def get_reduced_scell(self):
"""
enforces the surface coverage criterion and generates
the list all reduced lattice vectors that correspond to
the computed supercell size and returns the one with similar
lattice vector norms
"""
scell, nlig = self.enforce_coverage()
if scell and nlig:
ab = [self.lattice.matrix[0,:], self.lattice.matrix[1,:]]
uv_list, _ = reduced_supercell_vectors(ab, scell)
norm_list = []
for uv in uv_list:
unorm = np.linalg.norm(uv[0])
vnorm = np.linalg.norm(uv[1])
norm_list.append(abs(1. - unorm/vnorm))
return nlig, uv_list[np.argmin(norm_list)]
else:
logger.warn("couldn't find supercell and number of ligands that satisfy the required surface coverage. exiting.")
sys.exit()
def get_reduced_scell(self):
"""
enforces the surface coverage criterion and generates
the list all reduced lattice vectors that correspond to
the computed supercell size and returns the one with similar
lattice vector norms
"""
scell, nlig = self.enforce_coverage()
if scell and nlig:
ab = [self.lattice.matrix[0, :], self.lattice.matrix[1, :]]
uv_list, _ = reduced_supercell_vectors(ab, scell)
norm_list = []
for uv in uv_list:
unorm = np.linalg.norm(uv[0])
vnorm = np.linalg.norm(uv[1])
norm_list.append(abs(1. - unorm / vnorm))
return nlig, uv_list[np.argmin(norm_list)]
else:
logger.warn(
"couldn't find supercell and number of ligands that satisfy the required surface coverage. exiting.")
sys.exit()
def get_matching_lattices(iface1,
iface2,
max_area=100,
max_mismatch=0.01,
max_angle_diff=1,
r1r2_tol=0.02):
"""
computes a list of matching reduced lattice vectors that satify
the max_area, max_mismatch and max_anglele_diff criteria
"""
if iface1 is None and iface2 is None:
# test : the numbers from the paper
a1 = 5.653
a2 = 6.481
# for 100 plane
ab1 = [[0, a1 / 2, -a1 / 2], [0, a1 / 2, a1 / 2]]
ab2 = [[0, a2 / 2, -a2 / 2], [0, a2 / 2, a2 / 2]]
area1 = a1**2 / 2
area2 = a2**2 / 2
# for 110 plane
ab1 = [[a1 / 2, -a1 / 2, 0], [0, 0, a1]]
ab2 = [[a2 / 2, -a2 / 2, 0], [0, 0, a2]]
area1 = a1**2 / sqrt(2)
area2 = a2**2 / sqrt(2)
# for 111 surface
# ab1 = [ [a1/2, 0, a1/2], [a1/2, a1/2, 0]]
# ab2 = [ [a2/2, 0, a2/2], [a2/2, a2/2, 0]]
# area1 = a1**2 * sqrt(3)/4 #/ 2 /sqrt(2)
# area2 = a2**2 * sqrt(3)/4 #/ 2 / sqrt(2)
else:
area1 = iface1.surface_area
area2 = iface2.surface_area
# a, b vectors that define the surface
ab1 = [iface1.lattice.matrix[0, :], iface1.lattice.matrix[1, :]]
ab2 = [iface2.lattice.matrix[0, :], iface2.lattice.matrix[1, :]]
print('area1, area2', area1, area2)
r_list = get_r_list(area1, area2, max_area, tol=r1r2_tol)
if not r_list:
print(
'r_list is empty. Try increasing the max surface area or/and the other tolerance paramaters'
)
sys.exit()
for r1r2 in r_list:
# print('r1, r2', r1r2, '\n')
uv1_list = reduced_supercell_vectors(ab1, r1r2[0])
uv2_list = reduced_supercell_vectors(ab2, r1r2[1])
for uv1 in uv1_list:
for uv2 in uv2_list:
u_mismatch = get_mismatch(uv1[0], uv2[0])
v_mismatch = get_mismatch(uv1[1], uv2[1])
