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Add DFTB+ gen fmt parser
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@peterspackman
peterspackman committed Feb 14, 2024
1 parent 522eebe commit e2e1c2e
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66 changes: 66 additions & 0 deletions src/chmpy/fmt/gen.py
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import logging
from pathlib import Path
import numpy as np
from chmpy.core.element import Element

LOG = logging.getLogger(__name__)


def parse_gen_string(contents, filename=None):
"""Convert provided xmol .xyz file contents into an array of
atomic numbers and cartesian positions
Parameters
----------
contents: str
text contents of the .xyz file to read
Returns
-------
tuple of :obj:`np.ndarray`
List[Element], (N, 3) positions, (4, 3) lattice vectors, bool (if fractional)
read from the given file
"""
lines = contents.splitlines()
natom_str, kind = lines[0].split()
natom = int(natom_str)
kind = kind.strip()
LOG.debug("Expecting %d atoms %s", natom, "in " + filename if filename else "")
elements_map = [Element[x.strip()] for x in lines[1].split()]

arr = [[float(x) for x in line.split()] for line in lines[natom + 2 : natom + 6]]
elements = []
positions = []
for line in lines[2 : natom + 2]:
if not line.strip():
break
tokens = line.strip().split()
xyz = tuple(float(x) for x in tokens[2:5])
positions.append(xyz)
el = elements_map[int(tokens[1]) - 1]
elements.append(el)
LOG.debug(
"Found %d atoms lines in %s",
len(elements),
"in " + filename if filename else "",
)
return elements, np.asarray(positions), np.asarray(arr), kind == "F"


def parse_gen_file(filename):
"""Convert a provided DFTB+ .gen file into an array of
atomic numbers, positions and
Parameters
----------
filename: str
path to the .xyz file to read
Returns
-------
tuple of :obj:`np.ndarray`
List[Element], (N, 3) positions, (4, 3) lattice vectors, bool (if fractional)
read from the given file
"""
path = Path(filename)
return parse_gen_string(path.read_text(), filename=str(path.absolute()))
19 changes: 19 additions & 0 deletions src/chmpy/tests/fmt/test_gen.py
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from chmpy.fmt.gen import parse_gen_string, parse_gen_file
import unittest
import numpy as np
from .. import TEST_FILES


class GenFileTestCase(unittest.TestCase):
def test_parse_file(self):
els, pos, vecs, frac = parse_gen_file(TEST_FILES["example.gen"])
self.assertEqual(len(els), 76)
self.assertEqual(els[0].atomic_number, 1)
self.assertEqual(els[75].atomic_number, 8)

expected_coords_46 = np.array((0.3623979304, 0.6637420302, 0.8677686357))
np.testing.assert_allclose(pos[46, :], expected_coords_46, atol=1e-5)

np.testing.assert_allclose(np.zeros(3), vecs[0, :])

self.assertAlmostEqual(vecs[1, 0], 13.171)
82 changes: 82 additions & 0 deletions src/chmpy/tests/test_files/example.gen
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76 F
H C O
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