fixed bug with pair hybrid/overaly and manybody potentials finding the right skip neighbor method (9161bd98) · Commits · 郑智淋 / lammps

src/atom_vec_body.cpp

+4 −0

Original line number	Diff line number	Diff line
		@@ -847,6 +847,7 @@ void AtomVecBody::unpack_border(int n, int first, double *buf)
		inertia[2] = buf[m++];
		bonus[j].ninteger = (int) ubuf(buf[m++]).i;
		bonus[j].ndouble = (int) ubuf(buf[m++]).i;
		// corresponding put() calls are in clear_bonus()
		bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
		bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
		m += bptr->unpack_border_body(&bonus[j],&buf[m]);
		@@ -897,6 +898,7 @@ void AtomVecBody::unpack_border_vel(int n, int first, double *buf)
		inertia[2] = buf[m++];
		bonus[j].ninteger = (int) ubuf(buf[m++]).i;
		bonus[j].ndouble = (int) ubuf(buf[m++]).i;
		// corresponding put() calls are in clear_bonus()
		bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
		bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
		m += bptr->unpack_border_body(&bonus[j],&buf[m]);
		@@ -946,6 +948,7 @@ int AtomVecBody::unpack_border_hybrid(int n, int first, double *buf)
		inertia[2] = buf[m++];
		bonus[j].ninteger = (int) ubuf(buf[m++]).i;
		bonus[j].ndouble = (int) ubuf(buf[m++]).i;
		// corresponding put() calls are in clear_bonus()
		bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
		bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
		m += bptr->unpack_border_body(&bonus[j],&buf[m]);
		@@ -1050,6 +1053,7 @@ int AtomVecBody::unpack_exchange(double *buf)
		inertia[2] = buf[m++];
		bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
		bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
		// corresponding put() calls are in copy()
		bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
		bonus[nlocal_bonus].iindex);
		bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,

src/my_page.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -57,10 +57,10 @@ namespace LAMMPS_NS {

		template<class T>
		class MyPage {
		public:
		int ndatum; // total # of stored datums
		int nchunk; // total # of stored chunks

		public:
		MyPage() {
		ndatum = nchunk = 0;
		pages = NULL;

src/neigh_list.cpp

+1 −0

Original line number	Diff line number	Diff line
		@@ -192,6 +192,7 @@ void NeighList::setup_pages(int pgsize_caller, int oneatom_caller)
		gran calls grow() in granhistory
		respaouter calls grow() in respainner, respamiddle
		triggered by neighbor list build
		not called if a copy list
		------------------------------------------------------------------------- */

		void NeighList::grow(int nlocal, int nall)

src/neighbor.cpp

+43 −15

Original line number	Diff line number	Diff line
		@@ -1369,6 +1369,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
		"with ghost neighbors");

		// flags for settings the request + system requires of NPair class
		// some are set to 0/1, others are set to mask bit
		// comparisons below in loop over classes reflect that
		// copyflag = no/yes copy request
		// skipflag = no/yes skip request
		// halfflag = half request (gran and respa are also half lists)
		@@ -1402,7 +1404,7 @@ int Neighbor::choose_pair(NeighRequest *rq)
		// NOTE: exactly one of these request flags is set (see neigh_request.h)
		// this requires gran/respaouter also set halfflag
		// can simplify this logic, if follow NOTE in neigh_request.h
		// all why do size/off2on and size/off2on/oneside set NP_HALF
		// why do size/off2on and size/off2on/oneside set NP_HALF
		// either should set both half & full, or half should be in file name
		// to be consistent with how other NP classes use "half"

		@@ -1433,9 +1435,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
		else if (rq->newton == 1) newtflag = 1;
		else if (rq->newton == 2) newtflag = 0;

		// use flags to match exactly one of NPair class masks, bit by bit
		// copyflag match returns with no further checks
		// exactly one of halfflag,fullflag,halffullflag is set and thus must match
		// use flags to match exactly one of NPair class masks
		// sequence of checks is bit by bit in NeighConst

		int mask;

