def reindex_sites(structure, lattice, tolerance=0.5):
""" Reindexes atoms of structure according to lattice sites.
Expects that the structure is an exact supercell of the lattice, as far
cell vectors are concerned. The atoms, however, may have moved around a
bit. To get an index, an atom must be clearly closer to one ideal lattice
site than to any other, within a given tolerance (in units of `structure.scale`?).
"""
from pylada.crystal import neighbors, supercell
from copy import deepcopy
# haowei: should not change lattice
lat = deepcopy(lattice)
# first give a natural index for the sites in lattice
for i, a in enumerate(lat):
a.site = i
# in the supercell, each atom carry the site from the lat above, and will
# goes into the neighs
lat = supercell(lattice=lat, supercell=structure.cell *
structure.scale / lat.scale)
for atom in structure:
neighs_in_str = [n for n in neighbors(structure, 1, atom.pos)]
d = neighs_in_str[0][2]
# if two atoms from structure and lattice have exactly the same coordination
# and hence dist = 0, it will be neglected by neighbors
# add 1E-6 to atom.pos to avoid this, but aparrently this is not a perfect
# solution, Haowei
neighs = [n for n in neighbors(lat, 2, atom.pos + 1E-6)]
assert abs(neighs[1][2]) > 1e-12,\
RuntimeError('Found two sites occupying the same position.')
if neighs[0][2] * lat.scale > tolerance * d:
atom.site = -1
else:
atom.site = neighs[0][0].site
def reindex_sites(structure, lattice, tolerance=0.5):
""" Reindexes atoms of structure according to lattice sites.
Expects that the structure is an exact supercell of the lattice, as far
cell vectors are concerned. The atoms, however, may have moved around a
bit. To get an index, an atom must be clearly closer to one ideal lattice
site than to any other, within a given tolerance (in units of `structure.scale`?).
"""
from pylada.crystal import neighbors, supercell
from copy import deepcopy
# haowei: should not change lattice
lat = deepcopy(lattice)
# first give a natural index for the sites in lattice
for i, a in enumerate(lat):
a.site = i
# in the supercell, each atom carry the site from the lat above, and will
# goes into the neighs
lat = supercell(lattice=lat,
supercell=structure.cell * structure.scale / lat.scale)
for atom in structure:
neighs_in_str = [n for n in neighbors(structure, 1, atom.pos)]
d = neighs_in_str[0][2]
# if two atoms from structure and lattice have exactly the same coordination
# and hence dist = 0, it will be neglected by neighbors
# add 1E-6 to atom.pos to avoid this, but aparrently this is not a perfect
# solution, Haowei
neighs = [n for n in neighbors(lat, 2, atom.pos + 1E-6)]
assert abs(neighs[1][2]) > 1e-12,\
RuntimeError('Found two sites occupying the same position.')
if neighs[0][2] * lat.scale > tolerance * d:
atom.site = -1
else:
atom.site = neighs[0][0].site
def relax_structure_v1(structure, min_dist_AA=1., min_dist_AB=1., Niter=500):
from itertools import combinations
from pylada.crystal import neighbors
indexes = range(len(structure))
for iter in range(Niter):
succes = 1
np.random.shuffle(indexes)
for index_A in indexes:
neighs = [
n for n in neighbors(structure, 1, structure[index_A].pos)
]
index_B = get_index(structure, neighs[0][0])
if not same_kind(structure, index_A, index_B):
min_dist = min_dist_AB / float(structure.scale)
else:
min_dist = min_dist_AA / float(structure.scale)
if neighs[0][-1] < min_dist:
move_by = min_dist - neighs[0][-1]
if move_by * structure.scale > 0.02:
succes = 0
relax_pair_cm(structure, index_A, index_B, 1.2 * move_by,
min_dist)
move_to_cell(structure, index_A)
move_to_cell(structure, index_B)
if succes:
return 1
return 0
def get_cn(structure, cut_off = 2.8, index = -1, **kwargs):
atom_types, N = get_types(structure)
types_pdf = kwargs.get("types_pdf", get_pdf_types(atom_types))
scale = float(structure.scale)
cn = {}
max_coord = 15
for type in types_pdf:
cn[type] = np.zeros(max_coord)
for index_A in range(len(structure)):
A = structure[index_A].type
pos_A = structure[index_A].pos
neighs = [n for n in neighbors(structure, max_coord-1, pos_A)]
d2_AB_prev = 10.
