Merge pull request #1314 from charlessievers/OptimizedDynamicalMatrix (14e6c126) · Commits · 郑智淋 / lammps

doc/src/Commands_all.txt

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		@@ -55,6 +55,7 @@ An alphabetic list of all general LAMMPS commands.
		"dump netcdf"_dump_netcdf.html,
		"dump netcdf/mpiio"_dump_netcdf.html,
		"dump vtk"_dump_vtk.html,
		"dynamical_matrix"_dynamical_matrix.html,
		"echo"_echo.html,
		"fix"_fix.html,
		"fix_modify"_fix_modify.html,

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		@@ -1725,14 +1725,19 @@ USER-PHONON package :link(PKG-USER-PHONON),h4
		A "fix phonon"_fix_phonon.html command that calculates dynamical
		matrices, which can then be used to compute phonon dispersion
		relations, directly from molecular dynamics simulations.
		And a "dynamical_matrix" command to compute the dynamical matrix
		from finite differences.

		[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
		and Charlie Sievers (UC Davis) for "dynamical_matrix"

		[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).

		[Supporting info:]

		src/USER-PHONON: filenames -> commands
		src/USER-PHONON/README
		"fix phonon"_fix_phonon.html
		"dynamical_matrix"_dynamical_matrix.html
		examples/USER/phonon :ul

		:line

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0 → 100644

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		"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

		:link(lws,http://lammps.sandia.gov)
		:link(ld,Manual.html)
		:link(lc,Commands_all.html)

		:line

		dynamical_matrix command :h3

		[Syntax:]

		dynamical_matrix group-ID style gamma args keyword value ... :pre

		group-ID = ID of group of atoms to displace :ulb,l
		style = {regular} or {eskm} :l
		gamma = finite different displacement length (distance units) :l
		one or more keyword/arg pairs may be appended :l
		keyword = {file} or {binary}
		{file} name = name of output file for the dynamical matrix
		{binary} arg = {yes} or {no} or {gzip} :pre
		:ule

		[Examples:]

		dynamical_matrix 1 regular 0.000001
		dynamical_matrix 1 eskm 0.000001
		dynamical_matrix 3 regular 0.00004 file dynmat.dat
		dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes :pre

		[Description:]

		Calculate the dynamical matrix of the selected group.

		[Restrictions:]

		The command collects the entire dynamical matrix a single MPI rank,
		so the memory requirements can be very significant for large systems.

		This command assumes a periodic system.

		This command is part of the USER-PHONON package. It is only enabled if
		LAMMPS was built with that package. See the "Build
		package"_Build_package.html doc page for more info.

		[Related commands:]

		"fix phonon"_fix_phonon.html

		[Default:]

		The default settings are file = "dynmat.dyn", binary = no

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		@@ -179,7 +179,8 @@ settings"_Build_settings.html doc page for details.

		[Related commands:]

		"compute msd"_compute_msd.html
		"compute msd"_compute_msd.html,
		"dynamical_matrix"_dynamical_matrix.html

		[Default:]