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cif2json.py
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#!/usr/bin/env python3
import glob
import os
import sys
import math
import json
import copy
import time
import itertools
import CifFile
import numpy as np
import qcelemental as qcel
from itertools import permutations
sys.path.append("/home/jorgegv/work/qcp-python-app/qcp")
from system import systemData
class Timer:
def __init__(self, to_print):
self.start = time.time()
self.t1 = time.time()
self.print = to_print
def stop(self, descr=None):
if not self.print: return
now = time.time()
if descr:
print(round(now - self.t1, 2), round(now - self.start, 2), descr)
else:
print(round(now - self.t1, 2), round(now - self.start, 2))
self.t1 = time.time()
### CRYSTAL STRUCTURE --------------------------------------------
def find_cif(inp_dict):
try:
cif_file = inp_dict["Cif"]
except KeyError:
print("ERROR: cannot find 'Cif' in the input file.")
return(cif_file)
def cell_lengths(r, cif_data):
"""Number of boxes to consider in each axis where one box is one additional unit cell in that direction."""
print("Radius: {} A".format(r))
# Nx = math.ceil(r/cif_data["_cell_length_a"])+1
# Ny = math.ceil(r/cif_data["_cell_length_b"])+1
# Nz = math.ceil(r/cif_data["_cell_length_c"])+1
l_max = max(cif_data["_cell_length_a"], cif_data["_cell_length_b"], cif_data["_cell_length_c"])
n_max = math.ceil(r/l_max)+2
Nx, Ny, Nz = n_max, n_max, n_max
return Nx, Ny, Nz
def factors_convert_fract2cartes(cif_data):
"""
Edge vectors (a, b, c) in fractional coordinate –> (x, y, z) in Cartesian coordinate
cos(alpha) = b*c/(|b||c|)
cos(beta) = a*c/(|a||c|)
cos(gamma) = a*b/(|a||b|)
a = (a, 0, 0)
b = (bcos(gamma), bsin(gamma), 0)
c = (cx, cy, cz)
x = La*u + Lb*cos(gamma)*v + Lc*cos(beta)*w
y = Lb*sin(gamma)*v + Lc*((cos(alpha)cos(gamma) - cos(alpha))/sin(gamma))*w
z = Lc * (sqrt(1 - cos_a**2 - cos_b**2 - cos_g**2 + 2*cos_a*cos_b*cos_g)/sin_g)*w
"""
# Lengths of the unit cell
La = cif_data["_cell_length_a"]
Lb = cif_data["_cell_length_b"]
Lc = cif_data["_cell_length_c"]
# Angles in the unit cell
alpha = math.radians(cif_data["_cell_angle_alpha"])
beta = math.radians(cif_data["_cell_angle_beta"])
gamma = math.radians(cif_data["_cell_angle_gamma"])
cos_a = math.cos(alpha)
sin_a = math.sin(alpha)
cos_b = math.cos(beta)
sin_b = math.sin(beta)
cos_g = math.cos(gamma)
sin_g = math.sin(gamma)
ax = La
# ay = az = 0
bx = Lb * cos_g
by = Lb * sin_g
# bz = 0
cx = Lc * cos_b
cy = Lc * (cos_a - cos_g*cos_b)/sin_g
cz = Lc * math.sqrt(1 - cos_a**2 - cos_b**2 - cos_g**2 + 2*cos_a*cos_b*cos_g)/sin_g
# Use the volume to check that we calculated the vectors correctly
V = ax * by * cz
if abs(V - cif_data["_cell_volume"]) > 0.1:
print("WARNING: Volume calculated with the real vectors is not the same as the volume in CIF file.")
