Merge pull request #541 from lammps/charmm (25a5d12a) · Commits · 郑智淋 / lammps

doc/src/kspace_modify.txt

+5 −5

Original line number	Diff line number	Diff line
		@@ -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.

src/KSPACE/pair_lj_charmmfsw_coul_long.cpp

+19 −0

Original line number	Diff line number	Diff line
		@@ -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;
		}
		}

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

src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp

+19 −0

Original line number	Diff line number	Diff line
		@@ -25,6 +25,7 @@
		#include <string.h>
		#include "pair_lj_charmmfsw_coul_charmmfsh.h"
		#include "atom.h"
		#include "update.h"
		#include "comm.h"
		#include "force.h"
		#include "neighbor.h"
		@@ -46,6 +47,15 @@ PairLJCharmmfswCoulCharmmfsh::PairLJCharmmfswCoulCharmmfsh(LAMMPS *lmp) :
		// short-range/long-range flag accessed by DihedralCharmmfsw

		dihedflag = 0;

		// 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;
		}
		}

		/* ---------------------------------------------------------------------- */
		@@ -71,6 +81,15 @@ PairLJCharmmfswCoulCharmmfsh::~PairLJCharmmfswCoulCharmmfsh()
		memory->destroy(lj14_4);
		}
		}

		// 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;
		}
		}

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

src/force.cpp

+2 −0

Original line number	Diff line number	Diff line
		@@ -53,6 +53,8 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
		special_extra = 0;

		dielectric = 1.0;
		qqr2e_lammps_real = 332.06371; // these constants are toggled
		qqr2e_charmm_real = 332.0716; // by new CHARMM pair styles

		pair = NULL;
		bond = NULL;

src/force.h

+3 −0

Original line number	Diff line number	Diff line
		@@ -43,6 +43,9 @@ class Force : protected Pointers {
		double femtosecond; // 1 femtosecond in native units
		double qelectron; // 1 electron charge abs() in native units

		double qqr2e_lammps_real; // different versions of this constant
		double qqr2e_charmm_real; // used by new CHARMM pair styles

		int newton,newton_pair,newton_bond; // Newton's 3rd law settings

		class Pair *pair;

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