Source code for acat.utilities

from ase.data import covalent_radii, atomic_numbers, atomic_masses
from ase.geometry.geometry import _row_col_from_pdist
from ase.geometry import find_mic
from ase.formula import Formula
from itertools import product, permutations, combinations
from collections import abc
import networkx as nx
import numpy as np
import scipy
import math


[docs]def neighbor_shell_list(atoms, dx=0.3, neighbor_number=1, different_species=False, mic=False, radius=None, span=False): """Make dict of neighboring shell atoms for both periodic and non-periodic systems. Possible to return neighbors from defined neighbor shell e.g. 1st, 2nd, 3rd by changing the neighbor number. Parameters ---------- atoms : ase.Atoms object Accept any ase.Atoms object. No need to be built-in. dx : float, default 0.3 Buffer to calculate nearest neighbor pairs. neighbor_number : int, default 1 Neighbor shell number. different_species : boolean, default False Whether each neighbor pair are different species. mic : boolean, default False Whether to apply minimum image convention. Remember to set mic=True for periodic systems. radius : float, default None The radius of each shell. Works exactly as a conventional neighbor list when specified. If not specified, use covalent radii instead. span : boolean, default False Whether to include all neighbors spanned within the shell. """ natoms = len(atoms) if natoms == 1: return {0: []} cell = atoms.cell positions = atoms.positions nums = set(atoms.numbers) pairs = product(nums, nums) if not radius: cr_dict = {(i, j): (covalent_radii[i] + covalent_radii[j]) for i, j in pairs} ds = atoms.get_all_distances(mic=mic) conn = {k: [] for k in range(natoms)} for atomi in atoms: for atomj in atoms: i, j = atomi.index, atomj.index if i != j: if not (different_species & (atomi.symbol == atomj.symbol)): d = ds[i,j] crij = 2 * radius if radius else cr_dict[(atomi.number, atomj.number)] if neighbor_number == 1 or span: d_max1 = 0. else: d_max1 = (neighbor_number - 1) * crij + dx d_max2 = neighbor_number * crij + dx if d > d_max1 and d < d_max2: conn[atomi.index].append(atomj.index) return conn
[docs]def get_connectivity_matrix(neighborlist): """Returns a connectivity matrix from a neighborlist object. Parameters ---------- neighborlist : dict A neighborlist (dictionary) that contains keys of each atom index and values of their neighbor atom indices. """ conn_mat = [] index = range(len(neighborlist.keys())) # Create binary matrix denoting connections. for index1 in index: conn_x = [] for index2 in index: if index2 in neighborlist[index1]: conn_x.append(1) else: conn_x.append(0) conn_mat.append(conn_x) return np.asarray(conn_mat)
[docs]def get_mic(p1, p2, cell, pbc=[1,1,0], max_cell_multiple=1e5, return_squared_distance=False): """A highly efficient function for getting all vectors from p1 to p2. Also able to calculate the squared distance using the minimum image convention (mic). This function is useful when you want to constantly calculate mic between two given positions. Please use ase.geometry.find_mic if you want to calculate an array of vectors all at a time (useful for e.g. neighborlist). Parameters ---------- p1 : numpy.array The 3D Cartesian coordinate of the position 1. p2 : numpy.array The 3D Cartesian coordinate of the position 2. cell : numpy.array The 3D parallel epipedal unit cell. pbc : numpy.array or list, default [1, 1, 0] Whether cell is periodic in each direction. max_cell_multiple : int, default 1e5 A large number to account for the maximum repetitions of each of the lattice vectors. The minimum number of repetitions is hence calculated by the algorithm using the intersection of a sphere and the unit cell. return_squared_distance : bool, default False Whether to return the squared mic distance instead of the mic vector. """ # Precompute some useful values a, b, c = cell[0], cell[1], cell[2] vol = np.abs(a @ np.cross(b, c)) a_cross_b = np.cross(a, b) a_cross_b_len = np.linalg.norm(a_cross_b) a_cross_b_hat = a_cross_b / a_cross_b_len b_cross_c = np.cross(b, c) b_cross_c_len = np.linalg.norm(b_cross_c) b_cross_c_hat = b_cross_c / b_cross_c_len a_cross_c = np.cross(a, c) a_cross_c_len = np.linalg.norm(a_cross_c) a_cross_c_hat = a_cross_c / a_cross_c_len # TODO: Wrap p1, and p2 into the current unit cell dr = p2 - p1 min_dr_sq = dr @ dr min_length = math.sqrt(min_dr_sq) a_max = math.ceil(min_length / vol * b_cross_c_len) a_max = min(a_max, max_cell_multiple) b_max = math.ceil(min_length / vol * a_cross_c_len) b_max = min(b_max, max_cell_multiple) if not pbc[2]: c_max = 0 else: c_max = math.ceil(min_length / vol * a_cross_b_len) c_max = min(c_max, max_cell_multiple) min_dr = dr for i in range(-a_max, a_max + 1): ra = i * a for j in range(-b_max, b_max + 1): rab = ra + j * b for k in range(-c_max, c_max + 1): if i == 0 and j == 0 and k == 0: continue out_vec = rab + k * c + dr len_sq = out_vec @ out_vec if len_sq < min_dr_sq: min_dr = out_vec min_dr_sq = len_sq if not return_squared_distance: return min_dr else: return np.sum(min_dr**2)