return({"ax": ax, "ay": 0, "az": 0, "bx": bx, "by": by, "bz": 0, "cx": cx, "cy": cy, "cz": cz})
def convert_fract2carte_atom(u, v, w, factors_dict, print_=False):
ax = factors_dict["ax"]
bx = factors_dict["bx"]
cx = factors_dict["cx"]
by = factors_dict["by"]
cy = factors_dict["cy"]
cz = factors_dict["cz"]
x = ax*u + bx*v + cx*w
y = by*v + cy*w
z = cz*w
if print_:
print('convert_fract2carte_atom')
print("u, v, w", u, v, w)
print("ax, bx, cx, by, cy, cz", ax, bx, cx, by, cy, cz)
print('x, y, z', x, y, z)
return x, y, z
def convert_carte2fract_atom(x, y, z, factors_dict, print_=None):
ax = factors_dict["ax"]
bx = factors_dict["bx"]
cx = factors_dict["cx"]
by = factors_dict["by"]
cy = factors_dict["cy"]
cz = factors_dict["cz"]
w = z/cz
v = (y - cy * w) / by
u = (x - bx*v - cx*w) / ax
if print_:
print('convert_carte2fract_atom')
print('x, y, z', x, y, z)
print("ax, bx, cx, by, cy, cz", ax, bx, cx, by, cy, cz)
print("u, v, w", u, v, w)
return(u, v, w)
def read_cif(cif_name):
cif = CifFile.ReadCif(cif_name)
for data in cif:
cif_dblock = data
break
cif_data = {}
# Extract CIF data and remove the square brackets in the numbers
cif_data["_chemical_name"] = cif_dblock["_chemical_name_systematic"]
if cif_dblock["_chemical_name_systematic"] == "?":
cif_data["_chemical_name"] = cif_dblock["_chemical_name_common"]
cif_data["_chemical_formula_moiety"] = cif_dblock["_chemical_formula_moiety"]
cif_data["_cell_length_a"] = float(cif_dblock["_cell_length_a"].replace("(", "").replace(")", ""))
cif_data["_cell_length_b"] = float(cif_dblock["_cell_length_b"].replace("(", "").replace(")", ""))
cif_data["_cell_length_c"] = float(cif_dblock["_cell_length_c"].replace("(", "").replace(")", ""))
cif_data["_cell_angle_alpha"] = float(cif_dblock["_cell_angle_alpha"].replace("(", "").replace(")", ""))
cif_data["_cell_angle_beta"] = float(cif_dblock["_cell_angle_beta"].replace("(", "").replace(")", ""))
cif_data["_cell_angle_gamma"] = float(cif_dblock["_cell_angle_gamma"].replace("(", "").replace(")", ""))
cif_data["_cell_volume"] = float(cif_dblock["_cell_volume"].replace("(", "").replace(")", ""))
# Extract the symmetry operations that define the space group
'''
In some cases, it might be called "_space_group_symop_operation_xyz".
In the CIF file, the symmetry-equivalent position in the xyz format look like:
```
loop_
_symmetry_equiv_pos_as_xyz
'x,y,z'
'y,x,2/3-z'
'-y,x-y,2/3+z'
'-x,-x+y,1/3-z'
'-x+y,-x,1/3+z'
'x-y,-y,-z'
```
Except for the space group P1, these data will be repeated in a loop.
'''
cif_data["_symmetry_equiv_pos_as_xyz"] = []
try:
sym_op = cif_dblock["_symmetry_equiv_pos_as_xyz"]
except KeyError:
try:
sym_op = cif_dblock["_space_group_symop_operation_xyz"]
except KeyError:
print("\n ERROR: Cif file does not have an item: either \"_symmetry_equiv_pos_as_xyz\" or \"_space_group_symop_operation_xyz\".")
sys.exit()
for xyz_op in sym_op:
cif_data["_symmetry_equiv_pos_as_xyz"].append(xyz_op)
# Get the fractional coordinates u, v, w (x, y, z) of the atoms
cif_data["_atom_site_label"] = cif_dblock["_atom_site_label"]
cif_data["_atom_site_type_symbol"] = cif_dblock["_atom_site_type_symbol"]
cif_data["_atom_site_fract_x"] = []
for u in cif_dblock["_atom_site_fract_x"]:
cif_data["_atom_site_fract_x"].append(float(u.split("(")[0]))
cif_data["_atom_site_fract_y"] = []
for v in cif_dblock["_atom_site_fract_y"]:
cif_data["_atom_site_fract_y"].append(float(v.split("(")[0]))
cif_data["_atom_site_fract_z"] = []
for w in cif_dblock["_atom_site_fract_z"]:
cif_data["_atom_site_fract_z"].append(float(w.split("(")[0]))
return(cif_data)
def asym_unit(cif_data):
# Atom labels
atom_labels = cif_data["_atom_site_type_symbol"]
# Atom coordinates
atom_u = cif_data["_atom_site_fract_x"]
atom_v = cif_data["_atom_site_fract_y"]
atom_w = cif_data["_atom_site_fract_z"]
asym_unit = []
asym_unit = [(atom_labels[i], atom_u[i], atom_v[i], atom_w[i]) for i in range(len(atom_labels))]
# Move atoms into a unit cell
asym_unit = [(atom[0], atom[1]%1.0, atom[2]%1.0, atom[3]%1.0) for atom in asym_unit]
return(asym_unit)
def unit_cell(atoms, cif_data):
'''
Use symmetry operations to create the unit cell
The CIF file consists of a few atom positions and several "symmetry operations" that indicate the other atom positions within the unit cell.
