(460976db) · Commits · 郑智淋 / lammps

src/force.cpp

+0 −1

Original line number	Diff line number	Diff line
		@@ -105,7 +105,6 @@ void Force::init()

		if (kspace) kspace->init(); // kspace must come before pair
		if (pair) pair->init(); // so g_ewald is defined
		if (bond) bond->init();
		if (angle) angle->init();
		if (dihedral) dihedral->init();
		if (improper) improper->init();

src/neighbor.cpp

+24 −5

Original line number	Diff line number	Diff line
		@@ -208,6 +208,10 @@ void Neighbor::init()
		// cutneigh = force cutoff + skin if cutforce > 0, else cutneigh = 0

		triggersq = 0.25skinskin;
		shrinkcheck = 0;
		if (domain->box_change && (domain->xperiodic \|\| domain->yperiodic \|\|
		(dimension == 3 && domain->zperiodic)))
		shrinkcheck = 1;

		n = atom->ntypes;
		if (cutneighsq == NULL) {
		@@ -996,11 +1000,23 @@ int Neighbor::decide()
		} else return 0;
		}

		/* ---------------------------------------------------------------------- */
		/* ----------------------------------------------------------------------
		if any atom moved trigger distance (half of neighbor skin) return 1
		shrink trigger distance if periodic box dimension has decreased
		------------------------------------------------------------------------- */

		int Neighbor::check_distance()
		{
		double delx,dely,delz,rsq;
		double delx,dely,delz,rsq,deltasq;

		if (shrinkcheck) {
		double delta = 0.0;
		if (domain->xperiodic) delta = MIN(delta,domain->xprd-xprdhold);
		if (domain->yperiodic) delta = MIN(delta,domain->yprd-yprdhold);
		if (domain->zperiodic) delta = MIN(delta,domain->zprd-zprdhold);
		delta = 0.5*skin - delta;
		deltasq = delta*delta;
		} else deltasq = triggersq;

		double **x = atom->x;
		int nlocal = atom->nlocal;
		@@ -1012,7 +1028,7 @@ int Neighbor::check_distance()
		dely = x[i][1] - xhold[i][1];
		delz = x[i][2] - xhold[i][2];
		rsq = delxdelx + delydely + delz*delz;
		if (rsq > triggersq) flag = 1;
		if (rsq > deltasq) flag = 1;
		}

		int flagall;
		@@ -1033,7 +1049,7 @@ void Neighbor::build()
		ago = 0;
		ncalls++;

		// store current atom positions if needed
		// store current atom positions and box size if needed

		if (dist_check) {
		double **x = atom->x;
		@@ -1049,6 +1065,9 @@ void Neighbor::build()
		xhold[i][1] = x[i][1];
		xhold[i][2] = x[i][2];
		}
		xprdhold = domain->xprd;
		yprdhold = domain->yprd;
		zprdhold = domain->zprd;
		}

		// if necessary, extend atom arrays in pairwise lists

src/neighbor.h

+4 −2

Original line number	Diff line number	Diff line
		@@ -93,6 +93,8 @@ class Neighbor : protected Pointers {

		double **xhold; // atom coords at last neighbor build
		int maxhold; // size of xhold array
		double xprdhold,yprdhold,zprdhold; // box size at last neighbor build
		int shrinkcheck;

		int nbinx,nbiny,nbinz; // # of global bins
		int *bins; // ptr to next atom in each bin

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