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fix: write velocities or forces alone in restart files #193

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fix: write velocities or forces alone in restart files #193

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2 changes: 1 addition & 1 deletion PQAnalysis/io/restart_file/restart_writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,7 @@ def _get_atom_lines(
line += f"{atom.name} {atom_counter[i]} {residue} "
line += f"{pos[0]} {pos[1]} {pos[2]}"

if (frame.has_vel and frame.has_forces) or md_engine_format != MDEngineFormat.PQ:
if (frame.has_vel or frame.has_forces) or md_engine_format != MDEngineFormat.PQ:
line += f" {vel[0]} {vel[1]} {vel[2]}"
line += f" {force[0]} {force[1]} {force[2]}"

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30 changes: 27 additions & 3 deletions tests/io/test_restartWriter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from . import pytestmark

from PQAnalysis.io import RestartFileWriter
from PQAnalysis.io.restart_file.api import read_restart_file, write_restart_file
from PQAnalysis.traj import MDEngineFormat
from PQAnalysis.core import Cell, Atom
from PQAnalysis.atomic_system import AtomicSystem
Expand Down Expand Up @@ -184,9 +185,9 @@ def test_write(self, capsys):
captured = capsys.readouterr()
assert captured.out == """
Box 10.0 10.0 10.0 90 90 90
C 0 0 0.0 0.0 0.0
H 1 0 1.0 1.0 1.0
H 2 0 2.0 2.0 2.0
C 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
H 1 0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0
H 2 0 2.0 2.0 2.0 2.0 2.0 2.0 0.0 0.0 0.0
"""

forces = np.array([[0.0, 0.0, 0.0], [1.0, 1.0, 1.0], [2.0, 2.0, 2.0]])
Expand Down Expand Up @@ -214,3 +215,26 @@ def test_write(self, capsys):
H 1 0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
H 2 0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
"""

@pytest.mark.usefixtures("tmpdir")
def test_write_only_velocities_or_forces_round_trip(self):
atoms = [Atom("C"), Atom("H")]
positions = np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]])
values = np.array([[0.1, 0.2, 0.3], [0.4, 0.5, 0.6]])
cell = Cell(10.0, 10.0, 10.0)

frame = AtomicSystem(atoms=atoms, pos=positions, vel=values, cell=cell)
write_restart_file(frame, "vel_only.rst", mode="o")
system = read_restart_file("vel_only.rst")

assert np.allclose(system.vel, values)
assert np.allclose(system.forces, np.zeros((2, 3)))

frame = AtomicSystem(
atoms=atoms, pos=positions, forces=values, cell=cell
)
write_restart_file(frame, "forces_only.rst", mode="o")
system = read_restart_file("forces_only.rst")

assert np.allclose(system.forces, values)
assert np.allclose(system.vel, np.zeros((2, 3)))
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