add coul/wolf/cs and born/coul/wolf/cs pair styles for CORESHELL package (71c4edda) · Commits · 郑智淋 / lammps

src/CORESHELL/Install.sh

+15 −9

Original line number	Diff line number	Diff line
		@@ -30,6 +30,7 @@ action () {

		action compute_temp_cs.cpp
		action compute_temp_cs.h

		action pair_born_coul_long_cs.cpp pair_born_coul_long.cpp
		action pair_born_coul_dsf_cs.cpp pair_born_coul_dsf.cpp
		action pair_buck_coul_long_cs.cpp pair_buck_coul_long.cpp
		@@ -40,3 +41,8 @@ action pair_coul_long_cs.cpp pair_coul_long.cpp
		action pair_coul_long_cs.h pair_coul_long.h
		action pair_lj_cut_coul_long_cs.cpp pair_lj_cut_coul_long.cpp
		action pair_lj_cut_coul_long_cs.h pair_lj_cut_coul_long.h

		action pair_born_coul_wolf_cs.cpp pair_born_coul_wolf.cpp
		action pair_born_coul_wolf_cs.h pair_born_coul_wolf.h
		action pair_coul_wolf_cs.cpp pair_coul_wolf.cpp
		action pair_coul_wolf_cs.h pair_coul_wolf.h

src/CORESHELL/pair_born_coul_wolf_cs.cpp

0 → 100644

+170 −0

Original line number	Diff line number	Diff line
		/* ----------------------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov

		Copyright (2003) Sandia Corporation. Under the terms of Contract
		DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		certain rights in this software. This software is distributed under
		the GNU General Public License.

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */


		#include <math.h>
		#include <stdio.h>
		#include <stdlib.h>
		#include <string.h>
		#include "pair_born_coul_wolf_cs.h"
		#include "atom.h"
		#include "comm.h"
		#include "force.h"
		#include "neighbor.h"
		#include "neigh_list.h"
		#include "math_const.h"
		#include "math_special.h"
		#include "memory.h"
		#include "error.h"

		using namespace LAMMPS_NS;
		using namespace MathConst;
		using namespace MathSpecial;

		#define EPSILON 1.0e-20

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

		PairBornCoulWolfCS::PairBornCoulWolfCS(LAMMPS *lmp) : PairBornCoulWolf(lmp)
		{
		single_enable = 0;
		}

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

		void PairBornCoulWolfCS::compute(int eflag, int vflag)
		{
		int i,j,ii,jj,inum,jnum,itype,jtype;
		double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
		double rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;
		double prefactor;
		double r,rexp;
		int ilist,jlist,numneigh,*firstneigh;
		double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq;

		evdwl = ecoul = 0.0;
		if (eflag \|\| vflag) ev_setup(eflag,vflag);
		else evflag = vflag_fdotr = 0;

		double **x = atom->x;
		double **f = atom->f;
		double *q = atom->q;
		int *type = atom->type;
		int nlocal = atom->nlocal;
		double *special_coul = force->special_coul;
		double *special_lj = force->special_lj;
		int newton_pair = force->newton_pair;
		double qqrd2e = force->qqrd2e;

		// self and shifted coulombic energy

		e_self = v_sh = 0.0;
		e_shift = erfc(alf*cut_coul)/cut_coul;
		f_shift = -(e_shift+ 2.0alf/MY_PIS exp(-alfalfcut_coul*cut_coul)) /
		cut_coul;

		inum = list->inum;
		ilist = list->ilist;
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;

		// loop over neighbors of my atoms

		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		qtmp = q[i];
		xtmp = x[i][0];
		ytmp = x[i][1];
		ztmp = x[i][2];
		itype = type[i];
		jlist = firstneigh[i];
		jnum = numneigh[i];

		qisq = qtmp*qtmp;
		e_self = -(e_shift/2.0 + alf/MY_PIS) * qisq*qqrd2e;
		if (eflag) ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);

		for (jj = 0; jj < jnum; jj++) {
		j = jlist[jj];
		factor_lj = special_lj[sbmask(j)];
		factor_coul = special_coul[sbmask(j)];
		j &= NEIGHMASK;

		delx = xtmp - x[j][0];
		dely = ytmp - x[j][1];
		delz = ztmp - x[j][2];
		rsq = delxdelx + delydely + delz*delz;
		jtype = type[j];

		if (rsq < cutsq[itype][jtype]) {
		rsq += EPSILON;
		// Add EPISLON for case: r = 0; Interaction must be removed
		// by special bond
		r2inv = 1.0/rsq;

