@ -156,7 +156,7 @@ def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
def scale_to_coprime(v):
"""Scale vector to co-prime (relatively prime) integers."""
MAX_DENOMINATOR = 1000
MAX_DENOMINATOR = 1000000
def get_square_denominator(x):
"""Denominator of the square of a number."""
@ -166,10 +166,13 @@ def scale_to_coprime(v):
"""Least common multiple."""
return a * b // np.gcd(a, b)
denominators = [int(get_square_denominator(i)) for i in v]
s = reduce(lcm, denominators) ** 0.5
m = (np.array(v)*s).astype(np.int)
return m//reduce(np.gcd,m)
m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(np.int)
m = m//reduce(np.gcd,m)
if not np.allclose(v[v.nonzero()]/m[v.nonzero()],v[v.nonzero()][0]/m[m.nonzero()][0]):
raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?')
return m
####################################################################################################
@ -223,21 +226,20 @@ class _ProgressBar:
self.start_time = datetime.datetime.now()
self.last_fraction = 0.0
sys.stderr.write('{} {} 0% ETA n/a'.format(self.prefix, '░'*self.bar_length))
sys.stderr.write(f"{self.prefix} {'░'*self.bar_length} 0% ETA n/a")
sys.stderr.flush()
def update(self,iteration):
fraction = (iteration+1) / self.total
filled_length = int(self.bar_length * fraction)
if int(self.bar_length * fraction) > int(self.bar_length * self.last_fraction):
if filled_length > int(self.bar_length * self.last_fraction):
bar = '█' * filled_length + '░' * (self.bar_length - filled_length)
delta_time = datetime.datetime.now() - self.start_time
remaining_time = (self.total - (iteration+1)) * delta_time / (iteration+1)
remaining_time -= datetime.timedelta(microseconds=remaining_time.microseconds) # remove μs
filled_length = int(self.bar_length * fraction)
bar = '█' * filled_length + '░' * (self.bar_length - filled_length)
sys.stderr.write('\r{} {} {:>4.0%} ETA {}'.format(self.prefix, bar, fraction, remaining_time))
sys.stderr.write(f'\r{self.prefix} {bar} {fraction:>4.0%} ETA {remaining_time}')
sys.stderr.flush()
self.last_fraction = fraction
@ -249,7 +251,7 @@ class _ProgressBar:
class bcolors:
"""
ASCII Colors.
ASCII colors.
https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py
https://stackoverflow.com/questions/287871

4
python/tests/conftest.py
View File

@ -1,4 +1,4 @@
import os
from pathlib import Path
import numpy as np
import pytest
@ -16,7 +16,7 @@ def update(request):
@pytest.fixture
def reference_dir_base():
"""Directory containing reference results."""
return os.path.join(os.path.dirname(__file__),'reference')
return Path(__file__).parent/'reference'
@pytest.fixture
def set_of_quaternions():

67
python/tests/reference/VTK/polyData.vtp Normal file
View File

@ -0,0 +1,67 @@
<?xml version="1.0"?>
<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<PolyData>
<Piece NumberOfPoints="10" NumberOfVerts="0" NumberOfLines="0" NumberOfStrips="0" NumberOfPolys="0">
<PointData>
<DataArray type="Float64" Name="coordinates" NumberOfComponents="3" format="binary" RangeMin="0.7453559924999299" RangeMax="2.449489742783178">
AQAAAACAAADwAAAAagAAAA==eF5jYMAGPuyXOV4IRHvsIfQZe8u+xxZ9j1/sh/Eh9B37IjDj4f5QMLhqD6Gf2odB+Pth6iD0G3sFiLn7ofqg+j/CxOH6IfRX+xCouRYQ+6H0D/sCqH6YuRD6D1wd1B9QmsEBxgcAJsNfhw==
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
<Value index="0">
0.7453559925
</Value>
<Value index="1">
2.4494897428
</Value>
</InformationKey>
</DataArray>
</PointData>
<CellData>
</CellData>
<Points>
<DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="0.7453559924999299" RangeMax="2.449489742783178">
AQAAAACAAADwAAAAagAAAA==eF5jYMAGPuyXOV4IRHvsIfQZe8u+xxZ9j1/sh/Eh9B37IjDj4f5QMLhqD6Gf2odB+Pth6iD0G3sFiLn7ofqg+j/CxOH6IfRX+xCouRYQ+6H0D/sCqH6YuRD6D1wd1B9QmsEBxgcAJsNfhw==
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
<Value index="0">
0.7453559925
</Value>
<Value index="1">
2.4494897428
</Value>
</InformationKey>
</DataArray>
</Points>
<Verts>
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
</Verts>
<Lines>
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
</Lines>
<Strips>
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
</Strips>
<Polys>
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
</Polys>
</Piece>
</PolyData>
</VTKFile>

44
python/tests/reference/VTK/rectilinearGrid.vtr Normal file
View File

@ -0,0 +1,44 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 5 0 6 0 7">
<Piece Extent="0 5 0 6 0 7">
<PointData>
<DataArray type="Float64" Name="node" NumberOfComponents="3" format="binary" RangeMin="0" RangeMax="1.268857754044952">
AQAAAACAAACAHwAAywMAAA==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
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
<Value index="0">
0
</Value>
<Value index="1">
1.268857754
</Value>
</InformationKey>
</DataArray>
</PointData>
<CellData>
<DataArray type="Float64" Name="cell" NumberOfComponents="3" format="binary" RangeMin="0.10871961482881586" RangeMax="1.160792402743735">
AQAAAACAAACwEwAAZQIAAA==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
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
<Value index="0">
0.10871961483
</Value>
<Value index="1">
1.1607924027
</Value>
</InformationKey>
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.6">
AQAAAACAAAAwAAAAJwAAAA==eF5jYICAHXKtrwN37LOH0Ofsua4vLrDlug7l37M3BoPH9gCdQxK6
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAAA4AAAAIgAAAA==eF5jYICAUDA4ag+hr9pDRB9A+U/tV4HBK6j4B3sAk7wQqg==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.5">
AQAAAACAAABAAAAALAAAAA==eF5jYICASSqeQLTJHkIfsr+9LReITkP5l+zB3NvXoOK37SG6HtgDANusGUo=
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

17
python/tests/test_Geom.py
View File

@ -6,6 +6,7 @@ import numpy as np
from damask import Geom
from damask import Rotation
from damask import util
def geom_equal(a,b):
@ -85,8 +86,8 @@ class TestGeom:
def test_mirror(self,default,update,reference_dir,directions,reflect):
modified = copy.deepcopy(default)
modified.mirror(directions,reflect)
tag = 'directions={}_reflect={}'.format('-'.join(directions),reflect)
reference = os.path.join(reference_dir,'mirror_{}.geom'.format(tag))
tag = f'directions={"-".join(directions)}_reflect={reflect}'
reference = os.path.join(reference_dir,f'mirror_{tag}.geom')
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
@ -94,8 +95,8 @@ class TestGeom:
def test_clean(self,default,update,reference_dir,stencil):
modified = copy.deepcopy(default)
modified.clean(stencil)
tag = 'stencil={}'.format(stencil)
reference = os.path.join(reference_dir,'clean_{}.geom'.format(tag))
tag = f'stencil={stencil}'
reference = os.path.join(reference_dir,f'clean_{tag}.geom')
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
@ -111,8 +112,8 @@ class TestGeom:
def test_scale(self,default,update,reference_dir,grid):
modified = copy.deepcopy(default)
modified.scale(grid)
tag = 'grid={}'.format('-'.join([str(x) for x in grid]))
reference = os.path.join(reference_dir,'scale_{}.geom'.format(tag))
tag = f'grid={util.srepr(grid,"-")}'
reference = os.path.join(reference_dir,f'scale_{tag}.geom')
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
@ -150,8 +151,8 @@ class TestGeom:
def test_rotate(self,default,update,reference_dir,Eulers):
modified = copy.deepcopy(default)
modified.rotate(Rotation.from_Eulers(Eulers,degrees=True))
tag = 'Eulers={}-{}-{}'.format(*Eulers)
reference = os.path.join(reference_dir,'rotate_{}.geom'.format(tag))
tag = f'Eulers={util.srepr(Eulers,"-")}'
reference = os.path.join(reference_dir,f'rotate_{tag}.geom')
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))

2
python/tests/test_Lattice.py
View File

@ -154,4 +154,4 @@ class TestSymmetry:
def test_invalid_argument(self,function):
s = Symmetry() # noqa
with pytest.raises(ValueError):
eval('s.{}(np.ones(4))'.format(function))
eval(f's.{function}(np.ones(4))')

2
python/tests/test_Orientation.py
View File

@ -80,7 +80,7 @@ class TestOrientation:
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
@pytest.mark.parametrize('lattice',['fcc','bcc'])
def test_relationship_reference(self,update,reference_dir,model,lattice):
reference = os.path.join(reference_dir,'{}_{}.txt'.format(lattice,model))
reference = os.path.join(reference_dir,f'{lattice}_{model}.txt')
ori = Orientation(Rotation(),lattice)
eu = np.array([o.rotation.as_Eulers(degrees=True) for o in ori.related(model)])
if update:

