From af748745162c73b51153a399a63e2811e55da536 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 26 Apr 2017 19:27:13 -0400
Subject: [PATCH] rename references to USER-CG-CMM to USER-CGSDK
---
doc/src/Section_intro.txt | 2 +-
doc/src/Section_packages.txt | 32 +++++++++++++++++---------------
doc/src/angle_sdk.txt | 2 +-
doc/src/pair_sdk.txt | 2 +-
4 files changed, 20 insertions(+), 18 deletions(-)
diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt
index 33c3cf395f..0c438c6ce0 100644
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@@ -515,7 +515,7 @@ the packages they have written are somewhat unique to LAMMPS and the
code would not be as general-purpose as it is without their expertise
and efforts.
-Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages
+Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK and USER-OMP packages
Roy Pollock (LLNL), Ewald and PPPM solvers
Mike Brown (ORNL), brownw at ornl.gov, GPU package
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index b327b7b1ce..bd81361fa9 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -1139,8 +1139,8 @@ The current list of user-contributed packages is as follows:
Package, Description, Author(s), Doc page, Example, Pic/movie, Library
"USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
"USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
-"USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Strathclyde Glasgow), src/USER-CGDNA/README, USER/cgdna, -, -
+"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, "cgsdk"_cgsdk, -
"USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
"USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
@@ -1169,7 +1169,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
:tb(ea=c)
:link(atc,http://lammps.sandia.gov/pictures.html#atc)
-:link(cg,http://lammps.sandia.gov/pictures.html#cg)
+:link(cgsdk,http://lammps.sandia.gov/pictures.html#cg)
:link(eff,http://lammps.sandia.gov/movies.html#eff)
:link(manifold,http://lammps.sandia.gov/movies.html#manifold)
:link(sph,http://lammps.sandia.gov/movies.html#sph)
@@ -1267,18 +1267,18 @@ physik.hu-berlin.de). Contact him directly if you have questions.
:line
-USER-CG-CMM package :link(USER-CG-CMM),h5
+USER-CGSDK package :link(USER-CGSDK),h5
-Contents: CG-CMM stands for coarse-grained ??. This package
-implements several pair styles and an angle style using the coarse
-grained parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27
-(2007) (SDK), with extensions to simulate ionic liquids, electrolytes,
-lipids and charged amino acids. See src/USER-CG-CMM/README for more
-details.
+Contents: CGSDK stands for Shinoda-DeVane-Klein (SDK) coarse-grained
+molecular dynamics force field. This package implements several pair
+styles and an angle style using the coarse grained parametrization of
+Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007) (SDK), with extensions
+to simulate ionic liquids, electrolytes, lipids and charged amino acids.
+See src/USER-CGSDK/README for more details.
-Supporting info: src/USER-CG-CMM/README, "pair lj/sdk"_pair_sdk.html,
+Supporting info: src/USER-CGSDK/README, "pair lj/sdk"_pair_sdk.html,
"pair lj/sdk/coul/long"_pair_sdk.html, "angle sdk"_angle_sdk.html,
-examples/USER/cg-cmm
+examples/USER/cgsdk
Author: Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact
him directly if you have questions.
@@ -1329,10 +1329,12 @@ src/USER-COLVARS/README, lib/colvars/README, "fix
colvars"_fix_colvars.html, examples/USER/colvars
Authors: Axel Kohlmeyer at Temple U (akohlmey at gmail.com) wrote the
-fix. The COLVARS library itself is written and maintained by Giacomo
-Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome
-Henin (LISM, CNRS, Marseille, France). Contact them directly if you
-have questions.
+interface that integrates colvars into LAMMPS. The COLVARS library
+itself is written and maintained by Giacomo Fiorin (ICMS, Temple
+University, Philadelphia, PA, USA) and Jerome Henin (LISM, CNRS,
+Marseille, France). For more info, and to communicate with the COLVARS
+developers, please go to COLVARS home page at
+"http://colvars.github.io"_http://colvars.github.io/.
:line
diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt
index 785585f840..0cc535e543 100644
--- a/doc/src/angle_sdk.txt
+++ b/doc/src/angle_sdk.txt
@@ -46,7 +46,7 @@ from the pair_style.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-CG-CMM package. See the "Making
+USER-CGSDK package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt
index 212760e03d..1c348eaaf7 100644
--- a/doc/src/pair_sdk.txt
+++ b/doc/src/pair_sdk.txt
@@ -134,7 +134,7 @@ respa"_run_style.html command.
[Restrictions:]
-All of the lj/sdk pair styles are part of the USER-CG-CMM package.
+All of the lj/sdk pair styles are part of the USER-CGSDK package.
The {lj/sdk/coul/long} style also requires the KSPACE package to be
built (which is enabled by default). They are only enabled if LAMMPS
was built with that package. See the "Making
--
GitLab