functions theta(), theta_mod(), and cutoff() are never used in pair style bop (245f949e) · Commits · 郑智淋 / lammps

src/MANYBODY/pair_bop.cpp

+0 −159

Original line number	Diff line number	Diff line
		@@ -1035,145 +1035,6 @@ void PairBOP::gneigh()

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

		void PairBOP::theta()
		{
		int i,j,ii,jj,kk;
		int itype,jtype,i12;
		int temp_ij,temp_ik,temp_ijk;
		int n,nlocal,nall,ks;
		int nlisti;
		int *ilist;
		int *iilist;
		int **firstneigh;
		double rj2,rk2,rsq,ps;
		double rj1k1,rj2k2;
		double **x = atom->x;
		int *type = atom->type;

		nlocal = atom->nlocal;
		nall = nlocal+atom->nghost;
		ilist = list->ilist;
		firstneigh = list->firstneigh;
		if(update_list!=0)
		memory_theta_grow();
		else
		memory_theta_create();
		for (ii = 0; ii < nall; ii++) {
		if(ii<nlocal)
		i= ilist[ii];
		else
		i=ii;
		itype = map[type[i]]+1;

		iilist=firstneigh[i];
		nlisti=BOP_total[i];
		for(jj=0;jj<nlisti;jj++) {
		temp_ij=BOP_index[i]+jj;
		j=iilist[neigh_index[temp_ij]];
		jtype = map[type[j]]+1;
		if(itype==jtype)
		i12=itype-1;
		else if(itype<jtype)
		i12=itypebop_types-itype(itype+1)/2+jtype-1;
		else
		i12=jtypebop_types-jtype(jtype+1)/2+itype-1;
		if(i12>=npairs) {
		error->one(FLERR,"Too many atom pairs for pair bop");
		}
		disij[0][temp_ij]=x[j][0]-x[i][0];
		disij[1][temp_ij]=x[j][1]-x[i][1];
		disij[2][temp_ij]=x[j][2]-x[i][2];
		rsq=disij[0][temp_ij]*disij[0][temp_ij]
		+disij[1][temp_ij]*disij[1][temp_ij]
		+disij[2][temp_ij]*disij[2][temp_ij];
		rij[temp_ij]=sqrt(rsq);
		if(rij[temp_ij]<=rcut[i12])
		neigh_flag[temp_ij]=1;
		else
		neigh_flag[temp_ij]=0;
		if(rij[temp_ij]<=rcut3[i12])
		neigh_flag3[temp_ij]=1;
		else
		neigh_flag3[temp_ij]=0;
		ps=rij[temp_ij]*rdr[i12]+1.0;
		ks=(int)ps;
		if(nr-1<ks)
		ks=nr-1;
		ps=ps-ks;
		if(ps>1.0)
		ps=1.0;
		betaS[temp_ij]=((pBetaS3[i12][ks-1]ps+pBetaS2[i12][ks-1])ps+pBetaS1[i12][ks-1])*ps+pBetaS[i12][ks-1];
		dBetaS[temp_ij]=(pBetaS6[i12][ks-1]ps+pBetaS5[i12][ks-1])ps
		+pBetaS4[i12][ks-1];
		betaP[temp_ij]=((pBetaP3[i12][ks-1]ps+pBetaP2[i12][ks-1])ps
		+pBetaP1[i12][ks-1])*ps+pBetaP[i12][ks-1];
		dBetaP[temp_ij]=(pBetaP6[i12][ks-1]ps+pBetaP5[i12][ks-1])ps
		+pBetaP4[i12][ks-1];
		repul[temp_ij]=((pRepul3[i12][ks-1]ps+pRepul2[i12][ks-1])ps
		+pRepul1[i12][ks-1])*ps+pRepul[i12][ks-1];
		dRepul[temp_ij]=(pRepul6[i12][ks-1]ps+pRepul5[i12][ks-1])ps
		+pRepul4[i12][ks-1];
		}
		}
		for (ii = 0; ii < nall; ii++) {
		n=0;
		if(ii<nlocal)
		i= ilist[ii];
		else
		i=ii;
		iilist=firstneigh[i];
		nlisti=BOP_total[i];
		for(jj=0;jj<nlisti;jj++) {
		temp_ij=BOP_index[i]+jj;
		j=iilist[neigh_index[temp_ij]];
		rj2=rij[temp_ij]*rij[temp_ij];
		for(kk=jj+1;kk<nlisti;kk++) {
		if(cos_index[i]+n>=cos_total) {
		error->one(FLERR,"Too many atom triplets for pair bop");
		}
		temp_ik=BOP_index[i]+kk;
		temp_ijk=cos_index[i]+n;
		if(temp_ijk>=cos_total) {
		error->one(FLERR,"Too many atom triplets for pair bop");
		}
		rk2=rij[temp_ik]*rij[temp_ik];
		rj1k1=rij[temp_ij]*rij[temp_ik];
		rj2k2=rj1k1*rj1k1;
		if(temp_ijk>=cos_total) {
		error->one(FLERR,"Too many atom triplets for pair bop");
		}
		cosAng[temp_ijk]=(disij[0][temp_ij]*disij[0][temp_ik]+disij[1][temp_ij]
		disij[1][temp_ik]+disij[2][temp_ij]disij[2][temp_ik])/rj1k1;
		dcAng[temp_ijk][0][0]=(disij[0][temp_ik]*rj1k1-cosAng[temp_ijk]
		disij[0][temp_ij]rk2)/(rj2k2);
		dcAng[temp_ijk][1][0]=(disij[1][temp_ik]*rj1k1-cosAng[temp_ijk]
		disij[1][temp_ij]rk2)/(rj2k2);
		dcAng[temp_ijk][2][0]=(disij[2][temp_ik]*rj1k1-cosAng[temp_ijk]
		disij[2][temp_ij]rk2)/(rj2k2);
		dcAng[temp_ijk][0][1]=(disij[0][temp_ij]*rj1k1-cosAng[temp_ijk]
		disij[0][temp_ik]rj2)/(rj2k2);
		dcAng[temp_ijk][1][1]=(disij[1][temp_ij]*rj1k1-cosAng[temp_ijk]
		disij[1][temp_ik]rj2)/(rj2k2);
		dcAng[temp_ijk][2][1]=(disij[2][temp_ij]*rj1k1-cosAng[temp_ijk]
		disij[2][temp_ik]rj2)/(rj2k2);
		n++;
		}
		}
		}
		}

