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DAMASK_EICMD
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Merge remote-tracking branch 'origin/development' into vector-mechanics

This commit is contained in:
Martin Diehl 2020-11-18 13:46:48 +01:00
parent 9a1e8e3c38 a0b6c2690b
commit 89c748fdf1
60 changed files with 615 additions and 587 deletions
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24
.gitlab-ci.yml
View File

@ -187,8 +187,6 @@ grid_mech_compile_Intel:
stage: compilePETSc
script:
- module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
- cp -r grid_mech_compile grid_mech_compile_Intel
- grid_mech_compile_Intel/test.py
- cd pytest
- pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_Intel
except:
@ -199,8 +197,6 @@ Compile_FEM_Intel:
stage: compilePETSc
script:
- module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
- cp -r FEM_compile FEM_compile_Intel
- FEM_compile_Intel/test.py
- cd pytest
- pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_Intel
except:
@ -211,8 +207,6 @@ grid_mech_compile_GNU:
stage: compilePETSc
script:
- module load $GNUCompiler $MPICH_GNU $PETSc_MPICH_GNU
- cp -r grid_mech_compile grid_mech_compile_GNU
- grid_mech_compile_GNU/test.py
- cd pytest
- pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_GNU
except:
@ -223,8 +217,6 @@ Compile_FEM_GNU:
stage: compilePETSc
script:
- module load $GNUCompiler $MPICH_GNU $PETSc_MPICH_GNU
- cp -r FEM_compile FEM_compile_GNU
- FEM_compile_GNU/test.py
- cd pytest
- pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_GNU
except:
@ -274,22 +266,6 @@ Nonlocal_Damage_DetectChanges:
- master
- release
grid_all_restart:
stage: grid
script: grid_all_restart/test.py
except:
- master
- release
grid_all_restartMPI:
stage: grid
script:
- module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
- grid_all_restartMPI/test.py
except:
- master
- release
Plasticity_DetectChanges:
stage: grid
script: Plasticity_DetectChanges/test.py

2
PRIVATE

@ -1 +1 @@
Subproject commit 281e7eb84f76a2974a50eb54faf35ea25ec89b20
Subproject commit 2d00aa541f071dbfc200f32e358d324995a061f5

2
VERSION
View File

@ -1 +1 @@
v3.0.0-alpha-726-g1f59f6301
v3.0.0-alpha-777-g523a0979e

4
examples/SpectralMethod/Polycrystal/material.yaml
View File

@ -2,7 +2,7 @@
homogenization:
SX:
N_constituents: 1
mech: {type: none}
mechanics: {type: none}
material:
- homogenization: SX
@ -109,7 +109,7 @@ material:
phase:
Aluminum:
lattice: fcc
mech:
mechanics:
output: [F, P, F_e, F_p, L_p, O]
elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
plasticity:

2
examples/SpectralMethod/Polycrystal/shearXY.yaml
View File

@ -1,5 +1,5 @@
step:
- mech:
- mechanics:
dot_F: [0, 0, 0,
1e-3, 0, 0,
0, 0, 0]

2
examples/SpectralMethod/Polycrystal/shearZX.yaml
View File

@ -1,6 +1,6 @@
---
step:
- mech:
- mechanics:
dot_F: [0, 0, 1e-3,
0, 0, 0,
0, 0, 0]

4
examples/SpectralMethod/Polycrystal/tensionX.yaml
View File

@ -1,7 +1,7 @@
---
step:
- mech:
- mechanics:
dot_F: [1.0e-3, 0, 0,
0, x, 0,
0, 0, x]
@ -12,7 +12,7 @@ step:
t: 10
N: 40
f_out: 4
- mech:
- mechanics:
dot_F: [1.0e-3, 0, 0,
0, x, 0,
0, 0, x]

2
processing/post/addCompatibilityMismatch.py
View File

@ -136,7 +136,7 @@ def shapeMismatch(size,F,nodes,centres):
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
parser = OptionParser(usage='%prog options [ASCIItable(s)]', description = """
Add column(s) containing the shape and volume mismatch resulting from given deformation gradient.
Operates on periodic three-dimensional x,y,z-ordered data sets.

2
processing/post/addDisplacement.py
View File

@ -16,7 +16,7 @@ scriptID = ' '.join([scriptName,damask.version])
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
parser = OptionParser(usage='%prog options [ASCIItable(s)]', description = """
Add displacments resulting from deformation gradient field.
Operates on periodic three-dimensional x,y,z-ordered data sets.
Outputs at cell centers or cell nodes (into separate file).

2
processing/post/addSchmidfactors.py
View File

@ -98,7 +98,7 @@ slipSystems = {
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
parser = OptionParser(usage='%prog options [ASCIItable(s)]', description = """
Add columns listing Schmid factors (and optional trace vector of selected system) for given Euler angles.
""", version = scriptID)

2
processing/pre/geom_fromDREAM3D.py
View File

@ -14,7 +14,7 @@ scriptID = ' '.join([scriptName,damask.version])
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [DREAM.3Dfile(s)]', description = """
parser = OptionParser(usage='%prog options [DREAM.3Dfile(s)]', description = """
Converts DREAM.3D file. Input can be cell data (direct pointwise takeover) or grain data (individual
grains are segmented). Requires orientation data as quaternion.

69
processing/pre/geom_fromMinimalSurface.py
View File

@ -1,69 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
minimal_surfaces = list(damask.Geom._minimal_surface.keys())
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile]', description = """
Generate a bicontinuous structure of given type.
""", version = scriptID)
parser.add_option('-t','--type',
dest = 'type',
choices = minimal_surfaces, metavar = 'string',
help = 'type of minimal surface [primitive] {%s}' %(','.join(minimal_surfaces)))
parser.add_option('-f','--threshold',
dest = 'threshold',
type = 'float', metavar = 'float',
help = 'threshold value defining minimal surface [%default]')
parser.add_option('-g', '--grid',
dest = 'grid',
type = 'int', nargs = 3, metavar = 'int int int',
help = 'a,b,c grid of hexahedral box [%default]')
parser.add_option('-s', '--size',
dest = 'size',
type = 'float', nargs = 3, metavar = 'float float float',
help = 'x,y,z size of hexahedral box [%default]')
parser.add_option('-p', '--periods',
dest = 'periods',
type = 'int', metavar = 'int',
help = 'number of repetitions of unit cell [%default]')
parser.add_option('--m',
dest = 'microstructure',
type = 'int', nargs = 2, metavar = 'int int',
help = 'two microstructure indices to be used [%default]')
parser.set_defaults(type = minimal_surfaces[0],
threshold = 0.0,
periods = 1,
grid = (16,16,16),
size = (1.0,1.0,1.0),
microstructure = (1,2),
)
(options,filename) = parser.parse_args()
name = None if filename == [] else filename[0]
damask.util.report(scriptName,name)
geom=damask.Geom.from_minimal_surface(options.grid,options.size,options.type,options.threshold,
options.periods,options.microstructure)
damask.util.croak(geom)
geom.save_ASCII(sys.stdout if name is None else name)

2
processing/pre/geom_fromOsteonGeometry.py
View File

@ -17,7 +17,7 @@ scriptID = ' '.join([scriptName,damask.version])
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile]', description = """
parser = OptionParser(usage='%prog options [geomfile]', description = """
Generate description of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
The osteon phase is lamellar with a twisted plywood structure.
Its fiber orientation is oscillating by +/- amplitude within one period.

2
processing/pre/mentat_pbcOnBoxMesh.py
View File

@ -208,7 +208,7 @@ def add_servoLinks(mfd_data,active=[True,True,True]): # directions on which to
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
parser = OptionParser(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)

2
processing/pre/mentat_spectralBox.py
View File

@ -168,7 +168,7 @@ def initial_conditions(material):
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
parser = OptionParser(usage='%prog options [file[s]]', description = """
Generate MSC.Marc FE hexahedral mesh from geom file.
""", version = scriptID)

2
processing/pre/seeds_fromDistribution.py
View File

@ -164,7 +164,7 @@ class myThread (threading.Thread):
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
parser = OptionParser(usage='%prog options [file[s]]', description = """
Monte Carlo simulation to produce seed file that gives same size distribution like given geometry file.
""", version = scriptID)

2
processing/pre/seeds_fromPokes.py
View File

@ -16,7 +16,7 @@ scriptID = ' '.join([scriptName,damask.version])
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
parser = OptionParser(usage='%prog options [file[s]]', description = """
Create seeds file by poking at 45 degree through given geom file.
Mimics APS Beamline 34-ID-E DAXM poking.

