Merge branch 'master' into doc-updates (1f38e1a7) · Commits · 郑智淋 / lammps

doc/src/Manual.txt

+2 −2

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		<!-- HTML_ONLY -->
		<HEAD>
		<TITLE>LAMMPS Users Manual</TITLE>
		<META NAME="docnumber" CONTENT="27 Oct 2016 version">
		<META NAME="docnumber" CONTENT="9 Nov 2016 version">
		<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
		<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
		</HEAD>
		@@ -21,7 +21,7 @@
		<H1></H1>

		LAMMPS Documentation :c,h3
		27 Oct 2016 version :c,h4
		9 Nov 2016 version :c,h4

		Version info: :h4

doc/src/Section_commands.txt

+2 −0

Original line number	Diff line number	Diff line
		@@ -886,6 +886,8 @@ KOKKOS, o = USER-OMP, t = OPT.
		"body"_pair_body.html,
		"bop"_pair_bop.html,
		"born (go)"_pair_born.html,
		"born/coul/dsf"_pair_born.html,
		"born/coul/dsf/cs"_pair_born.html,
		"born/coul/long (go)"_pair_born.html,
		"born/coul/long/cs"_pair_born.html,
		"born/coul/msm (o)"_pair_born.html,

doc/src/Section_intro.txt

+3 −3

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		@@ -366,11 +366,11 @@ complementary modeling tasks.
		"DL_POLY"_dlpoly
		"Tinker"_tinker :ul

		:link(charmm,http://www.scripps.edu/brooks)
		:link(amber,http://amber.scripps.edu)
		:link(charmm,http://www.charmm.org)
		:link(amber,http://ambermd.org)
		:link(namd,http://www.ks.uiuc.edu/Research/namd/)
		:link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
		:link(dlpoly,http://www.cse.clrc.ac.uk/msi/software/DL_POLY)
		:link(dlpoly,http://www.ccp5.ac.uk/DL_POLY_CLASSIC)
		:link(tinker,http://dasher.wustl.edu/tinker)

		CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for

doc/src/pair_born.txt

+20 −5

Original line number	Diff line number	Diff line
		@@ -19,6 +19,8 @@ pair_style born/coul/msm/omp command :h3
		pair_style born/coul/wolf command :h3
		pair_style born/coul/wolf/gpu command :h3
		pair_style born/coul/wolf/omp command :h3
		pair_style born/coul/dsf command :h3
		pair_style born/coul/dsf/cs command :h3

		[Syntax:]

		@@ -37,7 +39,11 @@ args = list of arguments for a particular style :ul
		{born/coul/wolf} args = alpha cutoff (cutoff2)
		alpha = damping parameter (inverse distance units)
		cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
		cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
		cutoff2 = global cutoff for Coulombic (optional) (distance units)
		{born/coul/dsf} or {born/coul/dsf/cs} args = alpha cutoff (cutoff2)
		alpha = damping parameter (inverse distance units)
		cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
		cutoff2 = global cutoff for Coulombic (distance units) :pre

		[Examples:]

		@@ -62,6 +68,10 @@ pair_style born/coul/wolf 0.25 10.0 9.0
		pair_coeff * * 6.08 0.317 2.340 24.18 11.51
		pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre

		pair_style born/coul/dsf 0.1 10.0 12.0
		pair_coeff * * 0.0 1.00 0.00 0.00 0.00
		pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre

		[Description:]

		The {born} style computes the Born-Mayer-Huggins or Tosi/Fumi
		@@ -90,10 +100,14 @@ term.
		The {born/coul/wolf} style adds a Coulombic term as described for the
		Wolf potential in the "coul/wolf"_pair_coul.html pair style.

		The {born/coul/dsf} style computes the Coulomb contribution with the
		damped shifted force model as in the "coul/dsf"_pair_coul.html style.

		Style {born/coul/long/cs} is identical to {born/coul/long} except that
		a term is added for the "core/shell model"_Section_howto.html#howto_25
		to allow charges on core and shell particles to be separated by r =
		0.0.
		0.0. The same correction is introduced for {born/coul/dsf/cs} style
		which is identical to {born/coul/dsf}.

		Note that these potentials are related to the "Buckingham
		potential"_pair_buck.html.
		@@ -116,9 +130,10 @@ The second coefficient, rho, must be greater than zero.
		The last coefficient is optional. If not specified, the global A,C,D
		cutoff specified in the pair_style command is used.

		For {born/coul/long} and {born/coul/wolf} no Coulombic cutoff can be
		specified for an individual I,J type pair. All type pairs use the
		same global Coulombic cutoff specified in the pair_style command.
		For {born/coul/long}, {born/coul/wolf} and {born/coul/dsf} no
		Coulombic cutoff can be specified for an individual I,J type pair.
		All type pairs use the same global Coulombic cutoff specified in the
		pair_style command.

		:line

doc/src/pair_cs.txt

+20 −3

Original line number	Diff line number	Diff line
		@@ -8,19 +8,24 @@

		pair_style born/coul/long/cs command :h3
		pair_style buck/coul/long/cs command :h3
		pair_style born/coul/dsf/cs command :h3

		[Syntax:]

		pair_style style args :pre

		style = {born/coul/long/cs} or {buck/coul/long/cs}
		style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs}
		args = list of arguments for a particular style :ul
		{born/coul/long/cs} args = cutoff (cutoff2)
		cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
		cutoff2 = global cutoff for Coulombic (optional) (distance units)
		{buck/coul/long/cs} args = cutoff (cutoff2)
		cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
		cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
		cutoff2 = global cutoff for Coulombic (optional) (distance units)
		{born/coul/dsf/cs} args = alpha cutoff (cutoff2)
		alpha = damping parameter (inverse distance units)
		cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
		cutoff2 = global cutoff for Coulombic (distance units) :pre

		[Examples:]

		@@ -32,6 +37,10 @@ pair_style buck/coul/long/cs 10.0 8.0
		pair_coeff * * 100.0 1.5 200.0
		pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre

		pair_style born/coul/dsf/cs 0.1 10.0 12.0
		pair_coeff * * 0.0 1.00 0.00 0.00 0.00
		pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre

		[Description:]

		These pair styles are designed to be used with the adiabatic
		@@ -39,7 +48,7 @@ core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham. See
		"Section 6.25"_Section_howto.html#howto_25 of the manual for an
		overview of the model as implemented in LAMMPS.

		These pair styles are identical to the "pair_style
		The styles with a {coul/long} term are identical to the "pair_style
		born/coul/long"_pair_born.html and "pair_style
		buck/coul/long"_pair_buck.html styles, except they correctly treat the
		special case where the distance between two charged core and shell
		@@ -63,6 +72,14 @@ where C is an energy-conversion constant, Qi and Qj are the charges on
		the core and shell, epsilon is the dielectric constant and r_min is the
		minimal distance.

		The pair style {born/coul/dsf/cs} is identical to the
		"pair_style born/coul/dsf"_pair_born.html style, which uses the
		the damped shifted force model as in "coul/dsf"_pair_coul.html
		to compute the Coulomb contribution. This approach does not require
		a long-range solver, thus the only correction is the addition of a
		minimal distance to avoid the possible r = 0.0 case for a
		core/shell pair.

		[Restrictions:]

		These pair styles are part of the CORESHELL package. They are only

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