4075885785

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github

Committed by Shyue Ping Ong

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Merge branch 'master' of github.com:materialsproject/pymatgen

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90.77

/pymatgen/io/atat.py

# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

"""
Classes for reading/writing mcsqs files following the rndstr.in format.
"""

from __future__ import annotations

import numpy as np

from pymatgen.core.lattice import Lattice
from pymatgen.core.periodic_table import get_el_sp
from pymatgen.core.structure import Structure

__author__ = "Matthew Horton"
__copyright__ = "Copyright 2017, The Materials Project"
__maintainer__ = "Matthew Horton"
__email__ = "mkhorton@lbl.gov"
__status__ = "Production"
__date__ = "October 2017"


class Mcsqs:
    """
    Handle input/output for the crystal definition format
    used by mcsqs and other ATAT codes.
    """

    def __init__(self, structure):
        """
        :param structure: input Structure
        """
        self.structure = structure

    def to_string(self):
        """
        Returns a structure in mcsqs rndstr.in format.
        :return (str):
        """
        # add lattice vectors
        m = self.structure.lattice.matrix
        output = [f"{l[0]:6f} {l[1]:6f} {l[2]:6f}" for l in m]

        # define coord system, use Cartesian
        output.append("1.0 0.0 0.0")
        output.append("0.0 1.0 0.0")
        output.append("0.0 0.0 1.0")

        # add species
        for site in self.structure:
            species_str = []
            for sp, occu in sorted(site.species.items()):
                sp = str(sp)
                if ("," in sp) or ("=" in sp):
                    # Invalid species string for AT-AT input, so modify
                    sp = sp.replace(",", "__").replace("=", "___")
                species_str.append(f"{sp}={occu}")
            species_str = ",".join(species_str)
            a, b, c = site.frac_coords
            output.append(f"{a:6f} {b:6f} {c:6f} {species_str}")

        return "\n".join(output)

    @staticmethod
    def structure_from_string(data):
        """
        Parses a rndstr.in, lat.in or bestsqs.out file into pymatgen's
        Structure format.

        :param data: contents of a rndstr.in, lat.in or bestsqs.out file
        :return: Structure object
        """
        data = data.splitlines()
        data = [x.split() for x in data if x]  # remove empty lines

        # following specification/terminology given in manual
        if len(data[0]) == 6:  # lattice parameters
            a, b, c, alpha, beta, gamma = map(float, data[0])
            coord_system = Lattice.from_parameters(a, b, c, alpha, beta, gamma).matrix
            lattice_vecs = np.array(
                [
                    [data[1][0], data[1][1], data[1][2]],
                    [data[2][0], data[2][1], data[2][2]],
                    [data[3][0], data[3][1], data[3][2]],
                ],
                dtype=float,
            )
            first_species_line = 4
        else:
            coord_system = np.array(
                [
                    [data[0][0], data[0][1], data[0][2]],
                    [data[1][0], data[1][1], data[1][2]],
                    [data[2][0], data[2][1], data[2][2]],
                ],
                dtype=float,
            )
            lattice_vecs = np.array(
                [
                    [data[3][0], data[3][1], data[3][2]],
                    [data[4][0], data[4][1], data[4][2]],
                    [data[5][0], data[5][1], data[5][2]],
                ],
                dtype=float,
            )
            first_species_line = 6

        scaled_matrix = np.matmul(lattice_vecs, coord_system)
        lattice = Lattice(scaled_matrix)

        all_coords = []
        all_species = []
        for l in data[first_species_line:]:
            coords = np.array([l[0], l[1], l[2]], dtype=float)
            scaled_coords = np.matmul(coords, np.linalg.inv(lattice_vecs))
            all_coords.append(scaled_coords)

            species_strs = "".join(l[3:])  # join multiple strings back together
            species_strs = species_strs.replace(" ", "")  # trim any white space
            species_strs = species_strs.split(",")  # comma-delimited

            species = {}

            for species_occ in species_strs:
                # gets a species, occupancy pair
                species_occ = species_occ.split("=")

                if len(species_occ) == 1:
                    # assume occupancy is 1.0
                    species_occ = [species_occ[0], 1.0]

                if "_" in species_occ[0]:
                    # see to_string() method in this file, since , and = are not valid
                    # species names in AT-AT we replace "," with "__" and "=" with "___",
                    # for pymatgen to parse these back correctly we have to replace them back
                    species_occ[0] = species_occ[0].replace("___", "=").replace("__", ",")

                species[get_el_sp(species_occ[0])] = float(species_occ[1])

            all_species.append(species)

        return Structure(lattice, all_species, all_coords)

