Bugfix no 3 nearest neighbors for ghost atoms near boundary (4c19eab6) · Commits · 郑智淋 / lammps

potentials/C.drip

+7 −3

Original line number	Diff line number	Diff line
		@@ -6,10 +6,14 @@
		# Cite as M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, 98, 235404 (2018).


		# C0 C2 C4 C delta lambda A z0 B eta rho_cut r_cut
		C C 1.1598e-02 1.2981e-02 3.2515e-02 7.8151e-03 8.3679e-01 2.7158 2.2216e-02 3.34 7.6799e-03 1.1432 1.562 12.0
		# C0 C2 C4 C delta lambda A z0 B eta rho_cut r_cut normal_cut
		C C 1.1598e-02 1.2981e-02 3.2515e-02 7.8151e-03 8.3679e-01 2.7158 2.2216e-02 3.34 7.6799e-03 1.1432 1.562 12.0 3.7


		# C0, C2, C4, C, A, and B in [eV]
		# delta, z0, eta, rho_cut, and r_cut in [Angstrom]
		# delta, z0, eta, rho_cut, r_cut, and normal_cut in [Angstrom]
		# lambda in [1/Angstrom]
		#
		# normal_cut is a parameter not present in the Wen paper, but specific to the
		# LAMMPS implementation, which is used to find the 3 nearest neighbors of an
		# atom to construct the normal.

src/USER-MISC/pair_drip.cpp

+35 −9

Original line number	Diff line number	Diff line
		@@ -197,6 +197,14 @@ double PairDRIP::init_one(int i, int j)
		{
		if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");

		int itype = map[i];
		int jtype = map[j];
		int iparam_ij = elem2param[itype][jtype];
		Param& p = params[iparam_ij];

		// max cutoff is the main cutoff plus the normal cutoff such that
		double cutmax = p.rcut + p.ncut;

		return cutmax;
		}

		@@ -206,7 +214,7 @@ double PairDRIP::init_one(int i, int j)

		void PairDRIP::read_file(char *filename)
		{
		int params_per_line = 14;
		int params_per_line = 15;
		char *words = new char[params_per_line+1];
		memory->sfree(params);
		int nparams = 0;
		@@ -311,13 +319,12 @@ void PairDRIP::read_file(char *filename)
		params[nparams].eta = atof(words[11]);
		params[nparams].rhocut = atof(words[12]);
		params[nparams].rcut = atof(words[13]);
		params[nparams].ncut = atof(words[14]);

		// convenient precomputations
		params[nparams].rhocutsq = params[nparams].rhocut * params[nparams].rhocut;
		params[nparams].rcutsq = params[nparams].rcut * params[nparams].rcut;

		// set max cutoff
		if(params[nparams].rcut > cutmax) cutmax = params[nparams].rcut;
		params[nparams].ncutsq = params[nparams].ncut * params[nparams].ncut;

		nparams++;
		}
		@@ -371,6 +378,9 @@ void PairDRIP::compute(int eflag, int vflag)

		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		if (nearest3neigh[i][0] == -1) {
		continue;
		}
		itag = tag[i];
		xtmp = x[i][0];
		ytmp = x[i][1];
		@@ -387,6 +397,9 @@ void PairDRIP::compute(int eflag, int vflag)
		for (jj = 0; jj < jnum; jj++) {
		j = jlist[jj];
		j &= NEIGHMASK;
		if (nearest3neigh[j][0] == -1) {
		continue;
		}
		jtype = map[type[j]];
		jtag = tag[j];

		@@ -604,7 +617,7 @@ double PairDRIP::calc_repulsive(int const i, int const j, Param& p,

		void PairDRIP::find_nearest3neigh()
		{
		int i, j, ii, jj, n, allnum, jnum, itype, jtype, size;
		int i, j, ii, jj, n, allnum, inum, jnum, itype, jtype, size;
		double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
		int ilist, jlist, numneigh, *firstneigh;

		@@ -613,6 +626,7 @@ void PairDRIP::find_nearest3neigh()


		allnum = list->inum + list->gnum;
		inum = list->inum;
		ilist = list->ilist;
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;
		@@ -647,6 +661,7 @@ void PairDRIP::find_nearest3neigh()
		double nb3_rsq = 3.0e10;

		for (jj = 0; jj < jnum; jj++) {

		j = jlist[jj];
		j &= NEIGHMASK;
		jtype = map[type[j]];
		@@ -656,9 +671,9 @@ void PairDRIP::find_nearest3neigh()
		rsq = delx * delx + dely * dely + delz * delz;

		int iparam_ij = elem2param[itype][jtype];
		double rcutsq = params[iparam_ij].rcutsq;
		double ncutsq = params[iparam_ij].ncutsq;

		if (rsq < rcutsq && atom->molecule[i] == atom->molecule[j]) {
		if (rsq < ncutsq && atom->molecule[i] == atom->molecule[j]) {
		// find the 3 nearest neigh
		if (rsq < nb1_rsq) {
		nb3 = nb2;
		@@ -683,8 +698,19 @@ void PairDRIP::find_nearest3neigh()
		} // loop over jj

		// store neighbors to be used later to compute normal
		if (nb1_rsq >= 1.0e10 \|\| nb2_rsq >= 1.0e10 \|\| nb3_rsq >= 1.0e10) {
		if (nb3_rsq >= 1.0e10) {
		if (i<inum) {
		error->one(FLERR, "No enough neighbors to construct normal.");
		} else {
		// This only happens for ghost atoms that are near the boundary of the
		// domain (i.e. r > r_cut + n_cut). These ghost atoms will not be
		// the i j atoms in the compute function, but only neighbors of j atoms.
		// It is allowed not to have three neighbors for these atoms, since
		// their normals are not needed.
		nearest3neigh[i][0] = -1;
		nearest3neigh[i][1] = -1;
		nearest3neigh[i][2] = -1;
		}
		}
		else{
		nearest3neigh[i][0] = nb1;

src/USER-MISC/pair_drip.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -55,8 +55,8 @@ protected:
		struct Param
		{
		int ielement, jelement;
		double C0, C2, C4, C, delta, lambda, A, z0, B, eta, rhocut, rcut;
		double rhocutsq, rcutsq;
		double C0, C2, C4, C, delta, lambda, A, z0, B, eta, rhocut, rcut, ncut;
		double rhocutsq, rcutsq, ncutsq;
		};
		Param *params; // parameter set for I-J interactions
		int **nearest3neigh; // nearest 3 neighbors of atoms

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