Using these symmetry operations, create copies of the atoms until no new copies can be made.
For each atom, apply each symmetry operation to create a new atom.
'''
# Symmetry operation
sym_op = cif_data["_symmetry_equiv_pos_as_xyz"]
imax = len(atoms)
i = 0
atoms_uc = []
while i < imax:
label, x, y, z = atoms[i]
# Keep x, y, z as they are! Cause they will be inserted in the eval(op) later.
for op in sym_op:
# eval will convert the string into a 3-tuple using the current values for x, y, z
u, v, w = eval(op)
# Move new atom into the unit cell
u = u % 1.0
v = v % 1.0
w = w % 1.0
# Check if the new position is actually new, or already exists
# Two atoms are on top of each other if they are less than "eps" away.
eps = 0.01
new_atom = True
for atom in atoms:
if (abs(atom[1] - u) < eps) and (abs(atom[2] - v) < eps) and (abs(atom[3] - w) < eps):
new_atom = False
# Check that this is the same atom type.
if atom[0] != label:
print("\nERROR: Invalid CIF file: atom of type %s overlaps with atom of type %s" % (atom[0], label))
if (new_atom):
atoms.append((label, u, v, w))
i = i + 1
imax = len(atoms)
atoms_uc = atoms
return(atoms_uc)
def supercell(atoms_uc, Nx, Ny, Nz):
atoms_sc = []
for atom in atoms_uc:
label, u, v, w = atom
for i in range(Nx):
uu = i + u
for j in range(Ny):
vv = j + v
for k in range(Nz):
ww = k + w
atoms_sc.append((label, uu, vv, ww))
return(atoms_sc)
def convert_supercell_tocartes(atoms_sc, cif_data, Nx, Ny, Nz, print_=None):
factors_fract2carte_dict = factors_convert_fract2cartes(cif_data)
# Check if we have a rectangular box
rect_box = False
bx = factors_fract2carte_dict["bx"]
cx = factors_fract2carte_dict["cx"]
cy = factors_fract2carte_dict["cy"]
eps = 0.1
if (bx < eps) and (cx < eps) and (cy < eps):
rect_box = True
# Calculate the box size
Lx = Nx * cif_data['_cell_length_a']
Ly = Ny * cif_data['_cell_length_b']
Lz = Nz * cif_data['_cell_length_c']
atoms_rsc = []
for val, atom in enumerate(atoms_sc):
label, xf, yf, zf = atom
(xn1, yn1, zn1) = convert_fract2carte_atom(xf, yf, zf, factors_fract2carte_dict, print_)
# if rect_box:
if False:
# only changes values below zero
xn2 = (xn1 + Lx) % Lx
yn2 = (yn1 + Ly) % Ly
zn2 = (zn1 + Lz) % Lz
else:
xn2 = xn1
yn2 = yn1
zn2 = zn1
atoms_rsc.append((label, xn2, yn2, zn2))
if print_:
print("convert_supercell_tocartes")
print("label, xf, yf, zf", label, xf, yf, zf)
print("label, xn, yn, zn", label, xn1, yn1, zn1)
print("label, xn, yn, zn", label, xn2, yn2, zn2)
return(atoms_rsc)
def convert_tofracts(atoms_sc, cif_data):
factors_fract2carte_dict = factors_convert_fract2cartes(cif_data)
atoms_rsc = []
for label, xf, yf, zf in atoms_sc:
(xn, yn, zn) = convert_carte2fract_atom(xf, yf, zf, factors_fract2carte_dict)
atoms_rsc.append((label, xn, yn, zn))
return(atoms_rsc)
def finalise_supercell(atoms_rsc):
'''
