Merge branch 'misc-improvements' of magit1.mpie.de:/damask/DAMASK into misc-improvements
This commit is contained in:
Martin Diehl
commit
9d7158b51a
2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit 72d526e5750366a9efe4d1fd9d92e0d1ecd2cd38
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Subproject commit 8dde2a68538b7cffbe9d370e2b60be90a31627ab
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@ -2,6 +2,7 @@
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import os
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import sys
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from io import StringIO
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from optparse import OptionParser
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import numpy as np
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@ -15,91 +16,82 @@ scriptID = ' '.join([scriptName,damask.version])
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slipSystems = {
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'fcc':
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np.array([
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# Slip direction Plane normal
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[ 0, 1,-1, 1, 1, 1, ],
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[-1, 0, 1, 1, 1, 1, ],
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[ 1,-1, 0, 1, 1, 1, ],
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[ 0,-1,-1, -1,-1, 1, ],
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[ 1, 0, 1, -1,-1, 1, ],
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[-1, 1, 0, -1,-1, 1, ],
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[ 0,-1, 1, 1,-1,-1, ],
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[-1, 0,-1, 1,-1,-1, ],
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[ 1, 1, 0, 1,-1,-1, ],
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[ 0, 1, 1, -1, 1,-1, ],
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[ 1, 0,-1, -1, 1,-1, ],
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[-1,-1, 0, -1, 1,-1, ],
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],'f'),
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[+0,+1,-1 , +1,+1,+1],
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[-1,+0,+1 , +1,+1,+1],
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[+1,-1,+0 , +1,+1,+1],
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[+0,-1,-1 , -1,-1,+1],
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[+1,+0,+1 , -1,-1,+1],
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[-1,+1,+0 , -1,-1,+1],
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[+0,-1,+1 , +1,-1,-1],
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[-1,+0,-1 , +1,-1,-1],
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[+1,+1,+0 , +1,-1,-1],
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[+0,+1,+1 , -1,+1,-1],
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[+1,+0,-1 , -1,+1,-1],
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[-1,-1,+0 , -1,+1,-1],
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],'d'),
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'bcc':
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np.array([
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# Slip system <111>{110}
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[ 1,-1, 1, 0, 1, 1, ],
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[-1,-1, 1, 0, 1, 1, ],
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[ 1, 1, 1, 0,-1, 1, ],
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[-1, 1, 1, 0,-1, 1, ],
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[-1, 1, 1, 1, 0, 1, ],
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[-1,-1, 1, 1, 0, 1, ],
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[ 1, 1, 1, -1, 0, 1, ],
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[ 1,-1, 1, -1, 0, 1, ],
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[-1, 1, 1, 1, 1, 0, ],
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[-1, 1,-1, 1, 1, 0, ],
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[ 1, 1, 1, -1, 1, 0, ],
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[ 1, 1,-1, -1, 1, 0, ],
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# Slip system <111>{112}
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[-1, 1, 1, 2, 1, 1, ],
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[ 1, 1, 1, -2, 1, 1, ],
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[ 1, 1,-1, 2,-1, 1, ],
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[ 1,-1, 1, 2, 1,-1, ],
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[ 1,-1, 1, 1, 2, 1, ],
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[ 1, 1,-1, -1, 2, 1, ],
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[ 1, 1, 1, 1,-2, 1, ],
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[-1, 1, 1, 1, 2,-1, ],
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[ 1, 1,-1, 1, 1, 2, ],
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[ 1,-1, 1, -1, 1, 2, ],
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[-1, 1, 1, 1,-1, 2, ],
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[ 1, 1, 1, 1, 1,-2, ],
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],'f'),
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[+1,-1,+1 , +0,+1,+1],
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[-1,-1,+1 , +0,+1,+1],
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[+1,+1,+1 , +0,-1,+1],
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[-1,+1,+1 , +0,-1,+1],
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[-1,+1,+1 , +1,+0,+1],
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[-1,-1,+1 , +1,+0,+1],
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[+1,+1,+1 , -1,+0,+1],
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[+1,-1,+1 , -1,+0,+1],
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[-1,+1,+1 , +1,+1,+0],
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[-1,+1,-1 , +1,+1,+0],
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[+1,+1,+1 , -1,+1,+0],
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[+1,+1,-1 , -1,+1,+0],
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[-1,+1,+1 , +2,+1,+1],
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[+1,+1,+1 , -2,+1,+1],
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[+1,+1,-1 , +2,-1,+1],
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[+1,-1,+1 , +2,+1,-1],
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[+1,-1,+1 , +1,+2,+1],
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[+1,+1,-1 , -1,+2,+1],
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[+1,+1,+1 , +1,-2,+1],
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[-1,+1,+1 , +1,+2,-1],
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[+1,+1,-1 , +1,+1,+2],
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[+1,-1,+1 , -1,+1,+2],
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[-1,+1,+1 , +1,-1,+2],
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[+1,+1,+1 , +1,+1,-2],
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],'d'),
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'hex':
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np.array([
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# Basal systems <11.0>{00.1} (independent of c/a-ratio, Bravais notation (4 coordinate base))
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[ 2, -1, -1, 0, 0, 0, 0, 1, ],
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[-1, 2, -1, 0, 0, 0, 0, 1, ],
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[-1, -1, 2, 0, 0, 0, 0, 1, ],
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# 1st type prismatic systems <11.0>{10.0} (independent of c/a-ratio)
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[ 2, -1, -1, 0, 0, 1, -1, 0, ],
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[-1, 2, -1, 0, -1, 0, 1, 0, ],
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[-1, -1, 2, 0, 1, -1, 0, 0, ],
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# 2nd type prismatic systems <10.0>{11.0} -- a slip; plane normals independent of c/a-ratio
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[ 0, 1, -1, 0, 2, -1, -1, 0, ],
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[-1, 0, 1, 0, -1, 2, -1, 0, ],
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[ 1, -1, 0, 0, -1, -1, 2, 0, ],
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# 1st type 1st order pyramidal systems <11.0>{-11.1} -- plane normals depend on the c/a-ratio
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[ 2, -1, -1, 0, 0, 1, -1, 1, ],
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[-1, 2, -1, 0, -1, 0, 1, 1, ],
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[-1, -1, 2, 0, 1, -1, 0, 1, ],
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[ 1, 1, -2, 0, -1, 1, 0, 1, ],
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[-2, 1, 1, 0, 0, -1, 1, 1, ],
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[ 1, -2, 1, 0, 1, 0, -1, 1, ],
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# pyramidal system: c+a slip <11.3>{-10.1} -- plane normals depend on the c/a-ratio
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[ 2, -1, -1, 3, -1, 1, 0, 1, ],
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[ 1, -2, 1, 3, -1, 1, 0, 1, ],
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[-1, -1, 2, 3, 1, 0, -1, 1, ],
