| 5 |
|
"strange" atom types that are not normally handled by other simulation |
| 6 |
|
packages. This includes atoms with orientational degrees of freedom |
| 7 |
|
(point dipoles, sticky atoms), as well as transition metals under the |
| 8 |
< |
Embedded Atom Method (EAM). |
| 8 |
> |
Embedded Atom Method (EAM) or Sutton-Chen (SC) potentials. |
| 9 |
|
|
| 10 |
< |
Simulations are started in OOPSE using two files: |
| 10 |
> |
Simulations are started in OOPSE using a single Molecular Dynamics (.md) |
| 11 |
> |
file. These files must start with the <OOPSE> tag and must |
| 12 |
> |
have two sections: |
| 13 |
|
|
| 14 |
< |
1) a C-based meta-data (.md) file, and |
| 14 |
> |
1) a C-based <MetaData> section, and |
| 15 |
|
|
| 16 |
< |
2) a modified XYZ format for initial coordinate and velocity information. |
| 16 |
> |
2) a <Snapshot> block for initial coordinate and velocity information. |
| 17 |
|
|
| 18 |
< |
Detailed descriptions of the structures of these two files are |
| 18 |
> |
Detailed descriptions of the structures of these files are |
| 19 |
|
available in the "doc" directory. Sample simulations are |
| 20 |
|
available in the "samples" directory. |
| 21 |
|
|
| 24 |
|
1) Good C, C++ and Fortran95 compilers. We've built and tested OOPSE |
| 25 |
|
on the following architecture & compiler combinations: |
| 26 |
|
|
| 27 |
< |
Architecture CC CXX F90 Notes |
| 28 |
< |
------------------------- ---- ----- ----- ---------------------- |
| 29 |
< |
ix86-pc-linux-gnu icc icpc ifort (Intel versions 7 & 8) |
| 30 |
< |
powerpc-apple-darwin7.4.0 xlc xlc++ xlf (IBM XL v. 6.0/8.1) |
| 31 |
< |
mips-sgi-irix6.5 cc CC f90 (MIPSpro 7.4) |
| 32 |
< |
sparc-sun-solaris2.8 cc CC f95 (Forte Developer 7) |
| 27 |
> |
Architecture CC CXX F90 Notes |
| 28 |
> |
------------------------- ---- ----- ----- ---------------------- |
| 29 |
> |
ix86-pc-linux-gnu icc icpc ifort (Intel versions 7-9) |
| 30 |
> |
i386-apple-darwin8.7.1 icc icpc ifort (Intel version 9.1) |
| 31 |
> |
powerpc-apple-darwin8.7.0 gcc g++ xlf95 (GNU v.4 / IBM XL v. 8.1) |
| 32 |
> |
x86_64-unknown-linux-gnu gcc g++ pathf95 (GNU v.4 / Pathscale 2.5) |
| 33 |
> |
sparc-sun-solaris2.10 cc CC f95 (Sun ONE Studio 10) |
| 34 |
|
|
| 35 |
< |
We've successfully compiled OOPSE with gcc and g++, as well as |
| 36 |
< |
pgcc and pgCC in linux environments. However, you will need to |
| 37 |
< |
use a Fortran *95* compler for the fortran side of OOPSE, and |
| 38 |
< |
pgf90 does not implement the required portions of the f95 |
| 39 |
< |
language. Fortran77 and Fortran90 (i.e. g77 and pgf90) are *not* |
| 40 |
< |
sufficient to compile the fortran portions of OOPSE. |
| 35 |
> |
We've also successfully compiled OOPSE with the Portland Group c, c++, |
| 36 |
> |
and Fortran95 compilers on the x86_64-unknown-linux-gnu architecture. |
| 37 |
> |
|
| 38 |
> |
OOPSE uses features of the Fortran 95 language. The fortran |
| 39 |
> |
portions of our code will not compile if your compiler does not |
| 40 |
> |
support these particular features. Some (but not all) Fortran 90 |
| 41 |
> |
compilers do support these features. None of the Fortran 77 |
| 42 |
> |
compilers can be used to compile OOPSE. |
| 43 |
|
|
| 44 |
< |
2) The Scalable Parallel Random Number Generators Library (SPRNG). You |
| 45 |
< |
can obtain SPRNG here: http://sprng.cs.fsu.edu/ |
| 41 |
< |
SPRNG is a *requirement* for compiling OOPSE. |
| 44 |
> |
Fortran compilers that are known to fail on OOPSE: g77, Gfortran, |
| 45 |
> |
Older Portland Group compilers (pgf77, pgf90). |
| 46 |
|
|
| 47 |
< |
3) MPI. We like MPICH. Other implementations might work, but we |
| 48 |
< |
haven't tried. You can get MPICH here: |
| 49 |
< |
http://www-unix.mcs.anl.gov/mpi/mpich/ |
| 46 |
< |
MPI is only required if you want a parallel version of OOPSE. |
| 47 |
> |
Fortran compilers that are known to work on OOPSE: Intel's ifort, |
| 48 |
> |
Pathscale's pathf95, IBM's xlf95, Portland's pgf95 (version 6 or |
| 49 |
> |
higher), Sun's f95. There may be others that work also. |
| 50 |
|
|
| 51 |
< |
4) Assorted unix utilities (lexx, yacc, make) or their GNU |
| 52 |
< |
equivalents. The Gnu version of make is pretty much a requirement on |
| 53 |
< |
SGI machines. |
| 54 |
< |
|
| 51 |
> |
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 |
|
|
| 56 |
+ |
3) Perl. Compilation dependencies in Fortran95 are somewhat |
| 57 |
+ |
complicated, so the build process uses a perl script called |
| 58 |
+ |
filepp to do this job. You need perl for filepp, so you |
| 59 |
+ |
need perl to build OOPSE. |
| 60 |
+ |
|
| 61 |
+ |
4) MPI is optional for the single processor version of OOPSE, |
| 62 |
+ |
but is required if you want OOPSE to run in parallel. |
| 63 |
+ |
|
| 64 |
+ |
We like Open MPI. Other implementations might work, but we |
| 65 |
+ |
haven't tried. You can get Open MPI here: http://www.open-mpi.org/ |
| 66 |
+ |
|
| 67 |
|
INSTRUCTIONS |
| 68 |
|
|
| 69 |
|
1) Get, build, and test the required pieces above. |
| 70 |
< |
2) ./configure |
| 70 |
> |
2) ./configure (or ./configure --with-mpi=/usr/local/openmpi) |
| 71 |
|
3) make |
| 72 |
|
4) make install |
| 73 |
|
|
| 74 |
< |
That's it. Documentation will be forthcoming after the paper is |
| 61 |
< |
published. |
| 62 |
< |
|
| 74 |
> |
That's it. |
