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WIP: Lammpsdump velocities (and other fields) #3448

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WIP: Lammpsdump velocities (and other fields) #3448

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387f0ad
Parse velocities from LAMMPSDUMP
schlaicha Oct 26, 2021
6f86e50
Add unit conversion for LAMMPS real units
schlaicha Oct 29, 2021
10723cf
Correct frame numbering
schlaicha Oct 29, 2021
c130c18
Adjust documentation
schlaicha Oct 29, 2021
a985b43
PEP8
schlaicha Oct 29, 2021
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25 changes: 22 additions & 3 deletions package/MDAnalysis/coordinates/LAMMPS.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,8 +55,9 @@
Dump files
----------

The DumpReader expects ascii dump files written with the default
`LAMMPS dump format`_ of 'atom'
The DumpReader expects ascii dump files. Currently supported are
coordinates (dump style atom) and velocities for custom dump styles.
Other columns are ignored.


Example: Loading a LAMMPS simulation
Expand Down Expand Up @@ -462,6 +463,7 @@ class DumpReader(base.ReaderBase):
coordinate convention (xs,ys,zs) or scaled unwrapped coordinate convention
(xsu,ysu,zsu) they will automatically be converted from their
scaled/fractional representation to their real values.
Velocities (vx, vy, vz) can be parsed, too.


.. versionchanged:: 2.0.0
Expand Down Expand Up @@ -502,7 +504,7 @@ def _reopen(self):
self.close()
self._file = util.anyopen(self.filename)
self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs)
self.ts.frame = -1
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this is deliberately -1 as it gets incremented in the loading process

self.ts.frame = 0

@property
@cached('n_atoms')
Expand Down Expand Up @@ -606,15 +608,32 @@ def _read_next_timestep(self):

coord_cols = convention_to_col_ix[self.lammps_coordinate_convention]

# pass possible additional fields from LAMMPS dump
# pass velocities
velocity_col_names = ["vx", "vy", "vz"]
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I would make this a class attribute, much like self._conventions is, as the data is not mutable or instance dependent. :)

if any(item in attrs for item in velocity_col_names):
for cv_name, cv_col_names in enumerate(velocity_col_names):
try:
velocity_cols = [attr_to_col_ix[x] for x in velocity_col_names]
ts.has_velocities = True
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This works, but I think we only want to set ts.has_velocities = True on exit from this loop, slightly cleaner IMO.

except KeyError:
raise ValueError("Velocities detected in LAMMPS Dump file but MDAnalysis can only deal with all entries vx, vy, vz present")

ids = "id" in attr_to_col_ix
for i in range(self.n_atoms):
fields = f.readline().split()
if ids:
indices[i] = fields[attr_to_col_ix["id"]]
ts.positions[i] = [fields[dim] for dim in coord_cols]
if ts.has_velocities:
ts.velocities[i] = [fields[dim] for dim in velocity_cols]

order = np.argsort(indices)
ts.positions = ts.positions[order]
if ts.has_velocities:
ts.velocities = ts.velocities[order]
# LAMMPS reader only supports real units
ts.velocities *= units.speedUnit_factor['Angstrom/femtosecond']
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Query @richardjgowers on units? I'm no lammps expert, what are the range of possible units?

if (self.lammps_coordinate_convention.startswith("scaled")):
# if coordinates are given in scaled format, undo that
ts.positions = distances.transform_StoR(ts.positions,
Expand Down