[Openmd-users] [Openmd-developers] OpenMD version 1.1

[Dan Gezelter]

Brett,

  If you've built the code with MPI, then there should be a second binary called openmd_MPI in the same directory as the openmd binary.   Assuming you've got a queueing system to handle the MPI machine file for you, all you need to do is:

mpirun -np $nprocs openmd_MPI  file.md


 --Dan

On Jul 9, 2010, at 8:38 AM, Brett Donovan wrote:

> Hi Dan
> 
> I'm running on the clusters which is good and now I'm looking to use
> multiple processors to get some initial stats for how big we can go. I
> cannot see much in the documentation for running with MPI, I'm
> guessing its:
> 
> mpirun -np $nprocs openmd ??
> 
> Best
> 
> B
> 
> On Wed, Jul 7, 2010 at 8:09 PM, Dan Gezelter <gezelter at nd.edu> wrote:
>> We are pleased to announce the release of OpenMD version 1.1. This version fixes a number of bugs and provides extended functionality for some of the utility programs. It is recommended for all users of OpenMD.
>> 
>> New features include:
>> 
>> • Added a Progress bar to print out how long the simulation has remaining.
>> • Fixed ConvexHull code and added “select hull” as valid selection syntax.
>> • Fixed over-specificity in md-solvator and fixed installation bug.
>> • Fixed parameter typo for minimizer.
>> • Fixed gradients for minimization of rigid bodies
>> • Added EAM line for Art Voter’s aluminium potential
>> • Added NaN / INF detectors to DumpWriter and StatWriter
>> • Added a new correlation function (gofrz) to do slab-segregated g(r) calculations. This computes at g(r) for pairs while requiring the z coordinates of the two sites to be at fixed separations. The data is output in: r, z, g(r,z).
>> • Fixed a number of bugs in GhostBend and GhostTorsion.
>> • Fixed a bug in Torsion (and GhostTorsion) triggered by configurations with colinear atoms. The problem was discovered by Brett Donovan. Thanks, Brett!
>> • Added a new CosineBendType
>> • Updated the visitor architecture to make it easier to extend
>> • Updated Dump2XYZ to output velocities, forces, or vectors if requested.
>> 
>> Download the package here:  http://openmd.net/?page_id=20
>> 
>> Or simply do an "svn update" and remake the program if you have a development copy.
>> 
>> Enjoy!
>> 
>>  --Dan
>> 
>> 
>> ***********************************************************************
>>  J. Daniel Gezelter
>>  Associate Professor                                        Director
>>  University of Notre Dame                    The OpenScience Project
>> 
>>  gezelter at nd.edu                            gezelter at openscience.org
>>  http://www.nd.edu/~gezelter              http://www.openscience.org
>> ***********************************************************************
>> 
>> 
>> _______________________________________________
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>> 

***********************************************
  J. Daniel Gezelter
  Associate Professor of Chemistry
  Director of Graduate Admissions
  Department of Chemistry and Biochemistry
  251 Nieuwland Science Hall
  University of Notre Dame
  Notre Dame, IN 46556-5670

  phone:  +1 (574) 631-7595
  fax:    +1 (574) 631-6652
  e-mail: gezelter at nd.edu
  web:    http://www.nd.edu/~gezelter
************************************************