replace outdated ASCIItable class
This commit is contained in:
Martin Diehl
parent
7aecc37219
commit
06e4327c0b
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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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@ -102,11 +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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@ -129,88 +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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# ------------------------------------------ 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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table.head_read()
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o = damask.Rotation.from_quaternion(table.get(options.quaternion))
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# ------------------------------------------ sanity checks ----------------------------------------
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if not table.label_dimension(options.quaternion) == 4:
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damask.util.croak('input {} does not have dimension 4.'.format(options.quaternion))
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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,))
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normal = np.broadcast_to(normal,o.shape+(3,))
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slip_direction = np.broadcast_to(slip_direction,o.shape+slip_direction.shape)
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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)))
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column = table.label_index(options.quaternion)
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for i,label in enumerate(labels):
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table.add(label,S[:,i],scriptID+' '+' '.join(sys.argv[1:]))
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# ------------------------------------------ assemble header ---------------------------------------
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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table.labels_append(['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,
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direction = theDirection,
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) for theNormal,theDirection in zip(slip_normal,slip_direction)])
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table.head_write()
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# ------------------------------------------ process data ------------------------------------------
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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o = damask.Rotation(np.array(list(map(float,table.data[column:column+4]))))
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table.data_append( np.abs( np.sum(slip_direction * (o * force) ,axis=1) \
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* np.sum(slip_normal * (o * normal),axis=1)))
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close ASCII tables
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table.to_ASCII(sys.stdout if name is None else name)
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