count = {}
for i, nB in enumerate(neighs):
B = nB[0].type
d2_AB = (scale *nB[2])
delta_dist = d2_AB - d2_AB_prev
d2_AB_prev = d2_AB
if d2_AB > cut_off:
break
#if delta_dist>0.5:
# break
else:
if A+B not in count.keys():
count[A+B] = 0
count[A+B] += 1
for key in count.keys():
cn[key][count[key]] += 1./N[A]
return cn
def count_tot_broken_bonds(bulk=None, slab=None):
"""Counts total number of broken bonds"""
from pylada.crystal import neighbors
under_coord = sort_under_coord(bulk=bulk, slab=slab)
rc = z_center(slab=slab)
# Check the coordination in the bulk first shell
bulk_first_shell = []
for atom in bulk:
bulk_first_shell.append(
[atom.type, len(neighbors(structure=bulk, nmax=1, center=atom.pos, tolerance=1e-1 / bulk.scale))])
broken_bonds = []
for i in range(len(under_coord)):
atom = slab[under_coord[i][0]]
coordination = under_coord[i][1]
for j in range(len(bulk)):
eq_site = float(atom.site - j) / float(len(bulk))
if abs(int(eq_site) - eq_site) < 1e-5:
break
broken_bonds.append(abs(coordination - bulk_first_shell[j][1]))
return sum(array(broken_bonds))
def count_broken_bonds_per_area(bulk=None, slab=None):
"""Counts broken bonds per atom"""
from pylada.crystal import neighbors
under_coord = sort_under_coord(bulk=bulk, slab=slab)
rc = z_center(slab=slab)
# Check the coordination in the bulk first shell
bulk_first_shell = []
for atom in bulk:
bulk_first_shell.append(
[atom.type, len(neighbors(structure=bulk, nmax=1, center=atom.pos, tolerance=1e-1 / bulk.scale))])
broken_bonds = []
for i in range(len(under_coord)):
atom = slab[under_coord[i][0]]
coordination = under_coord[i][1]
for j in range(len(bulk)):
eq_site = float(atom.site - j) / float(len(bulk))
if abs(int(eq_site) - eq_site) < 1e-5:
break
broken_bonds.append(abs(coordination - bulk_first_shell[j][1]))
c = cross(slab.cell[0], slab.cell[1])
area = sqrt(dot(c, c)) * float(slab.scale)**2
return sum(array(broken_bonds)) / area / 2 # there are two surfaces
def relax_structure_v1(structure, min_dist_AA=1., min_dist_AB=1., Niter = 500):
from itertools import combinations
from pylada.crystal import neighbors
indexes = range(len(structure))
for iter in range(Niter):
succes = 1
np.random.shuffle(indexes)
for index_A in indexes:
neighs = [n for n in neighbors(structure, 1, structure[index_A].pos)]
index_B = get_index(structure, neighs[0][0])
if not same_kind(structure, index_A, index_B):
min_dist = min_dist_AB /float(structure.scale)
else:
min_dist = min_dist_AA /float(structure.scale)
if neighs[0][-1] < min_dist:
move_by = min_dist - neighs[0][-1]
if move_by*structure.scale > 0.02:
succes = 0
relax_pair_cm(structure, index_A, index_B, 1.2*move_by, min_dist)
move_to_cell(structure, index_A)
move_to_cell(structure, index_B)
if succes:
return 1
return 0
def get_duplicates(massextr, te_diff=0.01):
""" function to identify unique intersitials
Parameters
massextr = Pylada mass extraction object (directory with all intersitials directories)
te_diff = difference in total energy among interstitials, default = 0.01 eV
Returns
dict = {key='foldername', total_energy, index}
