Remove unused variables and methods (d6f3a955) · Commits · 郑智淋 / lammps

src/USER-MISC/pair_drip.cpp

+24 −159

Original line number	Diff line number	Diff line
		@@ -56,27 +56,21 @@ PairDRIP::PairDRIP(LAMMPS *lmp) : Pair(lmp)
		params = NULL;
		elem2param = NULL;
		map = NULL;

		cutmax = 0.0;
		nmax = 0;
		maxlocal = 0;
		ipage = NULL;
		pgsize = oneatom = 0;

		nearest3neigh = NULL;


		//no_virial_fdotr_compute = 1;
		//j nmax = 0;
		//j maxlocal = 0;
		//j ipage = NULL;
		//j pgsize = oneatom = 0;

		// set comm size needed by this Pair
		//comm_forward = 39;
		nearest3neigh = NULL;
		}

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

		PairDRIP::~PairDRIP()
		{
		delete [] ipage;
		// delete [] ipage;

		if (allocated) {
		memory->destroy(setflag);
		@@ -110,26 +104,6 @@ void PairDRIP::init_style()
		neighbor->requests[irequest]->half = 0;
		neighbor->requests[irequest]->full = 1;
		neighbor->requests[irequest]->ghost = 1;

		// TODO this can be deleted
		// local DRIP neighbor list
		// create pages if first time or if neighbor pgsize/oneatom has changed

		int create = 0;
		if (ipage == NULL) create = 1;
		if (pgsize != neighbor->pgsize) create = 1;
		if (oneatom != neighbor->oneatom) create = 1;

		if (create) {
		delete [] ipage;
		pgsize = neighbor->pgsize;
		oneatom = neighbor->oneatom;

		int nmypage= comm->nthreads;
		ipage = new MyPage<int>[nmypage];
		for (int i = 0; i < nmypage; i++)
		ipage[i].init(oneatom,pgsize,PGDELTA);
		}
		}

		/* ----------------------------------------------------------------------
		@@ -377,73 +351,6 @@ void PairDRIP::read_file(char *filename)

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

		//int PairDRIP::pack_forward_comm(int n, int list, double buf,
		// int /pbc_flag/, int * /pbc/)
		//{
		// int i,j,m,l,ip,id;
		//
		// m = 0;
		//// for (i = 0; i < n; i++) {
		//// j = list[i];
		//// buf[m++] = normal[j][0];
		//// buf[m++] = normal[j][1];
		//// buf[m++] = normal[j][2];
		//// buf[m++] = dnormdri[0][0][j];
		//// buf[m++] = dnormdri[0][1][j];
		//// buf[m++] = dnormdri[0][2][j];
		//// buf[m++] = dnormdri[1][0][j];
		//// buf[m++] = dnormdri[1][1][j];
		//// buf[m++] = dnormdri[1][2][j];
		//// buf[m++] = dnormdri[2][0][j];
		//// buf[m++] = dnormdri[2][1][j];
		//// buf[m++] = dnormdri[2][2][j];
		//// for (l = 0; l < 3; l++){
		//// for (id = 0; id < 3; id++){
		//// for (ip = 0; ip < 3; ip++){
		//// buf[m++] = dnormal[id][ip][l][j];
		//// }
		//// }
		//// }
		//// }
		//
		// return m;
		//}

		/* ---------------------------------------------------------------------- */
		//
		//void PairDRIP::unpack_forward_comm(int n, int first, double *buf)
		//{
		// int i,m,last,l,ip,id;
		//
		//// m = 0;
		//// last = first + n;
		//// for (i = first; i < last; i++) {
		//// normal[i][0] = buf[m++];
		//// normal[i][1] = buf[m++];
		//// normal[i][2] = buf[m++];
		//// dnormdri[0][0][i] = buf[m++];
		//// dnormdri[0][1][i] = buf[m++];
		//// dnormdri[0][2][i] = buf[m++];
		//// dnormdri[1][0][i] = buf[m++];
		//// dnormdri[1][1][i] = buf[m++];
		//// dnormdri[1][2][i] = buf[m++];
		//// dnormdri[2][0][i] = buf[m++];
		//// dnormdri[2][1][i] = buf[m++];
		//// dnormdri[2][2][i] = buf[m++];
		//// for (l = 0; l < 3; l++){
		//// for (id = 0; id < 3; id++){
		//// for (ip = 0; ip < 3; ip++){
		//// dnormal[id][ip][l][i] = buf[m++];
		//// }
		//// }
		//// }
		//// }
		////
		//}
		//

