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changing DL_Poly units #4983

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e787218
modifying force units
Mar 20, 2025
ad9c571
removing force from TRZ
Mar 20, 2025
445ec3a
modifying dlpoly test case
Mar 20, 2025
5585acc
changing conversion location
Mar 20, 2025
cfa4e25
typo fix
Mar 20, 2025
f11800b
fix inconsistencies
Mar 20, 2025
a267752
disregarding TRZ (dropped in 3.0)
Mar 21, 2025
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4 changes: 2 additions & 2 deletions package/MDAnalysis/coordinates/DLPoly.py
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@ def _read_first_frame(self):
if has_vels:
velocities = np.array(velocities, dtype=np.float32)
if has_forces:
forces = np.array(forces, dtype=np.float32)
forces = np.array(forces, dtype=np.float32) / 100
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add a comment above this line stating that forces in DL_POLY are 10 J/(mol.Å) and mention issue #2393 — this is weird enough to warrant a hint for future coders

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Actually, we should not just divide by 100 here. Instead we should use the normal conversion machinery where you store the native force units in _DLPOLY_UNITS and store the conversion factor in units, then use convert_from_native.

See also https://userguide.mdanalysis.org/stable/units.html .

self.n_atoms = len(coords)

if ids:
Expand Down Expand Up @@ -196,7 +196,7 @@ def _read_next_timestep(self, ts=None):
if self._has_vels:
ts._velocities[i] = self._file.readline().split()
if self._has_forces:
ts._forces[i] = self._file.readline().split()
ts._forces[i] = np.array(self._file.readline().split(), dtype=np.float32) / 100
i += 1

if ids:
Expand Down
22 changes: 0 additions & 22 deletions package/MDAnalysis/coordinates/TRZ.py
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Expand Up @@ -130,7 +130,6 @@ def __init__(self, trzfilename, n_atoms=None, **kwargs):
self._read_trz_header()
self.ts = Timestep(self.n_atoms,
velocities=True,
forces=self.has_force,
reader=self,
**self._ts_kwargs)

Expand Down Expand Up @@ -164,17 +163,6 @@ def __init__(self, trzfilename, n_atoms=None, **kwargs):
('vy', readarg),
('pad6', '<2i4'),
('vz', readarg)]
if not self.has_force:
frame_contents += [('pad7', '<i4')]
else:
frame_contents += [
('pad7', '<2i4'),
('fx', readarg),
('pad8', '<2i4'),
('fy', readarg),
('pad9', '<2i4'),
('fz', readarg),
('pad10', '<i4')]
self._dtype = np.dtype(frame_contents)

self._read_next_timestep()
Expand All @@ -189,12 +177,6 @@ def _read_trz_header(self):
('p3', '<i4')])
data = np.fromfile(self.trzfile, dtype=self._headerdtype, count=1)
self.title = ''.join(c.decode('utf-8') for c in data['title'][0]).strip()
if data['force'] == 10:
self.has_force = False
elif data['force'] == 20:
self.has_force = True
else:
raise IOError

def _read_next_timestep(self, ts=None):
if ts is None:
Expand Down Expand Up @@ -223,10 +205,6 @@ def _read_next_timestep(self, ts=None):
ts._velocities[:, 0] = data['vx']
ts._velocities[:, 1] = data['vy']
ts._velocities[:, 2] = data['vz']
if self.has_force:
ts._forces[:, 0] = data['fx']
ts._forces[:, 1] = data['fy']
ts._forces[:, 2] = data['fz']
except IndexError: # Raises indexerror if data has no data (EOF)
raise IOError from None
else:
Expand Down
3 changes: 2 additions & 1 deletion testsuite/MDAnalysisTests/coordinates/test_dlpoly.py
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Original file line number Diff line number Diff line change
Expand Up @@ -118,8 +118,9 @@ def test_vel(self, u):
ref = np.array([2.637614561, 0.5778767520e-01, -1.704765568])
assert_allclose(u.atoms[2].velocity, ref)

# modified to original numbers / 100
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remove comment

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@cbouy cbouy Apr 2, 2025 •
edited
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@lexi-x removing this would also fix the linters / black error here https://github.com/MDAnalysis/mdanalysis/actions/runs/13984105125/job/39154722804?pr=4983#step:5:151

def test_for(self, u):
ref = np.array([150.3309776, -812.6932914, 1429.413120])
ref = np.array([1.503309776, -8.126932914, 14.29413120])
assert_allclose(u.atoms[2].force, ref)

def test_number(self, u):
Expand Down
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