Fix triclinic cell at 0,0,0 #368
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WalkthroughModify _vector_to_lammps to treat zero-valued vectors as valid input (check now uses Changes
Sequence Diagram(s)sequenceDiagram
autonumber
participant Caller
participant ASEWrapper as ASE Wrapper
participant _Vec as _vector_to_lammps
participant Prism
participant LAMMPS as LAMMPS Engine
Caller->>ASEWrapper: interactive_structure_setter(structure, ...)
ASEWrapper->>_Vec: _vector_to_lammps(vector, prism)
alt vector is None
_Vec->>ASEWrapper: return None
else vector is not None (including zeros)
_Vec->>Prism: apply prism conversion (if provided)
Prism-->>_Vec: transformed vector
_Vec->>_Vec: flatten() -> 1D array
_Vec-->>ASEWrapper: return flattened vector
end
ASEWrapper->>LAMMPS: create_atoms(pos_vec_or_none, ...)
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~20 minutes Possibly related PRs
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #368 +/- ##
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+ Coverage 81.93% 82.31% +0.37%
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Files 5 5
Lines 559 554 -5
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- Hits 458 456 -2
+ Misses 101 98 -3 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Actionable comments posted: 1
🧹 Nitpick comments (4)
pylammpsmpi/wrapper/ase.py (3)
480-487: np.any(vector) drops legitimate all-zero data; make “None” mean “unset” onlycurrent behavior: all-zero arrays are treated as “absent” and collapsed to None. That’s why you needed a special fallback for positions. A simpler, more predictable rule: only treat vector is None as unset, otherwise transform+flatten regardless of values. This also preserves intentional zero velocities rather than silently omitting them.
Proposed patch:
def _vector_to_lammps(vector, prism): - if vector is not None and np.any(vector): - if not _check_ortho_prism(prism=prism): - vector = prism.vector_to_lammps(vector) - return vector.flatten() - else: - return None + if vector is None: + return None + if not _check_ortho_prism(prism=prism): + vector = prism.vector_to_lammps(vector) + return np.asarray(vector).flatten()This change would also make the new positions fallback unnecessary in most cases, but keeping the defensive fallback is fine.
291-296: Incorrect exception type and broken “missing elements” messageget_lammps_indicies_from_ase_structure will raise a ValueError (not KeyError) if an element in the structure is not mapped; and the current message uses el_dict (always empty here) and expects an Abbreviation attribute on strings. Fix both.
- except KeyError: - missing = set(get_species_symbols(structure)).difference(el_dict.keys()) - missing = ", ".join([el.Abbreviation for el in missing]) + except ValueError: + present = set(get_species_symbols(structure)) + allowed = set(el_eam_lst) + missing = ", ".join(sorted(present - allowed)) raise ValueError( - f"Structure contains elements [{missing}], that are not present in the potential!" + f"Structure contains elements [{missing}] that are not present in the potential!" )
142-145: Typos in warning text (“upper trangular”)Minor wording fix improves clarity and searchability of logs.
- "Warning: setting upper trangular matrix might slow down the calculation", + "Warning: setting an upper triangular matrix might slow down the calculation",Also applies to: 221-225
tests/test_ase_interface.py (1)
480-489: Expanded structure set and expected energies look consistent; consider naming and coverage tweaks
- The added bulk_al_small = bulk("Al").repeat([2, 2, 2]) is a nice addition to exercise the triclinic/default cell path; LGTM overall.
- Minor naming nit: bulk_al_small doesn’t convey why it’s added; bulk_al_skewed or bulk_al_default would be clearer.
- To fully cover the new positions fallback (and the mirrored fix I suggested), add a test where positions are explicitly set to all zeros to ensure no crash and correct propagation.
Sketch for an extra test:
def test_set_all_zero_positions(self): lmp = LammpsASELibrary(working_directory=None, cores=1, comm=None, logger=logging.getLogger("ZeroPosLogger"), log_file=None, library=LammpsLibrary(cores=2), disable_log_file=True) structure = bulk("Al", cubic=True) lmp.interactive_structure_setter( structure=structure, units="lj", dimension=3, boundary=" ".join(["p" if c else "f" for c in structure.pbc]), atom_style="atomic", el_eam_lst=["Al"], calc_md=False ) zeros = np.zeros_like(structure.positions) lmp.interactive_positions_setter(positions=zeros) lmp.interactive_lib_command("run 0") self.assertTrue(np.allclose(lmp.interactive_positions_getter(), zeros))
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📒 Files selected for processing (2)
pylammpsmpi/wrapper/ase.py(1 hunks)tests/test_ase_interface.py(1 hunks)
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Summary by CodeRabbit
Bug Fixes
Tests