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) |
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> |
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 |
|
|
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|
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-darwin7.8.0 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. Tests |
41 |
< |
with the PATHSCALE compiler on 64-bit AMD Opteron machines |
42 |
< |
are ongoing. |
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) GNU make. Regular make won't work. Really. We've tried. |
45 |
< |
Don't bother with regular make. Seriously. You need GNU make. |
43 |
< |
Did we mention that you need GNU make? |
44 |
> |
Fortran compilers that are known to fail on OOPSE: g77, Gfortran, |
45 |
> |
Older Portland Group compilers (pgf77, pgf90). |
46 |
|
|
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 |
+ |
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. |
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 MPICH-1.2.*. Other implementations might work, but we |
65 |
< |
haven't tried. You can get MPICH here: |
54 |
< |
http://www-unix.mcs.anl.gov/mpi/mpich/ |
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 |
|
|
56 |
– |
5) Assorted unix utilities (lexx, yacc) or their GNU equivalents. |
57 |
– |
|
67 |
|
INSTRUCTIONS |
68 |
|
|
69 |
|
1) Get, build, and test the required pieces above. |
70 |
< |
2) ./configure (or ./configure --with-mpi=/usr/local/mpich) |
70 |
> |
2) ./configure (or ./configure --with-mpi=/usr/local/openmpi) |
71 |
|
3) make |
72 |
|
4) make install |
73 |
|
|