152
python/damask/_colormap.py
View File

@ -22,6 +22,19 @@ _ref_white = np.array([.95047, 1.00000, 1.08883])
# - support NaN color (paraview)
class Colormap(mpl.colors.ListedColormap):
"""
Enhance matplotlib colormap functionality to be used within DAMASK.
References
----------
[1] DAMASK colormap theory
https://www.kennethmoreland.com/color-maps/ColorMapsExpanded.pdf
[2] DAMASK colormaps first use
https://doi.org/10.1016/j.ijplas.2012.09.012
[3] Matplotlib colormaps overview
https://matplotlib.org/tutorials/colors/colormaps.html
"""
def __add__(self,other):
"""Concatenate colormaps."""
@ -36,6 +49,17 @@ class Colormap(mpl.colors.ListedColormap):
"""Return inverted colormap."""
return self.reversed()
def __repr__(self):
"""Show colormap as matplotlib figure."""
fig = plt.figure(self.name,figsize=(5,.5))
ax1 = fig.add_axes([0, 0, 1, 1])
ax1.set_axis_off()
ax1.imshow(np.linspace(0,1,self.N).reshape(1,-1),
aspect='auto', cmap=self, interpolation='nearest')
plt.show(block = False)
return self.name
@staticmethod
def from_range(low,high,name='DAMASK colormap',N=256,model='rgb'):
"""
@ -126,51 +150,27 @@ class Colormap(mpl.colors.ListedColormap):
"""
# matplotlib presets
for cat in Colormap._predefined_mpl:
for n in cat[1]:
if n == name:
try:
colormap = cm.__dict__[name]
if isinstance(colormap,mpl.colors.LinearSegmentedColormap):
return Colormap(np.array(list(map(colormap,np.linspace(0,1,N)))),name=name)
else:
return Colormap(np.array(colormap.colors),name=name)
return Colormap(np.array(list(map(colormap,np.linspace(0,1,N)))
if isinstance(colormap,mpl.colors.LinearSegmentedColormap) else
colormap.colors),
name=name)
except KeyError:
# DAMASK presets
definition = Colormap._predefined_DAMASK[name]
return Colormap.from_range(definition['low'],definition['high'],name,N)
@staticmethod
def list_predefined():
"""
List predefined colormaps by category.
References
----------
[1] DAMASK colormap theory
https://www.kennethmoreland.com/color-maps/ColorMapsExpanded.pdf
[2] DAMASK colormaps first use
https://doi.org/10.1016/j.ijplas.2012.09.012
[3] Matplotlib colormaps overview
https://matplotlib.org/tutorials/colors/colormaps.html
"""
print('DAMASK colormaps')
print(' '+', '.join(Colormap._predefined_DAMASK.keys()))
for cat in Colormap._predefined_mpl:
print(f'{cat[0]}')
print(' '+', '.join(cat[1]))
def shade(self,field,bounds=None,gap=None):
"""
Generate PIL image of 2D field using colormap.
Parameters
----------
field : numpy.array of shape(:,:)
field : numpy.array of shape (:,:)
Data to be shaded.
bounds : iterable of len(2), optional
bounds : iterable of len (2), optional
Colormap value range (low,high).
gap : field.dtype, optional
Transparent value. NaN will always be rendered transparent.
@ -203,18 +203,6 @@ class Colormap(mpl.colors.ListedColormap):
mode='RGBA')
def show(self,aspect=10,vertical=False):
"""Show colormap as matplotlib figure."""
fig = plt.figure(figsize=(5/aspect,5) if vertical else (5,5/aspect))
ax1 = fig.add_axes([0, 0, 1, 1])
ax1.set_axis_off()
ax1.imshow(np.linspace(1 if vertical else 0,
0 if vertical else 1,
self.N).reshape((-1,1) if vertical else (1,-1)),
aspect='auto', cmap=self, interpolation='nearest')
plt.show()
def reversed(self,name=None):
"""
Make a reversed instance of the colormap.
@ -235,7 +223,6 @@ class Colormap(mpl.colors.ListedColormap):
return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
def save_paraview(self,fname=None):
"""
Write colormap to JSON file for Paraview.
@ -247,13 +234,13 @@ class Colormap(mpl.colors.ListedColormap):
consist of the name of the colormap and extension '.json'.
"""
if fname is not None:
if fname is None:
fhandle = None
else:
try:
fhandle = open(fname,'w')
except TypeError:
fhandle = fname
else:
fhandle = None
colors = []
for i,c in enumerate(np.round(self.colors,6).tolist()):
@ -266,11 +253,9 @@ class Colormap(mpl.colors.ListedColormap):
'DefaultMap':True,
'RGBPoints':colors
}]
if fhandle is None:
with open(self.name.replace(' ','_')+'.json', 'w') as f:
with open(self.name.replace(' ','_')+'.json', 'w') if fhandle is None else fhandle as f:
json.dump(out, f,indent=4)
else:
json.dump(out,fhandle,indent=4)
def save_ASCII(self,fname=None):
@ -284,22 +269,19 @@ class Colormap(mpl.colors.ListedColormap):
consist of the name of the colormap and extension '.txt'.
"""
if fname is not None:
if fname is None:
fhandle = None
else:
try:
fhandle = open(fname,'w')
except TypeError:
fhandle = fname
else:
fhandle = None
labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
t = Table(self.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
if fhandle is None:
with open(self.name.replace(' ','_')+'.txt', 'w') as f:
with open(self.name.replace(' ','_')+'.txt', 'w') if fhandle is None else fhandle as f:
t.save(f)
else:
t.save(fhandle)
def save_GOM(self,fname=None):
@ -313,24 +295,21 @@ class Colormap(mpl.colors.ListedColormap):
consist of the name of the colormap and extension '.legend'.
"""
if fname is not None:
if fname is None:
fhandle = None
else:
try:
fhandle = open(fname,'w')
except TypeError:
fhandle = fname
else:
fhandle = None
# ToDo: test in GOM
GOM_str = '1 1 {name} 9 {name} '.format(name=self.name.replace(" ","_")) \
+ '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(self.colors)}' \
+ ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(int))]) \
+ '\n'
if fhandle is None:
with open(self.name.replace(' ','_')+'.legend', 'w') as f:
with open(self.name.replace(' ','_')+'.legend', 'w') if fhandle is None else fhandle as f:
f.write(GOM_str)
else:
fhandle.write(GOM_str)
def save_gmsh(self,fname=None):
@ -344,22 +323,19 @@ class Colormap(mpl.colors.ListedColormap):
consist of the name of the colormap and extension '.msh'.
"""
if fname is not None:
if fname is None:
fhandle = None
else:
try:
fhandle = open(fname,'w')
except TypeError:
fhandle = fname
else:
fhandle = None
# ToDo: test in gmsh
gmsh_str = 'View.ColorTable = {\n' \
+'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
+'\n}\n'
if fhandle is None:
with open(self.name.replace(' ','_')+'.msh', 'w') as f:
with open(self.name.replace(' ','_')+'.msh', 'w') if fhandle is None else fhandle as f:
f.write(gmsh_str)
else:
fhandle.write(gmsh_str)
@staticmethod
@ -387,7 +363,6 @@ class Colormap(mpl.colors.ListedColormap):
if msh_sat[2] < - np.pi/3.0: hSpin *= -1.0
return msh_sat[2] + hSpin
lo = np.array(low)
hi = np.array(high)
@ -407,28 +382,28 @@ class Colormap(mpl.colors.ListedColormap):
return (1.0 - frac) * lo + frac * hi
_predefined_mpl= [('Perceptually Uniform Sequential', [
'viridis', 'plasma', 'inferno', 'magma', 'cividis']),
('Sequential', [
_predefined_mpl= {'Perceptually Uniform Sequential': [
'viridis', 'plasma', 'inferno', 'magma', 'cividis'],
'Sequential': [
'Greys', 'Purples', 'Blues', 'Greens', 'Oranges', 'Reds',
'YlOrBr', 'YlOrRd', 'OrRd', 'PuRd', 'RdPu', 'BuPu',
'GnBu', 'PuBu', 'YlGnBu', 'PuBuGn', 'BuGn', 'YlGn']),
('Sequential (2)', [
'GnBu', 'PuBu', 'YlGnBu', 'PuBuGn', 'BuGn', 'YlGn'],
'Sequential (2)': [
'binary', 'gist_yarg', 'gist_gray', 'gray', 'bone', 'pink',
'spring', 'summer', 'autumn', 'winter', 'cool', 'Wistia',
'hot', 'afmhot', 'gist_heat', 'copper']),
('Diverging', [
'hot', 'afmhot', 'gist_heat', 'copper'],
'Diverging': [
'PiYG', 'PRGn', 'BrBG', 'PuOr', 'RdGy', 'RdBu',
'RdYlBu', 'RdYlGn', 'Spectral', 'coolwarm', 'bwr', 'seismic']),
('Cyclic', ['twilight', 'twilight_shifted', 'hsv']),
('Qualitative', [
'RdYlBu', 'RdYlGn', 'Spectral', 'coolwarm', 'bwr', 'seismic'],
'Cyclic': ['twilight', 'twilight_shifted', 'hsv'],
'Qualitative': [
'Pastel1', 'Pastel2', 'Paired', 'Accent',
'Dark2', 'Set1', 'Set2', 'Set3',
'tab10', 'tab20', 'tab20b', 'tab20c']),
('Miscellaneous', [
'tab10', 'tab20', 'tab20b', 'tab20c'],
'Miscellaneous': [
'flag', 'prism', 'ocean', 'gist_earth', 'terrain', 'gist_stern',
'gnuplot', 'gnuplot2', 'CMRmap', 'cubehelix', 'brg',
'gist_rainbow', 'rainbow', 'jet', 'nipy_spectral', 'gist_ncar'])]
'gist_rainbow', 'rainbow', 'jet', 'nipy_spectral', 'gist_ncar']}
_predefined_DAMASK = {'orientation': {'low': [0.933334,0.878432,0.878431],
'high': [0.250980,0.007843,0.000000]},
@ -437,6 +412,9 @@ class Colormap(mpl.colors.ListedColormap):
'stress': {'low': [0.878432,0.874511,0.949019],
'high': [0.000002,0.000000,0.286275]}}
predefined = dict(**{'DAMASK':list(_predefined_DAMASK)},**_predefined_mpl)
@staticmethod
def _hsv2rgb(hsv):
"""

27
python/damask/_configmaterial.py
View File

@ -226,13 +226,13 @@ class ConfigMaterial(Config):
return dup
def material_add(self,constituents,**kwargs):
def material_add(self,constituents=None,**kwargs):
"""
Add material entries.
Parameters
----------
constituents : dict
constituents : dict, optional
Entries for 'constituents' as key-value pair.
**kwargs
Key-value pairs.
@ -263,13 +263,26 @@ class ConfigMaterial(Config):
homogenization: SX
"""
c = [{'constituents':u} for u in ConfigMaterial._constituents(**constituents)]
length = -1
for v in kwargs.values():
if hasattr(v,'__len__') and not isinstance(v,str):
if length != -1 and len(v) != length:
raise ValueError('Cannot add entries of different length')
else:
length = len(v)
length = max(1,length)
c = [{} for _ in range(length)] if constituents is None else \
[{'constituents':u} for u in ConfigMaterial._constituents(**constituents)]
if len(c) == 1: c = [copy.deepcopy(c[0]) for _ in range(length)]
if length != 1 and length != len(c):
raise ValueError('Cannot add entries of different length')
for k,v in kwargs.items():
if hasattr(v,'__len__') and not isinstance(v,str):
if len(v) != len(c):
raise ValueError('Cannot add entries of different length')
for i,vv in enumerate(v):
c[i][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
c[i][k] = vv.item() if isinstance(vv,np.generic) else vv
else:
for i in range(len(c)):
c[i][k] = v
@ -293,7 +306,7 @@ class ConfigMaterial(Config):
if len(v) != N_material:
raise ValueError('Cannot add entries of different length')
for i,vv in enumerate(np.array(v)):
m[i][0][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
m[i][0][k] = vv.item() if isinstance(vv,np.generic) else vv
else:
for i in range(N_material):
m[i][0][k] = v

15
python/damask/_environment.py
View File

@ -3,14 +3,8 @@ from pathlib import Path
class Environment:
def __init__(self):
"""Do Nothing."""
pass
@property
def screen_size(self):
width = 1024
height = 768
try:
import wx
_ = wx.App(False) # noqa
@ -23,7 +17,9 @@ class Environment:
height = tk.winfo_screenheight()
tk.destroy()
except Exception as e:
pass
width = 1024
height = 768
return (width,height)
@ -43,8 +39,3 @@ class Environment:
def root_dir(self):
"""Return DAMASK root path."""
return Path(__file__).parents[2]
# for compatibility
def rootDir(self):
return str(self.root_dir)

