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fix_phonon.txt
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fix_phonon.txt
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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,Section_commands.html#comm)

			:line

			fix phonon command :h3

			[Syntax:]

			fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ... :pre

			ID, group-ID are documented in "fix"_fix.html command :ulb,l
			phonon = style name of this fix command :l
			N = measure the Green's function every this many timesteps :l
			Noutput = output the dynamical matrix every this many measurements :l
			Nwait = wait this many timesteps before measuring :l
			map_file = {file} or {GAMMA} :l
			{file} is the file that contains the mapping info between atom ID and the lattice indices. :pre

			{GAMMA} flags to treate the whole simulation box as a unit cell, so that the mapping
			info can be generated internally. In this case, dynamical matrix at only the gamma-point
			will/can be evaluated. :pre
			prefix = prefix for output files :l
			one or none keyword/value pairs may be appended :l
			keyword = {sysdim} or {nasr} :l
			{sysdim} value = d
			d = dimension of the system, usually the same as the MD model dimension
			{nasr} value = n
			n = number of iterations to enforce the acoustic sum rule :pre
			:ule

			[Examples:]

			fix 1 all phonon 20 5000 200000 map.in LJ1D sysdim 1
			fix 1 all phonon 20 5000 200000 map.in EAM3D
			fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100 :pre

			[Description:]

			Calculate the dynamical matrix from molecular dynamics simulations
			based on fluctuation-dissipation theory for a group of atoms.

			Consider a crystal with {N} unit cells in three dimensions labelled {l
			= (l<sub>1</sub>,l<sub>2</sub>,l<sub>3</sub>)} where {l<sub>i</sub>}
			are integers. Each unit cell is defined by three linearly independent
			vectors [a]<sub>1</sub>, [a]<sub>2</sub>, [a]<sub>3</sub> forming a
			parallelipiped, containing {K} basis atoms labelled {k}.

			Based on fluctuation-dissipation theory, the force constant
			coefficients of the system in reciprocal space are given by
			("Campañá"_#Campana , "Kong"_#Kong)
			<center><b>Φ</b><sub>kα,k'β</sub>(<b>q</b>) =
			k<sub>B</sub>T
			<b>G</b><sup>-1</sup><sub>kα,k'β</sub>(<b>q</b>),</center>

			where [G] is the Green's functions coefficients given by

			<center><b>G</b><sub>kα,k'β</sub>(<b>q</b>) =
			<<b>u</b><sub>kα</sub>(<b>q</b>)<b>u</b><sub>k'β</sub><sup>*</sup>(<b>q</b>)>,</center>

			where <...> denotes the ensemble average, and
			<center>[u]<sub>kα</sub>(<b>q</b>) = ∑<sub>l</sub>
			<b>u</b><sub>lkα</sub> exp(i[qr]<sub>l</sub>)</center>

			is the α component of the atomic displacement for the {k}th atom
			in the unit cell in reciprocal space at [q]. In practice, the Green's
			functions coefficients can also be measured according to the following
			formula,

			<center><b>G</b><sub>kα,k'β</sub>(<b>q</b>) =
			<<b>R</b><sub>kα</sub>(<b>q</b>)<b>R</b><sup>*</sup><sub>k'β</sub>(<b>q</b>)>
			- <<b>R</b>><sub>kα</sub>(<b>q</b>)<<b>R</b>><sup>*</sup><sub>k'β</sub>(<b>q</b>),
			</center>

			where [R] is the instantaneous positions of atoms, and <[R]> is the
			averaged atomic positions. It gives essentially the same results as
			the displacement method and is easier to implement in an MD code.

			Once the force constant matrix is known, the dynamical matrix [D] can
			then be obtained by

			<center><b>D</b><sub>kα, k'β</sub>(<b>q</b>) = (m<sub>k</sub>m<sub>k'</sub>)<sup>-1/2</sup> <b>Φ</b><sub>kα,k'β</sub>(<b>q</b>)</center>

			whose eigenvalues are exactly the phonon frequencies at [q].

			This fix uses positions of atoms in the specified group and calculates
			two-point correlations. To achieve this. the positions of the atoms
			are examined every {Nevery} steps and are Fourier-transformed into
			reciprocal space, where the averaging process and correlation
			computation is then done. After every {Noutput} measurements, the
			matrix [G]([q]) is calculated and inverted to obtain the elastic
			stiffness coefficients. The dynamical matrices are then constructed
			and written to {prefix}.bin.timestep files in binary format and to the
			file {prefix}.log for each wavevector [q].

			A detailed description of this method can be found in
			("Kong2011"_#Kong2011).

