Merge branch 'fix-inhomogeneous-phase-physics' into development
This commit is contained in:
Samad Vakili
commit
6f4d93627b
2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit a16d1e45a2ed925e12244b0879b9d7e5a58d973b
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Subproject commit 1ca2223c68475bbcb9da633353dbe4a98c18db0d
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2
README
2
README
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@ -8,6 +8,6 @@ Max-Planck-Str. 1
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40237 Düsseldorf
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Germany
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Email: DAMASK@mpie.de
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damask@mpie.de
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https://damask.mpie.de
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https://magit1.mpie.de
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@ -2,4 +2,3 @@
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omit = tests/*
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damask/_asciitable.py
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damask/_test.py
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damask/config/*
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@ -24,5 +24,4 @@ from . import solver # noqa
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Environment = _
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from ._asciitable import ASCIItable # noqa
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from ._test import Test # noqa
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from .config import Material # noqa
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from .util import extendableOption # noqa
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@ -401,8 +401,9 @@ class Result:
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if sets is True:
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groups.append(group)
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else:
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match = [e for e_ in [glob.fnmatch.filter(f[group].keys(),s) for s in sets] for e in e_]
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if len(set(match)) == len(sets): groups.append(group)
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if group in f.keys():
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match = [e for e_ in [glob.fnmatch.filter(f[group].keys(),s) for s in sets] for e in e_]
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if len(set(match)) == len(sets): groups.append(group)
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return groups
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@ -1,3 +0,0 @@
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"""Aggregator for configuration file handling."""
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from .material import Material # noqa
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@ -1,282 +0,0 @@
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import re
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import os
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from damask import util
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class Section():
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def __init__(self,data = {'__order__':[]},part = ''):
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"""New material.config section."""
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classes = {
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'homogenization':Homogenization,
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'microstructure':Microstructure,
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'crystallite':Crystallite,
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'phase':Phase,
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'texture':Texture,
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}
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self.parameters = {}
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for key in data:
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self.parameters[key] = data[key] if isinstance(data[key], list) else [data[key]]
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if '__order__' not in self.parameters:
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self.parameters['__order__'] = list(self.parameters.keys())
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if part.lower() in classes:
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self.__class__ = classes[part.lower()]
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self.__init__(data)
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def add_multiKey(self,key,data):
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multiKey = '(%s)'%key
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if multiKey not in self.parameters: self.parameters[multiKey] = []
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if multiKey not in self.parameters['__order__']: self.parameters['__order__'] += [multiKey]
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self.parameters[multiKey] += [[item] for item in data] if isinstance(data, list) else [[data]]
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def data(self):
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return self.parameters
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class Homogenization(Section):
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def __init__(self,data = {'__order__':[]}):
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"""New material.config <homogenization> section."""
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Section.__init__(self,data)
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class Crystallite(Section):
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def __init__(self,data = {'__order__':[]}):
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"""New material.config <crystallite> section."""
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Section.__init__(self,data)
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class Phase(Section):
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def __init__(self,data = {'__order__':[]}):
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"""New material.config <Phase> section."""
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Section.__init__(self,data)
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class Microstructure(Section):
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def __init__(self,data = {'__order__':[]}):
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"""New material.config <microstructure> section."""
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Section.__init__(self,data)
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class Texture(Section):
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def __init__(self,data = {'__order__':[]}):
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"""New material.config <texture> section."""
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Section.__init__(self,data)
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def add_component(self,theType,properties):
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scatter = properties['scatter'] if 'scatter' in list(map(str.lower,list(properties.keys()))) else 0.0
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fraction = properties['fraction'] if 'fraction' in list(map(str.lower,list(properties.keys()))) else 1.0
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try:
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multiKey = theType.lower()
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except AttributeError:
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pass
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if multiKey == 'gauss':
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self.add_multiKey(multiKey,'phi1 %g\tPhi %g\tphi2 %g\tscatter %g\tfraction %g'%(
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properties['eulers'][0],
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properties['eulers'][1],
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properties['eulers'][2],
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scatter,
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fraction,
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)
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)
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class Material():
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"""Read, manipulate, and write material.config files."""
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def __init__(self,verbose=True):
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"""Generates ordered list of parts."""
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self.parts = [
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'homogenization',
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'crystallite',
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'phase',
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'texture',
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'microstructure',
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]
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self.data = {
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'homogenization': {'__order__': []},
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'microstructure': {'__order__': []},
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'crystallite': {'__order__': []},
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'phase': {'__order__': []},
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'texture': {'__order__': []},
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}
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self.verbose = verbose
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def __repr__(self):
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"""Returns current data structure in material.config format."""
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me = []
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for part in self.parts:
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if self.verbose: print(f'processing <{part}>')
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me += ['',
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'#'*100,
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f'<{part}>',
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'#'*100,
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]
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for section in self.data[part]['__order__']:
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me += [f'[{section}] {"#"+"-"*max(0,96-len(section))}']
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for key in self.data[part][section]['__order__']:
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if key.startswith('(') and key.endswith(')'): # multiple (key)
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me += [f'{key}\t{" ".join(values)}' for values in self.data[part][section][key]]
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else: # plain key
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me += [f'{key}\t{util.srepr(self.data[part][section][key]," ")}']
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return '\n'.join(me) + '\n'
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def parse(self, part=None, sections=[], content=None):
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re_part = re.compile(r'^<(.+)>$') # pattern for part
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re_sec = re.compile(r'^\[(.+)\]$') # pattern for section
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name_section = ''
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active = False
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for line in content:
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line = line.split('#')[0].strip() # kill comments and extra whitespace
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line = line.split('/echo/')[0].strip() # remove '/echo/' tags
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line = line.lower() # be case insensitive
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if line: # content survives...
