| 1 |
gezelter |
1490 |
OOPSE |
| 2 |
|
|
|
| 3 |
|
|
OOPSE is an open-source Object-Oriented Parallel Simulation Engine. |
| 4 |
|
|
It is primarily used to perform molecular dynamics simulations on |
| 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 |
gezelter |
2568 |
Embedded Atom Method (EAM) or Sutton-Chen (SC) potentials. |
| 9 |
gezelter |
1490 |
|
| 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 |
|
|
on the following architecture & compiler combinations: |
| 24 |
|
|
|
| 25 |
|
|
Architecture CC CXX F90 Notes |
| 26 |
|
|
------------------------- ---- ----- ----- ---------------------- |
| 27 |
gezelter |
2568 |
ix86-pc-linux-gnu icc icpc ifort (Intel versions 7-9) |
| 28 |
|
|
powerpc-apple-darwin8.4.0 gcc g++ xlf (GNU v.4 / IBM XL v. 8.1) |
| 29 |
|
|
x86_64-unknown-linux-gnu pgcc pgCC pgf95 (Portland Group v. 6.0) |
| 30 |
gezelter |
2572 |
sparc-sun-solaris2.10 cc CC f95 (Sun ONE Studio 10) |
| 31 |
gezelter |
1490 |
|
| 32 |
gezelter |
2568 |
We've successfully compiled OOPSE with the Pathscale c, c++, and |
| 33 |
|
|
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. |
| 37 |
|
|
|
| 38 |
gezelter |
2572 |
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 |
gezelter |
1490 |
|
| 44 |
gezelter |
2572 |
Compilers that are known to fail on OOPSE: g77, Gfortran, Older |
| 45 |
|
|
Portland Group compilers (pgf77, pgf90). |
| 46 |
|
|
|
| 47 |
|
|
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 |
gezelter |
2208 |
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 |
gezelter |
1490 |
|
| 56 |
gezelter |
2205 |
3) Perl. Compilation dependencies in Fortran95 are somewhat |
| 57 |
|
|
complicated, so the build process uses a perl script called |
| 58 |
gezelter |
2208 |
filepp to do this job. You need perl for filepp, so you |
| 59 |
|
|
need perl to build OOPSE. |
| 60 |
gezelter |
2205 |
|
| 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 |
gezelter |
1490 |
haven't tried. You can get MPICH here: |
| 66 |
|
|
http://www-unix.mcs.anl.gov/mpi/mpich/ |
| 67 |
|
|
|
| 68 |
|
|
INSTRUCTIONS |
| 69 |
|
|
|
| 70 |
|
|
1) Get, build, and test the required pieces above. |
| 71 |
gezelter |
2205 |
2) ./configure (or ./configure --with-mpi=/usr/local/mpich) |
| 72 |
gezelter |
1490 |
3) make |
| 73 |
|
|
4) make install |
| 74 |
|
|
|
| 75 |
gezelter |
2205 |
That's it. |
