Merge branch 'master' into collected-small-changes (2fea8f88) · Commits · 郑智淋 / lammps

doc/src/bond_none.rst

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -13,7 +13,7 @@ Syntax
	Examples		Examples
	""""""""		""""""""

	.. code-blocK:: LAMMPS		.. code-block:: LAMMPS

	bond_style none		bond_style none

doc/src/pair_meam_spline.rst

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -16,7 +16,7 @@ Syntax
	Examples		Examples
	""""""""		""""""""

	.. code:: LAMMPS		.. code-block:: LAMMPS

	pair_style meam/spline		pair_style meam/spline
	pair_coeff * * Ti.meam.spline Ti		pair_coeff * * Ti.meam.spline Ti

src/KOKKOS/kokkos_type.h

+12 −1

Original line number	Original line	Diff line number	Diff line
	@@ -1058,7 +1058,7 @@ struct alignas(2*sizeof(real)) SNAComplex
	{		{
	real re,im;		real re,im;

	KOKKOS_FORCEINLINE_FUNCTION SNAComplex() = default;		SNAComplex() = default;

	KOKKOS_FORCEINLINE_FUNCTION SNAComplex(real re)		KOKKOS_FORCEINLINE_FUNCTION SNAComplex(real re)
	: re(re), im(static_cast<real>(0.)) { ; }		: re(re), im(static_cast<real>(0.)) { ; }
	@@ -1100,6 +1100,17 @@ KOKKOS_FORCEINLINE_FUNCTION SNAComplex<real> operator*(const real& r, const SNAC

	typedef SNAComplex<SNAreal> SNAcomplex;		typedef SNAComplex<SNAreal> SNAcomplex;

			// Cayley-Klein pack
			// Can guarantee it's aligned to 2 complex
			struct alignas(32) CayleyKleinPack {

			SNAcomplex a, b;
			SNAcomplex da[3], db[3];
			SNAreal sfac;
			SNAreal dsfacu[3];

			};


	#if defined(KOKKOS_ENABLE_CXX11)		#if defined(KOKKOS_ENABLE_CXX11)
	#undef ISFINITE		#undef ISFINITE

src/KOKKOS/pair_snap_kokkos.h

+5 −4

Original line number	Original line	Diff line number	Diff line
	@@ -50,6 +50,7 @@ struct TagPairSNAPComputeFusedDeidrj{};
	// CPU backend only		// CPU backend only
	struct TagPairSNAPPreUiCPU{};		struct TagPairSNAPPreUiCPU{};
	struct TagPairSNAPComputeUiCPU{};		struct TagPairSNAPComputeUiCPU{};
			struct TagPairSNAPTransformUiCPU{};
	struct TagPairSNAPComputeZiCPU{};		struct TagPairSNAPComputeZiCPU{};
	struct TagPairSNAPBetaCPU{};		struct TagPairSNAPBetaCPU{};
	struct TagPairSNAPComputeBiCPU{};		struct TagPairSNAPComputeBiCPU{};
	@@ -104,7 +105,7 @@ public:
	void operator() (TagPairSNAPComputeUi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi>::member_type& team) const;		void operator() (TagPairSNAPComputeUi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi>::member_type& team) const;

	KOKKOS_INLINE_FUNCTION		KOKKOS_INLINE_FUNCTION
	void operator() (TagPairSNAPTransformUi,const int iatom_mod, const int idxu, const int iatom_div) const;		void operator() (TagPairSNAPTransformUi,const int iatom_mod, const int j, const int iatom_div) const;

	KOKKOS_INLINE_FUNCTION		KOKKOS_INLINE_FUNCTION
	void operator() (TagPairSNAPComputeZi,const int iatom_mod, const int idxz, const int iatom_div) const;		void operator() (TagPairSNAPComputeZi,const int iatom_mod, const int idxz, const int iatom_div) const;
	@@ -135,13 +136,13 @@ public:
	void operator() (TagPairSNAPComputeUiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiCPU>::member_type& team) const;		void operator() (TagPairSNAPComputeUiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiCPU>::member_type& team) const;

	KOKKOS_INLINE_FUNCTION		KOKKOS_INLINE_FUNCTION
	void operator() (TagPairSNAPComputeZiCPU,const int& ii) const;		void operator() (TagPairSNAPTransformUiCPU, const int j, const int iatom) const;