Clean the duplicates in the supercell coordinates
Translate the supercell to the origin
'''
# Make sure there is no duplicate rows in the super cell coordinates
clean_sc, uniq_idx_1 = np.unique(atoms_rsc, return_index=True, axis=0)
sc_coord = []
test_sc_coord = [] # testing if there are coordinates that are similar
sc_elem = []
#test_sc_elem = []
for atom in clean_sc:
x = round(float(atom[1]), 2)
y = round(float(atom[2]), 2)
z = round(float(atom[3]), 2)
sc_coord.append([float(atom[1]), float(atom[2]), float(atom[3])])
test_sc_coord.append([x, y, z])
sc_elem.append(atom[0])
sc_elem = np.array(sc_elem)
test_sc_coord = np.array(test_sc_coord)
clean_sc, uniq_idx_2 = np.unique(test_sc_coord, return_index=True, axis=0)
fin_sc_coord = []
fin_sc_elem = []
for i in uniq_idx_2:
atom = sc_coord[i]
fin_sc_coord.append(sc_coord[i])
fin_sc_elem.append(sc_elem[i])
# Find the origin of the super cell
center_sc = (np.max(fin_sc_coord, axis=0) - np.min(fin_sc_coord, axis=0))/2
# Translate the supercell to the origin
fin_sc_coord -= center_sc
# Glue the coordinate and elements together
sc_rcoord = [(fin_sc_elem[i], fin_sc_coord[i][0], fin_sc_coord[i][1], fin_sc_coord[i][2]) for i in range(len(fin_sc_elem))]
return(sc_rcoord)
def fract_min_max_from_cart(coords, cif_data):
"""Convert carts to fracts and get min and max in x, y and z."""
coords = convert_tofracts(coords, cif_data)
ua, va, wa = [], [], []
for sym, u, v, w in coords:
ua.append(u)
va.append(v)
wa.append(w)
(minu, maxu), (minv, maxv), (minw, maxw) = min_max(ua), min_max(va), min_max(wa)
# SHOULD BE JUST UNDER 3
if not 2.8 < maxu - minu < 3:
print("WARNING: maxu-minu not as expected", maxu, minu)
elif not 2.8 < maxv - minv < 3:
print("WARNING: maxv-minv not as expected", maxv, minv)
elif not 2.8 < maxw - minw < 3:
print("WARNING: maxw-minw not as expected", maxw, minw)
return minu, maxu, minv, maxv, minw, maxw
### COORDS/FRAGS/ATOMS --------------------------------------------
angstrom2bohr = 1.88973
hartree2kjmol = 2625.4996
osvdz2srs = 1.752
osvtz2srs = 1.64
def dist_threshold(atom_list, tolerance_value):
rcov = {}
for i in atom_list:
rcov[i] = {}
for j in atom_list:
r = (qcel.covalentradii.get(i, units="angstrom") + qcel.covalentradii.get(j, units="angstrom")) * tolerance_value
#r = round((covalent_radius_dict[atom_i] + covalent_radius_dict[atom_j]) * tolerance_value, 5)
rcov[i][j] = r
return rcov
def closest_distance(x, y, z, atmList):
"""Get closest distance between atmList and x, y, z."""
min_d = 100000
for atm in atmList:
dist = distance([x, y, z], [atm['x'], atm['y'], atm['z']])
min_d = min(dist, min_d)
return min_d
def distance(i, j):
dist = math.sqrt((i[0] - j[0])**2 + (i[1] - j[1])**2 + (i[2] - j[2])**2)
return dist
def centroid(mol_coord):
"""
mol_coord is a list of tuples. Each tuple holds an atomic coordinate.
