[ViewVC] Annotation of: OpenMD/trunk/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 10.9 (intel)       c++    (Apple LLVM version 5.0)
    Mac OS X 10.9 (intel)       g++    (GNU version 4.8.1)
    Mac OS X 10.9 (intel)       icpc   (Intel version 14.0)
    Linux (Ubuntu 13 – x86_64)        g++    (GNU version 4.7.3)
    Linux (RHEL 6.4 - x86_64)   icpc   (Intel version 14.0)
    Linux (RHEL 6.4 - 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:	1947
Committed:	Wed Nov 13 22:03:48 2013 UTC (11 years, 7 months ago) by gezelter
File size:	3136 byte(s)
Log Message:	Updated in prep for 2.1 release
#	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	1837	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	1837	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	1837	1) A good C++ compiler. We've built and tested OpenMD on the
30			following architecture & compiler combinations:
31	gezelter	2
32	gezelter	1837	Architecture CXX Notes
33			------------------------- ---- ----------------------
34	gezelter	1947	Mac OS X 10.9 (intel) c++ (Apple LLVM version 5.0)
35			Mac OS X 10.9 (intel) g++ (GNU version 4.8.1)
36			Mac OS X 10.9 (intel) icpc (Intel version 14.0)
37			Linux (Ubuntu 13 – x86_64) g++ (GNU version 4.7.3)
38			Linux (RHEL 6.4 - x86_64) icpc (Intel version 14.0)
39			Linux (RHEL 6.4 - x86_64) pgCC (Portland Group version 12.3)
40	gezelter	1390
41	gezelter	1837	OpenMD uses features in the standard template library (STL). Most
42			(but not all) C++ compilers support these features.
43
44	gezelter	1782	2) CMake, a cross-platform build system which is available at
45			http://www.cmake.org Most Linux and some Unix distributions
46			provide CMake as a standard package. If not, please download it,
47			and make sure you get a recent version. Mac OS X users can either
48			download the CMake installer or install it from the command line
49			using macports.
50	gezelter	2
51	gezelter	1837	3) An implementation of MPI-2 is optional for the single processor
52			version of OpenMD, but is required if you want OpenMD to run in
53			parallel. We like OpenMPI. Other implementations of MPI-2 might
54			work, but we haven't tried. You can get Open MPI here:
55			http://www.open-mpi.org/
56	gezelter	873
57	gezelter	1782	4) Other optional (but quite useful) libraries that will unlock some
58			features of OpenMD:
59	gezelter	873
60	gezelter	1782	Open Babel: http://openbabel.org
61			Qhull: http://www.qhull.org
62			FFTW: http://www.fftw.org
63			Doxygen: http://www.doxygen.org
64	gezelter	2
65	gezelter	1782	5) Some of the utility scripts depend on Python and Perl. These
66			interpreters are common installations on most flavors of Unix and
67			Mac OS X.
68	gezelter	508
69	gezelter	2	INSTRUCTIONS
70
71			1) Get, build, and test the required pieces above.
72	gezelter	1782	2) mkdir build
73			3) cd build
74			4) cmake ..
75			5) make
76			6) sudo make install
77	gezelter	2
78	gezelter	508	That's it.