Merge remote-tracking branch 'origin/development' into clean-and-polish-damage
This commit is contained in:
commit
705ee908a2
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@ -8,3 +8,10 @@
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*.jpg binary
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*.jpg binary
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||||||
*.hdf5 binary
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*.hdf5 binary
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||||||
*.pdf binary
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*.pdf binary
|
||||||
|
|
||||||
|
# ignore files from MSC.Marc in language statistics
|
||||||
|
installation/mods_MarcMentat/* linguist-vendored
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||||||
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src/MarcInclude/* linguist-vendored
|
||||||
|
|
||||||
|
# ignore reference files for tests in language statistics
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||||||
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python/tests/reference/* linguist-vendored
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||||||
|
|
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@ -142,13 +142,6 @@ Pre_General:
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||||||
- master
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- master
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||||||
- release
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- release
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||||||
|
|
||||||
grid_geometryPacking:
|
|
||||||
stage: preprocessing
|
|
||||||
script: grid_geometryPacking/test.py
|
|
||||||
except:
|
|
||||||
- master
|
|
||||||
- release
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|
||||||
|
|
||||||
###################################################################################################
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###################################################################################################
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||||||
Post_AverageDown:
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Post_AverageDown:
|
||||||
stage: postprocessing
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stage: postprocessing
|
||||||
|
|
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@ -52,15 +52,15 @@ for filename in options.filenames:
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||||||
table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)})
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table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)})
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||||||
table.add('pos',coords.reshape((-1,3)))
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table.add('pos',coords.reshape((-1,3)))
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||||||
|
|
||||||
results.set_visible('materialpoints',False)
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results.pick('materialpoints',False)
|
||||||
results.set_visible('constituents', True)
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results.pick('constituents', True)
|
||||||
for label in options.con:
|
for label in options.con:
|
||||||
x = results.get_dataset_location(label)
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x = results.get_dataset_location(label)
|
||||||
if len(x) != 0:
|
if len(x) != 0:
|
||||||
table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1)))
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table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1)))
|
||||||
|
|
||||||
results.set_visible('constituents', False)
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results.pick('constituents', False)
|
||||||
results.set_visible('materialpoints',True)
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results.pick('materialpoints',True)
|
||||||
for label in options.mat:
|
for label in options.mat:
|
||||||
x = results.get_dataset_location(label)
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x = results.get_dataset_location(label)
|
||||||
if len(x) != 0:
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if len(x) != 0:
|
||||||
|
|
File diff suppressed because it is too large
Load Diff
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@ -221,13 +221,9 @@ baseFile=os.path.splitext(os.path.basename(options.seedFile))[0]
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points = np.array(options.grid).prod().astype('float')
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points = np.array(options.grid).prod().astype('float')
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||||||
|
|
||||||
# ----------- calculate target distribution and bin edges
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# ----------- calculate target distribution and bin edges
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||||||
targetGeomFile = os.path.splitext(os.path.basename(options.target))[0]+'.geom'
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targetGeom = damask.Geom.from_file(os.path.splitext(os.path.basename(options.target))[0]+'.geom')
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targetGeomTable = damask.ASCIItable(targetGeomFile,None,labeled=False,readonly=True)
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nMicrostructures = len(np.unique(targetGeom.microstructure))
|
||||||
targetGeomTable.head_read()
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targetVolFrac = np.bincount(targetGeom.microstructure.flatten())/targetGeom.grid.prod().astype(np.float)
|
||||||
info,devNull = targetGeomTable.head_getGeom()
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|
||||||
nMicrostructures = info['microstructures']
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|
||||||
targetVolFrac = np.bincount(targetGeomTable.microstructure_read(info['grid']))[1:nMicrostructures+1]/\
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|
||||||
float(info['grid'].prod())
|
|
||||||
target=[]
|
target=[]
|
||||||
for i in range(1,nMicrostructures+1):
|
for i in range(1,nMicrostructures+1):
|
||||||
targetHist,targetBins = np.histogram(targetVolFrac,bins=i) #bin boundaries
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targetHist,targetBins = np.histogram(targetVolFrac,bins=i) #bin boundaries
|
||||||
|
@ -251,13 +247,12 @@ initialGeomVFile = StringIO()
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||||||
initialGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
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initialGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
|
||||||
' -g '+' '.join(list(map(str, options.grid))),bestSeedsVFile)[0])
|
' -g '+' '.join(list(map(str, options.grid))),bestSeedsVFile)[0])
|
||||||
initialGeomVFile.seek(0)
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initialGeomVFile.seek(0)
|
||||||
initialGeomTable = damask.ASCIItable(initialGeomVFile,None,labeled=False,readonly=True)
|
initialGeom = damask.Geom.from_file(initialGeomVFile)
|
||||||
initialGeomTable.head_read()
|
|
||||||
info,devNull = initialGeomTable.head_getGeom()
|
|
||||||
|
|
||||||
if info['microstructures'] != nMicrostructures: damask.util.croak('error. Microstructure count mismatch')
|
if len(np.unique(targetGeom.microstructure)) != nMicrostructures:
|
||||||
|
damask.util.croak('error. Microstructure count mismatch')
|
||||||
|
|
||||||
initialData = np.bincount(initialGeomTable.microstructure_read(info['grid']))/points
|
initialData = np.bincount(initialGeom.microstructure.flatten())/points
|
||||||
for i in range(nMicrostructures):
|
for i in range(nMicrostructures):
|
||||||
initialHist = np.histogram(initialData,bins=target[i]['bins'])[0]
|
initialHist = np.histogram(initialData,bins=target[i]['bins'])[0]
|
||||||
target[i]['error']=np.sqrt(np.square(np.array(target[i]['histogram']-initialHist)).sum())
|
target[i]['error']=np.sqrt(np.square(np.array(target[i]['histogram']-initialHist)).sum())
|
||||||
|
@ -273,7 +268,7 @@ for i in range(nMicrostructures):
|
||||||
|
|
||||||
|
|
||||||
if options.maxseeds < 1:
|
if options.maxseeds < 1:
|
||||||
maxSeeds = info['microstructures']
|
maxSeeds = len(np.unique(initialGeom.microstructure))
|
||||||
else:
|
else:
|
||||||
maxSeeds = options.maxseeds
|
maxSeeds = options.maxseeds
|
||||||
|
|
||||||
|
|
|
@ -1,13 +0,0 @@
|
||||||
DAMASK - The Düsseldorf Advanced Material Simulation Kit
|
|
||||||
Visit damask.mpie.de for installation and usage instructions
|
|
||||||
|
|
||||||
CONTACT INFORMATION
|
|
||||||
|
|
||||||
Max-Planck-Institut für Eisenforschung GmbH
|
|
||||||
Max-Planck-Str. 1
|
|
||||||
40237 Düsseldorf
|
|
||||||
Germany
|
|
||||||
|
|
||||||
Email: DAMASK@mpie.de
|
|
||||||
https://damask.mpie.de
|
|
||||||
https://magit1.mpie.de
|
|
|
@ -0,0 +1 @@
|
||||||
|
../README
|
|
@ -6,27 +6,27 @@
|
||||||
# Copyright (c) 2013-2014, Marc De Graef/Carnegie Mellon University
|
# Copyright (c) 2013-2014, Marc De Graef/Carnegie Mellon University
|
||||||
# All rights reserved.
|
# All rights reserved.
|
||||||
#
|
#
|
||||||
# Redistribution and use in source and binary forms, with or without modification, are
|
# Redistribution and use in source and binary forms, with or without modification, are
|
||||||
# permitted provided that the following conditions are met:
|
# permitted provided that the following conditions are met:
|
||||||
#
|
#
|
||||||
# - Redistributions of source code must retain the above copyright notice, this list
|
# - Redistributions of source code must retain the above copyright notice, this list
|
||||||
# of conditions and the following disclaimer.
|
# of conditions and the following disclaimer.
|
||||||
# - Redistributions in binary form must reproduce the above copyright notice, this
|
# - Redistributions in binary form must reproduce the above copyright notice, this
|
||||||
# list of conditions and the following disclaimer in the documentation and/or
|
# list of conditions and the following disclaimer in the documentation and/or
|
||||||
# other materials provided with the distribution.
|
# other materials provided with the distribution.
|
||||||
# - Neither the names of Marc De Graef, Carnegie Mellon University nor the names
|
# - Neither the names of Marc De Graef, Carnegie Mellon University nor the names
|
||||||
# of its contributors may be used to endorse or promote products derived from
|
# of its contributors may be used to endorse or promote products derived from
|
||||||
# this software without specific prior written permission.
|
# this software without specific prior written permission.
|
||||||
#
|
#
|
||||||
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
||||||
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||||
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
||||||
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
|
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
|
||||||
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
||||||
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
||||||
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
||||||
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
|
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
|
||||||
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
|
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
|
||||||
# USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
# USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||||
####################################################################################################
|
####################################################################################################
|
||||||
|
|
||||||
|
@ -44,7 +44,7 @@ def CubeToBall(cube):
|
||||||
----------
|
----------
|
||||||
cube : numpy.ndarray
|
cube : numpy.ndarray
|
||||||
coordinates of a point in a uniform refinable cubical grid.
|
coordinates of a point in a uniform refinable cubical grid.
|
||||||
|
|
||||||
References
|
References
|
||||||
----------
|
----------
|
||||||
D. Roşca et al., Modelling and Simulation in Materials Science and Engineering 22:075013, 2014
|
D. Roşca et al., Modelling and Simulation in Materials Science and Engineering 22:075013, 2014
|
||||||
|
@ -52,37 +52,37 @@ def CubeToBall(cube):
|
||||||
|
|
||||||
"""
|
"""
|
||||||
if np.abs(np.max(cube))>np.pi**(2./3.) * 0.5:
|
if np.abs(np.max(cube))>np.pi**(2./3.) * 0.5:
|
||||||
raise ValueError
|
raise ValueError
|
||||||
|
|
||||||
# transform to the sphere grid via the curved square, and intercept the zero point
|
# transform to the sphere grid via the curved square, and intercept the zero point
|
||||||
if np.allclose(cube,0.0,rtol=0.0,atol=1.0e-300):
|
if np.allclose(cube,0.0,rtol=0.0,atol=1.0e-300):
|
||||||
ball = np.zeros(3)
|
ball = np.zeros(3)
|
||||||
else:
|
else:
|
||||||
# get pyramide and scale by grid parameter ratio
|
# get pyramide and scale by grid parameter ratio
|
||||||
p = get_order(cube)
|
p = get_order(cube)
|
||||||
XYZ = cube[p] * sc
|
XYZ = cube[p] * sc
|
||||||
|
|
||||||
# intercept all the points along the z-axis
|
# intercept all the points along the z-axis
|
||||||
if np.allclose(XYZ[0:2],0.0,rtol=0.0,atol=1.0e-300):
|
if np.allclose(XYZ[0:2],0.0,rtol=0.0,atol=1.0e-300):
|
||||||
ball = np.array([0.0, 0.0, np.sqrt(6.0/np.pi) * XYZ[2]])
|
ball = np.array([0.0, 0.0, np.sqrt(6.0/np.pi) * XYZ[2]])
|
||||||
else:
|
else:
|
||||||
order = [1,0] if np.abs(XYZ[1]) <= np.abs(XYZ[0]) else [0,1]
|
order = [1,0] if np.abs(XYZ[1]) <= np.abs(XYZ[0]) else [0,1]
|
||||||
q = np.pi/12.0 * XYZ[order[0]]/XYZ[order[1]]
|
q = np.pi/12.0 * XYZ[order[0]]/XYZ[order[1]]
|
||||||
c = np.cos(q)
|
c = np.cos(q)
|
||||||
s = np.sin(q)
|
s = np.sin(q)
|
||||||
q = R1*2.0**0.25/beta * XYZ[order[1]] / np.sqrt(np.sqrt(2.0)-c)
|
q = R1*2.0**0.25/beta * XYZ[order[1]] / np.sqrt(np.sqrt(2.0)-c)
|
||||||
T = np.array([ (np.sqrt(2.0)*c - 1.0), np.sqrt(2.0) * s]) * q
|
T = np.array([ (np.sqrt(2.0)*c - 1.0), np.sqrt(2.0) * s]) * q
|
||||||
|
|
||||||
# transform to sphere grid (inverse Lambert)
|
# transform to sphere grid (inverse Lambert)
|
||||||
# note that there is no need to worry about dividing by zero, since XYZ[2] can not become zero
|
# note that there is no need to worry about dividing by zero, since XYZ[2] can not become zero
|
||||||
c = np.sum(T**2)
|
c = np.sum(T**2)
|
||||||
s = c * np.pi/24.0 /XYZ[2]**2
|
s = c * np.pi/24.0 /XYZ[2]**2
|
||||||
c = c * np.sqrt(np.pi/24.0)/XYZ[2]
|
c = c * np.sqrt(np.pi/24.0)/XYZ[2]
|
||||||
q = np.sqrt( 1.0 - s )
|
q = np.sqrt( 1.0 - s )
|
||||||
ball = np.array([ T[order[1]] * q, T[order[0]] * q, np.sqrt(6.0/np.pi) * XYZ[2] - c ])
|
ball = np.array([ T[order[1]] * q, T[order[0]] * q, np.sqrt(6.0/np.pi) * XYZ[2] - c ])
|
||||||
|
|
||||||
# reverse the coordinates back to the regular order according to the original pyramid number
|
# reverse the coordinates back to the regular order according to the original pyramid number
|
||||||
ball = ball[p]
|
ball = ball[p]
|
||||||
|
|
||||||
return ball
|
return ball
|
||||||
|
|
||||||
|
@ -103,46 +103,46 @@ def BallToCube(ball):
|
||||||
|
|
||||||
"""
|
"""
|
||||||
rs = np.linalg.norm(ball)
|
rs = np.linalg.norm(ball)
|
||||||
if rs > R1:
|
if rs > R1:
|
||||||
raise ValueError
|
raise ValueError
|
||||||
|
|
||||||
if np.allclose(ball,0.0,rtol=0.0,atol=1.0e-300):
|
if np.allclose(ball,0.0,rtol=0.0,atol=1.0e-300):
|
||||||
cube = np.zeros(3)
|
cube = np.zeros(3)
|
||||||
else:
|
else:
|
||||||
p = get_order(ball)
|
p = get_order(ball)
|
||||||
xyz3 = ball[p]
|
xyz3 = ball[p]
|
||||||
|
|
||||||
# inverse M_3
|
# inverse M_3
|
||||||
xyz2 = xyz3[0:2] * np.sqrt( 2.0*rs/(rs+np.abs(xyz3[2])) )
|
xyz2 = xyz3[0:2] * np.sqrt( 2.0*rs/(rs+np.abs(xyz3[2])) )
|
||||||
|
|
||||||
# inverse M_2
|
# inverse M_2
|
||||||
qxy = np.sum(xyz2**2)
|
qxy = np.sum(xyz2**2)
|
||||||
|
|
||||||
if np.isclose(qxy,0.0,rtol=0.0,atol=1.0e-300):
|
if np.isclose(qxy,0.0,rtol=0.0,atol=1.0e-300):
|
||||||
Tinv = np.zeros(2)
|
Tinv = np.zeros(2)
|
||||||
else:
|
else:
|
||||||
q2 = qxy + np.max(np.abs(xyz2))**2
|
q2 = qxy + np.max(np.abs(xyz2))**2
|
||||||
sq2 = np.sqrt(q2)
|
sq2 = np.sqrt(q2)
|
||||||
q = (beta/np.sqrt(2.0)/R1) * np.sqrt(q2*qxy/(q2-np.max(np.abs(xyz2))*sq2))
|
q = (beta/np.sqrt(2.0)/R1) * np.sqrt(q2*qxy/(q2-np.max(np.abs(xyz2))*sq2))
|
||||||
tt = np.clip((np.min(np.abs(xyz2))**2+np.max(np.abs(xyz2))*sq2)/np.sqrt(2.0)/qxy,-1.0,1.0)
|
tt = np.clip((np.min(np.abs(xyz2))**2+np.max(np.abs(xyz2))*sq2)/np.sqrt(2.0)/qxy,-1.0,1.0)
|
||||||
Tinv = np.array([1.0,np.arccos(tt)/np.pi*12.0]) if np.abs(xyz2[1]) <= np.abs(xyz2[0]) else \
|
Tinv = np.array([1.0,np.arccos(tt)/np.pi*12.0]) if np.abs(xyz2[1]) <= np.abs(xyz2[0]) else \
|
||||||
np.array([np.arccos(tt)/np.pi*12.0,1.0])
|
np.array([np.arccos(tt)/np.pi*12.0,1.0])
|
||||||
Tinv = q * np.where(xyz2<0.0,-Tinv,Tinv)
|
Tinv = q * np.where(xyz2<0.0,-Tinv,Tinv)
|
||||||
|
|
||||||
# inverse M_1
|
# inverse M_1
|
||||||
cube = np.array([ Tinv[0], Tinv[1], (-1.0 if xyz3[2] < 0.0 else 1.0) * rs / np.sqrt(6.0/np.pi) ]) /sc
|
cube = np.array([ Tinv[0], Tinv[1], (-1.0 if xyz3[2] < 0.0 else 1.0) * rs / np.sqrt(6.0/np.pi) ]) /sc
|
||||||
|
# reverse the coordinates back to the regular order according to the original pyramid number
|
||||||
|
cube = cube[p]
|
||||||
|
|
||||||
# reverse the coordinates back to the regular order according to the original pyramid number
|
|
||||||
cube = cube[p]
|
|
||||||
|
|
||||||
return cube
|
return cube
|
||||||
|
|
||||||
|
|
||||||
def get_order(xyz):
|
def get_order(xyz):
|
||||||
"""
|
"""
|
||||||
Get order of the coordinates.
|
Get order of the coordinates.
|
||||||
|
|
||||||
Depending on the pyramid in which the point is located, the order need to be adjusted.
|
Depending on the pyramid in which the point is located, the order need to be adjusted.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
xyz : numpy.ndarray
|
xyz : numpy.ndarray
|
||||||
|
@ -157,10 +157,10 @@ def get_order(xyz):
|
||||||
"""
|
"""
|
||||||
if (abs(xyz[0])<= xyz[2]) and (abs(xyz[1])<= xyz[2]) or \
|
if (abs(xyz[0])<= xyz[2]) and (abs(xyz[1])<= xyz[2]) or \
|
||||||
(abs(xyz[0])<=-xyz[2]) and (abs(xyz[1])<=-xyz[2]):
|
(abs(xyz[0])<=-xyz[2]) and (abs(xyz[1])<=-xyz[2]):
|
||||||
return [0,1,2]
|
return [0,1,2]
|
||||||
elif (abs(xyz[2])<= xyz[0]) and (abs(xyz[1])<= xyz[0]) or \
|
elif (abs(xyz[2])<= xyz[0]) and (abs(xyz[1])<= xyz[0]) or \
|
||||||
(abs(xyz[2])<=-xyz[0]) and (abs(xyz[1])<=-xyz[0]):
|
(abs(xyz[2])<=-xyz[0]) and (abs(xyz[1])<=-xyz[0]):
|
||||||
return [1,2,0]
|
return [1,2,0]
|
||||||
elif (abs(xyz[0])<= xyz[1]) and (abs(xyz[2])<= xyz[1]) or \
|
elif (abs(xyz[0])<= xyz[1]) and (abs(xyz[2])<= xyz[1]) or \
|
||||||
(abs(xyz[0])<=-xyz[1]) and (abs(xyz[2])<=-xyz[1]):
|
(abs(xyz[0])<=-xyz[1]) and (abs(xyz[2])<=-xyz[1]):
|
||||||
return [2,0,1]
|
return [2,0,1]
|
||||||
|
|
|
@ -13,9 +13,11 @@ from .asciitable import ASCIItable # noqa
|
||||||
|
|
||||||
from .config import Material # noqa
|
from .config import Material # noqa
|
||||||
from .colormaps import Colormap, Color # noqa
|
from .colormaps import Colormap, Color # noqa
|
||||||
from .orientation import Symmetry, Lattice, Rotation, Orientation # noqa
|
from .rotation import Rotation # noqa
|
||||||
from .dadf5 import DADF5 # noqa
|
from .lattice import Symmetry, Lattice# noqa
|
||||||
from .dadf5 import DADF5 as Result # noqa
|
from .orientation import Orientation # noqa
|
||||||
|
from .result import Result # noqa
|
||||||
|
from .result import Result as DADF5 # noqa
|
||||||
|
|
||||||
from .geom import Geom # noqa
|
from .geom import Geom # noqa
|
||||||
from .solver import Solver # noqa
|
from .solver import Solver # noqa
|
||||||
|
|
|
@ -11,12 +11,12 @@ class ASCIItable():
|
||||||
"""Read and write to ASCII tables."""
|
"""Read and write to ASCII tables."""
|
||||||
|
|
||||||
tmpext = '_tmp' # filename extension for in-place access
|
tmpext = '_tmp' # filename extension for in-place access
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
# ------------------------------------------------------------------
|
||||||
def __init__(self,
|
def __init__(self,
|
||||||
name = None,
|
name = None,
|
||||||
outname = None,
|
outname = None,
|
||||||
buffered = False, # flush writes
|
buffered = False, # is ignored, only exists for compatibility reasons
|
||||||
labeled = True, # assume table has labels
|
labeled = True, # assume table has labels
|
||||||
readonly = False, # no reading from file
|
readonly = False, # no reading from file
|
||||||
):
|
):
|
||||||
|
@ -52,7 +52,7 @@ class ASCIItable():
|
||||||
|
|
||||||
if self.__IO__['in'] is None \
|
if self.__IO__['in'] is None \
|
||||||
or self.__IO__['out'] is None: raise IOError # complain if any required file access not possible
|
or self.__IO__['out'] is None: raise IOError # complain if any required file access not possible
|
||||||
|
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
# ------------------------------------------------------------------
|
||||||
def _removeCRLF(self,
|
def _removeCRLF(self,
|
||||||
|
@ -63,7 +63,6 @@ class ASCIItable():
|
||||||
except AttributeError:
|
except AttributeError:
|
||||||
return str(string)
|
return str(string)
|
||||||
|
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
# ------------------------------------------------------------------
|
||||||
def _quote(self,
|
def _quote(self,
|
||||||
what):
|
what):
|
||||||
|
@ -71,6 +70,7 @@ class ASCIItable():
|
||||||
return '{quote}{content}{quote}'.format(
|
return '{quote}{content}{quote}'.format(
|
||||||
quote = ('"' if str(what)=='' or re.search(r"\s",str(what)) else ''),
|
quote = ('"' if str(what)=='' or re.search(r"\s",str(what)) else ''),
|
||||||
content = what)
|
content = what)
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
# ------------------------------------------------------------------
|
||||||
def close(self,
|
def close(self,
|
||||||
dismiss = False):
|
dismiss = False):
|
||||||
|
@ -110,7 +110,7 @@ class ASCIItable():
|
||||||
def head_read(self):
|
def head_read(self):
|
||||||
"""
|
"""
|
||||||
Get column labels.
|
Get column labels.
|
||||||
|
|
||||||
by either reading the first row or,
|
by either reading the first row or,
|
||||||
if keyword "head[*]" is present, the last line of the header
|
if keyword "head[*]" is present, the last line of the header
|
||||||
"""
|
"""
|
||||||
|
@ -121,7 +121,7 @@ class ASCIItable():
|
||||||
|
|
||||||
firstline = self.__IO__['in'].readline().strip()
|
firstline = self.__IO__['in'].readline().strip()
|
||||||
m = re.search(r'(\d+)\s+head', firstline.lower()) # search for "head" keyword
|
m = re.search(r'(\d+)\s+head', firstline.lower()) # search for "head" keyword
|
||||||
|
|
||||||
if m: # proper ASCIItable format
|
if m: # proper ASCIItable format
|
||||||
|
|
||||||
if self.__IO__['labeled']: # table features labels
|
if self.__IO__['labeled']: # table features labels
|
||||||
|
@ -145,7 +145,7 @@ class ASCIItable():
|
||||||
if self.__IO__['labeled']: # table features labels
|
if self.__IO__['labeled']: # table features labels
|
||||||
self.tags = self.data # get tags from last line in "header"...
|
self.tags = self.data # get tags from last line in "header"...
|
||||||
self.data_read() # ...and remove from buffer
|
self.data_read() # ...and remove from buffer
|
||||||
|
|
||||||
if self.__IO__['labeled']: # table features tags
|
if self.__IO__['labeled']: # table features tags
|
||||||
self.__IO__['tags'] = list(self.tags) # backup tags (make COPY, not link)
|
self.__IO__['tags'] = list(self.tags) # backup tags (make COPY, not link)
|
||||||
|
|
||||||
|
@ -163,7 +163,7 @@ class ASCIItable():
|
||||||
if self.__IO__['labeled']:
|
if self.__IO__['labeled']:
|
||||||
head.append('\t'.join(map(self._quote,self.tags)))
|
head.append('\t'.join(map(self._quote,self.tags)))
|
||||||
if len(self.tags) == 0: raise ValueError('no labels present.')
|
if len(self.tags) == 0: raise ValueError('no labels present.')
|
||||||
|
|
||||||
return self.output_write(head)
|
return self.output_write(head)
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
# ------------------------------------------------------------------
|
||||||
|
@ -178,15 +178,11 @@ class ASCIItable():
|
||||||
'grid': lambda x: int(x),
|
'grid': lambda x: int(x),
|
||||||
'size': lambda x: float(x),
|
'size': lambda x: float(x),
|
||||||
'origin': lambda x: float(x),
|
'origin': lambda x: float(x),
|
||||||
'homogenization': lambda x: int(x),
|
|
||||||
'microstructures': lambda x: int(x),
|
|
||||||
}
|
}
|
||||||
info = {
|
info = {
|
||||||
'grid': np.zeros(3,'i'),
|
'grid': np.zeros(3,'i'),
|
||||||
'size': np.zeros(3,'d'),
|
'size': np.zeros(3,'d'),
|
||||||
'origin': np.zeros(3,'d'),
|
'origin': np.zeros(3,'d'),
|
||||||
'homogenization': 0,
|
|
||||||
'microstructures': 0,
|
|
||||||
}
|
}
|
||||||
extra_header = []
|
extra_header = []
|
||||||
|
|
||||||
|
@ -234,7 +230,7 @@ class ASCIItable():
|
||||||
raw = False):
|
raw = False):
|
||||||
"""
|
"""
|
||||||
Tell abstract labels.
|
Tell abstract labels.
|
||||||
|
|
||||||
"x" for "1_x","2_x",... unless raw output is requested.
|
"x" for "1_x","2_x",... unless raw output is requested.
|
||||||
operates on object tags or given list.
|
operates on object tags or given list.
|
||||||
"""
|
"""
|
||||||
|
@ -347,7 +343,7 @@ class ASCIItable():
|
||||||
"""
|
"""
|
||||||
start = self.label_index(labels)
|
start = self.label_index(labels)
|
||||||
dim = self.label_dimension(labels)
|
dim = self.label_dimension(labels)
|
||||||
|
|
||||||
return np.hstack([range(s,s+d) for s,d in zip(start,dim)]).astype(int) \
|
return np.hstack([range(s,s+d) for s,d in zip(start,dim)]).astype(int) \
|
||||||
if isinstance(labels, Iterable) and not isinstance(labels, str) \
|
if isinstance(labels, Iterable) and not isinstance(labels, str) \
|
||||||
else range(start,start+dim)
|
else range(start,start+dim)
|
||||||
|
@ -375,15 +371,6 @@ class ASCIItable():
|
||||||
self.tags = list(self.__IO__['tags']) # restore label info found in header (as COPY, not link)
|
self.tags = list(self.__IO__['tags']) # restore label info found in header (as COPY, not link)
|
||||||
self.__IO__['labeled'] = len(self.tags) > 0
|
self.__IO__['labeled'] = len(self.tags) > 0
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
|
||||||
def data_skipLines(self,
|
|
||||||
count):
|
|
||||||
"""Wind forward by count number of lines."""
|
|
||||||
for i in range(count):
|
|
||||||
alive = self.data_read()
|
|
||||||
|
|
||||||
return alive
|
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
# ------------------------------------------------------------------
|
||||||
def data_read(self,
|
def data_read(self,
|
||||||
advance = True,
|
advance = True,
|
||||||
|
@ -425,8 +412,8 @@ class ASCIItable():
|
||||||
columns = []
|
columns = []
|
||||||
for i,(c,d) in enumerate(zip(indices[present],dimensions[present])): # for all valid labels ...
|
for i,(c,d) in enumerate(zip(indices[present],dimensions[present])): # for all valid labels ...
|
||||||
# ... transparently add all components unless column referenced by number or with explicit dimension
|
# ... transparently add all components unless column referenced by number or with explicit dimension
|
||||||
columns += list(range(c,c +
|
columns += list(range(c,c +
|
||||||
(d if str(c) != str(labels[present[i]]) else
|
(d if str(c) != str(labels[present[i]]) else
|
||||||
1)))
|
1)))
|
||||||
use = np.array(columns) if len(columns) > 0 else None
|
use = np.array(columns) if len(columns) > 0 else None
|
||||||
|
|
||||||
|
@ -457,7 +444,7 @@ class ASCIItable():
|
||||||
output = [fmt % value for value in row] if fmt else list(map(repr,row))
|
output = [fmt % value for value in row] if fmt else list(map(repr,row))
|
||||||
except Exception:
|
except Exception:
|
||||||
output = [fmt % row] if fmt else [repr(row)]
|
output = [fmt % row] if fmt else [repr(row)]
|
||||||
|
|
||||||
try:
|
try:
|
||||||
self.__IO__['out'].write(delimiter.join(output) + '\n')
|
self.__IO__['out'].write(delimiter.join(output) + '\n')
|
||||||
except Exception:
|
except Exception:
|
||||||
|
@ -473,33 +460,3 @@ class ASCIItable():
|
||||||
for item in what: self.data_append(item)
|
for item in what: self.data_append(item)
|
||||||
except TypeError:
|
except TypeError:
|
||||||
self.data += [str(what)]
|
self.data += [str(what)]
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
|
||||||
def microstructure_read(self,
|
|
||||||
grid,
|
|
||||||
type = 'i',
|
|
||||||
strict = False):
|
|
||||||
"""Read microstructure data (from .geom format)."""
|
|
||||||
def datatype(item):
|
|
||||||
return int(item) if type.lower() == 'i' else float(item)
|
|
||||||
|
|
||||||
N = grid.prod() # expected number of microstructure indices in data
|
|
||||||
microstructure = np.zeros(N,type) # initialize as flat array
|
|
||||||
|
|
||||||
i = 0
|
|
||||||
while i < N and self.data_read():
|
|
||||||
items = self.data
|
|
||||||
if len(items) > 2:
|
|
||||||
if items[1].lower() == 'of':
|
|
||||||
items = np.ones(datatype(items[0]))*datatype(items[2])
|
|
||||||
elif items[1].lower() == 'to':
|
|
||||||
items = np.linspace(datatype(items[0]),datatype(items[2]),
|
|
||||||
abs(datatype(items[2])-datatype(items[0]))+1,dtype=int)
|
|
||||||
else: items = list(map(datatype,items))
|
|
||||||
else: items = list(map(datatype,items))
|
|
||||||
|
|
||||||
s = min(len(items), N-i) # prevent overflow of microstructure array
|
|
||||||
microstructure[i:i+s] = items[:s]
|
|
||||||
i += len(items)
|
|
||||||
|
|
||||||
return (microstructure, i == N and not self.data_read()) if strict else microstructure # check for proper point count and end of file
|
|
||||||
|
|
|
@ -1,359 +1,355 @@
|
||||||
import numpy as np
|
import numpy as np
|
||||||
|
|
||||||
class Color():
|
class Color():
|
||||||
"""Color representation in and conversion between different color-spaces."""
|
"""Color representation in and conversion between different color-spaces."""
|
||||||
|
|
||||||
__slots__ = [
|
__slots__ = [
|
||||||
'model',
|
'model',
|
||||||
'color',
|
'color',
|
||||||
'__dict__',
|
'__dict__',
|
||||||
]
|
]
|
||||||
|
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
def __init__(self,
|
||||||
def __init__(self,
|
model = 'RGB',
|
||||||
model = 'RGB',
|
color = np.zeros(3,'d')):
|
||||||
color = np.zeros(3,'d')):
|
"""
|
||||||
"""
|
Create a Color object.
|
||||||
Create a Color object.
|
|
||||||
|
|
||||||
Parameters
|
|
||||||
----------
|
|
||||||
model : string
|
|
||||||
color model
|
|
||||||
color : numpy.ndarray
|
|
||||||
vector representing the color according to the selected model
|
|
||||||
|
|
||||||
"""
|
Parameters
|
||||||
self.__transforms__ = \
|
----------
|
||||||
{'HSV': {'index': 0, 'next': self._HSV2HSL},
|
model : string
|
||||||
'HSL': {'index': 1, 'next': self._HSL2RGB, 'prev': self._HSL2HSV},
|
color model
|
||||||
'RGB': {'index': 2, 'next': self._RGB2XYZ, 'prev': self._RGB2HSL},
|
color : numpy.ndarray
|
||||||
'XYZ': {'index': 3, 'next': self._XYZ2CIELAB, 'prev': self._XYZ2RGB},
|
vector representing the color according to the selected model
|
||||||
'CIELAB': {'index': 4, 'next': self._CIELAB2MSH, 'prev': self._CIELAB2XYZ},
|
|
||||||
'MSH': {'index': 5, 'prev': self._MSH2CIELAB},
|
|
||||||
}
|
|
||||||
|
|
||||||
model = model.upper()
|
"""
|
||||||
if model not in list(self.__transforms__.keys()): model = 'RGB'
|
self.__transforms__ = \
|
||||||
if model == 'RGB' and max(color) > 1.0: # are we RGB255 ?