	KOKKOS_INLINE_FUNCTION		KOKKOS_INLINE_FUNCTION
	void operator() (TagPairSNAPComputeBiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeBiCPU>::member_type& team) const;		void operator() (TagPairSNAPComputeZiCPU,const int& ii) const;

	KOKKOS_INLINE_FUNCTION		KOKKOS_INLINE_FUNCTION
	void operator() (TagPairSNAPZeroYiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPZeroYiCPU>::member_type& team) const;		void operator() (TagPairSNAPComputeBiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeBiCPU>::member_type& team) const;

	KOKKOS_INLINE_FUNCTION		KOKKOS_INLINE_FUNCTION
	void operator() (TagPairSNAPComputeYiCPU,const int& ii) const;		void operator() (TagPairSNAPComputeYiCPU,const int& ii) const;

src/KOKKOS/pair_snap_kokkos_impl.h

+112 −47

Original line number	Original line	Diff line number	Diff line
	@@ -206,8 +206,6 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)

	EV_FLOAT ev;		EV_FLOAT ev;

	int idxu_max = snaKK.idxu_max;

	while (chunk_offset < inum) { // chunk up loop to prevent running out of memory		while (chunk_offset < inum) { // chunk up loop to prevent running out of memory

	EV_FLOAT ev_tmp;		EV_FLOAT ev_tmp;
	@@ -246,6 +244,13 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
	Kokkos::parallel_for("ComputeUiCPU",policy_ui_cpu,*this);		Kokkos::parallel_for("ComputeUiCPU",policy_ui_cpu,*this);
	}		}

			{
			// Expand ulisttot -> ulisttot_full
			// Zero out ylist
			typename Kokkos::MDRangePolicy<DeviceType, Kokkos::IndexType<int>, Kokkos::Rank<2, Kokkos::Iterate::Left, Kokkos::Iterate::Left>, TagPairSNAPTransformUiCPU> policy_transform_ui_cpu({0,0},{twojmax+1,chunk_size});
			Kokkos::parallel_for("TransformUiCPU",policy_transform_ui_cpu,*this);
			}

	//Compute bispectrum		//Compute bispectrum
	if (quadraticflag \|\| eflag) {		if (quadraticflag \|\| eflag) {
	//ComputeZi		//ComputeZi
	@@ -261,20 +266,12 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
	Kokkos::parallel_for("ComputeBiCPU",policy_bi_cpu,*this);		Kokkos::parallel_for("ComputeBiCPU",policy_bi_cpu,*this);
	}		}

	//ZeroYi,ComputeYi		//ComputeYi
	{		{
	int vector_length = vector_length_default;
	int team_size = team_size_default;

	//Compute beta = dE_i/dB_i for all i in list		//Compute beta = dE_i/dB_i for all i in list
	typename Kokkos::RangePolicy<DeviceType,TagPairSNAPBetaCPU> policy_beta(0,chunk_size);		typename Kokkos::RangePolicy<DeviceType,TagPairSNAPBetaCPU> policy_beta(0,chunk_size);
	Kokkos::parallel_for("ComputeBetaCPU",policy_beta,*this);		Kokkos::parallel_for("ComputeBetaCPU",policy_beta,*this);

	//ZeroYi
	check_team_size_for<TagPairSNAPZeroYiCPU>(chunk_size,team_size,vector_length);
	typename Kokkos::TeamPolicy<DeviceType,TagPairSNAPZeroYiCPU> policy_zero_yi(((idxu_max+team_size-1)/team_size)*chunk_size,team_size,vector_length);
	Kokkos::parallel_for("ZeroYiCPU",policy_zero_yi,*this);

	//ComputeYi		//ComputeYi
	int idxz_max = snaKK.idxz_max;		int idxz_max = snaKK.idxz_max;
	typename Kokkos::RangePolicy<DeviceType,TagPairSNAPComputeYiCPU> policy_yi_cpu(0,chunk_size*idxz_max);		typename Kokkos::RangePolicy<DeviceType,TagPairSNAPComputeYiCPU> policy_yi_cpu(0,chunk_size*idxz_max);
	@@ -294,6 +291,7 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)

	Kokkos::parallel_for("ComputeDeidrjCPU",policy_deidrj_cpu,*this);		Kokkos::parallel_for("ComputeDeidrjCPU",policy_deidrj_cpu,*this);
	}		}

