(b0ce5b39) · Commits · 郑智淋 / lammps

src/ASPHERE/pair_gayberne.cpp

+41 −34

Original line number	Diff line number	Diff line
		@@ -25,9 +25,8 @@
		#include "comm.h"
		#include "force.h"
		#include "neighbor.h"
		#include "update.h"
		#include "neigh_list.h"
		#include "integrate.h"
		#include "respa.h"
		#include "memory.h"
		#include "error.h"

		@@ -75,20 +74,18 @@ PairGayBerne::~PairGayBerne()

		void PairGayBerne::compute(int eflag, int vflag)
		{
		int i,j,k,m,numneigh,itype,jtype;
		int i,j,ii,jj,m,inum,jnum,itype,jtype;
		double one_eng,rsq,r2inv,r6inv,forcelj;
		double fforce[3],ttor[3],rtor[3],r12[3];
		double a1[3][3],b1[3][3],g1[3][3],a2[3][3],b2[3][3],g2[3][3],temp[3][3];
		int *neighs;
		int ilist,jlist,numneigh,*firstneigh;
		double factor_lj;
		double **f;

		eng_vdwl = 0.0;
		if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;

		if (vflag == 2) f = update->f_pair;
		else f = atom->f;
		double **x = atom->x;
		double **f = atom->f;
		double **quat = atom->quat;
		double **tor = atom->torque;
		int *type = atom->type;
		@@ -97,12 +94,16 @@ void PairGayBerne::compute(int eflag, int vflag)
		double *special_lj = force->special_lj;
		int newton_pair = force->newton_pair;

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

		// loop over neighbors of my atoms

		for (i = 0; i < nlocal; i++) {
		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		itype = type[i];
		neighs = neighbor->firstneigh[i];
		numneigh = neighbor->numneigh[i];

		MathExtra::quat_to_mat_trans(quat[i],a1);
		MathExtra::diag_times3(well[itype],a1,temp);
		@@ -110,8 +111,11 @@ void PairGayBerne::compute(int eflag, int vflag)
		MathExtra::diag_times3(shape[itype],a1,temp);
		MathExtra::transpose_times3(a1,temp,g1);

		for (k = 0; k < numneigh; k++) {
		j = neighs[k];
		jlist = firstneigh[i];
		jnum = numneigh[i];

		for (jj = 0; jj < jnum; jj++) {
		j = jlist[jj];

		if (j < nall) factor_lj = 1.0;
		else {
		@@ -315,6 +319,31 @@ void PairGayBerne::coeff(int narg, char **arg)
		if (count == 0) error->all("Incorrect args for pair coefficients");
		}


		/* ----------------------------------------------------------------------
		init specific to this pair style
		------------------------------------------------------------------------- */

		void PairGayBerne::init_style()
		{
		if (!atom->quat_flag \|\| !atom->torque_flag)
		error->all("Pair gayberne requires atom attributes quat, torque");

		int irequest = neighbor->request(this);

		// per-type shape precalculations

		for (int i = 1; i <= atom->ntypes; i++) {
		if (setwell[i]) {
		double *one = atom->shape[i];
		shape[i][0] = one[0]*one[0];
		shape[i][1] = one[1]*one[1];
		shape[i][2] = one[2]*one[2];
		lshape[i] = (one[0]one[1]+one[2]one[2])sqrt(one[0]one[1]);
		}
		}
		}

		/* ----------------------------------------------------------------------
		init for one type pair i,j and corresponding j,i
		------------------------------------------------------------------------- */
		@@ -369,28 +398,6 @@ double PairGayBerne::init_one(int i, int j)
		return cut[i][j];
		}

		/* ----------------------------------------------------------------------
		check for necessary atom arrays
		------------------------------------------------------------------------- */

		void PairGayBerne::init_style()
		{
		if (!atom->quat_flag \|\| !atom->torque_flag)
		error->all("Pair gayberne requires atom attributes quat, torque");

		// per-type shape precalculations

		for (int i = 1; i <= atom->ntypes; i++) {
		if (setwell[i]) {
		double *one = atom->shape[i];
		shape[i][0] = one[0]*one[0];
		shape[i][1] = one[1]*one[1];
		shape[i][2] = one[2]*one[2];
		lshape[i] = (one[0]one[1]+one[2]one[2])sqrt(one[0]one[1]);
		}
		}
		}

		/* ----------------------------------------------------------------------
		proc 0 writes to restart file
		------------------------------------------------------------------------- */

src/ASPHERE/pair_gayberne.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -25,8 +25,8 @@ class PairGayBerne : public Pair {
		void compute(int, int);
		void settings(int, char **);
		void coeff(int, char **);
		double init_one(int, int);
		void init_style();
		double init_one(int, int);
		void write_restart(FILE *);
		void read_restart(FILE *);
		void write_restart_settings(FILE *);

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