		if (rsq < cut_coulsq) {
		r = sqrt(rsq);
		prefactor = qqrd2eqtmpq[j]/r;
		erfcc = erfc(alf*r);
		erfcd = exp(-alfalfr*r);
		v_sh = (erfcc - e_shiftr) prefactor;
		dvdrr = (erfcc/rsq + 2.0alf/MY_PIS erfcd/r) + f_shift;
		forcecoul = dvdrrrsqprefactor;
		if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
		} else forcecoul = 0.0;

		if (rsq < cut_ljsq[itype][jtype]) {
		r6inv = r2invr2invr2inv;
		r = sqrt(rsq);
		rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
		forceborn = born1[itype][jtype]rrexp - born2[itype][jtype]*r6inv
		+ born3[itype][jtype]r2invr6inv;
		} else forceborn = 0.0;

		fpair = (forcecoul + factor_ljforceborn) r2inv;

		f[i][0] += delx*fpair;
		f[i][1] += dely*fpair;
		f[i][2] += delz*fpair;
		if (newton_pair \|\| j < nlocal) {
		f[j][0] -= delx*fpair;
		f[j][1] -= dely*fpair;
		f[j][2] -= delz*fpair;
		}

		if (eflag) {
		if (rsq < cut_coulsq) {
		ecoul = v_sh;
		if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
		} else ecoul = 0.0;
		if (rsq < cut_ljsq[itype][jtype]) {
		evdwl = a[itype][jtype]rexp - c[itype][jtype]r6inv +
		d[itype][jtype]r6invr2inv - offset[itype][jtype];
		evdwl *= factor_lj;
		} else evdwl = 0.0;
		}

		if (evflag) ev_tally(i,j,nlocal,newton_pair,
		evdwl,ecoul,fpair,delx,dely,delz);
		}
		}
		}

		if (vflag_fdotr) virial_fdotr_compute();
		}

		/*
		Using erfc and expmsq provided by math_special.h

		See: http://lammps.sandia.gov/threads/msg61934.html
		*/

src/CORESHELL/pair_born_coul_wolf_cs.h

0 → 100644

+60 −0

Original line number	Diff line number	Diff line
		/* ----------------------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov

		Copyright (2003) Sandia Corporation. Under the terms of Contract
		DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		certain rights in this software. This software is distributed under
		the GNU General Public License.

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		#ifdef PAIR_CLASS

		PairStyle(born/coul/wolf/cs,PairBornCoulWolfCS)

		#else

		#ifndef LMP_PAIR_BORN_COUL_WOLF_CS_H
		#define LMP_PAIR_BORN_COUL_WOLF_CS_H

		#include "pair_born_coul_wolf.h"

		namespace LAMMPS_NS {

		class PairBornCoulWolfCS : public PairBornCoulWolf {
		public:
		PairBornCoulWolfCS(class LAMMPS *);
		virtual void compute(int, int);
		};

		}

		#endif
		#endif

		/* ERROR/WARNING messages:

		E: Illegal ... command

		Self-explanatory. Check the input script syntax and compare to the
		documentation for the command. You can use -echo screen as a
		command-line option when running LAMMPS to see the offending line.

		E: Incorrect args for pair coefficients

		Self-explanatory. Check the input script or data file.

		E: All pair coeffs are not set

		All pair coefficients must be set in the data file or by the
		pair_coeff command before running a simulation.

		E: Pair style born/coul/wolf/cs requires atom attribute q

		An atom style that defines this attribute must be used.


		*/

src/CORESHELL/pair_coul_wolf_cs.cpp

0 → 100644

+145 −0

Original line number	Diff line number	Diff line
		/* ----------------------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov

		Copyright (2003) Sandia Corporation. Under the terms of Contract
		DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		certain rights in this software. This software is distributed under
		the GNU General Public License.

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */


		#include <math.h>
		#include <stdio.h>
		#include <stdlib.h>
		#include <string.h>
		#include "pair_coul_wolf_cs.h"
		#include "atom.h"
		#include "comm.h"
		#include "force.h"
		#include "neighbor.h"
		#include "neigh_list.h"
		#include "math_const.h"
		#include "math_special.h"
		#include "memory.h"
		#include "error.h"

		using namespace LAMMPS_NS;
		using namespace MathConst;
		using namespace MathSpecial;

		#define EPSILON 1.0e-20

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

		PairCoulWolfCS::PairCoulWolfCS(LAMMPS *lmp) : PairCoulWolf( lmp )
		{
		single_enable = 0;
		}

