class Bicrystal(OrthorhombicPbcModel):
def __init__(self, lattice1, lattice2, dim, rot_u, rot_b, title):
OrthorhombicPbcModel.__init__(self, lattice1, dim, title=title)
self.mono_u = RotatedMonocrystal(lattice1, dim, rot_u)
self.mono_b = RotatedMonocrystal(lattice2, dim, rot_b)
def generate_atoms(self, z_margin=0.):
#print "Bicrystal.generate_atoms"
self.atoms = (self.mono_u.generate_atoms(upper=True, z_margin=z_margin)
+ self.mono_b.generate_atoms(upper=False, z_margin=z_margin))
print "Number of atoms in bicrystal: %i" % len(self.atoms)
self.print_boundary_angle()
def print_boundary_angle(self):
def calc_angle(v1, v2):
return acos( dot(v1, v2) / sqrt(inner(v1,v1) * inner(v2,v2)) )
u0 = self.mono_u.unit_cell.get_unit_shift(0)
b = [self.mono_b.unit_cell.get_unit_shift(i) for i in range(3)]
b += [-i for i in b]
angles = [degrees(calc_angle(u0, i)) for i in b]
print "angles between upper and bottom:", \
", ".join("%.1f" % i for i in angles)
class Bicrystal(OrthorhombicPbcModel):
def __init__(self, lattice1, lattice2, dim, rot_u, rot_b, title):
OrthorhombicPbcModel.__init__(self, lattice1, dim, title=title)
self.mono_u = RotatedMonocrystal(lattice1, dim, rot_u)
self.mono_b = RotatedMonocrystal(lattice2, dim, rot_b)
def generate_atoms(self, z_margin=0.):
#print "Bicrystal.generate_atoms"
self.atoms = (self.mono_u.generate_atoms(upper=True, z_margin=z_margin)
+ self.mono_b.generate_atoms(upper=False, z_margin=z_margin))
print "Number of atoms in bicrystal: %i" % len(self.atoms)
self.print_boundary_angle()
def print_boundary_angle(self):
def calc_angle(v1, v2):
return acos( dot(v1, v2) / sqrt(inner(v1,v1) * inner(v2,v2)) )
u0 = self.mono_u.unit_cell.get_unit_shift(0)
b = [self.mono_b.unit_cell.get_unit_shift(i) for i in range(3)]
b += [-i for i in b]
angles = [degrees(calc_angle(u0, i)) for i in b]
print "angles between upper and bottom:", \
", ".join("%.1f" % i for i in angles)
def __init__(self, lattice1, lattice2, dim, rot_u, rot_b, title):
OrthorhombicPbcModel.__init__(self, lattice1, dim, title=title)
self.mono_u = RotatedMonocrystal(lattice1, dim, rot_u)
self.mono_b = RotatedMonocrystal(lattice2, dim, rot_b)
def main():
opts = parse_args()
# R is a matrix that transforms lattice in the bottom monocrystal
# to lattice in the upper monocrystal
R = rodrigues(opts.axis, opts.theta)
if opts.sigma:
# C is CSL primitive cell
C = csl.find_csl_matrix(opts.sigma, R)
print_matrix("CSL primitive cell", C)
## and now we determine CSL for fcc lattice
#C = csl.pc2fcc(C)
#C = csl.beautify_matrix(C)
#print_matrix("CSL cell for fcc:", C)
else:
C = identity(3)
# CSL-lattice must be periodic is our system.
# * PBC box must be orthonormal
# * boundaries must be perpendicular to z axis of PBC box
print "CSL cell with z || [%s %s %s]" % tuple(opts.plane),
Cp = csl.make_parallel_to_axis(C, col=2, axis=opts.plane)
print_matrix("", Cp)
min_pbc = csl.find_orthorhombic_pbc(Cp)
print_matrix("Minimal(?) orthorhombic PBC", min_pbc)
min_dim = []
pbct = min_pbc.transpose().astype(float)
rot = zeros((3, 3))
for i in range(3):
length = sqrt(inner(pbct[i], pbct[i]))
rot[i] = pbct[i] / length
min_dim.append(length)
invrot = rot.transpose()
assert (numpy.abs(invrot - linalg.inv(rot)) < 1e-9).all(), "%s != %s" % (
invrot, linalg.inv(rot))
#print "hack warning: min_dim[1] /= 2."