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

		void PairDRIP::compute(int eflag, int vflag)
		{

		@@ -452,7 +359,6 @@ void PairDRIP::compute(int eflag, int vflag)
		double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1,fpair2, r, rsq;
		int ilist,jlist,numneigh,*firstneigh;

		int nbi1, nbi2, nbi3;
		double ni[DIM];
		double dni_dri[DIM][DIM], dni_drnb1[DIM][DIM];
		double dni_drnb2[DIM][DIM], dni_drnb3[DIM][DIM];
		@@ -461,9 +367,6 @@ void PairDRIP::compute(int eflag, int vflag)
		evdwl = 0.0;
		ev_init(eflag,vflag);

		// TODO
		//vflag_global = 1;

		double **x = atom->x;
		double **f = atom->f;
		int *type = atom->type;
		@@ -476,14 +379,8 @@ void PairDRIP::compute(int eflag, int vflag)
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;


		// find nearest 3 neighbors of each atom
		find_nearest3neigh();

		//TODO what does this comm do?
		// communicate the normal vector and its derivatives
		// comm->forward_comm_pair(this);

		// loop over neighbors of my atoms
		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		@@ -497,7 +394,7 @@ void PairDRIP::compute(int eflag, int vflag)


		// normal and its derivatives w.r.t. atom i and its 3 nearest neighs
		calc_normal(i, nbi1, nbi2, nbi3, ni, dni_dri,dni_drnb1, dni_drnb2, dni_drnb3);
		calc_normal(i, ni, dni_dri,dni_drnb1, dni_drnb2, dni_drnb3);

		double fi[DIM] = {0., 0., 0.};

		@@ -507,17 +404,6 @@ void PairDRIP::compute(int eflag, int vflag)
		jtype = map[type[j]];
		jtag = tag[j];

		// // two-body interactions from full neighbor list, skip half of them
		// if (itag > jtag) {
		// if ((itag+jtag) % 2 == 0) continue;
		// } else if (itag < jtag) {
		// if ((itag+jtag) % 2 == 1) continue;
		// } else {
		// if (x[j][2] < ztmp) continue;
		// if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
		// if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
		// }

		delx = x[j][0] - xtmp;
		dely = x[j][1] - ytmp;
		delz = x[j][2] - ztmp;
		@@ -535,26 +421,12 @@ void PairDRIP::compute(int eflag, int vflag)

		double phi_attr = calc_attractive(i,j,p, rsq, rvec, fi, fj);

		double phi_repul = calc_repulsive(i, j, p, rsq, rvec, nbi1, nbi2,
		nbi3, ni, dni_dri, dni_drnb1, dni_drnb2, dni_drnb3, fi, fj);
		double phi_repul = calc_repulsive(i, j, p, rsq, rvec,
		ni, dni_dri, dni_drnb1, dni_drnb2, dni_drnb3, fi, fj);

		if (eflag) evdwl = HALF * (phi_repul + phi_attr);

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

		if (evflag) ev_tally(i,j,nlocal,newton_pair, evdwl,0.0,0,0,0,0);


		// ev_tally_xyz(int i, int j, int nlocal, int newton_pair,
		// double evdwl, double ecoul,
		// double fx, double fy, double fz,
		// double delx, double dely, double delz)