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

		void PairCoulWolfCS::compute(int eflag, int vflag)
		{
		int i,j,ii,jj,inum,jnum;
		double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
		double rsq,forcecoul,factor_coul;
		double prefactor;
		double r;
		int ilist,jlist,numneigh,*firstneigh;
		double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq;

		ecoul = 0.0;
		if (eflag \|\| vflag) ev_setup(eflag,vflag);
		else evflag = vflag_fdotr = 0;

		double **x = atom->x;
		double **f = atom->f;
		double *q = atom->q;
		int nlocal = atom->nlocal;
		double *special_coul = force->special_coul;
		int newton_pair = force->newton_pair;
		double qqrd2e = force->qqrd2e;

		// self and shifted coulombic energy

		e_self = v_sh = 0.0;
		e_shift = erfc(alf*cut_coul)/cut_coul;
		f_shift = -(e_shift+ 2.0alf/MY_PIS exp(-alfalfcut_coul*cut_coul)) /
		cut_coul;

		inum = list->inum;
		ilist = list->ilist;
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;

		// loop over neighbors of my atoms

		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		qtmp = q[i];
		xtmp = x[i][0];
		ytmp = x[i][1];
		ztmp = x[i][2];
		jlist = firstneigh[i];
		jnum = numneigh[i];

		qisq = qtmp*qtmp;
		e_self = -(e_shift/2.0 + alf/MY_PIS) * qisq*qqrd2e;
		if (evflag) ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);

		for (jj = 0; jj < jnum; jj++) {
		j = jlist[jj];
		factor_coul = special_coul[sbmask(j)];
		j &= NEIGHMASK;

		delx = xtmp - x[j][0];
		dely = ytmp - x[j][1];
		delz = ztmp - x[j][2];
		rsq = delxdelx + delydely + delz*delz;

		if (rsq < cut_coulsq) {
		rsq += EPSILON;
		// Add EPISLON for case: r = 0; Interaction must be removed
		// by special bond
		r = sqrt(rsq);
		prefactor = qqrd2eqtmpq[j]/r;
		erfcc = erfc(alf*r);
		erfcd = exp(-alfalfr*r);
		v_sh = (erfcc - e_shiftr) prefactor;
		dvdrr = (erfcc/rsq + 2.0alf/MY_PIS erfcd/r) + f_shift;
		forcecoul = dvdrrrsqprefactor;
		if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
		fpair = forcecoul / rsq;

		f[i][0] += delx*fpair;
		f[i][1] += dely*fpair;
		f[i][2] += delz*fpair;
		if (newton_pair \|\| j < nlocal) {
		f[j][0] -= delx*fpair;
		f[j][1] -= dely*fpair;
		f[j][2] -= delz*fpair;
		}

		if (eflag) {
		ecoul = v_sh;
		if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
		} else ecoul = 0.0;

		if (evflag) ev_tally(i,j,nlocal,newton_pair,
		0.0,ecoul,fpair,delx,dely,delz);
		}
		}
		}

		if (vflag_fdotr) virial_fdotr_compute();
		}

		/* NOTES
		Using erfc and expmsq provided by math_special.h

		See: http://lammps.sandia.gov/threads/msg61934.html
		*/

src/CORESHELL/pair_coul_wolf_cs.h

0 → 100644

+54 −0

Original line number	Diff line number	Diff line
		/* -- c++ -- ----------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov

		Copyright (2003) Sandia Corporation. Under the terms of Contract
		DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		certain rights in this software. This software is distributed under
		the GNU General Public License.

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		#ifdef PAIR_CLASS

		PairStyle(coul/wolf/cs,PairCoulWolfCS)

		#else

		#ifndef LMP_PAIR_COUL_WOLF_CS_H_
		#define LMP_PAIR_COUL_WOLF_CS_H_

		#include "pair_coul_wolf.h"

		namespace LAMMPS_NS {

		class PairCoulWolfCS : public PairCoulWolf {
		public:
		PairCoulWolfCS( class LAMMPS *);
		virtual void compute( int, int);
		};

		}

		#endif
		#endif /* LMP_PAIR_COUL_WOLF_CS_H_ */

		/* ERROR/WARNING messages:

		E: Illegal ... command

		Self-explanatory. Check the input script syntax and compare to the
		documentation for the command. You can use -echo screen as a
		command-line option when running LAMMPS to see the offending line.

		E: Incorrect args for pair coefficients

		Self-explanatory. Check the input script or data file.

		E: Pair coul/wolf/cs requires atom attribute q

		The atom style defined does not have this attribute.

		*/

Admin message