	} else { // GPU		} else { // GPU

	#ifdef LMP_KOKKOS_GPU		#ifdef LMP_KOKKOS_GPU
	@@ -313,10 +311,10 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
	int team_size = 4; // need to cap b/c of shared memory reqs		int team_size = 4; // need to cap b/c of shared memory reqs
	check_team_size_for<TagPairSNAPComputeUi>(chunk_size,team_size,vector_length);		check_team_size_for<TagPairSNAPComputeUi>(chunk_size,team_size,vector_length);

	// scratch size: 2 * team_size * (twojmax+1)^2, to cover all `m1`,`m2` values		// scratch size: 2 * team_size * (twojmax+1)^2, to cover all `m1`,`m2` values, div 2 for symmetry
	// 2 is for double buffer		// 2 is for double buffer

	const int tile_size = (twojmax+1)*(twojmax+1);		const int tile_size = (twojmax+1)*(twojmax/2+1);
	typedef Kokkos::View< SNAcomplex*,		typedef Kokkos::View< SNAcomplex*,
	Kokkos::DefaultExecutionSpace::scratch_memory_space,		Kokkos::DefaultExecutionSpace::scratch_memory_space,
	Kokkos::MemoryTraits<Kokkos::Unmanaged> >		Kokkos::MemoryTraits<Kokkos::Unmanaged> >
	@@ -329,7 +327,7 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
	Kokkos::parallel_for("ComputeUi",policy_ui,*this);		Kokkos::parallel_for("ComputeUi",policy_ui,*this);

	//Transform data layout of ulisttot to AoSoA, zero ylist		//Transform data layout of ulisttot to AoSoA, zero ylist
	typename Kokkos::MDRangePolicy<DeviceType, Kokkos::IndexType<int>, Kokkos::Rank<3, Kokkos::Iterate::Left, Kokkos::Iterate::Left>, TagPairSNAPTransformUi> policy_transform_ui({0,0,0},{32,idxu_max,(chunk_size + 32 - 1) / 32},{32,4,1});		typename Kokkos::MDRangePolicy<DeviceType, Kokkos::IndexType<int>, Kokkos::Rank<3, Kokkos::Iterate::Left, Kokkos::Iterate::Left>, TagPairSNAPTransformUi> policy_transform_ui({0,0,0},{32,twojmax+1,(chunk_size + 32 - 1) / 32},{32,4,1});
	Kokkos::parallel_for("TransformUi",policy_transform_ui,*this);		Kokkos::parallel_for("TransformUi",policy_transform_ui,*this);

	}		}
	@@ -367,7 +365,8 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
	Kokkos::parallel_for("ComputeYi",policy_compute_yi,*this);		Kokkos::parallel_for("ComputeYi",policy_compute_yi,*this);

	//Transform data layout of ylist out of AoSoA		//Transform data layout of ylist out of AoSoA
	typename Kokkos::MDRangePolicy<DeviceType, Kokkos::IndexType<int>, Kokkos::Rank<3, Kokkos::Iterate::Left, Kokkos::Iterate::Left>, TagPairSNAPTransformYi> policy_transform_yi({0,0,0},{32,idxu_max,(chunk_size + 32 - 1) / 32},{32,4,1});		const int idxu_half_max = snaKK.idxu_half_max;
			typename Kokkos::MDRangePolicy<DeviceType, Kokkos::IndexType<int>, Kokkos::Rank<3, Kokkos::Iterate::Left, Kokkos::Iterate::Left>, TagPairSNAPTransformYi> policy_transform_yi({0,0,0},{32,idxu_half_max,(chunk_size + 32 - 1) / 32},{32,4,1});
	Kokkos::parallel_for("TransformYi",policy_transform_yi,*this);		Kokkos::parallel_for("TransformYi",policy_transform_yi,*this);

	}		}
	@@ -397,7 +396,7 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
	}		}
	}		}