10
python/tests/test_Result.py
View File

@ -137,7 +137,7 @@ class TestResult:
default.add_Cauchy('P','F')
default.add_eigenvalue('sigma',eigenvalue)
loc = {'sigma' :default.get_dataset_location('sigma'),
'lambda':default.get_dataset_location('lambda_{}(sigma)'.format(eigenvalue))}
'lambda':default.get_dataset_location(f'lambda_{eigenvalue}(sigma)')}
in_memory = function(mechanics.eigenvalues(default.read_dataset(loc['sigma'],0)),axis=1,keepdims=True)
in_file = default.read_dataset(loc['lambda'],0)
assert np.allclose(in_memory,in_file)
@ -147,7 +147,7 @@ class TestResult:
default.add_Cauchy('P','F')
default.add_eigenvector('sigma',eigenvalue)
loc = {'sigma' :default.get_dataset_location('sigma'),
'v(sigma)':default.get_dataset_location('v_{}(sigma)'.format(eigenvalue))}
'v(sigma)':default.get_dataset_location(f'v_{eigenvalue}(sigma)')}
in_memory = mechanics.eigenvectors(default.read_dataset(loc['sigma'],0))[:,idx]
in_file = default.read_dataset(loc['v(sigma)'],0)
assert np.allclose(in_memory,in_file)
@ -179,7 +179,7 @@ class TestResult:
t = ['V','U'][np.random.randint(0,2)]
m = np.random.random()*2.0 - 1.0
default.add_strain_tensor('F',t,m)
label = 'epsilon_{}^{}(F)'.format(t,m)
label = f'epsilon_{t}^{m}(F)'
default.add_Mises(label)
loc = {label :default.get_dataset_location(label),
label+'_vM':default.get_dataset_location(label+'_vM')}
@ -248,7 +248,7 @@ class TestResult:
t = ['V','U'][np.random.randint(0,2)]
m = np.random.random()*2.0 - 1.0
default.add_strain_tensor('F',t,m)
label = 'epsilon_{}^{}(F)'.format(t,m)
label = f'epsilon_{t}^{m}(F)'
loc = {'F': default.get_dataset_location('F'),
label: default.get_dataset_location(label)}
in_memory = mechanics.strain_tensor(default.read_dataset(loc['F'],0),t,m)
@ -302,8 +302,8 @@ class TestResult:
@pytest.mark.parametrize('allowed',['off','on'])
def test_rename(self,default,allowed):
F = default.read_dataset(default.get_dataset_location('F'))
if allowed == 'on':
F = default.read_dataset(default.get_dataset_location('F'))
default.allow_modification()
default.rename('F','new_name')
assert np.all(F == default.read_dataset(default.get_dataset_location('new_name')))

36
python/tests/test_Rotation.py
View File

@ -97,7 +97,7 @@ def qu2ax(qu):
Modified version of the original formulation, should be numerically more stable
"""
if np.isclose(qu[0],1.,rtol=0.0): # set axis to [001] if the angle is 0/360
if np.isclose(qu[0],1.,rtol=0.0): # set axis to [001] if the angle is 0/360
ax = np.array([ 0.0, 0.0, 1.0, 0.0 ])
elif qu[0] > 1.e-8:
s = np.sign(qu[0])/np.sqrt(qu[1]**2+qu[2]**2+qu[3]**2)
@ -461,7 +461,7 @@ def mul(me, other):
other_p = other.quaternion[1:]
R = me.__class__(np.append(me_q*other_q - np.dot(me_p,other_p),
me_q*other_p + other_q*me_p + _P * np.cross(me_p,other_p)))
return R.standardize()
return R._standardize()
elif isinstance(other, np.ndarray):
if other.shape == (3,):
A = me.quaternion[0]**2.0 - np.dot(me.quaternion[1:],me.quaternion[1:])
@ -481,9 +481,9 @@ def mul(me, other):
axes = ((0, 2, 4, 6), (0, 1, 2, 3))
return np.tensordot(RRRR, other, axes)
else:
raise ValueError('Can only rotate vectors, 2nd order ternsors, and 4th order tensors')
raise ValueError('Can only rotate vectors, 2nd order tensors, and 4th order tensors')
else:
raise TypeError('Cannot rotate {}'.format(type(other)))
raise TypeError(f'Cannot rotate {type(other)}')
class TestRotation:
@ -781,6 +781,10 @@ class TestRotation:
rot = Rotation.from_basis(om,False,reciprocal=reciprocal)
assert np.isclose(np.linalg.det(rot.as_matrix()),1.0)
@pytest.mark.parametrize('shape',[None,1,(4,4)])
def test_random(self,shape):
Rotation.from_random(shape)
@pytest.mark.parametrize('function',[Rotation.from_quaternion,
Rotation.from_Eulers,
Rotation.from_axis_angle,
@ -793,6 +797,16 @@ class TestRotation:
with pytest.raises(ValueError):
function(invalid_shape)
@pytest.mark.parametrize('fr,to',[(Rotation.from_quaternion,'as_quaternion'),
(Rotation.from_axis_angle,'as_axis_angle'),
(Rotation.from_Rodrigues, 'as_Rodrigues'),
(Rotation.from_homochoric,'as_homochoric'),
(Rotation.from_cubochoric,'as_cubochoric')])
def test_invalid_P(self,fr,to):
R = Rotation.from_random(np.random.randint(8,32,(3))) # noqa
with pytest.raises(ValueError):
fr(eval(f'R.{to}()'),P=-30)
@pytest.mark.parametrize('shape',[None,(3,),(4,2)])
def test_broadcast(self,shape):
rot = Rotation.from_random(shape)
@ -859,14 +873,18 @@ class TestRotation:
phi_2 = 2*np.pi - phi_1
R_1 = Rotation.from_Eulers(np.array([phi_1,0.,0.]))
R_2 = Rotation.from_Eulers(np.array([0.,0.,phi_2]))
assert np.allclose(data,R_2*(R_1*data))
assert np.allclose(data,R_2@(R_1@data))
def test_rotate_inverse(self):
R = Rotation.from_random()
assert np.allclose(np.eye(3),(~R@R).as_matrix())
@pytest.mark.parametrize('data',[np.random.rand(3),
np.random.rand(3,3),
np.random.rand(3,3,3,3)])
def test_rotate_inverse(self,data):
def test_rotate_inverse_array(self,data):
R = Rotation.from_random()
assert np.allclose(data,R.inversed()*(R*data))
assert np.allclose(data,~R@(R@data))
@pytest.mark.parametrize('data',[np.random.rand(4),
np.random.rand(3,2),
@ -883,3 +901,7 @@ class TestRotation:
R = Rotation.from_random()
with pytest.raises(TypeError):
R*data
def test_misorientation(self):
R = Rotation.from_random()
assert np.allclose(R.misorientation(R).as_matrix(),np.eye(3))