23
python/damask/_geom.py
View File

@ -2,6 +2,7 @@ import copy
import multiprocessing as mp
from functools import partial
from os import path
import warnings
import numpy as np
import pandas as pd
@ -73,23 +74,23 @@ class Geom:
"""
message = []
if np.any(other.grid != self.grid):
message.append(util.delete(f'grid a b c: {util.srepr(other.grid," x ")}'))
message.append(util.deemph(f'grid a b c: {util.srepr(other.grid," x ")}'))
message.append(util.emph( f'grid a b c: {util.srepr( self.grid," x ")}'))
if not np.allclose(other.size,self.size):
message.append(util.delete(f'size x y z: {util.srepr(other.size," x ")}'))
message.append(util.deemph(f'size x y z: {util.srepr(other.size," x ")}'))
message.append(util.emph( f'size x y z: {util.srepr( self.size," x ")}'))
if not np.allclose(other.origin,self.origin):
message.append(util.delete(f'origin x y z: {util.srepr(other.origin," ")}'))
message.append(util.deemph(f'origin x y z: {util.srepr(other.origin," ")}'))
message.append(util.emph( f'origin x y z: {util.srepr( self.origin," ")}'))
if other.N_materials != self.N_materials:
message.append(util.delete(f'# materials: {other.N_materials}'))
message.append(util.deemph(f'# materials: {other.N_materials}'))
message.append(util.emph( f'# materials: { self.N_materials}'))
if np.nanmax(other.material) != np.nanmax(self.material):
message.append(util.delete(f'max material: {np.nanmax(other.material)}'))
message.append(util.deemph(f'max material: {np.nanmax(other.material)}'))
message.append(util.emph( f'max material: {np.nanmax( self.material)}'))
return util.return_message(message)
@ -188,12 +189,16 @@ class Geom:
"""
Read a geom file.
Storing geometry files in ASCII format is deprecated.
This function will be removed in a future version of DAMASK.
Parameters
----------
fname : str, pathlib.Path, or file handle
Geometry file to read.
"""
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning)
try:
f = open(fname)
except TypeError:
@ -247,7 +252,6 @@ class Geom:
return Geom(material.reshape(grid,order='F'),size,origin,comments)
@staticmethod
def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
"""
@ -523,6 +527,9 @@ class Geom:
"""
Write a geom file.
Storing geometry files in ASCII format is deprecated.
This function will be removed in a future version of DAMASK.
Parameters
----------
fname : str or file handle
@ -531,6 +538,7 @@ class Geom:
Compress geometry with 'x of y' and 'a to b'.
"""
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning)
header = [f'{len(self.comments)+4} header'] + self.comments \
+ ['grid a {} b {} c {}'.format(*self.grid),
'size x {} y {} z {}'.format(*self.size),
@ -547,8 +555,7 @@ class Geom:
def show(self):
"""Show on screen."""
v = VTK.from_rectilinear_grid(self.grid,self.size,self.origin)
v.show()
VTK.from_rectilinear_grid(self.grid,self.size,self.origin).show()
def add_primitive(self,dimension,center,exponent,

114
python/damask/_orientation.py
View File

@ -4,7 +4,7 @@ from . import Rotation
from . import util
from . import tensor
__parameter_doc__ = \
_parameter_doc = \
"""lattice : str
Either a crystal family out of [triclinic, monoclinic, orthorhombic, tetragonal, hexagonal, cubic]
or a Bravais lattice out of [aP, mP, mS, oP, oS, oI, oF, tP, tI, hP, cP, cI, cF].
@ -27,22 +27,6 @@ __parameter_doc__ = \
"""
def extend_docstring():
"""Decorator: Append Orientation parameter documentation to function's docstring."""
def _decorator(func):
func.__doc__ += __parameter_doc__
return func
return _decorator
def extended_docstring(f):
"""Decorator: Combine Orientation parameter documentation with another function's docstring."""
def _decorator(func):
func.__doc__ = f.__doc__ + __parameter_doc__
return func
return _decorator
class Orientation(Rotation):
"""
Representation of crystallographic orientation as combination of rotation and either crystal family or Bravais lattice.
@ -83,20 +67,9 @@ class Orientation(Rotation):
Examples
--------
An array of 3 x 5 random orientations reduced to the fundamental zone of tetragonal symmetry:
>>> damask.Orientation.from_random(shape=(3,5),lattice='tetragonal').reduced
Disorientation between two specific orientations of hexagonal symmetry:
>>> a = damask.Orientation.from_Euler_angles(phi=[123,32,21],degrees=True,lattice='hexagonal')
>>> b = damask.Orientation.from_Euler_angles(phi=[104,11,87],degrees=True,lattice='hexagonal')
>>> a.disorientation(b)
Inverse pole figure color of the e_3 direction for a crystal in "Cube" orientation with cubic symmetry:
>>> o = damask.Orientation(lattice='cubic')
>>> o.IPF_color(o.to_SST(np.array([0,0,1])))
Schmid matrix (in lab frame) of slip systems of a face-centered cubic crystal in "Goss" orientation:
>>> damask.Orientation.from_Euler_angles(phi=[0,45,0],degrees=True,lattice='cF').Schmid('slip')
"""
crystal_families = ['triclinic',
@ -128,7 +101,7 @@ class Orientation(Rotation):
}
@extend_docstring()
@util.extend_docstring(_parameter_doc)
def __init__(self,
rotation = None,
lattice = None,
@ -279,73 +252,73 @@ class Orientation(Rotation):
@classmethod
@extended_docstring(Rotation.from_random)
@util.extended_docstring(Rotation.from_random,_parameter_doc)
def from_random(cls,**kwargs):
return cls(rotation=Rotation.from_random(**kwargs),**kwargs)
@classmethod
@extended_docstring(Rotation.from_quaternion)
@util.extended_docstring(Rotation.from_quaternion,_parameter_doc)
def from_quaternion(cls,**kwargs):
return cls(rotation=Rotation.from_quaternion(**kwargs),**kwargs)
@classmethod
@extended_docstring(Rotation.from_Euler_angles)
@util.extended_docstring(Rotation.from_Euler_angles,_parameter_doc)
def from_Euler_angles(cls,**kwargs):
return cls(rotation=Rotation.from_Euler_angles(**kwargs),**kwargs)
@classmethod
@extended_docstring(Rotation.from_axis_angle)
@util.extended_docstring(Rotation.from_axis_angle,_parameter_doc)
def from_axis_angle(cls,**kwargs):
return cls(rotation=Rotation.from_axis_angle(**kwargs),**kwargs)
@classmethod
@extended_docstring(Rotation.from_basis)
@util.extended_docstring(Rotation.from_basis,_parameter_doc)
def from_basis(cls,**kwargs):
return cls(rotation=Rotation.from_basis(**kwargs),**kwargs)
@classmethod
@extended_docstring(Rotation.from_matrix)
@util.extended_docstring(Rotation.from_matrix,_parameter_doc)
def from_matrix(cls,**kwargs):
return cls(rotation=Rotation.from_matrix(**kwargs),**kwargs)
@classmethod
@extended_docstring(Rotation.from_Rodrigues_vector)
@util.extended_docstring(Rotation.from_Rodrigues_vector,_parameter_doc)
def from_Rodrigues_vector(cls,**kwargs):
return cls(rotation=Rotation.from_Rodrigues_vector(**kwargs),**kwargs)
@classmethod
@extended_docstring(Rotation.from_homochoric)
@util.extended_docstring(Rotation.from_homochoric,_parameter_doc)
def from_homochoric(cls,**kwargs):
return cls(rotation=Rotation.from_homochoric(**kwargs),**kwargs)
@classmethod
@extended_docstring(Rotation.from_cubochoric)
@util.extended_docstring(Rotation.from_cubochoric,_parameter_doc)
def from_cubochoric(cls,**kwargs):
return cls(rotation=Rotation.from_cubochoric(**kwargs),**kwargs)
@classmethod
@extended_docstring(Rotation.from_spherical_component)
@util.extended_docstring(Rotation.from_spherical_component,_parameter_doc)
def from_spherical_component(cls,**kwargs):
return cls(rotation=Rotation.from_spherical_component(**kwargs),**kwargs)
@classmethod
@extended_docstring(Rotation.from_fiber_component)
@util.extended_docstring(Rotation.from_fiber_component,_parameter_doc)
def from_fiber_component(cls,**kwargs):
return cls(rotation=Rotation.from_fiber_component(**kwargs),**kwargs)
@classmethod
@extend_docstring()
@util.extend_docstring(_parameter_doc)
def from_directions(cls,uvw,hkl,**kwargs):
"""
Initialize orientation object from two crystallographic directions.
@ -847,6 +820,14 @@ class Orientation(Rotation):
rgb : numpy.ndarray of shape (...,3)
RGB array of IPF colors.
Examples
--------
Inverse pole figure color of the e_3 direction for a crystal in "Cube" orientation with cubic symmetry:
>>> o = damask.Orientation(lattice='cubic')
>>> o.IPF_color(o.to_SST([0,0,1]))
array([1., 0., 0.])
References
----------
Bases are computed from
@ -957,6 +938,22 @@ class Orientation(Rotation):
Currently requires same crystal family for both orientations.
For extension to cases with differing symmetry see A. Heinz and P. Neumann 1991 and 10.1107/S0021889808016373.
Examples
--------
Disorientation between two specific orientations of hexagonal symmetry:
>>> import damask
>>> a = damask.Orientation.from_Eulers(phi=[123,32,21],degrees=True,lattice='hexagonal')
>>> b = damask.Orientation.from_Eulers(phi=[104,11,87],degrees=True,lattice='hexagonal')
>>> a.disorientation(b)
Crystal family hexagonal
Quaternion: (real=0.976, imag=<+0.189, +0.018, +0.103>)
Matrix:
[[ 0.97831006 0.20710935 0.00389135]
[-0.19363288 0.90765544 0.37238141]
[ 0.07359167 -0.36505797 0.92807163]]
Bunge Eulers / deg: (11.40, 21.86, 0.60)
"""
if self.family is None or other.family is None:
raise ValueError('Missing crystal symmetry')
@ -1065,8 +1062,8 @@ class Orientation(Rotation):
raise ValueError('Missing crystal symmetry')
eq = self.equivalent
blend = util.shapeblender(eq.shape,vector.shape[:-1])
poles = eq.broadcast_to(blend,mode='right') @ np.broadcast_to(vector,blend+(3,))
blend = util.shapeblender(eq.shape,np.array(vector).shape[:-1])
poles = eq.broadcast_to(blend,mode='right') @ np.broadcast_to(np.array(vector),blend+(3,))
ok = self.in_SST(poles,proper=proper)
ok &= np.cumsum(ok,axis=0) == 1
loc = np.where(ok)
@ -1085,12 +1082,12 @@ class Orientation(Rotation):
Parameters
----------
uvtw | hkil : numpy.ndarray of shape (...,4)
uvtw|hkil : numpy.ndarray of shape (...,4)
Miller–Bravais indices of crystallographic direction [uvtw] or plane normal (hkil).
Returns
-------
uvw | hkl : numpy.ndarray of shape (...,3)
uvw|hkl : numpy.ndarray of shape (...,3)
Miller indices of [uvw] direction or (hkl) plane normal.
"""
@ -1113,12 +1110,12 @@ class Orientation(Rotation):
Parameters
----------
uvw | hkl : numpy.ndarray of shape (...,3)
uvw|hkl : numpy.ndarray of shape (...,3)
Miller indices of crystallographic direction [uvw] or plane normal (hkl).
Returns
-------
uvtw | hkil : numpy.ndarray of shape (...,4)
uvtw|hkil : numpy.ndarray of shape (...,4)
Miller–Bravais indices of [uvtw] direction or (hkil) plane normal.
"""
@ -1142,7 +1139,7 @@ class Orientation(Rotation):
Parameters
----------
direction | normal : numpy.ndarray of shape (...,3)
direction|normal : numpy.ndarray of shape (...,3)
Vector along direction or plane normal.
Returns
@ -1166,7 +1163,7 @@ class Orientation(Rotation):
Parameters
----------
uvw | hkl : numpy.ndarray of shape (...,3)
uvw|hkl : numpy.ndarray of shape (...,3)
Miller indices of crystallographic direction or plane normal.
with_symmetry : bool, optional
Calculate all N symmetrically equivalent vectors.
@ -1194,7 +1191,7 @@ class Orientation(Rotation):
Parameters
----------
uvw | hkl : numpy.ndarray of shape (...,3)
uvw|hkl : numpy.ndarray of shape (...,3)
Miller indices of crystallographic direction or plane normal.
with_symmetry : bool, optional
Calculate all N symmetrically equivalent vectors.
@ -1217,13 +1214,26 @@ class Orientation(Rotation):
Parameters
----------
mode : str
Type of kinematics, e.g. 'slip' or 'twin'.
Type of kinematics, i.e. 'slip' or 'twin'.
Returns
-------
P : numpy.ndarray of shape (...,N,3,3)
Schmid matrix for each of the N deformation systems.
Examples
--------
Schmid matrix (in lab frame) of slip systems of a face-centered
cubic crystal in "Goss" orientation.
>>> import damask
>>> import numpy as np
>>> np.set_printoptions(3,suppress=True,floatmode='fixed')
>>> damask.Orientation.from_Eulers(phi=[0,45,0],degrees=True,lattice='cF').Schmid('slip')[0]
array([[ 0.000, 0.000, 0.000],
[ 0.577, -0.000, 0.816],
[ 0.000, 0.000, 0.000]])
"""
d = self.to_frame(uvw=self.kinematics[mode]['direction'],with_symmetry=False)
p = self.to_frame(hkl=self.kinematics[mode]['plane'] ,with_symmetry=False)

