Calculating short neighbor lists (e37d2b5c) · Commits · 郑智淋 / lammps

src/KOKKOS/pair_vashishta_kokkos.cpp

+58 −1

Original line number	Diff line number	Diff line
		@@ -108,7 +108,7 @@ void PairVashishtaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
		newton_pair = force->newton_pair;
		nall = atom->nlocal + atom->nghost;

		const int inum = list->inum;
		inum = list->inum;
		const int ignum = inum + list->gnum;
		NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
		d_ilist = k_list->d_ilist;
		@@ -121,6 +121,29 @@ void PairVashishtaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
		EV_FLOAT ev;
		EV_FLOAT ev_all;

		int max_neighs = d_neighbors.dimension_1();

		if ((d_neighbors_short_2body.dimension_1() != max_neighs) \|\|
		(d_neighbors_short_2body.dimension_0() != ignum)) {
		d_neighbors_short_2body = Kokkos::View<int**,DeviceType>("Vashishta::neighbors_short_2body",ignum,max_neighs);
		}
		if (d_numneigh_short_2body.dimension_0()!=ignum) {
		d_numneigh_short_2body = Kokkos::View<int*,DeviceType>("Vashishta::numneighs_short_2body",ignum);
		}

		if ((d_neighbors_short_3body.dimension_1() != max_neighs) \|\|
		(d_neighbors_short_3body.dimension_0() != ignum)) {
		d_neighbors_short_3body = Kokkos::View<int**,DeviceType>("Vashishta::neighbors_short_3body",ignum,max_neighs);
		}

		if (d_numneigh_short_3body.dimension_0()!=ignum) {
		d_numneigh_short_3body = Kokkos::View<int*,DeviceType>("Vashishta::numneighs_short_3body",ignum);
		}

		Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairVashishtaComputeShortNeigh>(0,neighflag==FULL?ignum:inum), *this);



		// loop over neighbor list of my atoms

		if (neighflag == HALF) {
		@@ -174,6 +197,40 @@ void PairVashishtaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
		copymode = 0;
		}

		template<class DeviceType>
		KOKKOS_INLINE_FUNCTION
		void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeShortNeigh, const int& ii) const {
		const int i = d_ilist[ii];
		const X_FLOAT xtmp = x(i,0);
		const X_FLOAT ytmp = x(i,1);
		const X_FLOAT ztmp = x(i,2);

		const int jnum = d_numneigh[i];
		int inside_2body = 0;
		int inside_3body = 0;
		for (int jj = 0; jj < jnum; jj++) {
		int j = d_neighbors(i,jj);
		j &= NEIGHMASK;

		const X_FLOAT delx = xtmp - x(j,0);
		const X_FLOAT dely = ytmp - x(j,1);
		const X_FLOAT delz = ztmp - x(j,2);
		const F_FLOAT rsq = delxdelx + delydely + delz*delz;

		if (rsq < cutmax*cutmax) {
		d_neighbors_short_2body(i,inside_2body) = j;
		inside_2body++;
		}

		if (rsq < cutmax_3body*cutmax_3body) {
		d_neighbors_short_3body(i,inside_3body) = j;
		inside_3body++;
		}
		}
		d_numneigh_short_2body(i) = inside_2body;
		d_numneigh_short_3body(i) = inside_3body;
		}

		template<class DeviceType>
		template<int NEIGHFLAG, int EVFLAG>
		KOKKOS_INLINE_FUNCTION

src/KOKKOS/pair_vashishta_kokkos.h

+9 −1

Original line number	Diff line number	Diff line
		@@ -34,6 +34,8 @@ struct TagPairVashishtaComputeFullA{};
		template<int NEIGHFLAG, int EVFLAG>
		struct TagPairVashishtaComputeFullB{};

		struct TagPairVashishtaComputeShortNeigh{};

		namespace LAMMPS_NS {

		template<class DeviceType>
		@@ -75,6 +77,9 @@ class PairVashishtaKokkos : public PairVashishta {
		KOKKOS_INLINE_FUNCTION
		void operator()(TagPairVashishtaComputeFullB<NEIGHFLAG,EVFLAG>, const int&) const;

		KOKKOS_INLINE_FUNCTION
		void operator()(TagPairVashishtaComputeShortNeigh, const int&) const;

		template<int NEIGHFLAG>
		KOKKOS_INLINE_FUNCTION
		void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
		@@ -136,7 +141,10 @@ class PairVashishtaKokkos : public PairVashishta {
		int nlocal,nall,eflag,vflag;

		int inum;

		Kokkos::View<int**,DeviceType> d_neighbors_short_2body;
		Kokkos::View<int*,DeviceType> d_numneigh_short_2body;
		Kokkos::View<int**,DeviceType> d_neighbors_short_3body;
		Kokkos::View<int*,DeviceType> d_numneigh_short_3body;
		friend void pair_virial_fdotr_compute<PairVashishtaKokkos>(PairVashishtaKokkos*);
		};

src/MANYBODY/pair_vashishta.cpp

+2 −1

Original line number	Diff line number	Diff line
		@@ -532,11 +532,12 @@ void PairVashishta::setup_params()
		}

		// set cutmax to max of all params

		cutmax_3body = 0.0;
		cutmax = 0.0;
		for (m = 0; m < nparams; m++) {
		if (params[m].cut > cutmax) cutmax = params[m].cut;
		if (params[m].r0 > cutmax) cutmax = params[m].r0;
		if (params[m].r0 > cutmax_3body) cutmax_3body = params[m].r0;
		}
		}

src/MANYBODY/pair_vashishta.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -46,6 +46,7 @@ class PairVashishta : public Pair {
		};
		protected:
		double cutmax; // max cutoff for all elements
		double cutmax_3body; // max cutoff for all elements
		int nelements; // # of unique elements
		char **elements; // names of unique elements
		int ***elem2param; // mapping from element triplets to parameters

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