71
python/tests/test_VTK.py
View File

@ -1,14 +1,13 @@
import os
import pytest
import numpy as np
from damask import VTK
from damask import grid_filters
@pytest.fixture
def reference_dir(reference_dir_base):
"""Directory containing reference results."""
return os.path.join(reference_dir_base,'Result')
return reference_dir_base/'VTK'
class TestVTK:
@ -17,18 +16,24 @@ class TestVTK:
size = np.random.random(3) + 1.0
origin = np.random.random(3)
v = VTK.from_rectilinearGrid(grid,size,origin)
s = v.__repr__()
v.write(os.path.join(tmp_path,'rectilinearGrid'))
v = VTK.from_file(os.path.join(tmp_path,'rectilinearGrid.vtr'))
assert(s == v.__repr__())
string = v.__repr__()
v.write(tmp_path/'rectilinearGrid')
vtr = VTK.from_file(tmp_path/'rectilinearGrid.vtr')
with open(tmp_path/'rectilinearGrid.vtk','w') as f:
f.write(string)
vtk = VTK.from_file(tmp_path/'rectilinearGrid.vtk','VTK_rectilinearGrid')
assert(string == vtr.__repr__() == vtk.__repr__())
def test_polyData(self,tmp_path):
points = np.random.rand(3,100)
v = VTK.from_polyData(points)
s = v.__repr__()
v.write(os.path.join(tmp_path,'polyData'))
v = VTK.from_file(os.path.join(tmp_path,'polyData.vtp'))
assert(s == v.__repr__())
string = v.__repr__()
v.write(tmp_path/'polyData')
vtp = VTK.from_file(tmp_path/'polyData.vtp')
with open(tmp_path/'polyData.vtk','w') as f:
f.write(string)
vtk = VTK.from_file(tmp_path/'polyData.vtk','polyData')
assert(string == vtp.__repr__() == vtk.__repr__())
@pytest.mark.parametrize('cell_type,n',[
('VTK_hexahedron',8),
@ -41,7 +46,43 @@ class TestVTK:
nodes = np.random.rand(n,3)
connectivity = np.random.choice(np.arange(n),n,False).reshape(-1,n)
v = VTK.from_unstructuredGrid(nodes,connectivity,cell_type)
s = v.__repr__()
v.write(os.path.join(tmp_path,'unstructuredGrid'))
v = VTK.from_file(os.path.join(tmp_path,'unstructuredGrid.vtu'))
assert(s == v.__repr__())
string = v.__repr__()
v.write(tmp_path/'unstructuredGrid')
vtu = VTK.from_file(tmp_path/'unstructuredGrid.vtu')
with open(tmp_path/'unstructuredGrid.vtk','w') as f:
f.write(string)
vtk = VTK.from_file(tmp_path/'unstructuredGrid.vtk','unstructuredgrid')
assert(string == vtu.__repr__() == vtk.__repr__())
@pytest.mark.parametrize('name,dataset_type',[('this_file_does_not_exist.vtk',None),
('this_file_does_not_exist.vtk','vtk'),
('this_file_does_not_exist.vtx', None)])
def test_invalid_dataset_type(self,dataset_type,name):
with pytest.raises(TypeError):
VTK.from_file('this_file_does_not_exist.vtk',dataset_type)
def test_compare_reference_polyData(self,update,reference_dir,tmp_path):
points=np.dstack((np.linspace(0.,1.,10),np.linspace(0.,2.,10),np.linspace(-1.,1.,10))).squeeze()
polyData = VTK.from_polyData(points)
polyData.add(points,'coordinates')
if update:
polyData.write(reference_dir/'polyData')
else:
reference = VTK.from_file(reference_dir/'polyData.vtp')
assert polyData.__repr__() == reference.__repr__()
def test_compare_reference_rectilinearGrid(self,update,reference_dir,tmp_path):
grid = np.array([5,6,7],int)
size = np.array([.6,1.,.5])
rectilinearGrid = VTK.from_rectilinearGrid(grid,size)
c = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
n = grid_filters.node_coord0(grid,size).reshape(-1,3,order='F')
rectilinearGrid.add(c,'cell')
rectilinearGrid.add(n,'node')
if update:
rectilinearGrid.write(reference_dir/'rectilinearGrid')
else:
reference = VTK.from_file(reference_dir/'rectilinearGrid.vtr')
assert rectilinearGrid.__repr__() == reference.__repr__()

8
python/tests/test_grid_filters.py
View File

@ -30,8 +30,8 @@ class TestGridFilters:
grid = np.random.randint(8,32,(3))
size = np.random.random(3)
origin = np.random.random(3)
coord0 = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode)) # noqa
_grid,_size,_origin = eval('grid_filters.{}_coord0_gridSizeOrigin(coord0.reshape(-1,3,order="F"))'.format(mode))
coord0 = eval(f'grid_filters.{mode}_coord0(grid,size,origin)') # noqa
_grid,_size,_origin = eval(f'grid_filters.{mode}_coord0_gridSizeOrigin(coord0.reshape(-1,3,order="F"))')
assert np.allclose(grid,_grid) and np.allclose(size,_size) and np.allclose(origin,_origin)
def test_displacement_fluct_equivalence(self):
@ -67,8 +67,8 @@ class TestGridFilters:
origin= np.random.random(3)
size = np.random.random(3) # noqa
grid = np.random.randint(8,32,(3))
shifted = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode))
unshifted = eval('grid_filters.{}_coord0(grid,size)'.format(mode))
shifted = eval(f'grid_filters.{mode}_coord0(grid,size,origin)')
unshifted = eval(f'grid_filters.{mode}_coord0(grid,size)')
if mode == 'cell':
assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid) +(3,)))
elif mode == 'node':

33
python/tests/test_util.py Normal file
View File

@ -0,0 +1,33 @@
import pytest
import numpy as np
from damask import util
class TestUtil:
def test_execute_direct(self):
out,err = util.execute('echo test')
assert out=='test\n' and err==''
def test_execute_env(self):
out,err = util.execute('sh -c "echo $test_for_execute"',env={'test_for_execute':'test'})
assert out=='test\n' and err==''
def test_croak(self):
util.croak('Burp!')
@pytest.mark.parametrize('input,output',
[
([2,0],[1,0]),
([0.5,0.5],[1,1]),
([1./2.,1./3.],[3,2]),
([2./3.,1./2.,1./3.],[4,3,2]),
])
def test_scale2coprime(self,input,output):
assert np.allclose(util.scale_to_coprime(np.array(input)),
np.array(output).astype(int))
def test_lackofprecision(self):
with pytest.raises(ValueError):
util.scale_to_coprime(np.array([1/3333,1,1]))

