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

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, C++ and Fortran95 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 v. 10)
    i686-apple-darwin10.0.0     gcc    g++     gfortran (GNU v.4.3)
    i686-apple-darwin10.0.0     icc    icpc    ifort    (Intel v. 11)
    x86_64-unknown-linux-gnu    gcc    g++     pathf95  (Pathscale 3.2)

    OpenMD uses features of the Fortran 95 language. The fortran
    portions of our code will not compile if your compiler does not
    support these particular features. Some (but not all) Fortran 90
    compilers do support these features.

    Compilers that are known to fail on OpenMD: g77, older versions of
    gfortran, older Portland Group compilers (pgf77, pgf90).

    Compilers that are known to work on OpenMD: Intel's ifort,
    Pathscale's pathf95, IBM's xlf95, Portland-F�s pgf95 (version 6 or-A
    higher), Sun's f95. There may be others that work also.

 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.  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 OpenMD.

 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-F�t-A
    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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 11 months ago) by gezelter
Original Path:	*trunk/README*
File size:	3136 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	gezelter	1390	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	1390	1) Good C, C++ and Fortran95 compilers. We've built and tested OpenMD
30	gezelter	2	on the following architecture & compiler combinations:
31
32	gezelter	1055	Architecture CC CXX F90 Notes
33			------------------------- ---- ----- ----- ----------------------
34	gezelter	1390	ix86-pc-linux-gnu icc icpc ifort (Intel v. 10)
35			i686-apple-darwin10.0.0 gcc g++ gfortran (GNU v.4.3)
36			i686-apple-darwin10.0.0 icc icpc ifort (Intel v. 11)
37			x86_64-unknown-linux-gnu gcc g++ pathf95 (Pathscale 3.2)
38
39			OpenMD uses features of the Fortran 95 language. The fortran
40	gezelter	873	portions of our code will not compile if your compiler does not
41			support these particular features. Some (but not all) Fortran 90
42	gezelter	1390	compilers do support these features.
43	gezelter	2
44	gezelter	1390	Compilers that are known to fail on OpenMD: g77, older versions of
45			gfortran, older Portland Group compilers (pgf77, pgf90).
46	gezelter	873
47	gezelter	1390	Compilers that are known to work on OpenMD: Intel's ifort,
48			Pathscale's pathf95, IBM's xlf95, Portland-F�s pgf95 (version 6 or-A
49	gezelter	873	higher), Sun's f95. There may be others that work also.
50
51	gezelter	511	2) GNU make (also known as gmake). Regular make won't work.
52			Really. We've tried. Don't bother with regular make.
53			Seriously. You need GNU make. Did we mention that you
54			need GNU make?
55	gezelter	2
56	gezelter	508	3) Perl. Compilation dependencies in Fortran95 are somewhat
57			complicated, so the build process uses a perl script called
58	gezelter	511	filepp to do this job. You need perl for filepp, so you
59	gezelter	1390	need perl to build OpenMD.
60	gezelter	508
61	gezelter	1390	4) MPI-2 is optional for the single processor version of OpenMD, but
62			is required if you want OpenMD to run in parallel. We like
63			OpenMPI. Other implementations of MPI-2 might work, but we haven-F�t-A
64			tried. You can get Open MPI here: http://www.open-mpi.org/
65	gezelter	508
66	gezelter	2	INSTRUCTIONS
67
68			1) Get, build, and test the required pieces above.
69	gezelter	1390	2) ./configure
70	gezelter	2	3) make
71			4) make install
72
73	gezelter	508	That's it.