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initial implementation of lammps support #114

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initial implementation of lammps support #114

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MSiggel
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@MSiggel MSiggel commented Oct 21, 2018

Initial support for lammps simulations.
lammps module added, parsing added and test files added.

PR Checklist

  • Added changelog fragment in ./changelog/ (more information)?
  • Issue raised/referenced?

@MSiggel MSiggel requested a review from mimischi October 21, 2018 09:44
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MSiggel commented Oct 21, 2018

I added most of the stuff to use the code with LAMMPS in a crude manner. Same as in namd an issue here is that multiple files are required to run a simulation. Similiar issue will be the case when using AMBER. In light of this we should also discuss in this PR how we handle files which have to be provided i.e. whether we just assume that the user has to provide all files with the same name or not.
This would decrease reliability for those engines because the user might make mistakes.

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mimischi suggested changes Oct 21, 2018
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Do we have any log files so we can test the file parsers?

mdbenchmark/mdengines/lammps.py Outdated
continue

path = line.split()[1]
if "$" in path:
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This is all NAMD specific.

mdbenchmark/generate.py
LAMMPS_WARNING = (
"LAMMPS support is experimental."
"All input files must be in the same directory and have the same base name!"
"We hope you know what you're doing..."
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Suggested change
"We hope you know what you're doing..."

mdbenchmark/mdengines/lammps.py
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDBenchmark
# Copyright (c) 2017 Max Linke & Michael Gecht and contributors
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# Copyright (c) 2017 Max Linke & Michael Gecht and contributors
# Copyright (c) 2017-2018 The MDBenchmark development team and contributors

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MSiggel commented Oct 21, 2018

I added the analyze-files-lammps folder. There is a sample log file in folder /1.
I'll have to rerun this simulation the cluster.

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@MSiggel @mimischi