Note"
index = all the foldername (intersitials) with same index are effectively considered equivalent
Criteria for duplicates
1. Total_energy_difference <= 0.01 eV
2. Space_group
3. comparing first neighbor list for all the sites in the structure
"""
dict_E = massextr.total_energies
dict_Str = massextr.structure
dict2 = {}
g = 0
for k in dict_E.keys():
g = g + 1
dict2[k] = [dict_E[k]]
dict2[k].append(g)
folder_list = [l for l in massextr]
folder_combs = combinations(folder_list, 2)
for i in folder_combs:
diff_E = abs(dict2[i[0]][0] - dict2[i[1]][0])
str1 = dict_Str[i[0]]
str2 = dict_Str[i[1]]
spg1 = spglib.get_spacegroup(str1)
spg2 = spglib.get_spacegroup(str2)
ngh_list_1 = sorted(
[len(neighbors(str1, 1, atom.pos, 0.2)) for atom in str1])
ngh_list_2 = sorted(
[len(neighbors(str2, 1, atom.pos, 0.2)) for atom in str2])
if diff_E <= te_diff:
if spg1 == spg2:
if ngh_list_1 == ngh_list_2:
dict2[i[1]][1] = dict2[i[0]][1]
return (dict2)
def Dz(point, structure, k=1, d0=1.5):
from pylada.crystal import neighbors
neighs = [n for n in neighbors(structure, k, point)]
d0 /= float(structure.scale)
value = 0
for i in range(k):
value += (abs(neighs[k-1][-1]-d0))**2
return value
def Dz(point, structure, k=1, d0=1.5):
from pylada.crystal import neighbors
neighs = [n for n in neighbors(structure, k, point)]
d0 /= float(structure.scale)
value = 0
for i in range(k):
value += (abs(neighs[k - 1][-1] - d0))**2
return value
def test_symmetrized():
""" Tests that symmetrized clusters are determined correctly. """
from numpy import all, any
from pylada.ce import Cluster
from pylada.crystal import binary, neighbors
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge']
a = Cluster(lattice)
a.add_spin(lattice[0].pos)
a.add_spin(lattice[0].pos + [0.0, -0.5, -0.5])
a._create_symmetrized()
assert len(a._symmetrized) == 2 * 12
for i, (atom, vec, d) in enumerate(neighbors(lattice, 16, lattice[0].pos)):
if i < 4: continue
b = Cluster(lattice)
b.add_spin(lattice[0].pos)
b.add_spin(vec)
assert any(all(b.spins == u) for u in a._symmetrized)
for i, (atom, vec, d) in enumerate(neighbors(lattice, 16, lattice[1].pos)):
if i < 4: continue
b = Cluster(lattice)
b.add_spin(lattice[1].pos)
b.add_spin(vec)
assert any(all(b.spins == u) for u in a._symmetrized)
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
a = Cluster(lattice)
a.add_spin(lattice[1].pos)
a.add_spin(lattice[1].pos + [1.0, 0, 0])
a._create_symmetrized()
assert len(a._symmetrized) == 6
for i, (atom, vec, d) in enumerate(neighbors(lattice, 24, lattice[0].pos)):
if i < 16: continue
b = Cluster(lattice)
b.add_spin(lattice[1].pos)
b.add_spin(vec)
assert any(all(b.spins == u) for u in a._symmetrized)
def check_against_neighbors(structure, tolerance=1e-8):
from bisect import bisect_right
from pylada.crystal import coordination_shells, neighbors
distances = [u[-1] for u in neighbors(structure, 150, [0, 0, 0], tolerance)]
shells = coordination_shells(structure, 10, [0, 0, 0], tolerance)
for j in range(8):
i = bisect_right(distances, max([u[-1] for u in shells[j]]))
