jacapo-bsub myscript.py jacapo-ver-bsub 9a myscript.py (select a specific version) |
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:
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.
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 |
Version |
Date |
Comment |
jacapov3 |
4/29/11 |
copy of v2, but ase from svn head to pick up Lars parallel neb code (and dacapo.run) |
jacapov4 |
7/8/11 |
softlink to jacapov3, change setupenv/dacapo.run to use torque/maui aware openmpi |
jacapov5 |
2/23/12 |
softlink to javapov3, change setupenv/dacapo.run to use lcls filesystem naming /reg/d/suncat |
jacapov6 |
3/7/12 |
like v5, but use the TaskStarter/mympirun_wrapper script in dacapo.run so we can bstop/bresume jobs and fix accounting for non parneb jobs |
jacapov7 |
4/12/12 |
like v6, but change dacapo.run script so that it can be used for normal jobs and parallel nebs |
jacapov8 |
11/5/12 |
like v7, but change dacapo.run script to not use /afs version of mpirun. Appears to fix intermittent hang problem with parallel NEBs |
jacapov9a |
11/9/12 |
(suncat3 farm only) python packages rebuilt for RHEL6 |
jacapov10 |
2/21/13 |
like v8, but more recent version of ASE (3.6.1.2694) |