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"""GPUMD input file parser.
Implemented:
* Input file (xyz.in)
"""
import numpy as np
from ase import io
from ase.build import bulk
from ase.io.gpumd import load_xyz_input_gpumd
# This file is parsed correctly by GPUMD, since it include
# among the examples distributed with the package, i.e.
# GPUMD/examples/ex5/xyz.in
gpumd_input_text = """16 4 1.1 0 1 2
1 1 1 6.18408 6.18408 6.18408
0 24.6747 -9.37798 21.2733 28.085 0.0250834 -0.00953331 0.0216256 0 0
1 29.7632 16.4709 -20.349 12.011 0.0291449 0.0156324 -0.0217974 1 1
0 -11.3942 20.7898 -16.1723 28.085 -0.0138055 0.0189116 -0.0164401 2 0
1 14.1056 -16.6803 15.5969 12.011 0.0110053 -0.0202905 0.0147439 3 1
0 -6.83647 -7.06634 33.159 28.085 -0.00917232 -0.00718339 0.0314857 4 0
1 44.7294 -12.1643 19.0095 12.011 0.0421363 -0.0134771 0.0159904 5 1
0 -20.8261 1.14004 -38.0268 28.085 -0.0256162 -0.00106368 -0.0408793 6 0
1 -4.53023 -50.3483 27.9666 12.011 -0.0101618 -0.0545161 0.0250959 7 1
0 -24.0175 -12.38 -22.0283 28.085 -0.0244153 -0.0148076 -0.0246158 8 0
1 -19.4088 19.7935 -10.8377 12.011 -0.0208416 0.0167874 -0.0143511 9 1
0 7.39496 22.8278 17.9552 28.085 0.00529484 0.0187607 0.01603 10 0
1 -1.24082 -7.64731 15.2911 12.011 -0.00459528 -0.0133305 0.0122104 11 1
0 8.12018 25.4121 -10.6444 28.085 0.00603208 0.0236104 -0.0152659 12 0
1 38.2451 -24.2186 31.0212 12.011 0.0355446 -0.0279537 0.0259785 13 1
0 4.30332 19.9209 -9.21584 28.085 -7.06147e-05 0.0158056 -0.0138137 14 0
1 8.91989 -1.32745 44.8546 12.011 0.00351112 -0.00690595 0.040041 15 1 """
def test_read_gpumd_input():
"""Read GPUMD input file."""
with open('xyz.in', 'w') as f:
f.write(gpumd_input_text)
# Test when specifying the species
species = ['Si', 'C']
atoms = io.read('xyz.in', format='gpumd', species=species)
groupings = [[[i] for i in range(len(atoms))],
[[i for i, s in
enumerate(atoms.get_chemical_symbols()) if s == 'Si'],
[i for i, s in
enumerate(atoms.get_chemical_symbols()) if s == 'C']]]
groups = [[[j for j, group in enumerate(grouping) if i in group][0]
for grouping in groupings] for i in range(len(atoms))]
assert len(atoms) == 16
assert set(atoms.symbols) == set(species)
assert all(atoms.get_pbc())
assert len(atoms.info) == len(atoms)
assert all(np.array_equal(
atoms.info[i]['groups'], np.array(groups[i])) for i in
range(len(atoms)))
assert len(atoms.get_velocities()) == len(atoms)
# Test without specifying the species-type map
atoms = io.read('xyz.in', format='gpumd')
assert set(atoms.symbols) == set(species)
# Test when specifying the isotope masses
isotope_masses = {'Si': [28.085], 'C': [12.011]}
atoms = io.read('xyz.in', format='gpumd',
isotope_masses=isotope_masses)
assert set(atoms.symbols) == set(species)
def test_load_gpumd_input():
"""Load all information from a GPUMD input file."""
with open('xyz.in', 'w') as f:
f.write(gpumd_input_text)
species_ref = ['Si', 'C']
with open('xyz.in', 'r') as f:
atoms, input_parameters, species =\
load_xyz_input_gpumd(f, species=species_ref)
input_parameters_ref = {'N': 16, 'M': 4, 'cutoff': 1.1,
'triclinic': 0, 'has_velocity': 1,
'num_of_groups': 2}
assert input_parameters == input_parameters_ref
assert species == species_ref
def test_gpumd_input_write():
"""Write a structure and read it back."""
atoms = bulk('NiO', 'rocksalt', 4.813, cubic=True)
# Test write and read
atoms.write('xyz.in')
readback = io.read('xyz.in')
assert np.allclose(atoms.positions, readback.positions)
assert np.allclose(atoms.cell, readback.cell)
# Test write and read with triclinic cell
atoms.write('xyz.in', use_triclinic=True)
with open('xyz.in', 'r') as f:
readback, input_parameters, _ = load_xyz_input_gpumd(f)
assert input_parameters['triclinic'] == 1
assert np.allclose(atoms.positions, readback.positions)
assert np.allclose(atoms.cell, readback.cell)
assert np.array_equal(atoms.numbers, readback.numbers)
# Test write and load with groupings
groupings = [[[i for i, s in
enumerate(atoms.get_chemical_symbols()) if s == 'Ni'],
[i for i, s in
enumerate(atoms.get_chemical_symbols()) if s == 'O']],
[[i] for i in range(len(atoms))]]
groups = [[[j for j, group in enumerate(grouping) if i in group][0]
for grouping in groupings] for i in range(len(atoms))]
atoms.write('xyz.in', groupings=groupings)
with open('xyz.in', 'r') as f:
readback, input_parameters, _ = load_xyz_input_gpumd(f)
assert input_parameters['num_of_groups'] == 2
assert len(readback.info) == len(atoms)
assert all(np.array_equal(
readback.info[i]['groups'], np.array(groups[i])) for i in
range(len(atoms)))
# Test write and read with velocities
velocities = np.array([[-0.3, 2.3, 0.7], [0.0, 0.3, 0.8],
[-0.6, 0.9, 0.1], [-1.7, -0.1, -0.5],
[-0.5, 0.0, 0.6], [-0.2, 0.1, 0.5],
[-0.1, 1.4, -1.9], [-1.0, -0.5, -1.2]])
atoms.set_velocities(velocities)
atoms.write('xyz.in')
with open('xyz.in', 'r') as f:
readback, input_parameters, _ = load_xyz_input_gpumd(f)
assert input_parameters['has_velocity'] == 1
assert np.allclose(readback.get_velocities(), atoms.get_velocities())
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