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[-2, 1, 1, 3, 1, 0, -1, 1, ],
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[-1, 2, -1, 3, 0, -1, 1, 1, ],
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[ 1, 1, -2, 3, 0, -1, 1, 1, ],
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[-2, 1, 1, 3, 1, -1, 0, 1, ],
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[-1, 2, -1, 3, 1, -1, 0, 1, ],
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[ 1, 1, -2, 3, -1, 0, 1, 1, ],
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[ 2, -1, -1, 3, -1, 0, 1, 1, ],
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[ 1, -2, 1, 3, 0, 1, -1, 1, ],
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[-1, -1, 2, 3, 0, 1, -1, 1, ],
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# pyramidal system: c+a slip <11.3>{-1-1.2} -- as for hexagonal ice (Castelnau et al. 1996, similar to twin system found below)
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[ 2, -1, -1, 3, -2, 1, 1, 2, ], # sorted according to similar twin system
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[-1, 2, -1, 3, 1, -2, 1, 2, ], # <11.3>{-1-1.2} shear = 2((c/a)^2-2)/(3 c/a)
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[-1, -1, 2, 3, 1, 1, -2, 2, ],
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[-2, 1, 1, 3, 2, -1, -1, 2, ],
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[ 1, -2, 1, 3, -1, 2, -1, 2, ],
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[ 1, 1, -2, 3, -1, -1, 2, 2, ],
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],'f'),
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[+2,-1,-1,+0 , +0,+0,+0,+1],
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[-1,+2,-1,+0 , +0,+0,+0,+1],
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[-1,-1,+2,+0 , +0,+0,+0,+1],
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[+2,-1,-1,+0 , +0,+1,-1,+0],
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[-1,+2,-1,+0 , -1,+0,+1,+0],
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[-1,-1,+2,+0 , +1,-1,+0,+0],
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[-1,+1,+0,+0 , +1,+1,-2,+0],
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[+0,-1,+1,+0 , -2,+1,+1,+0],
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[+1,+0,-1,+0 , +1,-2,+1,+0],
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[-1,+2,-1,+0 , +1,+0,-1,+1],
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[-2,+1,+1,+0 , +0,+1,-1,+1],
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[-1,-1,+2,+0 , -1,+1,+0,+1],
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[+1,-2,+1,+0 , -1,+0,+1,+1],
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[+2,-1,-1,+0 , +0,-1,+1,+1],
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[+1,+1,-2,+0 , +1,-1,+0,+1],
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[-2,+1,+1,+3 , +1,+0,-1,+1],
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[-1,-1,+2,+3 , +1,+0,-1,+1],
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[-1,-1,+2,+3 , +0,+1,-1,+1],
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[+1,-2,+1,+3 , +0,+1,-1,+1],
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[+1,-2,+1,+3 , -1,+1,+0,+1],
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[+2,-1,-1,+3 , -1,+1,+0,+1],
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[+2,-1,-1,+3 , -1,+0,+1,+1],
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[+1,+1,-2,+3 , -1,+0,+1,+1],
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[+1,+1,-2,+3 , +0,-1,+1,+1],
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[-1,+2,-1,+3 , +0,-1,+1,+1],
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[-1,+2,-1,+3 , +1,-1,+0,+1],
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[-2,+1,+1,+3 , +1,-1,+0,+1],
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[-1,-1,+2,+3 , +1,+1,-2,+2],
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[+1,-2,+1,+3 , -1,+2,-1,+2],
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[+2,-1,-1,+3 , -2,+1,+1,+2],
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[+1,+1,-2,+3 , -1,-1,+2,+2],
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[-1,+2,-1,+3 , +1,-2,+1,+2],
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[-2,+1,+1,+3 , +2,-1,-1,+2],
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],'d'),
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}
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# --------------------------------------------------------------------
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@ -111,11 +103,11 @@ Add columns listing Schmid factors (and optional trace vector of selected system
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""", version = scriptID)
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latticeChoices = ('fcc','bcc','hex')
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lattice_choices = list(slipSystems.keys())
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parser.add_option('-l',
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'--lattice',
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dest = 'lattice', type = 'choice', choices = latticeChoices, metavar='string',
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help = 'type of lattice structure [%default] {}'.format(latticeChoices))
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dest = 'lattice', type = 'choice', choices = lattice_choices, metavar='string',
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help = 'type of lattice structure [%default] {}'.format(lattice_choices))
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parser.add_option('--covera',
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dest = 'CoverA', type = 'float', metavar = 'float',
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help = 'C over A ratio for hexagonal systems [%default]')
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@ -138,88 +130,63 @@ parser.add_option('-o',
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parser.set_defaults(force = (0.0,0.0,1.0),
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quaternion='orientation',
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normal = None,
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lattice = latticeChoices[0],
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lattice = lattice_choices[0],
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CoverA = np.sqrt(8./3.),
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)
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(options, filenames) = parser.parse_args()
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force = np.array(options.force)
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force /= np.linalg.norm(force)
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if options.normal is not None:
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normal = np.array(options.normal)
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normal /= np.linalg.norm(normal)
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if abs(np.dot(force,normal)) > 1e-3:
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parser.error('stress plane normal not orthogonal to force direction')
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else:
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normal = force
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slip_direction = np.zeros((len(slipSystems[options.lattice]),3),'f')
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slip_normal = np.zeros_like(slip_direction)
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if options.lattice in latticeChoices[:2]:
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slip_direction = slipSystems[options.lattice][:,:3]
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slip_normal = slipSystems[options.lattice][:,3:]
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elif options.lattice == latticeChoices[2]:
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# convert 4 Miller index notation of hex to orthogonal 3 Miller index notation
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for i in range(len(slip_direction)):
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slip_direction[i] = np.array([slipSystems['hex'][i,0]*1.5,
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(slipSystems['hex'][i,0] + 2.*slipSystems['hex'][i,1])*0.5*np.sqrt(3),
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slipSystems['hex'][i,3]*options.CoverA,
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])
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slip_normal[i] = np.array([slipSystems['hex'][i,4],
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(slipSystems['hex'][i,4] + 2.*slipSystems['hex'][i,5])/np.sqrt(3),
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slipSystems['hex'][i,7]/options.CoverA,
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])
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slip_direction /= np.tile(np.linalg.norm(slip_direction,axis=1),(3,1)).T
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slip_normal /= np.tile(np.linalg.norm(slip_normal ,axis=1),(3,1)).T
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# --- loop over input files ------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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force = np.array(options.force)/np.linalg.norm(options.force)
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if options.normal is not None:
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normal = np.array(options.normal)/np.linalg.norm(options.ormal)
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if abs(np.dot(force,normal)) > 1e-3:
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parser.error('stress plane normal not orthogonal to force direction')
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else:
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normal = force
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if options.lattice in ['bcc','fcc']:
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slip_direction = slipSystems[options.lattice][:,:3]
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slip_normal = slipSystems[options.lattice][:,3:]
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elif options.lattice == 'hex':
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slip_direction = np.zeros((len(slipSystems['hex']),3),'d')
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slip_normal = np.zeros_like(slip_direction)
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# convert 4 Miller index notation of hex to orthogonal 3 Miller index notation
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for i in range(len(slip_direction)):
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slip_direction[i] = np.array([slipSystems['hex'][i,0]*1.5,
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(slipSystems['hex'][i,0] + 2.*slipSystems['hex'][i,1])*0.5*np.sqrt(3),
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slipSystems['hex'][i,3]*options.CoverA,
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])
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slip_normal[i] = np.array([slipSystems['hex'][i,4],
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(slipSystems['hex'][i,4] + 2.*slipSystems['hex'][i,5])/np.sqrt(3),
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slipSystems['hex'][i,7]/options.CoverA,
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])
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slip_direction /= np.linalg.norm(slip_direction,axis=1,keepdims=True)
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slip_normal /= np.linalg.norm(slip_normal, axis=1,keepdims=True)
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labels = ['S[{direction[0]:.1g}_{direction[1]:.1g}_{direction[2]:.1g}]'
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'({normal[0]:.1g}_{normal[1]:.1g}_{normal[2]:.1g})'\
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.format(normal = theNormal, direction = theDirection,
|
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) for theNormal,theDirection in zip(slip_normal,slip_direction)]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name)
|
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except IOError:
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continue
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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|
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# ------------------------------------------ read header ------------------------------------------
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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|
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table.head_read()
|
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o = damask.Rotation.from_quaternion(table.get(options.quaternion))
|
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|
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# ------------------------------------------ sanity checks ----------------------------------------
|
||||
if not table.label_dimension(options.quaternion) == 4:
|
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damask.util.croak('input {} does not have dimension 4.'.format(options.quaternion))
|
||||
table.close(dismiss = True) # close ASCIItable and remove empty file
|
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continue
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force = np.broadcast_to(force, o.shape+(3,))
|
||||
normal = np.broadcast_to(normal,o.shape+(3,))
|
||||
slip_direction = np.broadcast_to(slip_direction,o.shape+slip_direction.shape)
|
||||
slip_normal = np.broadcast_to(slip_normal, o.shape+slip_normal.shape)
|
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S = np.abs(np.einsum('ijk,ik->ij',slip_direction,(o@force))*
|
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np.einsum('ijk,ik->ij',slip_normal, (o@normal)))
|
||||
|
||||
column = table.label_index(options.quaternion)
|
||||
for i,label in enumerate(labels):
|
||||
table.add(label,S[:,i],scriptID+' '+' '.join(sys.argv[1:]))
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
|
||||
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
|
||||
table.labels_append(['S[{direction[0]:.1g}_{direction[1]:.1g}_{direction[2]:.1g}]'
|
||||
'({normal[0]:.1g}_{normal[1]:.1g}_{normal[2]:.1g})'\
|
||||
.format(normal = theNormal,
|
||||
direction = theDirection,
|
||||
) for theNormal,theDirection in zip(slip_normal,slip_direction)])
|
||||
table.head_write()
|
||||
|
||||
# ------------------------------------------ process data ------------------------------------------
|
||||
|
||||
outputAlive = True
|
||||
while outputAlive and table.data_read(): # read next data line of ASCII table
|
||||
o = damask.Rotation(np.array(list(map(float,table.data[column:column+4]))))
|
||||
|
||||
table.data_append( np.abs( np.sum(slip_direction * (o * force) ,axis=1) \
|
||||
* np.sum(slip_normal * (o * normal),axis=1)))
|
||||
outputAlive = table.data_write() # output processed line
|
||||
|
||||
# ------------------------------------------ output finalization -----------------------------------
|
||||
|
||||
table.close() # close ASCII tables
|
||||
table.to_ASCII(sys.stdout if name is None else name)
|
||||
|
|
|
|||
|
|
@ -40,35 +40,22 @@ parser.add_option('-f','--fill',
|
|||
parser.set_defaults(offset = (0,0,0))
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
|
||||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
origin = geom.get_origin()
|
||||
size = geom.get_size()
|
||||
old = new = geom.get_grid()
|
||||
offset = np.asarray(options.offset)
|
||||
|
||||
if options.grid is not None:
|
||||
new = np.maximum(1,
|
||||
np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
|
||||
else int(n) for o,n in zip(old,options.grid)],dtype=int))
|
||||
grid = np.maximum(1,
|
||||
np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
|
||||
else int(n) for o,n in zip(geom.grid,options.grid)],dtype=int))
|
||||
else:
|
||||
grid = np.array(options.grid,dtype=int)
|
||||
|
||||
canvas = np.full(new,options.fill if options.fill is not None
|
||||
else np.nanmax(geom.microstructure)+1,geom.microstructure.dtype)
|
||||
|
||||
l = np.clip( offset, 0,np.minimum(old +offset,new)) # noqa
|
||||
r = np.clip( offset+old,0,np.minimum(old*2+offset,new))
|
||||
L = np.clip(-offset, 0,np.minimum(new -offset,old))
|
||||
R = np.clip(-offset+new,0,np.minimum(new*2-offset,old))
|
||||
canvas[l[0]:r[0],l[1]:r[1],l[2]:r[2]] = geom.microstructure[L[0]:R[0],L[1]:R[1],L[2]:R[2]]
|
||||
|
||||
|
||||
damask.util.croak(geom.update(canvas,origin=origin+offset*size/old,rescale=True))
|
||||
damask.util.croak(geom.canvas(grid,np.asarray(options.offset),options.fill))
|
||||
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
|
||||
geom.to_file(sys.stdout if name is None else name,pack=False)
|
||||
|
|
|
|||
|
|
@ -22,14 +22,12 @@ Renumber sorted microstructure indices to 1,...,N.
|
|||
""", version=scriptID)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
damask.util.croak(geom.renumber())
|
||||
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
geom.to_file(sys.stdout if name is None else name,pack=False)
|
||||
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
damask.util.croak(geom.renumber())
|
||||
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
geom.to_file(sys.stdout if name is None else name,pack=False)
|
||||
|
|
|
|||
|
|
@ -5,7 +5,6 @@ import sys
|
|||
from io import StringIO
|
||||
from optparse import OptionParser
|
||||
|
||||
from scipy import ndimage
|
||||
import numpy as np
|
||||
|
||||
import damask
|
||||
|
|
@ -52,47 +51,27 @@ parser.add_option('-f', '--fill',
|
|||
parser.set_defaults(degrees = False)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
if [options.rotation,options.eulers,options.matrix,options.quaternion].count(None) < 3:
|
||||
parser.error('more than one rotation specified.')
|
||||
if [options.rotation,options.eulers,options.matrix,options.quaternion].count(None) > 3:
|
||||
parser.error('no rotation specified.')
|
||||
|
||||
if options.quaternion is not None:
|
||||
rot = damask.Rotation.from_quaternion(np.array(options.quaternion)) # we might need P=+1 here, too...
|
||||
if options.rotation is not None:
|
||||
rot = damask.Rotation.from_axis_angle(np.array(options.rotation),degrees=options.degrees,normalise=True,P=+1)
|
||||
if options.matrix is not None:
|
||||
rot = damask.Rotation.from_matrix(np.array(options.Matrix))
|
||||
if options.eulers is not None:
|
||||
rot = damask.Rotation.from_Eulers(np.array(options.eulers),degrees=options.degrees)
|
||||
|
||||
eulers = rot.as_Eulers(degrees=True)
|
||||
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
if [options.rotation,options.eulers,options.matrix,options.quaternion].count(None) < 3:
|
||||
parser.error('more than one rotation specified.')
