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DAMASK_EICMD
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added option to use seed coordinates that are not normalized to a unit cube

This commit is contained in:
Philip Eisenlohr 2017-08-16 16:24:45 -04:00
parent 255a465e8b
commit 12fed7a38f
1 changed files with 18 additions and 11 deletions
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29
processing/pre/geom_fromVoronoiTessellation.py
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@ -37,12 +37,9 @@ def findClosestSeed(fargs):
return np.argmin(dist) # seed point closest to point return np.argmin(dist) # seed point closest to point
def laguerreTessellation(undeformed, coords, weights, grains, nonperiodic = False, cpus = 2): def laguerreTessellation(undeformed, coords, weights, grains, periodic = True, cpus = 2):
copies = \ copies = \
np.array([
[ 0, 0, 0 ],
]).astype(float) if nonperiodic else \
np.array([ np.array([
[ -1,-1,-1 ], [ -1,-1,-1 ],
[ 0,-1,-1 ], [ 0,-1,-1 ],
@ -71,7 +68,10 @@ def laguerreTessellation(undeformed, coords, weights, grains, nonperiodic = Fals
[ -1, 1, 1 ], [ -1, 1, 1 ],
[ 0, 1, 1 ], [ 0, 1, 1 ],
[ 1, 1, 1 ], [ 1, 1, 1 ],
]).astype(float)*info['size'] ]).astype(float)*info['size'] if periodic else \
np.array([
[ 0, 0, 0 ],
]).astype(float)
repeatweights = np.tile(weights,len(copies)).flatten(order='F') # Laguerre weights (1,2,3,1,2,3,...,1,2,3) repeatweights = np.tile(weights,len(copies)).flatten(order='F') # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
for i,vec in enumerate(copies): # periodic copies of seed points ... for i,vec in enumerate(copies): # periodic copies of seed points ...
@ -121,8 +121,8 @@ group.add_option('--cpus',
type = 'int', metavar = 'int', type = 'int', metavar = 'int',
help = 'number of parallel processes to use for Laguerre tessellation [%default]') help = 'number of parallel processes to use for Laguerre tessellation [%default]')
group.add_option('--nonperiodic', group.add_option('--nonperiodic',
dest = 'nonperiodic', dest = 'periodic',
action = 'store_true', action = 'store_false',
help = 'nonperiodic tessellation') help = 'nonperiodic tessellation')
parser.add_option_group(group) parser.add_option_group(group)
@ -144,6 +144,10 @@ group.add_option('-o',
dest = 'origin', dest = 'origin',
type = 'float', nargs = 3, metavar=' '.join(['float']*3), type = 'float', nargs = 3, metavar=' '.join(['float']*3),
help = 'origin of grid') help = 'origin of grid')
group.add_option('--nonnormalized',
dest = 'normalized',
action = 'store_false',
help = 'seed coordinates are not normalized to a unit cube')
parser.add_option_group(group) parser.add_option_group(group)
@ -206,7 +210,8 @@ parser.set_defaults(pos = 'pos',
phase = 1, phase = 1,
cpus = 2, cpus = 2,
laguerre = False, laguerre = False,
nonperiodic = False, periodic = True,
normalized = True,
config = True, config = True,
) )
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
@ -248,7 +253,7 @@ for name in filenames:
for i in range(3): for i in range(3):
if info['size'][i] <= 0.0: # any invalid size? if info['size'][i] <= 0.0: # any invalid size?
info['size'][i] = float(info['grid'][i])/max(info['grid']) # normalize to grid info['size'][i] = float(info['grid'][i])/max(info['grid']) # normalize to grid
remarks.append('rescaling size {} to {}...'.format({0:'x',1:'y',2:'z'}[i],info['size'][i])) remarks.append('rescaling size {} to {}...'.format(['x','y','z'][i],info['size'][i]))
if table.label_dimension(options.pos) != 3: if table.label_dimension(options.pos) != 3:
errors.append('seed positions "{}" have dimension {}.'.format(options.pos, errors.append('seed positions "{}" have dimension {}.'.format(options.pos,
@ -256,6 +261,7 @@ for name in filenames:
else: else:
labels += [options.pos] labels += [options.pos]
if not options.normalized: remarks.append('using real-space seed coordinates...')
if not hasEulers: remarks.append('missing seed orientations...') if not hasEulers: remarks.append('missing seed orientations...')
else: labels += [options.eulers] else: labels += [options.eulers]
if not hasGrains: remarks.append('missing seed microstructure indices...') if not hasGrains: remarks.append('missing seed microstructure indices...')
@ -272,7 +278,8 @@ for name in filenames:
# ------------------------------------------ read seeds --------------------------------------- # ------------------------------------------ read seeds ---------------------------------------
table.data_readArray(labels) table.data_readArray(labels)
coords = table.data[:,table.label_indexrange(options.pos)] * info['size'] coords = table.data[:,table.label_indexrange(options.pos)] * info['size'] if options.normalized \
else table.data[:,table.label_indexrange(options.pos)] - info['origin']
eulers = table.data[:,table.label_indexrange(options.eulers)] if hasEulers \ eulers = table.data[:,table.label_indexrange(options.eulers)] if hasEulers \
else np.zeros(3*len(coords)) else np.zeros(3*len(coords))
grains = table.data[:,table.label_indexrange(options.microstructure)].astype('i') if hasGrains \ grains = table.data[:,table.label_indexrange(options.microstructure)].astype('i') if hasGrains \
@ -291,7 +298,7 @@ for name in filenames:
damask.util.croak('tessellating...') damask.util.croak('tessellating...')
grid = np.vstack(meshgrid2(x, y, z)).reshape(3,-1).T grid = np.vstack(meshgrid2(x, y, z)).reshape(3,-1).T
indices = laguerreTessellation(grid, coords, weights, grains, options.nonperiodic, options.cpus) indices = laguerreTessellation(grid, coords, weights, grains, options.periodic, options.cpus)
# --- write header ------------------------------------------------------------------------ # --- write header ------------------------------------------------------------------------