Merge branch 'gridcomm-tiled' of ssh://github.com/lammps/lammps into gridcomm-tiled (f1afa45b) · Commits · 郑智淋 / lammps

src/KSPACE/msm.cpp

+15 −14

Original line number	Diff line number	Diff line
		@@ -45,20 +45,21 @@ enum{FORWARD_RHO,FORWARD_AD,FORWARD_AD_PERATOM};

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

		MSM::MSM(LAMMPS *lmp) : KSpace(lmp),
		MSM::MSM(LAMMPS *lmp)
		: KSpace(lmp),
		factors(NULL), delxinv(NULL), delyinv(NULL), delzinv(NULL), nx_msm(NULL),
		ny_msm(NULL), nz_msm(NULL), nxlo_in(NULL), nylo_in(NULL), nzlo_in(NULL),
		nxhi_in(NULL), nyhi_in(NULL), nzhi_in(NULL), nxlo_out(NULL), nylo_out(NULL),
		nzlo_out(NULL), nxhi_out(NULL), nyhi_out(NULL), nzhi_out(NULL), ngrid(NULL),
		active_flag(NULL), alpha(NULL), betax(NULL), betay(NULL), betaz(NULL),
		peratom_allocate_flag(0),
		levels(0), world_levels(NULL), qgrid(NULL), egrid(NULL), v0grid(NULL), v1grid(NULL),
		v2grid(NULL), v3grid(NULL), v4grid(NULL), v5grid(NULL), g_direct(NULL),
		v0_direct(NULL), v1_direct(NULL), v2_direct(NULL), v3_direct(NULL), v4_direct(NULL),
		v5_direct(NULL), g_direct_top(NULL), v0_direct_top(NULL), v1_direct_top(NULL),
		v2_direct_top(NULL), v3_direct_top(NULL), v4_direct_top(NULL), v5_direct_top(NULL),
		phi1d(NULL), dphi1d(NULL), procneigh_levels(NULL), gc(NULL),
		gcall(NULL), part2grid(NULL), boxlo(NULL)
		peratom_allocate_flag(0),levels(0),world_levels(NULL),qgrid(NULL),egrid(NULL),
		v0grid(NULL), v1grid(NULL),v2grid(NULL),v3grid(NULL),v4grid(NULL),v5grid(NULL),
		g_direct(NULL),v0_direct(NULL),v1_direct(NULL),v2_direct(NULL),v3_direct(NULL),
		v4_direct(NULL),v5_direct(NULL),g_direct_top(NULL),v0_direct_top(NULL),
		v1_direct_top(NULL),v2_direct_top(NULL),v3_direct_top(NULL),v4_direct_top(NULL),
		v5_direct_top(NULL),phi1d(NULL),dphi1d(NULL),procneigh_levels(NULL),gcall(NULL),
		gc(NULL),gcall_buf1(NULL),gcall_buf2(NULL),gc_buf1(NULL),gc_buf2(NULL),
		ngc_buf1(NULL),ngc_buf2(NULL),part2grid(NULL),boxlo(NULL)
		{
		msmflag = 1;

src/USER-OMP/msm_cg_omp.cpp

+27 −23

Original line number	Diff line number	Diff line
		@@ -95,17 +95,7 @@ void MSMCGOMP::compute(int eflag, int vflag)

		// invoke allocate_peratom() if needed for first time

		if (vflag_atom && !peratom_allocate_flag) {
		allocate_peratom();
		cg_peratom_all->ghost_notify();
		cg_peratom_all->setup();
		for (int n=0; n<levels; n++) {
		if (!active_flag[n]) continue;
		cg_peratom[n]->ghost_notify();
		cg_peratom[n]->setup();
		}
		peratom_allocate_flag = 1;
		}
		if (vflag_atom && !peratom_allocate_flag) allocate_peratom();