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

		void PairBOP::theta_mod()
		{
		if(update_list!=0)
		memory_theta_grow();
		else
		memory_theta_create();
		}

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

		/* The formulation differs slightly to avoid negative square roots
		in the calculation of Sigma^(1/2) of (a) Eq. 6 and (b) Eq. 11 */

		@@ -5556,26 +5417,6 @@ void _noopt PairBOP::read_table(char *filename)
		}
		}

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

		double PairBOP::cutoff(double rp,double vrcut,int mode,double r)
		{
		double tmp,tmp_beta,tmp_alpha,cut_store;

		if(mode==1) {
		tmp=(rsmall-rbig)*(r-rp)/(vrcut-rp)+rbig;
		cut_store=(erfc(tmp)-erfc(rsmall))/(erfc(rbig)-erfc(rsmall));
		}
		else {
		tmp_beta=log(log(rbig)/log(rsmall))/log(rp/vrcut);
		tmp_alpha=-log(rbig)/pow(rp,tmp_beta);
		cut_store=(exp(-tmp_alphapow(r,tmp_beta))-exp(-tmp_alphapow(vrcut
		,tmp_beta)))/(exp(-tmp_alpha*pow(rp,tmp_beta))-exp(-tmp_alpha
		*pow(vrcut,tmp_beta)));
		}
		return(cut_store);
		}

		/* ----------------------------------------------------------------------
		memory usage of local atom-based arrays
		------------------------------------------------------------------------- */

src/MANYBODY/pair_bop.h

+0 −3

Original line number	Diff line number	Diff line
		@@ -199,14 +199,11 @@ class PairBOP : public Pair {
		void setPrepul();
		void setSign();
		void gneigh();
		void theta();
		void theta_mod();
		double sigmaBo(int, int);
		double PiBo(int, int);
		void memory_theta_create();
		void memory_theta_destroy();
		void memory_theta_grow();
		double cutoff(double, double, int, double);

		void read_table(char *);
		void allocate();

Admin message