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sjplimp 9fc1ec8d30 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14614 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:15:02 +00:00
..
README Added Si vacancy hop example 2014-01-29 22:51:52 +00:00
Si.sw git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13530 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-07-06 16:35:48 +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.15Feb16.neb.hop1.g++.4 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14610 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:06:11 +00:00
log.15Feb16.neb.hop2.g++.4 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14610 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:06:11 +00:00
log.15Feb16.neb.sivac.g++.3 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14610 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:06:11 +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 #