Kokkos updates by Stan (8756a101) · Commits · 郑智淋 / lammps

doc/src/compute_pressure.txt

+11 −3

Original line number	Diff line number	Diff line
		@@ -38,9 +38,17 @@ The pressure is computed by the formula
		where N is the number of atoms in the system (see discussion of DOF
		below), Kb is the Boltzmann constant, T is the temperature, d is the
		dimensionality of the system (2 or 3 for 2d/3d), V is the system
		volume (or area in 2d), and the second term is the virial, computed
		within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
		and long-range interactions. "Fixes"_fix.html that impose constraints
		volume (or area in 2d).
		The second term is the virial, -dU/dV, computed within LAMMPS for all
		pairwise as well as 2-body, 3-body, 4-body, many-body, and
		long-range interactions, where r_i and f_i are the position and
		force vector of atom i, and the big black dot indicates dot product.
		When periodic boundary conditions are used, the summation includes
		contributions from periodic images of the atoms in the central box,
		which involves computing partial forces on local and ghost atoms.
		A detailed description of how partial forces for 2-body and manybody
		potentials are computed is provided in "(Thompson)"_#Thompson.
		"Fixes"_fix.html that impose constraints
		(e.g. the "fix shake"_fix_shake.html command) also contribute to the
		virial term.

+1 −0

+12 −2

Original line number	Diff line number	Diff line
		@@ -83,8 +83,13 @@ class AtomVecKokkos : public AtomVec {
		std::is_same<typename ViewType::execution_space,LMPDeviceType>::value,
		Kokkos::CudaHostPinnedSpace,typename ViewType::memory_space>::type,
		Kokkos::MemoryTraits<Kokkos::Unmanaged> > mirror_type;
		if(buffer_size < src.capacity())
		if (buffer_size == 0) {
		buffer = Kokkos::kokkos_malloc<Kokkos::CudaHostPinnedSpace>(src.capacity());
		buffer_size = src.capacity();
		} else if (buffer_size < src.capacity()) {
		buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.capacity());
		buffer_size = src.capacity();
		}
		return mirror_type( buffer ,
		src.dimension_0() ,
		src.dimension_1() ,
		@@ -104,8 +109,13 @@ class AtomVecKokkos : public AtomVec {
		std::is_same<typename ViewType::execution_space,LMPDeviceType>::value,
		Kokkos::CudaHostPinnedSpace,typename ViewType::memory_space>::type,
		Kokkos::MemoryTraits<Kokkos::Unmanaged> > mirror_type;
		if(buffer_size < src.capacity())
		if (buffer_size == 0) {
		buffer = Kokkos::kokkos_malloc<Kokkos::CudaHostPinnedSpace>(src.capacity()*sizeof(typename ViewType::value_type));
		buffer_size = src.capacity();
		} else if (buffer_size < src.capacity()) {
		buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.capacity()*sizeof(typename ViewType::value_type));
		buffer_size = src.capacity();
		}
		mirror_type tmp_view( (typename ViewType::value_type*)buffer ,
		src.dimension_0() ,
		src.dimension_1() ,

+18 −1

Original line number	Diff line number	Diff line
		@@ -21,6 +21,11 @@
		#include "atom_masks.h"
		#include "error.h"
		#include "kokkos.h"
		#include "force.h"
		#include "bond.h"
		#include "angle.h"
		#include "dihedral.h"
		#include "improper.h"

		using namespace LAMMPS_NS;

		@@ -601,6 +606,18 @@ void NeighborKokkos::build_topology_kokkos() {
		k_anglelist.modify<LMPDeviceType>();
		k_dihedrallist.modify<LMPDeviceType>();
		k_improperlist.modify<LMPDeviceType>();

		// Transfer topology neighbor lists to Host for non-Kokkos styles

		if (force->bond && force->bond->execution_space == Host)
		k_bondlist.sync<LMPHostType>();
		if (force->angle && force->angle->execution_space == Host)
		k_anglelist.sync<LMPHostType>();
		if (force->dihedral && force->dihedral->execution_space == Host)
		k_dihedrallist.sync<LMPHostType>();
		if (force->improper && force->improper->execution_space == Host)
		k_improperlist.sync<LMPHostType>();

		} else {
		neighbond_host.build_topology_kk();

+20 −20

Original line number	Diff line number	Diff line
		@@ -126,7 +126,7 @@ void PairTersoffKokkos<DeviceType>::setup_params()
		for (i = 1; i <= n; i++)
		for (j = 1; j <= n; j++)
		for (k = 1; k <= n; k++) {
		m = elem2param[i-1][j-1][k-1];
		m = elem2param[map[i]][map[j]][map[k]];
		k_params.h_view(i,j,k).powerm = params[m].powerm;
		k_params.h_view(i,j,k).gamma = params[m].gamma;
		k_params.h_view(i,j,k).lam3 = params[m].lam3;