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changing DL_Poly units #4983

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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
dc7a2f5
reformatting
Mar 21, 2025
2b8b5bf
issue #2393 fix DLPoly unit conversion
Aug 4, 2025
b61ae52
merge latest updates
Aug 4, 2025
eedba55
merge changes
Aug 4, 2025
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2 changes: 1 addition & 1 deletion 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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@orbeckst orbeckst Mar 30, 2025

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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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@orbeckst orbeckst Mar 30, 2025

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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:
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2 changes: 1 addition & 1 deletion package/MDAnalysis/coordinates/TRZ.py
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Expand Up @@ -605,4 +605,4 @@ def close(self):
if self.trzfile is None:
return
self.trzfile.close()
self.trzfile = None
self.trzfile = None
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@orbeckst orbeckst Mar 30, 2025

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just undo

6 changes: 4 additions & 2 deletions testsuite/MDAnalysisTests/coordinates/test_dlpoly.py
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Expand Up @@ -70,8 +70,9 @@ def test_velocities(self, ts):
ref = np.array([1.056610291, -1.218664448, 3.345828610])
assert_allclose(ts._velocities[0], ref)

# modified to original numbers / 100
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@orbeckst orbeckst Mar 30, 2025

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remove comment – we can always look in the git blame to find out when something was changed

def test_forces(self, ts):
ref = np.array([-1979.558687, 739.7961625, 1027.996603])
ref = np.array([-19.79558687, 7.397961625, 10.27996603])
assert_allclose(ts._forces[0], ref)


Expand Down Expand Up @@ -118,8 +119,9 @@ 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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@orbeckst orbeckst Mar 30, 2025

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remove comment

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@cbouy cbouy Apr 2, 2025 •
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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):
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