enable multi-processor NEB replicas (35705217) · Commits · 郑智淋 / lammps

doc/src/Manual.txt

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		<!-- HTML_ONLY -->
		<HEAD>
		<TITLE>LAMMPS Users Manual</TITLE>
		<META NAME="docnumber" CONTENT="27 Sep 2016 version">
		<META NAME="docnumber" CONTENT="28 Sep 2016 version">
		<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
		<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
		</HEAD>
		@@ -21,7 +21,7 @@
		<H1></H1>

		LAMMPS Documentation :c,h3
		27 Sep 2016 version :c,h4
		28 Sep 2016 version :c,h4

		Version info: :h4

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		@@ -57,9 +57,6 @@ would see with one or more physical processors per replica. See
		"Section 6.5"_Section_howto.html#howto_5 of the manual for further
		discussion.

		NOTE: The current NEB implementation in LAMMPS only allows there to be
		one processor per replica.

		NOTE: As explained below, a NEB calculation perfoms a damped dynamics
		minimization across all the replicas. The mimimizer uses whatever
		timestep you have defined in your input script, via the
		@@ -255,12 +252,6 @@ An atom map must be defined which it is not by default for "atom_style
		atomic"_atom_style.html problems. The "atom_modify
		map"_atom_modify.html command can be used to do this.

		The "atom_modify sort 0 0.0" command should be used to turn off atom
		sorting.

		NOTE: This sorting restriction will be removed in a future version of
		NEB in LAMMPS.

		The minimizers in LAMMPS operate on all atoms in your system, even
		non-NEB atoms, as defined above. To prevent non-NEB atoms from moving
		during the minimization, you should use the "fix

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		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
		mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1
		mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2
		mpirun -np 3 lmp_g++ -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)
		mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1
		mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2
		mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac
		mpirun -np 9 lmp_g++ -partition 3x3 -in in.neb.sivac

		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

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