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# fmt: off
"""Testing lammpsdata reader."""
import re
from io import StringIO
import numpy as np
import pytest
from ase.io import read
CONTENTS = """
3 atoms
1 atom types
2 bonds
2 bond types
1 angles
1 angle types
1 dihedrals
1 dihedral types
0 10 xlo xhi
0 10 ylo yhi
0 10 zlo zhi
Masses
1 1
Atoms # full
3 1 1 0 2 0 0 # 3rd
1 1 1 0 0 0 0 # 1st
2 1 1 0 1 0 0 # 2nd
Bonds
1 1 1 2 # 1-2
2 2 2 3 # 2-3
Angles
1 1 1 2 3 # 1-2-3
Dihedrals
1 1 1 2 3 1 # 1-2-3-1
"""
SORTED = {
True: np.array([0, 1, 2]),
False: np.array([2, 0, 1]),
}
REFERENCE = {
'positions': np.array([
[0, 0, 0],
[1, 0, 0],
[2, 0, 0],
]),
'cell': np.eye(3) * 10,
'bonds': {
'atoms': np.array([
[0, 1],
[1, 2],
]),
'types': np.array([1, 2]),
},
'angles': {
'atoms': np.array([
[0, 1, 2],
]),
'types': np.array([1]),
},
'dihedrals': {
'atoms': np.array([
[0, 1, 2, 0],
]),
'types': np.array([1]),
},
}
@pytest.fixture()
def fmt():
return 'lammps-data'
@pytest.fixture(params=[True, False])
def sort_by_id(request):
return request.param
@pytest.fixture()
def lammpsdata(fmt, sort_by_id):
fd = StringIO(CONTENTS)
return read(fd, format=fmt, sort_by_id=sort_by_id), SORTED[sort_by_id]
def parse_tuples(atoms, regex, permutation, label):
"""Parse connectivity strings stored in atoms."""
all_tuples = np.zeros((0, len(permutation)), int)
types = np.array([], int)
tuples = atoms.arrays[label]
bonded = np.where(tuples != '_')[0]
for i, per_atom in zip(bonded, tuples[bonded]):
per_atom = np.array(regex.findall(per_atom), int)
new_tuples = np.array([
np.full(per_atom.shape[0], i, int),
*(per_atom[:, :-1].T)
])
all_tuples = np.append(all_tuples,
new_tuples[permutation, :].T,
axis=0)
types = np.append(types, per_atom[:, -1])
return all_tuples, types
def test_positions(lammpsdata):
atoms, sorted = lammpsdata
assert pytest.approx(atoms.positions) == REFERENCE['positions'][sorted]
def test_cell(lammpsdata):
atoms, _ = lammpsdata
assert pytest.approx(atoms.cell.array) == REFERENCE['cell']
def test_connectivity(lammpsdata):
atoms, sorted = lammpsdata
parser_data = {
'bonds': ((0, 1), re.compile(r'(\d+)\((\d+)\)')),
'angles': ((1, 0, 2), re.compile(r'(\d+)-(\d+)\((\d+)\)')),
'dihedrals': ((0, 1, 2, 3), re.compile(r'(\d+)-(\d+)-(\d+)\((\d+)\)')),
}
for k, v in parser_data.items():
tuples, types = parse_tuples(atoms, v[1], v[0], k)
tuples = sorted[tuples.flatten()].reshape(tuples.shape)
assert np.all(tuples == REFERENCE[k]['atoms'])
assert np.all(types == REFERENCE[k]['types'])
|