|
{'HSV': {'index': 0, 'next': self._HSV2HSL},
|
||||||
for i in range(3):
|
'HSL': {'index': 1, 'next': self._HSL2RGB, 'prev': self._HSL2HSV},
|
||||||
color[i] /= 255.0 # rescale to RGB
|
'RGB': {'index': 2, 'next': self._RGB2XYZ, 'prev': self._RGB2HSL},
|
||||||
|
'XYZ': {'index': 3, 'next': self._XYZ2CIELAB, 'prev': self._XYZ2RGB},
|
||||||
|
'CIELAB': {'index': 4, 'next': self._CIELAB2MSH, 'prev': self._CIELAB2XYZ},
|
||||||
|
'MSH': {'index': 5, 'prev': self._MSH2CIELAB},
|
||||||
|
}
|
||||||
|
|
||||||
if model == 'HSL': # are we HSL ?
|
model = model.upper()
|
||||||
if abs(color[0]) > 1.0: color[0] /= 360.0 # with angular hue?
|
if model not in list(self.__transforms__.keys()): model = 'RGB'
|
||||||
while color[0] >= 1.0: color[0] -= 1.0 # rewind to proper range
|
if model == 'RGB' and max(color) > 1.0: # are we RGB255 ?
|
||||||
while color[0] < 0.0: color[0] += 1.0 # rewind to proper range
|
for i in range(3):
|
||||||
|
color[i] /= 255.0 # rescale to RGB
|
||||||
|
|
||||||
self.model = model
|
if model == 'HSL': # are we HSL ?
|
||||||
self.color = np.array(color,'d')
|
if abs(color[0]) > 1.0: color[0] /= 360.0 # with angular hue?
|
||||||
|
while color[0] >= 1.0: color[0] -= 1.0 # rewind to proper range
|
||||||
|
while color[0] < 0.0: color[0] += 1.0 # rewind to proper range
|
||||||
|
|
||||||
|
self.model = model
|
||||||
|
self.color = np.array(color,'d')
|
||||||
|
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
def __repr__(self):
|
||||||
def __repr__(self):
|
"""Color model and values."""
|
||||||
"""Color model and values."""
|
return 'Model: %s Color: %s'%(self.model,str(self.color))
|
||||||
return 'Model: %s Color: %s'%(self.model,str(self.color))
|
|
||||||
|
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
def __str__(self):
|
||||||
def __str__(self):
|
"""Color model and values."""
|
||||||
"""Color model and values."""
|
return self.__repr__()
|
||||||
return self.__repr__()
|
|
||||||
|
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
def convert_to(self,toModel = 'RGB'):
|
||||||
def convertTo(self,toModel = 'RGB'):
|
"""
|
||||||
"""
|
Change the color model permanently.
|
||||||
Change the color model permanently.
|
|
||||||
|
|
||||||
Parameters
|
|
||||||
----------
|
|
||||||
toModel : string
|
|
||||||
color model
|
|
||||||
|
|
||||||
"""
|
Parameters
|
||||||
toModel = toModel.upper()
|
----------
|
||||||
if toModel not in list(self.__transforms__.keys()): return
|
toModel : string
|
||||||
|
color model
|
||||||
|
|
||||||
sourcePos = self.__transforms__[self.model]['index']
|
"""
|
||||||
targetPos = self.__transforms__[toModel]['index']
|
toModel = toModel.upper()
|
||||||
|
if toModel not in list(self.__transforms__.keys()): return
|
||||||
|
|
||||||
while sourcePos < targetPos:
|
sourcePos = self.__transforms__[self.model]['index']
|
||||||
self.__transforms__[self.model]['next']()
|
targetPos = self.__transforms__[toModel]['index']
|
||||||
sourcePos += 1
|
|
||||||
|
|
||||||
while sourcePos > targetPos:
|
while sourcePos < targetPos:
|
||||||
self.__transforms__[self.model]['prev']()
|
self.__transforms__[self.model]['next']()
|
||||||
sourcePos -= 1
|
sourcePos += 1
|
||||||
return self
|
|
||||||
|
while sourcePos > targetPos:
|
||||||
|
self.__transforms__[self.model]['prev']()
|
||||||
|
sourcePos -= 1
|
||||||
|
return self
|
||||||
|
|
||||||
|
|
||||||
# ------------------------------------------------------------------
|
def express_as(self,asModel = 'RGB'):
|
||||||
def expressAs(self,asModel = 'RGB'):
|
"""
|
||||||
"""
|
Return the color in a different model.
|
||||||
Return the color in a different model.
|
|
||||||
|
|
||||||
Parameters
|
|
||||||
----------
|
|
||||||
asModel : string
|
|
||||||
color model
|
|
||||||
|
|
||||||
"""
|
Parameters
|
||||||
return self.__class__(self.model,self.color).convertTo(asModel)
|
----------
|
||||||
|
asModel : string
|
||||||
|
color model
|
||||||
|
|
||||||
|
"""
|
||||||
|
return self.__class__(self.model,self.color).convert_to(asModel)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def _HSV2HSL(self):
|
def _HSV2HSL(self):
|
||||||
"""
|
"""
|
||||||
Convert H(ue) S(aturation) V(alue or brightness) to H(ue) S(aturation) L(uminance).
|
Convert H(ue) S(aturation) V(alue or brightness) to H(ue) S(aturation) L(uminance).
|
||||||
|
|
||||||
All values are in the range [0,1]
|
All values are in the range [0,1]
|
||||||
http://codeitdown.com/hsl-hsb-hsv-color
|
http://codeitdown.com/hsl-hsb-hsv-color
|
||||||
"""
|
"""
|
||||||
if self.model != 'HSV': return
|
if self.model != 'HSV': return
|
||||||
|
|
||||||
converted = Color('HSL',np.array([
|
converted = Color('HSL',np.array([
|
||||||
self.color[0],
|
self.color[0],
|
||||||
1. if self.color[2] == 0.0 or (self.color[1] == 0.0 and self.color[2] == 1.0) \
|
1. if self.color[2] == 0.0 or (self.color[1] == 0.0 and self.color[2] == 1.0) \
|
||||||
else self.color[1]*self.color[2]/(1.-abs(self.color[2]*(2.-self.color[1])-1.)),
|
else self.color[1]*self.color[2]/(1.-abs(self.color[2]*(2.-self.color[1])-1.)),
|
||||||
0.5*self.color[2]*(2.-self.color[1]),
|
0.5*self.color[2]*(2.-self.color[1]),
|
||||||
]))
|
]))
|
||||||
|
|
||||||
self.model = converted.model
|
self.model = converted.model
|
||||||
self.color = converted.color
|
self.color = converted.color
|
||||||
|
|
||||||
|
|
||||||
def _HSL2HSV(self):
|
def _HSL2HSV(self):
|
||||||
"""
|
"""
|
||||||
Convert H(ue) S(aturation) L(uminance) to H(ue) S(aturation) V(alue or brightness).
|
Convert H(ue) S(aturation) L(uminance) to H(ue) S(aturation) V(alue or brightness).
|
||||||
|
|
||||||
All values are in the range [0,1]
|
All values are in the range [0,1]
|
||||||
http://codeitdown.com/hsl-hsb-hsv-color
|
http://codeitdown.com/hsl-hsb-hsv-color
|
||||||
"""
|
"""
|
||||||
if self.model != 'HSL': return
|
if self.model != 'HSL': return
|
||||||
|
|
||||||
h = self.color[0]
|
h = self.color[0]
|
||||||
b = self.color[2]+0.5*(self.color[1]*(1.-abs(2*self.color[2]-1)))
|
b = self.color[2]+0.5*(self.color[1]*(1.-abs(2*self.color[2]-1)))
|
||||||
s = 1.0 if b == 0.0 else 2.*(b-self.color[2])/b
|
s = 1.0 if b == 0.0 else 2.*(b-self.color[2])/b
|
||||||
|
|
||||||
converted = Color('HSV',np.array([h,s,b]))
|
converted = Color('HSV',np.array([h,s,b]))
|
||||||
|
|
||||||
self.model = converted.model
|
self.model = converted.model
|
||||||
self.color = converted.color
|
self.color = converted.color
|
||||||
|
|
||||||
|
|
||||||
def _HSL2RGB(self):
|
def _HSL2RGB(self):
|
||||||
"""
|
"""
|
||||||
Convert H(ue) S(aturation) L(uminance) to R(red) G(reen) B(lue).
|
Convert H(ue) S(aturation) L(uminance) to R(red) G(reen) B(lue).
|
||||||
|
|
||||||
All values are in the range [0,1]
|
All values are in the range [0,1]
|
||||||
from http://en.wikipedia.org/wiki/HSL_and_HSV
|
from http://en.wikipedia.org/wiki/HSL_and_HSV
|
||||||
"""
|
"""
|
||||||
if self.model != 'HSL': return
|
if self.model != 'HSL': return
|
||||||
|
|
||||||
sextant = self.color[0]*6.0
|
sextant = self.color[0]*6.0
|
||||||
c = (1.0 - abs(2.0 * self.color[2] - 1.0))*self.color[1]
|
c = (1.0 - abs(2.0 * self.color[2] - 1.0))*self.color[1]
|
||||||
x = c*(1.0 - abs(sextant%2 - 1.0))
|
x = c*(1.0 - abs(sextant%2 - 1.0))
|
||||||
m = self.color[2] - 0.5*c
|
m = self.color[2] - 0.5*c
|
||||||
|
|
||||||
converted = Color('RGB',np.array([
|
converted = Color('RGB',np.array([
|
||||||
[c+m, x+m, m],
|
[c+m, x+m, m],
|
||||||
[x+m, c+m, m],
|
[x+m, c+m, m],
|
||||||
[m, c+m, x+m],
|
[m, c+m, x+m],
|
||||||
[m, x+m, c+m],
|
[m, x+m, c+m],
|
||||||
[x+m, m, c+m],
|
[x+m, m, c+m],
|
||||||
[c+m, m, x+m],
|
[c+m, m, x+m],
|
||||||
][int(sextant)],'d'))
|
][int(sextant)],'d'))
|
||||||
self.model = converted.model
|
self.model = converted.model
|
||||||
self.color = converted.color
|
self.color = converted.color
|
||||||
|
|
||||||
|
|
||||||
def _RGB2HSL(self):
|
def _RGB2HSL(self):
|
||||||
"""
|
"""
|
||||||
Convert R(ed) G(reen) B(lue) to H(ue) S(aturation) L(uminance).
|
Convert R(ed) G(reen) B(lue) to H(ue) S(aturation) L(uminance).
|
||||||
|
|
||||||
All values are in the range [0,1]
|
All values are in the range [0,1]
|
||||||
from http://130.113.54.154/~monger/hsl-rgb.html
|
from http://130.113.54.154/~monger/hsl-rgb.html
|
||||||
"""
|
"""
|
||||||
if self.model != 'RGB': return
|
if self.model != 'RGB': return
|
||||||
|
|
||||||
HSL = np.zeros(3,'d')
|
HSL = np.zeros(3,'d')
|
||||||
maxcolor = self.color.max()
|
maxcolor = self.color.max()
|
||||||
mincolor = self.color.min()
|
mincolor = self.color.min()
|
||||||
HSL[2] = (maxcolor + mincolor)/2.0
|
HSL[2] = (maxcolor + mincolor)/2.0
|
||||||
if(mincolor == maxcolor):
|
if(mincolor == maxcolor):
|
||||||
HSL[0] = 0.0
|
HSL[0] = 0.0
|
||||||
HSL[1] = 0.0
|
HSL[1] = 0.0
|
||||||
else:
|
|
||||||
if (HSL[2]<0.5):
|
|
||||||
HSL[1] = (maxcolor - mincolor)/(maxcolor + mincolor)
|
|
||||||
else:
|
else:
|
||||||
HSL[1] = (maxcolor - mincolor)/(2.0 - maxcolor - mincolor)
|
if (HSL[2]<0.5):
|
||||||
if (maxcolor == self.color[0]):
|
HSL[1] = (maxcolor - mincolor)/(maxcolor + mincolor)
|
||||||
HSL[0] = 0.0 + (self.color[1] - self.color[2])/(maxcolor - mincolor)
|
else:
|
||||||
elif (maxcolor == self.color[1]):
|
HSL[1] = (maxcolor - mincolor)/(2.0 - maxcolor - mincolor)
|
||||||
HSL[0] = 2.0 + (self.color[2] - self.color[0])/(maxcolor - mincolor)
|
if (maxcolor == self.color[0]):
|
||||||
elif (maxcolor == self.color[2]):
|
HSL[0] = 0.0 + (self.color[1] - self.color[2])/(maxcolor - mincolor)
|
||||||
HSL[0] = 4.0 + (self.color[0] - self.color[1])/(maxcolor - mincolor)
|
elif (maxcolor == self.color[1]):
|
||||||
HSL[0] = HSL[0]*60.0 # scaling to 360 might be dangerous for small values
|
HSL[0] = 2.0 + (self.color[2] - self.color[0])/(maxcolor - mincolor)
|
||||||
if (HSL[0] < 0.0):
|
elif (maxcolor == self.color[2]):
|
||||||
HSL[0] = HSL[0] + 360.0
|
HSL[0] = 4.0 + (self.color[0] - self.color[1])/(maxcolor - mincolor)
|
||||||
for i in range(2):
|
HSL[0] = HSL[0]*60.0 # scaling to 360 might be dangerous for small values
|
||||||
HSL[i+1] = min(HSL[i+1],1.0)
|
if (HSL[0] < 0.0):
|
||||||
HSL[i+1] = max(HSL[i+1],0.0)
|
HSL[0] = HSL[0] + 360.0
|
||||||
|
for i in range(2):
|
||||||
|
HSL[i+1] = min(HSL[i+1],1.0)
|
||||||
|
HSL[i+1] = max(HSL[i+1],0.0)
|
||||||
|
|
||||||
converted = Color('HSL', HSL)
|
converted = Color('HSL', HSL)
|
||||||
self.model = converted.model
|
self.model = converted.model
|
||||||
self.color = converted.color
|
self.color = converted.color
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def _RGB2XYZ(self):
|
def _RGB2XYZ(self):
|
||||||
"""
|
"""
|
||||||
Convert R(ed) G(reen) B(lue) to CIE XYZ.
|
Convert R(ed) G(reen) B(lue) to CIE XYZ.
|
||||||
|
|
||||||
All values are in the range [0,1]
|
All values are in the range [0,1]
|
||||||
from http://www.cs.rit.edu/~ncs/color/t_convert.html
|
from http://www.cs.rit.edu/~ncs/color/t_convert.html
|
||||||
"""
|
"""
|
||||||
if self.model != 'RGB': return
|
if self.model != 'RGB': return
|
||||||
|
|
||||||
XYZ = np.zeros(3,'d')
|
XYZ = np.zeros(3,'d')
|
||||||
RGB_lin = np.zeros(3,'d')
|
RGB_lin = np.zeros(3,'d')
|
||||||
convert = np.array([[0.412453,0.357580,0.180423],
|
convert = np.array([[0.412453,0.357580,0.180423],
|
||||||
[0.212671,0.715160,0.072169],
|
[0.212671,0.715160,0.072169],
|
||||||
[0.019334,0.119193,0.950227]])
|
[0.019334,0.119193,0.950227]])
|
||||||
|
|
||||||
for i in range(3):
|
for i in range(3):
|
||||||
if (self.color[i] > 0.04045): RGB_lin[i] = ((self.color[i]+0.0555)/1.0555)**2.4
|
if (self.color[i] > 0.04045): RGB_lin[i] = ((self.color[i]+0.0555)/1.0555)**2.4
|
||||||
else: RGB_lin[i] = self.color[i] /12.92
|
else: RGB_lin[i] = self.color[i] /12.92
|
||||||
XYZ = np.dot(convert,RGB_lin)
|
XYZ = np.dot(convert,RGB_lin)
|
||||||
for i in range(3):
|
for i in range(3):
|
||||||
|
|
||||||
XYZ[i] = max(XYZ[i],0.0)
|
XYZ[i] = max(XYZ[i],0.0)
|
||||||
|
|
||||||
converted = Color('XYZ', XYZ)
|
converted = Color('XYZ', XYZ)
|
||||||
self.model = converted.model
|
self.model = converted.model
|
||||||
self.color = converted.color
|
self.color = converted.color
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def _XYZ2RGB(self):
|
def _XYZ2RGB(self):
|
||||||
"""
|
"""
|
||||||
Convert CIE XYZ to R(ed) G(reen) B(lue).
|
Convert CIE XYZ to R(ed) G(reen) B(lue).
|
||||||
|
|
||||||
All values are in the range [0,1]
|
All values are in the range [0,1]
|
||||||
from http://www.cs.rit.edu/~ncs/color/t_convert.html
|
from http://www.cs.rit.edu/~ncs/color/t_convert.html
|
||||||
"""
|
"""
|
||||||
if self.model != 'XYZ':
|
if self.model != 'XYZ':
|
||||||
return
|
return
|
||||||
|
|
||||||
convert = np.array([[ 3.240479,-1.537150,-0.498535],
|
convert = np.array([[ 3.240479,-1.537150,-0.498535],
|
||||||
[-0.969256, 1.875992, 0.041556],
|
[-0.969256, 1.875992, 0.041556],
|
||||||
[ 0.055648,-0.204043, 1.057311]])
|
[ 0.055648,-0.204043, 1.057311]])
|
||||||
RGB_lin = np.dot(convert,self.color)
|
RGB_lin = np.dot(convert,self.color)
|
||||||
RGB = np.zeros(3,'d')
|
RGB = np.zeros(3,'d')
|
||||||
|
|
||||||
for i in range(3):
|
for i in range(3):
|
||||||
if (RGB_lin[i] > 0.0031308): RGB[i] = ((RGB_lin[i])**(1.0/2.4))*1.0555-0.0555
|
if (RGB_lin[i] > 0.0031308): RGB[i] = ((RGB_lin[i])**(1.0/2.4))*1.0555-0.0555
|
||||||
else: RGB[i] = RGB_lin[i] *12.92
|
else: RGB[i] = RGB_lin[i] *12.92
|
||||||
for i in range(3):
|
for i in range(3):
|
||||||
RGB[i] = min(RGB[i],1.0)
|
RGB[i] = min(RGB[i],1.0)
|
||||||
RGB[i] = max(RGB[i],0.0)
|
RGB[i] = max(RGB[i],0.0)
|
||||||
|
|
||||||
maxVal = max(RGB) # clipping colors according to the display gamut
|
maxVal = max(RGB) # clipping colors according to the display gamut
|
||||||
if (maxVal > 1.0): RGB /= maxVal
|
if (maxVal > 1.0): RGB /= maxVal
|
||||||
|
|
||||||
converted = Color('RGB', RGB)
|
converted = Color('RGB', RGB)
|
||||||
self.model = converted.model
|
self.model = converted.model
|
||||||
self.color = converted.color
|
self.color = converted.color
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def _CIELAB2XYZ(self):
|
def _CIELAB2XYZ(self):
|
||||||
"""
|
"""
|
||||||
Convert CIE Lab to CIE XYZ.
|
Convert CIE Lab to CIE XYZ.
|
||||||
|
|
||||||
All values are in the range [0,1]
|
All values are in the range [0,1]
|
||||||
from http://www.easyrgb.com/index.php?X=MATH&H=07#text7
|
from http://www.easyrgb.com/index.php?X=MATH&H=07#text7
|
||||||
"""
|
"""
|
||||||
if self.model != 'CIELAB': return
|
if self.model != 'CIELAB': return
|
||||||
|
|
||||||
ref_white = np.array([.95047, 1.00000, 1.08883],'d') # Observer = 2, Illuminant = D65
|
ref_white = np.array([.95047, 1.00000, 1.08883],'d') # Observer = 2, Illuminant = D65
|
||||||
XYZ = np.zeros(3,'d')
|
XYZ = np.zeros(3,'d')
|
||||||
|
|
||||||
XYZ[1] = (self.color[0] + 16.0 ) / 116.0
|
XYZ[1] = (self.color[0] + 16.0 ) / 116.0
|
||||||
XYZ[0] = XYZ[1] + self.color[1]/ 500.0
|
XYZ[0] = XYZ[1] + self.color[1]/ 500.0
|
||||||
XYZ[2] = XYZ[1] - self.color[2]/ 200.0
|
XYZ[2] = XYZ[1] - self.color[2]/ 200.0
|
||||||
|
|
||||||
for i in range(len(XYZ)):
|
for i in range(len(XYZ)):
|
||||||
if (XYZ[i] > 6./29. ): XYZ[i] = XYZ[i]**3.
|
if (XYZ[i] > 6./29. ): XYZ[i] = XYZ[i]**3.
|
||||||
else: XYZ[i] = 108./841. * (XYZ[i] - 4./29.)
|
else: XYZ[i] = 108./841. * (XYZ[i] - 4./29.)
|
||||||
|
|
||||||
converted = Color('XYZ', XYZ*ref_white)
|
converted = Color('XYZ', XYZ*ref_white)
|
||||||
self.model = converted.model
|
self.model = converted.model
|
||||||
self.color = converted.color
|
self.color = converted.color
|
||||||
|
|
||||||
def _XYZ2CIELAB(self):
|
|
||||||
"""
|
|
||||||
Convert CIE XYZ to CIE Lab.
|
|
||||||
|
|
||||||
All values are in the range [0,1]
|
|
||||||
from http://en.wikipedia.org/wiki/Lab_color_space,
|
|
||||||
http://www.cs.rit.edu/~ncs/color/t_convert.html
|
|
||||||
"""
|
|
||||||
if self.model != 'XYZ': return
|
|
||||||
|
|
||||||
ref_white = np.array([.95047, 1.00000, 1.08883],'d') # Observer = 2, Illuminant = D65
|
|
||||||
XYZ = self.color/ref_white
|
|
||||||
|
|
||||||
for i in range(len(XYZ)):
|
|
||||||
if (XYZ[i] > 216./24389 ): XYZ[i] = XYZ[i]**(1.0/3.0)
|
|
||||||
else: XYZ[i] = (841./108. * XYZ[i]) + 16.0/116.0
|
|
||||||
|
|
||||||
converted = Color('CIELAB', np.array([ 116.0 * XYZ[1] - 16.0,
|
|
||||||
500.0 * (XYZ[0] - XYZ[1]),
|
|
||||||
200.0 * (XYZ[1] - XYZ[2]) ]))
|
|
||||||
self.model = converted.model
|
|
||||||
self.color = converted.color
|
|
||||||
|
|
||||||
|
|
||||||
def _CIELAB2MSH(self):
|
def _XYZ2CIELAB(self):
|
||||||
"""
|
"""
|
||||||
Convert CIE Lab to Msh colorspace.
|
Convert CIE XYZ to CIE Lab.
|
||||||
|
|
||||||
from http://www.cs.unm.edu/~kmorel/documents/ColorMaps/DivergingColorMapWorkshop.xls
|
All values are in the range [0,1]
|
||||||
"""
|
from http://en.wikipedia.org/wiki/Lab_color_space,
|
||||||
if self.model != 'CIELAB': return
|
http://www.cs.rit.edu/~ncs/color/t_convert.html
|
||||||
|
"""
|
||||||
|
if self.model != 'XYZ': return
|
||||||
|
|
||||||
Msh = np.zeros(3,'d')
|
ref_white = np.array([.95047, 1.00000, 1.08883],'d') # Observer = 2, Illuminant = D65
|
||||||
Msh[0] = np.sqrt(np.dot(self.color,self.color))
|
XYZ = self.color/ref_white
|
||||||
if (Msh[0] > 0.001):
|
|
||||||
Msh[1] = np.arccos(self.color[0]/Msh[0])
|
|
||||||
if (self.color[1] != 0.0):
|
|
||||||
Msh[2] = np.arctan2(self.color[2],self.color[1])
|
|
||||||
|
|
||||||
converted = Color('MSH', Msh)
|
for i in range(len(XYZ)):
|
||||||
self.model = converted.model
|
if (XYZ[i] > 216./24389 ): XYZ[i] = XYZ[i]**(1.0/3.0)
|
||||||
self.color = converted.color
|
else: XYZ[i] = (841./108. * XYZ[i]) + 16.0/116.0
|
||||||
|
|
||||||
|
converted = Color('CIELAB', np.array([ 116.0 * XYZ[1] - 16.0,
|
||||||
|
500.0 * (XYZ[0] - XYZ[1]),
|
||||||
|
200.0 * (XYZ[1] - XYZ[2]) ]))
|
||||||
|
self.model = converted.model
|
||||||
|
self.color = converted.color
|
||||||
|
|
||||||
|
|
||||||
def _MSH2CIELAB(self):
|
def _CIELAB2MSH(self):
|
||||||
"""
|
"""
|
||||||
Convert Msh colorspace to CIE Lab.
|
Convert CIE Lab to Msh colorspace.
|
||||||
|
|
||||||
with s,h in radians
|
from http://www.cs.unm.edu/~kmorel/documents/ColorMaps/DivergingColorMapWorkshop.xls
|
||||||
from http://www.cs.unm.edu/~kmorel/documents/ColorMaps/DivergingColorMapWorkshop.xls
|
"""
|
||||||
"""
|
if self.model != 'CIELAB': return
|
||||||
if self.model != 'MSH': return
|
|
||||||
|
|
||||||
Lab = np.zeros(3,'d')
|
Msh = np.zeros(3,'d')
|
||||||
Lab[0] = self.color[0] * np.cos(self.color[1])
|
Msh[0] = np.sqrt(np.dot(self.color,self.color))
|
||||||
Lab[1] = self.color[0] * np.sin(self.color[1]) * np.cos(self.color[2])
|
if (Msh[0] > 0.001):
|
||||||
Lab[2] = self.color[0] * np.sin(self.color[1]) * np.sin(self.color[2])
|
Msh[1] = np.arccos(self.color[0]/Msh[0])
|
||||||
|
if (self.color[1] != 0.0):
|
||||||
|
Msh[2] = np.arctan2(self.color[2],self.color[1])
|
||||||
|
|
||||||
converted = Color('CIELAB', Lab)
|
converted = Color('MSH', Msh)
|
||||||
self.model = converted.model
|
self.model = converted.model
|
||||||
self.color = converted.color
|
self.color = converted.color
|
||||||
|
|
||||||
|
|
||||||
|
def _MSH2CIELAB(self):
|
||||||
|
"""
|
||||||
|
Convert Msh colorspace to CIE Lab.
|
||||||
|
|
||||||
|
with s,h in radians
|
||||||
|
from http://www.cs.unm.edu/~kmorel/documents/ColorMaps/DivergingColorMapWorkshop.xls
|
||||||
|
"""
|
||||||
|
if self.model != 'MSH': return
|
||||||
|
|
||||||
|
Lab = np.zeros(3,'d')
|
||||||
|
Lab[0] = self.color[0] * np.cos(self.color[1])
|
||||||
|
Lab[1] = self.color[0] * np.sin(self.color[1]) * np.cos(self.color[2])
|
||||||
|
Lab[2] = self.color[0] * np.sin(self.color[1]) * np.sin(self.color[2])
|
||||||
|
|
||||||
|
converted = Color('CIELAB', Lab)
|
||||||
|
self.model = converted.model
|
||||||
|
self.color = converted.color
|
||||||
|
|
||||||
|
|
||||||
class Colormap():
|
class Colormap():
|
||||||
|
@ -416,7 +412,7 @@ class Colormap():
|
||||||
):
|
):
|
||||||
"""
|
"""
|
||||||
Create a Colormap object.
|
Create a Colormap object.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
left : Color
|
left : Color
|
||||||
|
@ -498,13 +494,13 @@ class Colormap():
|
||||||
def interpolate_linear(lo, hi, frac):
|
def interpolate_linear(lo, hi, frac):
|
||||||
"""Linear interpolation between lo and hi color at given fraction; output in model of lo color."""
|
"""Linear interpolation between lo and hi color at given fraction; output in model of lo color."""
|
||||||
interpolation = (1.0 - frac) * np.array(lo.color[:]) \
|
interpolation = (1.0 - frac) * np.array(lo.color[:]) \
|
||||||
+ frac * np.array(hi.expressAs(lo.model).color[:])
|
+ frac * np.array(hi.express_as(lo.model).color[:])
|
||||||
|
|
||||||
return Color(lo.model,interpolation)
|
return Color(lo.model,interpolation)
|
||||||
|
|
||||||
if self.interpolate == 'perceptualuniform':
|
if self.interpolate == 'perceptualuniform':
|
||||||
return interpolate_Msh(self.left.expressAs('MSH').color,
|
return interpolate_Msh(self.left.express_as('MSH').color,
|
||||||
self.right.expressAs('MSH').color,fraction)
|
self.right.express_as('MSH').color,fraction)
|
||||||
elif self.interpolate == 'linear':
|
elif self.interpolate == 'linear':
|
||||||
return interpolate_linear(self.left,
|
return interpolate_linear(self.left,
|
||||||
self.right,fraction)
|
self.right,fraction)
|
||||||
|
@ -528,7 +524,7 @@ class Colormap():
|
||||||
"""
|
"""
|
||||||
format = format.lower() # consistent comparison basis
|
format = format.lower() # consistent comparison basis
|
||||||
frac = 0.5*(np.array(crop) + 1.0) # rescale crop range to fractions
|
frac = 0.5*(np.array(crop) + 1.0) # rescale crop range to fractions
|
||||||
colors = [self.color(float(i)/(steps-1)*(frac[1]-frac[0])+frac[0]).expressAs(model).color for i in range(steps)]
|
colors = [self.color(float(i)/(steps-1)*(frac[1]-frac[0])+frac[0]).express_as(model).color for i in range(steps)]
|
||||||
if format == 'paraview':
|
if format == 'paraview':
|
||||||
colormap = ['[\n {{\n "ColorSpace": "RGB", "Name": "{}", "DefaultMap": true,\n "RGBPoints" : ['.format(name)] \
|
colormap = ['[\n {{\n "ColorSpace": "RGB", "Name": "{}", "DefaultMap": true,\n "RGBPoints" : ['.format(name)] \
|
||||||
+ [' {:4d},{:8.6f},{:8.6f},{:8.6f},'.format(i,color[0],color[1],color[2],) \
|
+ [' {:4d},{:8.6f},{:8.6f},{:8.6f},'.format(i,color[0],color[1],color[2],) \
|
||||||
|
|
File diff suppressed because it is too large
Load Diff
|
@ -80,7 +80,7 @@ class Geom():
|
||||||
if size is not None:
|
if size is not None:
|
||||||
self.set_size(size)
|
self.set_size(size)
|
||||||
elif rescale:
|
elif rescale:
|
||||||
self.set_size(self.get_grid()/grid_old*self.size)
|
self.set_size(self.get_grid()/grid_old*self.size)
|
||||||
|
|
||||||
message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))]
|
message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))]
|
||||||
if np.any(grid_old != self.get_grid()):
|
if np.any(grid_old != self.get_grid()):
|
||||||
|
@ -269,7 +269,7 @@ class Geom():
|
||||||
comments = []
|
comments = []
|
||||||
for i,line in enumerate(content[:header_length]):
|
for i,line in enumerate(content[:header_length]):
|
||||||
items = line.lower().strip().split()
|
items = line.lower().strip().split()
|
||||||
key = items[0] if len(items) > 0 else ''
|
key = items[0] if items else ''
|
||||||
if key == 'grid':
|
if key == 'grid':
|
||||||
grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
|
grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
|
||||||
elif key == 'size':
|
elif key == 'size':
|
||||||
|
@ -524,7 +524,7 @@ class Geom():
|
||||||
"""Renumber sorted microstructure indices to 1,...,N."""
|
"""Renumber sorted microstructure indices to 1,...,N."""
|
||||||
renumbered = np.empty(self.get_grid(),dtype=self.microstructure.dtype)
|
renumbered = np.empty(self.get_grid(),dtype=self.microstructure.dtype)
|
||||||
for i, oldID in enumerate(np.unique(self.microstructure)):
|
for i, oldID in enumerate(np.unique(self.microstructure)):
|
||||||
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
|
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
|
||||||
|
|
||||||
return self.update(renumbered)
|
return self.update(renumbered)
|
||||||
#self.add_comments('tbd')
|
#self.add_comments('tbd')
|
||||||
|
|
|
@ -1,14 +1,14 @@
|
||||||
from scipy import spatial
|
from scipy import spatial
|
||||||
import numpy as np
|
import numpy as np
|
||||||
|
|
||||||
def __ks(size,grid,first_order=False):
|
def _ks(size,grid,first_order=False):
|
||||||
"""
|
"""
|
||||||
Get wave numbers operator.
|
Get wave numbers operator.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
k_sk = np.where(np.arange(grid[0])>grid[0]//2,np.arange(grid[0])-grid[0],np.arange(grid[0]))/size[0]
|
k_sk = np.where(np.arange(grid[0])>grid[0]//2,np.arange(grid[0])-grid[0],np.arange(grid[0]))/size[0]
|
||||||
|
@ -30,14 +30,14 @@ def curl(size,field):
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
n = np.prod(field.shape[3:])
|
n = np.prod(field.shape[3:])
|
||||||
k_s = __ks(size,field.shape[:3],True)
|
k_s = _ks(size,field.shape[:3],True)
|
||||||
|
|
||||||
e = np.zeros((3, 3, 3))
|
e = np.zeros((3, 3, 3))
|
||||||
e[0, 1, 2] = e[1, 2, 0] = e[2, 0, 1] = +1.0 # Levi-Civita symbol
|
e[0, 1, 2] = e[1, 2, 0] = e[2, 0, 1] = +1.0 # Levi-Civita symbol
|
||||||
e[0, 2, 1] = e[2, 1, 0] = e[1, 0, 2] = -1.0
|
e[0, 2, 1] = e[2, 1, 0] = e[1, 0, 2] = -1.0
|
||||||
|
|
||||||
field_fourier = np.fft.rfftn(field,axes=(0,1,2))
|
field_fourier = np.fft.rfftn(field,axes=(0,1,2))
|
||||||
|
@ -54,11 +54,11 @@ def divergence(size,field):
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
n = np.prod(field.shape[3:])
|
n = np.prod(field.shape[3:])
|
||||||
k_s = __ks(size,field.shape[:3],True)
|
k_s = _ks(size,field.shape[:3],True)
|
||||||
|
|
||||||
field_fourier = np.fft.rfftn(field,axes=(0,1,2))
|
field_fourier = np.fft.rfftn(field,axes=(0,1,2))
|
||||||
divergence = (np.einsum('ijkl,ijkl ->ijk', k_s,field_fourier)*2.0j*np.pi if n == 3 else # vector, 3 -> 1
|
divergence = (np.einsum('ijkl,ijkl ->ijk', k_s,field_fourier)*2.0j*np.pi if n == 3 else # vector, 3 -> 1
|
||||||
|
@ -74,11 +74,11 @@ def gradient(size,field):
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
n = np.prod(field.shape[3:])
|
n = np.prod(field.shape[3:])
|
||||||
k_s = __ks(size,field.shape[:3],True)
|
k_s = _ks(size,field.shape[:3],True)
|
||||||
|
|
||||||
field_fourier = np.fft.rfftn(field,axes=(0,1,2))
|
field_fourier = np.fft.rfftn(field,axes=(0,1,2))
|
||||||
gradient = (np.einsum('ijkl,ijkm->ijkm', field_fourier,k_s)*2.0j*np.pi if n == 1 else # scalar, 1 -> 3
|
gradient = (np.einsum('ijkl,ijkm->ijkm', field_fourier,k_s)*2.0j*np.pi if n == 1 else # scalar, 1 -> 3
|
||||||
|
@ -96,7 +96,7 @@ def cell_coord0(grid,size,origin=np.zeros(3)):
|
||||||
grid : numpy.ndarray
|
grid : numpy.ndarray
|
||||||
number of grid points.
|
number of grid points.