138
src/CPFEM.f90
View File

@ -35,29 +35,15 @@ module CPFEM
CPFEM_dcsdE !< Cauchy stress tangent
real(pReal), dimension (:,:,:,:), allocatable, private :: &
CPFEM_dcsdE_knownGood !< known good tangent
integer(pInt), public :: &
cycleCounter = 0_pInt, & !< needs description
theInc = -1_pInt, & !< needs description
lastLovl = 0_pInt !< lovl in previous call to marc hypela2
real(pReal), public :: &
theTime = 0.0_pReal, & !< needs description
theDelta = 0.0_pReal
logical, public :: &
outdatedFFN1 = .false., & !< needs description
lastIncConverged = .false., & !< needs description
outdatedByNewInc = .false. !< needs description
logical, public, protected :: &
CPFEM_init_done = .false. !< remember whether init has been done already
logical, private :: &
CPFEM_calc_done = .false. !< remember whether first ip has already calced the results
integer(pInt), public :: &
cycleCounter = 0_pInt !< needs description
integer(pInt), parameter, public :: &
CPFEM_COLLECT = 2_pInt**0_pInt, &
CPFEM_CALCRESULTS = 2_pInt**1_pInt, &
CPFEM_AGERESULTS = 2_pInt**2_pInt, &
CPFEM_BACKUPJACOBIAN = 2_pInt**3_pInt, &
CPFEM_RESTOREJACOBIAN = 2_pInt**4_pInt
CPFEM_CALCRESULTS = 2_pInt**0_pInt, &
CPFEM_AGERESULTS = 2_pInt**1_pInt, &
CPFEM_BACKUPJACOBIAN = 2_pInt**2_pInt, &
CPFEM_RESTOREJACOBIAN = 2_pInt**3_pInt
public :: &
CPFEM_general, &
@ -68,14 +54,10 @@ contains
!--------------------------------------------------------------------------------------------------
!> @brief call (thread safe) all module initializations
!> @brief call all module initializations
!--------------------------------------------------------------------------------------------------
subroutine CPFEM_initAll(el,ip)
subroutine CPFEM_initAll
integer(pInt), intent(in) :: el, & !< FE el number
ip !< FE integration point number
CPFEM_init_done = .true.
call DAMASK_interface_init
call prec_init
call IO_init
@ -88,7 +70,7 @@ subroutine CPFEM_initAll(el,ip)
call YAML_init
call HDF5_utilities_init
call results_init(.false.)
call discretization_marc_init(ip, el)
call discretization_marc_init
call lattice_init
call material_init(.false.)
call constitutive_init
@ -124,7 +106,7 @@ end subroutine CPFEM_init
!--------------------------------------------------------------------------------------------------
!> @brief perform initialization at first call, update variables and call the actual material model
!--------------------------------------------------------------------------------------------------
subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyStress, jacobian)
subroutine CPFEM_general(mode, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyStress, jacobian)
integer(pInt), intent(in) :: elFE, & !< FE element number
ip !< integration point number
@ -133,24 +115,21 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
ffn1 !< deformation gradient for t=t1
integer(pInt), intent(in) :: mode !< computation mode 1: regular computation plus aging of results
real(pReal), intent(in) :: temperature_inp !< temperature
logical, intent(in) :: parallelExecution !< flag indicating parallel computation of requested IPs
real(pReal), dimension(6), intent(out) :: cauchyStress !< stress as 6 vector
real(pReal), dimension(6,6), intent(out) :: jacobian !< jacobian as 66 tensor (Consistent tangent dcs/dE)
real(pReal) J_inverse, & ! inverse of Jacobian
rnd
real(pReal), dimension (3,3) :: Kirchhoff, & ! Piola-Kirchhoff stress
cauchyStress33 ! stress vector
real(pReal), dimension (3,3) :: Kirchhoff ! Piola-Kirchhoff stress
real(pReal), dimension (3,3,3,3) :: H_sym, &
H, &
jacobian3333 ! jacobian in Matrix notation
H
integer(pInt) elCP, & ! crystal plasticity element number
i, j, k, l, m, n, ph, homog, mySource
logical updateJaco ! flag indicating if Jacobian has to be updated
real(pReal), parameter :: ODD_STRESS = 1e15_pReal, & !< return value for stress in case of ping pong dummy cycle
ODD_JACOBIAN = 1e50_pReal !< return value for jacobian in case of ping pong dummy cycle
real(pReal), parameter :: ODD_STRESS = 1e15_pReal, & !< return value for stress if terminallyIll
ODD_JACOBIAN = 1e50_pReal !< return value for jacobian if terminallyIll
elCP = mesh_FEM2DAMASK_elem(elFE)
@ -159,9 +138,6 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
write(6,'(/,a)') '#############################################'
write(6,'(a1,a22,1x,i8,a13)') '#','element', elCP, '#'
write(6,'(a1,a22,1x,i8,a13)') '#','ip', ip, '#'
write(6,'(a1,a22,1x,f15.7,a6)') '#','theTime', theTime, '#'
write(6,'(a1,a22,1x,f15.7,a6)') '#','theDelta', theDelta, '#'
write(6,'(a1,a22,1x,i8,a13)') '#','theInc', theInc, '#'
write(6,'(a1,a22,1x,i8,a13)') '#','cycleCounter', cycleCounter, '#'
write(6,'(a1,a22,1x,i8,a13)') '#','computationMode',mode, '#'
if (terminallyIll) &
@ -174,13 +150,8 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
if (iand(mode, CPFEM_RESTOREJACOBIAN) /= 0_pInt) &
CPFEM_dcsde = CPFEM_dcsde_knownGood
!*** age results
if (iand(mode, CPFEM_AGERESULTS) /= 0_pInt) call CPFEM_forward
!*** collection of FEM input with returning of randomize odd stress and jacobian
!* If no parallel execution is required, there is no need to collect FEM input
if (.not. parallelExecution) then
chosenThermal1: select case (thermal_type(material_homogenizationAt(elCP)))
case (THERMAL_conduction_ID) chosenThermal1
temperature(material_homogenizationAt(elCP))%p(thermalMapping(material_homogenizationAt(elCP))%p(ip,elCP)) = &
@ -189,64 +160,22 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
materialpoint_F0(1:3,1:3,ip,elCP) = ffn
materialpoint_F(1:3,1:3,ip,elCP) = ffn1
elseif (iand(mode, CPFEM_COLLECT) /= 0_pInt) then
call random_number(rnd)
if (rnd < 0.5_pReal) rnd = rnd - 1.0_pReal
CPFEM_cs(1:6,ip,elCP) = rnd * ODD_STRESS
CPFEM_dcsde(1:6,1:6,ip,elCP) = ODD_JACOBIAN * math_identity2nd(6)
chosenThermal2: select case (thermal_type(material_homogenizationAt(elCP)))
case (THERMAL_conduction_ID) chosenThermal2
temperature(material_homogenizationAt(elCP))%p(thermalMapping(material_homogenizationAt(elCP))%p(ip,elCP)) = &
temperature_inp
end select chosenThermal2
materialpoint_F0(1:3,1:3,ip,elCP) = ffn
materialpoint_F(1:3,1:3,ip,elCP) = ffn1
CPFEM_calc_done = .false.
endif
!*** calculation of stress and jacobian
if (iand(mode, CPFEM_CALCRESULTS) /= 0_pInt) then
!*** deformation gradient outdated or any actual deformation gradient differs more than relevantStrain from the stored one
validCalculation: if (terminallyIll &
.or. outdatedFFN1 &
.or. any(abs(ffn1 - materialpoint_F(1:3,1:3,ip,elCP)) > defgradTolerance)) then
if (any(abs(ffn1 - materialpoint_F(1:3,1:3,ip,elCP)) > defgradTolerance)) then
if (iand(debug_level(debug_CPFEM), debug_levelBasic) /= 0_pInt) then
write(6,'(a,1x,i8,1x,i2)') '<< CPFEM >> OUTDATED at elFE ip',elFE,ip
write(6,'(a,/,3(12x,3(f10.6,1x),/))') '<< CPFEM >> FFN1 old:',&
transpose(materialpoint_F(1:3,1:3,ip,elCP))
write(6,'(a,/,3(12x,3(f10.6,1x),/))') '<< CPFEM >> FFN1 now:',transpose(ffn1)
endif
outdatedFFN1 = .true.
endif
validCalculation: if (terminallyIll) then
call random_number(rnd)
if (rnd < 0.5_pReal) rnd = rnd - 1.0_pReal
CPFEM_cs(1:6,ip,elCP) = ODD_STRESS * rnd
CPFEM_dcsde(1:6,1:6,ip,elCP) = ODD_JACOBIAN * math_identity2nd(6)
!*** deformation gradient is not outdated
else validCalculation
updateJaco = mod(cycleCounter,iJacoStiffness) == 0
!* no parallel computation, so we use just one single elFE and ip for computation
if (.not. parallelExecution) then
FEsolving_execElem = elCP
FEsolving_execIP = ip
if (iand(debug_level(debug_CPFEM), debug_levelExtensive) /= 0_pInt) &
write(6,'(a,i8,1x,i2)') '<< CPFEM >> calculation for elFE ip ',elFE,ip
call materialpoint_stressAndItsTangent(updateJaco, dt)
FEsolving_execElem = elCP
FEsolving_execIP = ip
if (iand(debug_level(debug_CPFEM), debug_levelExtensive) /= 0_pInt) &
write(6,'(a,i8,1x,i2)') '<< CPFEM >> calculation for elFE ip ',elFE,ip
call materialpoint_stressAndItsTangent(updateJaco, dt)
!* parallel computation and calulation not yet done
elseif (.not. CPFEM_calc_done) then
if (iand(debug_level(debug_CPFEM), debug_levelExtensive) /= 0_pInt) &
write(6,'(a,i8,a,i8)') '<< CPFEM >> calculation for elements ',FEsolving_execElem(1),&
' to ',FEsolving_execElem(2)
call materialpoint_stressAndItsTangent(updateJaco, dt)
CPFEM_calc_done = .true.
endif
!* map stress and stiffness (or return odd values if terminally ill)
terminalIllness: if (terminallyIll) then
call random_number(rnd)
@ -256,7 +185,7 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
else terminalIllness
! translate from P to CS
! translate from P to sigma
Kirchhoff = matmul(materialpoint_P(1:3,1:3,ip,elCP), transpose(materialpoint_F(1:3,1:3,ip,elCP)))
J_inverse = 1.0_pReal / math_det33(materialpoint_F(1:3,1:3,ip,elCP))
CPFEM_cs(1:6,ip,elCP) = math_sym33to6(J_inverse * Kirchhoff,weighted=.false.)
@ -280,7 +209,6 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
endif terminalIllness
endif validCalculation
!* report stress and stiffness
if ((iand(debug_level(debug_CPFEM), debug_levelExtensive) /= 0_pInt) &
.and. ((debug_e == elCP .and. debug_i == ip) &
.or. .not. iand(debug_level(debug_CPFEM), debug_levelSelective) /= 0_pInt)) then
@ -293,35 +221,11 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
endif
!*** warn if stiffness close to zero
if (all(abs(CPFEM_dcsdE(1:6,1:6,ip,elCP)) < 1e-10_pReal)) call IO_warning(601,elCP,ip)
!*** copy to output if using commercial FEM solver
cauchyStress = CPFEM_cs (1:6, ip,elCP)
jacobian = CPFEM_dcsdE(1:6,1:6,ip,elCP)
!*** remember extreme values of stress ...
cauchyStress33 = math_6toSym33(CPFEM_cs(1:6,ip,elCP),weighted=.false.)
if (maxval(cauchyStress33) > debug_stressMax) then
debug_stressMaxLocation = [elCP, ip]
debug_stressMax = maxval(cauchyStress33)
endif
if (minval(cauchyStress33) < debug_stressMin) then
debug_stressMinLocation = [elCP, ip]
debug_stressMin = minval(cauchyStress33)
endif
!*** ... and Jacobian
jacobian3333 = math_66toSym3333(CPFEM_dcsdE(1:6,1:6,ip,elCP),weighted=.false.)
if (maxval(jacobian3333) > debug_jacobianMax) then
debug_jacobianMaxLocation = [elCP, ip]
debug_jacobianMax = maxval(jacobian3333)
endif
if (minval(jacobian3333) < debug_jacobianMin) then
debug_jacobianMinLocation = [elCP, ip]
debug_jacobianMin = minval(jacobian3333)
endif
end subroutine CPFEM_general

