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(point dipoles, sticky atoms), as well as transition metals under the |
| 8 |
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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 |
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|
| 14 |
< |
1) a C-based meta-data (.md) file, and |
| 14 |
> |
1) a C-based <MetaData> section, and |
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|
| 16 |
< |
2) a modified XYZ format for initial coordinate and velocity information. |
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> |
2) a <Snapshot> block for initial coordinate and velocity information. |
| 17 |
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|
| 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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|
| 24 |
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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 7-9) |
| 30 |
< |
powerpc-apple-darwin8.4.0 gcc g++ xlf (GNU v.4 / IBM XL v. 8.1) |
| 31 |
< |
x86_64-unknown-linux-gnu pgcc pgCC pgf95 (Portland Group v. 6.0) |
| 32 |
< |
sparc-sun-solaris2.10 cc CC f95 (Sun ONE Studio 10) |
| 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 the Pathscale c, c++, and |
| 36 |
< |
Fortran95 compilers on the x86_64-unknown-linux-gnu architecture, |
| 34 |
< |
but a bug in the exception handling on these compilers causes |
| 35 |
< |
OOPSE to abort (rather than providing a useful error message) when |
| 36 |
< |
an error is found in the meta-data file. |
| 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 |
| 41 |
|
compilers do support these features. None of the Fortran 77 |
| 42 |
|
compilers can be used to compile OOPSE. |
| 43 |
|
|
| 44 |
< |
Compilers that are known to fail on OOPSE: g77, Gfortran, Older |
| 45 |
< |
Portland Group compilers (pgf77, pgf90). |
| 44 |
> |
Fortran compilers that are known to fail on OOPSE: g77, Gfortran, |
| 45 |
> |
Older Portland Group compilers (pgf77, pgf90). |
| 46 |
|
|
| 47 |
< |
Compilers that are known to work on OOPSE: Intel's ifort, |
| 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 |
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|
| 61 |
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4) MPI is optional for the single processor version of OOPSE, |
| 62 |
|
but is required if you want OOPSE to run in parallel. |
| 63 |
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|
| 64 |
< |
We like MPICH-1.2.*. Other implementations might work, but we |
| 65 |
< |
haven't tried. You can get MPICH here: |
| 66 |
< |
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 |
|
|
| 67 |
|
INSTRUCTIONS |
| 68 |
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|
| 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 |
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3) make |
| 72 |
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4) make install |
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|
