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Steve Plimpton authored
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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 #