--- trunk/README 2006/01/17 16:16:58 873 +++ branches/development/README 2013/01/28 15:44:32 1840 @@ -1,75 +1,77 @@ -OOPSE +What is OpenMD? -OOPSE is an open-source Object-Oriented Parallel Simulation Engine. -It is primarily used to perform molecular dynamics simulations on -"strange" atom types that are not normally handled by other simulation -packages. This includes atoms with orientational degrees of freedom -(point dipoles, sticky atoms), as well as transition metals under the -Embedded Atom Method (EAM) or Sutton-Chen (SC) potentials. +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 OOPSE using two files: +Simulations are started in OpenMD using a single Molecular Dynamics (.md) +file. These files must start with the tag and must have two +sections: - 1) a C-based meta-data (.md) file, and + 1) a C-based section, and - 2) a modified XYZ format for initial coordinate and velocity information. + 2) a block for initial coordinate and velocity information. -Detailed descriptions of the structures of these two files are -available in the "doc" directory. Sample simulations are -available in the "samples" directory. +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 OOPSE: +What you need to compile and use OpenMD: - 1) Good C, C++ and Fortran95 compilers. We've built and tested OOPSE - on the following architecture & compiler combinations: + 1) A good C++ compiler. We've built and tested OpenMD on the + following architecture & compiler combinations: - Architecture CC CXX F90 Notes - ------------------------- ---- ----- ----- ---------------------- - ix86-pc-linux-gnu icc icpc ifort (Intel versions 7-9) - powerpc-apple-darwin8.4.0 gcc g++ xlf (GNU v.4 / IBM XL v. 8.1) - x86_64-unknown-linux-gnu pgcc pgCC pgf95 (Portland Group v. 6.0) - sparc-sun-solaris2.10 cc CC f95 (Sun ONE Studio 10) - - We've successfully compiled OOPSE with the Pathscale c, c++, and - Fortran95 compilers on the x86_64-unknown-linux-gnu architecture, - but a bug in the exception handling on these compilers causes - OOPSE to abort (rather than providing a useful error message) when - an error is found in the meta-data file. - - OOPSE uses features of the Fortran 95 language. The fortran - portions of our code will not compile if your compiler does not - support these particular features. Some (but not all) Fortran 90 - compilers do support these features. None of the Fortran 77 - compilers can be used to compile OOPSE. + Architecture CXX Notes + ------------------------- ---- ---------------------- + Mac OS X 10.8 (intel) c++ (Apple clang version 4.1) + Mac OS X 10.8 (intel) g++ (GNU version 4.7) + Mac OS X 10.8 (intel) icpc (Intel version 12.1) + Linux (RHEL 5.9 - x86_64) icpc (Intel version 12.1) + Linux (RHEL 5.9 - x86_64) pgCC (Portland Group version 12.3) - Compilers that are known to fail on OOPSE: g77, Gfortran, Older - Portland Group compilers (pgf77, pgf90). + OpenMD uses features in the standard template library (STL). Most + (but not all) C++ compilers support these features. - Compilers that are known to work on OOPSE: Intel's ifort, - Pathscale's pathf95, IBM's xlf95, Portland's pgf95 (version 6 or - higher), Sun's f95. There may be others that work also. + 2) CMake, a cross-platform build system which is available at + http://www.cmake.org 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. - 2) GNU make (also known as gmake). Regular make won't work. - Really. We've tried. Don't bother with regular make. - Seriously. You need GNU make. Did we mention that you - need GNU make? + 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: + http://www.open-mpi.org/ - 3) Perl. Compilation dependencies in Fortran95 are somewhat - complicated, so the build process uses a perl script called - filepp to do this job. You need perl for filepp, so you - need perl to build OOPSE. + 4) Other optional (but quite useful) libraries that will unlock some + features of OpenMD: - 4) MPI is optional for the single processor version of OOPSE, - but is required if you want OOPSE to run in parallel. + Open Babel: http://openbabel.org + Qhull: http://www.qhull.org + FFTW: http://www.fftw.org + Doxygen: http://www.doxygen.org - We like MPICH-1.2.*. Other implementations might work, but we - haven't tried. You can get MPICH here: - http://www-unix.mcs.anl.gov/mpi/mpich/ + 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. INSTRUCTIONS 1) Get, build, and test the required pieces above. - 2) ./configure (or ./configure --with-mpi=/usr/local/mpich) - 3) make - 4) make install + 2) mkdir build + 3) cd build + 4) cmake .. + 5) make + 6) sudo make install That's it.