changes to integrate USER-BOCS into LAMMPS and to closer follow the LAMMPS...

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:]

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 

   fix_ave_time

   fix_aveforce

   fix_balance

   fix_bocs

   fix_bond_break

   fix_bond_create

   fix_bond_swap

fix_ave_time.html

fix_aveforce.html

fix_balance.html

fix_bocs.html

fix_bond_break.html

fix_bond_create.html

fix_bond_swap.html