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
origin : numpy.ndarray, optional
|
origin : numpy.ndarray, optional
|
||||||
physical origin of the periodic field. Default is [0.0,0.0,0.0].
|
physical origin of the periodic field. Default is [0.0,0.0,0.0].
|
||||||
|
|
||||||
|
@ -108,7 +108,8 @@ def cell_coord0(grid,size,origin=np.zeros(3)):
|
||||||
np.linspace(start[0],end[0],grid[0]),
|
np.linspace(start[0],end[0],grid[0]),
|
||||||
indexing = 'ij')
|
indexing = 'ij')
|
||||||
|
|
||||||
return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
|
return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
|
||||||
|
|
||||||
|
|
||||||
def cell_displacement_fluct(size,F):
|
def cell_displacement_fluct(size,F):
|
||||||
"""
|
"""
|
||||||
|
@ -117,14 +118,14 @@ def cell_displacement_fluct(size,F):
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
F : numpy.ndarray
|
F : numpy.ndarray
|
||||||
deformation gradient field.
|
deformation gradient field.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
integrator = 0.5j*size/np.pi
|
integrator = 0.5j*size/np.pi
|
||||||
|
|
||||||
k_s = __ks(size,F.shape[:3],False)
|
k_s = _ks(size,F.shape[:3],False)
|
||||||
k_s_squared = np.einsum('...l,...l',k_s,k_s)
|
k_s_squared = np.einsum('...l,...l',k_s,k_s)
|
||||||
k_s_squared[0,0,0] = 1.0
|
k_s_squared[0,0,0] = 1.0
|
||||||
|
|
||||||
|
@ -136,6 +137,7 @@ def cell_displacement_fluct(size,F):
|
||||||
|
|
||||||
return np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
|
return np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
|
||||||
|
|
||||||
|
|
||||||
def cell_displacement_avg(size,F):
|
def cell_displacement_avg(size,F):
|
||||||
"""
|
"""
|
||||||
Cell center displacement field from average part of the deformation gradient field.
|
Cell center displacement field from average part of the deformation gradient field.
|
||||||
|
@ -143,7 +145,7 @@ def cell_displacement_avg(size,F):
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
F : numpy.ndarray
|
F : numpy.ndarray
|
||||||
deformation gradient field.
|
deformation gradient field.
|
||||||
|
|
||||||
|
@ -151,6 +153,7 @@ def cell_displacement_avg(size,F):
|
||||||
F_avg = np.average(F,axis=(0,1,2))
|
F_avg = np.average(F,axis=(0,1,2))
|
||||||
return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),cell_coord0(F.shape[:3][::-1],size))
|
return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),cell_coord0(F.shape[:3][::-1],size))
|
||||||
|
|
||||||
|
|
||||||
def cell_displacement(size,F):
|
def cell_displacement(size,F):
|
||||||
"""
|
"""
|
||||||
Cell center displacement field from deformation gradient field.
|
Cell center displacement field from deformation gradient field.
|
||||||
|
@ -158,13 +161,14 @@ def cell_displacement(size,F):
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
F : numpy.ndarray
|
F : numpy.ndarray
|
||||||
deformation gradient field.
|
deformation gradient field.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return cell_displacement_avg(size,F) + cell_displacement_fluct(size,F)
|
return cell_displacement_avg(size,F) + cell_displacement_fluct(size,F)
|
||||||
|
|
||||||
|
|
||||||
def cell_coord(size,F,origin=np.zeros(3)):
|
def cell_coord(size,F,origin=np.zeros(3)):
|
||||||
"""
|
"""
|
||||||
Cell center positions.
|
Cell center positions.
|
||||||
|
@ -172,7 +176,7 @@ def cell_coord(size,F,origin=np.zeros(3)):
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
F : numpy.ndarray
|
F : numpy.ndarray
|
||||||
deformation gradient field.
|
deformation gradient field.
|
||||||
origin : numpy.ndarray, optional
|
origin : numpy.ndarray, optional
|
||||||
|
@ -181,6 +185,7 @@ def cell_coord(size,F,origin=np.zeros(3)):
|
||||||
"""
|
"""
|
||||||
return cell_coord0(F.shape[:3][::-1],size,origin) + cell_displacement(size,F)
|
return cell_coord0(F.shape[:3][::-1],size,origin) + cell_displacement(size,F)
|
||||||
|
|
||||||
|
|
||||||
def cell_coord0_gridSizeOrigin(coord0,ordered=True):
|
def cell_coord0_gridSizeOrigin(coord0,ordered=True):
|
||||||
"""
|
"""
|
||||||
Return grid 'DNA', i.e. grid, size, and origin from array of cell positions.
|
Return grid 'DNA', i.e. grid, size, and origin from array of cell positions.
|
||||||
|
@ -200,11 +205,11 @@ def cell_coord0_gridSizeOrigin(coord0,ordered=True):
|
||||||
size = grid/np.maximum(grid-1,1) * (maxcorner-mincorner)
|
size = grid/np.maximum(grid-1,1) * (maxcorner-mincorner)
|
||||||
delta = size/grid
|
delta = size/grid
|
||||||
origin = mincorner - delta*.5
|
origin = mincorner - delta*.5
|
||||||
|
|
||||||
# 1D/2D: size/origin combination undefined, set origin to 0.0
|
# 1D/2D: size/origin combination undefined, set origin to 0.0
|
||||||
size [np.where(grid==1)] = origin[np.where(grid==1)]*2.
|
size [np.where(grid==1)] = origin[np.where(grid==1)]*2.
|
||||||
origin[np.where(grid==1)] = 0.0
|
origin[np.where(grid==1)] = 0.0
|
||||||
|
|
||||||
if grid.prod() != len(coord0):
|
if grid.prod() != len(coord0):
|
||||||
raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
|
raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
|
||||||
|
|
||||||
|
@ -221,6 +226,7 @@ def cell_coord0_gridSizeOrigin(coord0,ordered=True):
|
||||||
|
|
||||||
return (grid,size,origin)
|
return (grid,size,origin)
|
||||||
|
|
||||||
|
|
||||||
def coord0_check(coord0):
|
def coord0_check(coord0):
|
||||||
"""
|
"""
|
||||||
Check whether coordinates lie on a regular grid.
|
Check whether coordinates lie on a regular grid.
|
||||||
|
@ -234,7 +240,6 @@ def coord0_check(coord0):
|
||||||
cell_coord0_gridSizeOrigin(coord0,ordered=True)
|
cell_coord0_gridSizeOrigin(coord0,ordered=True)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def node_coord0(grid,size,origin=np.zeros(3)):
|
def node_coord0(grid,size,origin=np.zeros(3)):
|
||||||
"""
|
"""
|
||||||
Nodal positions (undeformed).
|
Nodal positions (undeformed).
|
||||||
|
@ -244,7 +249,7 @@ def node_coord0(grid,size,origin=np.zeros(3)):
|
||||||
grid : numpy.ndarray
|
grid : numpy.ndarray
|
||||||
number of grid points.
|
number of grid points.
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
origin : numpy.ndarray, optional
|
origin : numpy.ndarray, optional
|
||||||
physical origin of the periodic field. Default is [0.0,0.0,0.0].
|
physical origin of the periodic field. Default is [0.0,0.0,0.0].
|
||||||
|
|
||||||
|
@ -253,8 +258,9 @@ def node_coord0(grid,size,origin=np.zeros(3)):
|
||||||
np.linspace(origin[1],size[1]+origin[1],1+grid[1]),
|
np.linspace(origin[1],size[1]+origin[1],1+grid[1]),
|
||||||
np.linspace(origin[0],size[0]+origin[0],1+grid[0]),
|
np.linspace(origin[0],size[0]+origin[0],1+grid[0]),
|
||||||
indexing = 'ij')
|
indexing = 'ij')
|
||||||
|
|
||||||
return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
|
return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
|
||||||
|
|
||||||
|
|
||||||
def node_displacement_fluct(size,F):
|
def node_displacement_fluct(size,F):
|
||||||
"""
|
"""
|
||||||
|
@ -263,13 +269,14 @@ def node_displacement_fluct(size,F):
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
F : numpy.ndarray
|
F : numpy.ndarray
|
||||||
deformation gradient field.
|
deformation gradient field.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return cell_2_node(cell_displacement_fluct(size,F))
|
return cell_2_node(cell_displacement_fluct(size,F))
|
||||||
|
|
||||||
|
|
||||||
def node_displacement_avg(size,F):
|
def node_displacement_avg(size,F):
|
||||||
"""
|
"""
|
||||||
Nodal displacement field from average part of the deformation gradient field.
|
Nodal displacement field from average part of the deformation gradient field.
|
||||||
|
@ -277,7 +284,7 @@ def node_displacement_avg(size,F):
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
F : numpy.ndarray
|
F : numpy.ndarray
|
||||||
deformation gradient field.
|
deformation gradient field.
|
||||||
|
|
||||||
|
@ -285,6 +292,7 @@ def node_displacement_avg(size,F):
|
||||||
F_avg = np.average(F,axis=(0,1,2))
|
F_avg = np.average(F,axis=(0,1,2))
|
||||||
return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),node_coord0(F.shape[:3][::-1],size))
|
return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),node_coord0(F.shape[:3][::-1],size))
|
||||||
|
|
||||||
|
|
||||||
def node_displacement(size,F):
|
def node_displacement(size,F):
|
||||||
"""
|
"""
|
||||||
Nodal displacement field from deformation gradient field.
|
Nodal displacement field from deformation gradient field.
|
||||||
|
@ -292,13 +300,14 @@ def node_displacement(size,F):
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
F : numpy.ndarray
|
F : numpy.ndarray
|
||||||
deformation gradient field.
|
deformation gradient field.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return node_displacement_avg(size,F) + node_displacement_fluct(size,F)
|
return node_displacement_avg(size,F) + node_displacement_fluct(size,F)
|
||||||
|
|
||||||
|
|
||||||
def node_coord(size,F,origin=np.zeros(3)):
|
def node_coord(size,F,origin=np.zeros(3)):
|
||||||
"""
|
"""
|
||||||
Nodal positions.
|
Nodal positions.
|
||||||
|
@ -306,7 +315,7 @@ def node_coord(size,F,origin=np.zeros(3)):
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
size : numpy.ndarray
|
size : numpy.ndarray
|
||||||
physical size of the periodic field.
|
physical size of the periodic field.
|
||||||
F : numpy.ndarray
|
F : numpy.ndarray
|
||||||
deformation gradient field.
|
deformation gradient field.
|
||||||
origin : numpy.ndarray, optional
|
origin : numpy.ndarray, optional
|
||||||
|
@ -315,22 +324,25 @@ def node_coord(size,F,origin=np.zeros(3)):
|
||||||
"""
|
"""
|
||||||
return node_coord0(F.shape[:3][::-1],size,origin) + node_displacement(size,F)
|
return node_coord0(F.shape[:3][::-1],size,origin) + node_displacement(size,F)
|
||||||
|
|
||||||
|
|
||||||
def cell_2_node(cell_data):
|
def cell_2_node(cell_data):
|
||||||
"""Interpolate periodic cell data to nodal data."""
|
"""Interpolate periodic cell data to nodal data."""
|
||||||
n = ( cell_data + np.roll(cell_data,1,(0,1,2))
|
n = ( cell_data + np.roll(cell_data,1,(0,1,2))
|
||||||
+ np.roll(cell_data,1,(0,)) + np.roll(cell_data,1,(1,)) + np.roll(cell_data,1,(2,))
|
+ np.roll(cell_data,1,(0,)) + np.roll(cell_data,1,(1,)) + np.roll(cell_data,1,(2,))
|
||||||
+ np.roll(cell_data,1,(0,1)) + np.roll(cell_data,1,(1,2)) + np.roll(cell_data,1,(2,0)))*0.125
|
+ np.roll(cell_data,1,(0,1)) + np.roll(cell_data,1,(1,2)) + np.roll(cell_data,1,(2,0)))*0.125
|
||||||
|
|
||||||
return np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
|
return np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
|
||||||
|
|
||||||
|
|
||||||
def node_2_cell(node_data):
|
def node_2_cell(node_data):
|
||||||
"""Interpolate periodic nodal data to cell data."""
|
"""Interpolate periodic nodal data to cell data."""
|
||||||
c = ( node_data + np.roll(node_data,1,(0,1,2))
|
c = ( node_data + np.roll(node_data,1,(0,1,2))
|
||||||
+ np.roll(node_data,1,(0,)) + np.roll(node_data,1,(1,)) + np.roll(node_data,1,(2,))
|
+ np.roll(node_data,1,(0,)) + np.roll(node_data,1,(1,)) + np.roll(node_data,1,(2,))
|
||||||
+ np.roll(node_data,1,(0,1)) + np.roll(node_data,1,(1,2)) + np.roll(node_data,1,(2,0)))*0.125
|
+ np.roll(node_data,1,(0,1)) + np.roll(node_data,1,(1,2)) + np.roll(node_data,1,(2,0)))*0.125
|
||||||
|
|
||||||
return c[:-1,:-1,:-1]
|
return c[:-1,:-1,:-1]
|
||||||
|
|
||||||
|
|
||||||
def node_coord0_gridSizeOrigin(coord0,ordered=False):
|
def node_coord0_gridSizeOrigin(coord0,ordered=False):
|
||||||
"""
|
"""
|
||||||
Return grid 'DNA', i.e. grid, size, and origin from array of nodal positions.
|
Return grid 'DNA', i.e. grid, size, and origin from array of nodal positions.
|
||||||
|
@ -349,7 +361,7 @@ def node_coord0_gridSizeOrigin(coord0,ordered=False):
|
||||||
grid = np.array(list(map(len,coords)),'i') - 1
|
grid = np.array(list(map(len,coords)),'i') - 1
|
||||||
size = maxcorner-mincorner
|
size = maxcorner-mincorner
|
||||||
origin = mincorner
|
origin = mincorner
|
||||||
|
|
||||||
if (grid+1).prod() != len(coord0):
|
if (grid+1).prod() != len(coord0):
|
||||||
raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
|
raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
|
||||||
|
|
||||||
|
|
|
@ -0,0 +1,641 @@
|
||||||
|
import numpy as np
|
||||||
|
|
||||||
|
from .rotation import Rotation
|
||||||
|
|
||||||
|
P = -1
|
||||||
|
|
||||||
|
# ******************************************************************************************
|
||||||
|
class Symmetry:
|
||||||
|
"""
|
||||||
|
Symmetry operations for lattice systems.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
https://en.wikipedia.org/wiki/Crystal_system
|
||||||
|
|
||||||
|
"""
|
||||||
|
|
||||||
|
lattices = [None,'orthorhombic','tetragonal','hexagonal','cubic',]
|
||||||
|
|
||||||
|
def __init__(self, symmetry = None):
|
||||||
|
"""
|
||||||
|
Symmetry Definition.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
symmetry : str, optional
|
||||||
|
label of the crystal system
|
||||||
|
|
||||||
|
"""
|
||||||
|
if symmetry is not None and symmetry.lower() not in Symmetry.lattices:
|
||||||
|
raise KeyError('Symmetry/crystal system "{}" is unknown'.format(symmetry))
|
||||||
|
|
||||||
|
self.lattice = symmetry.lower() if isinstance(symmetry,str) else symmetry
|
||||||
|
|
||||||
|
|
||||||
|
def __copy__(self):
|
||||||
|
"""Copy."""
|
||||||
|
return self.__class__(self.lattice)
|
||||||
|
|
||||||
|
copy = __copy__
|
||||||
|
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
"""Readable string."""
|
||||||
|
return '{}'.format(self.lattice)
|
||||||
|
|
||||||
|
|
||||||
|
def __eq__(self, other):
|
||||||
|
"""
|
||||||
|
Equal to other.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : Symmetry
|
||||||
|
Symmetry to check for equality.
|
||||||
|
|
||||||
|
"""
|
||||||
|
return self.lattice == other.lattice
|
||||||
|
|
||||||
|
def __neq__(self, other):
|
||||||
|
"""
|
||||||
|
Not Equal to other.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : Symmetry
|
||||||
|
Symmetry to check for inequality.
|
||||||
|
|
||||||
|
"""
|
||||||
|
return not self.__eq__(other)
|
||||||
|
|
||||||
|
def __cmp__(self,other):
|
||||||
|
"""
|
||||||
|
Linear ordering.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : Symmetry
|
||||||
|
Symmetry to check for for order.
|
||||||
|
|
||||||
|
"""
|
||||||
|
myOrder = Symmetry.lattices.index(self.lattice)
|
||||||
|
otherOrder = Symmetry.lattices.index(other.lattice)
|
||||||
|
return (myOrder > otherOrder) - (myOrder < otherOrder)
|
||||||
|
|
||||||
|
def symmetryOperations(self,members=[]):
|
||||||
|
"""List (or single element) of symmetry operations as rotations."""
|
||||||
|
if self.lattice == 'cubic':
|
||||||
|
symQuats = [
|
||||||
|
[ 1.0, 0.0, 0.0, 0.0 ],
|
||||||
|
[ 0.0, 1.0, 0.0, 0.0 ],
|
||||||
|
[ 0.0, 0.0, 1.0, 0.0 ],
|
||||||
|
[ 0.0, 0.0, 0.0, 1.0 ],
|
||||||
|
[ 0.0, 0.0, 0.5*np.sqrt(2), 0.5*np.sqrt(2) ],
|
||||||
|
[ 0.0, 0.0, 0.5*np.sqrt(2),-0.5*np.sqrt(2) ],
|
||||||
|
[ 0.0, 0.5*np.sqrt(2), 0.0, 0.5*np.sqrt(2) ],
|
||||||
|
[ 0.0, 0.5*np.sqrt(2), 0.0, -0.5*np.sqrt(2) ],
|
||||||
|
[ 0.0, 0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0 ],
|
||||||
|
[ 0.0, -0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0 ],
|
||||||
|
[ 0.5, 0.5, 0.5, 0.5 ],
|
||||||
|
[-0.5, 0.5, 0.5, 0.5 ],
|
||||||
|
[-0.5, 0.5, 0.5, -0.5 ],
|
||||||
|
[-0.5, 0.5, -0.5, 0.5 ],
|
||||||
|
[-0.5, -0.5, 0.5, 0.5 ],
|
||||||
|
[-0.5, -0.5, 0.5, -0.5 ],
|
||||||
|
[-0.5, -0.5, -0.5, 0.5 ],
|
||||||
|
[-0.5, 0.5, -0.5, -0.5 ],
|
||||||
|
[-0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
|
||||||
|
[ 0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
|
||||||
|
[-0.5*np.sqrt(2), 0.0, 0.5*np.sqrt(2), 0.0 ],
|
||||||
|
[-0.5*np.sqrt(2), 0.0, -0.5*np.sqrt(2), 0.0 ],
|
||||||
|
[-0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0, 0.0 ],
|
||||||
|
[-0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0, 0.0 ],
|
||||||
|
]
|
||||||
|
elif self.lattice == 'hexagonal':
|
||||||
|
symQuats = [
|
||||||
|
[ 1.0, 0.0, 0.0, 0.0 ],
|
||||||
|
[-0.5*np.sqrt(3), 0.0, 0.0, -0.5 ],
|
||||||
|
[ 0.5, 0.0, 0.0, 0.5*np.sqrt(3) ],
|
||||||
|
[ 0.0, 0.0, 0.0, 1.0 ],
|
||||||
|
[-0.5, 0.0, 0.0, 0.5*np.sqrt(3) ],
|
||||||
|
[-0.5*np.sqrt(3), 0.0, 0.0, 0.5 ],
|
||||||
|
[ 0.0, 1.0, 0.0, 0.0 ],
|
||||||
|
[ 0.0, -0.5*np.sqrt(3), 0.5, 0.0 ],
|
||||||
|
[ 0.0, 0.5, -0.5*np.sqrt(3), 0.0 ],
|
||||||
|
[ 0.0, 0.0, 1.0, 0.0 ],
|
||||||
|
[ 0.0, -0.5, -0.5*np.sqrt(3), 0.0 ],
|
||||||
|
[ 0.0, 0.5*np.sqrt(3), 0.5, 0.0 ],
|
||||||
|
]
|
||||||
|
elif self.lattice == 'tetragonal':
|
||||||
|
symQuats = [
|
||||||
|
[ 1.0, 0.0, 0.0, 0.0 ],
|
||||||
|
[ 0.0, 1.0, 0.0, 0.0 ],
|
||||||
|
[ 0.0, 0.0, 1.0, 0.0 ],
|
||||||
|
[ 0.0, 0.0, 0.0, 1.0 ],
|
||||||
|
[ 0.0, 0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0 ],
|
||||||
|
[ 0.0, -0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0 ],
|
||||||
|
[ 0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
|
||||||
|
[-0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
|
||||||
|
]
|
||||||
|
elif self.lattice == 'orthorhombic':
|
||||||
|
symQuats = [
|
||||||
|
[ 1.0,0.0,0.0,0.0 ],
|
||||||
|
[ 0.0,1.0,0.0,0.0 ],
|
||||||
|
[ 0.0,0.0,1.0,0.0 ],
|
||||||
|
[ 0.0,0.0,0.0,1.0 ],
|
||||||
|
]
|
||||||
|
else:
|
||||||
|
symQuats = [
|
||||||
|
[ 1.0,0.0,0.0,0.0 ],
|
||||||
|
]
|
||||||
|
|
||||||
|
symOps = list(map(Rotation,
|
||||||
|
np.array(symQuats)[np.atleast_1d(members) if members != [] else range(len(symQuats))]))
|
||||||
|
try:
|
||||||
|
iter(members) # asking for (even empty) list of members?
|
||||||
|
except TypeError:
|
||||||
|
return symOps[0] # no, return rotation object
|
||||||
|
else:
|
||||||
|
return symOps # yes, return list of rotations
|
||||||
|
|
||||||
|
|
||||||
|
def inFZ(self,rodrigues):
|
||||||
|
"""
|
||||||
|
Check whether given Rodrigues-Frank vector falls into fundamental zone of own symmetry.
|
||||||
|
|
||||||
|
Fundamental zone in Rodrigues space is point symmetric around origin.
|
||||||
|
"""
|
||||||
|
if (len(rodrigues) != 3):
|
||||||
|
raise ValueError('Input is not a Rodrigues-Frank vector.\n')
|
||||||
|
|
||||||
|
if np.any(rodrigues == np.inf): return False
|
||||||
|
|
||||||
|
Rabs = abs(rodrigues)
|
||||||
|
|
||||||
|
if self.lattice == 'cubic':
|
||||||
|
return np.sqrt(2.0)-1.0 >= Rabs[0] \
|
||||||
|
and np.sqrt(2.0)-1.0 >= Rabs[1] \
|
||||||
|
and np.sqrt(2.0)-1.0 >= Rabs[2] \
|
||||||
|
and 1.0 >= Rabs[0] + Rabs[1] + Rabs[2]
|
||||||
|
elif self.lattice == 'hexagonal':
|
||||||
|
return 1.0 >= Rabs[0] and 1.0 >= Rabs[1] and 1.0 >= Rabs[2] \
|
||||||
|
and 2.0 >= np.sqrt(3)*Rabs[0] + Rabs[1] \
|
||||||
|
and 2.0 >= np.sqrt(3)*Rabs[1] + Rabs[0] \
|
||||||
|
and 2.0 >= np.sqrt(3) + Rabs[2]
|
||||||
|
elif self.lattice == 'tetragonal':
|
||||||
|
return 1.0 >= Rabs[0] and 1.0 >= Rabs[1] \
|
||||||
|
and np.sqrt(2.0) >= Rabs[0] + Rabs[1] \
|
||||||
|
and np.sqrt(2.0) >= Rabs[2] + 1.0
|
||||||
|
elif self.lattice == 'orthorhombic':
|
||||||
|
return 1.0 >= Rabs[0] and 1.0 >= Rabs[1] and 1.0 >= Rabs[2]
|
||||||
|
else:
|
||||||
|
return True
|
||||||
|
|
||||||
|
|
||||||
|
def inDisorientationSST(self,rodrigues):
|
||||||
|
"""
|
||||||
|
Check whether given Rodrigues-Frank vector (of misorientation) falls into standard stereographic triangle of own symmetry.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
A. Heinz and P. Neumann, Acta Crystallographica Section A 47:780-789, 1991
|
||||||
|
https://doi.org/10.1107/S0108767391006864
|
||||||
|
|
||||||
|
"""
|
||||||
|
if (len(rodrigues) != 3):
|
||||||
|
raise ValueError('Input is not a Rodrigues-Frank vector.\n')
|
||||||
|
R = rodrigues
|
||||||
|
|
||||||
|
epsilon = 0.0
|
||||||
|
if self.lattice == 'cubic':
|
||||||
|
return R[0] >= R[1]+epsilon and R[1] >= R[2]+epsilon and R[2] >= epsilon
|
||||||
|
elif self.lattice == 'hexagonal':
|
||||||
|
return R[0] >= np.sqrt(3)*(R[1]-epsilon) and R[1] >= epsilon and R[2] >= epsilon
|
||||||
|
elif self.lattice == 'tetragonal':
|
||||||
|
return R[0] >= R[1]-epsilon and R[1] >= epsilon and R[2] >= epsilon
|
||||||
|
elif self.lattice == 'orthorhombic':
|
||||||
|
return R[0] >= epsilon and R[1] >= epsilon and R[2] >= epsilon
|
||||||
|
else:
|
||||||
|
return True
|
||||||
|
|
||||||
|
|
||||||
|
def inSST(self,
|
||||||
|
vector,
|
||||||
|
proper = False,
|
||||||
|
color = False):
|
||||||
|
"""
|
||||||
|
Check whether given vector falls into standard stereographic triangle of own symmetry.
|
||||||
|
|
||||||
|
proper considers only vectors with z >= 0, hence uses two neighboring SSTs.
|
||||||
|
Return inverse pole figure color if requested.
|
||||||
|
Bases are computed from
|
||||||
|
|
||||||
|
basis = {'cubic' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||||||
|
[1.,0.,1.]/np.sqrt(2.), # direction of green
|
||||||
|
[1.,1.,1.]/np.sqrt(3.)]).T), # direction of blue
|
||||||
|
'hexagonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||||||
|
[1.,0.,0.], # direction of green
|
||||||
|
[np.sqrt(3.),1.,0.]/np.sqrt(4.)]).T), # direction of blue
|
||||||
|
'tetragonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||||||
|
[1.,0.,0.], # direction of green
|
||||||
|
[1.,1.,0.]/np.sqrt(2.)]).T), # direction of blue
|
||||||
|
'orthorhombic' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||||||
|
[1.,0.,0.], # direction of green
|
||||||
|
[0.,1.,0.]]).T), # direction of blue
|
||||||
|
}
|
||||||
|
"""
|
||||||
|
if self.lattice == 'cubic':
|
||||||
|
basis = {'improper':np.array([ [-1. , 0. , 1. ],
|
||||||
|
[ np.sqrt(2.) , -np.sqrt(2.) , 0. ],
|
||||||
|
[ 0. , np.sqrt(3.) , 0. ] ]),
|
||||||
|
'proper':np.array([ [ 0. , -1. , 1. ],
|
||||||
|
[-np.sqrt(2.) , np.sqrt(2.) , 0. ],
|
||||||
|
[ np.sqrt(3.) , 0. , 0. ] ]),
|
||||||
|
}
|
||||||
|
elif self.lattice == 'hexagonal':
|
||||||
|
basis = {'improper':np.array([ [ 0. , 0. , 1. ],
|
||||||
|
[ 1. , -np.sqrt(3.) , 0. ],
|
||||||
|
[ 0. , 2. , 0. ] ]),
|
||||||
|
'proper':np.array([ [ 0. , 0. , 1. ],
|
||||||
|
[-1. , np.sqrt(3.) , 0. ],
|
||||||
|
[ np.sqrt(3.) , -1. , 0. ] ]),
|
||||||
|
}
|
||||||
|
elif self.lattice == 'tetragonal':
|
||||||
|
basis = {'improper':np.array([ [ 0. , 0. , 1. ],
|
||||||
|
[ 1. , -1. , 0. ],
|
||||||
|
[ 0. , np.sqrt(2.) , 0. ] ]),
|
||||||
|
'proper':np.array([ [ 0. , 0. , 1. ],
|
||||||
|
[-1. , 1. , 0. ],
|
||||||
|
[ np.sqrt(2.) , 0. , 0. ] ]),
|
||||||
|
}
|
||||||
|
elif self.lattice == 'orthorhombic':
|
||||||
|
basis = {'improper':np.array([ [ 0., 0., 1.],
|
||||||
|
[ 1., 0., 0.],
|
||||||
|
[ 0., 1., 0.] ]),
|
||||||
|
'proper':np.array([ [ 0., 0., 1.],
|
||||||
|
[-1., 0., 0.],
|
||||||
|
[ 0., 1., 0.] ]),
|
||||||
|
}
|
||||||
|
else: # direct exit for unspecified symmetry
|
||||||
|
if color:
|
||||||
|
return (True,np.zeros(3,'d'))
|
||||||
|
else:
|
||||||
|
return True
|
||||||
|
|
||||||
|
v = np.array(vector,dtype=float)
|
||||||
|
if proper: # check both improper ...
|
||||||
|
theComponents = np.around(np.dot(basis['improper'],v),12)
|
||||||
|
inSST = np.all(theComponents >= 0.0)
|
||||||
|
if not inSST: # ... and proper SST
|
||||||
|
theComponents = np.around(np.dot(basis['proper'],v),12)
|
||||||
|
inSST = np.all(theComponents >= 0.0)
|
||||||
|
else:
|
||||||
|
v[2] = abs(v[2]) # z component projects identical
|
||||||
|
theComponents = np.around(np.dot(basis['improper'],v),12) # for positive and negative values
|
||||||
|
inSST = np.all(theComponents >= 0.0)
|
||||||
|
|
||||||
|
if color: # have to return color array
|
||||||
|
if inSST:
|
||||||
|
rgb = np.power(theComponents/np.linalg.norm(theComponents),0.5) # smoothen color ramps
|
||||||
|
rgb = np.minimum(np.ones(3,dtype=float),rgb) # limit to maximum intensity
|
||||||
|
rgb /= max(rgb) # normalize to (HS)V = 1
|
||||||
|
else:
|
||||||
|
rgb = np.zeros(3,dtype=float)
|
||||||
|
return (inSST,rgb)
|
||||||
|
else:
|
||||||
|
return inSST
|
||||||
|
|
||||||
|
# code derived from https://github.com/ezag/pyeuclid
|
||||||
|
# suggested reading: http://web.mit.edu/2.998/www/QuaternionReport1.pdf
|
||||||
|
|
||||||
|
|
||||||
|
# ******************************************************************************************
|
||||||
|
class Lattice:
|
||||||
|
"""
|
||||||
|
Lattice system.
|
||||||
|
|
||||||
|
Currently, this contains only a mapping from Bravais lattice to symmetry
|
||||||
|
and orientation relationships. It could include twin and slip systems.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
https://en.wikipedia.org/wiki/Bravais_lattice
|
||||||
|
|
||||||
|
"""
|
||||||
|
|
||||||
|
lattices = {
|
||||||
|
'triclinic':{'symmetry':None},
|
||||||
|
'bct':{'symmetry':'tetragonal'},
|
||||||
|
'hex':{'symmetry':'hexagonal'},
|
||||||
|
'fcc':{'symmetry':'cubic','c/a':1.0},
|
||||||
|
'bcc':{'symmetry':'cubic','c/a':1.0},
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
def __init__(self, lattice):
|
||||||
|
"""
|
||||||
|
New lattice of given type.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
lattice : str
|
||||||
|
Bravais lattice.
|
||||||
|
|
||||||
|
"""
|
||||||
|
self.lattice = lattice
|
||||||
|
self.symmetry = Symmetry(self.lattices[lattice]['symmetry'])
|
||||||
|
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
"""Report basic lattice information."""
