[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) Good C++ and C compilers.  We've built and tested OpenMD
    on the following architecture & compiler combinations:

    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?

 3) Perl.

 4) 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/

INSTRUCTIONS

 1) Get, build, and test the required pieces above.
 2) ./configure  
 3) make
 4) make install

That's it.
Revision:	1632
Committed:	Wed Sep 14 21:44:08 2011 UTC (13 years, 7 months ago) by gezelter
File size:	2299 byte(s)
Log Message:	cleaning up configure script & readme
#	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	1390	Simulations are started in OpenMD using a single Molecular Dynamics (.md)
16			file. These files must start with the <OpenMD> tag and must
17	gezelter	1055	have two 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	1055	Detailed descriptions of the structures of these files are
24	gezelter	2	available in the "doc" directory. Sample simulations are
25			available in the "samples" directory.
26
27	gezelter	1390	What you need to compile and use OpenMD:
28	gezelter	2
29	gezelter	1632	1) Good C++ and C compilers. We've built and tested OpenMD
30	gezelter	2	on the following architecture & compiler combinations:
31
32	gezelter	1632	Architecture CC CXX Notes
33			------------------------- ---- ----- ----------------------
34			ix86-pc-linux-gnu icc icpc (Intel v. 10)
35			i386-apple-darwin11.1.0 gcc g++ (GNU v.4.3)
36			i386-apple-darwin11.1.0 icc icpc (Intel v. 12)
37			x86_64-unknown-linux-gnu gcc g++ (Pathscale 3.2)
38	gezelter	1390
39	gezelter	511	2) GNU make (also known as gmake). Regular make won't work.
40			Really. We've tried. Don't bother with regular make.
41			Seriously. You need GNU make. Did we mention that you
42			need GNU make?
43	gezelter	2
44	gezelter	1632	3) Perl.
45	gezelter	508
46	gezelter	1390	4) MPI-2 is optional for the single processor version of OpenMD, but
47			is required if you want OpenMD to run in parallel. We like
48	gezelter	1632	OpenMPI. Other implementations of MPI-2 might work, but we haven't
49	gezelter	1390	tried. You can get Open MPI here: http://www.open-mpi.org/
50	gezelter	508
51	gezelter	2	INSTRUCTIONS
52
53			1) Get, build, and test the required pieces above.
54	gezelter	1390	2) ./configure
55	gezelter	2	3) make
56			4) make install
57
58	gezelter	508	That's it.