Merge branch 'pr-747' into develop (dce6c9ed) · Commits · 郑智淋 / lammps

src/KOKKOS/fix_qeq_reax_kokkos.cpp

+83 −30

Original line number	Diff line number	Diff line
		@@ -72,6 +72,9 @@ template<class DeviceType>
		FixQEqReaxKokkos<DeviceType>::~FixQEqReaxKokkos()
		{
		if (copymode) return;

		memoryKK->destroy_kokkos(k_s_hist,s_hist);
		memoryKK->destroy_kokkos(k_t_hist,t_hist);
		}

		/* ---------------------------------------------------------------------- */
		@@ -157,25 +160,11 @@ void FixQEqReaxKokkos<DeviceType>::init_shielding_k()
		template<class DeviceType>
		void FixQEqReaxKokkos<DeviceType>::init_hist()
		{
		int i,j;

		k_s_hist = DAT::tdual_ffloat_2d("qeq/kk:s_hist",atom->nmax,nprev);
		d_s_hist = k_s_hist.template view<DeviceType>();
		h_s_hist = k_s_hist.h_view;
		k_t_hist = DAT::tdual_ffloat_2d("qeq/kk:t_hist",atom->nmax,nprev);
		d_t_hist = k_t_hist.template view<DeviceType>();
		h_t_hist = k_t_hist.h_view;

		for( i = 0; i < atom->nmax; i++ )
		for( j = 0; j < nprev; j++ )
		k_s_hist.h_view(i,j) = k_t_hist.h_view(i,j) = 0.0;

		k_s_hist.template modify<LMPHostType>();
		k_s_hist.template sync<DeviceType>();

		k_t_hist.template modify<LMPHostType>();
		k_t_hist.template sync<DeviceType>();
		Kokkos::deep_copy(d_s_hist,0.0);
		Kokkos::deep_copy(d_t_hist,0.0);

		k_s_hist.template modify<DeviceType>();
		k_t_hist.template modify<DeviceType>();
		}

		/* ---------------------------------------------------------------------- */
		@@ -235,6 +224,8 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
		Kokkos::parallel_scan(inum,computeH_functor);

		// init_matvec
		k_s_hist.template sync<DeviceType>();
		k_t_hist.template sync<DeviceType>();
		FixQEqReaxKokkosMatVecFunctor<DeviceType> matvec_functor(this);
		Kokkos::parallel_for(inum,matvec_functor);

		@@ -262,6 +253,8 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)

		// calculate_Q();
		calculate_q();
		k_s_hist.template modify<DeviceType>();
		k_t_hist.template modify<DeviceType>();

		copymode = 0;

		@@ -334,14 +327,6 @@ void FixQEqReaxKokkos<DeviceType>::allocate_array()
		k_d = DAT::tdual_ffloat_1d("qeq/kk:h_d",nmax);
		d_d = k_d.template view<DeviceType>();
		h_d = k_d.h_view;

		k_s_hist = DAT::tdual_ffloat_2d("qeq/kk:s_hist",nmax,nprev);
		d_s_hist = k_s_hist.template view<DeviceType>();
		h_s_hist = k_s_hist.h_view;

		k_t_hist = DAT::tdual_ffloat_2d("qeq/kk:t_hist",nmax,nprev);
		d_t_hist = k_t_hist.template view<DeviceType>();
		h_t_hist = k_t_hist.h_view;
		}

		// init_storage
		@@ -369,8 +354,6 @@ void FixQEqReaxKokkos<DeviceType>::zero_item(int ii) const
		d_o[i] = 0.0;
		d_r[i] = 0.0;
		d_d[i] = 0.0;
		//for( int j = 0; j < nprev; j++ )
		//d_s_hist(i,j) = d_t_hist(i,j) = 0.0;
		}

		}
		@@ -462,7 +445,7 @@ double FixQEqReaxKokkos<DeviceType>::calculate_H_k(const F_FLOAT &r, const F_FLO

		template<class DeviceType>
		KOKKOS_INLINE_FUNCTION
		void FixQEqReaxKokkos<DeviceType>::mat_vec_item(int ii) const
		void FixQEqReaxKokkos<DeviceType>::matvec_item(int ii) const
		{
		const int i = d_ilist[ii];
		const int itype = type(i);
		@@ -1183,7 +1166,77 @@ double FixQEqReaxKokkos<DeviceType>::memory_usage()
		return bytes;
		}

		/* ---------------------------------------------------------------------- */\
		/* ----------------------------------------------------------------------
		allocate fictitious charge arrays
		------------------------------------------------------------------------- */

		template<class DeviceType>
		void FixQEqReaxKokkos<DeviceType>::grow_arrays(int nmax)
		{
		k_s_hist.template sync<LMPHostType>(); // force reallocation on host
		k_t_hist.template sync<LMPHostType>();

		memoryKK->grow_kokkos(k_s_hist,s_hist,nmax,nprev,"qeq:s_hist");
		memoryKK->grow_kokkos(k_t_hist,t_hist,nmax,nprev,"qeq:t_hist");

		d_s_hist = k_s_hist.template view<DeviceType>();
		d_t_hist = k_t_hist.template view<DeviceType>();

		k_s_hist.template modify<LMPHostType>();
		k_t_hist.template modify<LMPHostType>();
		}