|
||||||
|
return 'Bravais lattice {} ({} symmetry)'.format(self.lattice,self.symmetry)
|
||||||
|
|
||||||
|
|
||||||
|
# Kurdjomov--Sachs orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from S. Morito et al., Journal of Alloys and Compounds 577:s587-s592, 2013
|
||||||
|
# also see K. Kitahara et al., Acta Materialia 54:1279-1288, 2006
|
||||||
|
KS = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ -1, 0, 1],[ -1, -1, 1]],
|
||||||
|
[[ -1, 0, 1],[ -1, 1, -1]],
|
||||||
|
[[ 0, 1, -1],[ -1, -1, 1]],
|
||||||
|
[[ 0, 1, -1],[ -1, 1, -1]],
|
||||||
|
[[ 1, -1, 0],[ -1, -1, 1]],
|
||||||
|
[[ 1, -1, 0],[ -1, 1, -1]],
|
||||||
|
[[ 1, 0, -1],[ -1, -1, 1]],
|
||||||
|
[[ 1, 0, -1],[ -1, 1, -1]],
|
||||||
|
[[ -1, -1, 0],[ -1, -1, 1]],
|
||||||
|
[[ -1, -1, 0],[ -1, 1, -1]],
|
||||||
|
[[ 0, 1, 1],[ -1, -1, 1]],
|
||||||
|
[[ 0, 1, 1],[ -1, 1, -1]],
|
||||||
|
[[ 0, -1, 1],[ -1, -1, 1]],
|
||||||
|
[[ 0, -1, 1],[ -1, 1, -1]],
|
||||||
|
[[ -1, 0, -1],[ -1, -1, 1]],
|
||||||
|
[[ -1, 0, -1],[ -1, 1, -1]],
|
||||||
|
[[ 1, 1, 0],[ -1, -1, 1]],
|
||||||
|
[[ 1, 1, 0],[ -1, 1, -1]],
|
||||||
|
[[ -1, 1, 0],[ -1, -1, 1]],
|
||||||
|
[[ -1, 1, 0],[ -1, 1, -1]],
|
||||||
|
[[ 0, -1, -1],[ -1, -1, 1]],
|
||||||
|
[[ 0, -1, -1],[ -1, 1, -1]],
|
||||||
|
[[ 1, 0, 1],[ -1, -1, 1]],
|
||||||
|
[[ 1, 0, 1],[ -1, 1, -1]]],dtype='float')}
|
||||||
|
|
||||||
|
# Greninger--Troiano orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
|
||||||
|
GT = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 1, 1, 1],[ 1, 0, 1]],
|
||||||
|
[[ 1, 1, 1],[ 1, 1, 0]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, -1, 1],[ -1, 0, 1]],
|
||||||
|
[[ -1, -1, 1],[ -1, -1, 0]],
|
||||||
|
[[ -1, -1, 1],[ 0, -1, 1]],
|
||||||
|
[[ -1, 1, 1],[ -1, 0, 1]],
|
||||||
|
[[ -1, 1, 1],[ -1, 1, 0]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 1, 0, 1]],
|
||||||
|
[[ 1, -1, 1],[ 1, -1, 0]],
|
||||||
|
[[ 1, -1, 1],[ 0, -1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 1, 1, 0]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 1, 0, 1]],
|
||||||
|
[[ -1, -1, 1],[ -1, -1, 0]],
|
||||||
|
[[ -1, -1, 1],[ 0, -1, 1]],
|
||||||
|
[[ -1, -1, 1],[ -1, 0, 1]],
|
||||||
|
[[ -1, 1, 1],[ -1, 1, 0]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ -1, 0, 1]],
|
||||||
|
[[ 1, -1, 1],[ 1, -1, 0]],
|
||||||
|
[[ 1, -1, 1],[ 0, -1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 1, 0, 1]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ -5,-12, 17],[-17, -7, 17]],
|
||||||
|
[[ 17, -5,-12],[ 17,-17, -7]],
|
||||||
|
[[-12, 17, -5],[ -7, 17,-17]],
|
||||||
|
[[ 5, 12, 17],[ 17, 7, 17]],
|
||||||
|
[[-17, 5,-12],[-17, 17, -7]],
|
||||||
|
[[ 12,-17, -5],[ 7,-17,-17]],
|
||||||
|
[[ -5, 12,-17],[-17, 7,-17]],
|
||||||
|
[[ 17, 5, 12],[ 17, 17, 7]],
|
||||||
|
[[-12,-17, 5],[ -7,-17, 17]],
|
||||||
|
[[ 5,-12,-17],[ 17, -7,-17]],
|
||||||
|
[[-17, -5, 12],[-17,-17, 7]],
|
||||||
|
[[ 12, 17, 5],[ 7, 17, 17]],
|
||||||
|
[[ -5, 17,-12],[-17, 17, -7]],
|
||||||
|
[[-12, -5, 17],[ -7,-17, 17]],
|
||||||
|
[[ 17,-12, -5],[ 17, -7,-17]],
|
||||||
|
[[ 5,-17,-12],[ 17,-17, -7]],
|
||||||
|
[[ 12, 5, 17],[ 7, 17, 17]],
|
||||||
|
[[-17, 12, -5],[-17, 7,-17]],
|
||||||
|
[[ -5,-17, 12],[-17,-17, 7]],
|
||||||
|
[[-12, 5,-17],[ -7, 17,-17]],
|
||||||
|
[[ 17, 12, 5],[ 17, 7, 17]],
|
||||||
|
[[ 5, 17, 12],[ 17, 17, 7]],
|
||||||
|
[[ 12, -5,-17],[ 7,-17,-17]],
|
||||||
|
[[-17,-12, 5],[-17,-7, 17]]],dtype='float')}
|
||||||
|
|
||||||
|
# Greninger--Troiano' orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
|
||||||
|
GTprime = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 7, 17, 17],[ 12, 5, 17]],
|
||||||
|
[[ 17, 7, 17],[ 17, 12, 5]],
|
||||||
|
[[ 17, 17, 7],[ 5, 17, 12]],
|
||||||
|
[[ -7,-17, 17],[-12, -5, 17]],
|
||||||
|
[[-17, -7, 17],[-17,-12, 5]],
|
||||||
|
[[-17,-17, 7],[ -5,-17, 12]],
|
||||||
|
[[ 7,-17,-17],[ 12, -5,-17]],
|
||||||
|
[[ 17, -7,-17],[ 17,-12, -5]],
|
||||||
|
[[ 17,-17, -7],[ 5,-17,-12]],
|
||||||
|
[[ -7, 17,-17],[-12, 5,-17]],
|
||||||
|
[[-17, 7,-17],[-17, 12, -5]],
|
||||||
|
[[-17, 17, -7],[ -5, 17,-12]],
|
||||||
|
[[ 7, 17, 17],[ 12, 17, 5]],
|
||||||
|
[[ 17, 7, 17],[ 5, 12, 17]],
|
||||||
|
[[ 17, 17, 7],[ 17, 5, 12]],
|
||||||
|
[[ -7,-17, 17],[-12,-17, 5]],
|
||||||
|
[[-17, -7, 17],[ -5,-12, 17]],
|
||||||
|
[[-17,-17, 7],[-17, -5, 12]],
|
||||||
|
[[ 7,-17,-17],[ 12,-17, -5]],
|
||||||
|
[[ 17, -7,-17],[ 5, -12,-17]],
|
||||||
|
[[ 17,-17, -7],[ 17, -5,-12]],
|
||||||
|
[[ -7, 17,-17],[-12, 17, -5]],
|
||||||
|
[[-17, 7,-17],[ -5, 12,-17]],
|
||||||
|
[[-17, 17, -7],[-17, 5,-12]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ 0, 1, -1],[ 1, 1, -1]],
|
||||||
|
[[ -1, 0, 1],[ -1, 1, 1]],
|
||||||
|
[[ 1, -1, 0],[ 1, -1, 1]],
|
||||||
|
[[ 0, -1, -1],[ -1, -1, -1]],
|
||||||
|
[[ 1, 0, 1],[ 1, -1, 1]],
|
||||||
|
[[ 1, -1, 0],[ 1, -1, -1]],
|
||||||
|
[[ 0, 1, -1],[ -1, 1, -1]],
|
||||||
|
[[ 1, 0, 1],[ 1, 1, 1]],
|
||||||
|
[[ -1, -1, 0],[ -1, -1, 1]],
|
||||||
|
[[ 0, -1, -1],[ 1, -1, -1]],
|
||||||
|
[[ -1, 0, 1],[ -1, -1, 1]],
|
||||||
|
[[ -1, -1, 0],[ -1, -1, -1]],
|
||||||
|
[[ 0, -1, 1],[ 1, -1, 1]],
|
||||||
|
[[ 1, 0, -1],[ 1, 1, -1]],
|
||||||
|
[[ -1, 1, 0],[ -1, 1, 1]],
|
||||||
|
[[ 0, 1, 1],[ -1, 1, 1]],
|
||||||
|
[[ -1, 0, -1],[ -1, -1, -1]],
|
||||||
|
[[ -1, 1, 0],[ -1, 1, -1]],
|
||||||
|
[[ 0, -1, 1],[ -1, -1, 1]],
|
||||||
|
[[ -1, 0, -1],[ -1, 1, -1]],
|
||||||
|
[[ 1, 1, 0],[ 1, 1, 1]],
|
||||||
|
[[ 0, 1, 1],[ 1, 1, 1]],
|
||||||
|
[[ 1, 0, -1],[ 1, -1, -1]],
|
||||||
|
[[ 1, 1, 0],[ 1, 1, -1]]],dtype='float')}
|
||||||
|
|
||||||
|
# Nishiyama--Wassermann orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from H. Kitahara et al., Materials Characterization 54:378-386, 2005
|
||||||
|
NW = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, -1, 1],[ 0, 1, 1]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ 2, -1, -1],[ 0, -1, 1]],
|
||||||
|
[[ -1, 2, -1],[ 0, -1, 1]],
|
||||||
|
[[ -1, -1, 2],[ 0, -1, 1]],
|
||||||
|
[[ -2, -1, -1],[ 0, -1, 1]],
|
||||||
|
[[ 1, 2, -1],[ 0, -1, 1]],
|
||||||
|
[[ 1, -1, 2],[ 0, -1, 1]],
|
||||||
|
[[ 2, 1, -1],[ 0, -1, 1]],
|
||||||
|
[[ -1, -2, -1],[ 0, -1, 1]],
|
||||||
|
[[ -1, 1, 2],[ 0, -1, 1]],
|
||||||
|
[[ 2, -1, 1],[ 0, -1, 1]], #It is wrong in the paper, but matrix is correct
|
||||||
|
[[ -1, 2, 1],[ 0, -1, 1]],
|
||||||
|
[[ -1, -1, -2],[ 0, -1, 1]]],dtype='float')}
|
||||||
|
|
||||||
|
# Pitsch orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from Y. He et al., Acta Materialia 53:1179-1190, 2005
|
||||||
|
Pitsch = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 0, 1, 0],[ -1, 0, 1]],
|
||||||
|
[[ 0, 0, 1],[ 1, -1, 0]],
|
||||||
|
[[ 1, 0, 0],[ 0, 1, -1]],
|
||||||
|
[[ 1, 0, 0],[ 0, -1, -1]],
|
||||||
|
[[ 0, 1, 0],[ -1, 0, -1]],
|
||||||
|
[[ 0, 0, 1],[ -1, -1, 0]],
|
||||||
|
[[ 0, 1, 0],[ -1, 0, -1]],
|
||||||
|
[[ 0, 0, 1],[ -1, -1, 0]],
|
||||||
|
[[ 1, 0, 0],[ 0, -1, -1]],
|
||||||
|
[[ 1, 0, 0],[ 0, -1, 1]],
|
||||||
|
[[ 0, 1, 0],[ 1, 0, -1]],
|
||||||
|
[[ 0, 0, 1],[ -1, 1, 0]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ 1, 0, 1],[ 1, -1, 1]],
|
||||||
|
[[ 1, 1, 0],[ 1, 1, -1]],
|
||||||
|
[[ 0, 1, 1],[ -1, 1, 1]],
|
||||||
|
[[ 0, 1, -1],[ -1, 1, -1]],
|
||||||
|
[[ -1, 0, 1],[ -1, -1, 1]],
|
||||||
|
[[ 1, -1, 0],[ 1, -1, -1]],
|
||||||
|
[[ 1, 0, -1],[ 1, -1, -1]],
|
||||||
|
[[ -1, 1, 0],[ -1, 1, -1]],
|
||||||
|
[[ 0, -1, 1],[ -1, -1, 1]],
|
||||||
|
[[ 0, 1, 1],[ -1, 1, 1]],
|
||||||
|
[[ 1, 0, 1],[ 1, -1, 1]],
|
||||||
|
[[ 1, 1, 0],[ 1, 1, -1]]],dtype='float')}
|
||||||
|
|
||||||
|
# Bain orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
|
||||||
|
Bain = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 1, 0, 0],[ 1, 0, 0]],
|
||||||
|
[[ 0, 1, 0],[ 0, 1, 0]],
|
||||||
|
[[ 0, 0, 1],[ 0, 0, 1]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ 0, 1, 0],[ 0, 1, 1]],
|
||||||
|
[[ 0, 0, 1],[ 1, 0, 1]],
|
||||||
|
[[ 1, 0, 0],[ 1, 1, 0]]],dtype='float')}
|
||||||
|
|
||||||
|
def relationOperations(self,model):
|
||||||
|
"""
|
||||||
|
Crystallographic orientation relationships for phase transformations.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
S. Morito et al., Journal of Alloys and Compounds 577:s587-s592, 2013
|
||||||
|
https://doi.org/10.1016/j.jallcom.2012.02.004
|
||||||
|
|
||||||
|
K. Kitahara et al., Acta Materialia 54(5):1279-1288, 2006
|
||||||
|
https://doi.org/10.1016/j.actamat.2005.11.001
|
||||||
|
|
||||||
|
Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
|
||||||
|
https://doi.org/10.1107/S0021889805038276
|
||||||
|
|
||||||
|
H. Kitahara et al., Materials Characterization 54(4-5):378-386, 2005
|
||||||
|
https://doi.org/10.1016/j.matchar.2004.12.015
|
||||||
|
|
||||||
|
Y. He et al., Acta Materialia 53(4):1179-1190, 2005
|
||||||
|
https://doi.org/10.1016/j.actamat.2004.11.021
|
||||||
|
|
||||||
|
"""
|
||||||
|
models={'KS':self.KS, 'GT':self.GT, 'GT_prime':self.GTprime,
|
||||||
|
'NW':self.NW, 'Pitsch': self.Pitsch, 'Bain':self.Bain}
|
||||||
|
try:
|
||||||
|
relationship = models[model]
|
||||||
|
except KeyError :
|
||||||
|
raise KeyError('Orientation relationship "{}" is unknown'.format(model))
|
||||||
|
|
||||||
|
if self.lattice not in relationship['mapping']:
|
||||||
|
raise ValueError('Relationship "{}" not supported for lattice "{}"'.format(model,self.lattice))
|
||||||
|
|
||||||
|
r = {'lattice':Lattice((set(relationship['mapping'])-{self.lattice}).pop()), # target lattice
|
||||||
|
'rotations':[] }
|
||||||
|
|
||||||
|
myPlane_id = relationship['mapping'][self.lattice]
|
||||||
|
otherPlane_id = (myPlane_id+1)%2
|
||||||
|
myDir_id = myPlane_id +2
|
||||||
|
otherDir_id = otherPlane_id +2
|
||||||
|
|
||||||
|
for miller in np.hstack((relationship['planes'],relationship['directions'])):
|
||||||
|
myPlane = miller[myPlane_id]/ np.linalg.norm(miller[myPlane_id])
|
||||||
|
myDir = miller[myDir_id]/ np.linalg.norm(miller[myDir_id])
|
||||||
|
myMatrix = np.array([myDir,np.cross(myPlane,myDir),myPlane])
|
||||||
|
|
||||||
|
otherPlane = miller[otherPlane_id]/ np.linalg.norm(miller[otherPlane_id])
|
||||||
|
otherDir = miller[otherDir_id]/ np.linalg.norm(miller[otherDir_id])
|
||||||
|
otherMatrix = np.array([otherDir,np.cross(otherPlane,otherDir),otherPlane])
|
||||||
|
|
||||||
|
r['rotations'].append(Rotation.fromMatrix(np.dot(otherMatrix.T,myMatrix)))
|
||||||
|
|
||||||
|
return r
|
|
@ -21,21 +21,21 @@ def Cauchy(P,F):
|
||||||
return symmetric(sigma)
|
return symmetric(sigma)
|
||||||
|
|
||||||
|
|
||||||
def deviatoric_part(x):
|
def deviatoric_part(T):
|
||||||
"""
|
"""
|
||||||
Return deviatoric part of a tensor.
|
Return deviatoric part of a tensor.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Tensor of which the deviatoric part is computed.
|
Tensor of which the deviatoric part is computed.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return x - np.eye(3)*spherical_part(x) if np.shape(x) == (3,3) else \
|
return T - np.eye(3)*spherical_part(T) if np.shape(T) == (3,3) else \
|
||||||
x - np.einsum('ijk,i->ijk',np.broadcast_to(np.eye(3),[x.shape[0],3,3]),spherical_part(x))
|
T - np.einsum('ijk,i->ijk',np.broadcast_to(np.eye(3),[T.shape[0],3,3]),spherical_part(T))
|
||||||
|
|
||||||
|
|
||||||
def eigenvalues(x):
|
def eigenvalues(T_sym):
|
||||||
"""
|
"""
|
||||||
Return the eigenvalues, i.e. principal components, of a symmetric tensor.
|
Return the eigenvalues, i.e. principal components, of a symmetric tensor.
|
||||||
|
|
||||||
|
@ -44,14 +44,14 @@ def eigenvalues(x):
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T_sym : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Symmetric tensor of which the eigenvalues are computed.
|
Symmetric tensor of which the eigenvalues are computed.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return np.linalg.eigvalsh(symmetric(x))
|
return np.linalg.eigvalsh(symmetric(T_sym))
|
||||||
|
|
||||||
|
|
||||||
def eigenvectors(x,RHS=False):
|
def eigenvectors(T_sym,RHS=False):
|
||||||
"""
|
"""
|
||||||
Return eigenvectors of a symmetric tensor.
|
Return eigenvectors of a symmetric tensor.
|
||||||
|
|
||||||
|
@ -59,47 +59,47 @@ def eigenvectors(x,RHS=False):
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T_sym : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Symmetric tensor of which the eigenvectors are computed.
|
Symmetric tensor of which the eigenvectors are computed.
|
||||||
RHS: bool, optional
|
RHS: bool, optional
|
||||||
Enforce right-handed coordinate system. Default is False.
|
Enforce right-handed coordinate system. Default is False.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
(u,v) = np.linalg.eigh(symmetric(x))
|
(u,v) = np.linalg.eigh(symmetric(T_sym))
|
||||||
|
|
||||||
if RHS:
|
if RHS:
|
||||||
if np.shape(x) == (3,3):
|
if np.shape(T_sym) == (3,3):
|
||||||
if np.linalg.det(v) < 0.0: v[:,2] *= -1.0
|
if np.linalg.det(v) < 0.0: v[:,2] *= -1.0
|
||||||
else:
|
else:
|
||||||
v[np.linalg.det(v) < 0.0,:,2] *= -1.0
|
v[np.linalg.det(v) < 0.0,:,2] *= -1.0
|
||||||
return v
|
return v
|
||||||
|
|
||||||
|
|
||||||
def left_stretch(x):
|
def left_stretch(T):
|
||||||
"""
|
"""
|
||||||
Return the left stretch of a tensor.
|
Return the left stretch of a tensor.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Tensor of which the left stretch is computed.
|
Tensor of which the left stretch is computed.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return __polar_decomposition(x,'V')[0]
|
return __polar_decomposition(T,'V')[0]
|
||||||
|
|
||||||
|
|
||||||
def maximum_shear(x):
|
def maximum_shear(T_sym):
|
||||||
"""
|
"""
|
||||||
Return the maximum shear component of a symmetric tensor.
|
Return the maximum shear component of a symmetric tensor.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T_sym : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Symmetric tensor of which the maximum shear is computed.
|
Symmetric tensor of which the maximum shear is computed.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
w = eigenvalues(x)
|
w = eigenvalues(T_sym)
|
||||||
return (w[0] - w[2])*0.5 if np.shape(x) == (3,3) else \
|
return (w[0] - w[2])*0.5 if np.shape(T_sym) == (3,3) else \
|
||||||
(w[:,0] - w[:,2])*0.5
|
(w[:,0] - w[:,2])*0.5
|
||||||
|
|
||||||
|
|
||||||
|
@ -147,53 +147,54 @@ def PK2(P,F):
|
||||||
S = np.einsum('ijk,ikl->ijl',np.linalg.inv(F),P)
|
S = np.einsum('ijk,ikl->ijl',np.linalg.inv(F),P)
|
||||||
return symmetric(S)
|
return symmetric(S)
|
||||||
|
|
||||||
def right_stretch(x):
|
|
||||||
|
def right_stretch(T):
|
||||||
"""
|
"""
|
||||||
Return the right stretch of a tensor.
|
Return the right stretch of a tensor.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Tensor of which the right stretch is computed.
|
Tensor of which the right stretch is computed.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return __polar_decomposition(x,'U')[0]
|
return __polar_decomposition(T,'U')[0]
|
||||||
|
|
||||||
|
|
||||||
def rotational_part(x):
|
def rotational_part(T):
|
||||||
"""
|
"""
|
||||||
Return the rotational part of a tensor.
|
Return the rotational part of a tensor.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Tensor of which the rotational part is computed.
|
Tensor of which the rotational part is computed.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return __polar_decomposition(x,'R')[0]
|
return __polar_decomposition(T,'R')[0]
|
||||||
|
|
||||||
|
|
||||||
def spherical_part(x,tensor=False):
|
def spherical_part(T,tensor=False):
|
||||||
"""
|
"""
|
||||||
Return spherical (hydrostatic) part of a tensor.
|
Return spherical (hydrostatic) part of a tensor.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Tensor of which the hydrostatic part is computed.
|
Tensor of which the hydrostatic part is computed.
|
||||||
tensor : bool, optional
|
tensor : bool, optional
|
||||||
Map spherical part onto identity tensor. Default is false
|
Map spherical part onto identity tensor. Default is false
|
||||||
|
|
||||||
"""
|
"""
|
||||||
if x.shape == (3,3):
|
if T.shape == (3,3):
|
||||||
sph = np.trace(x)/3.0
|
sph = np.trace(T)/3.0
|
||||||
return sph if not tensor else np.eye(3)*sph
|
return sph if not tensor else np.eye(3)*sph
|
||||||
else:
|
else:
|
||||||
sph = np.trace(x,axis1=1,axis2=2)/3.0
|
sph = np.trace(T,axis1=1,axis2=2)/3.0
|
||||||
if not tensor:
|
if not tensor:
|
||||||
return sph
|
return sph
|
||||||
else:
|
else:
|
||||||
return np.einsum('ijk,i->ijk',np.broadcast_to(np.eye(3),(x.shape[0],3,3)),sph)
|
return np.einsum('ijk,i->ijk',np.broadcast_to(np.eye(3),(T.shape[0],3,3)),sph)
|
||||||
|
|
||||||
|
|
||||||
def strain_tensor(F,t,m):
|
def strain_tensor(F,t,m):
|
||||||
|
@ -234,73 +235,73 @@ def strain_tensor(F,t,m):
|
||||||
eps
|
eps
|
||||||
|
|
||||||
|
|
||||||
def symmetric(x):
|
def symmetric(T):
|
||||||
"""
|
"""
|
||||||
Return the symmetrized tensor.
|
Return the symmetrized tensor.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Tensor of which the symmetrized values are computed.
|
Tensor of which the symmetrized values are computed.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return (x+transpose(x))*0.5
|
return (T+transpose(T))*0.5
|
||||||
|
|
||||||
|
|
||||||
def transpose(x):
|
def transpose(T):
|
||||||
"""
|
"""
|
||||||
Return the transpose of a tensor.
|
Return the transpose of a tensor.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Tensor of which the transpose is computed.
|
Tensor of which the transpose is computed.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return x.T if np.shape(x) == (3,3) else \
|
return T.T if np.shape(T) == (3,3) else \
|
||||||
np.transpose(x,(0,2,1))
|
np.transpose(T,(0,2,1))
|
||||||
|
|
||||||
|
|
||||||
def __polar_decomposition(x,requested):
|
def __polar_decomposition(T,requested):
|
||||||
"""
|
"""
|
||||||
Singular value decomposition.
|
Singular value decomposition.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Tensor of which the singular values are computed.
|
Tensor of which the singular values are computed.
|
||||||
requested : iterable of str
|
requested : iterable of str
|
||||||
Requested outputs: ‘R’ for the rotation tensor,
|
Requested outputs: ‘R’ for the rotation tensor,
|
||||||
‘V’ for left stretch tensor and ‘U’ for right stretch tensor.
|
‘V’ for left stretch tensor and ‘U’ for right stretch tensor.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
u, s, vh = np.linalg.svd(x)
|
u, s, vh = np.linalg.svd(T)
|
||||||
R = np.dot(u,vh) if np.shape(x) == (3,3) else \
|
R = np.dot(u,vh) if np.shape(T) == (3,3) else \
|
||||||
np.einsum('ijk,ikl->ijl',u,vh)
|
np.einsum('ijk,ikl->ijl',u,vh)
|
||||||
|
|
||||||
output = []
|
output = []
|
||||||
if 'R' in requested:
|
if 'R' in requested:
|
||||||
output.append(R)
|
output.append(R)
|
||||||
if 'V' in requested:
|
if 'V' in requested:
|
||||||
output.append(np.dot(x,R.T) if np.shape(x) == (3,3) else np.einsum('ijk,ilk->ijl',x,R))
|
output.append(np.dot(T,R.T) if np.shape(T) == (3,3) else np.einsum('ijk,ilk->ijl',T,R))
|
||||||
if 'U' in requested:
|
if 'U' in requested:
|
||||||
output.append(np.dot(R.T,x) if np.shape(x) == (3,3) else np.einsum('ikj,ikl->ijl',R,x))
|
output.append(np.dot(R.T,T) if np.shape(T) == (3,3) else np.einsum('ikj,ikl->ijl',R,T))
|
||||||
|
|
||||||
return tuple(output)
|
return tuple(output)
|
||||||
|
|
||||||
|
|
||||||
def __Mises(x,s):
|
def __Mises(T_sym,s):
|
||||||
"""
|
"""
|
||||||
Base equation for Mises equivalent of a stres or strain tensor.
|
Base equation for Mises equivalent of a stres or strain tensor.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
x : numpy.array of shape (:,3,3) or (3,3)
|
T_sym : numpy.array of shape (:,3,3) or (3,3)
|
||||||
Symmetric tensor of which the von Mises equivalent is computed.
|
Symmetric tensor of which the von Mises equivalent is computed.
|
||||||
s : float
|
s : float
|
||||||
Scaling factor (2/3 for strain, 3/2 for stress).
|
Scaling factor (2/3 for strain, 3/2 for stress).
|
||||||
|
|
||||||
"""
|
"""
|
||||||
d = deviatoric_part(x)
|
d = deviatoric_part(T_sym)
|
||||||
return np.sqrt(s*(np.sum(d**2.0))) if np.shape(x) == (3,3) else \
|
return np.sqrt(s*(np.sum(d**2.0))) if np.shape(T_sym) == (3,3) else \
|
||||||
np.sqrt(s*np.einsum('ijk->i',d**2.0))
|
np.sqrt(s*np.einsum('ijk->i',d**2.0))
|
||||||
|
|
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
@ -0,0 +1,837 @@
|
||||||
|
import numpy as np
|
||||||
|
|
||||||
|
from . import Lambert
|
||||||
|
|
||||||
|
P = -1
|
||||||
|
|
||||||
|
def iszero(a):
|
||||||
|
return np.isclose(a,0.0,atol=1.0e-12,rtol=0.0)
|
||||||
|
|
||||||
|
|
||||||
|
class Rotation:
|
||||||
|
u"""
|
||||||
|
Orientation stored with functionality for conversion to different representations.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
D. Rowenhorst et al., Modelling and Simulation in Materials Science and Engineering 23:083501, 2015
|
||||||
|
https://doi.org/10.1088/0965-0393/23/8/083501
|
||||||
|
|
||||||
|
Conventions
|
||||||
|
-----------
|
||||||
|
Convention 1: Coordinate frames are right-handed.
|
||||||
|
Convention 2: A rotation angle ω is taken to be positive for a counterclockwise rotation
|
||||||
|
when viewing from the end point of the rotation axis towards the origin.
|
||||||
|
Convention 3: Rotations will be interpreted in the passive sense.
|
||||||
|
Convention 4: Euler angle triplets are implemented using the Bunge convention,
|
||||||
|
with the angular ranges as [0, 2π],[0, π],[0, 2π].
|
||||||
|
Convention 5: The rotation angle ω is limited to the interval [0, π].
|
||||||
|
Convention 6: the real part of a quaternion is positive, Re(q) > 0
|
||||||
|
Convention 7: P = -1 (as default).
|
||||||
|
|
||||||
|
Usage
|
||||||
|
-----
|
||||||
|
Vector "a" (defined in coordinate system "A") is passively rotated
|
||||||
|
resulting in new coordinates "b" when expressed in system "B".
|
||||||
|
b = Q * a
|
||||||
|
b = np.dot(Q.asMatrix(),a)
|
||||||
|
|
||||||
|
"""
|
||||||
|
|
||||||
|
__slots__ = ['quaternion']
|
||||||
|
|
||||||
|
def __init__(self,quaternion = np.array([1.0,0.0,0.0,0.0])):
|
||||||
|
"""
|
||||||
|
Initializes to identity unless specified.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
quaternion : numpy.ndarray, optional
|
||||||
|
Unit quaternion that follows the conventions. Use .fromQuaternion to perform a sanity check.
|
||||||
|
|
||||||
|
"""
|
||||||
|
self.quaternion = quaternion.copy()
|
||||||
|
|
||||||
|
def __copy__(self):
|
||||||
|
"""Copy."""
|
||||||
|
return self.__class__(self.quaternion)
|
||||||
|
|
||||||
|
copy = __copy__
|
||||||
|
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
"""Orientation displayed as unit quaternion, rotation matrix, and Bunge-Euler angles."""
|
||||||
|
return '\n'.join([
|
||||||
|
'Quaternion: (real={:.3f}, imag=<{:+.3f}, {:+.3f}, {:+.3f}>)'.format(*(self.quaternion)),
|
||||||
|
'Matrix:\n{}'.format(self.asMatrix()),
|
||||||
|
'Bunge Eulers / deg: ({:3.2f}, {:3.2f}, {:3.2f})'.format(*self.asEulers(degrees=True)),
|
||||||
|
])
|
||||||
|
|
||||||
|
|
||||||
|
def __mul__(self, other):
|
||||||
|
"""
|
||||||
|
Multiplication.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : numpy.ndarray or Rotation
|
||||||
|
Vector, second or fourth order tensor, or rotation object that is rotated.
|
||||||
|
|
||||||
|
Todo
|
||||||
|
----
|
||||||
|
Document details active/passive)
|
||||||
|
considere rotation of (3,3,3,3)-matrix
|
||||||
|
|
||||||
|
"""
|
||||||
|
if isinstance(other, Rotation): # rotate a rotation
|
||||||
|
self_q = self.quaternion[0]
|
||||||
|
self_p = self.quaternion[1:]
|
||||||
|
other_q = other.quaternion[0]
|
||||||
|
other_p = other.quaternion[1:]
|
||||||
|
R = self.__class__(np.append(self_q*other_q - np.dot(self_p,other_p),
|
||||||
|
self_q*other_p + other_q*self_p + P * np.cross(self_p,other_p)))
|
||||||
|
return R.standardize()
|
||||||
|
elif isinstance(other, (tuple,np.ndarray)):
|
||||||
|
if isinstance(other,tuple) or other.shape == (3,): # rotate a single (3)-vector or meshgrid
|
||||||
|
A = self.quaternion[0]**2.0 - np.dot(self.quaternion[1:],self.quaternion[1:])
|
||||||
|
B = 2.0 * ( self.quaternion[1]*other[0]
|
||||||
|
+ self.quaternion[2]*other[1]
|
||||||
|
+ self.quaternion[3]*other[2])
|
||||||
|
C = 2.0 * P*self.quaternion[0]
|
||||||
|
|
||||||
|
return np.array([
|
||||||
|
A*other[0] + B*self.quaternion[1] + C*(self.quaternion[2]*other[2] - self.quaternion[3]*other[1]),
|
||||||
|
A*other[1] + B*self.quaternion[2] + C*(self.quaternion[3]*other[0] - self.quaternion[1]*other[2]),
|
||||||
|
A*other[2] + B*self.quaternion[3] + C*(self.quaternion[1]*other[1] - self.quaternion[2]*other[0]),
|
||||||
|
])
|
||||||
|
elif other.shape == (3,3,): # rotate a single (3x3)-matrix
|
||||||
|
return np.dot(self.asMatrix(),np.dot(other,self.asMatrix().T))
|
||||||
|
elif other.shape == (3,3,3,3,):
|
||||||
|
raise NotImplementedError
|
||||||
|
else:
|
||||||
|
return NotImplemented
|
||||||
|
else:
|
||||||
|
return NotImplemented
|
||||||
|
|
||||||
|
|
||||||
|
def inverse(self):
|
||||||
|
"""In-place inverse rotation/backward rotation."""
|
||||||
|
self.quaternion[1:] *= -1
|
||||||
|
return self
|
||||||
|
|
||||||
|
def inversed(self):
|
||||||
|
"""Inverse rotation/backward rotation."""
|
||||||
|
return self.copy().inverse()
|
||||||
|
|
||||||
|
|
||||||
|
def standardize(self):
|
||||||
|
"""In-place quaternion representation with positive q."""
|
||||||
|
if self.quaternion[0] < 0.0: self.quaternion*=-1
|
||||||
|
return self
|
||||||
|
|
||||||
|
def standardized(self):
|
||||||
|
"""Quaternion representation with positive q."""
|
||||||
|
return self.copy().standardize()
|
||||||
|
|
||||||
|
|
||||||
|
def misorientation(self,other):
|
||||||
|
"""
|
||||||
|
Get Misorientation.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : Rotation
|
||||||
|
Rotation to which the misorientation is computed.
|
||||||
|
|
||||||
|
"""
|
||||||
|
return other*self.inversed()
|
||||||
|
|
||||||
|
|
||||||
|
def average(self,other):
|
||||||
|
"""
|
||||||
|
Calculate the average rotation.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : Rotation
|
||||||
|
Rotation from which the average is rotated.
|
||||||
|
|
||||||
|
"""
|
||||||
|
return Rotation.fromAverage([self,other])
|
||||||
|
|
||||||
|
|
||||||
|
################################################################################################
|
||||||
|
# convert to different orientation representations (numpy arrays)
|
||||||
|
|
||||||
|
def asQuaternion(self):
|
||||||
|
"""
|
||||||
|
Unit quaternion [q, p_1, p_2, p_3] unless quaternion == True: damask.quaternion object.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
quaternion : bool, optional
|
||||||
|
return quaternion as DAMASK object.
|
||||||
|
|
||||||
|
"""
|
||||||
|
return self.quaternion
|
||||||
|
|
||||||
|
def asEulers(self,
|
||||||
|
degrees = False):
|
||||||
|
"""
|
||||||
|
Bunge-Euler angles: (φ_1, ϕ, φ_2).