#min_dim[1] /= 2.
if "," in opts.lattice_name:
name1, name2 = opts.lattice_name.split(",")
lattice1 = get_named_lattice(name1)
lattice2 = get_named_lattice(name2)
else:
lattice1 = get_named_lattice(opts.lattice_name)
lattice2 = deepcopy(lattice1)
if opts.lattice_shift:
lattice1.shift_nodes(opts.lattice_shift)
lattice2.shift_nodes(opts.lattice_shift)
# the anti-phase GB can be made by swapping two species in one grain
if opts.antiphase:
assert lattice2.count_species() == 2
lattice2.swap_node_atoms_names()
a = lattice1.unit_cell.a
opts.find_dim([i * a for i in min_dim])
#rot_mat1 = rodrigues(opts.axis, rot1)
#rot_mat2 = rodrigues(opts.axis, rot2)
rot_mat1 = dot(linalg.inv(R), invrot)
rot_mat2 = invrot
#print "rot1", "det=%g" % linalg.det(rot_mat1), rot_mat1
#print "rot2", "det=%g" % linalg.det(rot_mat2), rot_mat2
title = get_command_line()
if opts.mono1:
config = RotatedMonocrystal(lattice1, opts.dim, rot_mat1,
title=title)
elif opts.mono2:
config = RotatedMonocrystal(lattice2, opts.dim, rot_mat2,
title=title)
else:
config = Bicrystal(lattice1, lattice2, opts.dim, rot_mat1, rot_mat2,
title=title)
config.generate_atoms(z_margin=opts.vacuum)
if not opts.mono1 and not opts.mono2 and opts.remove_dist > 0:
print "Removing atoms in distance < %s ..." % opts.remove_dist
config.remove_close_neighbours(opts.remove_dist)
if opts.remove_dist2:
a_atoms = []
b_atoms = []
a_name = config.atoms[0].name
for i in config.atoms:
if i.name == a_name:
a_atoms.append(i)
else:
b_atoms.append(i)
config.atoms = []
for aa in a_atoms, b_atoms:
print "Removing atoms where %s-%s distance is < %s ..." % (
aa[0].name, aa[0].name, opts.remove_dist2)
config.remove_close_neighbours(distance=opts.remove_dist2, atoms=aa)
config.atoms += aa
if opts.edge:
z1, z2 = opts.edge
sel = [n for n, a in enumerate(config.atoms)
if 0 < a.pos[1] <= config.pbc[1][1] / 2. and z1 < a.pos[2] < z2]
print "edge: %d atoms is removed" % len(sel)
for i in reversed(sel):
del config.atoms[i]
if opts.all:
#config.output_all_removal_possibilities(opts.output_filename)
config.apply_all_possible_cutoffs_to_stgb(opts.output_filename,
single_cutoff=True)
return
if opts.allall:
config.apply_all_possible_cutoffs_to_stgb(opts.output_filename,
single_cutoff=False)
return
config.export_atoms(opts.output_filename)
def __init__(self, lattice1, lattice2, dim, rot_u, rot_b, title):
OrthorhombicPbcModel.__init__(self, lattice1, dim, title=title)
self.mono_u = RotatedMonocrystal(lattice1, dim, rot_u)
self.mono_b = RotatedMonocrystal(lattice2, dim, rot_b)
def main():
opts = parse_args()
# R is a matrix that transforms lattice in the bottom monocrystal
# to lattice in the upper monocrystal
R = rodrigues(opts.axis, opts.theta)
if opts.sigma:
# C is CSL primitive cell
C = csl.find_csl_matrix(opts.sigma, R)
print_matrix("CSL primitive cell", C)
## and now we determine CSL for fcc lattice
#C = csl.pc2fcc(C)
#C = csl.beautify_matrix(C)
#print_matrix("CSL cell for fcc:", C)
else:
C = identity(3)
