--- trunk/README 2004/09/24 04:16:43 2 +++ branches/development/README 2013/01/28 15:44:32 1840 @@ -1,62 +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). +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 & 8) - powerpc-apple-darwin7.4.0 xlc xlc++ xlf (IBM XL v. 6.0/8.1) - mips-sgi-irix6.5 cc CC f90 (MIPSpro 7.4) - sparc-sun-solaris2.8 cc CC f95 (Forte Developer 7) - - We've successfully compiled OOPSE with gcc and g++, as well as - pgcc and pgCC in linux environments. However, you will need to - use a Fortran *95* compler for the fortran side of OOPSE, and - pgf90 does not implement the required portions of the f95 - language. Fortran77 and Fortran90 (i.e. g77 and pgf90) are *not* - sufficient to compile the fortran portions of 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) - 2) The Scalable Parallel Random Number Generators Library (SPRNG). You - can obtain SPRNG here: http://sprng.cs.fsu.edu/ - SPRNG is a *requirement* for compiling OOPSE. + OpenMD uses features in the standard template library (STL). Most + (but not all) C++ compilers support these features. - 3) MPI. We like MPICH. Other implementations might work, but we - haven't tried. You can get MPICH here: - http://www-unix.mcs.anl.gov/mpi/mpich/ - MPI is only required if you want a parallel version of OOPSE. + 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. - 4) Assorted unix utilities (lexx, yacc, make) or their GNU - equivalents. The Gnu version of make is pretty much a requirement on - SGI machines. - + 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/ + 4) Other optional (but quite useful) libraries that will unlock some + features of OpenMD: + + Open Babel: http://openbabel.org + Qhull: http://www.qhull.org + FFTW: http://www.fftw.org + Doxygen: http://www.doxygen.org + + 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 - 3) make - 4) make install + 2) mkdir build + 3) cd build + 4) cmake .. + 5) make + 6) sudo make install -That's it. Documentation will be forthcoming after the paper is -published. - +That's it.