Merge pull request #2231 from stanmoore1/reax_hybrid (7a312ca8) · Commits · 郑智淋 / lammps

src/KOKKOS/fix_qeq_reax_kokkos.cpp

+7 −6

Original line number	Diff line number	Diff line
		@@ -195,7 +195,6 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
		type = atomKK->k_type.view<DeviceType>();
		mask = atomKK->k_mask.view<DeviceType>();
		nlocal = atomKK->nlocal;
		nall = atom->nlocal + atom->nghost;
		newton_pair = force->newton_pair;

		k_params.template sync<DeviceType>();
		@@ -207,6 +206,7 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
		d_neighbors = k_list->d_neighbors;
		d_ilist = k_list->d_ilist;
		inum = list->inum;
		ignum = inum + list->gnum;

		copymode = 1;

		@@ -289,6 +289,8 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)

		// calculate_Q();

		k_s_hist.template sync<DeviceType>();
		k_t_hist.template sync<DeviceType>();
		calculate_q();
		k_s_hist.template modify<DeviceType>();
		k_t_hist.template modify<DeviceType>();
		@@ -373,7 +375,6 @@ void FixQEqReaxKokkos<DeviceType>::allocate_array()
		}

		// init_storage
		const int ignum = atom->nlocal + atom->nghost;
		FixQEqReaxKokkosZeroFunctor<DeviceType> zero_functor(this);
		Kokkos::parallel_for(ignum,zero_functor);

		@@ -732,7 +733,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
		FixQEqReaxKokkosSparse12Functor<DeviceType> sparse12_functor(this);
		Kokkos::parallel_for(inum,sparse12_functor);
		if (neighflag != FULL) {
		Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
		Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
		if (neighflag == HALF) {
		FixQEqReaxKokkosSparse13Functor<DeviceType,HALF> sparse13_functor(this);
		Kokkos::parallel_for(inum,sparse13_functor);
		@@ -788,7 +789,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
		FixQEqReaxKokkosSparse22Functor<DeviceType> sparse22_functor(this);
		Kokkos::parallel_for(inum,sparse22_functor);
		if (neighflag != FULL) {
		Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
		Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
		if (need_dup)
		dup_o.reset_except(d_o);
		if (neighflag == HALF) {
		@@ -869,7 +870,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
		FixQEqReaxKokkosSparse32Functor<DeviceType> sparse32_functor(this);
		Kokkos::parallel_for(inum,sparse32_functor);
		if (neighflag != FULL) {
		Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
		Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
		if (need_dup)
		dup_o.reset_except(d_o);
		if (neighflag == HALF) {
		@@ -927,7 +928,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
		FixQEqReaxKokkosSparse22Functor<DeviceType> sparse22_functor(this);
		Kokkos::parallel_for(inum,sparse22_functor);
		if (neighflag != FULL) {
		Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
		Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
		if (need_dup)
		dup_o.reset_except(d_o);
		if (neighflag == HALF) {

src/KOKKOS/fix_qeq_reax_kokkos.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -151,7 +151,7 @@ class FixQEqReaxKokkos : public FixQEqReax {
		double memory_usage();

		private:
		int inum;
		int inum,ignum;
		int allocated_flag;
		int need_dup;

src/KOKKOS/pair_reaxc_kokkos.cpp

+14 −28

Original line number	Diff line number	Diff line
		@@ -199,6 +199,8 @@ void PairReaxCKokkos<DeviceType>::setup()
		hbond_parameters *hbp;

		for (i = 1; i <= n; i++) {
		if (map[i] == -1) continue;

		// general
		k_params_sing.h_view(i).mass = system->reax_param.sbp[map[i]].mass;

		@@ -229,6 +231,8 @@ void PairReaxCKokkos<DeviceType>::setup()
		k_params_sing.h_view(i).p_hbond = system->reax_param.sbp[map[i]].p_hbond;

		for (j = 1; j <= n; j++) {
		if (map[j] == -1) continue;

		twbp = &(system->reax_param.tbp[map[i]][map[j]]);

		// vdW
		@@ -270,6 +274,8 @@ void PairReaxCKokkos<DeviceType>::setup()
		k_params_twbp.h_view(i,j).p_ovun1 = twbp->p_ovun1;

		for (k = 1; k <= n; k++) {
		if (map[k] == -1) continue;

		// Angular
		thbh = &(system->reax_param.thbp[map[i]][map[j]][map[k]]);
		thbp = &(thbh->prm[0]);
		@@ -290,6 +296,8 @@ void PairReaxCKokkos<DeviceType>::setup()
		k_params_hbp.h_view(i,j,k).r0_hb = hbp->r0_hb;

		for (m = 1; m <= n; m++) {
		if (map[m] == -1) continue;

