Skip to content

fix: apply remove_pbc to mixed configurations #391

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
njzjz-bot wants to merge 1 commit into
base: master
Choose a base branch
from
Open

fix: apply remove_pbc to mixed configurations #391

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions dpgen2/conf/file_conf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,12 @@ def generate_mixed(
assert "deepmd/npy/mixed" == self.fmt
ms = dpdata.MultiSystems(type_map=type_map)
ms.from_deepmd_npy_mixed(self.files[0], fmt="deepmd/npy/mixed", labeled=False) # type: ignore
if self.remove_pbc:
# Keep mixed-format configurations consistent with the standard
# file path: every reconstructed chemical system must receive the
# requested non-periodic cell transformation.
for system in ms.systems.values():
system.remove_pbc()
return ms

@staticmethod
Expand Down
16 changes: 16 additions & 0 deletions tests/conf/test_file_conf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -203,6 +203,22 @@ def test_deepmd_mixed(self):
np.testing.assert_almost_equal(ms[1][tt], ms1[1][tt])
shutil.rmtree("test_mixed")

def test_deepmd_mixed_remove_pbc(self):
type_map = ["Cu", "Al", "Mg"]
ms = dpdata.MultiSystems(type_map=type_map)
ms.append(dpdata.System(Path(self.prefix) / "poscar.foo.0", fmt="vasp/poscar"))
ms.to("deepmd/npy/mixed", "test_mixed_remove_pbc")
self.addCleanup(shutil.rmtree, "test_mixed_remove_pbc", ignore_errors=True)

loaded = FileConfGenerator(
"test_mixed_remove_pbc",
fmt="deepmd/npy/mixed",
remove_pbc=True,
).generate(type_map)

np.testing.assert_allclose(loaded[0]["cells"][0], np.eye(3) * 18.0)
np.testing.assert_allclose(loaded[0]["coords"][0, 0], np.full(3, 9.0))


class TestFileConfGeneratorContent(unittest.TestCase):
def test_list_1(self):
Expand Down