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
degrees : bool, optional
|
||||||
|
return angles in degrees.
|
||||||
|
|
||||||
|
"""
|
||||||
|
eu = Rotation.qu2eu(self.quaternion)
|
||||||
|
if degrees: eu = np.degrees(eu)
|
||||||
|
return eu
|
||||||
|
|
||||||
|
def asAxisAngle(self,
|
||||||
|
degrees = False,
|
||||||
|
pair = False):
|
||||||
|
"""
|
||||||
|
Axis angle representation [n_1, n_2, n_3, ω] unless pair == True: ([n_1, n_2, n_3], ω).
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
degrees : bool, optional
|
||||||
|
return rotation angle in degrees.
|
||||||
|
pair : bool, optional
|
||||||
|
return tuple of axis and angle.
|
||||||
|
|
||||||
|
"""
|
||||||
|
ax = Rotation.qu2ax(self.quaternion)
|
||||||
|
if degrees: ax[3] = np.degrees(ax[3])
|
||||||
|
return (ax[:3],np.degrees(ax[3])) if pair else ax
|
||||||
|
|
||||||
|
def asMatrix(self):
|
||||||
|
"""Rotation matrix."""
|
||||||
|
return Rotation.qu2om(self.quaternion)
|
||||||
|
|
||||||
|
def asRodrigues(self,
|
||||||
|
vector = False):
|
||||||
|
"""
|
||||||
|
Rodrigues-Frank vector representation [n_1, n_2, n_3, tan(ω/2)] unless vector == True: [n_1, n_2, n_3] * tan(ω/2).
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
vector : bool, optional
|
||||||
|
return as actual Rodrigues--Frank vector, i.e. rotation axis scaled by tan(ω/2).
|
||||||
|
|
||||||
|
"""
|
||||||
|
ro = Rotation.qu2ro(self.quaternion)
|
||||||
|
return ro[:3]*ro[3] if vector else ro
|
||||||
|
|
||||||
|
def asHomochoric(self):
|
||||||
|
"""Homochoric vector: (h_1, h_2, h_3)."""
|
||||||
|
return Rotation.qu2ho(self.quaternion)
|
||||||
|
|
||||||
|
def asCubochoric(self):
|
||||||
|
"""Cubochoric vector: (c_1, c_2, c_3)."""
|
||||||
|
return Rotation.qu2cu(self.quaternion)
|
||||||
|
|
||||||
|
def asM(self):
|
||||||
|
"""
|
||||||
|
Intermediate representation supporting quaternion averaging.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
F. Landis Markley et al., Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
|
||||||
|
https://doi.org/10.2514/1.28949
|
||||||
|
|
||||||
|
"""
|
||||||
|
return np.outer(self.quaternion,self.quaternion)
|
||||||
|
|
||||||
|
|
||||||
|
################################################################################################
|
||||||
|
# static constructors. The input data needs to follow the convention, options allow to
|
||||||
|
# relax these convections
|
||||||
|
@staticmethod
|
||||||
|
def fromQuaternion(quaternion,
|
||||||
|
acceptHomomorph = False,
|
||||||
|
P = -1):
|
||||||
|
|
||||||
|
qu = quaternion if isinstance(quaternion,np.ndarray) and quaternion.dtype == np.dtype(float) \
|
||||||
|
else np.array(quaternion,dtype=float)
|
||||||
|
if P > 0: qu[1:4] *= -1 # convert from P=1 to P=-1
|
||||||
|
if qu[0] < 0.0:
|
||||||
|
if acceptHomomorph:
|
||||||
|
qu *= -1.
|
||||||
|
else:
|
||||||
|
raise ValueError('Quaternion has negative first component.\n{}'.format(qu[0]))
|
||||||
|
if not np.isclose(np.linalg.norm(qu), 1.0):
|
||||||
|
raise ValueError('Quaternion is not of unit length.\n{} {} {} {}'.format(*qu))
|
||||||
|
|
||||||
|
return Rotation(qu)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromEulers(eulers,
|
||||||
|
degrees = False):
|
||||||
|
|
||||||
|
eu = eulers if isinstance(eulers, np.ndarray) and eulers.dtype == np.dtype(float) \
|
||||||
|
else np.array(eulers,dtype=float)
|
||||||
|
eu = np.radians(eu) if degrees else eu
|
||||||
|
if np.any(eu < 0.0) or np.any(eu > 2.0*np.pi) or eu[1] > np.pi:
|
||||||
|
raise ValueError('Euler angles outside of [0..2π],[0..π],[0..2π].\n{} {} {}.'.format(*eu))
|
||||||
|
|
||||||
|
return Rotation(Rotation.eu2qu(eu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromAxisAngle(angleAxis,
|
||||||
|
degrees = False,
|
||||||
|
normalise = False,
|
||||||
|
P = -1):
|
||||||
|
|
||||||
|
ax = angleAxis if isinstance(angleAxis, np.ndarray) and angleAxis.dtype == np.dtype(float) \
|
||||||
|
else np.array(angleAxis,dtype=float)
|
||||||
|
if P > 0: ax[0:3] *= -1 # convert from P=1 to P=-1
|
||||||
|
if degrees: ax[ 3] = np.radians(ax[3])
|
||||||
|
if normalise: ax[0:3] /= np.linalg.norm(ax[0:3])
|
||||||
|
if ax[3] < 0.0 or ax[3] > np.pi:
|
||||||
|
raise ValueError('Axis angle rotation angle outside of [0..π].\n'.format(ax[3]))
|
||||||
|
if not np.isclose(np.linalg.norm(ax[0:3]), 1.0):
|
||||||
|
raise ValueError('Axis angle rotation axis is not of unit length.\n{} {} {}'.format(*ax[0:3]))
|
||||||
|
|
||||||
|
return Rotation(Rotation.ax2qu(ax))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromBasis(basis,
|
||||||
|
orthonormal = True,
|
||||||
|
reciprocal = False,
|
||||||
|
):
|
||||||
|
|
||||||
|
om = basis if isinstance(basis, np.ndarray) else np.array(basis).reshape((3,3))
|
||||||
|
if reciprocal:
|
||||||
|
om = np.linalg.inv(om.T/np.pi) # transform reciprocal basis set
|
||||||
|
orthonormal = False # contains stretch
|
||||||
|
if not orthonormal:
|
||||||
|
(U,S,Vh) = np.linalg.svd(om) # singular value decomposition
|
||||||
|
om = np.dot(U,Vh)
|
||||||
|
if not np.isclose(np.linalg.det(om),1.0):
|
||||||
|
raise ValueError('matrix is not a proper rotation.\n{}'.format(om))
|
||||||
|
if not np.isclose(np.dot(om[0],om[1]), 0.0) \
|
||||||
|
or not np.isclose(np.dot(om[1],om[2]), 0.0) \
|
||||||
|
or not np.isclose(np.dot(om[2],om[0]), 0.0):
|
||||||
|
raise ValueError('matrix is not orthogonal.\n{}'.format(om))
|
||||||
|
|
||||||
|
return Rotation(Rotation.om2qu(om))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromMatrix(om,
|
||||||
|
):
|
||||||
|
|
||||||
|
return Rotation.fromBasis(om)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromRodrigues(rodrigues,
|
||||||
|
normalise = False,
|
||||||
|
P = -1):
|
||||||
|
|
||||||
|
ro = rodrigues if isinstance(rodrigues, np.ndarray) and rodrigues.dtype == np.dtype(float) \
|
||||||
|
else np.array(rodrigues,dtype=float)
|
||||||
|
if P > 0: ro[0:3] *= -1 # convert from P=1 to P=-1
|
||||||
|
if normalise: ro[0:3] /= np.linalg.norm(ro[0:3])
|
||||||
|
if not np.isclose(np.linalg.norm(ro[0:3]), 1.0):
|
||||||
|
raise ValueError('Rodrigues rotation axis is not of unit length.\n{} {} {}'.format(*ro[0:3]))
|
||||||
|
if ro[3] < 0.0:
|
||||||
|
raise ValueError('Rodriques rotation angle not positive.\n'.format(ro[3]))
|
||||||
|
|
||||||
|
return Rotation(Rotation.ro2qu(ro))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromHomochoric(homochoric,
|
||||||
|
P = -1):
|
||||||
|
|
||||||
|
ho = homochoric if isinstance(homochoric, np.ndarray) and homochoric.dtype == np.dtype(float) \
|
||||||
|
else np.array(homochoric,dtype=float)
|
||||||
|
if P > 0: ho *= -1 # convert from P=1 to P=-1
|
||||||
|
|
||||||
|
return Rotation(Rotation.ho2qu(ho))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromCubochoric(cubochoric,
|
||||||
|
P = -1):
|
||||||
|
|
||||||
|
cu = cubochoric if isinstance(cubochoric, np.ndarray) and cubochoric.dtype == np.dtype(float) \
|
||||||
|
else np.array(cubochoric,dtype=float)
|
||||||
|
ho = Rotation.cu2ho(cu)
|
||||||
|
if P > 0: ho *= -1 # convert from P=1 to P=-1
|
||||||
|
|
||||||
|
return Rotation(Rotation.ho2qu(ho))
|
||||||
|
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromAverage(rotations,
|
||||||
|
weights = []):
|
||||||
|
"""
|
||||||
|
Average rotation.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
F. Landis Markley et al., Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
|
||||||
|
https://doi.org/10.2514/1.28949
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
rotations : list of Rotations
|
||||||
|
Rotations to average from
|
||||||
|
weights : list of floats, optional
|
||||||
|
Weights for each rotation used for averaging
|
||||||
|
|
||||||
|
"""
|
||||||
|
if not all(isinstance(item, Rotation) for item in rotations):
|
||||||
|
raise TypeError("Only instances of Rotation can be averaged.")
|
||||||
|
|
||||||
|
N = len(rotations)
|
||||||
|
if weights == [] or not weights:
|
||||||
|
weights = np.ones(N,dtype='i')
|
||||||
|
|
||||||
|
for i,(r,n) in enumerate(zip(rotations,weights)):
|
||||||
|
M = r.asM() * n if i == 0 \
|
||||||
|
else M + r.asM() * n # noqa add (multiples) of this rotation to average noqa
|
||||||
|
eig, vec = np.linalg.eig(M/N)
|
||||||
|
|
||||||
|
return Rotation.fromQuaternion(np.real(vec.T[eig.argmax()]),acceptHomomorph = True)
|
||||||
|
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromRandom():
|
||||||
|
r = np.random.random(3)
|
||||||
|
A = np.sqrt(r[2])
|
||||||
|
B = np.sqrt(1.0-r[2])
|
||||||
|
return Rotation(np.array([np.cos(2.0*np.pi*r[0])*A,
|
||||||
|
np.sin(2.0*np.pi*r[1])*B,
|
||||||
|
np.cos(2.0*np.pi*r[1])*B,
|
||||||
|
np.sin(2.0*np.pi*r[0])*A])).standardize()
|
||||||
|
|
||||||
|
|
||||||
|
####################################################################################################
|
||||||
|
# Code below available according to the following conditions on https://github.com/MarDiehl/3Drotations
|
||||||
|
####################################################################################################
|
||||||
|
# Copyright (c) 2017-2019, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
|
||||||
|
# Copyright (c) 2013-2014, Marc De Graef/Carnegie Mellon University
|
||||||
|
# All rights reserved.
|
||||||
|
#
|
||||||
|
# Redistribution and use in source and binary forms, with or without modification, are
|
||||||
|
# permitted provided that the following conditions are met:
|
||||||
|
#
|
||||||
|
# - Redistributions of source code must retain the above copyright notice, this list
|
||||||
|
# of conditions and the following disclaimer.
|
||||||
|
# - Redistributions in binary form must reproduce the above copyright notice, this
|
||||||
|
# list of conditions and the following disclaimer in the documentation and/or
|
||||||
|
# other materials provided with the distribution.
|
||||||
|
# - Neither the names of Marc De Graef, Carnegie Mellon University nor the names
|
||||||
|
# of its contributors may be used to endorse or promote products derived from
|
||||||
|
# this software without specific prior written permission.
|
||||||
|
#
|
||||||
|
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
||||||
|
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||||
|
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
||||||
|
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
|
||||||
|
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
||||||
|
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
||||||
|
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
||||||
|
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
|
||||||
|
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
|
||||||
|
# USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||||
|
####################################################################################################
|
||||||
|
#---------- Quaternion ----------
|
||||||
|
@staticmethod
|
||||||
|
def qu2om(qu):
|
||||||
|
"""Quaternion to rotation matrix."""
|
||||||
|
qq = qu[0]**2-(qu[1]**2 + qu[2]**2 + qu[3]**2)
|
||||||
|
om = np.diag(qq + 2.0*np.array([qu[1],qu[2],qu[3]])**2)
|
||||||
|
|
||||||
|
om[1,0] = 2.0*(qu[2]*qu[1]+qu[0]*qu[3])
|
||||||
|
om[0,1] = 2.0*(qu[1]*qu[2]-qu[0]*qu[3])
|
||||||
|
om[2,1] = 2.0*(qu[3]*qu[2]+qu[0]*qu[1])
|
||||||
|
om[1,2] = 2.0*(qu[2]*qu[3]-qu[0]*qu[1])
|
||||||
|
om[0,2] = 2.0*(qu[1]*qu[3]+qu[0]*qu[2])
|
||||||
|
om[2,0] = 2.0*(qu[3]*qu[1]-qu[0]*qu[2])
|
||||||
|
return om if P > 0.0 else om.T
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def qu2eu(qu):
|
||||||
|
"""Quaternion to Bunge-Euler angles."""
|
||||||
|
q03 = qu[0]**2+qu[3]**2
|
||||||
|
q12 = qu[1]**2+qu[2]**2
|
||||||
|
chi = np.sqrt(q03*q12)
|
||||||
|
|
||||||
|
if iszero(chi):
|
||||||
|
eu = np.array([np.arctan2(-P*2.0*qu[0]*qu[3],qu[0]**2-qu[3]**2), 0.0, 0.0]) if iszero(q12) else \
|
||||||
|
np.array([np.arctan2(2.0*qu[1]*qu[2],qu[1]**2-qu[2]**2), np.pi, 0.0])
|
||||||
|
else:
|
||||||
|
eu = np.array([np.arctan2((-P*qu[0]*qu[2]+qu[1]*qu[3])*chi, (-P*qu[0]*qu[1]-qu[2]*qu[3])*chi ),
|
||||||
|
np.arctan2( 2.0*chi, q03-q12 ),
|
||||||
|
np.arctan2(( P*qu[0]*qu[2]+qu[1]*qu[3])*chi, (-P*qu[0]*qu[1]+qu[2]*qu[3])*chi )])
|
||||||
|
|
||||||
|
# reduce Euler angles to definition range, i.e a lower limit of 0.0
|
||||||
|
eu = np.where(eu<0, (eu+2.0*np.pi)%np.array([2.0*np.pi,np.pi,2.0*np.pi]),eu)
|
||||||
|
return eu
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def qu2ax(qu):
|
||||||
|
"""
|
||||||
|
Quaternion to axis angle pair.
|
||||||
|
|
||||||
|
Modified version of the original formulation, should be numerically more stable
|
||||||
|
"""
|
||||||
|
if iszero(qu[1]**2+qu[2]**2+qu[3]**2): # set axis to [001] if the angle is 0/360
|
||||||
|
ax = [ 0.0, 0.0, 1.0, 0.0 ]
|
||||||
|
elif not iszero(qu[0]):
|
||||||
|
s = np.sign(qu[0])/np.sqrt(qu[1]**2+qu[2]**2+qu[3]**2)
|
||||||
|
omega = 2.0 * np.arccos(np.clip(qu[0],-1.0,1.0))
|
||||||
|
ax = [ qu[1]*s, qu[2]*s, qu[3]*s, omega ]
|
||||||
|
else:
|
||||||
|
ax = [ qu[1], qu[2], qu[3], np.pi]
|
||||||
|
return np.array(ax)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def qu2ro(qu):
|
||||||
|
"""Quaternion to Rodriques-Frank vector."""
|
||||||
|
if iszero(qu[0]):
|
||||||
|
ro = [qu[1], qu[2], qu[3], np.inf]
|
||||||
|
else:
|
||||||
|
s = np.linalg.norm([qu[1],qu[2],qu[3]])
|
||||||
|
ro = [0.0,0.0,P,0.0] if iszero(s) else \
|
||||||
|
[ qu[1]/s, qu[2]/s, qu[3]/s, np.tan(np.arccos(np.clip(qu[0],-1.0,1.0)))]
|
||||||
|
return np.array(ro)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def qu2ho(qu):
|
||||||
|
"""Quaternion to homochoric vector."""
|
||||||
|
omega = 2.0 * np.arccos(np.clip(qu[0],-1.0,1.0))
|
||||||
|
|
||||||
|
if iszero(omega):
|
||||||
|
ho = np.array([ 0.0, 0.0, 0.0 ])
|
||||||
|
else:
|
||||||
|
ho = np.array([qu[1], qu[2], qu[3]])
|
||||||
|
f = 0.75 * ( omega - np.sin(omega) )
|
||||||
|
ho = ho/np.linalg.norm(ho) * f**(1./3.)
|
||||||
|
return ho
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def qu2cu(qu):
|
||||||
|
"""Quaternion to cubochoric vector."""
|
||||||
|
return Rotation.ho2cu(Rotation.qu2ho(qu))
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Rotation matrix ----------
|
||||||
|
@staticmethod
|
||||||
|
def om2qu(om):
|
||||||
|
"""
|
||||||
|
Rotation matrix to quaternion.
|
||||||
|
|
||||||
|
The original formulation (direct conversion) had (numerical?) issues
|
||||||
|
"""
|
||||||
|
return Rotation.eu2qu(Rotation.om2eu(om))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def om2eu(om):
|
||||||
|
"""Rotation matrix to Bunge-Euler angles."""
|
||||||
|
if abs(om[2,2]) < 1.0:
|
||||||
|
zeta = 1.0/np.sqrt(1.0-om[2,2]**2)
|
||||||
|
eu = np.array([np.arctan2(om[2,0]*zeta,-om[2,1]*zeta),
|
||||||
|
np.arccos(om[2,2]),
|
||||||
|
np.arctan2(om[0,2]*zeta, om[1,2]*zeta)])
|
||||||
|
else:
|
||||||
|
eu = np.array([np.arctan2( om[0,1],om[0,0]), np.pi*0.5*(1-om[2,2]),0.0]) # following the paper, not the reference implementation
|
||||||
|
|
||||||
|
# reduce Euler angles to definition range, i.e a lower limit of 0.0
|
||||||
|
eu = np.where(eu<0, (eu+2.0*np.pi)%np.array([2.0*np.pi,np.pi,2.0*np.pi]),eu)
|
||||||
|
return eu
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def om2ax(om):
|
||||||
|
"""Rotation matrix to axis angle pair."""
|
||||||
|
ax=np.empty(4)
|
||||||
|
|
||||||
|
# first get the rotation angle
|
||||||
|
t = 0.5*(om.trace() -1.0)
|
||||||
|
ax[3] = np.arccos(np.clip(t,-1.0,1.0))
|
||||||
|
|
||||||
|
if iszero(ax[3]):
|
||||||
|
ax = [ 0.0, 0.0, 1.0, 0.0]
|
||||||
|
else:
|
||||||
|
w,vr = np.linalg.eig(om)
|
||||||
|
# next, find the eigenvalue (1,0j)
|
||||||
|
i = np.where(np.isclose(w,1.0+0.0j))[0][0]
|
||||||
|
ax[0:3] = np.real(vr[0:3,i])
|
||||||
|
diagDelta = np.array([om[1,2]-om[2,1],om[2,0]-om[0,2],om[0,1]-om[1,0]])
|
||||||
|
ax[0:3] = np.where(iszero(diagDelta), ax[0:3],np.abs(ax[0:3])*np.sign(-P*diagDelta))
|
||||||
|
return np.array(ax)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def om2ro(om):
|
||||||
|
"""Rotation matrix to Rodriques-Frank vector."""
|
||||||
|
return Rotation.eu2ro(Rotation.om2eu(om))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def om2ho(om):
|
||||||
|
"""Rotation matrix to homochoric vector."""
|
||||||
|
return Rotation.ax2ho(Rotation.om2ax(om))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def om2cu(om):
|
||||||
|
"""Rotation matrix to cubochoric vector."""
|
||||||
|
return Rotation.ho2cu(Rotation.om2ho(om))
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Bunge-Euler angles ----------
|
||||||
|
@staticmethod
|
||||||
|
def eu2qu(eu):
|
||||||
|
"""Bunge-Euler angles to quaternion."""
|
||||||
|
ee = 0.5*eu
|
||||||
|
cPhi = np.cos(ee[1])
|
||||||
|
sPhi = np.sin(ee[1])
|
||||||
|
qu = np.array([ cPhi*np.cos(ee[0]+ee[2]),
|
||||||
|
-P*sPhi*np.cos(ee[0]-ee[2]),
|
||||||
|
-P*sPhi*np.sin(ee[0]-ee[2]),
|
||||||
|
-P*cPhi*np.sin(ee[0]+ee[2]) ])
|
||||||
|
if qu[0] < 0.0: qu*=-1
|
||||||
|
return qu
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def eu2om(eu):
|
||||||
|
"""Bunge-Euler angles to rotation matrix."""
|
||||||
|
c = np.cos(eu)
|
||||||
|
s = np.sin(eu)
|
||||||
|
|
||||||
|
om = np.array([[+c[0]*c[2]-s[0]*s[2]*c[1], +s[0]*c[2]+c[0]*s[2]*c[1], +s[2]*s[1]],
|
||||||
|
[-c[0]*s[2]-s[0]*c[2]*c[1], -s[0]*s[2]+c[0]*c[2]*c[1], +c[2]*s[1]],
|
||||||
|
[+s[0]*s[1], -c[0]*s[1], +c[1] ]])
|
||||||
|
|
||||||
|
om[np.where(iszero(om))] = 0.0
|
||||||
|
return om
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def eu2ax(eu):
|
||||||
|
"""Bunge-Euler angles to axis angle pair."""
|
||||||
|
t = np.tan(eu[1]*0.5)
|
||||||
|
sigma = 0.5*(eu[0]+eu[2])
|
||||||
|
delta = 0.5*(eu[0]-eu[2])
|
||||||
|
tau = np.linalg.norm([t,np.sin(sigma)])
|
||||||
|
alpha = np.pi if iszero(np.cos(sigma)) else \
|
||||||
|
2.0*np.arctan(tau/np.cos(sigma))
|
||||||
|
|
||||||
|
if iszero(alpha):
|
||||||
|
ax = np.array([ 0.0, 0.0, 1.0, 0.0 ])
|
||||||
|
else:
|
||||||
|
ax = -P/tau * np.array([ t*np.cos(delta), t*np.sin(delta), np.sin(sigma) ]) # passive axis angle pair so a minus sign in front
|
||||||
|
ax = np.append(ax,alpha)
|
||||||
|
if alpha < 0.0: ax *= -1.0 # ensure alpha is positive
|
||||||
|
return ax
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def eu2ro(eu):
|
||||||
|
"""Bunge-Euler angles to Rodriques-Frank vector."""
|
||||||
|
ro = Rotation.eu2ax(eu) # convert to axis angle pair representation
|
||||||
|
if ro[3] >= np.pi: # Differs from original implementation. check convention 5
|
||||||
|
ro[3] = np.inf
|
||||||
|
elif iszero(ro[3]):
|
||||||
|
ro = np.array([ 0.0, 0.0, P, 0.0 ])
|
||||||
|
else:
|
||||||
|
ro[3] = np.tan(ro[3]*0.5)
|
||||||
|
return ro
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def eu2ho(eu):
|
||||||
|
"""Bunge-Euler angles to homochoric vector."""
|
||||||
|
return Rotation.ax2ho(Rotation.eu2ax(eu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def eu2cu(eu):
|
||||||
|
"""Bunge-Euler angles to cubochoric vector."""
|
||||||
|
return Rotation.ho2cu(Rotation.eu2ho(eu))
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Axis angle pair ----------
|
||||||
|
@staticmethod
|
||||||
|
def ax2qu(ax):
|
||||||
|
"""Axis angle pair to quaternion."""
|
||||||
|
if iszero(ax[3]):
|
||||||
|
qu = np.array([ 1.0, 0.0, 0.0, 0.0 ])
|
||||||
|
else:
|
||||||
|
c = np.cos(ax[3]*0.5)
|
||||||
|
s = np.sin(ax[3]*0.5)
|
||||||
|
qu = np.array([ c, ax[0]*s, ax[1]*s, ax[2]*s ])
|
||||||
|
return qu
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ax2om(ax):
|
||||||
|
"""Axis angle pair to rotation matrix."""
|
||||||
|
c = np.cos(ax[3])
|
||||||
|
s = np.sin(ax[3])
|
||||||
|
omc = 1.0-c
|
||||||
|
om=np.diag(ax[0:3]**2*omc + c)
|
||||||
|
|
||||||
|
for idx in [[0,1,2],[1,2,0],[2,0,1]]:
|
||||||
|
q = omc*ax[idx[0]] * ax[idx[1]]
|
||||||
|
om[idx[0],idx[1]] = q + s*ax[idx[2]]
|
||||||
|
om[idx[1],idx[0]] = q - s*ax[idx[2]]
|
||||||
|
return om if P < 0.0 else om.T
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ax2eu(ax):
|
||||||
|
"""Rotation matrix to Bunge Euler angles."""
|
||||||
|
return Rotation.om2eu(Rotation.ax2om(ax))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ax2ro(ax):
|
||||||
|
"""Axis angle pair to Rodriques-Frank vector."""
|
||||||
|
if iszero(ax[3]):
|
||||||
|
ro = [ 0.0, 0.0, P, 0.0 ]
|
||||||
|
else:
|
||||||
|
ro = [ax[0], ax[1], ax[2]]
|
||||||
|
# 180 degree case
|
||||||
|
ro += [np.inf] if np.isclose(ax[3],np.pi,atol=1.0e-15,rtol=0.0) else \
|
||||||
|
[np.tan(ax[3]*0.5)]
|
||||||
|
return np.array(ro)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ax2ho(ax):
|
||||||
|
"""Axis angle pair to homochoric vector."""
|
||||||
|
f = (0.75 * ( ax[3] - np.sin(ax[3]) ))**(1.0/3.0)
|
||||||
|
ho = ax[0:3] * f
|
||||||
|
return ho
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ax2cu(ax):
|
||||||
|
"""Axis angle pair to cubochoric vector."""
|
||||||
|
return Rotation.ho2cu(Rotation.ax2ho(ax))
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Rodrigues-Frank vector ----------
|
||||||
|
@staticmethod
|
||||||
|
def ro2qu(ro):
|
||||||
|
"""Rodriques-Frank vector to quaternion."""
|
||||||
|
return Rotation.ax2qu(Rotation.ro2ax(ro))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ro2om(ro):
|
||||||
|
"""Rodgrigues-Frank vector to rotation matrix."""
|
||||||
|
return Rotation.ax2om(Rotation.ro2ax(ro))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ro2eu(ro):
|
||||||
|
"""Rodriques-Frank vector to Bunge-Euler angles."""
|
||||||
|
return Rotation.om2eu(Rotation.ro2om(ro))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ro2ax(ro):
|
||||||
|
"""Rodriques-Frank vector to axis angle pair."""
|
||||||
|
ta = ro[3]
|
||||||
|
|
||||||
|
if iszero(ta):
|
||||||
|
ax = [ 0.0, 0.0, 1.0, 0.0 ]
|
||||||
|
elif not np.isfinite(ta):
|
||||||
|
ax = [ ro[0], ro[1], ro[2], np.pi ]
|
||||||
|
else:
|
||||||
|
angle = 2.0*np.arctan(ta)
|
||||||
|
ta = 1.0/np.linalg.norm(ro[0:3])
|
||||||
|
ax = [ ro[0]/ta, ro[1]/ta, ro[2]/ta, angle ]
|
||||||
|
return np.array(ax)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ro2ho(ro):
|
||||||
|
"""Rodriques-Frank vector to homochoric vector."""
|
||||||
|
if iszero(np.sum(ro[0:3]**2.0)):
|
||||||
|
ho = [ 0.0, 0.0, 0.0 ]
|
||||||
|
else:
|
||||||
|
f = 2.0*np.arctan(ro[3]) -np.sin(2.0*np.arctan(ro[3])) if np.isfinite(ro[3]) else np.pi
|
||||||
|
ho = ro[0:3] * (0.75*f)**(1.0/3.0)
|
||||||
|
return np.array(ho)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ro2cu(ro):
|
||||||
|
"""Rodriques-Frank vector to cubochoric vector."""
|
||||||
|
return Rotation.ho2cu(Rotation.ro2ho(ro))
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Homochoric vector----------
|
||||||
|
@staticmethod
|
||||||
|
def ho2qu(ho):
|
||||||
|
"""Homochoric vector to quaternion."""
|
||||||
|
return Rotation.ax2qu(Rotation.ho2ax(ho))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ho2om(ho):
|
||||||
|
"""Homochoric vector to rotation matrix."""
|
||||||
|
return Rotation.ax2om(Rotation.ho2ax(ho))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ho2eu(ho):
|
||||||
|
"""Homochoric vector to Bunge-Euler angles."""
|
||||||
|
return Rotation.ax2eu(Rotation.ho2ax(ho))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ho2ax(ho):
|
||||||
|
"""Homochoric vector to axis angle pair."""
|
||||||
|
tfit = np.array([+1.0000000000018852, -0.5000000002194847,
|
||||||
|
-0.024999992127593126, -0.003928701544781374,
|
||||||
|
-0.0008152701535450438, -0.0002009500426119712,
|
||||||
|
-0.00002397986776071756, -0.00008202868926605841,
|
||||||
|
+0.00012448715042090092, -0.0001749114214822577,
|
||||||
|
+0.0001703481934140054, -0.00012062065004116828,
|
||||||
|
+0.000059719705868660826, -0.00001980756723965647,
|
||||||
|
+0.000003953714684212874, -0.00000036555001439719544])
|
||||||
|
# normalize h and store the magnitude
|
||||||
|
hmag_squared = np.sum(ho**2.)
|
||||||
|
if iszero(hmag_squared):
|
||||||
|
ax = np.array([ 0.0, 0.0, 1.0, 0.0 ])
|
||||||
|
else:
|
||||||
|
hm = hmag_squared
|
||||||
|
|
||||||
|
# convert the magnitude to the rotation angle
|
||||||
|
s = tfit[0] + tfit[1] * hmag_squared
|
||||||
|
for i in range(2,16):
|
||||||
|
hm *= hmag_squared
|
||||||
|
s += tfit[i] * hm
|
||||||
|
ax = np.append(ho/np.sqrt(hmag_squared),2.0*np.arccos(np.clip(s,-1.0,1.0)))
|
||||||
|
return ax
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ho2ro(ho):
|
||||||
|
"""Axis angle pair to Rodriques-Frank vector."""
|
||||||
|
return Rotation.ax2ro(Rotation.ho2ax(ho))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ho2cu(ho):
|
||||||
|
"""Homochoric vector to cubochoric vector."""
|
||||||
|
return Lambert.BallToCube(ho)
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Cubochoric ----------
|
||||||
|
@staticmethod
|
||||||
|
def cu2qu(cu):
|
||||||
|
"""Cubochoric vector to quaternion."""
|
||||||
|
return Rotation.ho2qu(Rotation.cu2ho(cu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def cu2om(cu):
|
||||||
|
"""Cubochoric vector to rotation matrix."""
|
||||||
|
return Rotation.ho2om(Rotation.cu2ho(cu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def cu2eu(cu):
|
||||||
|
"""Cubochoric vector to Bunge-Euler angles."""
|
||||||
|
return Rotation.ho2eu(Rotation.cu2ho(cu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def cu2ax(cu):
|
||||||
|
"""Cubochoric vector to axis angle pair."""
|
||||||
|
return Rotation.ho2ax(Rotation.cu2ho(cu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def cu2ro(cu):
|
||||||
|
"""Cubochoric vector to Rodriques-Frank vector."""
|
||||||
|
return Rotation.ho2ro(Rotation.cu2ho(cu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def cu2ho(cu):
|
||||||
|
"""Cubochoric vector to homochoric vector."""
|
||||||
|
return Lambert.CubeToBall(cu)
|
|
@ -32,7 +32,7 @@ class Table():
|
||||||
"""Label data individually, e.g. v v v ==> 1_v 2_v 3_v."""
|
"""Label data individually, e.g. v v v ==> 1_v 2_v 3_v."""
|
||||||
labels = []
|
labels = []
|
||||||
for label,shape in self.shapes.items():
|
for label,shape in self.shapes.items():
|
||||||
size = np.prod(shape)
|
size = int(np.prod(shape))
|
||||||
labels += ['{}{}'.format('' if size == 1 else '{}_'.format(i+1),label) for i in range(size)]
|
labels += ['{}{}'.format('' if size == 1 else '{}_'.format(i+1),label) for i in range(size)]
|
||||||
self.data.columns = labels
|
self.data.columns = labels
|
||||||
|
|
||||||
|
@ -41,14 +41,14 @@ class Table():
|
||||||
"""Label data condensed, e.g. 1_v 2_v 3_v ==> v v v."""
|
"""Label data condensed, e.g. 1_v 2_v 3_v ==> v v v."""
