Merge pull request #464 from akohlmey/rename-cg-cmm-to-cgsdk (f5cf1f13) · Commits · 郑智淋 / lammps

doc/src/Section_intro.txt

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		@@ -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

doc/src/Section_packages.txt

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		@@ -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

doc/src/angle_sdk.txt

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		@@ -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:]

doc/src/pair_sdk.txt

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		@@ -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

examples/USER/cg-cmm/README→examples/USER/cgsdk/README

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		LAMMPS USER-CMM-CG example problems
		LAMMPS USER-CGSDK example problems

		Each of these sub-directories contains a sample problem for the SDK
		coarse grained MD potentials that you can run with LAMMPS.

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