Jacapo

Submitting Batch Jobs

jacapo-bsub myscript.py
jacapo-ver-bsub 9a myscript.py (select a specific version)

Jacapo Parallel NEB Example

You can find a Jacapo parallel NEB example here. This same script can be used for a restart (the interpolated traj files are only recreated if they don't exist).

Some important notes:

• the number of processors selected for a parallel NEB must be an integer multiple of the NumberOfImages-2 (the images at the end points are "fixed").
• Parallel NEB settings (e.g. number of cores) can be debugged running in the suncat-test queue with 1 processor per non-fixed image.
• Later on in the NEB (discussed here) it is good to set climbing=True and switch to the FIRE method, shown here. As best I can tell, this page doesn't provide good instructions for when to turn those on.

Perturbing Jacapo Calculations

When taking an existing Jacapo calculation and making changes (e.g. adding an external field) it is important to not instantiate a new calculator (to work around some Jacapo bugs) but instead read in the previous atoms/calculator from the .nc file. Johannes Voss has kindly provided an example with some comments here.

Stripping Wavefunctions from Jacapo .nc Files

To strip wavefunctions from all subdirectories of the current directory (".", in the find command):

source /afs/slac/g/suncat/jacapo/setupenv
find . -name \*nc -exec /nfs/slac/g/suncatfs/sw/jacapov3/ase/ase/calculators/jacapo/tools/stripnetcdf {} \; -print

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