4
python/damask/_result.py
View File

@ -168,9 +168,7 @@ class Result:
def allow_modification(self):
print(util.bcolors().WARNING+util.bcolors().BOLD+
'Warning: Modification of existing datasets allowed!'+
util.bcolors().ENDC)
print(util.warn('Warning: Modification of existing datasets allowed!'))
self._allow_modification = True
def disallow_modification(self):

58
python/damask/_rotation.py
View File

@ -107,22 +107,6 @@ class Rotation:
and np.allclose(self.quaternion,other.quaternion)
def __neq__(self,other):
"""
Not Equal to other.
Equality is determined taking limited floating point precision into
account. See numpy.allclose for details.
Parameters
----------
other : Rotation
Rotation to check for inequality.
"""
return not self.__eq__(other)
@property
def shape(self):
return self.quaternion.shape[:-1]
@ -404,7 +388,7 @@ class Rotation:
Returns
-------
h : numpy.ndarray of shape (...,3)
Homochoric vector: (h_1, h_2, h_3), ǀhǀ < 1/2*π^(2/3).
Homochoric vector: (h_1, h_2, h_3), ǀhǀ < (3/4*π)^(1/3).
"""
return Rotation._qu2ho(self.quaternion)
@ -698,7 +682,7 @@ class Rotation:
@staticmethod
def from_random(shape = None,
seed = None,
rng_seed = None,
**kwargs):
"""
Draw random rotation.
@ -710,12 +694,12 @@ class Rotation:
shape : tuple of ints, optional
Shape of the sample. Defaults to None which gives a
single rotation
seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. Defaults to None.
If None, then fresh, unpredictable entropy will be pulled from the OS.
"""
rng = np.random.default_rng(seed)
rng = np.random.default_rng(rng_seed)
r = rng.random(3 if shape is None else tuple(shape)+(3,) if hasattr(shape, '__iter__') else (shape,3))
A = np.sqrt(r[...,2])
@ -730,11 +714,11 @@ class Rotation:
@staticmethod
def from_ODF(weights,
Eulers,
phi,
N = 500,
degrees = True,
fractions = True,
seed = None,
rng_seed = None,
**kwargs):
"""
Sample discrete values from a binned ODF.
@ -743,7 +727,7 @@ class Rotation:
----------
weights : numpy.ndarray of shape (n)
Texture intensity values (probability density or volume fraction) at Euler grid points.
Eulers : numpy.ndarray of shape (n,3)
phi : numpy.ndarray of shape (n,3)
Grid coordinates in Euler space at which weights are defined.
N : integer, optional
Number of discrete orientations to be sampled from the given ODF.
@ -753,7 +737,7 @@ class Rotation:
fractions : boolean, optional
ODF values correspond to volume fractions, not probability density.
Defaults to True.
seed: {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
rng_seed: {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. Defaults to None, i.e. unpredictable entropy
will be pulled from the OS.
@ -776,15 +760,15 @@ class Rotation:
"""
def _dg(eu,deg):
"""Return infinitesimal Euler space volume of bin(s)."""
Eulers_sorted = eu[np.lexsort((eu[:,0],eu[:,1],eu[:,2]))]
steps,size,_ = grid_filters.cell_coord0_gridSizeOrigin(Eulers_sorted)
phi_sorted = eu[np.lexsort((eu[:,0],eu[:,1],eu[:,2]))]
steps,size,_ = grid_filters.cell_coord0_gridSizeOrigin(phi_sorted)
delta = np.radians(size/steps) if deg else size/steps
return delta[0]*2.0*np.sin(delta[1]/2.0)*delta[2] / 8.0 / np.pi**2 * np.sin(np.radians(eu[:,1]) if deg else eu[:,1])
dg = 1.0 if fractions else _dg(Eulers,degrees)
dg = 1.0 if fractions else _dg(phi,degrees)
dV_V = dg * np.maximum(0.0,weights.squeeze())
return Rotation.from_Euler_angles(Eulers[util.hybrid_IA(dV_V,N,seed)],degrees)
return Rotation.from_Euler_angles(phi[util.hybrid_IA(dV_V,N,rng_seed)],degrees)
@staticmethod
@ -792,7 +776,7 @@ class Rotation:
sigma,
N = 500,
degrees = True,
seed = None,
rng_seed = None,
**kwargs):
"""
Calculate set of rotations with Gaussian distribution around center.
@ -807,12 +791,12 @@ class Rotation:
Number of samples, defaults to 500.
degrees : boolean, optional
sigma is given in degrees.
seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. Defaults to None, i.e. unpredictable entropy
will be pulled from the OS.
"""
rng = np.random.default_rng(seed)
rng = np.random.default_rng(rng_seed)
sigma = np.radians(sigma) if degrees else sigma
u,Theta = (rng.random((N,2)) * 2.0 * np.array([1,np.pi]) - np.array([1.0, 0])).T
omega = abs(rng.normal(scale=sigma,size=N))
@ -829,7 +813,7 @@ class Rotation:
sigma = 0.0,
N = 500,
degrees = True,
seed = None,
rng_seed = None,
**kwargs):
"""
Calculate set of rotations with Gaussian distribution around direction.
@ -847,12 +831,12 @@ class Rotation:
Number of samples, defaults to 500.
degrees : boolean, optional
sigma, alpha, and beta are given in degrees.
seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. Defaults to None, i.e. unpredictable entropy
will be pulled from the OS.
"""
rng = np.random.default_rng(seed)
rng = np.random.default_rng(rng_seed)
sigma_,alpha_,beta_ = map(np.radians,(sigma,alpha,beta)) if degrees else (sigma,alpha,beta)
d_cr = np.array([np.sin(alpha_[0])*np.cos(alpha_[1]), np.sin(alpha_[0])*np.sin(alpha_[1]), np.cos(alpha_[0])])
@ -1440,9 +1424,3 @@ class Rotation:
np.where(np.maximum(np.abs(xyz[...,1]),np.abs(xyz[...,2])) <= np.abs(xyz[...,0]),1,2))
return order[direction][p]
# for compatibility with deprecated tests
Rotation.from_Eulers = Rotation.from_Euler_angles
Rotation.as_Eulers = Rotation.as_Euler_angles
Rotation.from_Rodrigues = Rotation.from_Rodrigues_vector

5
python/damask/_table.py
View File

@ -31,7 +31,7 @@ class Table:
def __repr__(self):
"""Brief overview."""
return util.srepr(self.comments)+'\n'+self.data.__repr__()
return '\n'.join(['# '+c for c in self.comments])+'\n'+self.data.__repr__()
def __len__(self):
"""Number of rows."""
@ -159,7 +159,7 @@ class Table:
comments = [util.execution_stamp('Table','from_ang')]
for line in content:
if line.startswith('#'):
comments.append(line.strip())
comments.append(line.split('#',1)[1].strip())
else:
break
@ -222,6 +222,7 @@ class Table:
dup.data[label] = data.reshape(dup.data[label].shape)
return dup
def add(self,label,data,info=None):
"""
Add column data.

12
python/damask/seeds.py
View File

@ -7,7 +7,7 @@ from . import util
from . import grid_filters
def from_random(size,N_seeds,grid=None,seed=None):
def from_random(size,N_seeds,grid=None,rng_seed=None):
"""
Random seeding in space.
@ -20,12 +20,12 @@ def from_random(size,N_seeds,grid=None,seed=None):
grid : numpy.ndarray of shape (3), optional.
If given, ensures that all seeds initiate one grain if using a
standard Voronoi tessellation.
seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. Defaults to None.
If None, then fresh, unpredictable entropy will be pulled from the OS.
"""
rng = _np.random.default_rng(seed)
rng = _np.random.default_rng(rng_seed)
if grid is None:
coords = rng.random((N_seeds,3)) * size
else:
@ -36,7 +36,7 @@ def from_random(size,N_seeds,grid=None,seed=None):
return coords
def from_Poisson_disc(size,N_seeds,N_candidates,distance,periodic=True,seed=None):
def from_Poisson_disc(size,N_seeds,N_candidates,distance,periodic=True,rng_seed=None):
"""
Seeding in space according to a Poisson disc distribution.
@ -52,12 +52,12 @@ def from_Poisson_disc(size,N_seeds,N_candidates,distance,periodic=True,seed=None
Minimum acceptable distance to other seeds.
periodic : boolean, optional
Calculate minimum distance for periodically repeated grid.
seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. Defaults to None.
If None, then fresh, unpredictable entropy will be pulled from the OS.
"""
rng = _np.random.default_rng(seed)
rng = _np.random.default_rng(rng_seed)
coords = _np.empty((N_seeds,3))
coords[0] = rng.random(3) * size

