Tools

Nudged Elastic Band parallelized over images (separate jobs)

WARNING: ONLY LIMITED TESTING AS OF 1/4/2004

The scripts (originally due to Sune Bahn) which allow a Nudged Elastic Band job to be parallelized over images, and each image/step unit to be submitted as one batch job to the queue, have been modified to use the ASE interface. There are two scripts. One, nebstep, is invisible to the user and is what actually gets run by each unit-job. The one that the user actually calls is setup_and_submit.py. All user-parameters are provided in the file MyParameters.py which is also a python script, defining certain variables as well as functions which specify the calculator and constraints. See MyParameters.py for an example. This file should be in the same directory where the job is to be run.

plottrajectory

Tool for vieving a NetCDF trajectory, see the plottrajectory tool for a full description.

trajectory2xyz

Tool for translating a trajectory to a multiple frame xyz formatted file:

trajectory2xyz [-r 2 2 2] trajectory xyzfile

The xyz file can be used with eg. the xmakemol program. The option -r will repeat the unitcell then creating the xyz file.

xyz2trajectory

Tool for translating a xyz formatted file to a trajectory:

xyz2trajectory  xyzfile trajectory

nebfit

A fitting program for a Nudged Elastic Band calculation Making a spline fit to the Nudged Elastic Band energies and forces:

nebfit prefix -f frameno

The script nebfit assumes you have a list of NetCDF trajectories called prefix<image-number>.nc. You can specify which frame number you want to read. Two output files are produced:

  • A ascii file for xmgr containing the spline fit
  • A NetCDF trajectory file containing the path for the specified frame number.

hessian

A program for estimating a Hessian matrix from one or more NetCDF trajectories:

hessian trajectory1.nc trajectory2.nc -u Bofill

bee_nebfit

This tool are using Bayesian Error estimation (BEE) ASE utility for predicting error bars on the Nudged Elastic Band energies. Two sets of error bars are produced, one with respect to the initial state and one with respect to the final state.

The script assumes you have a list of restart files from your DFT calculations, eg. initial.nc , out.[1,5].nc and final.nc, now you can use bee_nebfit like:

bee_nebfit initial.nc out.1.nc out.2.nc out.3.nc out.4.nc out.5.nc final.nc

In contrast to the nebfit tool you can not use NetCDF trajectories, because these do not contain the BEE information.

The result is written to a xmgrace file bee_-1.agr.

Note that you have to autoscale the second plot in xmgrace.

ase2: Tools (last edited 2010-10-20 09:11:16 by localhost)