		// void ev_tally_xyz_full(int i, double evdwl, double ecoul,
		// double fx, double fy, double fz,
		// double delx, double dely, double delz)

		f[j][0] += fj[0];
		f[j][1] += fj[1];
		f[j][2] += fj[2];
		@@ -582,8 +454,6 @@ if (vflag_fdotr)





		printf("@@@ evflags in compute\n");
		printf("@@@ eflag_either=%d\n", eflag_either);
		printf("@@@ eflag_global=%d\n", eflag_global);
		@@ -649,9 +519,9 @@ double PairDRIP::calc_attractive(int const i, int const j, Param& p,
		/* ---------------------------------------------------------------------- */
		double PairDRIP::calc_repulsive(int const i, int const j,
		Param& p, double const rsq, double const * rvec,
		int const nbi1, int const nbi2, int const nbi3, double const * ni,
		V3 const * dni_dri, V3 const * dni_drnb1, V3 const * dni_drnb2,
		V3 const * dni_drnb3, double * const fi, double * const fj)
		double const * ni, V3 const * dni_dri, V3 const * dni_drnb1,
		V3 const * dni_drnb2, V3 const * dni_drnb3,
		double * const fi, double * const fj)
		{
		double **f = atom->f;
		double **x = atom->x;
		@@ -666,7 +536,10 @@ double PairDRIP::calc_repulsive(int const i, int const j,
		double z0 = p.z0;
		double cutoff = p.rcut;

		// nearest 3 neighbors of atom j
		// nearest 3 neighbors of atoms i and j
		int nbi1 = nearest3neigh[i][0];
		int nbi2 = nearest3neigh[i][1];
		int nbi3 = nearest3neigh[i][2];
		int nbj1 = nearest3neigh[j][0];
		int nbj2 = nearest3neigh[j][1];
		int nbj3 = nearest3neigh[j][2];
		@@ -733,12 +606,12 @@ double PairDRIP::calc_repulsive(int const i, int const j,
		fi[k] -= HALF * tp * V1 * ((dtdij + dgij_drhosq) * drhosqij_dri[k] + dgij_dri[k]);
		fj[k] -= HALF * tp * V1 * ((dtdij + dgij_drhosq) * drhosqij_drj[k] + dgij_drj[k]);

		// derivative of V2 contribute to neighs of atom i
		// derivative of V2 contribute to nearest 3 neighs of atom i
		fnbi1[k] =- HALF * tp * V1 * ((dtdij + dgij_drhosq) * drhosqij_drnb1[k] + dgij_drk1[k]);
		fnbi2[k] =- HALF * tp * V1 * ((dtdij + dgij_drhosq) * drhosqij_drnb2[k] + dgij_drk2[k]);
		fnbi3[k] =- HALF * tp * V1 * ((dtdij + dgij_drhosq) * drhosqij_drnb3[k] + dgij_drk3[k]);

		// derivative of V2 contribute to neighs of atom j
		// derivative of V2 contribute to nearest 3 neighs of atom j
		fnbj1[k] =- HALF * tp * V1 * dgij_drl1[k];
		fnbj2[k] =- HALF * tp * V1 * dgij_drl2[k];
		fnbj3[k] =- HALF * tp * V1 * dgij_drl3[k];
		@@ -785,7 +658,7 @@ void PairDRIP::find_nearest3neigh()
		int i,j,ii,jj,n,allnum,jnum,itype,jtype;
		double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
		int ilist,jlist,numneigh,*firstneigh;
		int *neighptr;
		//int *neighptr;

		double **x = atom->x;
		int *type = atom->type;
		@@ -799,17 +672,10 @@ void PairDRIP::find_nearest3neigh()
		memory->destroy(nearest3neigh);
		memory->create(nearest3neigh, allnum, 3, "DRIP:nearest3neigh");

		// store all DRIP neighs of owned and ghost atoms
		// scan full neighbor list of I

		ipage->reset();

		for (ii = 0; ii < allnum; ii++) {
		i = ilist[ii];

		n = 0;
		neighptr = ipage->vget();

		xtmp = x[i][0];
		ytmp = x[i][1];
		ztmp = x[i][2];
		@@ -878,14 +744,13 @@ void PairDRIP::find_nearest3neigh()