		// Torsion
		fbh = &(system->reax_param.fbp[map[i]][map[j]][map[k]][map[m]]);
		fbp = &(fbh->prm[0]);
		@@ -377,7 +385,9 @@ void PairReaxCKokkos<DeviceType>::init_md()
		d_LR = k_LR.template view<DeviceType>();

		for (int i = 1; i <= ntypes; ++i) {
		if (map[i] == -1) continue;
		for (int j = i; j <= ntypes; ++j) {
		if (map[j] == -1) continue;
		int n = LR[i][j].n;
		if (n == 0) continue;
		k_LR.h_view(i,j).dx = LR[i][j].dx;
		@@ -539,7 +549,9 @@ void PairReaxCKokkos<DeviceType>::Deallocate_Lookup_Tables()
		ntypes = atom->ntypes;

		for( i = 0; i <= ntypes; ++i ) {
		for( j = i; j <= ntypes; ++j )
		if (map[i] == -1) continue;
		for( j = i; j <= ntypes; ++j ) {
		if (map[i] == -1) continue;
		if (LR[i][j].n) {
		sfree( control->error_ptr, LR[i][j].y, "LR[i,j].y" );
		sfree( control->error_ptr, LR[i][j].H, "LR[i,j].H" );
		@@ -548,6 +560,7 @@ void PairReaxCKokkos<DeviceType>::Deallocate_Lookup_Tables()
		sfree( control->error_ptr, LR[i][j].ele, "LR[i,j].ele" );
		sfree( control->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb" );
		}
		}
		sfree( control->error_ptr, LR[i], "LR[i]" );
		}
		sfree( control->error_ptr, LR, "LR" );
		@@ -3659,33 +3672,6 @@ void PairReaxCKokkos<DeviceType>::v_tally3_atom(EV_FLOAT_REAX &ev, const int &i,
		}
		}

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

		template<class DeviceType>
		void PairReaxCKokkos<DeviceType>::extract(const char str, int &dim)
		{
		dim = 1;
		if (strcmp(str,"chi") == 0 && chi) {
		for (int i = 1; i <= atom->ntypes; i++)
		if (map[i] >= 0) chi[i] = system->reax_param.sbp[map[i]].chi;
		else chi[i] = 0.0;
		return (void *) chi;
		}
		if (strcmp(str,"eta") == 0 && eta) {
		for (int i = 1; i <= atom->ntypes; i++)
		if (map[i] >= 0) eta[i] = system->reax_param.sbp[map[i]].eta;
		else eta[i] = 0.0;
		return (void *) eta;
		}
		if (strcmp(str,"gamma") == 0 && gamma) {
		for (int i = 1; i <= atom->ntypes; i++)
		if (map[i] >= 0) gamma[i] = system->reax_param.sbp[map[i]].gamma;
		else gamma[i] = 0.0;
		return (void *) gamma;
		}
		return NULL;
		}

		/* ----------------------------------------------------------------------
		setup for energy, virial computation
		see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)

src/KOKKOS/pair_reaxc_kokkos.h

+0 −1

Original line number	Diff line number	Diff line
		@@ -121,7 +121,6 @@ class PairReaxCKokkos : public PairReaxC {

		void ev_setup(int, int, int alloc = 1);
		void compute(int, int);
		void extract(const char , int &);
		void init_style();
		double memory_usage();
		void FindBond(int &);

src/USER-REAXC/fix_qeq_reax.cpp

+16 −9

Original line number	Diff line number	Diff line
		@@ -463,13 +463,19 @@ void FixQEqReax::min_setup_pre_force(int vflag)
		void FixQEqReax::init_storage()
		{
		int NN;
		int *ilist;

		if (reaxc)
		if (reaxc) {
		NN = reaxc->list->inum + reaxc->list->gnum;
		else
		ilist = reaxc->list->ilist;
		} else {
		NN = list->inum + list->gnum;
		ilist = list->ilist;
		}

		for (int i = 0; i < NN; i++) {
		for (int ii = 0; ii < NN; ii++) {
		int i = ilist[ii];
		if (atom->mask[i] & groupbit) {
		Hdia_inv[i] = 1. / eta[atom->type[i]];
		b_s[i] = -chi[atom->type[i]];
		b_t[i] = -1.0;
		@@ -478,6 +484,7 @@ void FixQEqReax::init_storage()
		s[i] = t[i] = 0;
		}
		}
		}

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

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