Dear all
Despite wondering computational ability of LAMMPS, I’ve faced a dilemma how to analysis my simulation outputs. That is, other simulators such as GROMACS provide convenient facilities for statistical analysis of results. For example, RDF, density, coordination number and so on.
Are there similar options or alternative programmes for LAMMPS?
Bests
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Dear all
Despite wondering computational ability of LAMMPS, I've faced a
dilemma how to analysis my simulation outputs.
i think that is more a dilemma of not searching the web and reading the
manual enough.
That is, other simulators such as GROMACS provide convenient facilities
for statistical analysis of results. For example, RDF, density,
coordination number and so on.
many of these features you can do in LAMMPS via computes and fixes
*during* the simulation (and often in parallel). the manual has many
examples in the HowTo sections and in the input examples folders.
apart from that, you can also use the tools bundled with other MD codes,
e.g. gromacs or standalone tools like https://www.mdanalysis.org/,
pizza.sandia.gov and others listed here:
http://lammps.sandia.gov/prepost.html
*Are there similar options or alternative programmes for LAMMPS?*
many. LAMMPS is very flexible in how it produces output and thus can
produce output compatible with all kinds of tools or output files that are
easy to parse with scripts of your own.
axel.
Typically LAMMPS has these analysis tasks as computed properties, and they can be computed while the simulation is running, or on an existing trajectory, using the rerun command:
http://lammps.sandia.gov/doc/rerun.html
A Google search for “lammps compute rdf” should give you what you need for the RDF or for other specific properties. It’ mostly all there, in the big but browseable and searchable manual.
Giacomo