Merge pull request #1099 from jrgissing/bond/react-efficient-competing_reactions (1f5885fc) · Commits · 郑智淋 / lammps

src/USER-MISC/fix_bond_react.cpp

+21 −10

Original line number	Diff line number	Diff line
		@@ -961,6 +961,10 @@ void FixBondReact::superimpose_algorithm()
		local_num_mega = 0;
		ghostly_num_mega = 0;

		// indicates local ghosts of other procs
		int tmp;
		localsendlist = (int *) comm->extract("localsendlist",tmp);

		// quick description of important global indices you'll see floating about:
		// 'pion' is the pioneer loop index
		// 'neigh' in the first neighbor index
		@@ -1857,17 +1861,24 @@ if so, flag for broadcasting for perusal by all processors

		void FixBondReact::glove_ghostcheck()
		{
		// it appears this little loop was deemed important enough for its own function!
		// noteworthy: it's only relevant for parallel

		// here we add glove to either local_mega_glove or ghostly_mega_glove
		int ghostly = 1;
		//for (int i = 0; i < onemol->natoms; i++) {
		// if (atom->map(glove[i][1]) >= atom->nlocal) {
		// ghostly = 1;
		// break;
		// }
		//}
		// ghostly_mega_glove includes atoms that are ghosts, either of this proc or another
		// 'ghosts of another' indication taken from comm->sendlist

		int ghostly = 0;
		if (comm->style == 0) {
		for (int i = 0; i < onemol->natoms; i++) {
		int ilocal = atom->map(glove[i][1]);
		if (ilocal >= atom->nlocal \|\| localsendlist[ilocal] == 1) {
		ghostly = 1;
		break;
		}
		}
		} else {
		#if !defined(MPI_STUBS)
		ghostly = 1;
		#endif
		}

		if (ghostly == 1) {
		ghostly_mega_glove[0][ghostly_num_mega] = rxnID;

src/USER-MISC/fix_bond_react.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -122,6 +122,7 @@ class FixBondReact : public Fix {
		tagint **local_mega_glove; // consolidation local of reaction instances
		tagint **ghostly_mega_glove; // consolidation nonlocal of reaction instances
		tagint **global_mega_glove; // consolidation (inter-processor) of gloves containing nonlocal atoms
		int *localsendlist; // indicates ghosts of other procs
		int local_num_mega; // num of local reaction instances
		int ghostly_num_mega; // num of ghostly reaction instances
		int global_megasize; // num of reaction instances in global_mega_glove

src/comm.h

+3 −0

Original line number	Diff line number	Diff line
		@@ -112,6 +112,9 @@ class Comm : protected Pointers {
		int read_lines_from_file(FILE , int, int, char );
		int read_lines_from_file_universe(FILE , int, int, char );

		// extract data useful to other classes
		virtual void extract(const char , int &) {return NULL;}

		protected:
		int bordergroup; // only communicate this group in borders

src/comm_brick.cpp

+30 −1

Original line number	Diff line number	Diff line
		@@ -55,7 +55,8 @@ CommBrick::CommBrick(LAMMPS *lmp) :
		size_reverse_send(NULL), size_reverse_recv(NULL),
		slablo(NULL), slabhi(NULL), multilo(NULL), multihi(NULL),
		cutghostmulti(NULL), pbc_flag(NULL), pbc(NULL), firstrecv(NULL),
		sendlist(NULL), maxsendlist(NULL), buf_send(NULL), buf_recv(NULL)
		sendlist(NULL), localsendlist(NULL), maxsendlist(NULL),
		buf_send(NULL), buf_recv(NULL)
		{
		style = 0;
		layout = Comm::LAYOUT_UNIFORM;
		@@ -74,6 +75,7 @@ CommBrick::~CommBrick()
		}

		if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]);
		if (localsendlist) memory->destroy(localsendlist);
		memory->sfree(sendlist);
		memory->destroy(maxsendlist);

		@@ -1469,6 +1471,33 @@ void CommBrick::free_multi()
		multilo = multihi = NULL;
		}

		/* ----------------------------------------------------------------------
		extract data potentially useful to other classes
		------------------------------------------------------------------------- */

		void CommBrick::extract(const char str, int &dim)
		{
		if (strcmp(str,"localsendlist") == 0) {
		int i, iswap, isend;
		if (!localsendlist)
		memory->create(localsendlist,atom->nlocal,"comm:localsendlist");
		else
		memory->grow(localsendlist,atom->nlocal,"comm:localsendlist");

		for (i = 0; i < atom->nlocal; i++)
		localsendlist[i] = 0;

		for (iswap = 0; iswap < nswap; iswap++)
		for (isend = 0; isend < sendnum[iswap]; isend++)
		if (sendlist[iswap][isend] < atom->nlocal)
		localsendlist[sendlist[iswap][isend]] = 1;

		return (void *) localsendlist;
		}

		return NULL;
		}

		/* ----------------------------------------------------------------------
		return # of bytes of allocated memory
		------------------------------------------------------------------------- */

src/comm_brick.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -46,6 +46,7 @@ class CommBrick : public Comm {

		void forward_comm_array(int, double **); // forward comm of array
		int exchange_variable(int, double , double &); // exchange on neigh stencil
		void extract(const char ,int &);
		virtual bigint memory_usage();

		protected:
		@@ -67,6 +68,7 @@ class CommBrick : public Comm {

		int *firstrecv; // where to put 1st recv atom in each swap
		int **sendlist; // list of atoms to send in each swap
		int *localsendlist; // indexed list of local sendlist atoms
		int *maxsendlist; // max size of send list for each swap

		double *buf_send; // send buffer for all comm

Admin message