|
||||||
labels = []
|
labels = []
|
||||||
for label,shape in self.shapes.items():
|
for label,shape in self.shapes.items():
|
||||||
labels += [label] * np.prod(shape)
|
labels += [label] * int(np.prod(shape))
|
||||||
self.data.columns = labels
|
self.data.columns = labels
|
||||||
|
|
||||||
|
|
||||||
def __add_comment(self,label,shape,info):
|
def __add_comment(self,label,shape,info):
|
||||||
if info is not None:
|
if info is not None:
|
||||||
self.comments.append('{}{}: {}'.format(label,
|
self.comments.append('{}{}: {}'.format(label,
|
||||||
' '+str(shape) if np.prod(shape) > 1 else '',
|
' '+str(shape) if np.prod(shape,dtype=int) > 1 else '',
|
||||||
info))
|
info))
|
||||||
|
|
||||||
|
|
||||||
|
|
|
@ -6,8 +6,6 @@ import shlex
|
||||||
from fractions import Fraction
|
from fractions import Fraction
|
||||||
from functools import reduce
|
from functools import reduce
|
||||||
from optparse import Option
|
from optparse import Option
|
||||||
from queue import Queue
|
|
||||||
from threading import Thread
|
|
||||||
|
|
||||||
import numpy as np
|
import numpy as np
|
||||||
|
|
||||||
|
@ -40,218 +38,212 @@ class bcolors:
|
||||||
self.BOLD = ''
|
self.BOLD = ''
|
||||||
self.UNDERLINE = ''
|
self.UNDERLINE = ''
|
||||||
self.CROSSOUT = ''
|
self.CROSSOUT = ''
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def srepr(arg,glue = '\n'):
|
def srepr(arg,glue = '\n'):
|
||||||
"""Joins arguments as individual lines."""
|
r"""
|
||||||
if (not hasattr(arg, "strip") and
|
Join arguments as individual lines.
|
||||||
(hasattr(arg, "__getitem__") or
|
|
||||||
hasattr(arg, "__iter__"))):
|
Parameters
|
||||||
return glue.join(str(x) for x in arg)
|
----------
|
||||||
return arg if isinstance(arg,str) else repr(arg)
|
arg : iterable
|
||||||
|
Items to join.
|
||||||
|
glue : str, optional
|
||||||
|
Defaults to \n.
|
||||||
|
|
||||||
|
"""
|
||||||
|
if (not hasattr(arg, "strip") and
|
||||||
|
(hasattr(arg, "__getitem__") or
|
||||||
|
hasattr(arg, "__iter__"))):
|
||||||
|
return glue.join(str(x) for x in arg)
|
||||||
|
return arg if isinstance(arg,str) else repr(arg)
|
||||||
|
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def croak(what, newline = True):
|
def croak(what, newline = True):
|
||||||
"""Writes formated to stderr."""
|
"""
|
||||||
if what is not None:
|
Write formated to stderr.
|
||||||
sys.stderr.write(srepr(what,glue = '\n') + ('\n' if newline else ''))
|
|
||||||
sys.stderr.flush()
|
Parameters
|
||||||
|
----------
|
||||||
|
what : str or iterable
|
||||||
|
Content to be displayed
|
||||||
|
newline : bool, optional
|
||||||
|
Separate items of what by newline. Defaults to True.
|
||||||
|
|
||||||
|
"""
|
||||||
|
if not what:
|
||||||
|
sys.stderr.write(srepr(what,glue = '\n') + ('\n' if newline else ''))
|
||||||
|
sys.stderr.flush()
|
||||||
|
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def report(who = None,
|
def report(who = None,
|
||||||
what = None):
|
what = None):
|
||||||
"""Reports script and file name."""
|
"""
|
||||||
croak( (emph(who)+': ' if who is not None else '') + (what if what is not None else '') + '\n' )
|
Reports script and file name.
|
||||||
|
|
||||||
|
DEPRECATED
|
||||||
|
|
||||||
|
"""
|
||||||
|
croak( (emph(who)+': ' if who is not None else '') + (what if what is not None else '') + '\n' )
|
||||||
|
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def emph(what):
|
def emph(what):
|
||||||
"""Formats string with emphasis."""
|
"""Formats string with emphasis."""
|
||||||
return bcolors.BOLD+srepr(what)+bcolors.ENDC
|
return bcolors.BOLD+srepr(what)+bcolors.ENDC
|
||||||
|
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def deemph(what):
|
def deemph(what):
|
||||||
"""Formats string with deemphasis."""
|
"""Formats string with deemphasis."""
|
||||||
return bcolors.DIM+srepr(what)+bcolors.ENDC
|
return bcolors.DIM+srepr(what)+bcolors.ENDC
|
||||||
|
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def delete(what):
|
def delete(what):
|
||||||
"""Formats string as deleted."""
|
"""Formats string as deleted."""
|
||||||
return bcolors.DIM+srepr(what)+bcolors.ENDC
|
return bcolors.DIM+srepr(what)+bcolors.ENDC
|
||||||
|
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def strikeout(what):
|
def strikeout(what):
|
||||||
"""Formats string as strikeout."""
|
"""Formats string as strikeout."""
|
||||||
return bcolors.CROSSOUT+srepr(what)+bcolors.ENDC
|
return bcolors.CROSSOUT+srepr(what)+bcolors.ENDC
|
||||||
|
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def execute(cmd,
|
def execute(cmd,
|
||||||
streamIn = None,
|
streamIn = None,
|
||||||
wd = './',
|
wd = './',
|
||||||
env = None):
|
env = None):
|
||||||
"""Executes a command in given directory and returns stdout and stderr for optional stdin."""
|
"""
|
||||||
initialPath = os.getcwd()
|
Execute command.
|
||||||
os.chdir(wd)
|
|
||||||
myEnv = os.environ if env is None else env
|
Parameters
|
||||||
process = subprocess.Popen(shlex.split(cmd),
|
----------
|
||||||
stdout = subprocess.PIPE,
|
cmd : str
|
||||||
stderr = subprocess.PIPE,
|
Command to be executed.
|
||||||
stdin = subprocess.PIPE,
|
streanIn :, optional
|
||||||
env = myEnv)
|
Input (via pipe) for executed process.
|
||||||
out,error = [i for i in (process.communicate() if streamIn is None
|
wd : str, optional
|
||||||
else process.communicate(streamIn.read().encode('utf-8')))]
|
Working directory of process. Defaults to ./ .
|
||||||
out = out.decode('utf-8').replace('\x08','')
|
env :
|
||||||
error = error.decode('utf-8').replace('\x08','')
|
Environment
|
||||||
os.chdir(initialPath)
|
|
||||||
if process.returncode != 0: raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
|
"""
|
||||||
return out,error
|
initialPath = os.getcwd()
|
||||||
|
os.chdir(wd)
|
||||||
|
myEnv = os.environ if env is None else env
|
||||||
|
process = subprocess.Popen(shlex.split(cmd),
|
||||||
|
stdout = subprocess.PIPE,
|
||||||
|
stderr = subprocess.PIPE,
|
||||||
|
stdin = subprocess.PIPE,
|
||||||
|
env = myEnv)
|
||||||
|
out,error = [i for i in (process.communicate() if streamIn is None
|
||||||
|
else process.communicate(streamIn.read().encode('utf-8')))]
|
||||||
|
out = out.decode('utf-8').replace('\x08','')
|
||||||
|
error = error.decode('utf-8').replace('\x08','')
|
||||||
|
os.chdir(initialPath)
|
||||||
|
if process.returncode != 0:
|
||||||
|
raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
|
||||||
|
return out,error
|
||||||
|
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
class extendableOption(Option):
|
class extendableOption(Option):
|
||||||
"""
|
"""
|
||||||
Used for definition of new option parser action 'extend', which enables to take multiple option arguments.
|
Used for definition of new option parser action 'extend', which enables to take multiple option arguments.
|
||||||
|
|
||||||
Adopted from online tutorial http://docs.python.org/library/optparse.html
|
Adopted from online tutorial http://docs.python.org/library/optparse.html
|
||||||
"""
|
DEPRECATED
|
||||||
|
"""
|
||||||
|
|
||||||
ACTIONS = Option.ACTIONS + ("extend",)
|
ACTIONS = Option.ACTIONS + ("extend",)
|
||||||
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
|
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
|
||||||
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
|
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
|
||||||
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
|
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
|
||||||
|
|
||||||
|
def take_action(self, action, dest, opt, value, values, parser):
|
||||||
|
if action == "extend":
|
||||||
|
lvalue = value.split(",")
|
||||||
|
values.ensure_value(dest, []).extend(lvalue)
|
||||||
|
else:
|
||||||
|
Option.take_action(self, action, dest, opt, value, values, parser)
|
||||||
|
|
||||||
def take_action(self, action, dest, opt, value, values, parser):
|
|
||||||
if action == "extend":
|
|
||||||
lvalue = value.split(",")
|
|
||||||
values.ensure_value(dest, []).extend(lvalue)
|
|
||||||
else:
|
|
||||||
Option.take_action(self, action, dest, opt, value, values, parser)
|
|
||||||
|
|
||||||
# Print iterations progress
|
|
||||||
# from https://gist.github.com/aubricus/f91fb55dc6ba5557fbab06119420dd6a
|
|
||||||
def progressBar(iteration, total, prefix='', bar_length=50):
|
def progressBar(iteration, total, prefix='', bar_length=50):
|
||||||
"""
|
"""
|
||||||
Call in a loop to create terminal progress bar.
|
Call in a loop to create terminal progress bar.
|
||||||
|
|
||||||
|
From https://gist.github.com/aubricus/f91fb55dc6ba5557fbab06119420dd6a
|
||||||
|
|
||||||
@params:
|
Parameters
|
||||||
iteration - Required : current iteration (Int)
|
----------
|
||||||
total - Required : total iterations (Int)
|
iteration : int
|
||||||
prefix - Optional : prefix string (Str)
|
Current iteration.
|
||||||
bar_length - Optional : character length of bar (Int)
|
total : int
|
||||||
"""
|
Total iterations.
|
||||||
fraction = iteration / float(total)
|
prefix : str, optional
|
||||||
if not hasattr(progressBar, "last_fraction"): # first call to function
|
Prefix string.
|
||||||
progressBar.start_time = time.time()
|
bar_length : int, optional
|
||||||
progressBar.last_fraction = -1.0
|
Character length of bar. Defaults to 50.
|
||||||
remaining_time = ' n/a'
|
|
||||||
else:
|
"""
|
||||||
if fraction <= progressBar.last_fraction or iteration == 0: # reset: called within a new loop
|
fraction = iteration / float(total)
|
||||||
progressBar.start_time = time.time()
|
if not hasattr(progressBar, "last_fraction"): # first call to function
|
||||||
progressBar.last_fraction = -1.0
|
progressBar.start_time = time.time()
|
||||||
remaining_time = ' n/a'
|
progressBar.last_fraction = -1.0
|
||||||
|
remaining_time = ' n/a'
|
||||||
else:
|
else:
|
||||||
progressBar.last_fraction = fraction
|
if fraction <= progressBar.last_fraction or iteration == 0: # reset: called within a new loop
|
||||||
remainder = (total - iteration) * (time.time()-progressBar.start_time)/iteration
|
progressBar.start_time = time.time()
|
||||||
remaining_time = '{: 3d}:'.format(int( remainder//3600)) + \
|
progressBar.last_fraction = -1.0
|
||||||
'{:02d}:'.format(int((remainder//60)%60)) + \
|
remaining_time = ' n/a'
|
||||||
'{:02d}' .format(int( remainder %60))
|
else:
|
||||||
|
progressBar.last_fraction = fraction
|
||||||
|
remainder = (total - iteration) * (time.time()-progressBar.start_time)/iteration
|
||||||
|
remaining_time = '{: 3d}:'.format(int( remainder//3600)) + \
|
||||||
|
'{:02d}:'.format(int((remainder//60)%60)) + \
|
||||||
|
'{:02d}' .format(int( remainder %60))
|
||||||
|
|
||||||
filled_length = int(round(bar_length * fraction))
|
filled_length = int(round(bar_length * fraction))
|
||||||
bar = '█' * filled_length + '░' * (bar_length - filled_length)
|
bar = '█' * filled_length + '░' * (bar_length - filled_length)
|
||||||
|
|
||||||
sys.stderr.write('\r{} {} {}'.format(prefix, bar, remaining_time)),
|
sys.stderr.write('\r{} {} {}'.format(prefix, bar, remaining_time)),
|
||||||
|
|
||||||
if iteration == total: sys.stderr.write('\n')
|
|
||||||
sys.stderr.flush()
|
|
||||||
|
|
||||||
|
if iteration == total:
|
||||||
|
sys.stderr.write('\n')
|
||||||
|
sys.stderr.flush()
|
||||||
|
|
||||||
|
|
||||||
def scale_to_coprime(v):
|
def scale_to_coprime(v):
|
||||||
"""Scale vector to co-prime (relatively prime) integers."""
|
"""Scale vector to co-prime (relatively prime) integers."""
|
||||||
MAX_DENOMINATOR = 1000
|
MAX_DENOMINATOR = 1000
|
||||||
|
|
||||||
def get_square_denominator(x):
|
def get_square_denominator(x):
|
||||||
"""Denominator of the square of a number."""
|
"""Denominator of the square of a number."""
|
||||||
return Fraction(x ** 2).limit_denominator(MAX_DENOMINATOR).denominator
|
return Fraction(x ** 2).limit_denominator(MAX_DENOMINATOR).denominator
|
||||||
|
|
||||||
def lcm(a, b):
|
def lcm(a, b):
|
||||||
"""Least common multiple."""
|
"""Least common multiple."""
|
||||||
return a * b // np.gcd(a, b)
|
return a * b // np.gcd(a, b)
|
||||||
|
|
||||||
denominators = [int(get_square_denominator(i)) for i in v]
|
denominators = [int(get_square_denominator(i)) for i in v]
|
||||||
s = reduce(lcm, denominators) ** 0.5
|
s = reduce(lcm, denominators) ** 0.5
|
||||||
m = (np.array(v)*s).astype(np.int)
|
m = (np.array(v)*s).astype(np.int)
|
||||||
return m//reduce(np.gcd,m)
|
return m//reduce(np.gcd,m)
|
||||||
|
|
||||||
|
|
||||||
class return_message():
|
class return_message():
|
||||||
"""Object with formatted return message."""
|
"""Object with formatted return message."""
|
||||||
|
|
||||||
|
def __init__(self,message):
|
||||||
|
"""
|
||||||
|
Sets return message.
|
||||||
|
|
||||||
def __init__(self,message):
|
Parameters
|
||||||
"""
|
----------
|
||||||
Sets return message.
|
message : str or list of str
|
||||||
|
message for output to screen
|
||||||
|
|
||||||
Parameters
|
"""
|
||||||
----------
|
self.message = message
|
||||||
message : str or list of str
|
|
||||||
message for output to screen
|
def __repr__(self):
|
||||||
|
"""Return message suitable for interactive shells."""
|
||||||
|
return srepr(self.message)
|
||||||
|
|
||||||
"""
|
|
||||||
self.message = message
|
|
||||||
|
|
||||||
def __repr__(self):
|
|
||||||
"""Return message suitable for interactive shells."""
|
|
||||||
return srepr(self.message)
|
|
||||||
|
|
||||||
|
|
||||||
class ThreadPool:
|
|
||||||
"""Pool of threads consuming tasks from a queue."""
|
|
||||||
|
|
||||||
class Worker(Thread):
|
|
||||||
"""Thread executing tasks from a given tasks queue."""
|
|
||||||
|
|
||||||
def __init__(self, tasks):
|
|
||||||
"""Worker for tasks."""
|
|
||||||
Thread.__init__(self)
|
|
||||||
self.tasks = tasks
|
|
||||||
self.daemon = True
|
|
||||||
self.start()
|
|
||||||
|
|
||||||
def run(self):
|
|
||||||
while True:
|
|
||||||
func, args, kargs = self.tasks.get()
|
|
||||||
try:
|
|
||||||
func(*args, **kargs)
|
|
||||||
except Exception as e:
|
|
||||||
# An exception happened in this thread
|
|
||||||
print(e)
|
|
||||||
finally:
|
|
||||||
# Mark this task as done, whether an exception happened or not
|
|
||||||
self.tasks.task_done()
|
|
||||||
|
|
||||||
|
|
||||||
def __init__(self, num_threads):
|
|
||||||
"""
|
|
||||||
Thread pool.
|
|
||||||
|
|
||||||
Parameters
|
|
||||||
----------
|
|
||||||
num_threads : int
|
|
||||||
number of threads
|
|
||||||
|
|
||||||
"""
|
|
||||||
self.tasks = Queue(num_threads)
|
|
||||||
for _ in range(num_threads):
|
|
||||||
self.Worker(self.tasks)
|
|
||||||
|
|
||||||
def add_task(self, func, *args, **kargs):
|
|
||||||
"""Add a task to the queue."""
|
|
||||||
self.tasks.put((func, args, kargs))
|
|
||||||
|
|
||||||
def map(self, func, args_list):
|
|
||||||
"""Add a list of tasks to the queue."""
|
|
||||||
for args in args_list:
|
|
||||||
self.add_task(func, args)
|
|
||||||
|
|
||||||
def wait_completion(self):
|
|
||||||
"""Wait for completion of all the tasks in the queue."""
|
|
||||||
self.tasks.join()
|
|
||||||
|
|
|
@ -0,0 +1,65 @@
|
||||||
|
import os
|
||||||
|
from itertools import permutations
|
||||||
|
|
||||||
|
import pytest
|
||||||
|
import numpy as np
|
||||||
|
|
||||||
|
import damask
|
||||||
|
from damask import Rotation
|
||||||
|
from damask import Orientation
|
||||||
|
from damask import Lattice
|
||||||
|
|
||||||
|
n = 1000
|
||||||
|
|
||||||
|
@pytest.fixture
|
||||||
|
def default():
|
||||||
|
"""A set of n random rotations."""
|
||||||
|
return [Rotation.fromRandom() for r in range(n)]
|
||||||
|
|
||||||
|
@pytest.fixture
|
||||||
|
def reference_dir(reference_dir_base):
|
||||||
|
"""Directory containing reference results."""
|
||||||
|
return os.path.join(reference_dir_base,'Rotation')
|
||||||
|
|
||||||
|
|
||||||
|
class TestOrientation:
|
||||||
|
|
||||||
|
@pytest.mark.parametrize('color',[{'label':'red', 'RGB':[1,0,0],'direction':[0,0,1]},
|
||||||
|
{'label':'green','RGB':[0,1,0],'direction':[0,1,1]},
|
||||||
|
{'label':'blue', 'RGB':[0,0,1],'direction':[1,1,1]}])
|
||||||
|
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
||||||
|
def test_IPF_cubic(self,default,color,lattice):
|
||||||
|
cube = damask.Orientation(damask.Rotation(),lattice)
|
||||||
|
for direction in set(permutations(np.array(color['direction']))):
|
||||||
|
assert np.allclose(cube.IPFcolor(direction),np.array(color['RGB']))
|
||||||
|
|
||||||
|
@pytest.mark.parametrize('lattice',Lattice.lattices)
|
||||||
|
def test_IPF(self,lattice):
|
||||||
|
direction = np.random.random(3)*2.0-1
|
||||||
|
for rot in [Rotation.fromRandom() for r in range(n//100)]:
|
||||||
|
R = damask.Orientation(rot,lattice)
|
||||||
|
color = R.IPFcolor(direction)
|
||||||
|
for equivalent in R.equivalentOrientations():
|
||||||
|
assert np.allclose(color,R.IPFcolor(direction))
|
||||||
|
|
||||||
|
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
|
||||||
|
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
||||||
|
def test_relationship_forward_backward(self,model,lattice):
|
||||||
|
ori = Orientation(Rotation.fromRandom(),lattice)
|
||||||
|
for i,r in enumerate(ori.relatedOrientations(model)):
|
||||||
|
ori2 = r.relatedOrientations(model)[i]
|
||||||
|
misorientation = ori.rotation.misorientation(ori2.rotation)
|
||||||
|
assert misorientation.asAxisAngle(degrees=True)[3]<1.0e-5
|
||||||
|
|
||||||
|
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
|
||||||
|
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
||||||
|
def test_relationship_reference(self,update,reference_dir,model,lattice):
|
||||||
|
reference = os.path.join(reference_dir,'{}_{}.txt'.format(lattice,model))
|
||||||
|
ori = Orientation(Rotation(),lattice)
|
||||||
|
eu = np.array([o.rotation.asEulers(degrees=True) for o in ori.relatedOrientations(model)])
|
||||||
|
if update:
|
||||||
|
coords = np.array([(1,i+1) for i,x in enumerate(eu)])
|
||||||
|
table = damask.Table(eu,{'Eulers':(3,)})
|
||||||
|
table.add('pos',coords)
|
||||||
|
table.to_ASCII(reference)
|
||||||
|
assert np.allclose(eu,damask.Table.from_ASCII(reference).get('Eulers'))
|
|
@ -4,25 +4,25 @@ import os
|
||||||
import pytest
|
import pytest
|
||||||
import numpy as np
|
import numpy as np
|
||||||
|
|
||||||
from damask import DADF5
|
from damask import Result
|
||||||
from damask import mechanics
|
from damask import mechanics
|
||||||
|
|
||||||
@pytest.fixture
|
@pytest.fixture
|
||||||
def default(tmp_path,reference_dir):
|
def default(tmp_path,reference_dir):
|
||||||
"""Small DADF5 file in temp location for modification."""
|
"""Small Result file in temp location for modification."""
|
||||||
fname = '12grains6x7x8_tensionY.hdf5'
|
fname = '12grains6x7x8_tensionY.hdf5'
|
||||||
shutil.copy(os.path.join(reference_dir,fname),tmp_path)
|
shutil.copy(os.path.join(reference_dir,fname),tmp_path)
|
||||||
f = DADF5(os.path.join(tmp_path,fname))
|
f = Result(os.path.join(tmp_path,fname))
|
||||||
f.set_by_time(20.0,20.0)
|
f.set_by_time(20.0,20.0)
|
||||||
return f
|
return f
|
||||||
|
|
||||||
@pytest.fixture
|
@pytest.fixture
|
||||||
def reference_dir(reference_dir_base):
|
def reference_dir(reference_dir_base):
|
||||||
"""Directory containing reference results."""
|
"""Directory containing reference results."""
|
||||||
return os.path.join(reference_dir_base,'DADF5')
|
return os.path.join(reference_dir_base,'Result')
|
||||||
|
|
||||||
|
|
||||||
class TestDADF5:
|
class TestResult:
|
||||||
|
|
||||||
def test_time_increments(self,default):
|
def test_time_increments(self,default):
|
||||||
shape = default.read_dataset(default.get_dataset_location('F'),0).shape
|
shape = default.read_dataset(default.get_dataset_location('F'),0).shape
|
|
@ -1,13 +1,9 @@
|
||||||
import os
|
import os
|
||||||
from itertools import permutations
|
|
||||||
|
|
||||||
import pytest
|
import pytest
|
||||||
import numpy as np
|
import numpy as np
|
||||||
|
|
||||||
import damask
|
|
||||||
from damask import Rotation
|
from damask import Rotation
|
||||||
from damask import Orientation
|
|
||||||
from damask import Lattice
|
|
||||||
|
|
||||||
n = 1000
|
n = 1000
|
||||||
|
|
||||||
|
@ -58,44 +54,3 @@ class TestRotation:
|
||||||
for rot in default:
|
for rot in default:
|
||||||
assert np.allclose(rot.asCubochoric(),
|
assert np.allclose(rot.asCubochoric(),
|
||||||
Rotation.fromQuaternion(rot.asQuaternion()).asCubochoric())
|
Rotation.fromQuaternion(rot.asQuaternion()).asCubochoric())
|
||||||
|
|
||||||
|
|
||||||
@pytest.mark.parametrize('color',[{'label':'red', 'RGB':[1,0,0],'direction':[0,0,1]},
|
|
||||||
{'label':'green','RGB':[0,1,0],'direction':[0,1,1]},
|
|
||||||
{'label':'blue', 'RGB':[0,0,1],'direction':[1,1,1]}])
|
|
||||||
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
|
||||||
def test_IPF_cubic(self,default,color,lattice):
|
|
||||||
cube = damask.Orientation(damask.Rotation(),lattice)
|
|
||||||
for direction in set(permutations(np.array(color['direction']))):
|
|
||||||
assert np.allclose(cube.IPFcolor(direction),np.array(color['RGB']))
|
|
||||||
|
|
||||||
@pytest.mark.parametrize('lattice',Lattice.lattices)
|
|
||||||
def test_IPF(self,lattice):
|
|
||||||
direction = np.random.random(3)*2.0-1
|
|
||||||
for rot in [Rotation.fromRandom() for r in range(n//100)]:
|
|
||||||
R = damask.Orientation(rot,lattice)
|
|
||||||
color = R.IPFcolor(direction)
|
|
||||||
for equivalent in R.equivalentOrientations():
|
|
||||||
assert np.allclose(color,R.IPFcolor(direction))
|
|
||||||
|
|
||||||
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
|
|
||||||
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
|
||||||
def test_relationship_forward_backward(self,model,lattice):
|
|
||||||
ori = Orientation(Rotation.fromRandom(),lattice)
|
|
||||||
for i,r in enumerate(ori.relatedOrientations(model)):
|
|
||||||
ori2 = r.relatedOrientations(model)[i]
|
|
||||||
misorientation = ori.rotation.misorientation(ori2.rotation)
|
|
||||||
assert misorientation.asAxisAngle(degrees=True)[3]<1.0e-5
|
|
||||||
|
|
||||||
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
|
|
||||||
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
|
||||||
def test_relationship_reference(self,update,reference_dir,model,lattice):
|
|
||||||
reference = os.path.join(reference_dir,'{}_{}.txt'.format(lattice,model))
|
|
||||||
ori = Orientation(Rotation(),lattice)
|
|
||||||
eu = np.array([o.rotation.asEulers(degrees=True) for o in ori.relatedOrientations(model)])
|
|
||||||
if update:
|
|
||||||
coords = np.array([(1,i+1) for i,x in enumerate(eu)])
|
|
||||||
table = damask.Table(eu,{'Eulers':(3,)})
|
|
||||||
table.add('pos',coords)
|
|
||||||
table.to_ASCII(reference)
|
|
||||||
assert np.allclose(eu,damask.Table.from_ASCII(reference).get('Eulers'))
|
|
||||||
|
|
|
@ -69,31 +69,32 @@ contains
|
||||||
!> @brief call (thread safe) all module initializations
|
!> @brief call (thread safe) all module initializations
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
subroutine CPFEM_initAll(el,ip)
|
subroutine CPFEM_initAll(el,ip)
|
||||||
integer(pInt), intent(in) :: el, & !< FE el number
|
|
||||||
ip !< FE integration point number
|
integer(pInt), intent(in) :: el, & !< FE el number
|
||||||
|
ip !< FE integration point number
|
||||||
|
|
||||||
!$OMP CRITICAL (init)
|
!$OMP CRITICAL(init)
|
||||||
if (.not. CPFEM_init_done) then
|
if (.not. CPFEM_init_done) then
|
||||||
call DAMASK_interface_init ! Spectral and FEM interface to commandline
|
call DAMASK_interface_init
|
||||||
call prec_init
|
call prec_init
|
||||||
call IO_init
|
call IO_init
|
||||||
call numerics_init
|
call numerics_init
|
||||||
call debug_init
|
call debug_init
|
||||||
call config_init
|
call config_init
|
||||||
call math_init
|
call math_init
|
||||||
call rotations_init
|
call rotations_init
|
||||||
call HDF5_utilities_init
|
call HDF5_utilities_init
|
||||||
call results_init
|
call results_init
|
||||||
call mesh_init(ip, el)
|
call mesh_init(ip, el)
|
||||||
call lattice_init
|
call lattice_init
|
||||||
call material_init
|
call material_init
|
||||||
call constitutive_init
|
call constitutive_init
|
||||||
call crystallite_init
|
call crystallite_init
|
||||||
call homogenization_init
|
call homogenization_init
|
||||||
call CPFEM_init
|
call CPFEM_init
|
||||||
CPFEM_init_done = .true.
|
CPFEM_init_done = .true.
|
||||||
endif
|
endif
|
||||||
!$OMP END CRITICAL (init)
|
!$OMP END CRITICAL(init)
|
||||||
|
|
||||||
end subroutine CPFEM_initAll
|
end subroutine CPFEM_initAll
|
||||||
|
|
||||||
|
@ -174,35 +175,7 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
|
||||||
CPFEM_dcsde = CPFEM_dcsde_knownGood
|
CPFEM_dcsde = CPFEM_dcsde_knownGood
|
||||||
|
|
||||||
!*** age results
|
!*** age results
|
||||||
if (iand(mode, CPFEM_AGERESULTS) /= 0_pInt) then
|
if (iand(mode, CPFEM_AGERESULTS) /= 0_pInt) call CPFEM_forward
|
||||||
crystallite_F0 = crystallite_partionedF ! crystallite deformation
|
|
||||||
crystallite_Fp0 = crystallite_Fp ! crystallite plastic deformation
|
|
||||||
crystallite_Lp0 = crystallite_Lp ! crystallite plastic velocity
|
|
||||||
crystallite_Fi0 = crystallite_Fi ! crystallite intermediate deformation
|
|
||||||
crystallite_Li0 = crystallite_Li ! crystallite intermediate velocity
|
|
||||||
crystallite_S0 = crystallite_S ! crystallite 2nd Piola Kirchhoff stress
|
|
||||||
|
|
||||||
forall (i = 1:size(plasticState)) plasticState(i)%state0 = plasticState(i)%state
|
|
||||||
do i = 1, size(sourceState)
|
|
||||||
do mySource = 1,phase_Nsources(i)
|
|
||||||
sourceState(i)%p(mySource)%state0 = sourceState(i)%p(mySource)%state
|
|
||||||
enddo; enddo
|
|
||||||
if (iand(debug_level(debug_CPFEM), debug_levelBasic) /= 0_pInt) then
|
|
||||||
write(6,'(a)') '<< CPFEM >> aging states'
|
|
||||||
if (debug_e <= discretization_nElem .and. debug_i <=discretization_nIP) then
|
|
||||||
write(6,'(a,1x,i8,1x,i2,1x,i4,/,(12x,6(e20.8,1x)),/)') &
|
|
||||||
'<< CPFEM >> aged state of elFE ip grain',debug_e, debug_i, 1, &
|
|
||||||
plasticState(material_phaseAt(1,debug_e))%state(:,material_phasememberAt(1,debug_i,debug_e))
|
|
||||||
endif
|
|
||||||
endif
|
|
||||||
|
|
||||||
do homog = 1_pInt, material_Nhomogenization
|
|
||||||
homogState (homog)%state0 = homogState (homog)%state
|
|
||||||
thermalState (homog)%state0 = thermalState (homog)%state
|
|
||||||
damageState (homog)%state0 = damageState (homog)%state
|
|
||||||
enddo
|
|
||||||
endif
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
!*** collection of FEM input with returning of randomize odd stress and jacobian
|
!*** collection of FEM input with returning of randomize odd stress and jacobian
|
||||||
|
@ -360,7 +333,17 @@ end subroutine CPFEM_general
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief triggers writing of the results
|
!> @brief Forward data for new time increment.
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
subroutine CPFEM_forward
|
||||||
|
|
||||||
|
call crystallite_forward
|
||||||
|
|
||||||
|
end subroutine CPFEM_forward
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Trigger writing of results.
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
subroutine CPFEM_results(inc,time)
|
subroutine CPFEM_results(inc,time)
|
||||||
|
|
||||||
|
|
118
src/CPFEM2.f90
118
src/CPFEM2.f90
|
@ -64,131 +64,45 @@ end subroutine CPFEM_initAll
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief allocate the arrays defined in module CPFEM and initialize them
|
!> @brief Read restart information if needed.
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
subroutine CPFEM_init
|
subroutine CPFEM_init
|
||||||
|
|
||||||
integer :: i
|
|
||||||
integer(HID_T) :: fileHandle, groupHandle
|
|
||||||
character(len=pStringLen) :: fileName, datasetName
|
|
||||||
|
|
||||||
write(6,'(/,a)') ' <<<+- CPFEM init -+>>>'; flush(6)
|
write(6,'(/,a)') ' <<<+- CPFEM init -+>>>'; flush(6)
|
||||||
|
|
||||||
if (interface_restartInc > 0) then
|
if (interface_restartInc > 0) call crystallite_restartRead
|
||||||
write(6,'(/,a,i0,a)') ' reading restart information of increment ', interface_restartInc, ' from file'
|
|
||||||
|
|
||||||
write(fileName,'(a,i0,a)') trim(getSolverJobName())//'_',worldrank,'.hdf5'
|
|
||||||
fileHandle = HDF5_openFile(fileName)
|
|
||||||
|
|
||||||
call HDF5_read(fileHandle,crystallite_F0, 'F')
|
|
||||||
call HDF5_read(fileHandle,crystallite_Fp0,'Fp')
|
|
||||||
call HDF5_read(fileHandle,crystallite_Fi0,'Fi')
|
|
||||||
call HDF5_read(fileHandle,crystallite_Lp0,'Lp')
|
|
||||||
call HDF5_read(fileHandle,crystallite_Li0,'Li')
|
|
||||||
call HDF5_read(fileHandle,crystallite_S0, 'S')
|
|
||||||
|
|
||||||
groupHandle = HDF5_openGroup(fileHandle,'constituent')
|
|
||||||
do i = 1,size(phase_plasticity)
|
|
||||||
write(datasetName,'(i0,a)') i,'_omega_plastic'
|
|
||||||
call HDF5_read(groupHandle,plasticState(i)%state0,datasetName)
|
|
||||||
enddo
|
|
||||||
call HDF5_closeGroup(groupHandle)
|
|
||||||
|
|
||||||
groupHandle = HDF5_openGroup(fileHandle,'materialpoint')
|
|
||||||
do i = 1, material_Nhomogenization
|
|
||||||
write(datasetName,'(i0,a)') i,'_omega_homogenization'
|
|
||||||
call HDF5_read(groupHandle,homogState(i)%state0,datasetName)
|
|
||||||
enddo
|
|
||||||
call HDF5_closeGroup(groupHandle)
|
|
||||||
|
|
||||||
call HDF5_closeFile(fileHandle)
|
|
||||||
endif
|
|
||||||
|
|
||||||
end subroutine CPFEM_init
|
end subroutine CPFEM_init
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief Forward data after successful increment.
|
!> @brief Write restart information.
|
||||||
! ToDo: Any guessing for the current states possible?