		// extend size of per-atom arrays if necessary

		@@ -175,7 +165,8 @@ void MSMCGOMP::compute(int eflag, int vflag)
		// to fully sum contribution in their 3d grid

		current_level = 0;
		cg_all->reverse_comm(this,REVERSE_RHO);
		gcall->reverse_comm_kspace(this,1,sizeof(double),REVERSE_RHO,
		gcall_buf1,gcall_buf2,MPI_DOUBLE);

		// forward communicate charge density values to fill ghost grid points
		// compute direct sum interaction and then restrict to coarser grid
		@@ -183,24 +174,30 @@ void MSMCGOMP::compute(int eflag, int vflag)
		for (int n=0; n<=levels-2; n++) {
		if (!active_flag[n]) continue;
		current_level = n;
		cg[n]->forward_comm(this,FORWARD_RHO);

		gc[n]->forward_comm_kspace(this,1,sizeof(double),FORWARD_RHO,
		gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
		direct(n);
		restriction(n);
		}


		// compute direct interaction for top grid level for non-periodic
		// and for second from top grid level for periodic

		if (active_flag[levels-1]) {
		if (domain->nonperiodic) {
		current_level = levels-1;
		cg[levels-1]->forward_comm(this,FORWARD_RHO);
		gc[levels-1]->
		forward_comm_kspace(this,1,sizeof(double),FORWARD_RHO,
		gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
		direct_top(levels-1);
		cg[levels-1]->reverse_comm(this,REVERSE_AD);
		gc[levels-1]->
		reverse_comm_kspace(this,1,sizeof(double),REVERSE_AD,
		gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
		if (vflag_atom)
		cg_peratom[levels-1]->reverse_comm(this,REVERSE_AD_PERATOM);
		gc[levels-1]->
		reverse_comm_kspace(this,6,sizeof(double),REVERSE_AD_PERATOM,
		gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);

		} else {
		// Here using MPI_Allreduce is cheaper than using commgrid
		grid_swap_forward(levels-1,qgrid[levels-1]);
		@@ -208,7 +205,9 @@ void MSMCGOMP::compute(int eflag, int vflag)
		grid_swap_reverse(levels-1,egrid[levels-1]);
		current_level = levels-1;
		if (vflag_atom)
		cg_peratom[levels-1]->reverse_comm(this,REVERSE_AD_PERATOM);
		gc[levels-1]->
		reverse_comm_kspace(this,6,sizeof(double),REVERSE_AD_PERATOM,
		gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
		}
		}

		@@ -220,24 +219,28 @@ void MSMCGOMP::compute(int eflag, int vflag)
		prolongation(n);

		current_level = n;
		cg[n]->reverse_comm(this,REVERSE_AD);
		gc[n]->reverse_comm_kspace(this,1,sizeof(double),REVERSE_AD,
		gc_buf1[n],gc_buf2[n],MPI_DOUBLE);

		// extra per-atom virial communication

		if (vflag_atom)
		cg_peratom[n]->reverse_comm(this,REVERSE_AD_PERATOM);
		gc[n]->reverse_comm_kspace(this,6,sizeof(double),REVERSE_AD_PERATOM,
		gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
		}

		// all procs communicate E-field values
		// to fill ghost cells surrounding their 3d bricks

		current_level = 0;
		cg_all->forward_comm(this,FORWARD_AD);
		gcall->forward_comm_kspace(this,1,sizeof(double),FORWARD_AD,
		gcall_buf1,gcall_buf2,MPI_DOUBLE);

		// extra per-atom energy/virial communication

		if (vflag_atom)
		cg_peratom_all->forward_comm(this,FORWARD_AD_PERATOM);
		gcall->forward_comm_kspace(this,6,sizeof(double),FORWARD_AD_PERATOM,
		gcall_buf1,gcall_buf2,MPI_DOUBLE);

		// calculate the force on my particles (interpolation)

		@@ -556,6 +559,7 @@ void MSMCGOMP::fieldforce_peratom()
		}
		}

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

		double MSMCGOMP::memory_usage()
		{

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