angle1 = get_angle(uv1[0], uv1[1])
angle2 = get_angle(uv2[0], uv2[1])
print('\nu1, u2', np.linalg.norm(uv1[0]),
np.linalg.norm(uv2[0]))
print('v1, v2', np.linalg.norm(uv1[1]), np.linalg.norm(uv2[1]))
print('angle1, angle2', angle1, angle2)
print('u and v mismatches', u_mismatch, v_mismatch)
if abs(u_mismatch) < max_mismatch and abs(
v_mismatch) < max_mismatch:
if abs(angle1 - angle2) < max_angle_diff:
print('\n FOUND ONE')
print('u mismatch in percentage = ', u_mismatch)
print('v mismatch in percentage = ', v_mismatch)
print('angle1, angle diff', angle1,
abs(angle1 - angle2))
print('uv1, uv2', uv1, uv2)
return uv1, uv2
def get_matching_lattices(
iface1,
iface2,
max_area=100,
max_mismatch=0.01,
max_angle_diff=1,
r1r2_tol=0.02,
):
"""
computes a list of matching reduced lattice vectors that satify
the max_area, max_mismatch and max_anglele_diff criteria
"""
#| - get_matching_lattices
if iface1 is None and iface2 is None:
# | - iface1 and 2 is None
# test : the numbers from the paper
a1 = 5.653
a2 = 6.481
# for 100 plane
ab1 = [[0, a1 / 2, -a1 / 2], [0, a1 / 2, a1 / 2]]
ab2 = [[0, a2 / 2, -a2 / 2], [0, a2 / 2, a2 / 2]]
area1 = a1 ** 2 / 2
area2 = a2 ** 2 / 2
# for 110 plane
ab1 = [[a1 / 2, -a1 / 2, 0], [0, 0, a1]]
ab2 = [[a2 / 2, -a2 / 2, 0], [0, 0, a2]]
area1 = a1 ** 2 / sqrt(2)
area2 = a2 ** 2 / sqrt(2)
# for 111 surface
# ab1 = [ [a1/2, 0, a1/2], [a1/2, a1/2, 0]]
# ab2 = [ [a2/2, 0, a2/2], [a2/2, a2/2, 0]]
# area1 = a1**2 * sqrt(3)/4 #/ 2 /sqrt(2)
# area2 = a2**2 * sqrt(3)/4 #/ 2 / sqrt(2)
#__|
else:
# | - else
area1 = iface1.surface_area
area2 = iface2.surface_area
# a, b vectors that define the surface
ab1 = [iface1.lattice.matrix[0, :], iface1.lattice.matrix[1, :]]
ab2 = [iface2.lattice.matrix[0, :], iface2.lattice.matrix[1, :]]
# __|
#| - r_list
print('initial values:\nuv1:\n{0}\nuv2:\n{1}\n '.format(ab1, ab2))
r_list = get_r_list(area1, area2, max_area, tol=r1r2_tol)
if not r_list:
print(
'r_list is empty.',
' Try increasing the max surface area or/and the other',
' tolerance paramaters',
)
sys.exit()
#__|
# | - Searching For-loop
found = []
print('searching ...')
for r1r2 in r_list:
uv1_list, tm1_list = reduced_supercell_vectors(ab1, r1r2[0])
uv2_list, tm2_list = reduced_supercell_vectors(ab2, r1r2[1])
if not uv1_list and not uv2_list:
continue
for i, uv1 in enumerate(uv1_list):
for j, uv2 in enumerate(uv2_list):
u_mismatch = get_mismatch(uv1[0], uv2[0])
v_mismatch = get_mismatch(uv1[1], uv2[1])
angle1 = get_angle(uv1[0], uv1[1])
angle2 = get_angle(uv2[0], uv2[1])
angle_mismatch = abs(angle1 - angle2)
area1 = get_area(uv1)
area2 = get_area(uv2)
if abs(u_mismatch) < max_mismatch and abs(
v_mismatch) < max_mismatch:
max_angle = max(angle1, angle2)
min_angle = min(angle1, angle2)
mod_angle = max_angle % min_angle
is_angle_factor = False
if abs(mod_angle) < 0.001 or abs(
mod_angle - min_angle) < 0.001:
is_angle_factor = True
if angle_mismatch < max_angle_diff or is_angle_factor:
if angle_mismatch > max_angle_diff:
if angle1 > angle2:
uv1[1] = uv1[0] + uv1[1]
tm1_list[i][1] = tm1_list[i][0] + tm1_list[i][
1]
else:
uv2[1] = uv2[0] + uv2[1]
tm2_list[j][1] = tm2_list[j][0] + tm2_list[j][
1]
found.append(
(
uv1, uv2, min(area1, area2),
u_mismatch,
v_mismatch,
angle_mismatch,
tm1_list[i],
tm2_list[j],
)
)
#__|
if found:
return(found)
#| - If structure found
# print('\nMATCH FOUND\n')
# uv_opt = sorted(found, key=lambda x: x[2])[0]
# print('optimum values:\nuv1:\n{0}\nuv2:\n{1}\narea:\n{2}\n'.format(
# uv_opt[0], uv_opt[1], uv_opt[2]))
# print('optimum transition matrices:\ntm1:\n{0}\ntm2:\n{1}\n'.format(
# uv_opt[6], uv_opt[7]))
# print('u,v & angle mismatches:\n{0}, {1}, {2}\n'.format(uv_opt[3],
# uv_opt[4],
# uv_opt[5]))
# return uv_opt[0], uv_opt[1]
#__|
else:
# | - else
print('\n NO MATCH FOUND')
return None, None
def get_matching_lattices(iface1, iface2, max_area = 100,
max_mismatch = 0.01, max_angle_diff = 1,
r1r2_tol= 0.02):
"""
computes a list of matching reduced lattice vectors that satify
the max_area, max_mismatch and max_anglele_diff criteria
"""
if iface1 is None and iface2 is None:
#test : the numbers from the paper
a1 = 5.653
a2 = 6.481
#for 100 plane
ab1 = [ [0, a1/2, -a1/2], [0, a1/2,a1/2]]
ab2 = [ [0, a2/2, -a2/2], [0, a2/2,a2/2]]
area1 = a1**2 / 2
area2 = a2**2 / 2
#for 110 plane
ab1 = [ [a1/2,-a1/2,0], [0, 0,a1]]
ab2 = [ [a2/2,-a2/2,0], [0, 0,a2]]
area1 = a1**2 / sqrt(2)
area2 = a2**2 / sqrt(2)
#for 111 surface
#ab1 = [ [a1/2, 0, a1/2], [a1/2, a1/2, 0]]
#ab2 = [ [a2/2, 0, a2/2], [a2/2, a2/2, 0]]
#area1 = a1**2 * sqrt(3)/4 #/ 2 /sqrt(2)
#area2 = a2**2 * sqrt(3)/4 #/ 2 / sqrt(2)
else:
area1 = iface1.surface_area
area2 = iface2.surface_area
#a, b vectors that define the surface
ab1 = [ iface1.lattice.matrix[0,:] , iface1.lattice.matrix[1,:] ]
ab2 = [ iface2.lattice.matrix[0,:] , iface2.lattice.matrix[1,:] ]
print('area1, area2', area1, area2)
r_list = get_r_list(area1, area2, max_area, tol=r1r2_tol)
if not r_list:
print('r_list is empty. Try increasing the max surface area or/and the other tolerance paramaters')
sys.exit()
for r1r2 in r_list:
#print('r1, r2', r1r2, '\n')
uv1_list = reduced_supercell_vectors(ab1, r1r2[0])
uv2_list = reduced_supercell_vectors(ab2, r1r2[1])
for uv1 in uv1_list:
for uv2 in uv2_list:
u_mismatch = get_mismatch(uv1[0], uv2[0])
v_mismatch = get_mismatch(uv1[1], uv2[1])
angle1 = get_angle(uv1[0], uv1[1])
angle2 = get_angle(uv2[0], uv2[1])
print('\nu1, u2', np.linalg.norm(uv1[0]), np.linalg.norm(uv2[0]))
print('v1, v2', np.linalg.norm(uv1[1]), np.linalg.norm(uv2[1]))
print('angle1, angle2', angle1, angle2)
print('u and v mismatches', u_mismatch, v_mismatch)
if abs(u_mismatch) < max_mismatch and abs(v_mismatch) < max_mismatch:
if abs(angle1 - angle2) < max_angle_diff:
print('\n FOUND ONE')
print('u mismatch in percentage = ', u_mismatch)
print('v mismatch in percentage = ', v_mismatch)
print('angle1, angle diff', angle1, abs(angle1 - angle2))
print('uv1, uv2', uv1, uv2)
return uv1, uv2