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
|
||||||
subroutine CPFEM_forward
|
|
||||||
|
|
||||||
integer :: i, j
|
|
||||||
|
|
||||||
if (iand(debug_level(debug_CPFEM), debug_levelBasic) /= 0) &
|
|
||||||
write(6,'(a)') '<< CPFEM >> aging states'
|
|
||||||
|
|
||||||
crystallite_F0 = crystallite_partionedF
|
|
||||||
crystallite_Fp0 = crystallite_Fp
|
|
||||||
crystallite_Lp0 = crystallite_Lp
|
|
||||||
crystallite_Fi0 = crystallite_Fi
|
|
||||||
crystallite_Li0 = crystallite_Li
|
|
||||||
crystallite_S0 = crystallite_S
|
|
||||||
|
|
||||||
do i = 1, size(plasticState)
|
|
||||||
plasticState(i)%state0 = plasticState(i)%state
|
|
||||||
enddo
|
|
||||||
do i = 1, size(sourceState)
|
|
||||||
do j = 1,phase_Nsources(i)
|
|
||||||
sourceState(i)%p(j)%state0 = sourceState(i)%p(j)%state
|
|
||||||
enddo; enddo
|
|
||||||
do i = 1, material_Nhomogenization
|
|
||||||
homogState (i)%state0 = homogState (i)%state
|
|
||||||
thermalState(i)%state0 = thermalState(i)%state
|
|
||||||
damageState (i)%state0 = damageState (i)%state
|
|
||||||
enddo
|
|
||||||
|
|
||||||
end subroutine CPFEM_forward
|
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Write current restart information (Field and constitutive data) to file.
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
subroutine CPFEM_restartWrite
|
subroutine CPFEM_restartWrite
|
||||||
|
|
||||||
integer :: i
|
call crystallite_restartWrite
|
||||||
integer(HID_T) :: fileHandle, groupHandle
|
|
||||||
character(len=pStringLen) :: fileName, datasetName
|
|
||||||
|
|
||||||
write(6,'(a)') ' writing field and constitutive data required for restart to file';flush(6)
|
|
||||||
|
|
||||||
write(fileName,'(a,i0,a)') trim(getSolverJobName())//'_',worldrank,'.hdf5'
|
|
||||||
fileHandle = HDF5_openFile(fileName,'a')
|
|
||||||
|
|
||||||
call HDF5_write(fileHandle,crystallite_partionedF,'F')
|
|
||||||
call HDF5_write(fileHandle,crystallite_Fp, 'Fp')
|
|
||||||
call HDF5_write(fileHandle,crystallite_Fi, 'Fi')
|
|
||||||
call HDF5_write(fileHandle,crystallite_Lp, 'Lp')
|
|
||||||
call HDF5_write(fileHandle,crystallite_Li, 'Li')
|
|
||||||
call HDF5_write(fileHandle,crystallite_S, 'S')
|
|
||||||
|
|
||||||
groupHandle = HDF5_addGroup(fileHandle,'constituent')
|
|
||||||
do i = 1,size(phase_plasticity)
|
|
||||||
write(datasetName,'(i0,a)') i,'_omega_plastic'
|
|
||||||
call HDF5_write(groupHandle,plasticState(i)%state,datasetName)
|
|
||||||
enddo
|
|
||||||
call HDF5_closeGroup(groupHandle)
|
|
||||||
|
|
||||||
groupHandle = HDF5_addGroup(fileHandle,'materialpoint')
|
|
||||||
do i = 1, material_Nhomogenization
|
|
||||||
write(datasetName,'(i0,a)') i,'_omega_homogenization'
|
|
||||||
call HDF5_write(groupHandle,homogState(i)%state,datasetName)
|
|
||||||
enddo
|
|
||||||
call HDF5_closeGroup(groupHandle)
|
|
||||||
|
|
||||||
call HDF5_closeFile(fileHandle)
|
|
||||||
|
|
||||||
end subroutine CPFEM_restartWrite
|
end subroutine CPFEM_restartWrite
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Forward data for new time increment.
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
subroutine CPFEM_forward
|
||||||
|
|
||||||
|
call crystallite_forward
|
||||||
|
|
||||||
|
end subroutine CPFEM_forward
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief Trigger writing of results.
|
!> @brief Trigger writing of results.
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
subroutine CPFEM_results(inc,time)
|
subroutine CPFEM_results(inc,time)
|
||||||
|
|
||||||
integer, intent(in) :: inc
|
integer, intent(in) :: inc
|
||||||
real(pReal), intent(in) :: time
|
real(pReal), intent(in) :: time
|
||||||
|
|
||||||
call results_openJobFile
|
call results_openJobFile
|
||||||
call results_addIncrement(inc,time)
|
call results_addIncrement(inc,time)
|
||||||
call constitutive_results
|
call constitutive_results
|
||||||
|
|
|
@ -40,9 +40,9 @@ module DAMASK_interface
|
||||||
implicit none
|
implicit none
|
||||||
private
|
private
|
||||||
|
|
||||||
logical, protected, public :: symmetricSolver
|
logical, protected, public :: symmetricSolver
|
||||||
character(len=*), parameter, public :: INPUTFILEEXTENSION = '.dat'
|
character(len=*), parameter, public :: INPUTFILEEXTENSION = '.dat'
|
||||||
|
|
||||||
public :: &
|
public :: &
|
||||||
DAMASK_interface_init, &
|
DAMASK_interface_init, &
|
||||||
getSolverJobName
|
getSolverJobName
|
||||||
|
@ -57,14 +57,14 @@ subroutine DAMASK_interface_init
|
||||||
integer, dimension(8) :: dateAndTime
|
integer, dimension(8) :: dateAndTime
|
||||||
integer :: ierr
|
integer :: ierr
|
||||||
character(len=pPathLen) :: wd
|
character(len=pPathLen) :: wd
|
||||||
|
|
||||||
write(6,'(/,a)') ' <<<+- DAMASK_marc init -+>>>'
|
write(6,'(/,a)') ' <<<+- DAMASK_marc init -+>>>'
|
||||||
|
|
||||||
write(6,'(/,a)') ' Roters et al., Computational Materials Science 158:420–478, 2019'
|
write(6,'(/,a)') ' Roters et al., Computational Materials Science 158:420–478, 2019'
|
||||||
write(6,'(a)') ' https://doi.org/10.1016/j.commatsci.2018.04.030'
|
write(6,'(a)') ' https://doi.org/10.1016/j.commatsci.2018.04.030'
|
||||||
|
|
||||||
write(6,'(/,a)') ' Version: '//DAMASKVERSION
|
write(6,'(/,a)') ' Version: '//DAMASKVERSION
|
||||||
|
|
||||||
! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md
|
! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md
|
||||||
#if __INTEL_COMPILER >= 1800
|
#if __INTEL_COMPILER >= 1800
|
||||||
write(6,'(/,a)') ' Compiled with: '//compiler_version()
|
write(6,'(/,a)') ' Compiled with: '//compiler_version()
|
||||||
|
@ -73,13 +73,13 @@ subroutine DAMASK_interface_init
|
||||||
write(6,'(/,a,i4.4,a,i8.8)') ' Compiled with Intel fortran version :', __INTEL_COMPILER,&
|
write(6,'(/,a,i4.4,a,i8.8)') ' Compiled with Intel fortran version :', __INTEL_COMPILER,&
|
||||||
', build date :', __INTEL_COMPILER_BUILD_DATE
|
', build date :', __INTEL_COMPILER_BUILD_DATE
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
write(6,'(/,a)') ' Compiled on: '//__DATE__//' at '//__TIME__
|
write(6,'(/,a)') ' Compiled on: '//__DATE__//' at '//__TIME__
|
||||||
|
|
||||||
call date_and_time(values = dateAndTime)
|
call date_and_time(values = dateAndTime)
|
||||||
write(6,'(/,a,2(i2.2,a),i4.4)') ' Date: ',dateAndTime(3),'/',dateAndTime(2),'/', dateAndTime(1)
|
write(6,'(/,a,2(i2.2,a),i4.4)') ' Date: ',dateAndTime(3),'/',dateAndTime(2),'/', dateAndTime(1)
|
||||||
write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':', dateAndTime(6),':', dateAndTime(7)
|
write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':', dateAndTime(6),':', dateAndTime(7)
|
||||||
|
|
||||||
inquire(5, name=wd)
|
inquire(5, name=wd)
|
||||||
wd = wd(1:scan(wd,'/',back=.true.))
|
wd = wd(1:scan(wd,'/',back=.true.))
|
||||||
ierr = CHDIR(wd)
|
ierr = CHDIR(wd)
|
||||||
|
|
|
@ -11,6 +11,8 @@
|
||||||
module crystallite
|
module crystallite
|
||||||
use prec
|
use prec
|
||||||
use IO
|
use IO
|
||||||
|
use HDF5_utilities
|
||||||
|
use DAMASK_interface
|
||||||
use config
|
use config
|
||||||
use debug
|
use debug
|
||||||
use numerics
|
use numerics
|
||||||
|
@ -36,25 +38,25 @@ module crystallite
|
||||||
crystallite_orientation !< current orientation
|
crystallite_orientation !< current orientation
|
||||||
real(pReal), dimension(:,:,:,:,:), allocatable, public, protected :: &
|
real(pReal), dimension(:,:,:,:,:), allocatable, public, protected :: &
|
||||||
crystallite_Fe, & !< current "elastic" def grad (end of converged time step)
|
crystallite_Fe, & !< current "elastic" def grad (end of converged time step)
|
||||||
crystallite_P !< 1st Piola-Kirchhoff stress per grain
|
crystallite_P, & !< 1st Piola-Kirchhoff stress per grain
|
||||||
|
crystallite_S0, & !< 2nd Piola-Kirchhoff stress vector at start of FE inc
|
||||||
|
crystallite_Fp0, & !< plastic def grad at start of FE inc
|
||||||
|
crystallite_Fi0, & !< intermediate def grad at start of FE inc
|
||||||
|
crystallite_F0, & !< def grad at start of FE inc
|
||||||
|
crystallite_Lp0, & !< plastic velocitiy grad at start of FE inc
|
||||||
|
crystallite_Li0 !< intermediate velocitiy grad at start of FE inc
|
||||||
real(pReal), dimension(:,:,:,:,:), allocatable, public :: &
|
real(pReal), dimension(:,:,:,:,:), allocatable, public :: &
|
||||||
crystallite_S, & !< current 2nd Piola-Kirchhoff stress vector (end of converged time step)
|
crystallite_S, & !< current 2nd Piola-Kirchhoff stress vector (end of converged time step)
|
||||||
crystallite_S0, & !< 2nd Piola-Kirchhoff stress vector at start of FE inc
|
|
||||||
crystallite_partionedS0, & !< 2nd Piola-Kirchhoff stress vector at start of homog inc
|
crystallite_partionedS0, & !< 2nd Piola-Kirchhoff stress vector at start of homog inc
|
||||||
crystallite_Fp, & !< current plastic def grad (end of converged time step)
|
crystallite_Fp, & !< current plastic def grad (end of converged time step)
|
||||||
crystallite_Fp0, & !< plastic def grad at start of FE inc
|
|
||||||
crystallite_partionedFp0,& !< plastic def grad at start of homog inc
|
crystallite_partionedFp0,& !< plastic def grad at start of homog inc
|
||||||
crystallite_Fi, & !< current intermediate def grad (end of converged time step)
|
crystallite_Fi, & !< current intermediate def grad (end of converged time step)
|
||||||
crystallite_Fi0, & !< intermediate def grad at start of FE inc
|
|
||||||
crystallite_partionedFi0,& !< intermediate def grad at start of homog inc
|
crystallite_partionedFi0,& !< intermediate def grad at start of homog inc
|
||||||
crystallite_F0, & !< def grad at start of FE inc
|
|
||||||
crystallite_partionedF, & !< def grad to be reached at end of homog inc
|
crystallite_partionedF, & !< def grad to be reached at end of homog inc
|
||||||
crystallite_partionedF0, & !< def grad at start of homog inc
|
crystallite_partionedF0, & !< def grad at start of homog inc
|
||||||
crystallite_Lp, & !< current plastic velocitiy grad (end of converged time step)
|
crystallite_Lp, & !< current plastic velocitiy grad (end of converged time step)
|
||||||
crystallite_Lp0, & !< plastic velocitiy grad at start of FE inc
|
|
||||||
crystallite_partionedLp0, & !< plastic velocity grad at start of homog inc
|
crystallite_partionedLp0, & !< plastic velocity grad at start of homog inc
|
||||||
crystallite_Li, & !< current intermediate velocitiy grad (end of converged time step)
|
crystallite_Li, & !< current intermediate velocitiy grad (end of converged time step)
|
||||||
crystallite_Li0, & !< intermediate velocitiy grad at start of FE inc
|
|
||||||
crystallite_partionedLi0 !< intermediate velocity grad at start of homog inc
|
crystallite_partionedLi0 !< intermediate velocity grad at start of homog inc
|
||||||
real(pReal), dimension(:,:,:,:,:), allocatable :: &
|
real(pReal), dimension(:,:,:,:,:), allocatable :: &
|
||||||
crystallite_subFp0,& !< plastic def grad at start of crystallite inc
|
crystallite_subFp0,& !< plastic def grad at start of crystallite inc
|
||||||
|
@ -104,7 +106,10 @@ module crystallite
|
||||||
crystallite_stressTangent, &
|
crystallite_stressTangent, &
|
||||||
crystallite_orientations, &
|
crystallite_orientations, &
|
||||||
crystallite_push33ToRef, &
|
crystallite_push33ToRef, &
|
||||||
crystallite_results
|
crystallite_results, &
|
||||||
|
crystallite_restartWrite, &
|
||||||
|
crystallite_restartRead, &
|
||||||
|
crystallite_forward
|
||||||
|
|
||||||
contains
|
contains
|
||||||
|
|
||||||
|
@ -130,38 +135,30 @@ subroutine crystallite_init
|
||||||
iMax = discretization_nIP
|
iMax = discretization_nIP
|
||||||
eMax = discretization_nElem
|
eMax = discretization_nElem
|
||||||
|
|
||||||
allocate(crystallite_S0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
allocate(crystallite_partionedF(3,3,cMax,iMax,eMax),source=0.0_pReal)
|
||||||
allocate(crystallite_partionedS0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_S(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
allocate(crystallite_S0, &
|
||||||
allocate(crystallite_P(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
crystallite_F0, crystallite_Fi0,crystallite_Fp0, &
|
||||||
allocate(crystallite_F0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
crystallite_Li0,crystallite_Lp0, &
|
||||||
allocate(crystallite_partionedF0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
crystallite_partionedS0, &
|
||||||
allocate(crystallite_partionedF(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
crystallite_partionedF0,crystallite_partionedFp0,crystallite_partionedFi0, &
|
||||||
allocate(crystallite_subF0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
crystallite_partionedLp0,crystallite_partionedLi0, &
|
||||||
allocate(crystallite_subF(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
crystallite_S,crystallite_P, &
|
||||||
allocate(crystallite_Fp0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
crystallite_Fe,crystallite_Fi,crystallite_Fp, &
|
||||||
allocate(crystallite_partionedFp0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
crystallite_Li,crystallite_Lp, &
|
||||||
allocate(crystallite_subFp0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
crystallite_subF,crystallite_subF0, &
|
||||||
allocate(crystallite_Fp(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
crystallite_subFp0,crystallite_subFi0, &
|
||||||
allocate(crystallite_Fi0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
crystallite_subLi0,crystallite_subLp0, &
|
||||||
allocate(crystallite_partionedFi0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
source = crystallite_partionedF)
|
||||||
allocate(crystallite_subFi0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_Fi(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
allocate(crystallite_dPdF(3,3,3,3,cMax,iMax,eMax),source=0.0_pReal)
|
||||||
allocate(crystallite_Fe(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_Lp0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
allocate(crystallite_dt(cMax,iMax,eMax),source=0.0_pReal)
|
||||||
allocate(crystallite_partionedLp0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
allocate(crystallite_subdt,crystallite_subFrac,crystallite_subStep, &
|
||||||
allocate(crystallite_subLp0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
source = crystallite_dt)
|
||||||
allocate(crystallite_Lp(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_Li0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_partionedLi0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_subLi0(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_Li(3,3,cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_dPdF(3,3,3,3,cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_dt(cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_subdt(cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_subFrac(cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_subStep(cMax,iMax,eMax), source=0.0_pReal)
|
|
||||||
allocate(crystallite_orientation(cMax,iMax,eMax))
|
allocate(crystallite_orientation(cMax,iMax,eMax))
|
||||||
|
|
||||||
allocate(crystallite_localPlasticity(cMax,iMax,eMax), source=.true.)
|
allocate(crystallite_localPlasticity(cMax,iMax,eMax), source=.true.)
|
||||||
allocate(crystallite_requested(cMax,iMax,eMax), source=.false.)
|
allocate(crystallite_requested(cMax,iMax,eMax), source=.false.)
|
||||||
allocate(crystallite_todo(cMax,iMax,eMax), source=.false.)
|
allocate(crystallite_todo(cMax,iMax,eMax), source=.false.)
|
||||||
|
@ -1844,4 +1841,117 @@ logical function stateJump(ipc,ip,el)
|
||||||
|
|
||||||
end function stateJump
|
end function stateJump
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Write current restart information (Field and constitutive data) to file.
|
||||||
|
! ToDo: Merge data into one file for MPI, move state to constitutive and homogenization, respectively
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
subroutine crystallite_restartWrite
|
||||||
|
|
||||||
|
integer :: i
|
||||||
|
integer(HID_T) :: fileHandle, groupHandle
|
||||||
|
character(len=pStringLen) :: fileName, datasetName
|
||||||
|
|
||||||
|
write(6,'(a)') ' writing field and constitutive data required for restart to file';flush(6)
|
||||||
|
|
||||||
|
write(fileName,'(a,i0,a)') trim(getSolverJobName())//'_',worldrank,'.hdf5'
|
||||||
|
fileHandle = HDF5_openFile(fileName,'a')
|
||||||
|
|
||||||
|
call HDF5_write(fileHandle,crystallite_partionedF,'F')
|
||||||
|
call HDF5_write(fileHandle,crystallite_Fp, 'Fp')
|
||||||
|
call HDF5_write(fileHandle,crystallite_Fi, 'Fi')
|
||||||
|
call HDF5_write(fileHandle,crystallite_Lp, 'Lp')
|
||||||
|
call HDF5_write(fileHandle,crystallite_Li, 'Li')
|
||||||
|
call HDF5_write(fileHandle,crystallite_S, 'S')
|
||||||
|
|
||||||
|
groupHandle = HDF5_addGroup(fileHandle,'constituent')
|
||||||
|
do i = 1,size(phase_plasticity)
|
||||||
|
write(datasetName,'(i0,a)') i,'_omega_plastic'
|
||||||
|
call HDF5_write(groupHandle,plasticState(i)%state,datasetName)
|
||||||
|
enddo
|
||||||
|
call HDF5_closeGroup(groupHandle)
|
||||||
|
|
||||||
|
groupHandle = HDF5_addGroup(fileHandle,'materialpoint')
|
||||||
|
do i = 1, material_Nhomogenization
|
||||||
|
write(datasetName,'(i0,a)') i,'_omega_homogenization'
|
||||||
|
call HDF5_write(groupHandle,homogState(i)%state,datasetName)
|
||||||
|
enddo
|
||||||
|
call HDF5_closeGroup(groupHandle)
|
||||||
|
|
||||||
|
call HDF5_closeFile(fileHandle)
|
||||||
|
|
||||||
|
end subroutine crystallite_restartWrite
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Read data for restart
|
||||||
|
! ToDo: Merge data into one file for MPI, move state to constitutive and homogenization, respectively
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
subroutine crystallite_restartRead
|
||||||
|
|
||||||
|
integer :: i
|
||||||
|
integer(HID_T) :: fileHandle, groupHandle
|
||||||
|
character(len=pStringLen) :: fileName, datasetName
|
||||||
|
|
||||||
|
write(6,'(/,a,i0,a)') ' reading restart information of increment from file'
|
||||||
|
|
||||||
|
write(fileName,'(a,i0,a)') trim(getSolverJobName())//'_',worldrank,'.hdf5'
|
||||||
|
fileHandle = HDF5_openFile(fileName)
|
||||||
|
|
||||||
|
call HDF5_read(fileHandle,crystallite_F0, 'F')
|
||||||
|
call HDF5_read(fileHandle,crystallite_Fp0,'Fp')
|
||||||
|
call HDF5_read(fileHandle,crystallite_Fi0,'Fi')
|
||||||
|
call HDF5_read(fileHandle,crystallite_Lp0,'Lp')
|
||||||
|
call HDF5_read(fileHandle,crystallite_Li0,'Li')
|
||||||
|
call HDF5_read(fileHandle,crystallite_S0, 'S')
|
||||||
|
|
||||||
|
groupHandle = HDF5_openGroup(fileHandle,'constituent')
|
||||||
|
do i = 1,size(phase_plasticity)
|
||||||
|
write(datasetName,'(i0,a)') i,'_omega_plastic'
|
||||||
|
call HDF5_read(groupHandle,plasticState(i)%state0,datasetName)
|
||||||
|
enddo
|
||||||
|
call HDF5_closeGroup(groupHandle)
|
||||||
|
|
||||||
|
groupHandle = HDF5_openGroup(fileHandle,'materialpoint')
|
||||||
|
do i = 1, material_Nhomogenization
|
||||||
|
write(datasetName,'(i0,a)') i,'_omega_homogenization'
|
||||||
|
call HDF5_read(groupHandle,homogState(i)%state0,datasetName)
|
||||||
|
enddo
|
||||||
|
call HDF5_closeGroup(groupHandle)
|
||||||
|
|
||||||
|
call HDF5_closeFile(fileHandle)
|
||||||
|
|
||||||
|
end subroutine crystallite_restartRead
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Forward data after successful increment.
|
||||||
|
! ToDo: Any guessing for the current states possible?
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
subroutine crystallite_forward
|
||||||
|
|
||||||
|
integer :: i, j
|
||||||
|
|
||||||
|
crystallite_F0 = crystallite_partionedF
|
||||||
|
crystallite_Fp0 = crystallite_Fp
|
||||||
|
crystallite_Lp0 = crystallite_Lp
|
||||||
|
crystallite_Fi0 = crystallite_Fi
|
||||||
|
crystallite_Li0 = crystallite_Li
|
||||||
|
crystallite_S0 = crystallite_S
|
||||||
|
|
||||||
|
do i = 1, size(plasticState)
|
||||||
|
plasticState(i)%state0 = plasticState(i)%state
|
||||||
|
enddo
|
||||||
|
do i = 1, size(sourceState)
|
||||||
|
do j = 1,phase_Nsources(i)
|
||||||
|
sourceState(i)%p(j)%state0 = sourceState(i)%p(j)%state
|
||||||
|
enddo; enddo
|
||||||
|
do i = 1, material_Nhomogenization
|
||||||
|
homogState (i)%state0 = homogState (i)%state
|
||||||
|
thermalState(i)%state0 = thermalState(i)%state
|
||||||
|
damageState (i)%state0 = damageState (i)%state
|
||||||
|
enddo
|
||||||
|
|
||||||
|
end subroutine crystallite_forward
|
||||||
|
|
||||||
end module crystallite
|
end module crystallite
|
||||||
|
|
|
@ -669,7 +669,7 @@ module procedure mech_RGC_updateState
|
||||||
nDef = 0.0_pReal
|
nDef = 0.0_pReal
|
||||||
do i = 1,3; do j = 1,3
|
do i = 1,3; do j = 1,3
|
||||||
do k = 1,3; do l = 1,3
|
do k = 1,3; do l = 1,3
|
||||||
nDef(i,j) = nDef(i,j) - nVect(k)*gDef(i,l)*math_civita(j,k,l) ! compute the interface mismatch tensor from the jump of deformation gradient
|
nDef(i,j) = nDef(i,j) - nVect(k)*gDef(i,l)*math_LeviCivita(j,k,l) ! compute the interface mismatch tensor from the jump of deformation gradient
|
||||||
enddo; enddo
|
enddo; enddo
|
||||||
nDefNorm = nDefNorm + nDef(i,j)**2.0_pReal ! compute the norm of the mismatch tensor
|
nDefNorm = nDefNorm + nDef(i,j)**2.0_pReal ! compute the norm of the mismatch tensor
|
||||||
enddo; enddo
|
enddo; enddo
|
||||||
|
@ -689,7 +689,7 @@ module procedure mech_RGC_updateState
|
||||||
rPen(i,j,iGrain) = rPen(i,j,iGrain) + 0.5_pReal*(muGrain*bgGrain + muGNghb*bgGNghb)*prm%xiAlpha &
|
rPen(i,j,iGrain) = rPen(i,j,iGrain) + 0.5_pReal*(muGrain*bgGrain + muGNghb*bgGNghb)*prm%xiAlpha &
|
||||||
*surfCorr(abs(intFace(1)))/prm%dAlpha(abs(intFace(1))) &
|
*surfCorr(abs(intFace(1)))/prm%dAlpha(abs(intFace(1))) &
|
||||||
*cosh(prm%ciAlpha*nDefNorm) &
|
*cosh(prm%ciAlpha*nDefNorm) &
|
||||||
*0.5_pReal*nVect(l)*nDef(i,k)/nDefNorm*math_civita(k,l,j) &
|
*0.5_pReal*nVect(l)*nDef(i,k)/nDefNorm*math_LeviCivita(k,l,j) &
|
||||||
*tanh(nDefNorm/xSmoo_RGC)
|
*tanh(nDefNorm/xSmoo_RGC)
|
||||||
enddo; enddo;enddo; enddo
|
enddo; enddo;enddo; enddo
|
||||||
enddo interfaceLoop
|
enddo interfaceLoop
|
||||||
|
|
186
src/math.f90
186
src/math.f90
|
@ -72,7 +72,12 @@ module math
|
||||||
3,2, &
|
3,2, &
|
||||||
3,3 &
|
3,3 &
|
||||||
],[2,9]) !< arrangement in Plain notation
|
],[2,9]) !< arrangement in Plain notation
|
||||||
|
|
||||||
|
|
||||||
|
interface math_mul33xx33
|
||||||
|
module procedure math_tensordot
|
||||||
|
end interface math_mul33xx33
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
!---------------------------------------------------------------------------------------------------
|
||||||
private :: &
|
private :: &
|
||||||
unitTest
|
unitTest
|
||||||
|
@ -88,7 +93,7 @@ subroutine math_init
|
||||||
real(pReal), dimension(4) :: randTest
|
real(pReal), dimension(4) :: randTest
|
||||||
integer :: randSize
|
integer :: randSize
|
||||||
integer, dimension(:), allocatable :: randInit
|
integer, dimension(:), allocatable :: randInit
|
||||||
|
|
||||||
write(6,'(/,a)') ' <<<+- math init -+>>>'; flush(6)
|
write(6,'(/,a)') ' <<<+- math init -+>>>'; flush(6)
|
||||||
|
|
||||||
call random_seed(size=randSize)
|
call random_seed(size=randSize)
|
||||||
|
@ -140,7 +145,7 @@ recursive subroutine math_sort(a, istart, iend, sortDim)
|
||||||
else
|
else
|
||||||
e = ubound(a,2)
|
e = ubound(a,2)
|
||||||
endif
|
endif
|
||||||
|
|
||||||
if(present(sortDim)) then
|
if(present(sortDim)) then
|
||||||
d = sortDim
|
d = sortDim
|
||||||
else
|
else
|
||||||
|
@ -160,12 +165,12 @@ recursive subroutine math_sort(a, istart, iend, sortDim)
|
||||||
!> @brief Partitioning required for quicksort
|
!> @brief Partitioning required for quicksort
|
||||||
!-------------------------------------------------------------------------------------------------
|
!-------------------------------------------------------------------------------------------------
|
||||||
integer function qsort_partition(a, istart, iend, sort)
|
integer function qsort_partition(a, istart, iend, sort)
|
||||||
|
|
||||||
integer, dimension(:,:), intent(inout) :: a
|
integer, dimension(:,:), intent(inout) :: a
|
||||||
integer, intent(in) :: istart,iend,sort
|
integer, intent(in) :: istart,iend,sort
|
||||||
integer, dimension(size(a,1)) :: tmp
|
integer, dimension(size(a,1)) :: tmp
|
||||||
integer :: i,j
|
integer :: i,j
|
||||||
|
|
||||||
do
|
do
|
||||||
! find the first element on the right side less than or equal to the pivot point
|
! find the first element on the right side less than or equal to the pivot point
|
||||||
do j = iend, istart, -1
|
do j = iend, istart, -1
|
||||||
|
@ -187,7 +192,7 @@ recursive subroutine math_sort(a, istart, iend, sortDim)
|
||||||
a(:,j) = tmp
|
a(:,j) = tmp
|
||||||
endif cross
|
endif cross
|
||||||
enddo
|
enddo
|
||||||
|
|
||||||
end function qsort_partition
|
end function qsort_partition
|
||||||
|
|
||||||
end subroutine math_sort
|
end subroutine math_sort
|
||||||
|
@ -196,7 +201,7 @@ end subroutine math_sort
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief vector expansion
|
!> @brief vector expansion
|
||||||
!> @details takes a set of numbers (a,b,c,...) and corresponding multiples (x,y,z,...)
|
!> @details takes a set of numbers (a,b,c,...) and corresponding multiples (x,y,z,...)
|
||||||
!> to return a vector of x times a, y times b, z times c, ...
|
!> to return a vector of x times a, y times b, z times c, ...