('O', -0.8310492693341551, -8.864856732599998, 5.019346296047775)
centoid
"""
x, y, z, i = 0, 0, 0, 0
for atom in mol_coord:
i += 1
x += atom[1]
y += atom[2]
z += atom[3]
x = x/i
y = y/i
z = z/i
return (x, y, z)
def mol_centroid_in_central_unit_cell(fragments, coords, cif_data, minu, minv, minw, atoms_uc):
"""Return list of atoms whose centroid is in central unit cell."""
factors_fract2carte_dict = factors_convert_fract2cartes(cif_data)
new_atoms = []
for frag in fragments:
atoms = [coords[i] for i in frag]
cx, cy, cz = centroid(atoms)
u, v, w = convert_carte2fract_atom(cx, cy, cz, factors_fract2carte_dict)
minu = round(minu, 3)
minv = round(minv, 3)
minw = round(minw, 3)
if (minu+1 <= u < minu+2) and (minv+1 <= v < minv+2) and (minw+1 <= w < minw+2):
new_atoms.extend(atoms)
# if len(new_atoms) != len(atoms_uc):
# sys.exit(f"Not the same number of atoms in the unit cell ({len(atoms_uc)}) as whole atom unit cell ({len(new_atoms)}). exiting ...")
return new_atoms
def min_max(list_):
"""Min and max of 1D array."""
return min(list_), max(list_)
def add_centroid_frags(fragList, atmList):
"""Add centroid to each fragment."""
for frag in fragList:
atoms = [atmList[i] for i in frag['ids']]
frag['cx'], frag['cy'], frag['cz'] = centroid_atmList(atoms)
return fragList
def centroid_atmList(atmList):
"""Get centroid for list of atoms."""
i, x, y, z = 0, 0, 0, 0
for atm in atmList:
x += atm["x"]
y += atm["y"]
z += atm["z"]
i += 1
return x/i, y/i, z/i
def coords_midpoint(atom_list):
"""Midpoint of all points of xyz."""
listx, listy, listz = [], [], []
for atm in atom_list:
listx.append(atm["x"])
listy.append(atm["y"])
listz.append(atm["z"])
return midpoint(listx), midpoint(listy), midpoint(listz)
def midpoint(list_):
"""Return midpoint between a list of values in 1D."""
return np.min(list_) + (np.max(list_) - np.min(list_))/2
def add_two_frags_together(fragList, atm_list, frag1_id, frag2_id):
"""Combine two fragments in fragList."""
new_id = min(frag1_id, frag2_id)
other_id = max(frag1_id, frag2_id)
new_fragList = fragList[:new_id] # copy up to the combined one
new_frag = { # combined frag
'ids': fragList[frag1_id]['ids'] + fragList[frag2_id]['ids'],
'syms': fragList[frag1_id]['syms'] + fragList[frag2_id]['syms'],
'grp': new_id,
'chrg': fragList[frag1_id]['chrg'] + fragList[frag2_id]['chrg'],
'mult': fragList[frag1_id]['mult'] + fragList[frag2_id]['mult'] - 1,
'name': fragList[new_id]['name'],
}
new_frag = add_centroid_frags([new_frag], atm_list)
new_fragList.extend(new_frag) # add new frag
# add up to removed frag
new_fragList.extend(fragList[new_id+1:other_id])
# change rest of values
for i in range(other_id+1,len(fragList)):
fragList[i]['grp'] = i-1
fragList[i]['name'] = f"frag{i-1}"
new_fragList.append(fragList[i])
for i in range(len(new_fragList)):
if i != new_fragList[i]["grp"]:
print(i, "does not")
return new_fragList, new_id
def combination_smallest_distance(fragList, combinations):
"""Return the list of anion-cation pairs that has the smallest distance."""
comb_use = None
min_dist = 1000
for comb in combinations:
tot_dist = 0
# FOR EACH CATION, ANION PAIR
for cat, an in comb:
tot_dist += distance(
[fragList[cat]['cx'], fragList[cat]['cy'], fragList[cat]['cz']],
[fragList[an]['cx'], fragList[an]['cy'], fragList[an]['cz']]
)
if tot_dist < min_dist:
min_dist = tot_dist
comb_use = comb
return comb_use, min_dist
def pair_ions_lowest_dist(fragList, atmList):
"""Get pairing of molecules that has lowest total distance."""
