Merge branch 'master' of https://www.github.com/lammps/lammps (12579556) · Commits · 郑智淋 / lammps

doc/src/Manual.txt

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		<!-- HTML_ONLY -->
		<HEAD>
		<TITLE>LAMMPS Users Manual</TITLE>
		<META NAME="docnumber" CONTENT="20 Jun 2017 version">
		<META NAME="docnumber" CONTENT="23 Jun 2017 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
		20 Jun 2017 version :c,h4
		23 Jun 2017 version :c,h4

		Version info: :h4

doc/src/kspace_modify.txt

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		@@ -219,10 +219,10 @@ instead of using the virial equation. This option cannot be used to access
		individual components of the pressure tensor, to compute per-atom virial,
		or with suffix kspace/pair styles of MSM, like OMP or GPU.

		The {fftbench} keyword applies only to PPPM. It is on by default. If
		this option is turned off, LAMMPS will not take the time at the end
		of a run to give FFT benchmark timings, and will finish a few seconds
		faster than it would if this option were on.
		The {fftbench} keyword applies only to PPPM. It is off by default. If
		this option is turned on, LAMMPS will perform a short FFT benchmark
		computation and report its timings, and will thus finish a some seconds
		later than it would if this option were off.

		The {collective} keyword applies only to PPPM. It is set to {no} by
		default, except on IBM BlueGene machines. If this option is set to
		@@ -306,7 +306,7 @@ parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
		The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
		5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
		gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
		yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik
		yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik
		(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
		split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order =
		order/disp = 7.

doc/src/pair_charmm.txt

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		@@ -104,7 +104,15 @@ charmmfsw"_dihedral_charmm.html command. Eventually code from the new
		styles will propagate into the related pair styles (e.g. implicit,
		accelerator, free energy variants).

		The general CHARMM formulas are as follows
		NOTE: The newest CHARMM pair styles reset the Coulombic energy
		conversion factor used internally in the code, from the LAMMPS value
		to the CHARMM value, as if it were effectively a parameter of the
		force field. This is because the CHARMM code uses a slightly
		different value for the this conversion factor in "real
		units"_units.html (Kcal/mole), namely CHARMM = 332.0716, LAMMPS =
		332.06371. This is to enable more precise agreement by LAMMPS with
		the CHARMM force field energies and forces, when using one of these
		two CHARMM pair styles.

		:c,image(Eqs/pair_charmm.jpg)

doc/src/pair_dipole.txt

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		@@ -71,6 +71,14 @@ and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
		torques do not act symmetrically. These formulas are discussed in
		"(Allen)"_#Allen2 and in "(Toukmaji)"_#Toukmaji2.

		Also note, that in the code, all of these terms (except Elj) have a
		C/epsilon prefactor, the same as the Coulombic term in the LJ +
		Coulombic pair styles discussed "here"_pair_lj.html. C is an
		energy-conversion constant and epsilon is the dielectric constant
		which can be set by the "dielectric"_dielectric.html command. The
		same is true of the equations that follow for other dipole pair
		styles.

		Style {lj/sf/dipole/sf} computes "shifted-force" interactions between
		pairs of particles that each have a charge and/or a point dipole
		moment. In general, a shifted-force potential is a (sligthly) modified

src/KSPACE/pair_lj_charmmfsw_coul_long.cpp

+19 −0

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		@@ -25,6 +25,7 @@
		#include <string.h>
		#include "pair_lj_charmmfsw_coul_long.h"
		#include "atom.h"
		#include "update.h"
		#include "comm.h"
		#include "force.h"
		#include "kspace.h"
		@@ -61,6 +62,15 @@ PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(LAMMPS *lmp) : Pair(lmp)
		// short-range/long-range flag accessed by DihedralCharmmfsw

		dihedflag = 1;

		// switch qqr2e from LAMMPS value to CHARMM value

		if (strcmp(update->unit_style,"real") == 0) {
		if ((comm->me == 0) && (force->qqr2e != force->qqr2e_charmm_real))
		error->message(FLERR,"Switching to CHARMM coulomb energy"
		" conversion constant");
		force->qqr2e = force->qqr2e_charmm_real;
		}
		}

		/* ---------------------------------------------------------------------- */
		@@ -87,6 +97,15 @@ PairLJCharmmfswCoulLong::~PairLJCharmmfswCoulLong()
		}
		if (ftable) free_tables();
		}

		// switch qqr2e back from CHARMM value to LAMMPS value

		if (update && strcmp(update->unit_style,"real") == 0) {
		if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real))
		error->message(FLERR,"Restoring original LAMMPS coulomb energy"
		" conversion constant");
		force->qqr2e = force->qqr2e_lammps_real;
		}
		}

		/* ---------------------------------------------------------------------- */

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