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Merge branch 'master' into USER-DPD_kokkos as of 21Dec16 patch

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Tim Mattox
2016-12-21 16:50:42 -05:00
parent 807d9529da 62dea1bb63
commit 26c21da45b
7 changed files with 55 additions and 21 deletions
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4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="17 Dec 2016 version">
<META NAME="docnumber" CONTENT="21 Dec 2016 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
17 Dec 2016 version :c,h4
21 Dec 2016 version :c,h4
Version info: :h4

4
src/atom_vec_body.cpp
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@ -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,

2
src/my_page.h
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@ -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;

1
src/neigh_list.cpp
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@ -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)

60
src/neighbor.cpp
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@ -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) {
@ -1470,19 +1479,38 @@ int Neighbor::choose_pair(NeighRequest *rq)
if (ssaflag != (mask & NP_SSA)) continue;
if (ompflag != (mask & NP_OMP)) continue;
if (intelflag != (mask & NP_INTEL)) 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 (triclinic) {
if (!(mask & NP_TRI)) continue;
} else if (!triclinic) {
if (!(mask & NP_ORTHO)) continue;
}
// Kokkos flags
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;
if (newtflag && !(mask & NP_NEWTON)) continue;
if (!newtflag && !(mask & NP_NEWTOFF)) continue;
if (!triclinic && !(mask & NP_ORTHO)) continue;
if (triclinic && !(mask & NP_TRI)) 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]);
}

3
src/npair_skip.h
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@ -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

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "17 Dec 2016"
#define LAMMPS_VERSION "21 Dec 2016"