def expand_cell(atoms, cutoff=None, padding=None): #Return Cartesian coordinates atoms within a supercell #which contains repetitions of the unit cell which contains #at least one neighboring atom. Borrowed from Catkit. cell = atoms.cell pbc = [1, 1, 0] pos = atoms.positions if padding is None and cutoff is None: diags = np.sqrt((([[1, 1, 1], [-1, 1, 1], [1, -1, 1], [-1, -1, 1]]
[docs] @ cell)**2).sum(1)) if pos.shape[0] == 1: cutoff = max(diags) / 2. else: dpos = (pos - pos[:, None]).reshape(-1, 3) Dr = dpos @ np.linalg.inv(cell) D = (Dr - np.round(Dr) * pbc) @ cell D_len = np.sqrt((D**2).sum(1)) cutoff = min(max(D_len), max(diags) / 2.) latt_len = np.sqrt((cell**2).sum(1)) V = abs(np.linalg.det(cell)) padding = pbc * np.array(np.ceil(cutoff * np.prod(latt_len) / (V * latt_len)), dtype=int) offsets = np.mgrid[-padding[0]:padding[0] + 1, -padding[1]:padding[1] + 1, -padding[2]:padding[2] + 1].T tvecs = offsets @ cell coords = pos[None, None, None, :, :] + tvecs[:, :, :, None, :] ncell = np.prod(offsets.shape[:-1]) index = np.arange(len(atoms))[None, :].repeat(ncell, axis=0).flatten() coords = coords.reshape(np.prod(coords.shape[:-1]), 3) offsets = offsets.reshape(ncell, 3) return index, coords, offsets def get_max_delta_sum_path(nodes): delta_sum = -10000 res_nodes = [] for i in range(len(nodes)): new_nodes = nodes[i:] + nodes[:i] ds = sum([new_nodes[j+1] - new_nodes[j] for j in range(len(nodes)-1)]) if ds > delta_sum: delta_sum = ds res_nodes = new_nodes if -ds > delta_sum: delta_sum = -ds res_nodes = new_nodes[::-1] return res_nodes
[docs]def bipartitions(shells, total): n = len(shells) for k in range(n + 1): for combo in combinations(range(n), k): if sum(len(shells[i]) for i in combo) == total: set_combo = set(combo) yield sorted(shells[i] for i in combo), sorted( shells[i] for i in range(n) if i not in set_combo)
[docs]def partitions_into_totals(shells, totals): assert totals if len(totals) == 1: yield [shells] else: for first, remaining_shells in bipartitions(shells, totals[0]): for rest in partitions_into_totals(remaining_shells, totals[1:]): yield [first] + rest
[docs]def get_close_atoms(atoms, cutoff=0.5, mic=False, delete=False): """Get a list of close atoms and delete one set of them if requested. Identify all atoms that lie within the cutoff radius of each other. Parameters ---------- atoms : ase.Atoms object Accept any ase.Atoms object. No need to be built-in. cutoff : float, default 0.5 The cutoff radius. Two atoms are too close if the distance between them is less than this cutoff mic : bool, default False Whether to apply minimum image convention. Remember to set mic=True for periodic systems. delete : bool, default False Whether to delete one set of the close atoms. """ res = np.asarray(list(combinations(np.asarray(range(len(atoms))),2))) indices1, indices2 = res[:, 0], res[:, 1] p1, p2 = atoms.positions[indices1], atoms.positions[indices2] if mic: _, dists = find_mic(p2 - p1, atoms.cell, pbc=True) else: dists = np.linalg.norm(p2 - p1, axis=1) dup = np.nonzero(dists < cutoff) rem = np.array(_row_col_from_pdist(len(atoms), dup[0])) if delete: if rem.size != 0: del atoms[rem[:, 0]] else: return rem
[docs]def atoms_too_close(atoms, cutoff=0.5, mic=False): """Check if there are atoms that are too close to each other. Parameters ---------- atoms : ase.Atoms object Accept any ase.Atoms object. No need to be built-in. cutoff : float, default 0.5 The cutoff radius. Two atoms are too close if the distance between them is less than this cutoff mic : bool, default False Whether to apply minimum image convention. Remember to set mic=True for periodic systems. """ res = np.asarray(list(combinations(np.asarray(range(len(atoms))), 2))) indices1, indices2 = res[:, 0], res[:, 1] p1, p2 = atoms.positions[indices1], atoms.positions[indices2] if mic: _, dists = find_mic(p2 - p1, atoms.cell, pbc=True) else: dists = np.linalg.norm(p2 - p1, axis=1) return any(dists < cutoff)
[docs]def atoms_too_close_after_addition(atoms, n_added, cutoff=1.5, mic=False): """Check if there are atoms that are too close to each other after adding some new atoms. Parameters ---------- atoms : ase.Atoms object Accept any ase.Atoms object. No need to be built-in. n_added : int Number of newly added atoms. cutoff : float, default 1.5 The cutoff radius. Two atoms are too close if the distance between them is less than this cutoff mic : bool, default False Whether to apply minimum image convention. Remember to set mic=True for periodic systems. """ newp, oldp = atoms.positions[-n_added:], atoms.positions[:-n_added] newps = np.repeat(newp, len(oldp), axis=0) oldps = np.tile(oldp, (n_added, 1)) if mic: _, dists = find_mic(newps - oldps, atoms.cell, pbc=True) else: dists = np.linalg.norm(newps - oldps, axis=1) return any(dists < cutoff)
[docs]def get_angle_between(v1, v2): """Returns the angle in radians between vectors 'v1' and 'v2'. Parameters ---------- v1 : numpy.array Vector 1. v2 : numpy.array Vector 2. """ v1_u = v1 / np.linalg.norm(v1) v2_u = v2 / np.linalg.norm(v2) return np.arccos(np.clip(v1_u @ v2_u, -1., 1.))