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match_part = re_part.match(line)
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if match_part: # found <...> separator
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active = (match_part.group(1) == part) # only active in <part>
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continue
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if active:
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match_sec = re_sec.match(line)
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if match_sec: # found [section]
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name_section = match_sec.group(1) # remember name ...
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if '__order__' not in self.data[part]: self.data[part]['__order__'] = []
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self.data[part]['__order__'].append(name_section) # ... and position
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self.data[part][name_section] = {'__order__':[]}
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continue
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if sections == [] or name_section in sections: # possibly restrict to subset
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items = line.split()
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if items[0] not in self.data[part][name_section]: # first encounter of key?
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self.data[part][name_section][items[0]] = [] # create item
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self.data[part][name_section]['__order__'].append(items[0])
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if items[0].startswith('(') and items[0].endswith(')'): # multiple "(key)"
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self.data[part][name_section][items[0]].append(items[1:])
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else: # plain key
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self.data[part][name_section][items[0]] = items[1:]
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def read(self,filename=None):
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"""Read material.config file."""
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def recursiveRead(filename):
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"""Takes care of include statements like '{}'."""
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result = []
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re_include = re.compile(r'^{(.+)}$')
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with open(filename) as f: lines = f.readlines()
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for line in lines:
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match = re_include.match(line.split()[0]) if line.strip() else False
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result += [line] if not match else \
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recursiveRead(match.group(1) if match.group(1).startswith('/') else
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os.path.normpath(os.path.join(os.path.dirname(filename),match.group(1))))
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return result
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c = recursiveRead(filename)
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for p in self.parts:
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self.parse(part=p, content=c)
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def write(self,filename='material.config', overwrite=False):
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"""Write to material.config."""
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i = 0
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outname = filename
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while os.path.exists(outname) and not overwrite:
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i += 1
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outname = f'{filename}_{i}'
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if self.verbose: print(f'Writing material data to {outname}')
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with open(outname,'w') as f:
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f.write(str(self))
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return outname
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def add_section(self, part=None, section=None, initialData=None, merge=False):
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"""Add Update."""
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part = part.lower()
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section = section.lower()
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if part not in self.parts: raise Exception(f'invalid part {part}')
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if not isinstance(initialData, dict):
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initialData = initialData.data()
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if section not in self.data[part]: self.data[part]['__order__'] += [section]
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if section in self.data[part] and merge:
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for existing in self.data[part][section]['__order__']: # replace existing
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if existing in initialData['__order__']:
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if existing.startswith('(') and existing.endswith(')'): # multiple (key)
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self.data[part][section][existing] += initialData[existing] # add new multiple entries to existing ones
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else: # regular key
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self.data[part][section][existing] = initialData[existing] # plain replice
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for new in initialData['__order__']: # merge new content
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if new not in self.data[part][section]['__order__']:
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self.data[part][section][new] = initialData[new]
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self.data[part][section]['__order__'] += [new]
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else:
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self.data[part][section] = initialData
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def add_microstructure(self, section='',
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components={}, # dict of phase,texture, and fraction lists
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):
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"""Experimental! Needs expansion to multi-constituent microstructures..."""
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microstructure = Microstructure()
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# make keys lower case (http://stackoverflow.com/questions/764235/dictionary-to-lowercase-in-python)
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components=dict((k.lower(), v) for k,v in components.items())
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for key in ['phase','texture','fraction','crystallite']:
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if isinstance(components[key], list):
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for i, x in enumerate(components[key]):
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try:
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components[key][i] = x.lower()
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except AttributeError:
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pass
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else:
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try:
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components[key] = [components[key].lower()]
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except AttributeError:
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components[key] = [components[key]]
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for (phase,texture,fraction,crystallite) in zip(components['phase'],components['texture'],
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components['fraction'],components['crystallite']):
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microstructure.add_multiKey('constituent','phase %i\ttexture %i\tfraction %g\ncrystallite %i'%(
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self.data['phase']['__order__'].index(phase)+1,
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self.data['texture']['__order__'].index(texture)+1,
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fraction,
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self.data['crystallite']['__order__'].index(crystallite)+1))
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self.add_section('microstructure',section,microstructure)
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def change_value(self, part=None,
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section=None,
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key=None,
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value=None):
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if not isinstance(value,list):
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if not isinstance(value,str):
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value = '%s'%value
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value = [value]
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newlen = len(value)
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oldval = self.data[part.lower()][section.lower()][key.lower()]
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oldlen = len(oldval)
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print('changing %s:%s:%s from %s to %s '%(part.lower(),section.lower(),key.lower(),oldval,value))
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self.data[part.lower()][section.lower()][key.lower()] = value
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if newlen is not oldlen:
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print('Length of value was changed from %i to %i!'%(oldlen,newlen))
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def add_value(self, part=None,
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section=None,
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key=None,
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value=None):
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if not isinstance(value,list):
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if not isinstance(value,str):
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value = '%s'%value
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value = [value]
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print('adding %s:%s:%s with value %s '%(part.lower(),section.lower(),key.lower(),value))
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self.data[part.lower()][section.lower()][key.lower()] = value
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self.data[part.lower()][section.lower()]['__order__'] += [key.lower()]
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@ -16,12 +16,11 @@ setuptools.setup(
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packages=setuptools.find_packages(),
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include_package_data=True,
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install_requires = [
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"pandas",
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"pandas", # requires numpy
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"scipy",
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"h5py",
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"h5py", # requires numpy
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"vtk",
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"matplotlib",
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"PIL",
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"matplotlib", # requires numpy, pillow
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],
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classifiers = [
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"Intended Audience :: Science/Research",
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