assert i == sum([len(shell) for shell in shells[:j + 1]])
def sort_under_coord(bulk=None, slab=None):
"""Returns indices and th coordinations of the undercoordinated atoms in a slab created from the bulk
:param bulk: pylada structure
:param slab: pylada structure
"""
from pylada.crystal import neighbors
# Check the coordination in the bulk first shell
bulk_first_shell = []
for atom in bulk:
bulk_first_shell.append(
[atom.type, len(neighbors(structure=bulk, nmax=1, center=atom.pos, tolerance=1e-1 / bulk.scale))])
del atom
maxz = max([x.pos[2] for x in slab])
minz = min([x.pos[2] for x in slab])
# Find the undercoordinated atoms in the slab
under_coord = []
indices = [br for br in range(len(slab)) if slab[br].pos[
2] <= minz + 4. / float(slab.scale) or maxz - 4. / float(slab.scale) <= slab[br].pos[2]]
for i in indices:
atom = slab[i]
coordination = len(neighbors(structure=slab, nmax=1,
center=atom.pos, tolerance=1e-1 / slab.scale))
# Find the equivalent bulk atom to compare the coordination with
for j in range(len(bulk)):
eq_site = float(atom.site - j) / float(len(bulk))
if abs(int(eq_site) - eq_site) < 1e-2:
break
# Comparing coordination with the "equivalent" bulk atom
if coordination != bulk_first_shell[j][1]:
under_coord.append([i, coordination])
del coordination
# returns the list of undercoordinated atoms,
# atom index in the slab, coordination
return under_coord
def calc_correlation(structure, rad, **kwargs):
scale = float(structure.scale)
Natoms = len(structure)
cell = structure.cell.T
abc = [ v for v in structure.cell]
ds = [np.dot(v, v)**0.5 for v in abc]
Vol = np.linalg.det(cell)
atom_types, N = get_types(structure)
print atom_types, N
types_pdf = kwargs.get("types_pdf", get_pdf_types(atom_types))
Npdfs = len(types_pdf)
pdf_cut = kwargs.get("pdf_cut", Vol**(1/3.) * scale)/scale
pdf_nbins = len(rad)
cut2 = 6.25 / (scale**2)
N_in_rcut = kwargs.get("N_in_rcut", int(1.2 *Natoms*4*np.pi*pdf_cut**3/(3*Vol)))
pdfs = {}
count = {}
for type in types_pdf:
[A, B] = re.findall('[A-Z][^A-Z]*', type)
pdfs[A+B] = np.zeros(pdf_nbins)
count[A+B] = 0
if 1:
A_range = range(Natoms)
for index_A in A_range:
A = structure[index_A].type
pos_A = structure[index_A].pos
neighs = [n for n in neighbors(structure, N_in_rcut, pos_A)]
for i, nB in enumerate(neighs):
index_B = get_index(structure, nB[0])
if index_B > index_A:
B = structure[index_B].type
dist = nB[2]*scale
for Nbin, d in enumerate(rad[1:]):
if dist < d:
pdf_width = rad[Nbin-1] - d
break
if Nbin < pdf_nbins:
pdf_width
weigth0 = 4 * np.pi * pdf_width**3 / Vol
val = np.zeros(pdf_nbins)
val[Nbin] = weigth0
pdfs[A+B] += val
pdfs[B+A] += val
for type in types_pdf:
[A, B] = re.findall('[A-Z][^A-Z]*', type)
pdfs[A+B] /= N[B] * N[A]
for i in range(pdf_nbins):
pdfs[A+B][i] /= (i + 1e-5)**2
return pdfs
def first_shell(structure, pos, tolerance=0.25): """ Iterates though first neighbor shell. """ from pylada.crystal import neighbors from copy import deepcopy struct = deepcopy(structure) for i, a in enumerate(struct): a.index = i neighs = [n for n in neighbors(struct, 12, pos)] d = neighs[0][2] return [n for n in neighs if abs(n[2] - d) < tolerance * d]
