def write_frame(self, frame, subset=None, **kwargs):
'''
Write a frame into the opened XTC file
Parameters
----------
frame : Frame
subset : list of int, optional
kwargs : dict
Ignored
'''
import chemfiles
if subset is None:
positions = frame.positions
else:
positions = frame.positions[subset]
cf_frame = chemfiles.Frame()
cf_frame.resize(len(positions))
cf_frame.positions[:] = positions * 10
cf_frame.cell = chemfiles.UnitCell(frame.cell.lengths * 10,
frame.cell.angles)
cf_frame.step = frame.step
self._xtc.write(cf_frame)
def _timestep_to_chemfiles(self, ts):
"""
Convert a Timestep to a chemfiles Frame
"""
# TODO: CONVERTERS?
frame = chemfiles.Frame()
frame.resize(ts.n_atoms)
if ts.has_positions:
frame.positions[:] = ts.positions[:]
if ts.has_velocities:
frame.add_velocities()
frame.velocities[:] = ts.velocities[:]
frame.cell = chemfiles.UnitCell(*ts.dimensions)
return frame
def test_cell(self):
frame = chemfiles.Frame()
system = ChemfilesSystem(frame)
self.assertTrue(np.all(system.cell() == 0))
frame.cell = chemfiles.UnitCell((3, 3, 3))
self.assertTrue(np.allclose(system.cell(), np.diag([3, 3, 3])))
frame.cell = chemfiles.UnitCell((3, 3, 3), (60, 60, 60))
expected = [
[3.0, 0.0, 0.0],
[1.5, 2.59807621, 0.0],
[1.5, 0.8660254, 2.44948974],
]
self.assertTrue(np.allclose(system.cell(), expected))
def test_system_implementation(self):
frame = chemfiles.Frame()
frame.add_atom(chemfiles.Atom("C"), (0, 0, 0))
frame.add_atom(chemfiles.Atom("CH3"), (0, 1, 0))
frame.add_atom(chemfiles.Atom("X"), (0, 2, 0))
frame.add_atom(chemfiles.Atom("Zn1", "Zn"), (0, 3, 0))
system = ChemfilesSystem(frame)
self.assertEqual(system.size(), 4)
self.assertTrue(np.all(system.species() == [6, 120, 121, 30]))
positions = [
(0, 0, 0),
(0, 1, 0),
(0, 2, 0),
(0, 3, 0),
]
self.assertTrue(np.all(system.positions() == positions))
def test_compute(self):
frame = chemfiles.Frame()
frame.add_atom(chemfiles.Atom("C"), (0, 0, 0))
frame.add_atom(chemfiles.Atom("C"), (0, 1, 0))
frame.add_atom(chemfiles.Atom("C"), (0, 2, 0))
frame.add_atom(chemfiles.Atom("C"), (0, 3, 0))
calculator = DummyCalculator(cutoff=3.4, delta=1, name="", gradients=False)
with self.assertRaises(RascalError) as cm:
calculator.compute(frame, use_native_system=False)
self.assertEqual(
cm.exception.__cause__.args[0],
"chemfiles systems can only be used with 'use_native_system=True'",
)
# use_native_system=True should work fine
descriptor = calculator.compute(frame, use_native_system=True)
self.assertEqual(descriptor.values.shape, (4, 2))