| 7 |
|
(point dipoles, sticky atoms), as well as transition metals under the |
| 8 |
|
Embedded Atom Method (EAM). |
| 9 |
|
|
| 10 |
< |
Input files are handled using the (included) Bizarre Atom Simulation |
| 11 |
< |
Syntax (BASS) library. |
| 10 |
> |
Simulations are started in OOPSE using two files: |
| 11 |
|
|
| 12 |
+ |
1) a C-based meta-data (.md) file, and |
| 13 |
+ |
|
| 14 |
+ |
2) a modified XYZ format for initial coordinate and velocity information. |
| 15 |
+ |
|
| 16 |
+ |
Detailed descriptions of the structures of these two files are |
| 17 |
+ |
available in the "doc" directory. Sample simulations are |
| 18 |
+ |
available in the "samples" directory. |
| 19 |
+ |
|
| 20 |
|
What you need to compile and use OOPSE: |
| 21 |
|
|
| 22 |
|
1) Good C, C++ and Fortran95 compilers. We've built and tested OOPSE |
| 23 |
< |
using version 8 of the Intel compilers (ifort, icpc and icc) on Linux |
| 17 |
< |
machines. We also routinely build and test under Mac OS X using the |
| 18 |
< |
IBM compilers (xlf95, vac++). OOPSE should build with g++ and gcc, |
| 19 |
< |
but you'll still need a good fortran *95* compiler. Fortran77 and |
| 20 |
< |
Fortran90 are *not* sufficient to compile OOPSE. |
| 23 |
> |
on the following architecture & compiler combinations: |
| 24 |
|
|
| 25 |
< |
2) MPI. We like MPICH. Other implementations might work, but we |
| 25 |
> |
Architecture CC CXX F90 Notes |
| 26 |
> |
------------------------- ---- ----- ----- ---------------------- |
| 27 |
> |
ix86-pc-linux-gnu icc icpc ifort (Intel versions 7 & 8) |
| 28 |
> |
powerpc-apple-darwin7.4.0 xlc xlc++ xlf (IBM XL v. 6.0/8.1) |
| 29 |
> |
mips-sgi-irix6.5 cc CC f90 (MIPSpro 7.4) |
| 30 |
> |
sparc-sun-solaris2.8 cc CC f95 (Forte Developer 7) |
| 31 |
> |
|
| 32 |
> |
We've successfully compiled OOPSE with gcc and g++, as well as |
| 33 |
> |
pgcc and pgCC in linux environments. However, you will need to |
| 34 |
> |
use a Fortran *95* compler for the fortran side of OOPSE, and |
| 35 |
> |
pgf90 does not implement the required portions of the f95 |
| 36 |
> |
language. Fortran77 and Fortran90 (i.e. g77 and pgf90) are *not* |
| 37 |
> |
sufficient to compile the fortran portions of OOPSE. |
| 38 |
> |
|
| 39 |
> |
2) The Scalable Parallel Random Number Generators Library (SPRNG). You |
| 40 |
> |
can obtain SPRNG here: http://sprng.cs.fsu.edu/ |
| 41 |
> |
SPRNG is a *requirement* for compiling OOPSE. |
| 42 |
> |
|
| 43 |
> |
3) MPI. We like MPICH. Other implementations might work, but we |
| 44 |
|
haven't tried. You can get MPICH here: |
| 45 |
|
http://www-unix.mcs.anl.gov/mpi/mpich/ |
| 46 |
+ |
MPI is only required if you want a parallel version of OOPSE. |
| 47 |
|
|
| 48 |
< |
3) The Scalable Parallel Random Number Generators Library (SPRNG). You |
| 49 |
< |
can obtain SPRNG here: |
| 50 |
< |
http://archive.ncsa.uiuc.edu/Apps/CMP/RNG/RNG-home.html |
| 48 |
> |
4) Assorted unix utilities (lexx, yacc, make) or their GNU |
| 49 |
> |
equivalents. The Gnu version of make is pretty much a requirement on |
| 50 |
> |
SGI machines. |
| 51 |
> |
|
| 52 |
|
|
| 30 |
– |
4) Assorted unix utilities (lexx, yacc, make) or their GNU equivalents. |
| 31 |
– |
|
| 53 |
|
INSTRUCTIONS |
| 54 |
|
|
| 55 |
|
1) Get, build, and test the required pieces above. |