# cation/anion lists
cations_list, anions_list = [], []
for i in range(len(fragList)):
if fragList[i]['chrg'] == 1:
cations_list.append(i)
elif fragList[i]['chrg'] == -1:
anions_list.append(i)
else:
sys.exit("Only written for singly charged species. exiting ...")
cutoff = 8
anion_pairs = []
for i in cations_list:
cat = fragList[i]
anion_pairs.append([])
for j in anions_list:
an = fragList[j]
d = distance([cat['cx'], cat['cy'], cat['cz']], [an['cx'], an['cy'], an['cz']])
if d < cutoff:
anion_pairs[-1].append(j)
# if anion only in one list
for an in anions_list:
i = 0
for an_list in anion_pairs:
if an in an_list:
i += 1
if i == 1:
for j in range(len(anion_pairs)):
if an in anion_pairs[j]:
anion_pairs[j] = [an]
# if list only has one anion
for an_list in anion_pairs:
if len(an_list) == 1:
id = an_list[0]
for an_list2 in anion_pairs:
if id in an_list2 and an_list2 != [id]:
an_list2.remove(id)
# if anion only in one list
for an in anions_list:
i = 0
for an_list in anion_pairs:
if an in an_list:
i += 1
if i == 1:
for j in range(len(anion_pairs)):
if an in anion_pairs[j]:
anion_pairs[j] = [an]
# if list only has one anion
for an_list in anion_pairs:
if len(an_list) == 1:
id = an_list[0]
for an_list2 in anion_pairs:
if id in an_list2 and an_list2 != [id]:
an_list2.remove(id)
# all combinations of one anion from each list
anion_combs_to_check = list(itertools.product(*anion_pairs))
# each anion in list only once
anions = []
for comb in anion_combs_to_check:
remove = False
for an in anions_list:
if comb.count(an) != 1:
remove = True
break
if not remove:
anions.append(comb)
cations = [cations_list] * len(anions_list) # make list of lists of cations
# make combinations
combinations = []
for an_list, cat_list in zip(anions, cations):
comb = []
for an, cat in zip(an_list, cat_list):
comb.append([cat, an])
combinations.append(comb)
# pair
comb, min_dist = combination_smallest_distance(fragList, combinations)
# sort combinations largest val to smallest so can combine frags safely
comb_sorted = []
starting_frags = len(fragList)
for i in range(starting_frags-1, -1, -1):
for _ in comb:
if i in _:
comb_sorted.append(_)
comb.remove(_)
break
# combine frags
for index1, index2 in comb_sorted:
lines = []
fragList, newid = add_two_frags_together(fragList, atmList, index1, index2)
# for id in fragList[newid]['ids']:
# atm = atmList[id]
# lines.append(f"{atm['sym']} {atm['x']} {atm['y']} {atm['z']}\n")
# write_xyz_zoe(f"{index1}-{index2}.xyz", lines)
return fragList
def central_frag_with_charge(frag_list, atmList, midpointx, midpointy, midpointz, charge=0):
"""Returns the frag_id/grp of the central fragment with charge=charge by finding the average
distance to the midpoint for each fragment."""
min_dist = 10000
min_ion = None
for frag in frag_list:
if frag['chrg'] == charge or charge == "any":
dist = 0
centroid = [0.0, 0.0, 0.0]
for id in frag['ids']:
# DIST
# dist += distance([midpointx, midpointy, midpointz],
# [atmList[id]['x'], atmList[id]['y'], atmList[id]['z']])
centroid[0] += atmList[id]['x']
centroid[1] += atmList[id]['y']
centroid[2] += atmList[id]['z']
# AVERAGE
centroid[0] /= len(frag['ids'])
centroid[1] /= len(frag['ids'])
centroid[2] /= len(frag['ids'])
dist = distance([midpointx, midpointy, midpointz], centroid)
# IF SMALLEST DIST
if dist < min_dist:
min_dist = dist
min_ion = frag['grp']
return min_ion
def pair_mols_by_type(fragList_uc, atmList_uc, mx, my, mz, pair_mols):
"""Pair ions by type and return new fragList and central fragment ID."""
