Molecular Dynamics in the Open
C++ Other
Latest commit 68f81dc Feb 21, 2017 @Patrick-Louden Patrick-Louden Seg faults when calling either the densityfield or vectorfield, I bel…
…ieve it has something to do with a (new) instantiation..


What is OpenMD?

OpenMD is an open source molecular dynamics engine which is capable of
efficiently simulating liquids, proteins, nanoparticles, interfaces,
and other complex systems using atom types with orientational degrees
of freedom (e.g. "sticky" atoms, point dipoles, and coarse-grained
assemblies). Proteins, zeolites, lipids, transition metals (bulk, flat
interfaces, and nanoparticles) have all been simulated using force
fields included with the code. OpenMD works on parallel computers
using the Message Passing Interface (MPI), and comes with a number of
analysis and utility programs that are easy to use and modify. An
OpenMD simulation is specified using a very simple meta-data language
that is easy to learn.

Simulations are started in OpenMD using a single Molecular Dynamics (.omd)
file.  These files must start with the <OpenMD> tag and must have two sections:

  1) a C-based <MetaData> section, and 

  2) a <Snapshot> block for initial coordinate and velocity information.

Detailed descriptions of the structures of these files are available
in the "doc" directory.  Sample simulations are available in the
"samples" directory.

What you need to compile and use OpenMD:

 1) A good C++ compiler.  We've built and tested OpenMD on the
    following architecture & compiler combinations:

  Architecture                  CXX  Notes
  -------------------------     ---- ----------------------
  macOS 10.12 (intel)           c++  (Apple LLVM version 8.0.0, Open MPI 1.10.3)
  macOS 10.12 (intel)           g++  (GNU version 6.2.0)
  Linux (Ubuntu 16.10 – x86_64) g++  (GNU version 6.2.0, Open MPI 1.10.3)
  Linux (RHEL 7.3 - x86_64)     icpc (Intel version 15.0, Open MPI 1.10.2)

    OpenMD uses features in the standard template library (STL). Most
    (but not all) C++ compilers support these features.

 2) CMake, a cross-platform build system which is available at    Most Linux and some Unix distributions
    provide CMake as a standard package. If not, please download it,
    and make sure you get a recent version. Mac OS X users can either
    download the CMake installer or install it from the command line
    using macports.

 3) An implementation of MPI-2 is optional for the single processor
    version of OpenMD, but is required if you want OpenMD to run in
    parallel. We like OpenMPI. Other implementations of MPI-2 might
    work, but we haven't tried.  You can get Open MPI here:

 4) Other optional (but quite useful) libraries that will unlock some
    features of OpenMD:

      Open Babel:

 5) Some of the utility scripts depend on Python and Perl.  These
    interpreters are common installations on most flavors of Unix and
    Mac OS X.


 1) Get, build, and test the required pieces above.
 2) mkdir build
 3) cd build
 4) cmake ..
 5) make
 6) umask 0022; sudo make install

That's it.