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This commit is contained in:
Steve Plimpton
2017-01-26 14:06:43 -07:00
parent 18e5584311
commit f8506fee23
11 changed files with 37 additions and 12 deletions
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4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="20 Jan 2017 version"> <META NAME="docnumber" CONTENT="26 Jan 2017 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <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."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
20 Jan 2017 version :c,h4 26 Jan 2017 version :c,h4
Version info: :h4 Version info: :h4

13
potentials/WL.meam Normal file
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@ -0,0 +1,13 @@
# DATE: 2017-01-25 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov, CITATION: Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001)
rc = 3.8
delr = 0.1
augt1 = 0
erose_form = 2
zbl(1,1) = 0
nn2(1,1) = 1
Ec(1,1) = 8.66
re(1,1) = 2.74
attrac(1,1) = 0
repuls(1,1) = 0
Cmin(1,1,1) = 0.49
Cmax(1,1,1) = 2.8

2
src/angle_hybrid.cpp
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@ -104,7 +104,7 @@ void AngleHybrid::compute(int eflag, int vflag)
// accumulate sub-style global/peratom energy/virial in hybrid // accumulate sub-style global/peratom energy/virial in hybrid
if (eflag || vflag) ev_setup(eflag,vflag); if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0; else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
for (m = 0; m < nstyles; m++) { for (m = 0; m < nstyles; m++) {
neighbor->nanglelist = nanglelist[m]; neighbor->nanglelist = nanglelist[m];

2
src/bond_hybrid.cpp
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@ -103,7 +103,7 @@ void BondHybrid::compute(int eflag, int vflag)
// accumulate sub-style global/peratom energy/virial in hybrid // accumulate sub-style global/peratom energy/virial in hybrid
if (eflag || vflag) ev_setup(eflag,vflag); if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0; else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
for (m = 0; m < nstyles; m++) { for (m = 0; m < nstyles; m++) {
neighbor->nbondlist = nbondlist[m]; neighbor->nbondlist = nbondlist[m];

2
src/dihedral_hybrid.cpp
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@ -105,7 +105,7 @@ void DihedralHybrid::compute(int eflag, int vflag)
// accumulate sub-style global/peratom energy/virial in hybrid // accumulate sub-style global/peratom energy/virial in hybrid
if (eflag || vflag) ev_setup(eflag,vflag); if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0; else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
for (m = 0; m < nstyles; m++) { for (m = 0; m < nstyles; m++) {
neighbor->ndihedrallist = ndihedrallist[m]; neighbor->ndihedrallist = ndihedrallist[m];

2
src/improper_hybrid.cpp
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@ -105,7 +105,7 @@ void ImproperHybrid::compute(int eflag, int vflag)
// accumulate sub-style global/peratom energy/virial in hybrid // accumulate sub-style global/peratom energy/virial in hybrid
if (eflag || vflag) ev_setup(eflag,vflag); if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0; else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
for (m = 0; m < nstyles; m++) { for (m = 0; m < nstyles; m++) {
neighbor->nimproperlist = nimproperlist[m]; neighbor->nimproperlist = nimproperlist[m];

7
src/neigh_request.cpp
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@ -46,7 +46,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
command_style = NULL; command_style = NULL;
// combination of settings, mutiple can be set to 1 // combination of settings, mutiple can be set to 1
// default is every reneighboring // default is every reneighboring, not occasional
// default is use newton_pair setting in force // default is use newton_pair setting in force
// default is no size history (when gran = 1) // default is no size history (when gran = 1)
// default is no one-sided sphere/surface interactions (when gran = 1) // default is no one-sided sphere/surface interactions (when gran = 1)
@ -55,6 +55,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
// default is no multi-threaded neighbor list build // default is no multi-threaded neighbor list build
// default is no Kokkos neighbor list build // default is no Kokkos neighbor list build
// default is no Shardlow Splitting Algorithm (SSA) neighbor list build // default is no Shardlow Splitting Algorithm (SSA) neighbor list build
// default is neighbors of atoms, not bonds
occasional = 0; occasional = 0;
newton = 0; newton = 0;
@ -65,6 +66,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
intel = 0; intel = 0;
kokkos_host = kokkos_device = 0; kokkos_host = kokkos_device = 0;
ssa = 0; ssa = 0;
bond = 0;
// copy/skip/derive info, default is no copy or skip // copy/skip/derive info, default is no copy or skip
// none or only one option is set // none or only one option is set
@ -142,6 +144,7 @@ int NeighRequest::identical(NeighRequest *other)
if (kokkos_host != other->kokkos_host) same = 0; if (kokkos_host != other->kokkos_host) same = 0;
if (kokkos_device != other->kokkos_device) same = 0; if (kokkos_device != other->kokkos_device) same = 0;
if (ssa != other->ssa) same = 0; if (ssa != other->ssa) same = 0;
if (bond != other->bond) same = 0;
if (copy != other->copy_original) same = 0; if (copy != other->copy_original) same = 0;
if (same_skip(other) == 0) same = 0; if (same_skip(other) == 0) same = 0;
@ -182,6 +185,7 @@ int NeighRequest::same_kind(NeighRequest *other)
if (kokkos_host != other->kokkos_host) same = 0; if (kokkos_host != other->kokkos_host) same = 0;
if (kokkos_device != other->kokkos_device) same = 0; if (kokkos_device != other->kokkos_device) same = 0;
if (ssa != other->ssa) same = 0; if (ssa != other->ssa) same = 0;
if (bond != other->bond) same = 0;
// copy/skip/derive info does not need to be the same // copy/skip/derive info does not need to be the same
@ -237,4 +241,5 @@ void NeighRequest::copy_request(NeighRequest *other)
kokkos_host = other->kokkos_host; kokkos_host = other->kokkos_host;
kokkos_device = other->kokkos_device; kokkos_device = other->kokkos_device;
ssa = other->ssa; ssa = other->ssa;
bond = other->bond;
} }

