(9e8c9fb0) · Commits · 郑智淋 / lammps

src/comm.cpp

+38 −17

Original line number	Diff line number	Diff line
		@@ -51,6 +51,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
		MPI_Comm_size(world,&nprocs);

		user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0;
		grid2proc = NULL;

		style = SINGLE;
		multilo = multihi = NULL;
		@@ -82,6 +83,8 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)

		Comm::~Comm()
		{
		if (grid2proc) memory->destroy_3d_int_array(grid2proc);

		free_swap();
		if (style == MULTI) {
		free_multi();
		@@ -162,6 +165,14 @@ void Comm::set_procs()
		if (force->dimension == 2 && procgrid[2] != 1)
		error->all("Proc grid in z != 1 for 2d simulation");

		if (grid2proc) memory->destroy_3d_int_array(grid2proc);
		grid2proc = memory->create_3d_int_array(procgrid[0],procgrid[1],procgrid[2],
		"comm:grid2proc");

		// use MPI Cartesian routines to setup 3d grid of procs
		// grid2proc[i][j][k] = proc that owns i,j,k location in grid
		// let MPI compute it instead of LAMMPS in case it is machine optimized

		int reorder = 0;
		int periods[3];
		periods[0] = periods[1] = periods[2] = 1;
		@@ -172,9 +183,19 @@ void Comm::set_procs()
		MPI_Cart_shift(cartesian,0,1,&procneigh[0][0],&procneigh[0][1]);
		MPI_Cart_shift(cartesian,1,1,&procneigh[1][0],&procneigh[1][1]);
		MPI_Cart_shift(cartesian,2,1,&procneigh[2][0],&procneigh[2][1]);

		int coords[3];
		int i,j,k;
		for (i = 0; i < procgrid[0]; i++)
		for (j = 0; j < procgrid[1]; j++)
		for (k = 0; k < procgrid[2]; k++) {
		coords[0] = i; coords[1] = j; coords[2] = k;
		MPI_Cart_rank(cartesian,coords,&grid2proc[i][j][k]);
		}

		MPI_Comm_free(&cartesian);

		// can't set lamda box params until procs are assigned
		// set lamda box params after procs are assigned

		if (triclinic) domain->set_lamda_box();

		@@ -206,10 +227,10 @@ void Comm::setup()

		int i;
		int ntypes = atom->ntypes;
		double prd,prd_border,sublo,subhi;
		double prd,sublo,*subhi;

		if (triclinic == 0) {
		prd = prd_border = domain->prd;
		prd = domain->prd;
		sublo = domain->sublo;
		subhi = domain->subhi;
		cutghost[0] = cutghost[1] = cutghost[2] = neighbor->cutghost;
		@@ -220,8 +241,7 @@ void Comm::setup()
		cuttype[i];
		}
		} else {
		prd = domain->prd;
		prd_border = domain->prd_lamda;
		prd = domain->prd_lamda;
		sublo = domain->sublo_lamda;
		subhi = domain->subhi_lamda;
		double *h_inv = domain->h_inv;
		@@ -245,9 +265,9 @@ void Comm::setup()
		// need = # of procs I need atoms from in each dim based on max cutoff
		// for 2d, don't communicate in z

		need[0] = static_cast<int> (cutghost[0] * procgrid[0] / prd_border[0]) + 1;
		need[1] = static_cast<int> (cutghost[1] * procgrid[1] / prd_border[1]) + 1;
		need[2] = static_cast<int> (cutghost[2] * procgrid[2] / prd_border[2]) + 1;
		need[0] = static_cast<int> (cutghost[0] * procgrid[0] / prd[0]) + 1;
		need[1] = static_cast<int> (cutghost[1] * procgrid[1] / prd[1]) + 1;
		need[2] = static_cast<int> (cutghost[2] * procgrid[2] / prd[2]) + 1;
		if (force->dimension == 2) need[2] = 0;

		// if non-periodic, do not communicate further than procgrid-1 away
		@@ -906,9 +926,11 @@ void Comm::reverse_comm_compute(Compute *compute)

		/* ----------------------------------------------------------------------
		communicate atoms to new owning procs via irregular communication
		unlike exchange(), allows for atoms to move arbitrary distances
		can be used in place of exchange()
		unlike exchange(), allows atoms to have moved arbitrarily long distances
		first setup irregular comm pattern, then invoke it
		for triclinic, atoms must be in lamda coords (0-1) before irregular is called
		for triclinic,
		atoms must be in lamda coords (0-1) before irregular is called
		------------------------------------------------------------------------- */

		void Comm::irregular()
		@@ -930,7 +952,7 @@ void Comm::irregular()

		// loop over atoms, flag any that are not in my sub-box
		// fill buffer with atoms leaving my box, using < and >=
		// assign which proc it belongs to
		// assign which proc it belongs to via irregular_lookup()
		// when atom is deleted, fill it in with last atom

		AtomVec *avec = atom->avec;
		@@ -1020,7 +1042,7 @@ Comm::Plan Comm::irregular_create(int n, int sizes, int *proclist,
		// nsend = # of messages I send

		for (i = 0; i < nprocs; i++) list[i] = 0;
		for (i = 0; i < n; i++) list[proclist[i]] += sizes[n];
		for (i = 0; i < n; i++) list[proclist[i]] += sizes[i];

		int nsend = 0;
		for (i = 0; i < nprocs; i++)
		@@ -1200,7 +1222,7 @@ void Comm::irregular_destroy(Plan *plan)
		}

		/* ----------------------------------------------------------------------
		compute which proc owns atom with x coord
		determine which proc owns atom with x coord
		x will be in box (orthogonal) or lamda coords (triclinic)
		------------------------------------------------------------------------- */

		@@ -1225,12 +1247,11 @@ int Comm::irregular_lookup(double *x)
		if (loc[0] < 0) loc[0] = 0;
		if (loc[0] >= procgrid[0]) loc[0] = procgrid[0] - 1;
		if (loc[1] < 0) loc[1] = 0;
		if (loc[1] >= procgrid[1]) loc[0] = procgrid[1] - 1;
		if (loc[1] >= procgrid[1]) loc[1] = procgrid[1] - 1;
		if (loc[2] < 0) loc[2] = 0;
		if (loc[2] >= procgrid[2]) loc[0] = procgrid[2] - 1;
		if (loc[2] >= procgrid[2]) loc[2] = procgrid[2] - 1;

		int proc = loc[2]procgrid[1]procgrid[0] + loc[1]*procgrid[0] + loc[0];
		return proc;
		return grid2proc[loc[0]][loc[1]][loc[2]];
		}

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

src/comm.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -70,6 +70,7 @@ class Comm : protected Pointers {
		int **pbc; // dimension flags for PBC adjustments
		int comm_x_only,comm_f_only; // 1 if only exchange x,f in for/rev comm
		int map_style; // non-0 if global->local mapping is done
		int ***grid2proc; // which proc owns i,j,k loc in 3d grid

		int *firstrecv; // where to put 1st recv atom in each swap
		int **sendlist; // list of atoms to send in each swap

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