|
||||
if [options.rotation,options.eulers,options.matrix,options.quaternion].count(None) > 3:
|
||||
parser.error('no rotation specified.')
|
||||
|
||||
if options.quaternion is not None:
|
||||
rot = damask.Rotation.from_quaternion(np.array(options.quaternion)) # we might need P=+1 here, too...
|
||||
if options.rotation is not None:
|
||||
rot = damask.Rotation.from_axis_angle(np.array(options.rotation),degrees=options.degrees,normalise=True,P=+1)
|
||||
if options.matrix is not None:
|
||||
rot = damask.Rotation.from_matrix(np.array(options.Matrix))
|
||||
if options.eulers is not None:
|
||||
rot = damask.Rotation.from_Eulers(np.array(options.eulers),degrees=options.degrees)
|
||||
|
||||
|
||||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
size = geom.get_size()
|
||||
grid = geom.get_grid()
|
||||
origin = geom.get_origin()
|
||||
microstructure = geom.get_microstructure()
|
||||
fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
|
||||
dtype = float if np.isnan(fill) or int(fill) != fill or microstructure.dtype==np.float else int
|
||||
|
||||
# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
|
||||
# this seems to be ok, see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
|
||||
microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,
|
||||
prefilter=False,output=dtype,cval=fill) # rotation around z
|
||||
microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,
|
||||
prefilter=False,output=dtype,cval=fill) # rotation around x
|
||||
microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,
|
||||
prefilter=False,output=dtype,cval=fill) # rotation around z
|
||||
|
||||
damask.util.croak(geom.update(microstructure,origin=origin-(np.asarray(microstructure.shape)-grid)/2*size/grid,rescale=True))
|
||||
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
|
||||
geom.to_file(sys.stdout if name is None else name,pack=False)
|
||||
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
damask.util.croak(geom.rotate(rot,options.fill))
|
||||
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
geom.to_file(sys.stdout if name is None else name,pack=False)
|
||||
|
|
|
|||
|
|
@ -40,22 +40,16 @@ parser.set_defaults(origin = (0.0,0.0,0.0),
|
|||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
sub = list(map(int,options.substitute))
|
||||
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
|
||||
substituted = geom.get_microstructure()
|
||||
for old,new in zip(sub[0::2],sub[1::2]): substituted[geom.microstructure==old] = new # substitute microstructure indices
|
||||
substituted += options.microstructure # constant shift
|
||||
|
||||
damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin))
|
||||
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
|
||||
geom.to_file(sys.stdout if name is None else name,pack=False)
|
||||
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
geom.renumber(sub[0::2],sub[1::2],origin=geom.origin+options.origin)
|
||||
geom.microstructure+= options.microstructure
|
||||
damask.util.croak(geom)
|
||||
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
geom.to_file(sys.stdout if name is None else name,pack=False)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
"""Main aggregator."""
|
||||
"""Tools for pre and post processing of DAMASK simulations."""
|
||||
import os as _os
|
||||
import re as _re
|
||||
|
||||
|
|
|
|||
|
|
@ -581,3 +581,58 @@ class Geom:
|
|||
|
||||
#self.add_comments('geom.py:renumber v{}'.format(version)
|
||||
return self.update(renumbered)
|
||||
|
||||
|
||||
def rotate(self,R,fill=None):
|
||||
"""Rotate microstructure (pad if required)."""
|
||||
if fill is None: fill = np.nanmax(self.microstructure) + 1
|
||||
dtype = float if np.isnan(fill) or int(fill) != fill or self.microstructure.dtype==np.float else int
|
||||
|
||||
Eulers = R.as_Eulers(degrees=True)
|
||||
microstructure_in = self.get_microstructure()
|
||||
|
||||
# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
|
||||
# see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
|
||||
for angle,axes in zip(Eulers[::-1], [(0,1),(1,2),(0,1)]):
|
||||
microstructure_out = ndimage.rotate(microstructure_in,angle,axes,order=0,
|
||||
prefilter=False,output=dtype,cval=fill)
|
||||
if np.prod(microstructure_in.shape) == np.prod(microstructure_out.shape):
|
||||
# avoid scipy interpolation errors for rotations close to multiples of 90°
|
||||
microstructure_in = np.rot90(microstructure_in,k=np.rint(angle/90.).astype(int),axes=axes)
|
||||
else:
|
||||
microstructure_in = microstructure_out
|
||||
|
||||
origin = self.origin-(np.asarray(microstructure_in.shape)-self.grid)*.5 * self.size/self.grid
|
||||
|
||||
#self.add_comments('geom.py:rotate v{}'.format(version)
|
||||
return self.update(microstructure_in,origin=origin,rescale=True)
|
||||
|
||||
|
||||
def canvas(self,grid=None,offset=None,fill=None):
|
||||
"""Crop or enlarge/pad microstructure."""
|
||||
if fill is None: fill = np.nanmax(self.microstructure) + 1
|
||||
if offset is None: offset = 0
|
||||
dtype = float if int(fill) != fill or self.microstructure.dtype==np.float else int
|
||||
|
||||
canvas = np.full(self.grid if grid is None else grid,
|
||||
fill if fill is not None else np.nanmax(self.microstructure)+1,dtype)
|
||||
|
||||
l = np.clip( offset, 0,np.minimum(self.grid +offset,grid)) # noqa
|
||||
r = np.clip( offset+self.grid,0,np.minimum(self.grid*2+offset,grid))
|
||||
L = np.clip(-offset, 0,np.minimum(grid -offset,self.grid))
|
||||
R = np.clip(-offset+grid, 0,np.minimum(grid*2 -offset,self.grid))
|
||||
|
||||
canvas[l[0]:r[0],l[1]:r[1],l[2]:r[2]] = self.microstructure[L[0]:R[0],L[1]:R[1],L[2]:R[2]]
|
||||
|
||||
#self.add_comments('geom.py:canvas v{}'.format(version)
|
||||
return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)
|
||||
|
||||
|
||||
def substitute(self,from_microstructure,to_microstructure):
|
||||
"""Substitude microstructure indices."""
|
||||
substituted = self.get_microstructure()
|
||||
for from_ms,to_ms in zip(from_microstructure,to_microstructure):
|
||||
substituted[self.microstructure==from_ms] = to_ms
|
||||
|
||||
#self.add_comments('geom.py:substitute v{}'.format(version)
|
||||
return self.update(substituted)
|
||||
|
|
|
|||
|
|
@ -229,19 +229,20 @@ class Symmetry:
|
|||
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
|
||||
}
|
||||
>>> 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. ],
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@ class Orientation:
|
|||
Crystallographic orientation.
|
||||
|
||||
A crystallographic orientation contains a rotation and a lattice.
|
||||
|
||||
"""
|
||||
|
||||
__slots__ = ['rotation','lattice']
|
||||
|
|
@ -49,8 +50,10 @@ class Orientation:
|
|||
Disorientation between myself and given other orientation.
|
||||
|
||||
Rotation axis falls into SST if SST == True.
|
||||
(Currently requires same symmetry for both orientations.