327
src/DAMASK_marc.f90
View File

@ -42,9 +42,7 @@ module DAMASK_interface
logical, protected, public :: symmetricSolver
character(len=*), parameter, public :: INPUTFILEEXTENSION = '.dat'
logical, dimension(:,:), public, allocatable :: &
calcMode !< calculate or collect (ping pong scheme)
public :: &
DAMASK_interface_init, &
@ -175,62 +173,62 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
dispt,coord,ffn,frotn,strechn,eigvn,ffn1,frotn1, &
strechn1,eigvn1,ncrd,itel,ndeg,ndm,nnode, &
jtype,lclass,ifr,ifu)
use prec
use DAMASK_interface
use numerics
use FEsolving
use debug
use discretization_marc
use homogenization
use CPFEM
use prec
use DAMASK_interface
use numerics
use FEsolving
use debug
use discretization_marc
use homogenization
use CPFEM
implicit none
!$ include "omp_lib.h" ! the openMP function library
integer, intent(in) :: & ! according to MSC.Marc 2012 Manual D
ngens, & !< size of stress-strain law
nn, & !< integration point number
ndi, & !< number of direct components
nshear, & !< number of shear components
ncrd, & !< number of coordinates
itel, & !< dimension of F and R, either 2 or 3
ndeg, & !< number of degrees of freedom
ndm, & !< not specified in MSC.Marc 2012 Manual D
nnode, & !< number of nodes per element
jtype, & !< element type
ifr, & !< set to 1 if R has been calculated
ifu !< set to 1 if stretch has been calculated
integer, dimension(2), intent(in) :: & ! according to MSC.Marc 2012 Manual D
m, & !< (1) user element number, (2) internal element number
matus, & !< (1) user material identification number, (2) internal material identification number
kcus, & !< (1) layer number, (2) internal layer number
lclass !< (1) element class, (2) 0: displacement, 1: low order Herrmann, 2: high order Herrmann
real(pReal), dimension(*), intent(in) :: & ! has dimension(1) according to MSC.Marc 2012 Manual D, but according to example hypela2.f dimension(*)
e, & !< total elastic strain
de, & !< increment of strain
dt !< increment of state variables
real(pReal), dimension(itel), intent(in) :: & ! according to MSC.Marc 2012 Manual D
strechn, & !< square of principal stretch ratios, lambda(i) at t=n
strechn1 !< square of principal stretch ratios, lambda(i) at t=n+1
real(pReal), dimension(3,3), intent(in) :: & ! has dimension(itel,*) according to MSC.Marc 2012 Manual D, but we alway assume dimension(3,3)
ffn, & !< deformation gradient at t=n
ffn1 !< deformation gradient at t=n+1
real(pReal), dimension(itel,*), intent(in) :: & ! according to MSC.Marc 2012 Manual D
frotn, & !< rotation tensor at t=n
eigvn, & !< i principal direction components for j eigenvalues at t=n
frotn1, & !< rotation tensor at t=n+1
eigvn1 !< i principal direction components for j eigenvalues at t=n+1
real(pReal), dimension(ndeg,*), intent(in) :: & ! according to MSC.Marc 2012 Manual D
disp, & !< incremental displacements
dispt !< displacements at t=n (at assembly, lovl=4) and displacements at t=n+1 (at stress recovery, lovl=6)
real(pReal), dimension(ncrd,*), intent(in) :: & ! according to MSC.Marc 2012 Manual D
coord !< coordinates
real(pReal), dimension(*), intent(inout) :: & ! according to MSC.Marc 2012 Manual D
t !< state variables (comes in at t=n, must be updated to have state variables at t=n+1)
real(pReal), dimension(ndi+nshear), intent(out) :: & ! has dimension(*) according to MSC.Marc 2012 Manual D, but we need to loop over it
s, & !< stress - should be updated by user
g !< change in stress due to temperature effects
real(pReal), dimension(ngens,ngens), intent(out) :: & ! according to MSC.Marc 2012 Manual D, but according to example hypela2.f dimension(ngens,*)
d !< stress-strain law to be formed
implicit none
include "omp_lib.h" ! the openMP function library
integer, intent(in) :: & ! according to MSC.Marc 2012 Manual D
ngens, & !< size of stress-strain law
nn, & !< integration point number
ndi, & !< number of direct components
nshear, & !< number of shear components
ncrd, & !< number of coordinates
itel, & !< dimension of F and R, either 2 or 3
ndeg, & !< number of degrees of freedom
ndm, & !< not specified in MSC.Marc 2012 Manual D
nnode, & !< number of nodes per element
jtype, & !< element type
ifr, & !< set to 1 if R has been calculated
ifu !< set to 1 if stretch has been calculated
integer, dimension(2), intent(in) :: & ! according to MSC.Marc 2012 Manual D
m, & !< (1) user element number, (2) internal element number
matus, & !< (1) user material identification number, (2) internal material identification number
kcus, & !< (1) layer number, (2) internal layer number
lclass !< (1) element class, (2) 0: displacement, 1: low order Herrmann, 2: high order Herrmann
real(pReal), dimension(*), intent(in) :: & ! has dimension(1) according to MSC.Marc 2012 Manual D, but according to example hypela2.f dimension(*)
e, & !< total elastic strain
de, & !< increment of strain
dt !< increment of state variables
real(pReal), dimension(itel), intent(in) :: & ! according to MSC.Marc 2012 Manual D
strechn, & !< square of principal stretch ratios, lambda(i) at t=n
strechn1 !< square of principal stretch ratios, lambda(i) at t=n+1
real(pReal), dimension(3,3), intent(in) :: & ! has dimension(itel,*) according to MSC.Marc 2012 Manual D, but we alway assume dimension(3,3)
ffn, & !< deformation gradient at t=n
ffn1 !< deformation gradient at t=n+1
real(pReal), dimension(itel,*), intent(in) :: & ! according to MSC.Marc 2012 Manual D
frotn, & !< rotation tensor at t=n
eigvn, & !< i principal direction components for j eigenvalues at t=n
frotn1, & !< rotation tensor at t=n+1
eigvn1 !< i principal direction components for j eigenvalues at t=n+1
real(pReal), dimension(ndeg,*), intent(in) :: & ! according to MSC.Marc 2012 Manual D
disp, & !< incremental displacements
dispt !< displacements at t=n (at assembly, lovl=4) and displacements at t=n+1 (at stress recovery, lovl=6)
real(pReal), dimension(ncrd,*), intent(in) :: & ! according to MSC.Marc 2012 Manual D
coord !< coordinates
real(pReal), dimension(*), intent(inout) :: & ! according to MSC.Marc 2012 Manual D
t !< state variables (comes in at t=n, must be updated to have state variables at t=n+1)
real(pReal), dimension(ndi+nshear), intent(out) :: & ! has dimension(*) according to MSC.Marc 2012 Manual D, but we need to loop over it
s, & !< stress - should be updated by user
g !< change in stress due to temperature effects
real(pReal), dimension(ngens,ngens), intent(out) :: & ! according to MSC.Marc 2012 Manual D, but according to example hypela2.f dimension(ngens,*)
d !< stress-strain law to be formed
!--------------------------------------------------------------------------------------------------
! Marc common blocks are in fixed format so they have to be reformated to free format (f90)
@ -239,137 +237,108 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
#include QUOTE(PASTE(./marc/include/concom,Marc4DAMASK)) ! concom is needed for inc, lovl
#include QUOTE(PASTE(./marc/include/creeps,Marc4DAMASK)) ! creeps is needed for timinc (time increment)
logical :: cutBack
real(pReal), dimension(6) :: stress
real(pReal), dimension(6,6) :: ddsdde
integer :: computationMode, i, cp_en, node, CPnodeID
!$ integer(4) :: defaultNumThreadsInt !< default value set by Marc
logical :: cutBack
real(pReal), dimension(6) :: stress
real(pReal), dimension(6,6) :: ddsdde
integer :: computationMode, i, cp_en, node, CPnodeID
integer(4) :: defaultNumThreadsInt !< default value set by Marc
if (iand(debug_level(debug_MARC),debug_LEVELBASIC) /= 0) then
write(6,'(a,/,i8,i8,i2)') ' MSC.MARC information on shape of element(2), IP:', m, nn
write(6,'(a,2(i1))') ' Jacobian: ', ngens,ngens
write(6,'(a,i1)') ' Direct stress: ', ndi
write(6,'(a,i1)') ' Shear stress: ', nshear
write(6,'(a,i2)') ' DoF: ', ndeg
write(6,'(a,i2)') ' Coordinates: ', ncrd
write(6,'(a,i12)') ' Nodes: ', nnode
write(6,'(a,i1)') ' Deformation gradient: ', itel
write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') ' Deformation gradient at t=n:', &
transpose(ffn)
write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') ' Deformation gradient at t=n+1:', &
transpose(ffn1)
endif
integer(pInt), save :: &
