(9cecf815) · Commits · 郑智淋 / lammps

src/atom.cpp

+19 −11

Original line number	Diff line number	Diff line
		@@ -53,7 +53,8 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
		extra_bond_per_atom = 0;

		firstgroupname = NULL;
		sortfreq = 1000;
		sortfreq = 0;
		//sortfreq = 1000;
		userbinsize = 0.0;
		maxbin = maxnext = 0;
		binhead = NULL;
		@@ -353,13 +354,15 @@ void Atom::modify_params(int narg, char **arg)
		iarg += 2;
		} else if (strcmp(arg[iarg],"first") == 0) {
		if (iarg+2 > narg) error->all("Illegal atom_modify command");
		if (strcmp(arg[iarg+1],"all") == 0) delete [] firstgroupname;
		else {
		if (strcmp(arg[iarg+1],"all") == 0) {
		delete [] firstgroupname;
		firstgroupname = NULL;
		} else {
		int n = strlen(arg[iarg+1]) + 1;
		firstgroupname = new char[n];
		strcpy(firstgroupname,arg[iarg+1]);
		}
		sortfreq = 0;
		}
		iarg += 2;
		} else if (strcmp(arg[iarg],"sort") == 0) {
		if (iarg+3 > narg) error->all("Illegal atom_modify command");
		@@ -1360,9 +1363,9 @@ void Atom::sort()
		for (i = 0; i < nbins; i++) binhead[i] = -1;

		for (i = nlocal-1; i >= 0; i--) {
		ix = static_cast<int> ((x[i][0]-bboxlo[0])*bininv);
		iy = static_cast<int> ((x[i][1]-bboxlo[1])*bininv);
		iz = static_cast<int> ((x[i][2]-bboxlo[2])*bininv);
		ix = static_cast<int> ((x[i][0]-bboxlo[0])*bininvx);
		iy = static_cast<int> ((x[i][1]-bboxlo[1])*bininvy);
		iz = static_cast<int> ((x[i][2]-bboxlo[2])*bininvz);
		ix = MAX(ix,0);
		iy = MAX(iy,0);
		iz = MAX(iz,0);
		@@ -1439,7 +1442,7 @@ void Atom::setup_sort_bins()
		else binsize = 0.5 * neighbor->cutneighmax;
		if (binsize == 0.0) error->all("Atom sorting has bin size = 0.0");

		bininv = 1.0/binsize;
		double bininv = 1.0/binsize;

		// nbin xyz = local bins
		// bbox lo/hi = bounding box of my sub-domain
		@@ -1458,10 +1461,15 @@ void Atom::setup_sort_bins()
		nbinx = static_cast<int> ((bboxhi[0]-bboxlo[0]) * bininv);
		nbiny = static_cast<int> ((bboxhi[1]-bboxlo[1]) * bininv);
		nbinz = static_cast<int> ((bboxhi[2]-bboxlo[2]) * bininv);
		if (domain->dimension == 2) nbinz = 1;

		if (nbinx == 0) nbinx = 1;
		if (nbiny == 0) nbiny = 1;
		if (nbinz == 0) nbinz = 1;

		nbinx = MAX(nbinx,1);
		nbinx = MAX(nbiny,1);
		nbinx = MAX(nbinz,1);
		bininvx = nbinx / (bboxhi[0]-bboxlo[0]);
		bininvy = nbiny / (bboxhi[1]-bboxlo[1]);
		bininvz = nbinz / (bboxhi[2]-bboxlo[2]);

		if (1.0nbinxnbiny*nbinz > INT_MAX)
		error->one("Too many atom sorting bins");

src/atom.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -203,8 +203,8 @@ class Atom : protected Pointers {
		int *binhead; // 1st atom in each bin
		int *next; // next atom in bin
		int *permute; // permutation vector
		double userbinsize; // sorting bin size
		double bininv;
		double userbinsize; // requested sort bin size
		double bininvx,bininvy,bininvz; // inverse actual bin sizes
		double bboxlo[3],bboxhi[3]; // bounding box of my sub-domain

		int memlength; // allocated size of memstr

src/universe.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -26,7 +26,7 @@ using namespace LAMMPS_NS;

		Universe::Universe(LAMMPS *lmp, MPI_Comm communicator) : Pointers(lmp)
		{
		version = (char *) "7 Jul 2009";
		version = (char *) "15 Jan 2010";

		uworld = communicator;
		MPI_Comm_rank(uworld,&me);

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