|
||||
Look into A. Heinz and P. Neumann 1991 for cases with differing sym.)
|
||||
|
||||
Currently requires same symmetry for both orientations.
|
||||
Look into A. Heinz and P. Neumann 1991 for cases with differing sym.
|
||||
|
||||
"""
|
||||
if self.lattice.symmetry != other.lattice.symmetry:
|
||||
raise NotImplementedError('disorientation between different symmetry classes not supported yet.')
|
||||
|
|
|
|||
|
|
@ -322,9 +322,10 @@ class Result:
|
|||
Return groups that contain all requested datasets.
|
||||
|
||||
Only groups within
|
||||
- inc?????/constituent/*_*/*
|
||||
- inc?????/materialpoint/*_*/*
|
||||
- inc?????/geometry/*
|
||||
- inc*/constituent/*/*
|
||||
- inc*/materialpoint/*/*
|
||||
- inc*/geometry/*
|
||||
|
||||
are considered as they contain user-relevant data.
|
||||
Single strings will be treated as list with one entry.
|
||||
|
||||
|
|
@ -599,9 +600,6 @@ class Result:
|
|||
|
||||
@staticmethod
|
||||
def _add_deviator(T):
|
||||
if not T['data'].shape[1:] == (3,3):
|
||||
raise ValueError
|
||||
|
||||
return {
|
||||
'data': mechanics.deviatoric_part(T['data']),
|
||||
'label': 's_{}'.format(T['label']),
|
||||
|
|
@ -832,14 +830,12 @@ class Result:
|
|||
pole = np.array(p)
|
||||
unit_pole = pole/np.linalg.norm(pole)
|
||||
m = util.scale_to_coprime(pole)
|
||||
coords = np.empty((len(q['data']),2))
|
||||
|
||||
for i,qu in enumerate(q['data']):
|
||||
o = Rotation(np.array([qu['w'],qu['x'],qu['y'],qu['z']]))
|
||||
rotatedPole = o*unit_pole # rotate pole according to crystal orientation
|
||||
(x,y) = rotatedPole[0:2]/(1.+abs(unit_pole[2])) # stereographic projection
|
||||
coords[i] = [np.sqrt(x*x+y*y),np.arctan2(y,x)] if polar else [x,y]
|
||||
rot = Rotation(q['data'].view(np.double).reshape(-1,4))
|
||||
|
||||
rotatedPole = rot @ np.broadcast_to(unit_pole,rot.shape+(3,)) # rotate pole according to crystal orientation
|
||||
xy = rotatedPole[:,0:2]/(1.+abs(unit_pole[2])) # stereographic projection
|
||||
coords = xy if not polar else \
|
||||
np.block([np.sqrt(xy[:,0:1]*xy[:,0:1]+xy[:,1:2]*xy[:,1:2]),np.arctan2(xy[:,1:2],xy[:,0:1])])
|
||||
return {
|
||||
'data': coords,
|
||||
'label': 'p^{}_[{} {} {})'.format(u'rφ' if polar else 'xy',*m),
|
||||
|
|
@ -869,8 +865,6 @@ class Result:
|
|||
|
||||
@staticmethod
|
||||
def _add_rotational_part(F):
|
||||
if not F['data'].shape[1:] == (3,3):
|
||||
raise ValueError
|
||||
return {
|
||||
'data': mechanics.rotational_part(F['data']),
|
||||
'label': 'R({})'.format(F['label']),
|
||||
|
|
@ -895,9 +889,6 @@ class Result:
|
|||
|
||||
@staticmethod
|
||||
def _add_spherical(T):
|
||||
if not T['data'].shape[1:] == (3,3):
|
||||
raise ValueError
|
||||
|
||||
return {
|
||||
'data': mechanics.spherical_part(T['data']),
|
||||
'label': 'p_{}'.format(T['label']),
|
||||
|
|
@ -922,9 +913,6 @@ class Result:
|
|||
|
||||
@staticmethod
|
||||
def _add_strain_tensor(F,t,m):
|
||||
if not F['data'].shape[1:] == (3,3):
|
||||
raise ValueError
|
||||
|
||||
return {
|
||||
'data': mechanics.strain_tensor(F['data'],t,m),
|
||||
'label': 'epsilon_{}^{}({})'.format(t,m,F['label']),
|
||||
|
|
@ -956,9 +944,6 @@ class Result:
|
|||
|
||||
@staticmethod
|
||||
def _add_stretch_tensor(F,t):
|
||||
if not F['data'].shape[1:] == (3,3):
|
||||
raise ValueError
|
||||
|
||||
return {
|
||||
'data': mechanics.left_stretch(F['data']) if t == 'V' else mechanics.right_stretch(F['data']),
|
||||
'label': '{}({})'.format(t,F['label']),
|
||||
|
|
@ -1041,7 +1026,7 @@ class Result:
|
|||
pool.join()
|
||||
|
||||
|
||||
def write_XMDF(self):
|
||||
def write_XDMF(self):
|
||||
"""
|
||||
Write XDMF file to directly visualize data in DADF5 file.
|
||||
|
||||
|
|
@ -1049,7 +1034,7 @@ class Result:
|
|||
Selection is not taken into account.
|
||||
"""
|
||||
if len(self.constituents) != 1 or not self.structured:
|
||||
raise NotImplementedError
|
||||
raise NotImplementedError('XDMF only available for grid results with 1 constituent.')
|
||||
|
||||
xdmf=ET.Element('Xdmf')
|
||||
xdmf.attrib={'Version': '2.0',
|
||||
|
|
@ -1217,14 +1202,6 @@ class Result:
|
|||
###################################################################################################
|
||||
# BEGIN DEPRECATED
|
||||
|
||||
def _time_to_inc(self,start,end):
|
||||
selected = []
|
||||
for i,time in enumerate(self.times):
|
||||
if start <= time <= end:
|
||||
selected.append(self.increments[i])
|
||||
return selected
|
||||
|
||||
|
||||
def set_by_time(self,start,end):
|
||||
"""
|
||||
Set active increments based on start and end time.
|
||||
|
|
@ -1237,4 +1214,4 @@ class Result:
|
|||
end time (included)
|
||||
|
||||
"""
|
||||
self._manage_selection('set','increments',self._time_to_inc(start,end))
|
||||
self._manage_selection('set','times',self.times_in_range(start,end))
|
||||
|
|
|
|||
|
|
@ -13,30 +13,31 @@ class Rotation:
|
|||
u"""
|
||||
Orientation stored with functionality for conversion to different representations.
|
||||
|
||||
The following conventions apply:
|
||||
|
||||
- coordinate frames are right-handed.
|
||||
- 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.
|
||||
- rotations will be interpreted in the passive sense.
|
||||
- Euler angle triplets are implemented using the Bunge convention,
|
||||
with the angular ranges as [0, 2π],[0, π],[0, 2π].
|
||||
- the rotation angle ω is limited to the interval [0, π].
|
||||
- the real part of a quaternion is positive, Re(q) > 0
|
||||
- P = -1 (as default).
