Merge pull request #728 from danicholson/cluster-fragment-aggregate-fixes (45555b01) · Commits · 郑智淋 / lammps

src/compute_aggregate_atom.cpp

+47 −2

Original line number	Diff line number	Diff line
		@@ -52,6 +52,7 @@ ComputeAggregateAtom::ComputeAggregateAtom(LAMMPS lmp, int narg, char *arg) :
		peratom_flag = 1;
		size_peratom_cols = 0;
		comm_forward = 1;
		comm_reverse = 1;

		nmax = 0;
		}
		@@ -120,8 +121,10 @@ void ComputeAggregateAtom::compute_peratom()
		}

		// invoke full neighbor list (will copy or build if necessary)
		// on the first step of a run, set preflag to one in neighbor->build_one(...)

		neighbor->build_one(list);
		if (update->firststep == update->ntimestep) neighbor->build_one(list,1);
		else neighbor->build_one(list);

		// if group is dynamic, insure ghost atom masks are current

		@@ -164,6 +167,11 @@ void ComputeAggregateAtom::compute_peratom()
		while (1) {
		comm->forward_comm_compute(this);

		// reverse communication when bonds are not stored on every processor

		if (force->newton_bond)
		comm->reverse_comm_compute(this);

		change = 0;
		while (1) {
		done = 1;
		@@ -253,13 +261,50 @@ void ComputeAggregateAtom::unpack_forward_comm(int n, int first, double *buf)
		m = 0;
		last = first + n;
		if (commflag)
		for (i = first; i < last; i++) aggregateID[i] = buf[m++];
		for (i = first; i < last; i++) {
		double x = buf[m++];

		// only overwrite ghost IDs with values lower than current ones

		aggregateID[i] = MIN(x,aggregateID[i]);
		}
		else {
		int *mask = atom->mask;
		for (i = first; i < last; i++) mask[i] = (int) ubuf(buf[m++]).i;
		}
		}

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

		int ComputeAggregateAtom::pack_reverse_comm(int n, int first, double *buf)
		{
		int i,m,last;

		m = 0;
		last = first + n;
		for (i = first; i < last; i++) {
		buf[m++] = aggregateID[i];
		}
		return m;
		}

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

		void ComputeAggregateAtom::unpack_reverse_comm(int n, int list, double buf)
		{
		int i,j,m;

		m = 0;
		for (i = 0; i < n; i++) {
		j = list[i];
		double x = buf[m++];

		// only overwrite local IDs with values lower than current ones

		aggregateID[j] = MIN(x,aggregateID[j]);
		}
		}

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

src/compute_aggregate_atom.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -33,6 +33,8 @@ class ComputeAggregateAtom : public Compute {
		void compute_peratom();
		int pack_forward_comm(int, int , double , int, int *);
		void unpack_forward_comm(int, int, double *);
		int pack_reverse_comm(int, int, double *);
		void unpack_reverse_comm(int, int , double );
		double memory_usage();

		private:

src/compute_cluster_atom.cpp

+3 −1

Original line number	Diff line number	Diff line
		@@ -112,8 +112,10 @@ void ComputeClusterAtom::compute_peratom()
		}

		// invoke full neighbor list (will copy or build if necessary)
		// on the first step of a run, set preflag to one in neighbor->build_one(...)

		neighbor->build_one(list);
		if (update->firststep == update->ntimestep) neighbor->build_one(list,1);
		else neighbor->build_one(list);

		inum = list->inum;
		ilist = list->ilist;

src/compute_fragment_atom.cpp

+44 −1

Original line number	Diff line number	Diff line
		@@ -44,6 +44,7 @@ ComputeFragmentAtom::ComputeFragmentAtom(LAMMPS lmp, int narg, char *arg) :
		peratom_flag = 1;
		size_peratom_cols = 0;
		comm_forward = 1;
		comm_reverse = 1;

		nmax = 0;
		}
		@@ -122,6 +123,11 @@ void ComputeFragmentAtom::compute_peratom()
		while (1) {
		comm->forward_comm_compute(this);

		// reverse communication when bonds are not stored on every processor

		if (force->newton_bond)
		comm->reverse_comm_compute(this);

		change = 0;
		while (1) {
		done = 1;
		@@ -183,13 +189,50 @@ void ComputeFragmentAtom::unpack_forward_comm(int n, int first, double *buf)
		m = 0;
		last = first + n;
		if (commflag)
		for (i = first; i < last; i++) fragmentID[i] = buf[m++];
		for (i = first; i < last; i++) {
		double x = buf[m++];

		// only overwrite ghost IDs with values lower than current ones

		fragmentID[i] = MIN(x,fragmentID[i]);
		}
		else {
		int *mask = atom->mask;
		for (i = first; i < last; i++) mask[i] = (int) ubuf(buf[m++]).i;
		}
		}

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

		int ComputeFragmentAtom::pack_reverse_comm(int n, int first, double *buf)
		{
		int i,m,last;

		m = 0;
		last = first + n;
		for (i = first; i < last; i++) {
		buf[m++] = fragmentID[i];
		}
		return m;
		}

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

		void ComputeFragmentAtom::unpack_reverse_comm(int n, int list, double buf)
		{
		int i,j,m;

		m = 0;
		for (i = 0; i < n; i++) {
		j = list[i];
		double x = buf[m++];

		// only overwrite local IDs with values lower than current ones

		fragmentID[j] = MIN(x,fragmentID[j]);
		}
		}

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

src/compute_fragment_atom.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -32,6 +32,8 @@ class ComputeFragmentAtom : public Compute {
		void compute_peratom();
		int pack_forward_comm(int, int , double , int, int *);
		void unpack_forward_comm(int, int, double *);
		int pack_reverse_comm(int, int, double *);
		void unpack_reverse_comm(int, int , double );
		double memory_usage();

		private:

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