--- trunk/README 2005/04/15 22:43:26 511 +++ branches/development/README 2011/09/27 14:48:28 1651 @@ -1,67 +1,73 @@ -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 +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 + 1) Good C++ and C compilers. 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-darwin7.8.0 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. Tests - with the PATHSCALE compiler on 64-bit AMD Opteron machines - are ongoing. + Architecture CC CXX Notes + ------------------------- ---- ----- ---------------------- + ix86-pc-linux-gnu icc icpc (Intel v. 10) + i386-apple-darwin11.1.0 gcc g++ (GNU v.4.3) + i386-apple-darwin11.1.0 icc icpc (Intel v. 12) + x86_64-unknown-linux-gnu gcc g++ (Pathscale 3.2) - 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? + 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. - 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. + 3) 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 + tested them. You can get Open MPI here: http://www.open-mpi.org/ - 4) MPI is optional for the single processor version of OOPSE, - but is required if you want OOPSE to run in parallel. + 4) Other optional (but quite useful) libraries that will unlock some + features of OpenMD: - 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/ + Open Babel: http://openbabel.org + Qhull: http://www.qhull.org + FFTW: http://www.fftw.org + Doxygen: http://www.doxygen.org - 5) Assorted unix utilities (lexx, yacc) or their GNU equivalents. + 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.