| 12 |
|
OpenMD simulation is specified using a very simple meta-data language |
| 13 |
|
that is easy to learn. |
| 14 |
|
|
| 15 |
< |
Simulations are started in OpenMD using a single Molecular Dynamics (.md) |
| 16 |
< |
file. These files must start with the <OpenMD> tag and must |
| 17 |
< |
have two sections: |
| 15 |
> |
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 |
|
|
| 19 |
|
1) a C-based <MetaData> section, and |
| 20 |
|
|
| 21 |
|
2) a <Snapshot> block for initial coordinate and velocity information. |
| 22 |
|
|
| 23 |
< |
Detailed descriptions of the structures of these files are |
| 24 |
< |
available in the "doc" directory. Sample simulations are |
| 25 |
< |
available in the "samples" directory. |
| 23 |
> |
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 |
|
|
| 27 |
|
What you need to compile and use OpenMD: |
| 28 |
|
|
| 29 |
< |
1) Good C++ and C compilers. We've built and tested OpenMD |
| 30 |
< |
on the following architecture & compiler combinations: |
| 29 |
> |
1) A good C++ compiler. We've built and tested OpenMD on the |
| 30 |
> |
following architecture & compiler combinations: |
| 31 |
|
|
| 32 |
< |
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) |
| 32 |
> |
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 |
|
|
| 40 |
+ |
OpenMD uses features in the standard template library (STL). Most |
| 41 |
+ |
(but not all) C++ compilers support these features. |
| 42 |
+ |
|
| 43 |
|
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, |
| 47 |
|
download the CMake installer or install it from the command line |
| 48 |
|
using macports. |
| 49 |
|
|
| 50 |
< |
3) MPI-2 is optional for the single processor version of OpenMD, but |
| 51 |
< |
is required if you want OpenMD to run in parallel. We like |
| 52 |
< |
OpenMPI. Other implementations of MPI-2 might work, but we haven't |
| 53 |
< |
tested them. You can get Open MPI here: http://www.open-mpi.org/ |
| 50 |
> |
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 |
|
|
| 56 |
|
4) Other optional (but quite useful) libraries that will unlock some |
| 57 |
|
features of OpenMD: |
| 65 |
|
interpreters are common installations on most flavors of Unix and |
| 66 |
|
Mac OS X. |
| 67 |
|
|
| 63 |
– |
|
| 68 |
|
INSTRUCTIONS |
| 69 |
|
|
| 70 |
|
1) Get, build, and test the required pieces above. |
