FMD - a classical molecular dynamics library

1) About FMD
============

Free Molecular Dynamics (FMD) is a library for performing classical
molecular dynamics (MD) simulations on different kinds of computers,
from personal computers to computer clusters. It is written in C.

FMD is a growing project. At the moment, its features and capabilities
include:

- It can run on personal computers, workstations, clusters and
  supercomputers;
   * uses MPI for distributed-memory message-passing parallelism;
   * uses OpenMP for shared-memory parallelism.
- It provides tools for performing combined atomistic-continuum
  simulations, where MD is combined with finite-difference-based
  solvers of PDEs [1];
   * An example is simulations which use TTM-MD model (see [2,3], for
     instance).
- It utilizes "events" and event-handlers to interact with calling
  programs;
   * Events are created when something significant occurs, e.g. when
     a user-defined "timer" ticks;
   * FMD calls the event-handler set by the calling program to handle
     those events.
- It can save atomic coordinates in XYZ [4], VTF [5] and CSV [6]
  formats.
- It supports EAM, Morse, and Lennard-Jones potentials.
- It provides Berendsen thermostat.
- It provides microcanonical NVE ensemble.
- It can save "state files" for continuing simulations.

2) Installation
===============

FMD depends on

- an MPI implementation (e.g. Open MPI or MPICH)
- GNU Scientific Library
- HDF5

To install FMD on Linux, open a terminal and change the current directory
to "src". Then simply enter the following command:

$ make install

It can also be uninstalled by

$ make uninstall

3) Where to get more information
================================

There is online documentation for this version at:
https://fmd.readthedocs.io/en/0.4.0/

We welcome questions and comments! If you would like to comment or ask
any questions related to this project, write to [email protected]

Endnotes and References:

[1] Partial Differential Equations
[2] https://doi.org/10.1103/PhysRevB.68.064114
[3] https://doi.org/10.1016/j.apsusc.2020.147775
[4] https://en.wikipedia.org/wiki/XYZ_file_format
[5] https://github.com/olenz/vtfplugin/wiki/VTF-format
[6] https://en.wikipedia.org/wiki/Comma-separated_values