theInc = -1_pInt, & !< needs description
lastLovl = 0_pInt !< lovl in previous call to marc hypela2
real(pReal), save :: &
theTime = 0.0_pReal, & !< needs description
theDelta = 0.0_pReal
logical, save :: &
lastIncConverged = .false., & !< needs description
outdatedByNewInc = .false., & !< needs description
CPFEM_init_done = .false. !< remember whether init has been done already
if (iand(debug_level(debug_MARC),debug_LEVELBASIC) /= 0) then
write(6,'(a,/,i8,i8,i2)') ' MSC.MARC information on shape of element(2), IP:', m, nn
write(6,'(a,2(i1))') ' Jacobian: ', ngens,ngens
write(6,'(a,i1)') ' Direct stress: ', ndi
write(6,'(a,i1)') ' Shear stress: ', nshear
write(6,'(a,i2)') ' DoF: ', ndeg
write(6,'(a,i2)') ' Coordinates: ', ncrd
write(6,'(a,i12)') ' Nodes: ', nnode
write(6,'(a,i1)') ' Deformation gradient: ', itel
write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') ' Deformation gradient at t=n:', &
transpose(ffn)
write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') ' Deformation gradient at t=n+1:', &
transpose(ffn1)
endif
!$ defaultNumThreadsInt = omp_get_num_threads() ! remember number of threads set by Marc
!$ call omp_set_num_threads(DAMASK_NumThreadsInt) ! set number of threads for parallel execution set by DAMASK_NUM_THREADS
defaultNumThreadsInt = omp_get_num_threads() ! remember number of threads set by Marc
call omp_set_num_threads(1) ! no openMP
if (.not. CPFEM_init_done) call CPFEM_initAll(m(1),nn)
if (.not. CPFEM_init_done) then
CPFEM_init_done = .true.
call CPFEM_initAll
endif
computationMode = 0 ! save initialization value, since it does not result in any calculation
if (lovl == 4 ) then ! jacobian requested by marc
if (timinc < theDelta .and. theInc == inc .and. lastLovl /= lovl) & ! first after cutback
computationMode = CPFEM_RESTOREJACOBIAN
elseif (lovl == 6) then ! stress requested by marc
cp_en = mesh_FEM2DAMASK_elem(m(1))
if (cptim > theTime .or. inc /= theInc) then ! reached "convergence"
terminallyIll = .false.
cycleCounter = -1 ! first calc step increments this to cycle = 0
if (inc == 0) then ! >> start of analysis <<
lastIncConverged = .false. ! no Jacobian backup
outdatedByNewInc = .false. ! no aging of state
calcMode = .false. ! pretend last step was collection
lastLovl = lovl ! pretend that this is NOT the first after a lovl change
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> start of analysis..! ',m(1),nn
flush(6)
else if (inc - theInc > 1) then ! >> restart of broken analysis <<
lastIncConverged = .false. ! no Jacobian backup
outdatedByNewInc = .false. ! no aging of state
calcMode = .true. ! pretend last step was calculation
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> restart of analysis..! ',m(1),nn
flush(6)
else ! >> just the next inc <<
lastIncConverged = .true. ! request Jacobian backup
outdatedByNewInc = .true. ! request aging of state
calcMode = .true. ! assure last step was calculation
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> new increment..! ',m(1),nn
flush(6)
endif
else if ( timinc < theDelta ) then ! >> cutBack <<
lastIncConverged = .false. ! no Jacobian backup
outdatedByNewInc = .false. ! no aging of state
terminallyIll = .false.
cycleCounter = -1 ! first calc step increments this to cycle = 0
calcMode = .true. ! pretend last step was calculation
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> cutback detected..! ',m(1),nn
flush(6)
endif ! convergence treatment end
computationMode = 0 ! save initialization value, since it does not result in any calculation
if (lovl == 4 ) then ! jacobian requested by marc
if (timinc < theDelta .and. theInc == inc .and. lastLovl /= lovl) & ! first after cutback
computationMode = CPFEM_RESTOREJACOBIAN
elseif (lovl == 6) then ! stress requested by marc
computationMode = CPFEM_CALCRESULTS
cp_en = mesh_FEM2DAMASK_elem(m(1))
if (cptim > theTime .or. inc /= theInc) then ! reached "convergence"
terminallyIll = .false.
cycleCounter = -1 ! first calc step increments this to cycle = 0
if (inc == 0) then ! >> start of analysis <<
lastIncConverged = .false.
outdatedByNewInc = .false.
lastLovl = lovl ! pretend that this is NOT the first after a lovl change
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> start of analysis..! ',m(1),nn
else if (inc - theInc > 1) then ! >> restart of broken analysis <<
lastIncConverged = .false.
outdatedByNewInc = .false.
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> restart of analysis..! ',m(1),nn
else ! >> just the next inc <<
lastIncConverged = .true.
outdatedByNewInc = .true.
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> new increment..! ',m(1),nn
endif
else if ( timinc < theDelta ) then ! >> cutBack <<
lastIncConverged = .false.
outdatedByNewInc = .false.
terminallyIll = .false.
cycleCounter = -1 ! first calc step increments this to cycle = 0
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> cutback detected..! ',m(1),nn
endif ! convergence treatment end
flush(6)
if (lastLovl /= lovl) then
cycleCounter = cycleCounter + 1
!mesh_cellnode = mesh_build_cellnodes() ! update cell node coordinates
!call mesh_build_ipCoordinates() ! update ip coordinates
endif
if (outdatedByNewInc) then
computationMode = ior(computationMode,CPFEM_AGERESULTS)
outdatedByNewInc = .false.
endif
if (lastIncConverged) then
computationMode = ior(computationMode,CPFEM_BACKUPJACOBIAN)
lastIncConverged = .false.
endif
if (usePingPong) then
calcMode(nn,cp_en) = .not. calcMode(nn,cp_en) ! ping pong (calc <--> collect)
if (calcMode(nn,cp_en)) then ! now --- CALC ---
computationMode = CPFEM_CALCRESULTS
if (lastLovl /= lovl) then ! first after ping pong
call debug_reset() ! resets debugging
outdatedFFN1 = .false.
cycleCounter = cycleCounter + 1
!mesh_cellnode = mesh_build_cellnodes() ! update cell node coordinates
!call mesh_build_ipCoordinates() ! update ip coordinates
endif
if (outdatedByNewInc) then
computationMode = ior(computationMode,CPFEM_AGERESULTS) ! calc and age results
outdatedByNewInc = .false. ! reset flag
endif
else ! now --- COLLECT ---
computationMode = CPFEM_COLLECT ! plain collect
if (lastLovl /= lovl .and. & .not. terminallyIll) &
call debug_info() ! first after ping pong reports (meaningful) debugging
if (lastIncConverged) then
computationMode = ior(computationMode,CPFEM_BACKUPJACOBIAN) ! collect and backup Jacobian after convergence
lastIncConverged = .false. ! reset flag
endif
!do node = 1,theMesh%elem%nNodes
!CPnodeID = mesh_element(4+node,cp_en)
!mesh_node(1:ndeg,CPnodeID) = mesh_node0(1:ndeg,CPnodeID) + numerics_unitlength * dispt(1:ndeg,node)
!enddo
endif
theTime = cptim
theDelta = timinc
theInc = inc
else ! --- PLAIN MODE ---
computationMode = CPFEM_CALCRESULTS ! always calc
if (lastLovl /= lovl) then
if (.not. terminallyIll) &
call debug_info() ! first reports (meaningful) debugging
call debug_reset() ! and resets debugging
outdatedFFN1 = .false.
cycleCounter = cycleCounter + 1
!mesh_cellnode = mesh_build_cellnodes() ! update cell node coordinates
!call mesh_build_ipCoordinates() ! update ip coordinates
endif
if (outdatedByNewInc) then
computationMode = ior(computationMode,CPFEM_AGERESULTS)
outdatedByNewInc = .false. ! reset flag
endif
if (lastIncConverged) then
computationMode = ior(computationMode,CPFEM_BACKUPJACOBIAN) ! backup Jacobian after convergence
lastIncConverged = .false. ! reset flag
endif
endif
endif
lastLovl = lovl
theTime = cptim ! record current starting time
theDelta = timinc ! record current time increment
theInc = inc ! record current increment number
call CPFEM_general(computationMode,ffn,ffn1,t(1),timinc,m(1),nn,stress,ddsdde)
endif
lastLovl = lovl ! record lovl
d = ddsdde(1:ngens,1:ngens)
s = stress(1:ndi+nshear)
g = 0.0_pReal
if(symmetricSolver) d = 0.5_pReal*(d+transpose(d))
call CPFEM_general(computationMode,usePingPong,ffn,ffn1,t(1),timinc,m(1),nn,stress,ddsdde)
d = ddsdde(1:ngens,1:ngens)
s = stress(1:ndi+nshear)
g = 0.0_pReal
if(symmetricSolver) d = 0.5_pReal*(d+transpose(d))
!$ call omp_set_num_threads(defaultNumThreadsInt) ! reset number of threads to stored default value
call omp_set_num_threads(defaultNumThreadsInt) ! reset number of threads to stored default value
end subroutine hypela2