	#endif // KOKKOS_ENABLE_CUDA		#endif // LMP_KOKKOS_GPU

	}		}

	@@ -608,12 +607,21 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeNeigh,const typen

	if ( rsq < rnd_cutsq(itype,jtype) ) {		if ( rsq < rnd_cutsq(itype,jtype) ) {
	if (final) {		if (final) {
			#ifdef LMP_KOKKOS_GPU
			if (std::is_same<DeviceType,Kokkos::Cuda>::value) {
			my_sna.compute_cayley_klein(ii, offset, dx, dy, dz, (radi + d_radelem[elem_j])*rcutfac,
			d_wjelem[elem_j]);
			} else {
			#endif
	my_sna.rij(ii,offset,0) = dx;		my_sna.rij(ii,offset,0) = dx;
	my_sna.rij(ii,offset,1) = dy;		my_sna.rij(ii,offset,1) = dy;
	my_sna.rij(ii,offset,2) = dz;		my_sna.rij(ii,offset,2) = dz;
	my_sna.inside(ii,offset) = j;
	my_sna.wj(ii,offset) = d_wjelem[elem_j];		my_sna.wj(ii,offset) = d_wjelem[elem_j];
	my_sna.rcutij(ii,offset) = (radi + d_radelem[elem_j])*rcutfac;		my_sna.rcutij(ii,offset) = (radi + d_radelem[elem_j])*rcutfac;
			#ifdef LMP_KOKKOS_GPU
			}
			#endif
			my_sna.inside(ii,offset) = j;
	if (chemflag)		if (chemflag)
	my_sna.element(ii,offset) = elem_j;		my_sna.element(ii,offset) = elem_j;
	else		else
	@@ -704,27 +712,54 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeUi,const typename

	template<class DeviceType>		template<class DeviceType>
	KOKKOS_INLINE_FUNCTION		KOKKOS_INLINE_FUNCTION
	void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPTransformUi,const int iatom_mod, const int idxu, const int iatom_div) const {		void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPTransformUi,const int iatom_mod, const int j, const int iatom_div) const {
	SNAKokkos<DeviceType> my_sna = snaKK;		SNAKokkos<DeviceType> my_sna = snaKK;

	const int iatom = iatom_mod + iatom_div * 32;		const int iatom = iatom_mod + iatom_div * 32;
	if (iatom >= chunk_size) return;		if (iatom >= chunk_size) return;

	if (idxu >= my_sna.idxu_max) return;		if (j > twojmax) return;

	int elem_count = chemflag ? nelements : 1;		int elem_count = chemflag ? nelements : 1;

	for (int ielem = 0; ielem < elem_count; ielem++) {		for (int ielem = 0; ielem < elem_count; ielem++) {
			const int jju_half = my_sna.idxu_half_block(j);
			const int jju = my_sna.idxu_block(j);

			for (int mb = 0; 2*mb <= j; mb++) {
			for (int ma = 0; ma <= j; ma++) {
			// Extract top half

	const auto utot_re = my_sna.ulisttot_re(idxu, ielem, iatom);		const int idxu_shift = mb * (j + 1) + ma;
	const auto utot_im = my_sna.ulisttot_im(idxu, ielem, iatom);		const int idxu_half = jju_half + idxu_shift;
			const int idxu = jju + idxu_shift;

			auto utot_re = my_sna.ulisttot_re(idxu_half, ielem, iatom);
			auto utot_im = my_sna.ulisttot_im(idxu_half, ielem, iatom);

			// Store
	my_sna.ulisttot_pack(iatom_mod, idxu, ielem, iatom_div) = { utot_re, utot_im };		my_sna.ulisttot_pack(iatom_mod, idxu, ielem, iatom_div) = { utot_re, utot_im };

	my_sna.ylist_pack_re(iatom_mod, idxu, ielem, iatom_div) = 0.;		// Also zero yi
	my_sna.ylist_pack_im(iatom_mod, idxu, ielem, iatom_div) = 0.;		my_sna.ylist_pack_re(iatom_mod, idxu_half, ielem, iatom_div) = 0.;
			my_sna.ylist_pack_im(iatom_mod, idxu_half, ielem, iatom_div) = 0.;

			// Symmetric term
			const int sign_factor = (((ma+mb)%2==0)?1:-1);
			const int idxu_flip = jju + (j + 1 - mb) * (j + 1) - (ma + 1);

			if (sign_factor == 1) {
			utot_im = -utot_im;
			} else {
			utot_re = -utot_re;
	}		}

			my_sna.ulisttot_pack(iatom_mod, idxu_flip, ielem, iatom_div) = { utot_re, utot_im };

