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# type: ignore
import numpy as np
from ase import Atoms
from ase.io import read, write
import ase.io.rmc6f as rmc6f
from ase.lattice.compounds import TRI_Fe2O3
rmc6f_input_text = """
(Version 6f format configuration file)
Metadata owner: Joe Smith
Metadata date: 31-01-1900
Metadata material: SF6
Metadata comment: Some comments go here...
Metadata source: GSAS
Number of moves generated: 89692
Number of moves tried: 85650
Number of moves accepted: 10074
Number of prior configuration saves: 0
Number of atoms: 7
Number density (Ang^-3): 0.068606
Supercell dimensions: 1 1 1
Cell (Ang/deg): 4.672816 4.672816 4.672816 90.0 90.0 90.0
Lattice vectors (Ang):
4.672816 0.000000 0.000000
0.000000 4.672816 0.000000
0.000000 0.000000 4.672816
Atoms:
1 S 0.600452 0.525100 0.442050 1 0 0 0
2 F 0.911952 0.450722 0.382733 2 0 0 0
3 F 0.283794 0.616712 0.500094 3 0 0 0
4 F 0.679823 0.854839 0.343915 4 0 0 0
5 F 0.531660 0.229024 0.535688 5 0 0 0
6 F 0.692514 0.584931 0.746683 6 0 0 0
7 F 0.509687 0.449350 0.111960 7 0 0 0
"""
# Information for system
positions = [
[0.600452, 0.525100, 0.442050],
[0.911952, 0.450722, 0.382733],
[0.283794, 0.616712, 0.500094],
[0.679823, 0.854839, 0.343915],
[0.531660, 0.229024, 0.535688],
[0.692514, 0.584931, 0.746683],
[0.509687, 0.449350, 0.111960]]
symbols = ['S', 'F', 'F', 'F', 'F', 'F', 'F']
lat = 4.672816
# Intermediate data structures to test against
symbol_xyz_list = [[s] + xyz for s, xyz in zip(symbols, positions)]
symbol_xyz_dict = {i + 1: row for i, row in enumerate(symbol_xyz_list)}
symbol_xyz_list_ext = [tuple([i + 1] + row + [0, 0, 0, 0])
for i, row in enumerate(symbol_xyz_list)]
# Target Atoms system
lat_positions = lat * np.array(positions)
cell = [lat, lat, lat]
rmc6f_atoms = Atoms(symbols, positions=lat_positions, cell=cell, pbc=[1, 1, 1])
def test_rmc6f_read():
"""Test for reading rmc6f input file."""
with open('input.rmc6f', 'w') as rmc6f_input_f:
rmc6f_input_f.write(rmc6f_input_text)
rmc6f_input_atoms = read('input.rmc6f')
assert len(rmc6f_input_atoms) == 7
assert rmc6f_input_atoms == rmc6f_atoms
def test_rmc6f_write():
"""Test for writing rmc6f input file."""
tol = 1e-5
write('output.rmc6f', rmc6f_atoms)
readback = read('output.rmc6f')
assert np.allclose(rmc6f_atoms.positions, readback.positions, rtol=tol)
assert readback == rmc6f_atoms
def test_rmc6f_write_with_order():
"""Test for writing rmc6f input file with order passed in."""
tol = 1e-5
write('output.rmc6f', rmc6f_atoms, order=['F', 'S'])
readback = read('output.rmc6f')
reordered_positions = np.vstack(
(rmc6f_atoms.positions[1:7], rmc6f_atoms.positions[0]))
assert np.allclose(reordered_positions, readback.positions, rtol=tol)
def test_rmc6f_write_with_triclinic_system():
"""Test for writing rmc6f input file for triclinic system
"""
tol = 1e-5
fe4o6 = TRI_Fe2O3(
symbol=('Fe', 'O'),
latticeconstant={
'a': 5.143,
'b': 5.383,
'c': 14.902,
'alpha': 90.391,
'beta': 90.014,
'gamma': 89.834},
size=(1, 1, 1))
# Make sure these are the returned cells (verified correct for rmc6f file)
va = [5.143, 0.0, 0.0]
vb = [0.015596, 5.382977, 0.0]
vc = [-0.00364124, -0.101684, 14.901653]
write('output.rmc6f', fe4o6)
readback = read('output.rmc6f')
assert np.allclose(fe4o6.positions, readback.positions, rtol=tol)
assert np.allclose(va, readback.cell[0], rtol=tol)
assert np.allclose(vb, readback.cell[1], rtol=tol)
assert np.allclose(vc, readback.cell[2], rtol=tol)
def test_rmc6f_read_construct_regex():
"""Test for utility function that constructs rmc6f header regex."""
