Merge branch 'master' into user-cgdna

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

  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ

  REAX REPLICA RIGID SHOCK SNAP SRD)

set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE

  USER-ATC USER-AWPMD USER-CGDNA USER-MESO

  USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO

  USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF

  USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC

  USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD

Package, Description, Doc page, Example, Library

"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int

"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int

"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -

"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -

"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -

"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int

:line

USER-BOCS package :link(USER-BOCS),h4

[Contents:]

This package provides "fix bocs"_fix_bocs.html, a modified version

of "fix npt"_fix_nh.html which includes the pressure correction to

the barostat as outlined in:

N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that 

accurately describe the structure, pressure, and compressibility of

molecular liquids," J. Chem. Phys. 143, 243148 (2015).

[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)

[Install or un-install:]

make yes-user-bocs

make machine :pre

make no-user-bocs

make machine :pre

[Supporting info:]

The USER-BOCS user package for LAMMPS is part of the BOCS software package:

"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS

See the following reference for information about the entire package:

Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.

"BOCS: Bottom-Up Open-Source Coarse-Graining Software."

J. Phys. Chem. B. 122, 13, 3363-3377 (2018).

Example inputs are in the examples/USER/bocs folder.

:line

USER-CGDNA package :link(USER-CGDNA),h4

[Contents:]

[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

<"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 bocs command :h3

[Syntax:]

fix  ID group-ID bocs keyword values ... :pre

keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}

  {temp} values = Tstart Tstop Tdamp

  {cgiso} values = Pstart Pstop Pdamp

  {basis set}

    {analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N

    {linear_spline} values = input_filename

    {cubic_spline} values = input_filename :pre

:ule

[Examples:]

fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre

fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre

thermo_modify press 1_press :pre

[Description:]

These commands incorporate a pressure correction as described by 

Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK

barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .

The first half of the command mimics a standard fix npt command:

fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre

The two differences are replacing {npt} with {bocs}, and replacing 

{iso}/{aniso}/{etc} with {cgiso}.

The rest of the command details what form you would like to use for 

the pressure correction equation. The choices are: {analytic}, {linear_spline}, 

or {cubic_spline}. 

With either spline method, the only argument that needs to follow it 

is the name of a file that contains the desired pressure correction 

as a function of volume. The file should be formatted so each line has:

Volume_i, PressureCorrection_i :pre

Note both the COMMA and the SPACE separating the volume's 

value and its corresponding pressure correction. The volumes in the file 

should be uniformly spaced. Both the volumes and the pressure corrections 

should be provided in the proper units, e.g. if you are using {units real}, 

the volumes should all be in cubic angstroms, and the pressure corrections 

should all be in atomspheres. Furthermore, the table should start/end at a 

volume considerably smaller/larger than you expect your system to sample 

during the simulation. If the system ever reaches a volume outside of the 

range provided, the simulation will stop.

With the {analytic} option, the arguments are as follows:

... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre

Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you 

are using {units real}, {V_avg} should be in cubic angstroms, and the 

coefficients should all be in atmospheres * cubic angstroms.

[Restrictions:]

As this is computing a (modified) pressure, group-ID should be {all}.

The pressure correction has only been tested for use with an isotropic 

pressure coupling in 3 dimensions.   

By default, LAMMPS will still report the normal value for the pressure

if the pressure is printed via a {thermo} command, or if the pressures

are written to a file every so often. In order to have LAMMPS report the

modified pressure, you must include the {thermo_modify} command given in 

the examples. For the last argument in the command, you should put 

XXXX_press, where XXXX is the ID given to the fix bocs command (in the

example, the ID of the fix bocs command is 1 ).

This fix is part of the USER-BOCS 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.

[Related:]

For more details about the pressure correction and the entire BOCS software 

package, visit the "BOCS package on github"_bocsgithub and read the release 

paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .

:link(bocsgithub,https://github.com/noid-group/BOCS)

:line

:link(bocs-Dunn1)

[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).

:link(bocs-Martyna)

[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).

:link(bocs-Dunn2)

[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).