94
python/damask/util.py
View File

@ -17,7 +17,7 @@ __all__=[
'srepr',
'croak',
'report',
'emph','deemph','delete','strikeout',
'emph','deemph','warn','strikeout',
'execute',
'show_progress',
'scale_to_coprime',
@ -26,8 +26,8 @@ __all__=[
'return_message',
'extendableOption',
'execution_stamp',
'shapeshifter',
'shapeblender',
'shapeshifter', 'shapeblender',
'extend_docstring', 'extended_docstring'
]
####################################################################################################
@ -42,7 +42,7 @@ def srepr(arg,glue = '\n'):
arg : iterable
Items to join.
glue : str, optional
Defaults to \n.
Glue used for joining operation. Defaults to \n.
"""
if (not hasattr(arg, "strip") and
@ -56,6 +56,8 @@ def croak(what, newline = True):
"""
Write formated to stderr.
DEPRECATED
Parameters
----------
what : str or iterable
@ -72,7 +74,7 @@ def croak(what, newline = True):
def report(who = None,
what = None):
"""
Reports script and file name.
Report script and file name.
DEPRECATED
@ -84,16 +86,13 @@ def emph(what):
"""Formats string with emphasis."""
return bcolors.BOLD+srepr(what)+bcolors.ENDC
def deemph(what):
"""Formats string with deemphasis."""
return bcolors.DIM+srepr(what)+bcolors.ENDC
def delete(what):
"""Formats string as deleted."""
return bcolors.DIM+srepr(what)+bcolors.ENDC
def warn(what):
"""Formats string for warning."""
return bcolors.WARNING+emph(what)+bcolors.ENDC
def strikeout(what):
"""Formats string as strikeout."""
@ -164,7 +163,15 @@ def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
def scale_to_coprime(v):
"""Scale vector to co-prime (relatively prime) integers."""
"""
Scale vector to co-prime (relatively prime) integers.
Parameters
----------
v : numpy.ndarray of shape (:)
Vector to scale.
"""
MAX_DENOMINATOR = 1000000
def get_square_denominator(x):
@ -215,7 +222,21 @@ def execution_stamp(class_name,function_name=None):
return f'damask.{class_name}{_function_name} v{version} ({now})'
def hybrid_IA(dist,N,seed=None):
def hybrid_IA(dist,N,rng_seed=None):
"""
Hybrid integer approximation.
Parameters
----------
dist : numpy.ndarray
Distribution to be approximated
N : int
Number of samples to draw.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. Defaults to None.
If None, then fresh, unpredictable entropy will be pulled from the OS.
"""
N_opt_samples,N_inv_samples = (max(np.count_nonzero(dist),N),0) # random subsampling if too little samples requested
scale_,scale,inc_factor = (0.0,float(N_opt_samples),1.0)
@ -226,7 +247,7 @@ def hybrid_IA(dist,N,seed=None):
if N_inv_samples < N_opt_samples else \
(scale_,0.5*(scale_ + scale), 1.0)
return np.repeat(np.arange(len(dist)),repeats)[np.random.default_rng(seed).permutation(N_inv_samples)[:N]]
return np.repeat(np.arange(len(dist)),repeats)[np.random.default_rng(rng_seed).permutation(N_inv_samples)[:N]]
def shapeshifter(fro,to,mode='left',keep_ones=False):
@ -300,6 +321,40 @@ def shapeblender(a,b):
return a + b[i:]
def extend_docstring(extra_docstring):
"""
Decorator: Append to function's docstring.
Parameters
----------
extra_docstring : str
Docstring to append.
"""
def _decorator(func):
func.__doc__ += extra_docstring
return func
return _decorator
def extended_docstring(f,extra_docstring):
"""
Decorator: Combine another function's docstring with a given docstring.
Parameters
----------
f : function
Function of which the docstring is taken.
extra_docstring : str
Docstring to append.
"""
def _decorator(func):
func.__doc__ = f.__doc__ + extra_docstring
return func
return _decorator
####################################################################################################
# Classes
####################################################################################################
@ -393,17 +448,6 @@ class bcolors:
UNDERLINE = '\033[4m'
CROSSOUT = '\033[9m'
def disable(self):
self.HEADER = ''
self.OKBLUE = ''
self.OKGREEN = ''
self.WARNING = ''
self.FAIL = ''
self.ENDC = ''
self.BOLD = ''
self.UNDERLINE = ''
self.CROSSOUT = ''
class return_message:
"""Object with formatted return message."""

18
python/tests/conftest.py
View File

@ -1,8 +1,13 @@
from pathlib import Path
import datetime
import os
import numpy as np
import pytest
import matplotlib as mpl
if os.name == 'posix' and 'DISPLAY' not in os.environ:
mpl.use('Agg')
import matplotlib.pyplot as plt
import damask
@ -25,8 +30,9 @@ def patch_datetime_now(monkeypatch):
monkeypatch.setattr(datetime, 'datetime', mydatetime)
@pytest.fixture
def execution_stamp(monkeypatch):
def patch_execution_stamp(monkeypatch):
"""Set damask.util.execution_stamp for reproducible tests results."""
def execution_stamp(class_name,function_name=None):
_function_name = '' if function_name is None else f'.{function_name}'
@ -35,21 +41,31 @@ def execution_stamp(monkeypatch):
monkeypatch.setattr(damask.util, 'execution_stamp', execution_stamp)
@pytest.fixture
def patch_plt_show(monkeypatch):
def _None(block=None):
pass
monkeypatch.setattr(plt, 'show', _None, raising=True)
def pytest_addoption(parser):
parser.addoption("--update",
action="store_true",
default=False)
@pytest.fixture
def update(request):
"""Store current results as new reference results."""
return request.config.getoption("--update")
@pytest.fixture
def reference_dir_base():
"""Directory containing reference results."""
return Path(__file__).parent/'reference'
@pytest.fixture
def set_of_quaternions():
"""A set of n random rotations."""

9
python/tests/test_Colormap.py
View File

@ -17,9 +17,12 @@ def reference_dir(reference_dir_base):
class TestColormap:
@pytest.fixture(autouse=True)
def _execution_stamp(self, execution_stamp):
def _patch_execution_stamp(self, patch_execution_stamp):
print('patched damask.util.execution_stamp')
def test_repr(self,patch_plt_show):
print(Colormap.from_predefined('stress'))
def test_conversion(self):
specials = np.array([[0.,0.,0.],
[1.,0.,0.],
@ -138,8 +141,8 @@ class TestColormap:
diff = ImageChops.difference(img_reference.convert('RGB'),img_current.convert('RGB'))
assert not diff.getbbox()
def test_list(self):
Colormap.list_predefined()
def test_predefined(self):
assert (isinstance(Colormap.predefined,dict))
@pytest.mark.parametrize('format,ext',[('ASCII','.txt'),
('paraview','.json'),

37
python/tests/test_ConfigMaterial.py
View File

@ -62,6 +62,12 @@ class TestConfigMaterial:
del material_config['material'][0]['homogenization']
assert not material_config.is_complete
def test_incomplete_homogenization_N_constituents(self,reference_dir):
material_config = ConfigMaterial.load(reference_dir/'material.yaml')
for h in material_config['homogenization'].keys():
del material_config['homogenization'][h]['N_constituents']
assert not material_config.is_complete
def test_incomplete_phase_lattice(self,reference_dir):
material_config = ConfigMaterial.load(reference_dir/'material.yaml')
del material_config['phase']['Aluminum']['lattice']
@ -85,9 +91,36 @@ class TestConfigMaterial:
assert len(c['material']) == N
for i,m in enumerate(c['material']):
c = m['constituents'][0]
assert m['c'] == 1 and c['b'] == 0 and c['a'] == [i,1]
assert m['c'] == 1 and c['b'] == 0 and (c['a'] == [i,1]).all()
def test__constituents(self):
def test_constituents(self):
c = ConfigMaterial._constituents(c=1,v=[2,3])
assert c[0][0]['c'] == c[1][0]['c'] == 1
assert c[0][0]['v'] == c[1][0]['v'] -1 ==2
@pytest.mark.parametrize('constituents',[{'W':1,'X':[2,3]},{'Y':4},{'Z':[5,6]}])
@pytest.mark.parametrize('a',[[7.,8.],9.])
@pytest.mark.parametrize('b',['bd',['efg','hi']])
def test_material_add(self,tmp_path,constituents,a,b):
len_c = len(ConfigMaterial()._constituents(1,**constituents))
len_a = len(a) if isinstance(a,list) else 1
len_b = len(b) if isinstance(b,list) else 1
m = ConfigMaterial().material_add(constituents,a=a,b=b)
m.save()
assert len(m['material']) == np.max([len_a,len_b,len_c])
@pytest.mark.parametrize('constituents',[{'W':1,'X':np.array([2,3])},{'Y':4},{'Z':np.array([5,6])}])
@pytest.mark.parametrize('a',[np.array([7,8]),9])
def test_material_add_np(self,tmp_path,constituents,a):
len_c = len(ConfigMaterial()._constituents(1,**constituents))
len_a = len(a) if isinstance(a,np.ndarray) else 1
m = ConfigMaterial().material_add(constituents,ld=a)
m.save()
assert len(m['material']) == np.max([len_a,len_c])
@pytest.mark.parametrize('constituents',[{'X':np.array([2,3,4,5])},{'Y':4}])
@pytest.mark.parametrize('a',[np.array([1,2,3]),[4,5,6]])
@pytest.mark.parametrize('b',[np.array([6.,7.]),[8.,9.]])
def test_material_add_invalid(self,constituents,a,b):
with pytest.raises(ValueError):
ConfigMaterial().material_add(constituents,a=a,u=b)

7
python/tests/test_Geom.py
View File

@ -34,7 +34,7 @@ def reference_dir(reference_dir_base):
class TestGeom:
@pytest.fixture(autouse=True)
def _execution_stamp(self, execution_stamp):
def _patch_execution_stamp(self, patch_execution_stamp):
print('patched damask.util.execution_stamp')
def test_diff_equal(self,default):
@ -45,6 +45,8 @@ class TestGeom:
new = Geom(default.material[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
assert str(default.diff(new)) != ''
def test_repr(self,default):
print(default)
def test_read_write_vtr(self,default,tmp_path):
default.save(tmp_path/'default')
@ -70,6 +72,9 @@ class TestGeom:
Geom(default.material[1:,1:,1:],
size=np.ones(2))
def test_save_load_ASCII(self,default,tmp_path):
default.save_ASCII(tmp_path/'ASCII')
assert geom_equal(Geom.load_ASCII(tmp_path/'ASCII'),default)
def test_invalid_origin(self,default):
with pytest.raises(ValueError):