header_lines = [
"Number of atoms:",
" Supercell dimensions: ",
" Cell (Ang/deg): ",
" Lattice vectors (Ang): "]
result = rmc6f._read_construct_regex(header_lines)
target = "(Number\\s+of\\s+atoms:|Supercell\\s+dimensions:|Cell\\s+\\(Ang/deg\\):|Lattice\\s+vectors\\s+\\(Ang\\):)" # noqa: E501
assert result == target
def test_rmc6f_read_line_of_atoms_section_style_no_labels():
"""Test for reading a line of atoms section
w/ 'no labels' style for rmc6f
"""
atom_line = "1 S 0.600452 0.525100 0.442050 1 0 0 0"
atom_id, props = rmc6f._read_line_of_atoms_section(atom_line.split())
target_id = 1
target_props = ['S', 0.600452, 0.5251, 0.44205]
assert atom_id == target_id
assert props == target_props
def test_rmc6f_read_line_of_atoms_section_style_labels():
"""Test for reading a line of atoms section
w/ 'labels'-included style for rmc6f
"""
atom_line = "1 S [1] 0.600452 0.525100 0.442050 1 0 0 0"
atom_id, props = rmc6f._read_line_of_atoms_section(atom_line.split())
target_id = 1
target_props = ['S', 0.600452, 0.5251, 0.44205]
assert atom_id == target_id
assert props == target_props
def test_rmc6f_read_line_of_atoms_section_style_magnetic():
"""Test for reading a line of atoms section
w/ 'magnetic' style for rmc6f
"""
atom_line = "1 S 0.600452 0.525100 0.442050 1 0 0 0 M: 0.1"
atom_id, props = rmc6f._read_line_of_atoms_section(atom_line.split())
target_id = 1
target_props = ['S', 0.600452, 0.5251, 0.44205, 0.1]
assert atom_id == target_id
assert props == target_props
def test_rmc6f_read_process_rmc6f_lines_to_pos_and_cell():
"""Test for utility function that processes lines of rmc6f using
regular expressions to capture atom properties and cell information
"""
tol = 1e-5
lines = rmc6f_input_text.split('\n')
props, cell = rmc6f._read_process_rmc6f_lines_to_pos_and_cell(lines)
target_cell = np.zeros((3, 3), float)
np.fill_diagonal(target_cell, 4.672816)
assert props == symbol_xyz_dict
assert np.allclose(cell, target_cell, rtol=tol)
def test_rmc6f_read_process_rmc6f_lines_to_pos_and_cell_padded_whitespace():
"""Test for utility function that processes lines of rmc6f using
regular expressions to capture atom properties and cell information
with puposeful whitespace padded on one line
"""
tol = 1e-5
lines = rmc6f_input_text.split('\n')
lines[14] = " {} ".format(lines[14]) # intentional whitespace
props, cell = rmc6f._read_process_rmc6f_lines_to_pos_and_cell(lines)
target_cell = np.zeros((3, 3), float)
np.fill_diagonal(target_cell, 4.672816)
assert props == symbol_xyz_dict
assert np.allclose(cell, target_cell, rtol=tol)
def test_rmc6f_write_output_column_format():
"""Test for utility function that processes the columns in array
and gets back out formatting information.
"""
cols = ['id', 'symbols', 'scaled_positions', 'ref_num', 'ref_cell']
arrays = {}
arrays['id'] = np.array([1, 2, 3, 4, 5, 6, 7])
arrays['symbols'] = np.array(symbols)
arrays['ref_num'] = np.zeros(7, int)
arrays['ref_cell'] = np.zeros((7, 3), int)
arrays['scaled_positions'] = lat_positions / lat
ncols, dtype_obj, fmt = rmc6f._write_output_column_format(cols, arrays)
target_ncols = [1, 1, 3, 1, 3]
target_fmt = "%8d %s%14.6f %14.6f %14.6f %8d %8d %8d %8d \n"
assert ncols == target_ncols
assert fmt == target_fmt
def test_rmc6f_write_output():
"""Test for utility function for writing rmc6f output
"""
fileobj = "output.rmc6f"
header_lines = [
'(Version 6f format configuration file)',
'(Generated by ASE - Atomic Simulation Environment https://wiki.fysik.dtu.dk/ase/ )', # noqa: E501
"Metadata date:18-007-'2019",
'Number of types of atoms: 2 ',
'Atom types present: S F',
'Number of each atom type: 1 6',
'Number of moves generated: 0',
'Number of moves tried: 0',
'Number of moves accepted: 0',
'Number of prior configuration saves: 0',
'Number of atoms: 7',
'Supercell dimensions: 1 1 1',
'Number density (Ang^-3): 0.06860598423060468',
'Cell (Ang/deg): 4.672816 4.672816 4.672816 90.0 90.0 90.0',
'Lattice vectors (Ang):',
' 4.672816 0.000000 0.000000',
' 0.000000 4.672816 0.000000',
' 0.000000 0.000000 4.672816',
'Atoms:']
data_array = symbol_xyz_list_ext
data_dtype = [
('id', '<i8'),
('symbols', '<U1'),
('scaled_positions0', '<f8'),
('scaled_positions1', '<f8'),
('scaled_positions2', '<f8'),
('ref_num', '<i8'),
('ref_cell0', '<i8'),
('ref_cell1', '<i8'),
('ref_cell2', '<i8')]
data = np.array(data_array, dtype=data_dtype)
fmt = "%8d %s%14.6f %14.6f %14.6f %8d %8d %8d %8d \n"
with open('output.rmc6f', 'w') as fileobj:
rmc6f._write_output(fileobj, header_lines, data, fmt)
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