[docs]def get_rejection_between(v1, v2): """Calculate the vector rejection of vector 'v1' perpendicular to vector 'v2'. Parameters ---------- v1 : numpy.array Vector 1. v2 : numpy.array Vector 2. """ return v1 - v2 * (v1 @ v2) / (v2 @ v2)
[docs]def get_rotation_matrix(v1, v2): """Return the rotation matrix R that rotates unit vector v1 onto unit vector v2. Parameters ---------- v1 : numpy.array Vector 1. v2 : numpy.array Vector 2. """ ax, ay, az = v1[0], v1[1], v1[2] bx, by, bz = v2[0], v2[1], v2[2] au = v1 / (np.sqrt(ax * ax + ay * ay + az * az)) bu = v2 / (np.sqrt(bx * bx + by * by + bz * bz)) R = np.asarray([[bu[0] * au[0], bu[0] * au[1], bu[0] * au[2]], [bu[1] * au[0], bu[1] * au[1], bu[1] * au[2]], [bu[2] * au[0], bu[2] * au[1], bu[2] * au[2]]]) return R
[docs]def get_rodrigues_rotation_matrix(axis, angle): """Return the Rodrigues rotation matrix associated with counter-clockwise rotation about the given axis by an angle. Parameters ---------- axis : numpy.array The axis (vector) to rotate around with. angle : numpy.array The angle (in radians) to rotate around. """ return scipy.linalg.expm(np.cross(np.eye(3), axis / np.linalg.norm(axis) * angle))
[docs]def get_total_masses(symbol): """Get the total molar mass given the chemical symbol of a molecule. Parameters ---------- symbol : str Chemical symbol of the molecule. """ return np.sum([atomic_masses[atomic_numbers[s]] for s in list(Formula(symbol))])
def is_list_or_tuple(obj): return (isinstance(obj, abc.Sequence) and not isinstance(obj, str))
[docs]def string_fragmentation(adsorbate): """A function for generating a fragment list (list of strings) from a given adsorbate (string). Parameters ---------- adsorbate : str The string of the adsorbate molecule. """ if adsorbate == 'H2': return ['H', 'H'] sym_list = list(Formula(adsorbate)) nsyms = len(sym_list) frag_list = [] for i, sym in enumerate(sym_list): if sym != 'H': j = i + 1 if j < nsyms: hlen = 0 while sym_list[j] == 'H': hlen += 1 j += 1 if j == nsyms: break if hlen == 0: frag = sym elif hlen == 1: frag = sym + 'H' else: frag = sym + 'H' + str(hlen) frag_list.append(frag) else: frag_list.append(sym) return frag_list
[docs]def numbers_from_ratio(sum_numbers, ratio): """Return the number of atoms for each element from ratio. Parameters ---------- sum_numbers : int The total number of atoms ratio : list A list of ratio for different elements """ sum_ratio = sum(ratio) totals = [int((sum_numbers * r) // sum_ratio) for r in ratio] residues = [(sum_numbers * r) % sum_ratio for r in ratio] for i in sorted(range(len(ratio)), key=lambda i: residues[i] * ratio[i], reverse=True)[:sum_numbers-sum(totals)]: totals[i] += 1 return totals
[docs]def draw_graph(G, savefig='graph.png'): """Draw the graph using matplotlib.pyplot. Parameters ---------- G : networkx.Graph object The graph object savefig : str, default 'graph.png' The name of the figure to be saved. """ import matplotlib.pyplot as plt labels = nx.get_node_attributes(G, 'symbol') # Get unique groups groups = sorted(set(labels.values())) mapping = {x: "C{}".format(i) for i, x in enumerate(groups)} nodes = G.nodes() colors = [mapping[G.nodes[n]['symbol']] for n in nodes] # Drawing nodes, edges and labels separately pos = nx.spring_layout(G) nx.draw_networkx_edges(G, pos, alpha=0.5) nx.draw_networkx_nodes(G, pos, nodelist=nodes, node_color=colors, node_size=500) nx.draw_networkx_labels(G, pos, labels, font_size=10, font_color='w') plt.axis('off') plt.savefig(savefig) plt.clf()