2
src/constitutive_plastic_dislotwin.f90
View File

@ -830,7 +830,7 @@ module subroutine plastic_dislotwin_results(instance,group)
'mobile dislocation density','1/m²')
case('rho_dip')
if(prm%sum_N_sl>0) call results_writeDataset(group,stt%rho_dip,'rho_dip',&
'dislocation dipole density''1/m²')
'dislocation dipole density','1/m²')
case('gamma_sl')
if(prm%sum_N_sl>0) call results_writeDataset(group,stt%gamma_sl,'gamma_sl',&
'plastic shear','1')

9
src/crystallite.f90
View File

@ -245,7 +245,7 @@ subroutine crystallite_init
enddo
!$OMP END PARALLEL DO
if(any(plasticState%nonlocal) .and. .not. usePingPong) call IO_error(601) ! exit if nonlocal but no ping-pong ToDo: Why not check earlier? or in nonlocal?
!if(any(plasticState%nonlocal) .and. .not. usePingPong) call IO_error(601)
crystallite_partionedFp0 = crystallite_Fp0
crystallite_partionedFi0 = crystallite_Fi0
@ -276,9 +276,6 @@ subroutine crystallite_init
write(6,'(a42,1x,i10)') 'max # of constituents/integration point: ', cMax
flush(6)
endif
call debug_info
call debug_reset
#endif
end subroutine crystallite_init
@ -287,11 +284,9 @@ end subroutine crystallite_init
!--------------------------------------------------------------------------------------------------
!> @brief calculate stress (P)
!--------------------------------------------------------------------------------------------------
function crystallite_stress(dummyArgumentToPreventInternalCompilerErrorWithGCC)
function crystallite_stress()
logical, dimension(discretization_nIP,discretization_nElem) :: crystallite_stress
real(pReal), intent(in), optional :: &
dummyArgumentToPreventInternalCompilerErrorWithGCC
real(pReal) :: &
formerSubStep
integer :: &

55
src/debug.f90
View File

@ -49,26 +49,11 @@ module debug
debug_i = 1, &
debug_g = 1
integer, dimension(2), public :: &
debug_stressMaxLocation = 0, &
debug_stressMinLocation = 0, &
debug_jacobianMaxLocation = 0, &
debug_jacobianMinLocation = 0
real(pReal), public :: &
debug_stressMax = -huge(1.0_pReal), &
debug_stressMin = huge(1.0_pReal), &
debug_jacobianMax = -huge(1.0_pReal), &
debug_jacobianMin = huge(1.0_pReal)
#ifdef PETSc
character(len=1024), parameter, public :: &
PETSCDEBUG = ' -snes_view -snes_monitor '
#endif
public :: debug_init, &
debug_reset, &
debug_info
public :: debug_init
contains
@ -230,42 +215,4 @@ subroutine debug_init
end subroutine debug_init
!--------------------------------------------------------------------------------------------------
!> @brief resets all debug values
!--------------------------------------------------------------------------------------------------
subroutine debug_reset
debug_stressMaxLocation = 0
debug_stressMinLocation = 0
debug_jacobianMaxLocation = 0
debug_jacobianMinLocation = 0
debug_stressMax = -huge(1.0_pReal)
debug_stressMin = huge(1.0_pReal)
debug_jacobianMax = -huge(1.0_pReal)
debug_jacobianMin = huge(1.0_pReal)
end subroutine debug_reset
!--------------------------------------------------------------------------------------------------
!> @brief writes debug statements to standard out
!--------------------------------------------------------------------------------------------------
subroutine debug_info
!$OMP CRITICAL (write2out)
debugOutputCPFEM: if (iand(debug_level(debug_CPFEM),debug_LEVELBASIC) /= 0 &
.and. any(debug_stressMinLocation /= 0) &
.and. any(debug_stressMaxLocation /= 0) ) then
write(6,'(2/,a,/)') ' Extreme values of returned stress and Jacobian'
write(6,'(a39)') ' value el ip'
write(6,'(a14,1x,e12.3,1x,i8,1x,i4)') ' stress min :', debug_stressMin, debug_stressMinLocation
write(6,'(a14,1x,e12.3,1x,i8,1x,i4)') ' max :', debug_stressMax, debug_stressMaxLocation
write(6,'(a14,1x,e12.3,1x,i8,1x,i4)') ' Jacobian min :', debug_jacobianMin, debug_jacobianMinLocation
write(6,'(a14,1x,e12.3,1x,i8,1x,i4,/)') ' max :', debug_jacobianMax, debug_jacobianMaxLocation
endif debugOutputCPFEM
!$OMP END CRITICAL (write2out)
end subroutine debug_info
end module debug

2
src/discretization.f90
View File

@ -49,7 +49,7 @@ subroutine discretization_init(homogenizationAt,microstructureAt,&
IPcoords0, &
NodeCoords0
integer, optional, intent(in) :: &
sharedNodesBegin
sharedNodesBegin !< index of first node shared among different processes (MPI)
write(6,'(/,a)') ' <<<+- discretization init -+>>>'; flush(6)

3
src/homogenization.f90
View File

@ -249,7 +249,8 @@ subroutine materialpoint_stressAndItsTangent(updateJaco,dt)
NiterationHomog = 0
cutBackLooping: do while (.not. terminallyIll .and. &
any(subStep(:,FEsolving_execELem(1):FEsolving_execElem(2)) > num%subStepMinHomog))
any(subStep(FEsolving_execIP(1):FEsolving_execIP(2),&
FEsolving_execElem(1):FEsolving_execElem(2)) > num%subStepMinHomog))
!$OMP PARALLEL DO PRIVATE(myNgrains)
elementLooping1: do e = FEsolving_execElem(1),FEsolving_execElem(2)

10
src/marc/discretization_marc.f90
View File

@ -45,10 +45,8 @@ contains
!> @brief initializes the mesh by calling all necessary private routines the mesh module
!! Order and routines strongly depend on type of solver
!--------------------------------------------------------------------------------------------------
subroutine discretization_marc_init(ip,el)
subroutine discretization_marc_init
integer, intent(in) :: el, ip
real(pReal), dimension(:,:), allocatable :: &
node0_elem, & !< node x,y,z coordinates (initially!)
node0_cell
@ -70,7 +68,7 @@ subroutine discretization_marc_init(ip,el)
real(pReal), dimension(:,:,:,:),allocatable :: &
unscaledNormals
write(6,'(/,a)') ' <<<+- mesh init -+>>>'; flush(6)
write(6,'(/,a)') ' <<<+- discretization_marc init -+>>>'; flush(6)
mesh_unitlength = numerics_unitlength ! set physical extent of a length unit in mesh
@ -83,10 +81,6 @@ subroutine discretization_marc_init(ip,el)
FEsolving_execElem = [1,nElems]
FEsolving_execIP = [1,elem%nIPs]
allocate(calcMode(elem%nIPs,nElems),source=.false.) ! pretend to have collected what first call is asking (F = I)
calcMode(ip,mesh_FEM2DAMASK_elem(el)) = .true. ! first ip,el needs to be already pingponged to "calc"
allocate(cellNodeDefinition(elem%nNodes-1))
allocate(connectivity_cell(elem%NcellNodesPerCell,elem%nIPs,nElems))
call buildCells(connectivity_cell,cellNodeDefinition,&