print(f"{len(fragList_uc)} molecules in whole unit cell")
# Pair all ions
if pair_mols == "all":
# Add centroid
fragList_uc = add_centroid_frags(fragList_uc, atmList_uc)
# Pair molecules by lowest total pairing distance
fragList_uc = pair_ions_lowest_dist(fragList_uc, atmList_uc)
# central frag
center_frag_id = central_frag_with_charge(fragList_uc, atmList_uc, mx, my, mz, 0)
# Only pair central ion pair
elif pair_mols == "central":
# Find central anion and cations
center_cat = central_frag_with_charge(fragList_uc, atmList_uc, mx, my, mz, 1)
center_an = central_frag_with_charge(fragList_uc, atmList_uc, mx, my, mz, -1)
fragList_uc, center_frag_id = add_two_frags_together(fragList_uc, atmList_uc, center_cat, center_an)
# Do not pair any ions
elif pair_mols == "none":
center_frag_id = central_frag_with_charge(fragList_uc, atmList_uc, mx, my, mz, "any")
print(f"{len(fragList_uc)} fragments in whole unit cell")
return fragList_uc, center_frag_id
### FIND FRAGMENTS --------------------------------------------
def pairing_atoms(coords):
"""Put atoms in boxes and loop through boxes to get atom pairs."""
uniq_atoms = list(set([i[0] for i in coords]))
rcov_dict = dist_threshold(uniq_atoms, 1.2)
# BOX LENGTH
box_length = 4
# GET MIN AND MAX X, Y, Z
group_dict = {} # STORE GROUP NUMBER
minx, miny, minz = 1000, 1000, 1000
maxx, maxy, maxz = -1000, -1000, -1000
for val, (sym, x, y, z) in enumerate(coords):
if x < minx:
minx = x
if x > maxx:
maxx = x
if y < miny:
miny = y
if y > maxy:
maxy = y
if z < minz:
minz = z
if z > maxz:
maxz = z
group_dict[val] = None
# NUMBER OF BOXES
Nbx = math.ceil((maxx - minx) / box_length)
Nby = math.ceil((maxy - miny) / box_length)
Nbz = math.ceil((maxz - minz) / box_length)
# BOXES CONTAINER
Box_list = {}
for bx in range(Nbx+1):
for by in range(Nby+1):
for bz in range(Nbz+1):
Box_list[bx + Nbx*by + Nbx*Nby*bz] = []
# print("Number of boxes = ", len(Box_list))
# ASSIGN ATOMS TO BOXES
for id, atom in enumerate(coords):
bx = math.floor((atom[1] - minx) / box_length)
by = math.floor((atom[2] - miny) / box_length)
bz = math.floor((atom[3] - minz) / box_length)
Box_list[bx + Nbx*by + Nbx*Nby*bz].append([id, atom])
# LOOP OVER BOXES
group = 0
for bx in range(Nbx):
for by in range(Nby):
for bz in range(Nbz):
box_id = bx + Nbx*by + Nbx*Nby*bz # BOX ID
# FOR ATOMS IN BOX
for id1, atom1 in Box_list[box_id]:
con_vwd = False # CONNECTED TO OTHER ATOMS
# LOOP OVER SURROUNDING BOXES
for sbx in range(max(0, bx-1), min(bx+2, Nbx+1)):
for sby in range(max(0, by-1), min(by+2, Nby+1)):
for sbz in range(max(0, bz-1), min(bz+2, Nbz+1)):
sbox_id = sbx + Nbx*sby + Nbx*Nby*sbz
for id2, atom2 in Box_list[sbox_id]:
# DONT DO FOR SAME ATOM
if not id2 == id1:
# DO THE THING THAT NEEDS DOING FOR EACH PAIR
group, group_dict, con_vwd = \
update_groups(id1, id2, coords, group, group_dict, con_vwd, rcov_dict)
# IF NELLY NO MATES
if not con_vwd:
group_dict[id1] = group
group += 1
# CONVERT TO LIST OF LISTS
groups_list = listFromGroups(group, group_dict)
return groups_list
def update_groups(atm1_id, atm2_id, coords, ngroups, group_dict, con_vwd, rcov_dict):
"""If two atoms are within vdW's radii update group_dict."""