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
pure function math_expand(what,how)
|
pure function math_expand(what,how)
|
||||||
|
|
||||||
|
@ -204,9 +209,9 @@ pure function math_expand(what,how)
|
||||||
integer, dimension(:), intent(in) :: how
|
integer, dimension(:), intent(in) :: how
|
||||||
real(pReal), dimension(sum(how)) :: math_expand
|
real(pReal), dimension(sum(how)) :: math_expand
|
||||||
integer :: i
|
integer :: i
|
||||||
|
|
||||||
if (sum(how) == 0) return
|
if (sum(how) == 0) return
|
||||||
|
|
||||||
do i = 1, size(how)
|
do i = 1, size(how)
|
||||||
math_expand(sum(how(1:i-1))+1:sum(how(1:i))) = what(mod(i-1,size(what))+1)
|
math_expand(sum(how(1:i-1))+1:sum(how(1:i))) = what(mod(i-1,size(what))+1)
|
||||||
enddo
|
enddo
|
||||||
|
@ -266,31 +271,30 @@ end function math_identity4th
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief permutation tensor e_ijk used for computing cross product of two tensors
|
!> @brief permutation tensor e_ijk
|
||||||
! e_ijk = 1 if even permutation of ijk
|
! e_ijk = 1 if even permutation of ijk
|
||||||
! e_ijk = -1 if odd permutation of ijk
|
! e_ijk = -1 if odd permutation of ijk
|
||||||
! e_ijk = 0 otherwise
|
! e_ijk = 0 otherwise
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
real(pReal) pure function math_civita(i,j,k)
|
real(pReal) pure function math_LeviCivita(i,j,k)
|
||||||
|
|
||||||
integer, intent(in) :: i,j,k
|
integer, intent(in) :: i,j,k
|
||||||
|
|
||||||
math_civita = 0.0_pReal
|
if (all([i,j,k] == [1,2,3]) .or. all([i,j,k] == [2,3,1]) .or. all([i,j,k] == [3,1,2])) then
|
||||||
if (((i == 1).and.(j == 2).and.(k == 3)) .or. &
|
math_LeviCivita = +1.0_pReal
|
||||||
((i == 2).and.(j == 3).and.(k == 1)) .or. &
|
elseif (all([i,j,k] == [3,2,1]) .or. all([i,j,k] == [2,1,3]) .or. all([i,j,k] == [1,3,2])) then
|
||||||
((i == 3).and.(j == 1).and.(k == 2))) math_civita = 1.0_pReal
|
math_LeviCivita = -1.0_pReal
|
||||||
if (((i == 1).and.(j == 3).and.(k == 2)) .or. &
|
else
|
||||||
((i == 2).and.(j == 1).and.(k == 3)) .or. &
|
math_LeviCivita = 0.0_pReal
|
||||||
((i == 3).and.(j == 2).and.(k == 1))) math_civita = -1.0_pReal
|
endif
|
||||||
|
|
||||||
end function math_civita
|
end function math_LeviCivita
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief kronecker delta function d_ij
|
!> @brief kronecker delta function d_ij
|
||||||
! d_ij = 1 if i = j
|
! d_ij = 1 if i = j
|
||||||
! d_ij = 0 otherwise
|
! d_ij = 0 otherwise
|
||||||
! inspired by http://fortraninacworld.blogspot.de/2012/12/ternary-operator.html
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
real(pReal) pure function math_delta(i,j)
|
real(pReal) pure function math_delta(i,j)
|
||||||
|
|
||||||
|
@ -317,7 +321,7 @@ end function math_cross
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief outer product A \otimes B of arbitrary sized vectors A and B
|
!> @brief outer product of arbitrary sized vectors (A ⊗ B / i,j)
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
pure function math_outer(A,B)
|
pure function math_outer(A,B)
|
||||||
|
|
||||||
|
@ -333,7 +337,7 @@ end function math_outer
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief outer product A \otimes B of arbitrary sized vectors A and B
|
!> @brief inner product of arbitrary sized vectors (A · B / i,i)
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
real(pReal) pure function math_inner(A,B)
|
real(pReal) pure function math_inner(A,B)
|
||||||
|
|
||||||
|
@ -346,31 +350,26 @@ end function math_inner
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief matrix multiplication 33xx33 = 1 (double contraction --> ij * ij)
|
!> @brief double contraction of 3x3 matrices (A : B / ij,ij)
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
real(pReal) pure function math_mul33xx33(A,B)
|
real(pReal) pure function math_tensordot(A,B)
|
||||||
|
|
||||||
real(pReal), dimension(3,3), intent(in) :: A,B
|
real(pReal), dimension(3,3), intent(in) :: A,B
|
||||||
integer :: i,j
|
|
||||||
real(pReal), dimension(3,3) :: C
|
|
||||||
|
|
||||||
do i=1,3; do j=1,3
|
math_tensordot = sum(A*B)
|
||||||
C(i,j) = A(i,j) * B(i,j)
|
|
||||||
enddo; enddo
|
|
||||||
math_mul33xx33 = sum(C)
|
|
||||||
|
|
||||||
end function math_mul33xx33
|
end function math_tensordot
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief matrix multiplication 3333x33 = 33 (double contraction --> ijkl *kl = ij)
|
!> @brief matrix double contraction 3333x33 = 33 (ijkl,kl)
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
pure function math_mul3333xx33(A,B)
|
pure function math_mul3333xx33(A,B)
|
||||||
|
|
||||||
real(pReal), dimension(3,3,3,3), intent(in) :: A
|
real(pReal), dimension(3,3,3,3), intent(in) :: A
|
||||||
real(pReal), dimension(3,3), intent(in) :: B
|
real(pReal), dimension(3,3), intent(in) :: B
|
||||||
real(pReal), dimension(3,3) :: math_mul3333xx33
|
real(pReal), dimension(3,3) :: math_mul3333xx33
|
||||||
integer :: i,j
|
integer :: i,j
|
||||||
|
|
||||||
do i=1,3; do j=1,3
|
do i=1,3; do j=1,3
|
||||||
math_mul3333xx33(i,j) = sum(A(i,j,1:3,1:3)*B(1:3,1:3))
|
math_mul3333xx33(i,j) = sum(A(i,j,1:3,1:3)*B(1:3,1:3))
|
||||||
|
@ -380,7 +379,7 @@ end function math_mul3333xx33
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief matrix multiplication 3333x3333 = 3333 (ijkl *klmn = ijmn)
|
!> @brief matrix multiplication 3333x3333 = 3333 (ijkl,klmn)
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
pure function math_mul3333xx3333(A,B)
|
pure function math_mul3333xx3333(A,B)
|
||||||
|
|
||||||
|
@ -402,8 +401,9 @@ end function math_mul3333xx3333
|
||||||
pure function math_exp33(A,n)
|
pure function math_exp33(A,n)
|
||||||
|
|
||||||
real(pReal), dimension(3,3), intent(in) :: A
|
real(pReal), dimension(3,3), intent(in) :: A
|
||||||
integer, intent(in), optional :: n
|
integer, intent(in), optional :: n
|
||||||
real(pReal), dimension(3,3) :: B, math_exp33
|
real(pReal), dimension(3,3) :: B, math_exp33
|
||||||
|
|
||||||
real(pReal) :: invFac
|
real(pReal) :: invFac
|
||||||
integer :: n_,i
|
integer :: n_,i
|
||||||
|
|
||||||
|
@ -428,15 +428,16 @@ end function math_exp33
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
!> @brief Cramer inversion of 33 matrix (function)
|
!> @brief Cramer inversion of 33 matrix (function)
|
||||||
!> @details Direct Cramer inversion of matrix A. Returns all zeroes if not possible, i.e.
|
!> @details Direct Cramer inversion of matrix A. Returns all zeroes if not possible, i.e.
|
||||||
! if determinant is close to zero
|
! if determinant is close to zero
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
pure function math_inv33(A)
|
pure function math_inv33(A)
|
||||||
|
|
||||||
real(pReal),dimension(3,3),intent(in) :: A
|
real(pReal), dimension(3,3), intent(in) :: A
|
||||||
real(pReal) :: DetA
|
real(pReal), dimension(3,3) :: math_inv33
|
||||||
real(pReal),dimension(3,3) :: math_inv33
|
|
||||||
logical :: error
|
real(pReal) :: DetA
|
||||||
|
logical :: error
|
||||||
|
|
||||||
call math_invert33(math_inv33,DetA,error,A)
|
call math_invert33(math_inv33,DetA,error,A)
|
||||||
if(error) math_inv33 = 0.0_pReal
|
if(error) math_inv33 = 0.0_pReal
|
||||||
|
@ -451,10 +452,10 @@ end function math_inv33
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
pure subroutine math_invert33(InvA, DetA, error, A)
|
pure subroutine math_invert33(InvA, DetA, error, A)
|
||||||
|
|
||||||
logical, intent(out) :: error
|
real(pReal), dimension(3,3), intent(out) :: InvA
|
||||||
real(pReal),dimension(3,3),intent(in) :: A
|
real(pReal), intent(out) :: DetA
|
||||||
real(pReal),dimension(3,3),intent(out) :: InvA
|
logical, intent(out) :: error
|
||||||
real(pReal), intent(out) :: DetA
|
real(pReal), dimension(3,3), intent(in) :: A
|
||||||
|
|
||||||
InvA(1,1) = A(2,2) * A(3,3) - A(2,3) * A(3,2)
|
InvA(1,1) = A(2,2) * A(3,3) - A(2,3) * A(3,2)
|
||||||
InvA(2,1) = -A(2,1) * A(3,3) + A(2,3) * A(3,1)
|
InvA(2,1) = -A(2,1) * A(3,3) + A(2,3) * A(3,1)
|
||||||
|
@ -529,12 +530,12 @@ subroutine math_invert(InvA, error, A)
|
||||||
dgetrf, &
|
dgetrf, &
|
||||||
dgetri
|
dgetri
|
||||||
|
|
||||||
invA = A
|
invA = A
|
||||||
call dgetrf(size(A,1),size(A,1),invA,size(A,1),ipiv,ierr)
|
call dgetrf(size(A,1),size(A,1),invA,size(A,1),ipiv,ierr)
|
||||||
error = (ierr /= 0)
|
error = (ierr /= 0)
|
||||||
call dgetri(size(A,1),InvA,size(A,1),ipiv,work,size(work,1),ierr)
|
call dgetri(size(A,1),InvA,size(A,1),ipiv,work,size(work,1),ierr)
|
||||||
error = error .or. (ierr /= 0)
|
error = error .or. (ierr /= 0)
|
||||||
|
|
||||||
end subroutine math_invert
|
end subroutine math_invert
|
||||||
|
|
||||||
|
|
||||||
|
@ -621,7 +622,7 @@ end function math_trace33
|
||||||
real(pReal) pure function math_det33(m)
|
real(pReal) pure function math_det33(m)
|
||||||
|
|
||||||
real(pReal), dimension(3,3), intent(in) :: m
|
real(pReal), dimension(3,3), intent(in) :: m
|
||||||
|
|
||||||
math_det33 = m(1,1)* (m(2,2)*m(3,3)-m(2,3)*m(3,2)) &
|
math_det33 = m(1,1)* (m(2,2)*m(3,3)-m(2,3)*m(3,2)) &
|
||||||
- m(1,2)* (m(2,1)*m(3,3)-m(2,3)*m(3,1)) &
|
- m(1,2)* (m(2,1)*m(3,3)-m(2,3)*m(3,1)) &
|
||||||
+ m(1,3)* (m(2,1)*m(3,2)-m(2,2)*m(3,1))
|
+ m(1,3)* (m(2,1)*m(3,2)-m(2,2)*m(3,1))
|
||||||
|
@ -635,7 +636,7 @@ end function math_det33
|
||||||
real(pReal) pure function math_detSym33(m)
|
real(pReal) pure function math_detSym33(m)
|
||||||
|
|
||||||
real(pReal), dimension(3,3), intent(in) :: m
|
real(pReal), dimension(3,3), intent(in) :: m
|
||||||
|
|
||||||
math_detSym33 = -(m(1,1)*m(2,3)**2 + m(2,2)*m(1,3)**2 + m(3,3)*m(1,2)**2) &
|
math_detSym33 = -(m(1,1)*m(2,3)**2 + m(2,2)*m(1,3)**2 + m(3,3)*m(1,2)**2) &
|
||||||
+ m(1,1)*m(2,2)*m(3,3) + 2.0_pReal * m(1,2)*m(1,3)*m(2,3)
|
+ m(1,1)*m(2,2)*m(3,3) + 2.0_pReal * m(1,2)*m(1,3)*m(2,3)
|
||||||
|
|
||||||
|
@ -649,9 +650,9 @@ pure function math_33to9(m33)
|
||||||
|
|
||||||
real(pReal), dimension(9) :: math_33to9
|
real(pReal), dimension(9) :: math_33to9
|
||||||
real(pReal), dimension(3,3), intent(in) :: m33
|
real(pReal), dimension(3,3), intent(in) :: m33
|
||||||
|
|
||||||
integer :: i
|
integer :: i
|
||||||
|
|
||||||
do i = 1, 9
|
do i = 1, 9
|
||||||
math_33to9(i) = m33(MAPPLAIN(1,i),MAPPLAIN(2,i))
|
math_33to9(i) = m33(MAPPLAIN(1,i),MAPPLAIN(2,i))
|
||||||
enddo
|
enddo
|
||||||
|
@ -666,7 +667,7 @@ pure function math_9to33(v9)
|
||||||
|
|
||||||
real(pReal), dimension(3,3) :: math_9to33
|
real(pReal), dimension(3,3) :: math_9to33
|
||||||
real(pReal), dimension(9), intent(in) :: v9
|
real(pReal), dimension(9), intent(in) :: v9
|
||||||
|
|
||||||
integer :: i
|
integer :: i
|
||||||
|
|
||||||
do i = 1, 9
|
do i = 1, 9
|
||||||
|
@ -687,10 +688,10 @@ pure function math_sym33to6(m33,weighted)
|
||||||
real(pReal), dimension(6) :: math_sym33to6
|
real(pReal), dimension(6) :: math_sym33to6
|
||||||
real(pReal), dimension(3,3), intent(in) :: m33 !< symmetric matrix (no internal check)
|
real(pReal), dimension(3,3), intent(in) :: m33 !< symmetric matrix (no internal check)
|
||||||
logical, optional, intent(in) :: weighted !< weight according to Mandel (.true. by default)
|
logical, optional, intent(in) :: weighted !< weight according to Mandel (.true. by default)
|
||||||
|
|
||||||
real(pReal), dimension(6) :: w
|
real(pReal), dimension(6) :: w
|
||||||
integer :: i
|
integer :: i
|
||||||
|
|
||||||
if(present(weighted)) then
|
if(present(weighted)) then
|
||||||
w = merge(NRMMANDEL,1.0_pReal,weighted)
|
w = merge(NRMMANDEL,1.0_pReal,weighted)
|
||||||
else
|
else
|
||||||
|
@ -699,7 +700,7 @@ pure function math_sym33to6(m33,weighted)
|
||||||
|
|
||||||
do i = 1, 6
|
do i = 1, 6
|
||||||
math_sym33to6(i) = w(i)*m33(MAPNYE(1,i),MAPNYE(2,i))
|
math_sym33to6(i) = w(i)*m33(MAPNYE(1,i),MAPNYE(2,i))
|
||||||
enddo
|
enddo
|
||||||
|
|
||||||
end function math_sym33to6
|
end function math_sym33to6
|
||||||
|
|
||||||
|
@ -718,7 +719,7 @@ pure function math_6toSym33(v6,weighted)
|
||||||
|
|
||||||
real(pReal), dimension(6) :: w
|
real(pReal), dimension(6) :: w
|
||||||
integer :: i
|
integer :: i
|
||||||
|
|
||||||
if(present(weighted)) then
|
if(present(weighted)) then
|
||||||
w = merge(INVNRMMANDEL,1.0_pReal,weighted)
|
w = merge(INVNRMMANDEL,1.0_pReal,weighted)
|
||||||
else
|
else
|
||||||
|
@ -781,7 +782,7 @@ pure function math_sym3333to66(m3333,weighted)
|
||||||
|
|
||||||
real(pReal), dimension(6) :: w
|
real(pReal), dimension(6) :: w
|
||||||
integer :: i,j
|
integer :: i,j
|
||||||
|
|
||||||
if(present(weighted)) then
|
if(present(weighted)) then
|
||||||
w = merge(NRMMANDEL,1.0_pReal,weighted)
|
w = merge(NRMMANDEL,1.0_pReal,weighted)
|
||||||
else
|
else
|
||||||
|
@ -806,10 +807,10 @@ pure function math_66toSym3333(m66,weighted)
|
||||||
real(pReal), dimension(3,3,3,3) :: math_66toSym3333
|
real(pReal), dimension(3,3,3,3) :: math_66toSym3333
|
||||||
real(pReal), dimension(6,6), intent(in) :: m66
|
real(pReal), dimension(6,6), intent(in) :: m66
|
||||||
logical, optional, intent(in) :: weighted !< weight according to Mandel (.true. by default)
|
logical, optional, intent(in) :: weighted !< weight according to Mandel (.true. by default)
|
||||||
|
|
||||||
real(pReal), dimension(6) :: w
|
real(pReal), dimension(6) :: w
|
||||||
integer :: i,j
|
integer :: i,j
|
||||||
|
|
||||||
if(present(weighted)) then
|
if(present(weighted)) then
|
||||||
w = merge(INVNRMMANDEL,1.0_pReal,weighted)
|
w = merge(INVNRMMANDEL,1.0_pReal,weighted)
|
||||||
else
|
else
|
||||||
|
@ -909,48 +910,48 @@ end subroutine math_eigenValuesVectorsSym
|
||||||
! ToDo: has wrong oder of arguments
|
! ToDo: has wrong oder of arguments
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
subroutine math_eigenValuesVectorsSym33(m,values,vectors)
|
subroutine math_eigenValuesVectorsSym33(m,values,vectors)
|
||||||
|
|
||||||
real(pReal), dimension(3,3),intent(in) :: m
|
real(pReal), dimension(3,3),intent(in) :: m
|
||||||
real(pReal), dimension(3), intent(out) :: values
|
real(pReal), dimension(3), intent(out) :: values
|
||||||
real(pReal), dimension(3,3),intent(out) :: vectors
|
real(pReal), dimension(3,3),intent(out) :: vectors
|
||||||
real(pReal) :: T, U, norm, threshold
|
real(pReal) :: T, U, norm, threshold
|
||||||
logical :: error
|
logical :: error
|
||||||
|
|
||||||
values = math_eigenvaluesSym33(m)
|
values = math_eigenvaluesSym33(m)
|
||||||
|
|
||||||
vectors(1:3,2) = [ m(1, 2) * m(2, 3) - m(1, 3) * m(2, 2), &
|
vectors(1:3,2) = [ m(1, 2) * m(2, 3) - m(1, 3) * m(2, 2), &
|
||||||
m(1, 3) * m(1, 2) - m(2, 3) * m(1, 1), &
|
m(1, 3) * m(1, 2) - m(2, 3) * m(1, 1), &
|
||||||
m(1, 2)**2]
|
m(1, 2)**2]
|
||||||
|
|
||||||
T = maxval(abs(values))
|
T = maxval(abs(values))
|
||||||
U = max(T, T**2)
|
U = max(T, T**2)
|
||||||
threshold = sqrt(5.68e-14_pReal * U**2)
|
threshold = sqrt(5.68e-14_pReal * U**2)
|
||||||
|
|
||||||
! Calculate first eigenvector by the formula v[0] = (m - lambda[0]).e1 x (m - lambda[0]).e2
|
! Calculate first eigenvector by the formula v[0] = (m - lambda[0]).e1 x (m - lambda[0]).e2
|
||||||
vectors(1:3,1) = [ vectors(1,2) + m(1, 3) * values(1), &
|
vectors(1:3,1) = [ vectors(1,2) + m(1, 3) * values(1), &
|
||||||
vectors(2,2) + m(2, 3) * values(1), &
|
vectors(2,2) + m(2, 3) * values(1), &
|
||||||
(m(1,1) - values(1)) * (m(2,2) - values(1)) - vectors(3,2)]
|
(m(1,1) - values(1)) * (m(2,2) - values(1)) - vectors(3,2)]
|
||||||
norm = norm2(vectors(1:3, 1))
|
norm = norm2(vectors(1:3, 1))
|
||||||
|
|
||||||
fallback1: if(norm < threshold) then
|
fallback1: if(norm < threshold) then
|
||||||
call math_eigenValuesVectorsSym(m,values,vectors,error)
|
call math_eigenValuesVectorsSym(m,values,vectors,error)
|
||||||
return
|
return
|
||||||
endif fallback1
|
endif fallback1
|
||||||
|
|
||||||
vectors(1:3,1) = vectors(1:3, 1) / norm
|
vectors(1:3,1) = vectors(1:3, 1) / norm
|
||||||
|
|
||||||
! Calculate second eigenvector by the formula v[1] = (m - lambda[1]).e1 x (m - lambda[1]).e2
|
! Calculate second eigenvector by the formula v[1] = (m - lambda[1]).e1 x (m - lambda[1]).e2
|
||||||
vectors(1:3,2) = [ vectors(1,2) + m(1, 3) * values(2), &
|
vectors(1:3,2) = [ vectors(1,2) + m(1, 3) * values(2), &
|
||||||
vectors(2,2) + m(2, 3) * values(2), &
|
vectors(2,2) + m(2, 3) * values(2), &
|
||||||
(m(1,1) - values(2)) * (m(2,2) - values(2)) - vectors(3,2)]
|
(m(1,1) - values(2)) * (m(2,2) - values(2)) - vectors(3,2)]
|
||||||
norm = norm2(vectors(1:3, 2))
|
norm = norm2(vectors(1:3, 2))
|
||||||
|
|
||||||
fallback2: if(norm < threshold) then
|
fallback2: if(norm < threshold) then
|
||||||
call math_eigenValuesVectorsSym(m,values,vectors,error)
|
call math_eigenValuesVectorsSym(m,values,vectors,error)
|
||||||
return
|
return
|
||||||
endif fallback2
|
endif fallback2
|
||||||
vectors(1:3,2) = vectors(1:3, 2) / norm
|
vectors(1:3,2) = vectors(1:3, 2) / norm
|
||||||
|
|
||||||
! Calculate third eigenvector according to v[2] = v[0] x v[1]
|
! Calculate third eigenvector according to v[2] = v[0] x v[1]
|
||||||
vectors(1:3,3) = math_cross(vectors(1:3,1),vectors(1:3,2))
|
vectors(1:3,3) = math_cross(vectors(1:3,1),vectors(1:3,2))
|
||||||
|
|
||||||
|
@ -968,11 +969,11 @@ function math_eigenvectorBasisSym(m)
|
||||||
real(pReal), dimension(size(m,1),size(m,1)) :: math_eigenvectorBasisSym
|
real(pReal), dimension(size(m,1),size(m,1)) :: math_eigenvectorBasisSym
|
||||||
logical :: error
|
logical :: error
|
||||||
integer :: i
|
integer :: i
|
||||||
|
|
||||||
math_eigenvectorBasisSym = 0.0_pReal
|
math_eigenvectorBasisSym = 0.0_pReal
|
||||||
call math_eigenValuesVectorsSym(m,values,vectors,error)
|
call math_eigenValuesVectorsSym(m,values,vectors,error)
|
||||||
if(error) return
|
if(error) return
|
||||||
|
|
||||||
do i=1, size(m,1)
|
do i=1, size(m,1)
|
||||||
math_eigenvectorBasisSym = math_eigenvectorBasisSym &
|
math_eigenvectorBasisSym = math_eigenvectorBasisSym &
|
||||||
+ sqrt(values(i)) * math_outer(vectors(:,i),vectors(:,i))
|
+ sqrt(values(i)) * math_outer(vectors(:,i),vectors(:,i))
|
||||||
|
@ -992,13 +993,13 @@ pure function math_eigenvectorBasisSym33(m)
|
||||||
real(pReal) :: P, Q, rho, phi
|
real(pReal) :: P, Q, rho, phi
|
||||||
real(pReal), parameter :: TOL=1.e-14_pReal
|
real(pReal), parameter :: TOL=1.e-14_pReal
|
||||||
real(pReal), dimension(3,3,3) :: N, EB
|
real(pReal), dimension(3,3,3) :: N, EB
|
||||||
|
|
||||||
invariants = math_invariantsSym33(m)
|
invariants = math_invariantsSym33(m)
|
||||||
EB = 0.0_pReal
|
EB = 0.0_pReal
|
||||||
|
|
||||||
P = invariants(2)-invariants(1)**2.0_pReal/3.0_pReal
|
P = invariants(2)-invariants(1)**2.0_pReal/3.0_pReal
|
||||||
Q = -2.0_pReal/27.0_pReal*invariants(1)**3.0_pReal+product(invariants(1:2))/3.0_pReal-invariants(3)
|
Q = -2.0_pReal/27.0_pReal*invariants(1)**3.0_pReal+product(invariants(1:2))/3.0_pReal-invariants(3)
|
||||||
|
|
||||||
threeSimilarEigenvalues: if(all(abs([P,Q]) < TOL)) then
|
threeSimilarEigenvalues: if(all(abs([P,Q]) < TOL)) then
|
||||||
values = invariants(1)/3.0_pReal
|
values = invariants(1)/3.0_pReal
|
||||||
! this is not really correct, but at least the basis is correct
|
! this is not really correct, but at least the basis is correct
|
||||||
|
@ -1016,7 +1017,7 @@ pure function math_eigenvectorBasisSym33(m)
|
||||||
N(1:3,1:3,1) = m-values(1)*math_I3
|
N(1:3,1:3,1) = m-values(1)*math_I3
|
||||||
N(1:3,1:3,2) = m-values(2)*math_I3
|
N(1:3,1:3,2) = m-values(2)*math_I3
|
||||||
N(1:3,1:3,3) = m-values(3)*math_I3
|
N(1:3,1:3,3) = m-values(3)*math_I3
|
||||||
twoSimilarEigenvalues: if(abs(values(1)-values(2)) < TOL) then
|
twoSimilarEigenvalues: if(abs(values(1)-values(2)) < TOL) then
|
||||||
EB(1:3,1:3,3)=matmul(N(1:3,1:3,1),N(1:3,1:3,2))/ &
|
EB(1:3,1:3,3)=matmul(N(1:3,1:3,1),N(1:3,1:3,2))/ &
|
||||||
((values(3)-values(1))*(values(3)-values(2)))
|
((values(3)-values(1))*(values(3)-values(2)))
|
||||||
EB(1:3,1:3,1)=math_I3-EB(1:3,1:3,3)
|
EB(1:3,1:3,1)=math_I3-EB(1:3,1:3,3)
|
||||||
|
@ -1024,7 +1025,7 @@ pure function math_eigenvectorBasisSym33(m)
|
||||||
EB(1:3,1:3,1)=matmul(N(1:3,1:3,2),N(1:3,1:3,3))/ &
|
EB(1:3,1:3,1)=matmul(N(1:3,1:3,2),N(1:3,1:3,3))/ &
|
||||||
((values(1)-values(2))*(values(1)-values(3)))
|
((values(1)-values(2))*(values(1)-values(3)))
|
||||||
EB(1:3,1:3,2)=math_I3-EB(1:3,1:3,1)
|
EB(1:3,1:3,2)=math_I3-EB(1:3,1:3,1)
|
||||||
elseif(abs(values(3)-values(1)) < TOL) then twoSimilarEigenvalues
|
elseif(abs(values(3)-values(1)) < TOL) then twoSimilarEigenvalues
|
||||||
EB(1:3,1:3,2)=matmul(N(1:3,1:3,1),N(1:3,1:3,3))/ &
|
EB(1:3,1:3,2)=matmul(N(1:3,1:3,1),N(1:3,1:3,3))/ &
|
||||||
((values(2)-values(1))*(values(2)-values(3)))
|
((values(2)-values(1))*(values(2)-values(3)))
|
||||||
EB(1:3,1:3,1)=math_I3-EB(1:3,1:3,2)
|
EB(1:3,1:3,1)=math_I3-EB(1:3,1:3,2)
|
||||||
|
@ -1080,7 +1081,7 @@ pure function math_eigenvectorBasisSym33_log(m)
|
||||||
N(1:3,1:3,1) = m-values(1)*math_I3
|
N(1:3,1:3,1) = m-values(1)*math_I3
|
||||||
N(1:3,1:3,2) = m-values(2)*math_I3
|
N(1:3,1:3,2) = m-values(2)*math_I3
|
||||||
N(1:3,1:3,3) = m-values(3)*math_I3
|
N(1:3,1:3,3) = m-values(3)*math_I3
|
||||||
twoSimilarEigenvalues: if(abs(values(1)-values(2)) < TOL) then
|
twoSimilarEigenvalues: if(abs(values(1)-values(2)) < TOL) then
|
||||||
EB(1:3,1:3,3)=matmul(N(1:3,1:3,1),N(1:3,1:3,2))/ &
|
EB(1:3,1:3,3)=matmul(N(1:3,1:3,1),N(1:3,1:3,2))/ &
|
||||||
((values(3)-values(1))*(values(3)-values(2)))
|
((values(3)-values(1))*(values(3)-values(2)))
|
||||||
EB(1:3,1:3,1)=math_I3-EB(1:3,1:3,3)
|
EB(1:3,1:3,1)=math_I3-EB(1:3,1:3,3)
|
||||||
|
@ -1088,7 +1089,7 @@ pure function math_eigenvectorBasisSym33_log(m)
|
||||||
EB(1:3,1:3,1)=matmul(N(1:3,1:3,2),N(1:3,1:3,3))/ &
|
EB(1:3,1:3,1)=matmul(N(1:3,1:3,2),N(1:3,1:3,3))/ &
|
||||||
((values(1)-values(2))*(values(1)-values(3)))
|
((values(1)-values(2))*(values(1)-values(3)))
|
||||||
EB(1:3,1:3,2)=math_I3-EB(1:3,1:3,1)
|
EB(1:3,1:3,2)=math_I3-EB(1:3,1:3,1)
|
||||||
elseif(abs(values(3)-values(1)) < TOL) then twoSimilarEigenvalues
|
elseif(abs(values(3)-values(1)) < TOL) then twoSimilarEigenvalues
|
||||||
EB(1:3,1:3,2)=matmul(N(1:3,1:3,1),N(1:3,1:3,3))/ &
|
EB(1:3,1:3,2)=matmul(N(1:3,1:3,1),N(1:3,1:3,3))/ &
|
||||||
((values(2)-values(1))*(values(2)-values(3)))
|
((values(2)-values(1))*(values(2)-values(3)))
|
||||||
EB(1:3,1:3,1)=math_I3-EB(1:3,1:3,2)
|
EB(1:3,1:3,1)=math_I3-EB(1:3,1:3,2)
|
||||||
|
@ -1136,7 +1137,7 @@ end function math_rotationalPart33
|
||||||
! will return NaN on error
|
! will return NaN on error
|
||||||
!--------------------------------------------------------------------------------------------------
|
!--------------------------------------------------------------------------------------------------
|
||||||
function math_eigenvaluesSym(m)
|
function math_eigenvaluesSym(m)
|
||||||
|
|
||||||
real(pReal), dimension(:,:), intent(in) :: m
|
real(pReal), dimension(:,:), intent(in) :: m
|
||||||
real(pReal), dimension(size(m,1)) :: math_eigenvaluesSym
|
real(pReal), dimension(size(m,1)) :: math_eigenvaluesSym
|
||||||
real(pReal), dimension(size(m,1),size(m,1)) :: m_
|
real(pReal), dimension(size(m,1),size(m,1)) :: m_
|
||||||
|
@ -1221,7 +1222,7 @@ integer pure function math_binomial(n,k)
|
||||||
|
|
||||||
integer, intent(in) :: n, k
|
integer, intent(in) :: n, k
|
||||||
integer :: i, k_, n_
|
integer :: i, k_, n_
|
||||||
|
|
||||||
k_ = min(k,n-k)
|
k_ = min(k,n-k)
|
||||||
n_ = n
|
n_ = n
|
||||||
math_binomial = merge(1,0,k_>-1) ! handling special cases k < 0 or k > n
|
math_binomial = merge(1,0,k_>-1) ! handling special cases k < 0 or k > n
|
||||||
|
@ -1244,7 +1245,7 @@ integer pure function math_multinomial(alpha)
|
||||||
math_multinomial = 1
|
math_multinomial = 1
|
||||||
do i = 1, size(alpha)
|
do i = 1, size(alpha)
|
||||||
math_multinomial = math_multinomial*math_binomial(sum(alpha(1:i)),alpha(i))
|
math_multinomial = math_multinomial*math_binomial(sum(alpha(1:i)),alpha(i))
|
||||||
enddo
|
enddo
|
||||||
|
|
||||||
end function math_multinomial
|
end function math_multinomial
|
||||||
|
|
||||||
|
@ -1307,6 +1308,7 @@ subroutine unitTest
|
||||||
sort_out_ = reshape([-1,-1, +1,+5, +5,+6, +3,-2],[2,4])
|
sort_out_ = reshape([-1,-1, +1,+5, +5,+6, +3,-2],[2,4])
|
||||||
|
|
||||||
integer, dimension(5) :: range_out_ = [1,2,3,4,5]
|
integer, dimension(5) :: range_out_ = [1,2,3,4,5]
|
||||||
|
integer, dimension(3) :: ijk
|
||||||
|
|
||||||
real(pReal) :: det
|
real(pReal) :: det
|
||||||
real(pReal), dimension(3) :: v3_1,v3_2,v3_3,v3_4
|
real(pReal), dimension(3) :: v3_1,v3_2,v3_3,v3_4
|
||||||
|
@ -1349,7 +1351,7 @@ subroutine unitTest
|
||||||
call random_number(v9)
|
call random_number(v9)
|
||||||
if(any(dNeq(math_33to9(math_9to33(v9)),v9))) &
|
if(any(dNeq(math_33to9(math_9to33(v9)),v9))) &
|
||||||
call IO_error(0,ext_msg='math_33to9/math_9to33')
|
call IO_error(0,ext_msg='math_33to9/math_9to33')
|
||||||
|
|
||||||
call random_number(t99)
|
call random_number(t99)
|
||||||
if(any(dNeq(math_3333to99(math_99to3333(t99)),t99))) &
|
if(any(dNeq(math_3333to99(math_99to3333(t99)),t99))) &
|
||||||
call IO_error(0,ext_msg='math_3333to99/math_99to3333')
|
call IO_error(0,ext_msg='math_3333to99/math_99to3333')
|
||||||
|
@ -1378,7 +1380,7 @@ subroutine unitTest
|
||||||
call random_number(t33)
|
call random_number(t33)
|
||||||
if(dNeq(math_det33(math_symmetric33(t33)),math_detSym33(math_symmetric33(t33)),tol=1.0e-12_pReal)) &
|
if(dNeq(math_det33(math_symmetric33(t33)),math_detSym33(math_symmetric33(t33)),tol=1.0e-12_pReal)) &
|
||||||
call IO_error(0,ext_msg='math_det33/math_detSym33')
|
call IO_error(0,ext_msg='math_det33/math_detSym33')
|
||||||
|
|
||||||
if(any(dNeq0(math_identity2nd(3),math_inv33(math_I3)))) &
|
if(any(dNeq0(math_identity2nd(3),math_inv33(math_I3)))) &
|
||||||
call IO_error(0,ext_msg='math_inv33(math_I3)')
|
call IO_error(0,ext_msg='math_inv33(math_I3)')
|
||||||
|
|
||||||
|
@ -1410,18 +1412,28 @@ subroutine unitTest
|
||||||
if(any(dNeq0(txx_2,txx) .or. e)) &
|
if(any(dNeq0(txx_2,txx) .or. e)) &
|
||||||
call IO_error(0,ext_msg='math_invert(txx)/math_identity2nd')
|
call IO_error(0,ext_msg='math_invert(txx)/math_identity2nd')
|
||||||
|
|
||||||
call math_invert(t99_2,e,t99) ! not sure how likely it is that we get a singular matrix
|
call math_invert(t99_2,e,t99) ! not sure how likely it is that we get a singular matrix
|
||||||
if(any(dNeq0(matmul(t99_2,t99)-math_identity2nd(9),tol=1.0e-9_pReal)) .or. e) &
|
if(any(dNeq0(matmul(t99_2,t99)-math_identity2nd(9),tol=1.0e-9_pReal)) .or. e) &
|
||||||
call IO_error(0,ext_msg='math_invert(t99)')
|
call IO_error(0,ext_msg='math_invert(t99)')
|
||||||
|
|
||||||
if(any(dNeq(math_clip([4.0_pReal,9.0_pReal],5.0_pReal,6.5_pReal),[5.0_pReal,6.5_pReal]))) &
|
if(any(dNeq(math_clip([4.0_pReal,9.0_pReal],5.0_pReal,6.5_pReal),[5.0_pReal,6.5_pReal]))) &
|
||||||
call IO_error(0,ext_msg='math_clip')
|
call IO_error(0,ext_msg='math_clip')
|
||||||
|
|
||||||
if(math_factorial(10) /= 3628800) &
|
if(math_factorial(10) /= 3628800) &
|
||||||
call IO_error(0,ext_msg='math_factorial')
|
call IO_error(0,ext_msg='math_factorial')
|
||||||
|
|
||||||
if(math_binomial(49,6) /= 13983816) &
|
if(math_binomial(49,6) /= 13983816) &
|
||||||
call IO_error(0,ext_msg='math_binomial')
|
call IO_error(0,ext_msg='math_binomial')
|
||||||
|
|
||||||
|
ijk = cshift([1,2,3],int(r*1.0e2_pReal))
|
||||||
|
if(dNeq(math_LeviCivita(ijk(1),ijk(2),ijk(3)),+1.0_pReal)) &
|
||||||
|
call IO_error(0,ext_msg='math_LeviCivita(even)')
|
||||||
|
ijk = cshift([3,2,1],int(r*2.0e2_pReal))
|
||||||
|
if(dNeq(math_LeviCivita(ijk(1),ijk(2),ijk(3)),-1.0_pReal)) &
|
||||||
|
call IO_error(0,ext_msg='math_LeviCivita(odd)')
|
||||||
|
ijk = cshift([2,2,1],int(r*2.0e2_pReal))
|
||||||
|
if(dNeq0(math_LeviCivita(ijk(1),ijk(2),ijk(3))))&
|
||||||
|
call IO_error(0,ext_msg='math_LeviCivita')
|
||||||
|
|
||||||
end subroutine unitTest
|
end subroutine unitTest
|
||||||
|
|
||||||
|
|
Loading…
Reference in New Issue