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fix(pwmat): use selected frame cell for coordinates #1021

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fix(pwmat): use selected frame cell for coordinates #1021

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4 changes: 3 additions & 1 deletion dpdata/formats/pwmat/atomconfig.py
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,9 @@ def from_system_data(system, f_idx=0, skip_zeros=True):
atomic_numbers.append(ELEMENTS.index(ii) + 1)
posi_list = []
for jj, ii in zip(atomic_numbers, posis):
ii = np.matmul(ii, np.linalg.inv(system["cells"][0]))
# Fractional coordinates must be computed in the same frame's cell;
# frame zero is only valid for a fixed-cell trajectory.
ii = np.matmul(ii, np.linalg.inv(system["cells"][f_idx]))
posi_list.append("%d %15.10f %15.10f %15.10f 1 1 1" % (jj, ii[0], ii[1], ii[2])) # noqa: UP031
for kk in range(len(posi_list)):
min = kk
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15 changes: 15 additions & 0 deletions tests/test_pwmat_config_dump.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,11 @@
import os
import unittest

import numpy as np
from pwmat.config_ref_oh import Testconfigoh

import dpdata
from dpdata.formats.pwmat.atomconfig import from_system_data


def myfilecmp(test, f0, f1):
Expand Down Expand Up @@ -58,5 +60,18 @@ def test_dump_pwmat_type_map(self):
myfilecmp(self, "atom.config.tmp.1", "atom.config.tmp.2")


class TestAtomconfigFrameCell(unittest.TestCase):
def test_fractional_coordinates_use_selected_frame_cell(self):
system = {
"atom_names": ["H"],
"atom_numbs": [1],
"atom_types": np.array([0]),
"cells": np.array([np.eye(3), np.eye(3) * 2.0]),
"coords": np.array([[[1.0, 0.0, 0.0]], [[1.0, 0.0, 0.0]]]),
}
output = from_system_data(system, f_idx=1)
self.assertIn("0.5000000000 0.0000000000 0.0000000000", output)


if __name__ == "__main__":
unittest.main()
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