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OOPSE |
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What is OpenMD? |
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OOPSE is an open-source Object-Oriented Parallel Simulation Engine. |
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It is primarily used to perform molecular dynamics simulations on |
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"strange" atom types that are not normally handled by other simulation |
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packages. This includes atoms with orientational degrees of freedom |
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(point dipoles, sticky atoms), as well as transition metals under the |
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Embedded Atom Method (EAM) or Sutton-Chen (SC) potentials. |
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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 OOPSE using two files: |
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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 meta-data (.md) file, and |
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1) a C-based <MetaData> section, and |
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2) a modified XYZ format for initial coordinate and velocity information. |
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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 two files are |
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available in the "doc" directory. Sample simulations are |
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available in the "samples" directory. |
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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 OOPSE: |
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What you need to compile and use OpenMD: |
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1) Good C, C++ and Fortran95 compilers. We've built and tested OOPSE |
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on the following architecture & compiler combinations: |
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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 CC CXX F90 Notes |
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------------------------- ---- ----- ----- ---------------------- |
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ix86-pc-linux-gnu icc icpc ifort (Intel versions 7-9) |
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powerpc-apple-darwin8.4.0 gcc g++ xlf (GNU v.4 / IBM XL v. 8.1) |
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x86_64-unknown-linux-gnu pgcc pgCC pgf95 (Portland Group v. 6.0) |
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sparc-sun-solaris2.10 cc CC f95 (Sun ONE Studio 10) |
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We've successfully compiled OOPSE with the Pathscale c, c++, and |
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Fortran95 compilers on the x86_64-unknown-linux-gnu architecture, |
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but a bug in the exception handling on these compilers causes |
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OOPSE to abort (rather than providing a useful error message) when |
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an error is found in the meta-data file. |
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OOPSE uses features of the Fortran 95 language. The fortran |
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portions of our code will not compile if your compiler does not |
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support these particular features. Some (but not all) Fortran 90 |
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compilers do support these features. None of the Fortran 77 |
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compilers can be used to compile OOPSE. |
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Architecture CXX Notes |
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------------------------- ---- ---------------------- |
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Mac OS X 10.8 (intel) c++ (Apple clang version 4.1) |
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Mac OS X 10.8 (intel) g++ (GNU version 4.7) |
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Mac OS X 10.8 (intel) icpc (Intel version 12.1) |
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Linux (RHEL 5.9 - x86_64) icpc (Intel version 12.1) |
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Linux (RHEL 5.9 - x86_64) pgCC (Portland Group version 12.3) |
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Compilers that are known to fail on OOPSE: g77, Gfortran, Older |
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Portland Group compilers (pgf77, pgf90). |
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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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Compilers that are known to work on OOPSE: Intel's ifort, |
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Pathscale's pathf95, IBM's xlf95, Portland's pgf95 (version 6 or |
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higher), Sun's f95. There may be others that work also. |
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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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2) GNU make (also known as gmake). Regular make won't work. |
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Really. We've tried. Don't bother with regular make. |
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Seriously. You need GNU make. Did we mention that you |
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need GNU make? |
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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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3) Perl. Compilation dependencies in Fortran95 are somewhat |
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complicated, so the build process uses a perl script called |
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filepp to do this job. You need perl for filepp, so you |
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need perl to build OOPSE. |
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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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4) MPI is optional for the single processor version of OOPSE, |
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but is required if you want OOPSE to run in parallel. |
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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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We like MPICH-1.2.*. Other implementations might work, but we |
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haven't tried. You can get MPICH here: |
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http://www-unix.mcs.anl.gov/mpi/mpich/ |
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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) ./configure (or ./configure --with-mpi=/usr/local/mpich) |
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3) make |
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4) make install |
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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) sudo make install |
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That's it. |