|
||||
|
||||
Examples
|
||||
--------
|
||||
Rotate vector "a" (defined in coordinate system "A") to
|
||||
coordinates "b" expressed in system "B":
|
||||
|
||||
- b = Q @ a
|
||||
- b = np.dot(Q.asMatrix(),a)
|
||||
|
||||
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.as_matrix(),a)
|
||||
|
||||
"""
|
||||
|
||||
__slots__ = ['quaternion']
|
||||
|
|
@ -160,10 +161,10 @@ class Rotation:
|
|||
if self.shape == ():
|
||||
q = np.broadcast_to(self.quaternion,shape+(4,))
|
||||
else:
|
||||
q = np.block([np.broadcast_to(self.quaternion[...,0:1],shape+(1,)),
|
||||
np.broadcast_to(self.quaternion[...,1:2],shape+(1,)),
|
||||
np.broadcast_to(self.quaternion[...,2:3],shape+(1,)),
|
||||
np.broadcast_to(self.quaternion[...,3:4],shape+(1,))])
|
||||
q = np.block([np.broadcast_to(self.quaternion[...,0:1],shape).reshape(shape+(1,)),
|
||||
np.broadcast_to(self.quaternion[...,1:2],shape).reshape(shape+(1,)),
|
||||
np.broadcast_to(self.quaternion[...,2:3],shape).reshape(shape+(1,)),
|
||||
np.broadcast_to(self.quaternion[...,3:4],shape).reshape(shape+(1,))])
|
||||
return self.__class__(q)
|
||||
|
||||
|
||||
|
|
@ -537,7 +538,7 @@ class Rotation:
|
|||
)
|
||||
# reduce Euler angles to definition range
|
||||
eu[np.abs(eu)<1.e-6] = 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)
|
||||
eu = np.where(eu<0, (eu+2.0*np.pi)%np.array([2.0*np.pi,np.pi,2.0*np.pi]),eu) # needed?
|
||||
return eu
|
||||
|
||||
@staticmethod
|
||||
|
|
|
|||
|
|
@ -120,9 +120,9 @@ class VTK:
|
|||
Parameters
|
||||
----------
|
||||
fname : str
|
||||
Filename for reading. Valid extensions are *.vtr, *.vtu, *.vtp, and *.vtk.
|
||||
Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk.
|
||||
dataset_type : str, optional
|
||||
Name of the vtk.vtkDataSet subclass when opening an *.vtk file. Valid types are vtkRectilinearGrid,
|
||||
Name of the vtk.vtkDataSet subclass when opening an .vtk file. Valid types are vtkRectilinearGrid,
|
||||
vtkUnstructuredGrid, and vtkPolyData.
|
||||
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -0,0 +1,85 @@
|
|||
4 header
|
||||
grid a 8 b 10 c 8
|
||||
size x 8e-06 y 1e-05 z 8e-06
|
||||
origin x 0.0 y -2.5e-06 z -2e-06
|
||||
homogenization 1
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 30 14 18 42 42 42
|
||||
42 42 29 13 17 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 31 15 19 42 42 42
|
||||
42 6 10 2 2 42 42 42
|
||||
42 1 2 2 2 2 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 32 16 20 42 42 42
|
||||
42 7 11 2 2 42 42 42
|
||||
42 7 11 2 2 42 42 42
|
||||
42 2 2 2 2 2 42 42
|
||||
42 42 2 2 31 35 42 42
|
||||
42 42 22 26 10 14 1 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 4 2 2 2 2 42 42
|
||||
42 42 2 2 32 36 42 42
|
||||
42 42 24 28 12 16 1 42
|
||||
42 42 42 7 7 1 1 42
|
||||
42 42 42 7 7 1 1 42
|
||||
42 42 42 1 1 1 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 25 29 13 17 1 42
|
||||
42 42 42 8 8 1 1 42
|
||||
42 42 42 1 1 1 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 1 1 1 42 42
|
||||
42 42 42 1 1 1 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42
|
||||
|
|
@ -0,0 +1,104 @@
|
|||
4 header
|
||||
grid a 11 b 11 c 9
|
||||
size x 1.1e-05 y 1.1000000000000001e-05 z 9e-06
|
||||
origin x -1.5e-06 y -3.0000000000000005e-06 z -2.4999999999999998e-06
|
||||
homogenization 1
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 1 2 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 1 42 42 42 42 42 42
|
||||
42 42 42 42 1 5 42 42 42 42 42
|
||||
42 42 42 1 7 4 42 42 42 42 42
|
||||
42 42 42 42 42 27 42 42 42 42 42
|
||||
42 42 42 42 42 42 2 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 1 1 42 42 42 42 42 42
|
||||
42 42 42 1 1 9 29 42 42 42 42
|
||||
42 42 1 1 11 8 28 2 42 42 42
|
||||
42 42 42 1 10 31 2 42 42 42 42
|
||||
42 42 42 42 30 2 2 2 42 42 42
|
||||
42 42 42 42 42 42 2 1 42 42 42
|
||||
42 42 42 42 42 42 42 1 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 1 42 42 42 42 42 42 42
|
||||
42 42 42 1 1 42 42 42 42 42 42
|
||||
42 42 1 16 36 12 32 42 42 42 42
|
||||
42 42 42 15 35 2 2 2 42 42 42
|
||||
42 42 42 42 2 2 2 11 3 42 42
|
||||
42 42 42 42 42 42 10 6 42 42 42
|
||||
42 42 42 42 42 42 42 6 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 1 42 42 42 42 42 42 42
|
||||
42 42 42 1 17 42 42 42 42 42 42
|
||||
42 42 42 16 36 37 2 42 42 42 42
|
||||
42 42 42 42 39 2 2 12 42 42 42
|
||||
42 42 42 38 2 2 2 11 8 42 42
|
||||
42 42 42 42 2 2 14 30 42 42 42
|
||||
42 42 42 42 42 42 13 30 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 40 42 42 42 42 42 42
|
||||
42 42 42 42 42 2 42 42 42 42 42
|
||||
42 42 42 42 42 2 2 15 42 42 42
|
||||
42 42 42 42 42 2 18 42 42 42 42
|
||||
42 42 42 42 42 42 17 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 2 20 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
42 42 42 42 42 42 42 42 42 42 42
|
||||
|
|
@ -5,12 +5,13 @@ import pytest
|
|||
import numpy as np
|
||||
|
||||
from damask import Geom
|
||||
from damask import Rotation
|
||||
|
||||
|
||||
def geom_equal(a,b):
|
||||
return np.all(a.get_microstructure() == b.get_microstructure()) and \
|
||||
np.all(a.get_size() == b.get_size()) and \
|
||||
np.all(a.get_grid() == b.get_grid())
|
||||
np.all(a.get_grid() == b.get_grid()) and \
|
||||
np.allclose(a.get_size(), b.get_size())
|
||||
|
||||
@pytest.fixture
|
||||
def default():
|
||||
|
|
@ -36,6 +37,7 @@ class TestGeom:
|
|||
default.get_size(),
|
||||
default.get_origin()
|
||||
)
|
||||
print(modified)
|
||||
assert geom_equal(modified,default)
|
||||
|
||||
|
||||
|
|
@ -57,6 +59,22 @@ class TestGeom:
|
|||
new = Geom.from_file(tmpdir.join('default.geom'))
|
||||
assert geom_equal(new,default)
|
||||
|
||||