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

		void PairDRIP::calc_normal(int const i, int& k1, int& k2, int& k3,
		double * const normal, V3 const dn_dri, V3 const dn_drk1,
		V3 const dn_drk2, V3 const dn_drk3)
		void PairDRIP::calc_normal(int const i, double * const normal,
		V3 const dn_dri, V3 const dn_drk1, V3 const dn_drk2, V3 const dn_drk3)
		{

		k1 = nearest3neigh[i][0];
		k2 = nearest3neigh[i][1];
		k3 = nearest3neigh[i][2];
		int k1 = nearest3neigh[i][0];
		int k2 = nearest3neigh[i][1];
		int k3 = nearest3neigh[i][2];

		// normal does not depend on i, setting to zero
		for (int j = 0; j < DIM; j++) {

src/USER-MISC/pair_drip.h

+17 −23

Original line number	Diff line number	Diff line
		@@ -40,18 +40,8 @@ class PairDRIP : public Pair {
		void coeff(int, char **);
		double init_one(int, int);
		void init_style();
		// int pack_forward_comm(int, int , double , int, int *);
		// void unpack_forward_comm(int, int, double *);

		protected:
		double cutmax; // max cutoff for all species
		int me;
		int maxlocal; // size of numneigh, firstneigh arrays
		int pgsize; // size of neighbor page
		int oneatom; // max # of neighbors for one atom
		MyPage<int> *ipage; // neighbor list pages


		struct Param {
		int ielement,jelement;
		double C0,C2,C4,C,delta,lambda,A,z0,B,eta,rhocut,rcut;
		@@ -65,7 +55,7 @@ class PairDRIP : public Pair {
		int nelements; // # of unique elements
		int nparams; // # of stored parameter sets
		int maxparam; // max # of parameter sets
		int nmax; // max # of atoms
		double cutmax; // max cutoff for all species
		int ** nearest3neigh; // nearest 3 neighbors of atoms

		void read_file(char * );
		@@ -77,17 +67,16 @@ class PairDRIP : public Pair {

		double calc_repulsive(int const i, int const j,
		Param& p, double const rsq, double const * rvec,
		int const nbi1, int const nbi2, int const nbi3, double const * ni,
		V3 const * dni_dri, V3 const * dni_drnb1, V3 const * dni_drnb2,
		V3 const * dni_drnb3, double * const fi, double * const fj);
		double const * ni, V3 const * dni_dri,
		V3 const * dni_drnb1, V3 const * dni_drnb2, V3 const * dni_drnb3,
		double * const fi, double * const fj);


		void find_nearest3neigh();


		void calc_normal(int const i, int& k1, int& k2, int& k3,
		double * const normal, V3 const dn_dri, V3 const dn_drk1,
		V3 const dn_drk2, V3 const dn_drk3);
		void calc_normal(int const i, double * const normal,
		V3 const dn_dri, V3 const dn_drk1, V3 const dn_drk2, V3 const dn_drk3);



		@@ -122,15 +111,13 @@ void deriv_cross( double const* rk, double const* rl, double const* rm,
		double* const cross, V3 *const dcross_drk,
		V3 const dcross_drl, V3 const dcross_drm);



		// inline functions
		inline double dot(double const* x, double const* y) {
		return x[0] * y[0] + x[1] * y[1] + x[2] * y[2];
		}


		inline void mat_dot_vec(V3 const* X, double const* y, double* const z)
		{
		inline void mat_dot_vec(V3 const* X, double const* y, double* const z) {
		for (int k = 0; k < 3; k++) {
		z[k] = X[k][0] * y[0] + X[k][1] * y[1] + X[k][2] * y[2];
		}
		@@ -161,5 +148,12 @@ 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: No enough neighbors to construct normal

		Cannot find three neighbors within cutoff of the target atom.
		Check the configuration.




		*/

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