# CSL-lattice must be periodic is our system.
# * PBC box must be orthonormal
# * boundaries must be perpendicular to z axis of PBC box
print "CSL cell with z || [%s %s %s]" % tuple(opts.plane),
Cp = csl.make_parallel_to_axis(C, col=2, axis=opts.plane)
print_matrix("", Cp)
min_pbc = csl.find_orthorhombic_pbc(Cp)
print_matrix("Minimal(?) orthorhombic PBC", min_pbc)
min_dim = []
pbct = min_pbc.transpose().astype(float)
rot = zeros((3, 3))
for i in range(3):
length = sqrt(inner(pbct[i], pbct[i]))
rot[i] = pbct[i] / length
min_dim.append(length)
invrot = rot.transpose()
assert (numpy.abs(invrot - linalg.inv(rot)) <
1e-9).all(), "%s != %s" % (invrot, linalg.inv(rot))
#print "hack warning: min_dim[1] /= 2."
#min_dim[1] /= 2.
if "," in opts.lattice_name:
name1, name2 = opts.lattice_name.split(",")
lattice1 = get_named_lattice(name1)
lattice2 = get_named_lattice(name2)
else:
lattice1 = get_named_lattice(opts.lattice_name)
lattice2 = deepcopy(lattice1)
if opts.lattice_shift:
lattice1.shift_nodes(opts.lattice_shift)
lattice2.shift_nodes(opts.lattice_shift)
# the anti-phase GB can be made by swapping two species in one grain
if opts.antiphase:
assert lattice2.count_species() == 2
lattice2.swap_node_atoms_names()
a = lattice1.unit_cell.a
opts.find_dim([i * a for i in min_dim])
#rot_mat1 = rodrigues(opts.axis, rot1)
#rot_mat2 = rodrigues(opts.axis, rot2)
rot_mat1 = dot(linalg.inv(R), invrot)
rot_mat2 = invrot
#print "rot1", "det=%g" % linalg.det(rot_mat1), rot_mat1
#print "rot2", "det=%g" % linalg.det(rot_mat2), rot_mat2
title = get_command_line()
if opts.mono1:
config = RotatedMonocrystal(lattice1, opts.dim, rot_mat1, title=title)
elif opts.mono2:
config = RotatedMonocrystal(lattice2, opts.dim, rot_mat2, title=title)
else:
config = Bicrystal(lattice1,
lattice2,
opts.dim,
rot_mat1,
rot_mat2,
title=title)
config.generate_atoms(z_margin=opts.vacuum)
if not opts.mono1 and not opts.mono2 and opts.remove_dist > 0:
print "Removing atoms in distance < %s ..." % opts.remove_dist
config.remove_close_neighbours(opts.remove_dist)
if opts.remove_dist2:
a_atoms = []
b_atoms = []
a_name = config.atoms[0].name
for i in config.atoms:
if i.name == a_name:
a_atoms.append(i)
else:
b_atoms.append(i)
config.atoms = []
for aa in a_atoms, b_atoms:
print "Removing atoms where %s-%s distance is < %s ..." % (
aa[0].name, aa[0].name, opts.remove_dist2)
config.remove_close_neighbours(distance=opts.remove_dist2,
atoms=aa)
config.atoms += aa
if opts.edge:
z1, z2 = opts.edge
sel = [
n for n, a in enumerate(config.atoms)
if 0 < a.pos[1] <= config.pbc[1][1] / 2. and z1 < a.pos[2] < z2
]
print "edge: %d atoms is removed" % len(sel)
for i in reversed(sel):
del config.atoms[i]
if opts.all:
#config.output_all_removal_possibilities(opts.output_filename)
config.apply_all_possible_cutoffs_to_stgb(opts.output_filename,
single_cutoff=True)
return
if opts.allall:
config.apply_all_possible_cutoffs_to_stgb(opts.output_filename,
single_cutoff=False)
return
config.export_atoms(opts.output_filename)