def test_invalid_combination(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
default.update(default.microstructure[1:,1:,1:],size=np.ones(3), rescale=True)
|
||||
|
||||
def test_invalid_size(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
default.update(default.microstructure[1:,1:,1:],size=np.ones(2))
|
||||
|
||||
def test_invalid_microstructure(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
default.update(default.microstructure[1])
|
||||
|
||||
def test_invalid_homogenization(self,default):
|
||||
with pytest.raises(TypeError):
|
||||
default.set_homogenization(homogenization=0)
|
||||
|
||||
@pytest.mark.parametrize('directions,reflect',[
|
||||
(['x'], False),
|
||||
(['x','y','z'],True),
|
||||
|
|
@ -98,6 +116,52 @@ class TestGeom:
|
|||
if update: modified.to_file(reference)
|
||||
assert geom_equal(modified,Geom.from_file(reference))
|
||||
|
||||
def test_renumber(self,default):
|
||||
modified = copy.deepcopy(default)
|
||||
microstructure = modified.get_microstructure()
|
||||
for m in np.unique(microstructure):
|
||||
microstructure[microstructure==m] = microstructure.max() + np.random.randint(1,30)
|
||||
modified.update(microstructure)
|
||||
assert not geom_equal(modified,default)
|
||||
modified.renumber()
|
||||
assert geom_equal(modified,default)
|
||||
|
||||
def test_substitute(self,default):
|
||||
modified = copy.deepcopy(default)
|
||||
microstructure = modified.get_microstructure()
|
||||
offset = np.random.randint(1,500)
|
||||
microstructure+=offset
|
||||
modified.update(microstructure)
|
||||
assert not geom_equal(modified,default)
|
||||
modified.substitute(np.arange(default.microstructure.max())+1+offset,
|
||||
np.arange(default.microstructure.max())+1)
|
||||
assert geom_equal(modified,default)
|
||||
|
||||
@pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]),
|
||||
np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])])
|
||||
def test_rotate360(self,default,axis_angle):
|
||||
modified = copy.deepcopy(default)
|
||||
for i in range(np.rint(360/axis_angle[3]).astype(int)):
|
||||
modified.rotate(Rotation.from_axis_angle(axis_angle,degrees=True))
|
||||
assert geom_equal(modified,default)
|
||||
|
||||
@pytest.mark.parametrize('Eulers',[[32.0,68.0,21.0],
|
||||
[0.0,32.0,240.0]])
|
||||
def test_rotate(self,default,update,reference_dir,Eulers):
|
||||
modified = copy.deepcopy(default)
|
||||
modified.rotate(Rotation.from_Eulers(Eulers,degrees=True))
|
||||
tag = 'Eulers={}-{}-{}'.format(*Eulers)
|
||||
reference = os.path.join(reference_dir,'rotate_{}.geom'.format(tag))
|
||||
if update: modified.to_file(reference)
|
||||
assert geom_equal(modified,Geom.from_file(reference))
|
||||
|
||||
def test_canvas(self,default):
|
||||
grid_add = np.random.randint(0,30,(3))
|
||||
modified = copy.deepcopy(default)
|
||||
modified.canvas(modified.grid + grid_add)
|
||||
e = default.grid
|
||||
assert np.all(modified.microstructure[:e[0],:e[1],:e[2]] == default.microstructure)
|
||||
|
||||
@pytest.mark.parametrize('periodic',[True,False])
|
||||
def test_tessellation_approaches(self,periodic):
|
||||
grid = np.random.randint(10,20,3)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,41 @@
|
|||
import random
|
||||
|
||||
import pytest
|
||||
import numpy as np
|
||||
|
||||
from damask import Symmetry
|
||||
|
||||
class TestSymmetry:
|
||||
|
||||
@pytest.mark.parametrize('invalid_symmetry',['fcc','bcc','hello'])
|
||||
def test_invalid_symmetry(self,invalid_symmetry):
|
||||
with pytest.raises(KeyError):
|
||||
s = Symmetry(invalid_symmetry) # noqa
|
||||
|
||||
def test_equal(self):
|
||||
symmetry = random.choice(Symmetry.lattices)
|
||||
print(symmetry)
|
||||
assert Symmetry(symmetry) == Symmetry(symmetry)
|
||||
|
||||
def test_not_equal(self):
|
||||
symmetries = random.sample(Symmetry.lattices,k=2)
|
||||
assert Symmetry(symmetries[0]) != Symmetry(symmetries[1])
|
||||
|
||||
@pytest.mark.parametrize('lattice',Symmetry.lattices)
|
||||
def test_inFZ(self,lattice):
|
||||
assert Symmetry(lattice).inFZ(np.zeros(3))
|
||||
|
||||
@pytest.mark.parametrize('lattice',Symmetry.lattices)
|
||||
def test_inDisorientationSST(self,lattice):
|
||||
assert Symmetry(lattice).inDisorientationSST(np.zeros(3))
|
||||
|
||||
@pytest.mark.parametrize('lattice',Symmetry.lattices)
|
||||
@pytest.mark.parametrize('proper',[True,False])
|
||||
def test_inSST(self,lattice,proper):
|
||||
assert Symmetry(lattice).inSST(np.zeros(3),proper)
|
||||
|
||||
@pytest.mark.parametrize('function',['inFZ','inDisorientationSST'])
|
||||
def test_invalid_argument(self,function):
|
||||
s = Symmetry() # noqa
|
||||
with pytest.raises(ValueError):
|
||||
eval('s.{}(np.ones(4))'.format(function))
|
||||
|
|
@ -4,6 +4,7 @@ import os
|
|||
import pytest
|
||||
import numpy as np
|
||||
|
||||
import damask
|
||||
from damask import Result
|
||||
from damask import mechanics
|
||||
|
||||
|
|
@ -13,7 +14,7 @@ def default(tmp_path,reference_dir):
|
|||
fname = '12grains6x7x8_tensionY.hdf5'
|
||||
shutil.copy(os.path.join(reference_dir,fname),tmp_path)
|
||||
f = Result(os.path.join(tmp_path,fname))
|
||||
f.set_by_time(20.0,20.0)
|
||||
f.pick('times',20.0)
|
||||
return f
|
||||
|
||||
@pytest.fixture
|
||||
|
|
@ -28,12 +29,60 @@ class TestResult:
|
|||
print(default)
|
||||
|
||||
|
||||
def test_time_increments(self,default):
|
||||
shape = default.read_dataset(default.get_dataset_location('F'),0).shape
|
||||
default.set_by_time(0.0,20.0)
|
||||
for i in default.iterate('increments'):
|
||||
assert shape == default.read_dataset(default.get_dataset_location('F'),0).shape
|
||||
def test_pick_all(self,default):
|
||||
default.pick('increments',True)
|
||||
a = default.get_dataset_location('F')
|
||||
default.pick('increments','*')
