2010-10-01 07:12:46 +08:00
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Run these examples as:
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2016-09-28 05:24:10 +08:00
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mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1
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mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2
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2017-06-19 22:30:42 +08:00
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mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1.end
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2016-09-28 05:24:10 +08:00
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mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac
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2010-10-01 07:12:46 +08:00
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2016-09-28 05:24:10 +08:00
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mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1
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mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2
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2017-06-19 22:30:42 +08:00
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mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1.end
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2017-06-20 22:19:23 +08:00
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mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.sivac
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2017-05-29 21:49:04 +08:00
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Note that more than 4 replicas should be used for a precise estimate
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of the activation energy corresponding to a transition.
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2016-09-28 05:24:10 +08:00
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If you uncomment the dump command lines in the input scripts, you can
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create dump files to do visualization from via Python tools: (see
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lammps/tools/README and lammps/tools/python/README for more info on
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these Python scripts)
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2010-10-01 07:12:46 +08:00
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2010-10-07 07:33:17 +08:00
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python ~/lammps/tools/python/neb_combine.py -o dump.hop1.combine
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-b dump.nonneb.1
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-r dump.neb.*
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python ~/lammps/tools/python/neb_final.py -o dump.hop1.final
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-b dump.nonneb.1
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-r dump.neb.*
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2010-10-01 07:12:46 +08:00
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2010-10-07 07:33:17 +08:00
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produces:
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dump.hop1.combine = series of snapshots for all replicas together
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time = progression of NEB calculation
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dump.hop1.final = series of snapshots for final state of all replicas
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time = replica #
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