def analyze_voids(zipped_voids, structure):
''' Analysis voids'''
centers = []
for value, point in zipped_voids:
print '######', value * structure.scale
centers.append(-value * structure.scale)
neighs = [n for n in neighbors(structure, 7, point)]
for n in neighs:
print n[0].type, n[2] * structure.scale
return centers
def get_all_interstitials(prim_structure, positions):
""" function to return list of all interstitial sites using Voronoi.py
Parameters
prim = pylada primitive structure
positions = positions (numpy array) to compute interstitials for
Returns
Inst_list = list of list, with inner list containing ['atom type', [x,y,z]]
"""
ints_list = []
for site_num in range(len(positions)):
site = np.array([
positions[site_num][0], positions[site_num][1],
positions[site_num][2]
])
site_ngh = neighbors(prim_structure, 13, site, 0.1)
points = [site]
### creating list with site and its neighbors
for i in range(len(site_ngh)):
a = site + site_ngh[i][1]
points.append(a)
### converting list to numpy array
points = np.asarray(points)
### using tess object cntr to compute voronoi
cntr = compute_voronoi(points)
### Voronoi vertices
### the first position in points is the site, therefore '0'
v = get_vertices(0, cntr)
for i in range(len(v)):
ints_list.append(['B', v[i].tolist()])
### Voronoi face centers
f = get_facecentroid(0, cntr)
for j in range(len(f)):
ints_list.append(['C', f[j].tolist()])
### Voronoi edge centers
e = get_edgecenter(0, cntr)
for k in range(len(e)):
ints_list.append(['N', e[k].tolist()])
### return list of list ['Atom type', [x,y,z]]
return ints_list
def check(structure, center, tolerance=1e-8):
from numpy import abs, sqrt, all
from pylada.crystal import neighbors
# check we get the neighbors of zinc-blende.
neighs = neighbors(structure, 46, center, tolerance)
assert len(neighs) == 46
for atom, diff, dist in neighs[:4]:
assert abs(dist - sqrt(3.0) * 0.25) < tolerance
assert all(abs(abs(diff) - 0.25) < tolerance)
for atom, diff, dist in neighs[4: 16]:
assert abs(dist - sqrt(2.0) * 0.5) < tolerance
assert len([0 for u in diff if abs(u) < tolerance]) == 1
assert len([0 for u in diff if abs(abs(u) - 0.5) < tolerance]) == 2
for atom, diff, dist in neighs[16: 28]:
assert abs(dist - sqrt(0.75 * 0.75 + 2. * 0.25 * 0.25)) < tolerance
assert len([0 for u in diff if abs(abs(u) - 0.25) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u) - 0.75) < tolerance]) == 1
for atom, diff, dist in neighs[28:34]:
assert abs(dist - 1.) < tolerance
assert len([0 for u in diff if abs(u) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u) - 1.) < tolerance]) == 1
for atom, diff, dist in neighs[34:]:
assert abs(dist - sqrt(2 * 0.75 * 0.75 + 0.25 * 0.25)) < tolerance
assert len([0 for u in diff if abs(abs(u) - 0.75) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u) - 0.25) < tolerance]) == 1
# check input using position rather than atom.
neighs2 = neighbors(structure, 36, center.pos, tolerance)
for (a, b, c), (d, e, f) in zip(neighs, neighs2):
