lammps

History

sjplimp dd122f6a0b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11411 f3b2605a-c512-4ea7-a41b-209d697bcdaa		2014-01-30 22:50:33 +00:00
..
README	Added Si vacancy hop example	2014-01-29 22:51:52 +00:00
Si.sw	Added Si vacancy hop example	2014-01-29 22:51:52 +00:00
final.hop1	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11005 f3b2605a-c512-4ea7-a41b-209d697bcdaa	2013-11-08 20:49:16 +00:00
final.hop2	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11005 f3b2605a-c512-4ea7-a41b-209d697bcdaa	2013-11-08 20:49:16 +00:00
final.sivac	Added Si vacancy hop example	2014-01-29 22:51:52 +00:00
in.neb.hop1	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11402 f3b2605a-c512-4ea7-a41b-209d697bcdaa	2014-01-30 21:11:09 +00:00
in.neb.hop2	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11402 f3b2605a-c512-4ea7-a41b-209d697bcdaa	2014-01-30 21:11:09 +00:00
in.neb.sivac	Added Si vacancy hop example	2014-01-29 22:51:52 +00:00
log.neb.hop1.1Feb14.linux.4	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11411 f3b2605a-c512-4ea7-a41b-209d697bcdaa	2014-01-30 22:50:33 +00:00
log.neb.hop2.1Feb14.linux.4	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11411 f3b2605a-c512-4ea7-a41b-209d697bcdaa	2014-01-30 22:50:33 +00:00
log.neb.sivac.1Feb14.linux.3	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11411 f3b2605a-c512-4ea7-a41b-209d697bcdaa	2014-01-30 22:50:33 +00:00

README

Run these examples as:

mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop1
mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop2
mpirun -np 3 lmp_linux -partition 3x1 -in in.neb.sivac

Create dump files to do visualization from via Python tools:
(see lammps/tools/README and lammps/tools/python/README
for more info on these Python scripts)

python ~/lammps/tools/python/neb_combine.py -o dump.hop1.combine
					    -b dump.nonneb.1 
					    -r dump.neb.*
python ~/lammps/tools/python/neb_final.py -o dump.hop1.final 
					  -b dump.nonneb.1	
					  -r dump.neb.*

produces:

dump.hop1.combine = series of snapshots for all replicas together
		    time = progression of NEB calculation
dump.hop1.final = series of snapshots for final state of all replicas
		  time = replica #