1	# Copyright (c) Pymatgen Development Team.
2	# Distributed under the terms of the MIT License.
3
4	"""	1✔
5	Classes for reading/writing mcsqs files following the rndstr.in format.
6	"""
7
8	from __future__ import annotations	1✔
9
10	import numpy as np	1✔
11
12	from pymatgen.core.lattice import Lattice	1✔
13	from pymatgen.core.periodic_table import get_el_sp	1✔
14	from pymatgen.core.structure import Structure	1✔
15
16	__author__ = "Matthew Horton"	1✔
17	__copyright__ = "Copyright 2017, The Materials Project"	1✔
18	__maintainer__ = "Matthew Horton"	1✔
19	__email__ = "mkhorton@lbl.gov"	1✔
20	__status__ = "Production"	1✔
21	__date__ = "October 2017"	1✔
22
23
24	class Mcsqs:	1✔
25	"""
26	Handle input/output for the crystal definition format
27	used by mcsqs and other ATAT codes.
28	"""
29
30	def __init__(self, structure):	1✔
31	"""
32	:param structure: input Structure
33	"""
34	self.structure = structure	1✔
35
36	def to_string(self):	1✔
37	"""
38	Returns a structure in mcsqs rndstr.in format.
39	:return (str):
40	"""
41	# add lattice vectors
42	m = self.structure.lattice.matrix	1✔
43	output = [f"{l[0]:6f} {l[1]:6f} {l[2]:6f}" for l in m]	1✔
44
45	# define coord system, use Cartesian
46	output.append("1.0 0.0 0.0")	1✔
47	output.append("0.0 1.0 0.0")	1✔
48	output.append("0.0 0.0 1.0")	1✔
49
50	# add species
51	for site in self.structure:	1✔
52	species_str = []	1✔
53	for sp, occu in sorted(site.species.items()):	1✔
54	sp = str(sp)	1✔
55	if ("," in sp) or ("=" in sp):	1✔
56	# Invalid species string for AT-AT input, so modify
57	sp = sp.replace(",", "__").replace("=", "___")	×
58	species_str.append(f"{sp}={occu}")	1✔
59	species_str = ",".join(species_str)	1✔
60	a, b, c = site.frac_coords	1✔
61	output.append(f"{a:6f} {b:6f} {c:6f} {species_str}")	1✔
62
63	return "\n".join(output)	1✔
64
65	@staticmethod	1✔
66	def structure_from_string(data):	1✔
67	"""
68	Parses a rndstr.in, lat.in or bestsqs.out file into pymatgen's
69	Structure format.
70
71	:param data: contents of a rndstr.in, lat.in or bestsqs.out file
72	:return: Structure object
73	"""
74	data = data.splitlines()	1✔
75	data = [x.split() for x in data if x] # remove empty lines	1✔
76
77	# following specification/terminology given in manual
78	if len(data[0]) == 6: # lattice parameters	1✔
79	a, b, c, alpha, beta, gamma = map(float, data[0])	×
80	coord_system = Lattice.from_parameters(a, b, c, alpha, beta, gamma).matrix	×
81	lattice_vecs = np.array(	×
82	[
83	[data[1][0], data[1][1], data[1][2]],
84	[data[2][0], data[2][1], data[2][2]],
85	[data[3][0], data[3][1], data[3][2]],
86	],
87	dtype=float,
88	)
89	first_species_line = 4	×
90	else:
91	coord_system = np.array(	1✔
92	[
93	[data[0][0], data[0][1], data[0][2]],
94	[data[1][0], data[1][1], data[1][2]],
95	[data[2][0], data[2][1], data[2][2]],
96	],
97	dtype=float,
98	)
99	lattice_vecs = np.array(	1✔
100	[
101	[data[3][0], data[3][1], data[3][2]],
102	[data[4][0], data[4][1], data[4][2]],
103	[data[5][0], data[5][1], data[5][2]],
104	],
105	dtype=float,
106	)
107	first_species_line = 6	1✔
108
109	scaled_matrix = np.matmul(lattice_vecs, coord_system)	1✔
110	lattice = Lattice(scaled_matrix)	1✔
111
112	all_coords = []	1✔
113	all_species = []	1✔
114	for l in data[first_species_line:]:	1✔
115	coords = np.array([l[0], l[1], l[2]], dtype=float)	1✔
116	scaled_coords = np.matmul(coords, np.linalg.inv(lattice_vecs))	1✔
117	all_coords.append(scaled_coords)	1✔
118
119	species_strs = "".join(l[3:]) # join multiple strings back together	1✔
120	species_strs = species_strs.replace(" ", "") # trim any white space	1✔
121	species_strs = species_strs.split(",") # comma-delimited	1✔
122
123	species = {}	1✔
124
125	for species_occ in species_strs:	1✔
126	# gets a species, occupancy pair
127	species_occ = species_occ.split("=")	1✔
128
129	if len(species_occ) == 1:	1✔
130	# assume occupancy is 1.0
131	species_occ = [species_occ[0], 1.0]	1✔
132
133	if "_" in species_occ[0]:	1✔
134	# see to_string() method in this file, since , and = are not valid
135	# species names in AT-AT we replace "," with "__" and "=" with "___",
136	# for pymatgen to parse these back correctly we have to replace them back
137	species_occ[0] = species_occ[0].replace("___", "=").replace("__", ",")	×
138
139	species[get_el_sp(species_occ[0])] = float(species_occ[1])	1✔
140
141	all_species.append(species)	1✔
142
143	return Structure(lattice, all_species, all_coords)	1✔

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