assert a is d
assert all(abs(b - e)) < tolerance
assert abs(c - f) < tolerance
# check neighbor completeness.
assert len(neighbors(structure, 2, center, tolerance)) == 4
assert len(neighbors(structure, 4, center, tolerance)) == 4
assert len(neighbors(structure, 6, center, tolerance)) == 16
def first_shell(structure, pos, tolerance=0.25):
""" Iterates though first neighbor shell. """
from pylada.crystal import neighbors
from copy import deepcopy
struct = deepcopy(structure)
for i, a in enumerate(struct):
a.index = i
neighs = [n for n in neighbors(struct, 12, pos)]
d = neighs[0][2]
return [n for n in neighs if abs(n[2] - d) < tolerance * d]
def get_nnb(s, i, mytol):
nghs = neighbors(s, 20, s[i].pos, 0.001)
shortest_dist = nghs[0][-1]
shortest_type = nghs[0][0].type
hlp = []
for ng in nghs:
if ng[0].type != shortest_type: break
if ng[-1] > shortest_dist * (1 + mytol): continue
hlp.append(ng)
return len(hlp)
def find_ngh_indices(atomind,structure):
""" function to return ngh indices from given atomind
"""
nghs=neighbors(structure,1,structure[atomind],0.2)
ngh_indices=[]
for ii in range(len(structure)):
if any([ all(structure[ii].pos==ngh[0].pos) for ngh in nghs]) and any([ structure[ii].type==ngh[0].type for ngh in nghs]):
ngh_indices.append(ii)
return ngh_indices
def ffirst_shell(structure, pos, tolerance):
""" Function to iterate through the first neighbor shell
Parameters
structure = pylada structure object
pos = position (numpy array) of site, around which neighbor shell need to be computed
tolerance = for choosing neighbors whose distance from 'pos' is within first neighbor distance, d(1+tolerance)
Returns
list of neighbors, same format as pylada.crystal.neigbors
"""
struct = deepcopy(structure)
for i, a in enumerate(struct):
a.index = i
neighs = [n for n in neighbors(struct, 12, pos)]
d = neighs[0][2]
return [n for n in neighs if abs(n[2] - d) < tolerance * d]
def void_hop_type(structure,seed):
point, value = void.get_rnd_void_center(structure, seed=seed)
neighs = [n for n in neighbors(structure, 12, point)]
n0 = neighs[0]
type0 = n0[0].type
n_in = 0
n_o = 0
for n in neighs[1:]:
type_tmp = n[0].type
if (n[2] - n0[2])*structure.scale <0.4:
if type_tmp != 'O':
n_in +=1
if type_tmp == 'O':
n_o +=1
for n in neighs:
type = n[0].type
if n_in < n_o:
if type != 'O':
dp = point - n[0].pos
ddp = structure.scale*np.dot(dp,dp)**0.5
dp = impose_pbc(structure.cell, dp)
ddp1 = structure.scale*np.dot(dp,dp)**0.5
print type, ddp, ddp1, structure.scale*n[2]
n[0].pos = point
break
else:
if type == 'O':
dp = point - n[0].pos
ddp = structure.scale*np.dot(dp,dp)**0.5
dp = impose_pbc(structure.cell, dp)
ddp1 = structure.scale*np.dot(dp,dp)**0.5
print type, ddp, ddp1, structure.scale*n[2]
n[0].pos = point
break
#print '######moved', n_in, n_o, type, index, n[2]*structure.scale
return structure
def get_2shells(s, i, mytol):
nghs = neighbors(s, 50, s[i].pos, 0.001)
shortest_dist = nghs[0][-1]
shortest_type = nghs[0][0].type
hlp = []
for ii in range(len(nghs)):
ng = nghs[ii]
if ng[0].type != shortest_type: break
if ng[-1] > shortest_dist * (1 + mytol): continue
hlp.append(ng)
shortest_dist = nghs[ii][-1]
shortest_type = nghs[ii][0].type
hlphlp = []
for jj in range(ii, len(nghs)):
ng = nghs[jj]
if ng[0].type != shortest_type: break
if ng[-1] > shortest_dist * (1 + mytol): continue
hlphlp.append(ng)