20
python/tests/test_Orientation.py
View File

@ -125,9 +125,9 @@ class TestOrientation:
def test_from_fiber_component(self):
r = Rotation.from_fiber_component(alpha=np.zeros(2),beta=np.zeros(2),
sigma=0.0,N=1,seed=0)
sigma=0.0,N=1,rng_seed=0)
assert np.all(Orientation.from_fiber_component(alpha=np.zeros(2),beta=np.zeros(2),
sigma=0.0,N=1,seed=0,lattice='triclinic').quaternion
sigma=0.0,N=1,rng_seed=0,lattice='triclinic').quaternion
== r.quaternion)
@pytest.mark.parametrize('kwargs',[
@ -175,8 +175,8 @@ class TestOrientation:
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('N',[1,8,32])
def test_disorientation(self,lattice,N):
o = Orientation.from_random(lattice=lattice,shape=N,seed=0)
p = Orientation.from_random(lattice=lattice,shape=N,seed=1)
o = Orientation.from_random(lattice=lattice,shape=N)
p = Orientation.from_random(lattice=lattice,shape=N)
d,ops = o.disorientation(p,return_operators=True)
@ -198,8 +198,8 @@ class TestOrientation:
(None,None),
])
def test_disorientation_blending(self,lattice,a,b):
o = Orientation.from_random(lattice=lattice,shape=a,seed=0)
p = Orientation.from_random(lattice=lattice,shape=b,seed=1)
o = Orientation.from_random(lattice=lattice,shape=a)
p = Orientation.from_random(lattice=lattice,shape=b)
blend = util.shapeblender(o.shape,p.shape)
for loc in np.random.randint(0,blend,(10,len(blend))):
assert o[tuple(loc[:len(o.shape)])].disorientation(p[tuple(loc[-len(p.shape):])]) \
@ -214,7 +214,7 @@ class TestOrientation:
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
def test_reduced_vectorization(self,lattice,shape):
o = Orientation.from_random(lattice=lattice,shape=shape,seed=0)
o = Orientation.from_random(lattice=lattice,shape=shape)
for r, theO in zip(o.reduced.flatten(),o.flatten()):
assert r == theO.reduced
@ -223,7 +223,7 @@ class TestOrientation:
@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
@pytest.mark.parametrize('proper',[True,False])
def test_to_SST_vectorization(self,lattice,shape,vector,proper):
o = Orientation.from_random(lattice=lattice,shape=shape,seed=0)
o = Orientation.from_random(lattice=lattice,shape=shape)
for r, theO in zip(o.to_SST(vector=vector,proper=proper).reshape((-1,3)),o.flatten()):
assert np.allclose(r,theO.to_SST(vector=vector,proper=proper))
@ -232,7 +232,7 @@ class TestOrientation:
@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
@pytest.mark.parametrize('proper',[True,False])
def test_IPF_color_vectorization(self,lattice,shape,vector,proper):
o = Orientation.from_random(lattice=lattice,shape=shape,seed=0)
o = Orientation.from_random(lattice=lattice,shape=shape)
poles = o.to_SST(vector=vector,proper=proper)
for r, theO in zip(o.IPF_color(poles,proper=proper).reshape((-1,3)),o.flatten()):
assert np.allclose(r,theO.IPF_color(theO.to_SST(vector=vector,proper=proper),proper=proper))
@ -245,7 +245,7 @@ class TestOrientation:
(None,(3,)),
])
def test_to_SST_blending(self,lattice,a,b):
o = Orientation.from_random(lattice=lattice,shape=a,seed=0)
o = Orientation.from_random(lattice=lattice,shape=a)
v = np.random.random(b+(3,))
blend = util.shapeblender(o.shape,b)
for loc in np.random.randint(0,blend,(10,len(blend))):

17
python/tests/test_Rotation.py
View File

@ -769,18 +769,19 @@ class TestRotation:
@pytest.mark.parametrize('shape',[None,1,(4,4)])
def test_random(self,shape):
Rotation.from_random(shape)
r = Rotation.from_random(shape)
if shape is None:
assert r.shape == ()
elif shape == 1:
assert r.shape == (1,)
else:
assert r.shape == shape
def test_equal(self):
r = Rotation.from_random(seed=0)
assert r == r
def test_unequal(self):
r = Rotation.from_random(seed=0)
assert not (r != r)
assert Rotation.from_random(rng_seed=1) == Rotation.from_random(rng_seed=1)
def test_inversion(self):
r = Rotation.from_random(seed=0)
r = Rotation.from_random()
assert r == ~~r
@pytest.mark.parametrize('shape',[None,1,(1,),(4,2),(1,1,1)])

6
python/tests/test_Table.py
View File

@ -17,6 +17,12 @@ def reference_dir(reference_dir_base):
class TestTable:
def test_repr(self,default):
print(default)
def test_len(self):
len(Table(np.random.rand(7,3),{'X':3})) == 7
def test_get_scalar(self,default):
d = default.get('s')
assert np.allclose(d,1.0) and d.shape[1:] == (1,)

11
python/tests/test_VTK.py
View File

@ -23,7 +23,7 @@ def default():
class TestVTK:
@pytest.fixture(autouse=True)
def _execution_stamp(self, execution_stamp):
def _patch_execution_stamp(self, patch_execution_stamp):
print('patched damask.util.execution_stamp')
def test_rectilinearGrid(self,tmp_path):
@ -84,6 +84,15 @@ class TestVTK:
time.sleep(.5)
assert(False)
def test_compress(self,tmp_path):
points = np.random.rand(102,3)
v = VTK.from_poly_data(points)
fname_c = tmp_path/'compressed.vtp'
fname_p = tmp_path/'plain.vtp'
v.save(fname_c,parallel=False,compress=False)
v.save(fname_p,parallel=False,compress=True)
assert(VTK.load(fname_c).__repr__() == VTK.load(fname_p).__repr__())
@pytest.mark.parametrize('fname',['a','a.vtp','a.b','a.b.vtp'])
def test_filename_variations(self,tmp_path,fname):

8
python/tests/test_util.py
View File

@ -15,6 +15,10 @@ class TestUtil:
out,err = util.execute('sh -c "echo $test_for_execute"',env={'test_for_execute':'test'})
assert out=='test\n' and err==''
def test_execute_invalid(self):
with pytest.raises(RuntimeError):
util.execute('/bin/false')
def test_croak(self):
util.croak('Burp!')
@ -93,3 +97,7 @@ class TestUtil:
])
def test_shapeblender(self,a,b,answer):
assert util.shapeblender(a,b) == answer
@pytest.mark.parametrize('style',[util.emph,util.deemph,util.warn,util.strikeout])
def test_decorate(self,style):
assert 'DAMASK' in style('DAMASK')

36
src/C_routines.c
View File

@ -4,25 +4,24 @@
#include <dirent.h>
#include <string.h>
#include <signal.h>
#include <pwd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "zlib.h"
/* http://stackoverflow.com/questions/30279228/is-there-an-alternative-to-getcwd-in-fortran-2003-2008 */
#define PATHLEN 4096
#define STRLEN 256
int isdirectory_c(const char *dir){
struct stat statbuf;
if(stat(dir, &statbuf) != 0) /* error */
return 0; /* return "NO, this is not a directory" */
return S_ISDIR(statbuf.st_mode); /* 1 => is directory, 0 => this is NOT a directory */
int setcwd_c(const char *cwd){
return chdir(cwd);
}
void getcurrentworkdir_c(char cwd[], int *stat ){
char cwd_tmp[4096];
if(getcwd(cwd_tmp, sizeof(cwd_tmp)) == cwd_tmp){
strcpy(cwd,cwd_tmp);
void getcwd_c(char cwd[], int *stat ){
char cwd_tmp[PATHLEN+1];
if(getcwd(cwd_tmp, sizeof(cwd_tmp))){
strcpy(cwd,cwd_tmp); // getcwd guarantees a NULL-terminated string
*stat = 0;
}
else{
@ -32,9 +31,9 @@ void getcurrentworkdir_c(char cwd[], int *stat ){
void gethostname_c(char hostname[], int *stat){
char hostname_tmp[4096];
char hostname_tmp[STRLEN];
if(gethostname(hostname_tmp, sizeof(hostname_tmp)) == 0){
strcpy(hostname,hostname_tmp);
strncpy(hostname,hostname_tmp,sizeof(hostname_tmp)+1); // gethostname does not guarantee a NULL-terminated string
*stat = 0;
}
else{
@ -43,10 +42,18 @@ void gethostname_c(char hostname[], int *stat){
}
int chdir_c(const char *dir){
return chdir(dir);
void getusername_c(char username[], int *stat){
struct passwd *pw = getpwuid(geteuid());
if(pw && strlen(pw->pw_name) <= STRLEN){
strncpy(username,pw->pw_name,STRLEN+1);
*stat = 0;
}
else{
*stat = 1;
}
}
void signalterm_c(void (*handler)(int)){
signal(SIGTERM, handler);
}
@ -59,6 +66,7 @@ void signalusr2_c(void (*handler)(int)){
signal(SIGUSR2, handler);
}
void inflate_c(const uLong *s_deflated, const uLong *s_inflated, const Byte deflated[], Byte inflated[]){
/* make writable copy, uncompress will write to it */
uLong s_inflated_,i;

27
src/DAMASK_interface.f90
View File

@ -69,8 +69,6 @@ subroutine DAMASK_interface_init
loadCaseArg = '', & !< -l argument given to the executable
geometryArg = '', & !< -g argument given to the executable
workingDirArg = '' !< -w argument given to the executable
character(len=pStringLen) :: &
userName !< name of user calling the executable
integer :: &
stat, &
i
@ -117,6 +115,9 @@ subroutine DAMASK_interface_init
print'(/,a)', ' Compiled on: '//__DATE__//' at '//__TIME__
print'(/,a,i0,a,i0,a,i0)', &
' PETSc version: ',PETSC_VERSION_MAJOR,'.',PETSC_VERSION_MINOR,'.',PETSC_VERSION_SUBMINOR
call date_and_time(values = dateAndTime)
print'(/,a,2(i2.2,a),i4.4)', ' Date: ',dateAndTime(3),'/',dateAndTime(2),'/', dateAndTime(1)
print'(a,2(i2.2,a),i2.2)', ' Time: ',dateAndTime(5),':', dateAndTime(6),':', dateAndTime(7)
@ -126,9 +127,9 @@ subroutine DAMASK_interface_init
if (err /= 0) call quit(1)
select case(trim(arg)) ! extract key
case ('-h','--help')
print'(a)', ' #######################################################################'
print'(/,a)',' #######################################################################'
print'(a)', ' DAMASK Command Line Interface:'
print'(a)', ' For PETSc-based solvers for the Düsseldorf Advanced Material Simulation Kit'
print'(a)', ' Düsseldorf Advanced Material Simulation Kit with PETSc-based solvers'
print'(a,/)',' #######################################################################'
print'(a,/)',' Valid command line switches:'
print'(a)', ' --geom (-g, --geometry)'
@ -189,17 +190,15 @@ subroutine DAMASK_interface_init
interface_loadFile = getLoadCaseFile(loadCaseArg)
call get_command(commandLine)
call get_environment_variable('USER',userName)
! ToDo: https://stackoverflow.com/questions/8953424/how-to-get-the-username-in-c-c-in-linux
print'(a)', ' Host name: '//trim(getHostName())
print'(a)', ' User name: '//trim(userName)
print'(/,a)', ' Host name: '//getHostName()
print'(a)', ' User name: '//getUserName()
print'(/a)', ' Command line call: '//trim(commandLine)
if (len_trim(workingDirArg) > 0) &
print'(a)', ' Working dir argument: '//trim(workingDirArg)
print'(a)', ' Geometry argument: '//trim(geometryArg)
print'(a)', ' Load case argument: '//trim(loadcaseArg)
print'(a)', ' Working directory: '//getCWD()
print'(a)', ' Loadcase argument: '//trim(loadcaseArg)
print'(/,a)', ' Working directory: '//getCWD()
print'(a)', ' Geometry file: '//interface_geomFile
print'(a)', ' Loadcase file: '//interface_loadFile
print'(a)', ' Solver job name: '//getSolverJobName()
@ -223,7 +222,7 @@ end subroutine DAMASK_interface_init
subroutine setWorkingDirectory(workingDirectoryArg)
character(len=*), intent(in) :: workingDirectoryArg !< working directory argument
character(len=pPathLen) :: workingDirectory
character(len=:), allocatable :: workingDirectory
logical :: error
external :: quit
@ -359,12 +358,12 @@ end function rectifyPath
!--------------------------------------------------------------------------------------------------
!> @brief relative path from absolute a to absolute b
!> @brief Determine relative path from absolute a to absolute b
!--------------------------------------------------------------------------------------------------
function makeRelativePath(a,b)
character (len=*), intent(in) :: a,b
character (len=pPathLen) :: a_cleaned,b_cleaned
character(len=*), intent(in) :: a,b
character(len=pPathLen) :: a_cleaned,b_cleaned
character(len=:), allocatable :: makeRelativePath
integer :: i,posLastCommonSlash,remainingSlashes

