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lammps/examples/neb
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Steve Plimpton d2610d9e7c minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
..
README minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
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 minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
in.neb.hop1.end minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
in.neb.hop2 modified the documentation, first and last freeend can have different spring constants 2017-06-19 16:30:42 +02:00
in.neb.sivac made the command options more lammps standard style 2017-06-02 23:42:16 +02:00
initial.hop1 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15663 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-09-27 21:24:10 +00:00
initial.hop1.end USER-INTEL upgrade from M Brown 2017-06-16 16:56:28 -06:00
initial.hop2 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15663 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-09-27 21:24:10 +00:00
initial.sivac git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15663 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-09-27 21:24:10 +00:00
log.19Jun17.neb.hop1.end.g++.4 minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
log.19Jun17.neb.hop1.end.g++.8 minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
log.19Jun17.neb.hop1.g++.4 minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
log.19Jun17.neb.hop1.g++.8 minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
log.19Jun17.neb.hop2.g++.4 minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
log.19Jun17.neb.hop2.g++.8 minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
log.19Jun17.neb.sivac.g++.4 minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
log.19Jun17.neb.sivac.g++.8 minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00

README 

Run these examples as:

mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1.end
mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac

mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1.end
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.sivac

Note that more than 4 replicas should be used for a precise estimate 
of the activation energy corresponding to a transition.

If you uncomment the dump command lines in the input scripts, you can
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 #