return [hlp, hlphlp]
def check_bcc():
""" Check on BCC structure. """
from pylada.crystal import Structure, neighbors
structure = Structure([[-0.5, 0.5, 0.5], [0.5, -0.5, 0.5], [0.5, 0.5, -0.5]])\
.add_atom(0, 0, 0, "Mo")
print(neighbors(structure, 12, [0, 0, 0]))
def calc_Dx(point, structure):
'''Calculates the distnace to the nearest atom'''
neighs = [n for n in neighbors(structure, 3, point)]
return -neighs[0][2]
def calc_pdfs(structure, template = False, index = -1, **kwargs):
scale = float(structure.scale)
Natoms = len(structure)
cell = structure.cell.T
abc = [ v for v in structure.cell]
ds = [np.dot(v, v)**0.5 for v in abc]
Vol = np.linalg.det(cell)
atom_types, N = get_types(structure)
print atom_types, N
types_pdf = kwargs.get("types_pdf", get_pdf_types(atom_types))
Npdfs = len(types_pdf)
pdf_width = kwargs.get("pdf_width", 0.05)
smear_flag = kwargs.get("smear_flag", True)
pdf_sigma = kwargs.get("pdf_sigma", pdf_width)
pdf_nsigma = pdf_sigma/pdf_width
pdf_nsmear = int(3*pdf_nsigma+0.5)
pdf_cut = kwargs.get("pdf_cut", Vol**(1/3.) * scale)/scale
pdf_nbins = 2 * int(pdf_cut * scale / (2* pdf_width) ) + 1
pdf_width = pdf_cut / pdf_nbins
cut2 = 6.25 / (scale**2)
N_in_rcut = kwargs.get("N_in_rcut", int(1.2 *Natoms*4*np.pi*pdf_cut**3/(3*Vol)))
weight0 = 4 * np.pi * pdf_width**3 / Vol
pdfs = {}
count = {}
for type in types_pdf:
[A, B] = re.findall('[A-Z][^A-Z]*', type)
pdfs[A+B] = np.zeros(pdf_nbins)
count[A+B] = 0
if 1:
if index >=0:
A_range = [index]
weight0 = Natoms * weight0
else:
A_range = range(Natoms)
weight0 = weight0
for index_A in A_range:
A = structure[index_A].type
pos_A = structure[index_A].pos
neighs = [n for n in neighbors(structure, N_in_rcut, pos_A)]
for i, nB in enumerate(neighs):
index_B = get_index(structure, nB[0])
if index_B > index_A:
B = structure[index_B].type
Nbin = np.around(nB[2]/pdf_width)
if Nbin < pdf_nbins:
#val = gauss1D( 1., Nbin, pdf_nbins, 0, pdf_nsigma)
if smear_flag:
val = gauss1D( 1., Nbin, pdf_nbins, pdf_nsmear, pdf_nsigma)
else:
val = np.zeros(pdf_nbins)
val[Nbin] = 1
pdfs[A+B] += val
pdfs[B+A] += val
for type in types_pdf:
[A, B] = re.findall('[A-Z][^A-Z]*', type)
pdfs[A+B] /= weight0 * N[B] * N[A]
for i in range(pdf_nbins):
pdfs[A+B][i] /= (i + 1e-5)**2
r = pdf_width * np.arange(pdf_nbins) * scale
return pdfs, r
def void_hop(structure,seed):
point, value = void.get_rnd_void_center(structure, seed=seed)
neighs = [n for n in neighbors(structure, 1, point)]
n[0].pos = point
import numpy as np
d = json.load(open("data.json", 'r'))
cord = {}
coulomb = {"ZiZj/d": {},
"1/d": {}}
for item in d:
icsdstr = "{0:06d}".format(int(item["icsdnum"]))
atoms = read.icsd_cif_a("/scratch/jyan/allcifs/icsd_%s.cif"%(icsdstr))
ngh = defaultdict(float)
uniqueatom = defaultdict(int)
coul1 = defaultdict(float)
coul2 = defaultdict(float)
for i, atom in enumerate(atoms):
ngh_n = neighbors(structure=atoms,nmax=1,center=atom.pos,tolerance=0.05)
uniqueatom[atom.type] += 1
ngh[atom.type] += len(ngh_n)
Zi = getattr(pt, atom.type).atomic_number
# loop over neighbors
for j in range(len(ngh_n)):
Zj = getattr(pt, ngh_n[j][0].type).atomic_number
coul1[atom.type] += Zi * Zj / ngh_n[j][2]
coul2[atom.type] += 1. / ngh_n[j][2]
for atom in ngh.keys():
ngh[atom] /= float(uniqueatom[atom])
coul1[atom] /= float(uniqueatom[atom])
coul2[atom] /= float(uniqueatom[atom])