6
src/constitutive_mech.f90
View File

@ -217,7 +217,7 @@ module subroutine mech_init
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
elastic => mech%get('elasticity')
if(elastic%get_asString('type') == 'hooke') then
phase_elasticity(p) = ELASTICITY_HOOKE_ID
@ -234,7 +234,7 @@ module subroutine mech_init
if(maxVal(phase_NstiffnessDegradations)/=0) then
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
stiffDegradation => mech%get('stiffness_degradation',defaultVal=emptyList)
do stiffDegradationCtr = 1, stiffDegradation%length
if(stiffDegradation%get_asString(stiffDegradationCtr) == 'damage') &
@ -285,7 +285,7 @@ module function plastic_active(plastic_label) result(active_plastic)
allocate(active_plastic(phases%length), source = .false. )
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
pl => mech%get('plasticity')
if(pl%get_asString('type') == plastic_label) active_plastic(p) = .true.
enddo

2
src/constitutive_plastic_disloTungsten.f90
View File

@ -116,7 +116,7 @@ module function plastic_disloTungsten_init() result(myPlasticity)
i = 0
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
if(.not. myPlasticity(p)) cycle
i = i + 1
associate(prm => param(i), &

2
src/constitutive_plastic_dislotwin.f90
View File

@ -169,7 +169,7 @@ module function plastic_dislotwin_init() result(myPlasticity)
i = 0
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
if(.not. myPlasticity(p)) cycle
i = i + 1
associate(prm => param(i), &

2
src/constitutive_plastic_isotropic.f90
View File

@ -86,7 +86,7 @@ module function plastic_isotropic_init() result(myPlasticity)
i = 0
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
if(.not. myPlasticity(p)) cycle
i = i + 1
associate(prm => param(i), &

2
src/constitutive_plastic_kinehardening.f90
View File

@ -96,7 +96,7 @@ module function plastic_kinehardening_init() result(myPlasticity)
i = 0
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
if(.not. myPlasticity(p)) cycle
i = i + 1
associate(prm => param(i), &

2
src/constitutive_plastic_none.f90
View File

@ -31,7 +31,7 @@ module function plastic_none_init() result(myPlasticity)
allocate(myPlasticity(phases%length), source = .false.)
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
pl => mech%get ('plasticity')
if(pl%get_asString('type') == 'none') myPlasticity(p) = .true.
enddo

2
src/constitutive_plastic_nonlocal.f90
View File

@ -213,7 +213,7 @@ module function plastic_nonlocal_init() result(myPlasticity)
i = 0
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
if(.not. myPlasticity(p)) cycle
i = i + 1
associate(prm => param(i), &

2
src/constitutive_plastic_phenopowerlaw.f90
View File

@ -104,7 +104,7 @@ module function plastic_phenopowerlaw_init() result(myPlasticity)
i = 0
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
if(.not. myPlasticity(p)) cycle
i = i + 1
associate(prm => param(i), &

4
src/crystallite.f90
View File

@ -240,7 +240,7 @@ subroutine crystallite_init
allocate(output_constituent(phases%length))
do c = 1, phases%length
phase => phases%get(c)
mech => phase%get('mech',defaultVal = emptyDict)
mech => phase%get('mechanics',defaultVal = emptyDict)
#if defined(__GFORTRAN__)
output_constituent(c)%label = output_asStrings(mech)
#else
@ -739,7 +739,7 @@ subroutine crystallite_results
character(len=:), allocatable :: group,structureLabel
do p=1,size(material_name_phase)
group = trim('current/constituent')//'/'//trim(material_name_phase(p))//'/generic'
group = trim('current/constituent')//'/'//trim(material_name_phase(p))//'/mechanics'
call results_closeGroup(results_addGroup(group))

2
src/grid/DAMASK_grid.f90
View File

@ -176,7 +176,7 @@ program DAMASK_grid
load_step => load_steps%get(l)
step_mech => load_step%get('mech')
step_mech => load_step%get('mechanics')
loadCases(l)%stress%myType='P'
readMech: do m = 1, step_mech%length
select case (step_mech%getKey(m))

44
src/grid/discretization_grid.f90
View File

@ -56,25 +56,33 @@ subroutine discretization_grid_init(restart)
myGrid !< domain grid of this process
integer, dimension(:), allocatable :: &
materialAt
materialAt, materialAt_global
integer :: &
j, &
debug_element, &
debug_ip
debug_element, debug_ip, &
ierr
integer(C_INTPTR_T) :: &
devNull, z, z_offset
integer, dimension(worldsize) :: &
displs, sendcounts
print'(/,a)', ' <<<+- discretization_grid init -+>>>'; flush(IO_STDOUT)
call readVTR(grid,geomSize,origin,materialAt)
if(worldrank == 0) call readVTR(grid,geomSize,origin,materialAt_global)
call MPI_Bcast(grid,3,MPI_INTEGER,0,PETSC_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Bcast(geomSize,3,MPI_DOUBLE,0,PETSC_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Bcast(origin,3,MPI_DOUBLE,0,PETSC_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'
print'(/,a,3(i12 ))', ' grid a b c: ', grid
print'(a,3(es12.5))', ' size x y z: ', geomSize
print'(a,3(es12.5))', ' origin x y z: ', origin
!--------------------------------------------------------------------------------------------------
! grid solver specific quantities
if(worldsize>grid(3)) call IO_error(894, ext_msg='number of processes exceeds grid(3)')
call fftw_mpi_init
@ -93,14 +101,14 @@ subroutine discretization_grid_init(restart)
myGrid = [grid(1:2),grid3]
mySize = [geomSize(1:2),size3]
!-------------------------------------------------------------------------------------------------
! debug parameters
debug_element = config_debug%get_asInt('element',defaultVal=1)
debug_ip = config_debug%get_asInt('integrationpoint',defaultVal=1)
call MPI_Gather(product(grid(1:2))*grid3Offset,1,MPI_INTEGER,displs, 1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Gather(product(myGrid), 1,MPI_INTEGER,sendcounts,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
if (ierr /= 0) error stop 'MPI error'
!--------------------------------------------------------------------------------------------------
! general discretization
materialAt = materialAt(product(grid(1:2))*grid3Offset+1:product(grid(1:2))*(grid3Offset+grid3)) ! reallocate/shrink in case of MPI
allocate(materialAt(product(myGrid)))
call MPI_scatterv(materialAt_global,sendcounts,displs,MPI_INTEGER,materialAt,size(materialAt),MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
if (ierr /= 0) error stop 'MPI error'
call discretization_init(materialAt, &
IPcoordinates0(myGrid,mySize,grid3Offset), &
@ -131,10 +139,12 @@ subroutine discretization_grid_init(restart)
call geometry_plastic_nonlocal_setIPareaNormal (cellSurfaceNormal(product(myGrid)))
call geometry_plastic_nonlocal_setIPneighborhood(IPneighborhood(myGrid))
!--------------------------------------------------------------------------------------------------
! sanity checks for debugging
if (debug_element < 1 .or. debug_element > product(myGrid)) call IO_error(602,ext_msg='element') ! selected element does not exist
if (debug_ip /= 1) call IO_error(602,ext_msg='IP') ! selected IP does not exist
!-------------------------------------------------------------------------------------------------
! debug parameters
debug_element = config_debug%get_asInt('element',defaultVal=1)
if (debug_element < 1 .or. debug_element > product(myGrid)) call IO_error(602,ext_msg='element')
debug_ip = config_debug%get_asInt('integrationpoint',defaultVal=1)
if (debug_ip /= 1) call IO_error(602,ext_msg='IP')
end subroutine discretization_grid_init

23
src/grid/spectral_utilities.f90
View File

@ -993,12 +993,11 @@ subroutine utilities_updateCoords(F)
real(pReal), dimension(3, grid(1)+1,grid(2)+1,grid3+1) :: nodeCoords
integer :: &
i,j,k,n, &
rank_t, &
rank_b, &
c, r, &
rank_t, rank_b, &
c, &
ierr
integer, dimension(MPI_STATUS_SIZE) :: &
s
integer, dimension(4) :: request
integer, dimension(MPI_STATUS_SIZE,4) :: status
real(pReal), dimension(3) :: step
real(pReal), dimension(3,3) :: Favg
integer, dimension(3) :: me
@ -1044,20 +1043,20 @@ subroutine utilities_updateCoords(F)
rank_b = modulo(worldrank-1,worldsize)
! send bottom layer to process below
call MPI_Isend(IPfluct_padded(:,:,:,2), c,MPI_DOUBLE,rank_b,0,PETSC_COMM_WORLD,r,ierr)
call MPI_Isend(IPfluct_padded(:,:,:,2), c,MPI_DOUBLE,rank_b,0,PETSC_COMM_WORLD,request(1),ierr)
if(ierr /=0) error stop 'MPI error'
call MPI_Irecv(IPfluct_padded(:,:,:,grid3+2),c,MPI_DOUBLE,rank_t,0,PETSC_COMM_WORLD,r,ierr)
if(ierr /=0) error stop 'MPI error'
call MPI_Wait(r,s,ierr)
call MPI_Irecv(IPfluct_padded(:,:,:,grid3+2),c,MPI_DOUBLE,rank_t,0,PETSC_COMM_WORLD,request(2),ierr)
if(ierr /=0) error stop 'MPI error'
! send top layer to process above
call MPI_Isend(IPfluct_padded(:,:,:,grid3+1),c,MPI_DOUBLE,rank_t,0,PETSC_COMM_WORLD,r,ierr)
call MPI_Isend(IPfluct_padded(:,:,:,grid3+1),c,MPI_DOUBLE,rank_t,1,PETSC_COMM_WORLD,request(3),ierr)
if(ierr /=0) error stop 'MPI error'
call MPI_Irecv(IPfluct_padded(:,:,:,1), c,MPI_DOUBLE,rank_b,0,PETSC_COMM_WORLD,r,ierr)
call MPI_Irecv(IPfluct_padded(:,:,:,1), c,MPI_DOUBLE,rank_b,1,PETSC_COMM_WORLD,request(4),ierr)
if(ierr /=0) error stop 'MPI error'
call MPI_Wait(r,s,ierr)
call MPI_Waitall(4,request,status,ierr)
if(ierr /=0) error stop 'MPI error'
if(any(status(MPI_ERROR,:) /= 0)) error stop 'MPI error'
!--------------------------------------------------------------------------------------------------
! calculate nodal displacements