			The {sysdim} keyword is optional. If specified with a value smaller
			than the dimensionality of the LAMMPS simulation, its value is used
			for the dynamical matrix calculation. For example, using LAMMPS ot
			model a 2D or 3D system, the phonon dispersion of a 1D atomic chain
			can be computed using {sysdim} = 1.

			The {nasr} keyword is optional. An iterative procedure is employed to
			enforce the acoustic sum rule on Φ at Γ, and the number
			provided by keyword {nasr} gives the total number of iterations. For a
			system whose unit cell has only one atom, {nasr} = 1 is sufficient;
			for other systems, {nasr} = 10 is typically sufficient.

			The {map_file} contains the mapping information between the lattice
			indices and the atom IDs, which tells the code which atom sits at
			which lattice point; the lattice indices start from 0. An auxiliary
			code, "latgen"_http://code.google.com/p/latgen, can be employed to
			generate the compatible map file for various crystals.

			In case one simulates an aperiodic system, where the whole simulation box
			is treated as a unit cell, one can set {map_file} as {GAMMA}, so that the mapping
			info will be generated internally and a file is not needed. In this case, the
			dynamical matrix at only the gamma-point will/can be evaluated. Please keep in
			mind that fix-phonon is designed for cyrstals, it will be inefficient and
			even degrade the performance of lammps in case the unit cell is too large.

			The calculated dynamical matrix elements are written out in
			"energy/distance^2/mass"_units.html units. The coordinates for {q}
			points in the log file is in the units of the basis vectors of the
			corresponding reciprocal lattice.

			[Restart, fix_modify, output, run start/stop, minimize info:]

			No information about this fix is written to "binary restart
			files"_restart.html.

			The "fix_modify"_fix_modify.html {temp} option is supported by this
			fix. You can use it to change the temperature compute from thermo_temp
			to the one that reflects the true temperature of atoms in the group.

			No global scalar or vector or per-atom quantities are stored by this
			fix for access by various "output commands"_Section_howto.html#4_15.

			Instead, this fix outputs its initialization information (including
			mapping information) and the calculated dynamical matrices to the file
			{prefix}.log, with the specified {prefix}. The dynamical matrices are
			also written to files {prefix}.bin.timestep in binary format. These
			can be read by the post-processing tool in tools/phonon to compute the
			phonon density of states and/or phonon dispersion curves.

			No parameter of this fix can be used with the {start/stop} keywords
			of the "run"_run.html command.

			This fix is not invoked during "energy minimization"_minimize.html.

			[Restrictions:]

			This fix assumes a crystalline system with periodical lattice. The
			temperature of the system should not exceed the melting temperature to
			keep the system in its solid state.

			This fix is part of the USER-PHONON package. It is only enabled if
			LAMMPS was built with that package. See the "Making
			LAMMPS"_Section_start.html#start_3 section for more info.

			This fix requires LAMMPS be built with an FFT library. See the
			"Making LAMMPS"_Section_start.html#start_2 section for more info.

			[Related commands:]

			"compute msd"_compute_msd.html

			[Default:]

			The option defaults are sysdim = the same dimemsion as specified by
			the "dimension"_dimension command, and nasr = 20.

			:line

			:link(Campana)
			[(Campañá)] C. Campañá and
			M. H. Müser, {Practical Green's function approach to the
			simulation of elastic semi-infinite solids}, "Phys. Rev. B \[74\],
			075420 (2006)"_http://dx.doi.org/10.1103/PhysRevB.74.075420

			:link(Kong)
			[(Kong)] L.T. Kong, G. Bartels, C. Campañá,
			C. Denniston, and Martin H. Müser, {Implementation of Green's
			function molecular dynamics: An extension to LAMMPS}, "Computer
			Physics Communications \[180\](6):1004-1010
			(2009)."_http://dx.doi.org/10.1016/j.cpc.2008.12.035

			L.T. Kong, C. Denniston, and Martin H. Müser,
			{An improved version of the Green's function molecular dynamics
			method}, "Computer Physics Communications \[182\](2):540-541
			(2011)."_http://dx.doi.org/10.1016/j.cpc.2010.10.006

			:link(Kong2011)
			[(Kong2011)] L.T. Kong, {Phonon dispersion measured directly from
			molecular dynamics simulations}, "Computer Physics Communications
			\[182\](10):2201-2207,
			(2011)."_http://dx.doi.org/10.1016/j.cpc.2011.04.019

lammps/doc/fix_phonon.txt992d9ff3ea57efficient_neuronet

fix_phonon.txtView Options

lammps/doc/fix_phonon.txt
992d9ff3ea57efficient_neuronet

fix_phonon.txt
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