			// No need to zero symmetrized ylist
			}
			}
			}
	}		}

	template<class DeviceType>		template<class DeviceType>
	@@ -742,20 +777,20 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeYi,const int iato

	template<class DeviceType>		template<class DeviceType>
	KOKKOS_INLINE_FUNCTION		KOKKOS_INLINE_FUNCTION
	void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPTransformYi,const int iatom_mod, const int idxu, const int iatom_div) const {		void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPTransformYi,const int iatom_mod, const int idxu_half, const int iatom_div) const {
	SNAKokkos<DeviceType> my_sna = snaKK;		SNAKokkos<DeviceType> my_sna = snaKK;

	const int iatom = iatom_mod + iatom_div * 32;		const int iatom = iatom_mod + iatom_div * 32;
	if (iatom >= chunk_size) return;		if (iatom >= chunk_size) return;

	if (idxu >= my_sna.idxu_max) return;		if (idxu_half >= my_sna.idxu_half_max) return;

	int elem_count = chemflag ? nelements : 1;		int elem_count = chemflag ? nelements : 1;
	for (int ielem = 0; ielem < elem_count; ielem++) {		for (int ielem = 0; ielem < elem_count; ielem++) {
	const auto y_re = my_sna.ylist_pack_re(iatom_mod, idxu, ielem, iatom_div);		const auto y_re = my_sna.ylist_pack_re(iatom_mod, idxu_half, ielem, iatom_div);
	const auto y_im = my_sna.ylist_pack_im(iatom_mod, idxu, ielem, iatom_div);		const auto y_im = my_sna.ylist_pack_im(iatom_mod, idxu_half, ielem, iatom_div);

	my_sna.ylist(idxu, ielem, iatom) = { y_re, y_im };		my_sna.ylist(idxu_half, ielem, iatom) = { y_re, y_im };
	}		}

	}		}
	@@ -904,22 +939,52 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeUiCPU,const typen

	template<class DeviceType>		template<class DeviceType>
	KOKKOS_INLINE_FUNCTION		KOKKOS_INLINE_FUNCTION
	void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPZeroYiCPU,const typename Kokkos::TeamPolicy<DeviceType,TagPairSNAPZeroYiCPU>::member_type& team) const {		void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPTransformUiCPU, const int j, const int iatom) const {
	SNAKokkos<DeviceType> my_sna = snaKK;		SNAKokkos<DeviceType> my_sna = snaKK;

	// Extract the quantum number		if (iatom >= chunk_size) return;
	const int idx = team.team_rank() + team.team_size() * (team.league_rank() % ((my_sna.idxu_max+team.team_size()-1)/team.team_size()));
	if (idx >= my_sna.idxu_max) return;

	// Extract the atomic index		if (j > twojmax) return;
	const int ii = team.league_rank() / ((my_sna.idxu_max+team.team_size()-1)/team.team_size());
	if (ii >= chunk_size) return;

	if (chemflag)		int elem_count = chemflag ? nelements : 1;
	for(int ielem = 0; ielem < nelements; ielem++)
	my_sna.zero_yi_cpu(idx,ii,ielem);		// De-symmetrize ulisttot
	else		for (int ielem = 0; ielem < elem_count; ielem++) {
	my_sna.zero_yi_cpu(idx,ii,0);
			const int jju_half = my_sna.idxu_half_block(j);
			const int jju = my_sna.idxu_block(j);

			for (int mb = 0; 2*mb <= j; mb++) {
			for (int ma = 0; ma <= j; ma++) {
			// Extract top half

			const int idxu_shift = mb * (j + 1) + ma;
			const int idxu_half = jju_half + idxu_shift;
			const int idxu = jju + idxu_shift;

			// Load ulist
			auto utot = my_sna.ulisttot(idxu_half, ielem, iatom);

			// Store
			my_sna.ulisttot_full(idxu, ielem, iatom) = utot;

			// Zero Yi
			my_sna.ylist(idxu_half, ielem, iatom) = {0., 0.};

			// Symmetric term
			const int sign_factor = (((ma+mb)%2==0)?1:-1);
			const int idxu_flip = jju + (j + 1 - mb) * (j + 1) - (ma + 1);

			if (sign_factor == 1) {
			utot.im = -utot.im;
			} else {
			utot.re = -utot.re;
			}

			my_sna.ulisttot_full(idxu_flip, ielem, iatom) = utot;
			}
			}
			}
	}		}

	template<class DeviceType>		template<class DeviceType>

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