Merge pull request #891 from akohlmey/collected-small-changes

lib/molfile/*         @akohlmey

lib/qmmm/*            @akohlmey

lib/vtk/*             @rbberger

lib/kim/*             @ellio167

# packages

src/KOKKOS            @stanmoore1

src/USER-CGSDK        @akohlmey

src/USER-COLVARS      @giacomofiorin

src/USER-OMP          @akohlmey

src/USER-QMMM         @akohlmey

# whole packages

src/COMPRESS/*        @akohlmey

src/GPU/*             @ndtrung81

src/KOKKOS/*          @stanmoore1

src/KIM/*             @ellio167

src/USER-CGDNA/*      @ohenrich

src/USER-CGSDK/*      @akohlmey

src/USER-COLVARS/*    @giacomofiorin

src/USER-DPD/*        @timattox

src/USER-INTEL/*      @wmbrownintel

src/USER-MANIFOLD/*   @Pakketeretet2

src/USER-MEAMC/*      @martok

src/USER-MOFFF/*      @hheenen

src/USER-MOLFILE/*    @akohlmey

src/USER-NETCDF/*     @pastewka

src/USER-PHONON/*     @lingtikong

src/USER-OMP/*        @akohlmey

src/USER-QMMM/*       @akohlmey

src/USER-REAXC/*      @hasanmetin

src/USER-TALLY/*      @akohlmey

src/USER-UEF/*        @danicholson

src/USER-VTK/*        @rbberger

# individual files in packages

src/GPU/pair_vashishta_gpu.*        @andeplane

src/KOKKOS/pair_vashishta_kokkos.*  @andeplane

src/MANYBODY/pair_vashishta_table.* @andeplane

src/USER-MISC/fix_bond_react.*      @jrgissing

src/USER-MISC/*_grem.*              @dstelter92

# tools

tools/msi2lmp/*       @akohlmey

[Syntax:]

compute ID group-ID ackland/atom :pre

compute ID group-ID ackland/atom keyword/value :pre

ID, group-ID are documented in "compute"_compute.html command

ackland/atom = style name of this compute command :ul

ID, group-ID are documented in "compute"_compute.html command :ulb,l

ackland/atom = style name of this compute command :l

zero or more keyword/value pairs may be appended :l

keyword = {legacy} :l

  {legacy} yes/no = use ({yes}) or do not use ({no}) legacy ackland algorithm implementation :pre

:ule

[Examples:]

compute 1 all ackland/atom :pre

compute 1 all ackland/atom

compute 1 all ackland/atom legacy yes :pre

[Description:]

Defines a computation that calculates the local lattice structure

according to the formulation given in "(Ackland)"_#Ackland.

Historically, LAMMPS had two, slightly different implementations of

the algorithm from the paper. With the {legacy} keyword, it is

possible to switch between the pre-2015 ({legacy yes}) and post-2015

implemention ({legacy no}). The post-2015 variant is the default.

In contrast to the "centro-symmetry

parameter"_compute_centro_atom.html this method is stable against

"compute centro/atom"_compute_centro_atom.html

[Default:] none

[Default:]

The keyword {legacy} defaults to {no}.

:line

should be chosen low enough, so as to mimic as closely as possible the

self-consistent minimization. It must however be high enough, so that

the dipoles can follow the local electric field exerted by the

neighbouring atoms. The optimal value probably depends on the

neighboring atoms. The optimal value probably depends on the

temperature of the centers of mass and on the mass of the Drude

particles.

    atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom

    Kstart,Kstop = restraint coefficients at start/end of run (energy units)

    theta0 = equilibrium angle theta (degrees)

  {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0

  {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value

    atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order

    Kstart,Kstop = restraint coefficients at start/end of run (energy units)

    phi0 = equilibrium dihedral angle phi (degrees) :pre

    phi0 = equilibrium dihedral angle phi (degrees)

    keyword/value = optional keyword value pairs. supported keyword/value pairs:

      {mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre

:ule

[Examples:]

with the following coefficients:

K (energy)

n = 1

n (multiplicity, >= 0)

d (degrees) = phi0 + 180 :ul

K and phi0 are specified with the fix.  Note that the value of n is

hard-wired to 1.  Also note that the energy will be a minimum when the

K and phi0 are specified with the fix.  Note that the value of the

dihedral multiplicity {n} is set by default to 1. You can use the

optional {mult} keyword to set it to a different positive integer.

Also note that the energy will be a minimum when the

current dihedral angle phi is equal to phi0.

:line

This potential is intended for interactions between two layers of graphene.

Therefore, to avoid interaction between layers in multi-layered materials,

each layer should have a separate atom type and interactions should only

be computed between atom types of neighbouring layers.

be computed between atom types of neighboring layers.

The parameter file (e.g. CC.KC), is intended for use with metal

"units"_units.html, with energies in meV. An additional parameter, {S},