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Re: [lammps-users] Extracting per-atom potential energy with LAMMPS-Python interface
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Re: [lammps-users] Extracting per-atom potential energy with LAMMPS-Python interface


From: Steve Plimpton <sjplimp@...24...>
Date: Mon, 6 Nov 2017 11:36:33 -0700

If you read the doc headers for the extract_variable()
and gather_atoms() functions in src/library.cpp,
you will see that the former returns just a ptr to
the per-atom variable quantity, while the latter
does the gather operation Axel talked about.  But
it is only for per-atom quantities that already
have a name, like x, v, charge, etc.

Depending on the application, both kinds of
returns are useful (raw ptr on each proc versus
gathered data into one big vector).  Since
your Python driver is parallel, are you sure you
want one big vector on every proc?

It would not be hard to extend the interface for
gather_atoms() to enable it to work with per-atom
variables in addition to names like x,v.  Possibly
just extending the atom->extract() method to
find/return the pointers for per-atom varaibles.

It would also be useful to enable this for
per-atom compute and fix info.

Steve


On Mon, Oct 23, 2017 at 2:40 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
On Mon, Oct 23, 2017 at 10:52 AM, Wise, Ethan Allen <eawise@...2437...> wrote:
> Hi LAMMPS users,
>
>
>
> In my current project, I am using the python-LAMMPS interface from a python
> function embedded within my LAMMPS input script.  This python function is
> called during each timestep and accesses/changes per-atom properties using
> the “lmp.gather_atoms()” and “lmp.scatter_atoms()” methods.  I now want to
> access a per-atom potential energy variable (and corresponding per-atom id)
> in a similar fashion.  I am accessing this atom style variable from within
> python via the “lmp.extract_variable()” method.  However, I noticed that
> each processor seems to return a separate python list.  Is there a way to
> retrieve the per-atom potential energy as a single list in python?  If not,
> is there a way for me to combine these variables into a single variable?
> The python code is mpi4py enabled and I am running on LAMMPS version
> 20161117.  Thanks for your help.

two comments:

1) you should upgrade your LAMMPS version. there have been significant
improvements to the LAMMPS python interface over the last year.

2) you will have to do your own MPI communication in python to collect
the information into a properly ordered array. or extend the C library
interface and correspondingly the python wrapper.
  the procedure is straightforward: you get a suitable storage on rank
0 of size natoms ready for the data.
  then you loop over all ranks > 0 and receive a data chunk with all
atom tags and the property you are interested. those will be in
"local" order.
  then you loop over the received data (mind you, that each MPI rank
may have a different number of nlocal atoms)
  for (i=0; i < nlocal_rank; ++i) { data[tag[i]] = recv[i]; }
  now you have your data in order of the global atom id in the array
"data". this can be done more efficient (e.g. using MPI_Gatherv), but
this is the general principle.

axel.

>
>
>
> Ethan
>
>
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--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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