		@@ -1447,13 +1448,21 @@ int Neighbor::choose_pair(NeighRequest *rq)
		for (int i = 0; i < npclass; i++) {
		mask = pairmasks[i];

		if (copyflag && (mask & NP_COPY)) {
		// if copyflag set, return or continue with no further checks

		if (copyflag) {
		if (!(mask & NP_COPY)) continue;
		if (kokkos_device_flag != (mask & NP_KOKKOS_DEVICE)) continue;
		if (kokkos_host_flag != (mask & NP_KOKKOS_HOST)) continue;
		return i+1;
		}

		// skipflag must match along with other flags, so do not return

		if (skipflag != (mask & NP_SKIP)) continue;

		// exactly one of halfflag,fullflag,halffullflag is set and must match

		if (halfflag) {
		if (!(mask & NP_HALF)) continue;
		} else if (fullflag) {
		@@ -1470,18 +1479,37 @@ int Neighbor::choose_pair(NeighRequest *rq)
		if (ssaflag != (mask & NP_SSA)) continue;
		if (ompflag != (mask & NP_OMP)) continue;
		if (intelflag != (mask & NP_INTEL)) continue;
		if (kokkos_device_flag != (mask & NP_KOKKOS_DEVICE)) continue;
		if (kokkos_host_flag != (mask & NP_KOKKOS_HOST)) continue;

		if (style == NSQ && !(mask & NP_NSQ)) continue;
		if (style == BIN && !(mask & NP_BIN)) continue;
		if (style == MULTI && !(mask & NP_MULTI)) continue;
		// style is one of NSQ,BIN,MULTI and must match

		if (style == NSQ) {
		if (!(mask & NP_NSQ)) continue;
		} else if (style == BIN) {
		if (!(mask & NP_BIN)) continue;
		} else if (style == MULTI) {
		if (!(mask & NP_MULTI)) continue;
		}

		// newtflag is on or off and must match

		if (newtflag) {
		if (!(mask & NP_NEWTON)) continue;
		} else if (!newtflag) {
		if (!(mask & NP_NEWTOFF)) continue;
		}

		// triclinic flag is on or off and must match

		if (newtflag && !(mask & NP_NEWTON)) continue;
		if (!newtflag && !(mask & NP_NEWTOFF)) continue;
		if (triclinic) {
		if (!(mask & NP_TRI)) continue;
		} else if (!triclinic) {
		if (!(mask & NP_ORTHO)) continue;
		}

		// Kokkos flags

		if (!triclinic && !(mask & NP_ORTHO)) continue;
		if (triclinic && !(mask & NP_TRI)) continue;
		if (kokkos_device_flag != (mask & NP_KOKKOS_DEVICE)) continue;
		if (kokkos_host_flag != (mask & NP_KOKKOS_HOST)) continue;

		return i+1;
		}
		@@ -1727,7 +1755,7 @@ void Neighbor::build(int topoflag)

		for (i = 0; i < npair_perpetual; i++) {
		m = plist[i];
		lists[m]->grow(nlocal,nall);
		if (!lists[m]->copy) lists[m]->grow(nlocal,nall);
		neigh_pair[m]->build_setup();
		neigh_pair[m]->build(lists[m]);
		}

src/npair_skip.h

+2 −1

Original line number	Diff line number	Diff line
		@@ -15,7 +15,8 @@

		NPairStyle(skip,
		NPairSkip,
		NP_SKIP \| NP_HALF \| NP_FULL \| NP_NSQ \| NP_BIN \| NP_MULTI \|
		NP_SKIP \| NP_HALF \| NP_FULL \| NP_HALFFULL \|
		NP_NSQ \| NP_BIN \| NP_MULTI \|
		NP_NEWTON \| NP_NEWTOFF \| NP_ORTHO \| NP_TRI)

		#else

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