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What is OpenMD? |
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OpenMD is an open source molecular dynamics engine which is capable of |
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efficiently simulating liquids, proteins, nanoparticles, interfaces, |
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and other complex systems using atom types with orientational degrees |
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of freedom (e.g. "sticky" atoms, point dipoles, and coarse-grained |
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assemblies). Proteins, zeolites, lipids, transition metals (bulk, flat |
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interfaces, and nanoparticles) have all been simulated using force |
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fields included with the code. OpenMD works on parallel computers |
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using the Message Passing Interface (MPI), and comes with a number of |
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analysis and utility programs that are easy to use and modify. An |
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OpenMD simulation is specified using a very simple meta-data language |
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that is easy to learn. |
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Simulations are started in OpenMD using a single Molecular Dynamics (.md) |
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file. These files must start with the <OpenMD> tag and must have two |
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sections: |
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1) a C-based <MetaData> section, and |
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2) a <Snapshot> block for initial coordinate and velocity information. |
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Detailed descriptions of the structures of these files are available |
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in the "doc" directory. Sample simulations are available in the |
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"samples" directory. |
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What you need to compile and use OpenMD: |
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1) A good C++ compiler. We've built and tested OpenMD on the |
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following architecture & compiler combinations: |
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Architecture CXX Notes |
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------------------------- ---- ---------------------- |
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Mac OS X 10.10 (intel) c++ (Apple LLVM version 6.0, Open MPI 1.7.5) |
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Mac OS X 10.10 (intel) g++ (GNU version 4.8.3) |
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Mac OS X 10.10 (intel) icpc (Intel version 14.0.2) |
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Linux (Ubuntu 13 – x86_64) g++ (GNU version 4.8.1, Open MPI 1.4.5) |
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Linux (RHEL 6.6 - x86_64) icpc (Intel version 14.0, Open MPI 1.6.5) |
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Linux (RHEL 6.6 - x86_64) pgCC (Portland Group version 14.6) |
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OpenMD uses features in the standard template library (STL). Most |
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(but not all) C++ compilers support these features. |
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2) CMake, a cross-platform build system which is available at |
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http://www.cmake.org Most Linux and some Unix distributions |
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provide CMake as a standard package. If not, please download it, |
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and make sure you get a recent version. Mac OS X users can either |
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download the CMake installer or install it from the command line |
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using macports. |
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3) An implementation of MPI-2 is optional for the single processor |
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version of OpenMD, but is required if you want OpenMD to run in |
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parallel. We like OpenMPI. Other implementations of MPI-2 might |
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work, but we haven't tried. You can get Open MPI here: |
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http://www.open-mpi.org/ |
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4) Other optional (but quite useful) libraries that will unlock some |
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features of OpenMD: |
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Open Babel: http://openbabel.org |
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Qhull: http://www.qhull.org |
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FFTW: http://www.fftw.org |
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Doxygen: http://www.doxygen.org |
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5) Some of the utility scripts depend on Python and Perl. These |
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interpreters are common installations on most flavors of Unix and |
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Mac OS X. |
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INSTRUCTIONS |
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1) Get, build, and test the required pieces above. |
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2) mkdir build |
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3) cd build |
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4) cmake .. |
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5) make |
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6) umask 0022; sudo make install |
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That's it. |
