[ViewVC] Annotation of: OpenMD/branches/development/README

What is OpenMD?

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 OpenMD using a single Molecular Dynamics (.md) 
file.  These files must start with the <OpenMD> tag and must have two 
sections:

  1) a C-based <MetaData> section, and 

  2) a <Snapshot> block for initial coordinate and velocity information.

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 OpenMD:

 1) A good C++ compiler.  We've built and tested OpenMD on the
    following architecture & compiler combinations:

    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)

    OpenMD uses features in the standard template library (STL). Most
    (but not all) C++ compilers support these features.

 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) 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) mkdir build
 3) cd build
 4) cmake ..
 5) make
 6) sudo make install

That's it.
Revision:	1840
Committed:	Mon Jan 28 15:44:32 2013 UTC (12 years, 3 months ago) by gezelter
File size:	3075 byte(s)
Log Message:	Merging trunk changes back to development branch
#	User	Rev	Content
1	gezelter	1394	What is OpenMD?
2	gezelter	2
3	gezelter	1390	OpenMD is an open source molecular dynamics engine which is capable of
4			efficiently simulating liquids, proteins, nanoparticles, interfaces,
5			and other complex systems using atom types with orientational degrees
6			of freedom (e.g. "sticky" atoms, point dipoles, and coarse-grained
7			assemblies). Proteins, zeolites, lipids, transition metals (bulk, flat
8			interfaces, and nanoparticles) have all been simulated using force
9			fields included with the code. OpenMD works on parallel computers
10			using the Message Passing Interface (MPI), and comes with a number of
11			analysis and utility programs that are easy to use and modify. An
12			OpenMD simulation is specified using a very simple meta-data language
13			that is easy to learn.
14	gezelter	2
15	gezelter	1840	Simulations are started in OpenMD using a single Molecular Dynamics (.md)
16			file. These files must start with the <OpenMD> tag and must have two
17			sections:
18	gezelter	2
19	gezelter	1055	1) a C-based <MetaData> section, and
20	gezelter	2
21	gezelter	1055	2) a <Snapshot> block for initial coordinate and velocity information.
22	gezelter	2
23	gezelter	1840	Detailed descriptions of the structures of these files are available
24			in the "doc" directory. Sample simulations are available in the
25			"samples" directory.
26	gezelter	2
27	gezelter	1390	What you need to compile and use OpenMD:
28	gezelter	2
29	gezelter	1840	1) A good C++ compiler. We've built and tested OpenMD on the
30			following architecture & compiler combinations:
31	gezelter	2
32	gezelter	1840	Architecture CXX Notes
33			------------------------- ---- ----------------------
34			Mac OS X 10.8 (intel) c++ (Apple clang version 4.1)
35			Mac OS X 10.8 (intel) g++ (GNU version 4.7)
36			Mac OS X 10.8 (intel) icpc (Intel version 12.1)
37			Linux (RHEL 5.9 - x86_64) icpc (Intel version 12.1)
38			Linux (RHEL 5.9 - x86_64) pgCC (Portland Group version 12.3)
39	gezelter	1390
40	gezelter	1840	OpenMD uses features in the standard template library (STL). Most
41			(but not all) C++ compilers support these features.
42
43	gezelter	1639	2) CMake, a cross-platform build system which is available at
44			http://www.cmake.org Most Linux and some Unix distributions
45			provide CMake as a standard package. If not, please download it,
46			and make sure you get a recent version. Mac OS X users can either
47			download the CMake installer or install it from the command line
48			using macports.
49	gezelter	2
50	gezelter	1840	3) An implementation of MPI-2 is optional for the single processor
51			version of OpenMD, but is required if you want OpenMD to run in
52			parallel. We like OpenMPI. Other implementations of MPI-2 might
53			work, but we haven't tried. You can get Open MPI here:
54			http://www.open-mpi.org/
55	gezelter	508
56	gezelter	1639	4) Other optional (but quite useful) libraries that will unlock some
57			features of OpenMD:
58
59			Open Babel: http://openbabel.org
60			Qhull: http://www.qhull.org
61			FFTW: http://www.fftw.org
62	gezelter	1651	Doxygen: http://www.doxygen.org
63	gezelter	1639
64			5) Some of the utility scripts depend on Python and Perl. These
65			interpreters are common installations on most flavors of Unix and
66			Mac OS X.
67
68	gezelter	2	INSTRUCTIONS
69
70			1) Get, build, and test the required pieces above.
71	gezelter	1651	2) mkdir build
72			3) cd build
73			4) cmake ..
74			5) make
75			6) sudo make install
76	gezelter	2
77	gezelter	508	That's it.