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normalizing coordinates _before_ rotation causes wrong primitive shape for non-cubic VEs

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Philip Eisenlohr 2020-11-12 18:34:29 -05:00
parent e90c20ccd6
commit b3e8b85d25
1 changed files with 16 additions and 14 deletions
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30
python/damask/_geom.py
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@ -564,14 +564,14 @@ class Geom:
If given as floats, coordinates are addressed. If given as floats, coordinates are addressed.
center : int or float numpy.ndarray of shape (3) center : int or float numpy.ndarray of shape (3)
Center of the primitive. If given as integers, grid point Center of the primitive. If given as integers, grid point
locations (cell centers) are addressed. coordinates (cell centers) are addressed.
If given as floats, coordinates are addressed. If given as floats, coordinates in space are addressed.
exponent : numpy.ndarray of shape (3) or float exponent : numpy.ndarray of shape (3) or float
Exponents for the three axes. Exponents for the three axes.
0 gives octahedron (ǀxǀ^(2^0) + ǀyǀ^(2^0) + ǀzǀ^(2^0) < 1) 0 gives octahedron (ǀxǀ^(2^0) + ǀyǀ^(2^0) + ǀzǀ^(2^0) < 1)
1 gives sphere (ǀxǀ^(2^1) + ǀyǀ^(2^1) + ǀzǀ^(2^1) < 1) 1 gives sphere (ǀxǀ^(2^1) + ǀyǀ^(2^1) + ǀzǀ^(2^1) < 1)
fill : int, optional fill : int, optional
Fill value for primitive. Defaults to material.max() + 1. Fill value for primitive. Defaults to material.max()+1.
R : damask.Rotation, optional R : damask.Rotation, optional
Rotation of primitive. Defaults to no rotation. Rotation of primitive. Defaults to no rotation.
inverse : Boolean, optional inverse : Boolean, optional
@ -581,25 +581,27 @@ class Geom:
Repeat primitive over boundaries. Defaults to True. Repeat primitive over boundaries. Defaults to True.
""" """
# normalized 'radius' and center # radius and center
r = np.array(dimension)/self.grid/2.0 if np.array(dimension).dtype in np.sctypes['int'] else \ r = np.array(dimension)/2.0*self.size/self.grid if np.array(dimension).dtype in np.sctypes['int'] else \
np.array(dimension)/self.size/2.0 np.array(dimension)/2.0
c = (np.array(center) + .5)/self.grid if np.array(center).dtype in np.sctypes['int'] else \ c = (np.array(center) + .5)*self.size/self.grid if np.array(center).dtype in np.sctypes['int'] else \
(np.array(center) - self.origin)/self.size (np.array(center) - self.origin)
coords = grid_filters.cell_coord0(self.grid,np.ones(3)) \ coords = grid_filters.cell_coord0(self.grid,self.size,
- ((np.ones(3)-(1./self.grid if np.array(center).dtype in np.sctypes['int'] else 0))*0.5 if periodic else c) # periodic center is always at CoG -(0.5*(self.size + (self.size/self.grid
if np.array(center).dtype in np.sctypes['int'] else
0)) if periodic else c))
coords_rot = R.broadcast_to(tuple(self.grid))@coords coords_rot = R.broadcast_to(tuple(self.grid))@coords
with np.errstate(all='ignore'): with np.errstate(all='ignore'):
mask = np.sum(np.power(coords_rot/r,2.0**np.array(exponent)),axis=-1) > 1.0 mask = np.sum(np.power(coords_rot/r,2.0**np.array(exponent)),axis=-1) > 1.0
if periodic: # translate back to center if periodic: # translate back to center
mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2)) mask = np.roll(mask,((c/self.size-0.5)*self.grid).round().astype(int),(0,1,2))
fill_ = np.full_like(self.material,np.nanmax(self.material)+1 if fill is None else fill) return Geom(material = np.where(np.logical_not(mask) if inverse else mask,
self.material,
return Geom(material = np.where(np.logical_not(mask) if inverse else mask, self.material,fill_), np.nanmax(self.material)+1 if fill is None else fill),
size = self.size, size = self.size,
origin = self.origin, origin = self.origin,
comments = self.comments+[util.execution_stamp('Geom','add_primitive')], comments = self.comments+[util.execution_stamp('Geom','add_primitive')],