def print_boundary_type(axis, plane, theta):
if (plane == axis * sum(plane) / sum(axis)).all():
bt = "twist"
elif inner(plane, axis) == 0:
R = rodrigues(axis, theta, verbose=False)
p2 = dot(linalg.inv(R), plane)
plane2 = csl.scale_to_integers(p2)
bt = "tilt (%i %i %i) (%i %i %i)" % (tuple(plane) + tuple(plane2))
else:
bt = "mixed"
return bt
def print_boundary_type(axis, plane, theta):
if (plane == axis * sum(plane) / sum(axis)).all():
bt = "twist"
elif inner(plane, axis) == 0:
R = rodrigues(axis, theta, verbose=False)
p2 = dot(linalg.inv(R), plane)
plane2 = csl.scale_to_integers(p2)
bt = "tilt (%i %i %i) (%i %i %i)" % (tuple(plane) + tuple(plane2))
else:
bt = "mixed"
return bt
def parse_args():
if len(sys.argv) < 7:
print usage
sys.exit()
opts = BicrystalOptions()
opts.axis = csl.parse_miller(sys.argv[1])
print "-------> rotation axis: [%i %i %i]" % tuple(opts.axis)
opts.parse_sigma_and_find_theta(sys.argv[3])
plane = sys.argv[2]
if plane == "twist":
opts.plane = opts.axis.copy()
elif plane.startswith("m"):
m_plane = csl.parse_miller(plane[1:])
if inner(m_plane, opts.axis) != 0:
raise ValueError("Axis must be contained in median plane.")
R = rodrigues(opts.axis, opts.theta / 2., verbose=False)
plane_ = dot(R, m_plane)
opts.plane = csl.scale_to_integers(plane_)
else:
opts.plane = csl.parse_miller(plane)
print "-------> boundary plane: (%i %i %i)" % tuple(opts.plane)
bt = print_boundary_type(opts.axis, opts.plane, opts.theta)
print " boundary type:", bt
opts.req_dim = [float(eval(i, math.__dict__)) for i in sys.argv[4:7]]
options = sys.argv[7:-1]
for i in options:
if i == "nofit":
assert opts.fit is None
opts.fit = False
if i == "nozfit":
assert opts.zfit is None
opts.zfit = False
elif i == "mono1":
assert opts.mono1 is None
opts.mono1 = True
elif i == "mono2":
assert opts.mono2 is None
opts.mono2 = True
elif i == "all":
assert opts.all is None and opts.allall is None
opts.all = True
elif i == "allall":
assert opts.allall is None and opts.all is None
opts.allall = True
elif i.startswith("remove:"):
assert opts.remove_dist is None
opts.remove_dist = float(i[7:])
elif i.startswith("remove2:"):
assert opts.remove_dist2 is None
opts.remove_dist2 = float(i[8:])
elif i.startswith("vacuum:"):
assert opts.vacuum is None
opts.vacuum = float(i[7:]) * 10. #nm -> A
elif i.startswith("lattice:"):
opts.lattice_name = i[8:]
elif i.startswith("shift:"):
s = i[6:].split(",")
if len(s) != 3:
raise ValueError("Wrong format of shift parameter")
opts.lattice_shift = [float(i) for i in s]
elif i.startswith("edge:"):
try:
z1, z2 = i[5:].split(",")
opts.edge = (float(z1), float(z2))
except (TypeError, ValueError):
raise ValueError("Wrong format of edge parameter")
else:
raise ValueError("Unknown option: %s" % i)
# default values
if opts.fit is None:
opts.fit = True
if opts.zfit is None:
opts.zfit = True
if opts.mono1 is None:
opts.mono1 = False
if opts.mono2 is None:
opts.mono2 = False
#if opts.remove_dist is None:
# opts.remove_dist = 0.8 * opts.atom_min_dist
opts.output_filename = sys.argv[-1]
return opts
def parse_args():
if len(sys.argv) < 7:
print usage
sys.exit()
opts = BicrystalOptions()
opts.axis = csl.parse_miller(sys.argv[1])
print "-------> rotation axis: [%i %i %i]" % tuple(opts.axis)
opts.parse_sigma_and_find_theta(sys.argv[3])
plane = sys.argv[2]
if plane == "twist":
opts.plane = opts.axis.copy()
elif plane.startswith("m"):
m_plane = csl.parse_miller(plane[1:])
if inner(m_plane, opts.axis) != 0:
raise ValueError("Axis must be contained in median plane.")
R = rodrigues(opts.axis, opts.theta / 2., verbose=False)
plane_ = dot(R, m_plane)
opts.plane = csl.scale_to_integers(plane_)
else:
opts.plane = csl.parse_miller(plane)
print "-------> boundary plane: (%i %i %i)" % tuple(opts.plane)
bt = print_boundary_type(opts.axis, opts.plane, opts.theta)
print " boundary type:", bt
opts.req_dim = [float(eval(i, math.__dict__)) for i in sys.argv[4:7]]
options = sys.argv[7:-1]
for i in options:
if i == "nofit":
assert opts.fit is None
opts.fit = False
if i == "nozfit":
assert opts.zfit is None
opts.zfit = False
elif i == "mono1":
assert opts.mono1 is None
opts.mono1 = True
elif i == "mono2":
assert opts.mono2 is None
opts.mono2 = True
elif i == "all":
assert opts.all is None and opts.allall is None
opts.all = True
elif i == "allall":
assert opts.allall is None and opts.all is None
opts.allall = True
elif i.startswith("remove:"):
assert opts.remove_dist is None
opts.remove_dist = float(i[7:])
elif i.startswith("remove2:"):
assert opts.remove_dist2 is None
opts.remove_dist2 = float(i[8:])
elif i.startswith("vacuum:"):
assert opts.vacuum is None
opts.vacuum = float(i[7:]) * 10. #nm -> A
elif i.startswith("lattice:"):
opts.lattice_name = i[8:]
elif i.startswith("shift:"):
s = i[6:].split(",")
if len(s) != 3:
raise ValueError("Wrong format of shift parameter")
opts.lattice_shift = [float(i) for i in s]
elif i.startswith("edge:"):
try:
z1, z2 = i[5:].split(",")
opts.edge = (float(z1), float(z2))
except (TypeError, ValueError):
raise ValueError("Wrong format of edge parameter")
else:
raise ValueError("Unknown option: %s" % i)
# default values
if opts.fit is None:
opts.fit = True
if opts.zfit is None:
opts.zfit = True
if opts.mono1 is None:
opts.mono1 = False
if opts.mono2 is None:
opts.mono2 = False
#if opts.remove_dist is None:
# opts.remove_dist = 0.8 * opts.atom_min_dist
opts.output_filename = sys.argv[-1]
return opts