# CHECK IF DIST < VDW RADII
if distance(coords[atm1_id][1:], coords[atm2_id][1:]) < rcov_dict[coords[atm1_id][0]][coords[atm2_id][0]]:
# FOUND A MATE
con_vwd = True
# IF NEITHER ATOM1 NOR ATOM2 PART OF A GROUP ADD THEM TO A NEW GROUP
if group_dict[atm1_id] is None and group_dict[atm2_id] is None:
group_dict[atm1_id], group_dict[atm2_id] = ngroups, ngroups
ngroups += 1
# IF BOTH HAVE BEEN ASSIGNED TO A DIFF GROUP
elif not group_dict[atm1_id] is None and not group_dict[atm2_id] is None:
if group_dict[atm1_id] != group_dict[atm2_id]:
grp_chng = group_dict[atm2_id]
# CHANGE ALL IN SECOND GROUP TO FIRST
for key, value in group_dict.items():
if value == grp_chng:
group_dict[key] = group_dict[atm1_id]
# IF ATOM2 NOT ASSIGNED
elif not group_dict[atm1_id] is None and group_dict[atm2_id] is None:
group_dict[atm2_id] = group_dict[atm1_id]
# IF ATOM1 NOT ASSIGNED
elif not group_dict[atm2_id] is None and group_dict[atm1_id] is None:
group_dict[atm1_id] = group_dict[atm2_id]
return ngroups, group_dict, con_vwd
def listFromGroups(groups_, group_dict_):
"""Convert my dict of groups to list of lists."""
# INITIATE EMPTY LIST
list_ = [[] for i in range(groups_)]
# ADD INDEX TO LIST GROUP NUMBER
for atm_indx, group_no in group_dict_.items():
list_[group_no].append(atm_indx)
# REMOVE EMPTY LISTS
list_ = [ele for ele in list_ if ele != []]
return list_
### MAKE SPHERE --------------------------------------------
def make_sphere_from_whole_unit_cell(fragList_uc, atmList_uc, mx, my, mz, Nx, Ny, Nz, cif_data, r_thres, dist_cutoff):
"""Loop over number of boxes that will fit in radius with half on either side of initial unit cell and duplicate
frag."""
fragList = copy.deepcopy(fragList_uc)
atmList = copy.deepcopy(atmList_uc)
n_frags = len(fragList)
n_atoms = len(atmList)
# print(cif_data["_cell_length_a"], cif_data["_cell_length_b"], cif_data["_cell_length_c"])
# print(convert_fract2carte_atom(0, 0, 0, factors_convert_fract2cartes(cif_data)))
# print(convert_fract2carte_atom(1, 0, 0, factors_convert_fract2cartes(cif_data)))
# print(convert_fract2carte_atom(0, 1, 0, factors_convert_fract2cartes(cif_data)))
# print(convert_fract2carte_atom(0, 0, 1, factors_convert_fract2cartes(cif_data)))
# print(convert_fract2carte_atom(1, 1, 1, factors_convert_fract2cartes(cif_data)))
for nx in range(-Nx, Nx):
for ny in range(-Ny, Nx):
for nz in range(-Nz, Nz):
if nx == 0 and ny == 0 and nz == 0: continue
x, y, z = convert_fract2carte_atom(nx, ny, nz, factors_convert_fract2cartes(cif_data))
# loop over frags
for frag in fragList_uc:
n_atoms_copy = n_atoms # reset number of atoms in case last frag was not added
new_atoms = [] # store atoms of new_frag
new_atom_ids = [] # store ids as lists for frag data
for id in frag['ids']:
# new atom
new_atoms.append({
'id' : n_atoms_copy,
'sym' : atmList_uc[id]['sym'],
'x' : atmList_uc[id]['x'] + x,
'y' : atmList_uc[id]['y'] + y,
'z' : atmList_uc[id]['z'] + z,
'nu' : atmList_uc[id]['nu'],
'mas' : atmList_uc[id]['mas'],
'vdw' : atmList_uc[id]['vdw'],
})
new_atom_ids.append(n_atoms_copy)
n_atoms_copy += 1