157
src/mesh/discretization_mesh.f90
View File

@ -8,53 +8,50 @@ module discretization_mesh
#include <petsc/finclude/petscdmplex.h>
#include <petsc/finclude/petscis.h>
#include <petsc/finclude/petscdmda.h>
use PETScdmplex
use PETScdmda
use PETScis
use PETScdmplex
use PETScdmda
use PETScis
use DAMASK_interface
use IO
use debug
use discretization
use numerics
use FEsolving
use FEM_quadrature
use prec
implicit none
private
integer, public, protected :: &
mesh_Nboundaries, &
mesh_NcpElemsGlobal
use DAMASK_interface
use IO
use debug
use discretization
use numerics
use FEsolving
use FEM_quadrature
use prec
integer :: &
mesh_NcpElems !< total number of CP elements in mesh
implicit none
private
integer, public, protected :: &
mesh_Nboundaries, &
mesh_NcpElemsGlobal
integer :: &
mesh_NcpElems !< total number of CP elements in mesh
!!!! BEGIN DEPRECATED !!!!!
integer, public, protected :: &
mesh_maxNips !< max number of IPs in any CP element
integer, public, protected :: &
mesh_maxNips !< max number of IPs in any CP element
!!!! BEGIN DEPRECATED !!!!!
integer, dimension(:,:), allocatable :: &
mesh_element !DEPRECATED
real(pReal), dimension(:,:), allocatable :: &
mesh_ipVolume, & !< volume associated with IP (initially!)
mesh_node0 !< node x,y,z coordinates (initially!)
real(pReal), dimension(:,:), allocatable :: &
mesh_ipVolume, & !< volume associated with IP (initially!)
mesh_node0 !< node x,y,z coordinates (initially!)
real(pReal), dimension(:,:,:), allocatable :: &
mesh_ipCoordinates !< IP x,y,z coordinates (after deformation!)
real(pReal), dimension(:,:,:), allocatable :: &
mesh_ipCoordinates !< IP x,y,z coordinates (after deformation!)
DM, public :: geomMesh
PetscInt, dimension(:), allocatable, public, protected :: &
mesh_boundaries
DM, public :: geomMesh
public :: &
discretization_mesh_init, &
mesh_FEM_build_ipVolumes, &
mesh_FEM_build_ipCoordinates
PetscInt, dimension(:), allocatable, public, protected :: &
mesh_boundaries
public :: &
discretization_mesh_init, &
mesh_FEM_build_ipVolumes, &
mesh_FEM_build_ipCoordinates
contains
@ -67,39 +64,33 @@ subroutine discretization_mesh_init(restart)
logical, intent(in) :: restart
integer, dimension(1), parameter:: FE_geomtype = [1] !< geometry type of particular element type
integer, dimension(1) :: FE_Nips !< number of IPs in a specific type of element
integer, allocatable, dimension(:) :: chunkPos
integer :: dimPlex, &
mesh_Nnodes, & !< total number of nodes in mesh
j, l
integer, parameter :: &
mesh_ElemType=1 !< Element type of the mesh (only support homogeneous meshes)
PetscSF :: sf
DM :: globalMesh
PetscInt :: nFaceSets
PetscInt, pointer, dimension(:) :: pFaceSets
character(len=pStringLen), dimension(:), allocatable :: fileContent
IS :: faceSetIS
IS :: faceSetIS
PetscErrorCode :: ierr
integer, dimension(:), allocatable :: &
homogenizationAt, &
microstructureAt
write(6,'(/,a)') ' <<<+- mesh init -+>>>'
! read in file
call DMPlexCreateFromFile(PETSC_COMM_WORLD,geometryFile,PETSC_TRUE,globalMesh,ierr)
CHKERRQ(ierr)
! get spatial dimension (2 or 3?)
call DMGetDimension(globalMesh,dimPlex,ierr)
CHKERRQ(ierr)
write(6,*) 'dimension',dimPlex;flush(6)
call DMGetStratumSize(globalMesh,'depth',dimPlex,mesh_NcpElemsGlobal,ierr)
CHKERRQ(ierr)
! get number of IDs in face sets (for boundary conditions?)
call DMGetLabelSize(globalMesh,'Face Sets',mesh_Nboundaries,ierr)
CHKERRQ(ierr)
write(6,*) 'number of "Face Sets"',mesh_Nboundaries;flush(6)
call MPI_Bcast(mesh_Nboundaries,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
call MPI_Bcast(mesh_NcpElemsGlobal,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
call MPI_Bcast(dimPlex,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
@ -142,48 +133,42 @@ subroutine discretization_mesh_init(restart)
enddo
call DMClone(globalMesh,geomMesh,ierr)
CHKERRQ(ierr)
else
else
call DMPlexDistribute(globalMesh,0,sf,geomMesh,ierr)
CHKERRQ(ierr)
endif
endif
call DMDestroy(globalMesh,ierr); CHKERRQ(ierr)
call DMGetStratumSize(geomMesh,'depth',dimPlex,mesh_NcpElems,ierr)
CHKERRQ(ierr)
call DMGetStratumSize(geomMesh,'depth',0,mesh_Nnodes,ierr)
CHKERRQ(ierr)
FE_Nips(FE_geomtype(1)) = FEM_nQuadrature(dimPlex,integrationOrder)
mesh_maxNips = FE_Nips(1)
write(6,*) 'mesh_maxNips',mesh_maxNips
mesh_maxNips = FEM_nQuadrature(dimPlex,integrationOrder)
call mesh_FEM_build_ipCoordinates(dimPlex,FEM_quadrature_points(dimPlex,integrationOrder)%p)
call mesh_FEM_build_ipVolumes(dimPlex)
allocate (mesh_element (4,mesh_NcpElems)); mesh_element = 0
do j = 1, mesh_NcpElems
mesh_element( 1,j) = -1 ! DEPRECATED
mesh_element( 2,j) = mesh_elemType ! elem type
mesh_element( 3,j) = 1 ! homogenization
call DMGetLabelValue(geomMesh,'material',j-1,mesh_element(4,j),ierr)
CHKERRQ(ierr)
end do
if (debug_e < 1 .or. debug_e > mesh_NcpElems) &
call IO_error(602,ext_msg='element') ! selected element does not exist
if (debug_i < 1 .or. debug_i > FE_Nips(FE_geomtype(mesh_element(2,debug_e)))) &
call IO_error(602,ext_msg='IP') ! selected element does not have requested IP
FEsolving_execElem = [ 1,mesh_NcpElems ] ! parallel loop bounds set to comprise all DAMASK elements
FEsolving_execIP = [1,FE_Nips(FE_geomtype(mesh_element(2,1)))]
allocate(microstructureAt(mesh_NcpElems))
allocate(homogenizationAt(mesh_NcpElems),source=1)
do j = 1, mesh_NcpElems
call DMGetLabelValue(geomMesh,'material',j-1,microstructureAt(j),ierr)
CHKERRQ(ierr)
end do
if (debug_e < 1 .or. debug_e > mesh_NcpElems) call IO_error(602,ext_msg='element')
if (debug_i < 1 .or. debug_i > mesh_maxNips) call IO_error(602,ext_msg='IP')
FEsolving_execElem = [1,mesh_NcpElems] ! parallel loop bounds set to comprise all DAMASK elements
FEsolving_execIP = [1,mesh_maxNips]
allocate(mesh_node0(3,mesh_Nnodes),source=0.0_pReal)
call discretization_init(mesh_element(3,:),mesh_element(4,:),&
call discretization_init(microstructureAt,homogenizationAt,&
reshape(mesh_ipCoordinates,[3,mesh_maxNips*mesh_NcpElems]), &
mesh_node0)
end subroutine discretization_mesh_init
@ -191,23 +176,23 @@ end subroutine discretization_mesh_init
!> @brief Calculates IP volume. Allocates global array 'mesh_ipVolume'
!--------------------------------------------------------------------------------------------------
subroutine mesh_FEM_build_ipVolumes(dimPlex)
PetscInt,intent(in):: dimPlex
PetscReal :: vol
PetscReal, pointer,dimension(:) :: pCent, pNorm
PetscInt :: cellStart, cellEnd, cell
PetscErrorCode :: ierr
allocate(mesh_ipVolume(mesh_maxNips,mesh_NcpElems),source=0.0_pReal)
call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
allocate(pCent(dimPlex))
allocate(pNorm(dimPlex))
do cell = cellStart, cellEnd-1
call DMPlexComputeCellGeometryFVM(geomMesh,cell,vol,pCent,pNorm,ierr)
call DMPlexComputeCellGeometryFVM(geomMesh,cell,vol,pCent,pNorm,ierr)
CHKERRQ(ierr)
mesh_ipVolume(:,cell+1) = vol/real(mesh_maxNips,pReal)
enddo
enddo
end subroutine mesh_FEM_build_ipVolumes
@ -219,20 +204,20 @@ subroutine mesh_FEM_build_ipCoordinates(dimPlex,qPoints)
PetscInt, intent(in) :: dimPlex
PetscReal, intent(in) :: qPoints(mesh_maxNips*dimPlex)
PetscReal, pointer,dimension(:) :: pV0, pCellJ, pInvcellJ
PetscReal :: detJ
PetscInt :: cellStart, cellEnd, cell, qPt, dirI, dirJ, qOffset
PetscErrorCode :: ierr
allocate(mesh_ipCoordinates(3,mesh_maxNips,mesh_NcpElems),source=0.0_pReal)
allocate(pV0(dimPlex))
allocatE(pCellJ(dimPlex**2))
allocatE(pinvCellJ(dimPlex**2))
call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
do cell = cellStart, cellEnd-1 !< loop over all elements
do cell = cellStart, cellEnd-1 !< loop over all elements
call DMPlexComputeCellGeometryAffineFEM(geomMesh,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
CHKERRQ(ierr)
qOffset = 0
@ -246,7 +231,7 @@ subroutine mesh_FEM_build_ipCoordinates(dimPlex,qPoints)
enddo
qOffset = qOffset + dimPlex
enddo
enddo
enddo
end subroutine mesh_FEM_build_ipCoordinates

5
src/numerics.f90
View File

@ -28,8 +28,6 @@ module numerics
numerics_unitlength = 1.0_pReal, & !< determines the physical length of one computational length unit
charLength = 1.0_pReal, & !< characteristic length scale for gradient problems
residualStiffness = 1.0e-6_pReal !< non-zero residual damage
logical, protected, public :: &
usePingPong = .true.
!--------------------------------------------------------------------------------------------------
! field parameters:
@ -133,8 +131,6 @@ subroutine numerics_init
defgradTolerance = IO_floatValue(line,chunkPos,2)
case ('ijacostiffness')
iJacoStiffness = IO_intValue(line,chunkPos,2)
case ('usepingpong')
usepingpong = IO_intValue(line,chunkPos,2) > 0
case ('unitlength')
numerics_unitlength = IO_floatValue(line,chunkPos,2)
@ -221,7 +217,6 @@ subroutine numerics_init
! writing parameters to output
write(6,'(a24,1x,es8.1)') ' defgradTolerance: ',defgradTolerance
write(6,'(a24,1x,i8)') ' iJacoStiffness: ',iJacoStiffness
write(6,'(a24,1x,L8)') ' use ping pong scheme: ',usepingpong
write(6,'(a24,1x,es8.1,/)')' unitlength: ',numerics_unitlength
!--------------------------------------------------------------------------------------------------

2
src/quaternions.f90
View File

@ -101,6 +101,8 @@ module quaternions
assignment(=), &
conjg, aimag, &
log, exp, &
abs, dot_product, &
inverse, &
real
contains