|
||||
b = default.get_dataset_location('F')
|
||||
default.pick('increments',default.incs_in_range(0,np.iinfo(int).max))
|
||||
c = default.get_dataset_location('F')
|
||||
|
||||
default.pick('times',True)
|
||||
d = default.get_dataset_location('F')
|
||||
default.pick('times','*')
|
||||
e = default.get_dataset_location('F')
|
||||
default.pick('times',default.times_in_range(0.0,np.inf))
|
||||
f = default.get_dataset_location('F')
|
||||
assert a == b == c == d == e ==f
|
||||
|
||||
@pytest.mark.parametrize('what',['increments','times','constituents']) # ToDo: discuss materialpoints
|
||||
def test_pick_none(self,default,what):
|
||||
default.pick(what,False)
|
||||
a = default.get_dataset_location('F')
|
||||
default.pick(what,[])
|
||||
b = default.get_dataset_location('F')
|
||||
|
||||
assert a == b == []
|
||||
|
||||
@pytest.mark.parametrize('what',['increments','times','constituents']) # ToDo: discuss materialpoints
|
||||
def test_pick_more(self,default,what):
|
||||
default.pick(what,False)
|
||||
default.pick_more(what,'*')
|
||||
a = default.get_dataset_location('F')
|
||||
|
||||
default.pick(what,True)
|
||||
b = default.get_dataset_location('F')
|
||||
|
||||
assert a == b
|
||||
|
||||
@pytest.mark.parametrize('what',['increments','times','constituents']) # ToDo: discuss materialpoints
|
||||
def test_pick_less(self,default,what):
|
||||
default.pick(what,True)
|
||||
default.pick_less(what,'*')
|
||||
a = default.get_dataset_location('F')
|
||||
|
||||
default.pick(what,False)
|
||||
b = default.get_dataset_location('F')
|
||||
|
||||
assert a == b == []
|
||||
|
||||
def test_pick_invalid(self,default):
|
||||
with pytest.raises(AttributeError):
|
||||
default.pick('invalid',True)
|
||||
|
||||
def test_add_invalid(self,default):
|
||||
with pytest.raises(Exception):
|
||||
default.add_calculation('#invalid#*2')
|
||||
|
||||
def test_add_absolute(self,default):
|
||||
default.add_absolute('Fe')
|
||||
|
|
@ -95,6 +144,20 @@ class TestResult:
|
|||
in_file = default.read_dataset(loc['v(sigma)'],0)
|
||||
assert np.allclose(in_memory,in_file)
|
||||
|
||||
@pytest.mark.parametrize('d',[[1,0,0],[0,1,0],[0,0,1]])
|
||||
def test_add_IPFcolor(self,default,d):
|
||||
default.add_IPFcolor('orientation',d)
|
||||
loc = {'orientation': default.get_dataset_location('orientation'),
|
||||
'color': default.get_dataset_location('IPFcolor_[{} {} {}]'.format(*d))}
|
||||
qu = default.read_dataset(loc['orientation']).view(np.double).reshape(-1,4)
|
||||
crystal_structure = default.get_crystal_structure()
|
||||
in_memory = np.empty((qu.shape[0],3),np.uint8)
|
||||
for i,q in enumerate(qu):
|
||||
o = damask.Orientation(q,crystal_structure).reduced()
|
||||
in_memory[i] = np.uint8(o.IPFcolor(np.array(d))*255)
|
||||
in_file = default.read_dataset(loc['color'])
|
||||
assert np.allclose(in_memory,in_file)
|
||||
|
||||
def test_add_maximum_shear(self,default):
|
||||
default.add_Cauchy('P','F')
|
||||
default.add_maximum_shear('sigma')
|
||||
|
|
@ -143,6 +206,20 @@ class TestResult:
|
|||
in_file = default.read_dataset(loc['S'],0)
|
||||
assert np.allclose(in_memory,in_file)
|
||||
|
||||
@pytest.mark.parametrize('polar',[True,False])
|
||||
def test_add_pole(self,default,polar):
|
||||
pole = np.array([1.,0.,0.])
|
||||
default.add_pole('orientation',pole,polar)
|
||||
loc = {'orientation': default.get_dataset_location('orientation'),
|
||||
'pole': default.get_dataset_location('p^{}_[1 0 0)'.format(u'rφ' if polar else 'xy'))}
|
||||
rot = damask.Rotation(default.read_dataset(loc['orientation']).view(np.double))
|
||||
rotated_pole = rot * np.broadcast_to(pole,rot.shape+(3,))
|
||||
xy = rotated_pole[:,0:2]/(1.+abs(pole[2]))
|
||||
in_memory = xy if not polar else \
|
||||
np.block([np.sqrt(xy[:,0:1]*xy[:,0:1]+xy[:,1:2]*xy[:,1:2]),np.arctan2(xy[:,1:2],xy[:,0:1])])
|
||||
in_file = default.read_dataset(loc['pole'])
|
||||
assert np.allclose(in_memory,in_file)
|
||||
|
||||
def test_add_rotational_part(self,default):
|
||||
default.add_rotational_part('F')
|
||||
loc = {'F': default.get_dataset_location('F'),
|
||||
|
|
@ -185,3 +262,7 @@ class TestResult:
|
|||
in_memory = mechanics.left_stretch(default.read_dataset(loc['F'],0))
|
||||
in_file = default.read_dataset(loc['V(F)'],0)
|
||||
assert np.allclose(in_memory,in_file)
|
||||
|
||||
@pytest.mark.parametrize('output',['F',[],['F','P']])
|
||||
def test_vtk(self,default,output):
|
||||
default.to_vtk(output)
|
||||
|
|
|
|||
|
|
@ -866,12 +866,23 @@ class TestRotation:
|
|||
with pytest.raises(ValueError):
|
||||
function(invalid_shape)
|
||||
|
||||
@pytest.mark.parametrize('shape',[None,(3,),(4,2)])
|
||||
def test_broadcast(self,shape):
|
||||
rot = Rotation.from_random(shape)
|
||||
new_shape = tuple(np.random.randint(8,32,(3))) if shape is None else \
|
||||
rot.shape + (np.random.randint(8,32),)
|
||||
rot_broadcast = rot.broadcast_to(tuple(new_shape))
|
||||
for i in range(rot_broadcast.shape[-1]):
|
||||
assert np.allclose(rot_broadcast.quaternion[...,i,:], rot.quaternion)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('function,invalid',[(Rotation.from_quaternion, np.array([-1,0,0,0])),
|
||||
(Rotation.from_quaternion, np.array([1,1,1,0])),
|
||||
(Rotation.from_Eulers, np.array([1,4,0])),
|
||||
(Rotation.from_axis_angle, np.array([1,0,0,4])),
|
||||
(Rotation.from_axis_angle, np.array([1,1,0,1])),
|
||||
(Rotation.from_matrix, np.random.rand(3,3)),
|
||||
(Rotation.from_matrix, np.array([[1,1,0],[1,2,0],[0,0,1]])),
|
||||
(Rotation.from_Rodrigues, np.array([1,0,0,-1])),
|
||||
(Rotation.from_Rodrigues, np.array([1,1,0,1])),
|
||||
(Rotation.from_homochoric, np.array([2,2,2])),
|
||||
|
|
|
|||
Loading…
Reference in New Issue