		/* ----------------------------------------------------------------------
		copy values within fictitious charge arrays
		------------------------------------------------------------------------- */

		template<class DeviceType>
		void FixQEqReaxKokkos<DeviceType>::copy_arrays(int i, int j, int delflag)
		{
		k_s_hist.template sync<LMPHostType>();
		k_t_hist.template sync<LMPHostType>();

		for (int m = 0; m < nprev; m++) {
		s_hist[j][m] = s_hist[i][m];
		t_hist[j][m] = t_hist[i][m];
		}

		k_s_hist.template modify<LMPHostType>();
		k_t_hist.template modify<LMPHostType>();
		}

		/* ----------------------------------------------------------------------
		pack values in local atom-based array for exchange with another proc
		------------------------------------------------------------------------- */

		template<class DeviceType>
		int FixQEqReaxKokkos<DeviceType>::pack_exchange(int i, double *buf)
		{
		k_s_hist.template sync<LMPHostType>();
		k_t_hist.template sync<LMPHostType>();

		for (int m = 0; m < nprev; m++) buf[m] = s_hist[i][m];
		for (int m = 0; m < nprev; m++) buf[nprev+m] = t_hist[i][m];
		return nprev*2;
		}

		/* ----------------------------------------------------------------------
		unpack values in local atom-based array from exchange with another proc
		------------------------------------------------------------------------- */

		template<class DeviceType>
		int FixQEqReaxKokkos<DeviceType>::unpack_exchange(int nlocal, double *buf)
		{
		for (int m = 0; m < nprev; m++) s_hist[nlocal][m] = buf[m];
		for (int m = 0; m < nprev; m++) t_hist[nlocal][m] = buf[nprev+m];

		k_s_hist.template modify<LMPHostType>();
		k_t_hist.template modify<LMPHostType>();

		return nprev*2;
		}

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

		namespace LAMMPS_NS {
		template class FixQEqReaxKokkos<LMPDeviceType>;

src/KOKKOS/fix_qeq_reax_kokkos.h

+7 −3

Original line number	Diff line number	Diff line
		@@ -57,7 +57,7 @@ class FixQEqReaxKokkos : public FixQEqReax {
		void compute_h_item(int, int &, const bool &) const;

		KOKKOS_INLINE_FUNCTION
		void mat_vec_item(int) const;
		void matvec_item(int) const;

		KOKKOS_INLINE_FUNCTION
		void sparse12_item(int) const;
		@@ -145,7 +145,7 @@ class FixQEqReaxKokkos : public FixQEqReax {
		void unpack_reverse_comm(int, int , double );
		double memory_usage();

		protected:
		private:
		int inum;
		int allocated_flag;

		@@ -210,6 +210,10 @@ class FixQEqReaxKokkos : public FixQEqReax {
		typename AT::t_int_2d d_sendlist;
		typename AT::t_xfloat_1d_um v_buf;

		void grow_arrays(int);
		void copy_arrays(int, int, int);
		int pack_exchange(int, double *);
		int unpack_exchange(int, double *);
		};

		template <class DeviceType>
		@@ -235,7 +239,7 @@ struct FixQEqReaxKokkosMatVecFunctor {
		};
		KOKKOS_INLINE_FUNCTION
		void operator()(const int ii) const {
		c.mat_vec_item(ii);
		c.matvec_item(ii);
		}
		};

src/USER-REAXC/fix_qeq_reax.h

+9 −9

Original line number	Diff line number	Diff line
		@@ -122,15 +122,15 @@ class FixQEqReax : public Fix {
		//int GMRES(double,double);
		virtual void sparse_matvec(sparse_matrix,double,double*);

		int pack_forward_comm(int, int , double , int, int *);
		void unpack_forward_comm(int, int, double *);
		int pack_reverse_comm(int, int, double *);
		void unpack_reverse_comm(int, int , double );
		double memory_usage();
		void grow_arrays(int);
		void copy_arrays(int, int, int);
		int pack_exchange(int, double *);
		int unpack_exchange(int, double *);
		virtual int pack_forward_comm(int, int , double , int, int *);
		virtual void unpack_forward_comm(int, int, double *);
		virtual int pack_reverse_comm(int, int, double *);
		virtual void unpack_reverse_comm(int, int , double );
		virtual double memory_usage();
		virtual void grow_arrays(int);
		virtual void copy_arrays(int, int, int);
		virtual int pack_exchange(int, double *);
		virtual int unpack_exchange(int, double *);

		virtual double parallel_norm( double*, int );
		virtual double parallel_dot( double, double, int );

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