Finish off multi-neighbor list support for pair_kim (a7e3ccd8) · Commits · 郑智淋 / lammps

src/KIM/pair_kim.cpp

+28 −11

Original line number	Diff line number	Diff line
		@@ -61,6 +61,7 @@ PairKIM::PairKIM(LAMMPS *lmp) :
		lmps_maxalloc(0),
		kim_particleSpecies(0),
		kim_particleContributing(0),
		lmps_stripped_neigh_ptr(0),
		lmps_stripped_neigh_list(0)
		{
		// Initialize Pair data members to appropriate values
		@@ -94,6 +95,12 @@ PairKIM::~PairKIM()
		memory->destroy(kim_particleSpecies);
		memory->destroy(kim_particleContributing);
		memory->destroy(lmps_stripped_neigh_list);
		// clean up lmps_stripped_neigh_ptr
		if (lmps_stripped_neigh_ptr)
		{
		delete [] lmps_stripped_neigh_ptr;
		lmps_stripped_neigh_ptr = 0;
		}

		// clean up allocated memory for standard Pair class usage
		// also, we allocate lmps_map_species_to_uniuqe in the allocate() function
		@@ -241,10 +248,11 @@ void PairKIM::settings(int narg, char **arg)
		++settings_call_count;
		init_style_call_count = 0;

		if (narg < 2) error->all(FLERR,"Illegal pair_style command");
		if (narg != 2) error->all(FLERR,"Illegal pair_style command");
		// arg[0] is the virial handling option: "LAMMPSvirial" or "KIMvirial"
		// arg[1] is the KIM Model name
		// arg[2] is the print-kim-file flag: 0/1 do-not/do print (default 0)

		lmps_using_molecular = (atom->molecular > 0);

		// ensure we are in a clean state for KIM (needed on repeated call)
		// first time called will do nothing...
		@@ -382,6 +390,22 @@ void PairKIM::init_style()
		kim_init();
		}

		// setup lmps_stripped_neigh_list for neighbors of one atom, if needed
		if (lmps_using_molecular) {
		memory->destroy(lmps_stripped_neigh_list);
		memory->create(lmps_stripped_neigh_list,
		kim_number_of_cutoffs*neighbor->oneatom,
		"pair:lmps_stripped_neigh_list");
		delete [] lmps_stripped_neigh_ptr;
		lmps_stripped_neigh_ptr = new int*[kim_number_of_cutoffs];
		for (int i = 0; i < kim_number_of_cutoffs; ++i)
		{
		lmps_stripped_neigh_ptr[0]
		= &(lmps_stripped_neigh_list[(i-1)*(neighbor->oneatom)]);
		}

		}

		// make sure comm_reverse expects (at most) 9 values when newton is off
		if (!lmps_using_newton) comm_reverse_off = 9;

		@@ -595,7 +619,8 @@ int PairKIM::get_neigh(void const * const dataObject,
		{
		int n = *numberOfNeighbors;
		int *ptr = firstneigh[particleNumber];
		int *lmps_stripped_neigh_list = Model->lmps_stripped_neigh_list;
		int *lmps_stripped_neigh_list
		= Model->lmps_stripped_neigh_ptr[neighborListIndex];
		for (int i = 0; i < n; i++)
		lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK;
		*neighborsOfParticle = lmps_stripped_neigh_list;
		@@ -781,14 +806,6 @@ void PairKIM::set_lmps_flags()
		// determint if newton is on or off
		lmps_using_newton = (force->newton_pair == 1);

		// setup lmps_stripped_neigh_list for neighbors of one atom, if needed
		lmps_using_molecular = (atom->molecular > 0);
		if (lmps_using_molecular) {
		memory->destroy(lmps_stripped_neigh_list);
		memory->create(lmps_stripped_neigh_list,neighbor->oneatom,
		"pair:lmps_stripped_neigh_list");
		}

		// determine if running with pair hybrid
		if (force->pair_match("hybrid",0))
		{

src/KIM/pair_kim.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -116,6 +116,7 @@ namespace LAMMPS_NS {
		int* kim_particleContributing; // array of KIM particle contributing
		int* lmps_stripped_neigh_list; // neighbors of one atom, used when LAMMPS
		// is in molecular mode
		int** lmps_stripped_neigh_ptr; // pointer into lists

		// KIM specific helper functions
		void kim_init();

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