Accessing velocity of atoms in each frame

[Teslim Olayiwola]

Hi everyone,

Thanks for the great tool! I am trying to access the velocity of each atom in a lammps trajectory (see attached image for a screenshot of the lammpstrj file) for 1 frame at a time. In my code, I have the tried the following:

import MDAnalysis as mda

lammps_data = "npt_stp04.data"
lammps_trajectory = "dump_npt_step04.lammpstrj"

data = mda.Universe(lammps_data, lammps_trajectory, format="LAMMPSDUMP", has_velocities = True)

choice_atoms = data.select_atoms("type 63")

for ts in data.trajectory:
        reference = choice_atoms.ts.velocities

I got the following error

NoDataError Traceback (most recent call last) <ipython-input-108-7356210d6102> in <module> 

1 for ts in data.trajectory: 

----> 2 reference = choice_atoms.ts.velocities ~/opt/anaconda3/lib/python3.8/site-packages/MDAnalysis/coordinates/base.py in __getattr__(self, attr) 

488 # special-case timestep info 

489 if attr in ('velocities', 'forces', 'positions'):

--> 490 raise NoDataError('This Timestep has no ' + attr) 

491 err = "{selfcls} object has no attribute '{attr}'" 

492 raise AttributeError(err.format(selfcls=type(self).__name__, 

NoDataError: This Timestep has no velocities

Please advise on what to do. Thank you very much!

[Oliver Beckstein]



Hi Teslim,

I’m not sure if the LAMMPS reader actually read velocities. The table https://userguide.mdanalysis.org/stable/formats/index.html#coordinates says no but it may be outdated. 

Did you (or anyone else) have a look at the code to check that it actually reads velocities?

If it doesn’t then you can raise an issue and suggest it as an enhancement. 

Oliver 

Am 10/1/22 um 07:57 schrieb Teslim Olayiwola <olayiwol...@gmail.com>:

Hi everyone,

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[Hugo Macdermott-Opeskin]

There is an open PR with this fix. 

https://github.com/MDAnalysis/mdanalysis/pull/3844

You may be able to use that branch in the interim until it is merged. :)

[Teslim Olayiwola]

Thank you very much to you (Hugo), Oliver and the entire MDAnalysis team! How do I download this new fix and merge it to the existing version on my PC?

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[Teslim Olayiwola]

Thank you. I have been able to install it! I made use of the Github desktop to synchronize it to my PC.