2
src/homogenization_mech_RGC.f90
View File

@ -145,7 +145,7 @@ module subroutine mech_RGC_init(num_homogMech)
do h = 1, size(homogenization_type)
if (homogenization_type(h) /= HOMOGENIZATION_RGC_ID) cycle
homog => material_homogenization%get(h)
homogMech => homog%get('mech')
homogMech => homog%get('mechanics')
associate(prm => param(homogenization_typeInstance(h)), &
stt => state(homogenization_typeInstance(h)), &
st0 => state0(homogenization_typeInstance(h)), &

2
src/homogenization_mech_isostrain.f90
View File

@ -48,7 +48,7 @@ module subroutine mech_isostrain_init
do h = 1, size(homogenization_type)
if (homogenization_type(h) /= HOMOGENIZATION_ISOSTRAIN_ID) cycle
homog => material_homogenization%get(h)
homogMech => homog%get('mech')
homogMech => homog%get('mechanics')
associate(prm => param(homogenization_typeInstance(h)))
prm%N_constituents = homogenization_Nconstituents(h)

2
src/kinematics_slipplane_opening.f90
View File

@ -63,7 +63,7 @@ module function kinematics_slipplane_opening_init(kinematics_length) result(myKi
do p = 1, phases%length
if(any(myKinematics(:,p))) kinematics_slipplane_opening_instance(p) = count(myKinematics(:,1:p))
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
pl => mech%get('plasticity')
if(count(myKinematics(:,p)) == 0) cycle
kinematics => phase%get('kinematics')

2
src/lattice.f90
View File

@ -476,7 +476,7 @@ subroutine lattice_init
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
mech => phase%get('mechanics')
elasticity => mech%get('elasticity')
lattice_C66(1,1,p) = elasticity%get_asFloat('C_11')
lattice_C66(1,2,p) = elasticity%get_asFloat('C_12')

2
src/material.f90
View File

@ -226,7 +226,7 @@ subroutine material_parseHomogenization
do h=1, size(material_name_homogenization)
homog => material_homogenization%get(h)
homogMech => homog%get('mech')
homogMech => homog%get('mechanics')
select case (homogMech%get_asString('type'))
case('none')
homogenization_type(h) = HOMOGENIZATION_NONE_ID

5
src/mesh/DAMASK_mesh.f90
View File

@ -110,7 +110,8 @@ program DAMASK_mesh
enddo ! count all identifiers to allocate memory and do sanity check
enddo
allocate (loadCases(N_def))
if(N_def < 1) call IO_error(error_ID = 837)
allocate(loadCases(N_def))
do i = 1, size(loadCases)
allocate(loadCases(i)%fieldBC(nActiveFields))
@ -161,7 +162,7 @@ program DAMASK_mesh
do faceSet = 1, mesh_Nboundaries
if (mesh_boundaries(faceSet) == currentFace) currentFaceSet = faceSet
enddo
if (currentFaceSet < 0) call IO_error(error_ID = errorID, ext_msg = 'invalid BC')
if (currentFaceSet < 0) call IO_error(error_ID = 837, ext_msg = 'invalid BC')
case('t','time','delta') ! increment time
loadCases(currentLoadCase)%time = IO_floatValue(line,chunkPos,i+1)
case('n','incs','increments','steps') ! number of increments

5
src/mesh/discretization_mesh.f90
View File

@ -17,6 +17,7 @@ module discretization_mesh
use IO
use config
use discretization
use results
use FEsolving
use FEM_quadrature
use YAML_types
@ -182,6 +183,10 @@ subroutine discretization_mesh_init(restart)
reshape(mesh_ipCoordinates,[3,mesh_maxNips*mesh_NcpElems]), &
mesh_node0)
call results_openJobFile
call results_closeGroup(results_addGroup('geometry'))
call results_closeJobFile
end subroutine discretization_mesh_init

2
src/source_damage_anisoDuctile.f90
View File

@ -60,7 +60,7 @@ module function source_damage_anisoDuctile_init(source_length) result(mySources)
phase => phases%get(p)
if(any(mySources(:,p))) source_damage_anisoDuctile_instance(p) = count(mySources(:,1:p))
if(count(mySources(:,p)) == 0) cycle
mech => phase%get('mech')
mech => phase%get('mechanics')
pl => mech%get('plasticity')
sources => phase%get('source')
do sourceOffset = 1, sources%length

120
src/system_routines.f90
View File

@ -8,79 +8,65 @@ module system_routines
use prec
implicit none
private
public :: &
signalterm_C, &
signalusr1_C, &
signalusr2_C, &
isDirectory, &
setCWD, &
getCWD, &
getHostName, &
setCWD
getUserName, &
signalterm_C, &
signalusr1_C, &
signalusr2_C
interface
function isDirectory_C(path) bind(C)
use, intrinsic :: ISO_C_Binding, only: &
C_INT, &
C_CHAR
function setCWD_C(cwd) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
integer(C_INT) :: setCWD_C
character(kind=C_CHAR), dimension(*), intent(in) :: cwd
end function setCWD_C
subroutine getCWD_C(cwd, stat) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
use prec
integer(C_INT) :: isDirectory_C
character(kind=C_CHAR), dimension(pPathLen), intent(in) :: path ! C string is an array
end function isDirectory_C
subroutine getCurrentWorkDir_C(path, stat) bind(C)
use, intrinsic :: ISO_C_Binding, only: &
C_INT, &
C_CHAR
use prec
character(kind=C_CHAR), dimension(pPathLen), intent(out) :: path ! C string is an array
character(kind=C_CHAR), dimension(pPathLen+1), intent(out) :: cwd ! NULL-terminated array
integer(C_INT), intent(out) :: stat
end subroutine getCurrentWorkDir_C
subroutine getHostName_C(str, stat) bind(C)
use, intrinsic :: ISO_C_Binding, only: &
C_INT, &
C_CHAR
end subroutine getCWD_C
subroutine getHostName_C(hostname, stat) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
use prec
character(kind=C_CHAR), dimension(pStringLen), intent(out) :: str ! C string is an array
character(kind=C_CHAR), dimension(pStringLen+1), intent(out) :: hostname ! NULL-terminated array
integer(C_INT), intent(out) :: stat
end subroutine getHostName_C
function chdir_C(path) bind(C)
use, intrinsic :: ISO_C_Binding, only: &
C_INT, &
C_CHAR
subroutine getUserName_C(username, stat) bind(C)
use, intrinsic :: ISO_C_Binding, only: C_INT, C_CHAR
use prec
integer(C_INT) :: chdir_C
character(kind=C_CHAR), dimension(pPathLen), intent(in) :: path ! C string is an array
end function chdir_C
character(kind=C_CHAR), dimension(pStringLen+1), intent(out) :: username ! NULL-terminated array
integer(C_INT), intent(out) :: stat
end subroutine getUserName_C
subroutine signalterm_C(handler) bind(C)
use, intrinsic :: ISO_C_Binding, only: &
C_FUNPTR
use, intrinsic :: ISO_C_Binding, only: C_FUNPTR
type(C_FUNPTR), intent(in), value :: handler
end subroutine signalterm_C
subroutine signalusr1_C(handler) bind(C)
use, intrinsic :: ISO_C_Binding, only: &
C_FUNPTR
use, intrinsic :: ISO_C_Binding, only: C_FUNPTR
type(C_FUNPTR), intent(in), value :: handler
end subroutine signalusr1_C
subroutine signalusr2_C(handler) bind(C)
use, intrinsic :: ISO_C_Binding, only: &
C_FUNPTR
use, intrinsic :: ISO_C_Binding, only: C_FUNPTR
type(C_FUNPTR), intent(in), value :: handler
end subroutine signalusr2_C
@ -89,45 +75,48 @@ module system_routines
contains
!--------------------------------------------------------------------------------------------------
!> @brief figures out if a given path is a directory (and not an ordinary file)
!> @brief set the current working directory
!--------------------------------------------------------------------------------------------------
logical function isDirectory(path)
logical function setCWD(path)
character(len=*), intent(in) :: path
isDirectory=merge(.True.,.False.,isDirectory_C(f_c_string(path)) /= 0_C_INT)
setCWD=merge(.True.,.False.,setCWD_C(f_c_string(path)) /= 0_C_INT)
end function isDirectory
end function setCWD
!--------------------------------------------------------------------------------------------------
!> @brief gets the current working directory
!> @brief get the current working directory
!--------------------------------------------------------------------------------------------------
function getCWD()
character(kind=C_CHAR), dimension(pPathLen) :: getCWD_Cstring
character(len=:), allocatable :: getCWD
character(kind=C_CHAR), dimension(pPathLen+1) :: getCWD_Cstring
integer(C_INT) :: stat
call getCurrentWorkDir_C(getCWD_Cstring,stat)
call getCWD_C(getCWD_Cstring,stat)
if(stat == 0) then
getCWD = c_f_string(getCWD_Cstring)
else
getCWD = 'Error occured when getting currend working directory'
error stop 'invalid working directory'
endif
end function getCWD
!--------------------------------------------------------------------------------------------------
!> @brief gets the current host name
!> @brief get the host name
!--------------------------------------------------------------------------------------------------
function getHostName()
character(kind=C_CHAR), dimension(pPathLen) :: getHostName_Cstring
character(len=:), allocatable :: getHostName
character(kind=C_CHAR), dimension(pStringLen+1) :: getHostName_Cstring
integer(C_INT) :: stat
call getHostName_C(getHostName_Cstring,stat)
@ -135,22 +124,31 @@ function getHostName()
if(stat == 0) then
getHostName = c_f_string(getHostName_Cstring)
else
getHostName = 'Error occured when getting host name'
getHostName = 'n/a (Error!)'
endif
end function getHostName
!--------------------------------------------------------------------------------------------------
!> @brief changes the current working directory
!> @brief get the user name
!--------------------------------------------------------------------------------------------------
logical function setCWD(path)
function getUserName()
character(len=*), intent(in) :: path
character(len=:), allocatable :: getUserName
setCWD=merge(.True.,.False.,chdir_C(f_c_string(path)) /= 0_C_INT)
character(kind=C_CHAR), dimension(pStringLen+1) :: getUserName_Cstring
integer(C_INT) :: stat
end function setCWD
call getUserName_C(getUserName_Cstring,stat)
if(stat == 0) then
getUserName = c_f_string(getUserName_Cstring)
else
getUserName = 'n/a (Error!)'
endif
end function getUserName
!--------------------------------------------------------------------------------------------------
@ -183,13 +181,13 @@ end function c_f_string
pure function f_c_string(f_string) result(c_string)
character(len=*), intent(in) :: f_string
character(kind=C_CHAR), dimension(len(f_string)+1) :: c_string
character(kind=C_CHAR), dimension(len_trim(f_string)+1) :: c_string
integer :: i
do i=1,len(f_string)
do i=1,len_trim(f_string)
c_string(i)=f_string(i:i)
enddo
c_string(i) = C_NULL_CHAR
c_string(len_trim(f_string)+1) = C_NULL_CHAR
end function f_c_string