4
src/neigh_request.h
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@ -95,6 +95,10 @@ class NeighRequest : protected Pointers {
int ssa; int ssa;
// 1 if bond neighbors, not atom neighbors
int bond;
// ----------------- // -----------------
// end of optional settings // end of optional settings
// ----------------- // -----------------

10
src/neighbor.cpp
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@ -1411,11 +1411,11 @@ int Neighbor::choose_pair(NeighRequest *rq)
int copyflag,skipflag,halfflag,fullflag,halffullflag,sizeflag,respaflag, int copyflag,skipflag,halfflag,fullflag,halffullflag,sizeflag,respaflag,
ghostflag,off2onflag,onesideflag,ssaflag,ompflag,intelflag, ghostflag,off2onflag,onesideflag,ssaflag,ompflag,intelflag,
kokkos_device_flag,kokkos_host_flag; kokkos_device_flag,kokkos_host_flag,bondflag;
copyflag = skipflag = halfflag = fullflag = halffullflag = sizeflag = copyflag = skipflag = halfflag = fullflag = halffullflag = sizeflag =
ghostflag = respaflag = off2onflag = onesideflag = ssaflag = ghostflag = respaflag = off2onflag = onesideflag = ssaflag =
ompflag = intelflag = kokkos_device_flag = kokkos_host_flag = 0; ompflag = intelflag = kokkos_device_flag = kokkos_host_flag = bondflag = 0;
if (rq->copy) copyflag = NP_COPY; if (rq->copy) copyflag = NP_COPY;
if (rq->skip) skipflag = NP_SKIP; if (rq->skip) skipflag = NP_SKIP;
@ -1447,6 +1447,7 @@ int Neighbor::choose_pair(NeighRequest *rq)
if (rq->intel) intelflag = NP_INTEL; if (rq->intel) intelflag = NP_INTEL;
if (rq->kokkos_device) kokkos_device_flag = NP_KOKKOS_DEVICE; if (rq->kokkos_device) kokkos_device_flag = NP_KOKKOS_DEVICE;
if (rq->kokkos_host) kokkos_host_flag = NP_KOKKOS_HOST; if (rq->kokkos_host) kokkos_host_flag = NP_KOKKOS_HOST;
if (rq->bond) bondflag = NP_BOND;
int newtflag; int newtflag;
if (rq->newton == 0 && newton_pair) newtflag = 1; if (rq->newton == 0 && newton_pair) newtflag = 1;
@ -1459,10 +1460,10 @@ int Neighbor::choose_pair(NeighRequest *rq)
int mask; int mask;
//printf("FLAGS: %d %d %d %d %d %d %d %d %d %d %d %d %d %d\n", //printf("FLAGS: %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d\n",
// copyflag,skipflag,halfflag,fullflag,halffullflag, // copyflag,skipflag,halfflag,fullflag,halffullflag,
// sizeflag,respaflag,ghostflag,off2onflag,onesideflag,ssaflag, // sizeflag,respaflag,ghostflag,off2onflag,onesideflag,ssaflag,
// ompflag,intelflag,newtflag); // ompflag,intelflag,newtflag,bondflag);
for (int i = 0; i < npclass; i++) { for (int i = 0; i < npclass; i++) {
mask = pairmasks[i]; mask = pairmasks[i];
@ -1496,6 +1497,7 @@ int Neighbor::choose_pair(NeighRequest *rq)
if (off2onflag != (mask & NP_OFF2ON)) continue; if (off2onflag != (mask & NP_OFF2ON)) continue;
if (onesideflag != (mask & NP_ONESIDE)) continue; if (onesideflag != (mask & NP_ONESIDE)) continue;
if (ssaflag != (mask & NP_SSA)) continue; if (ssaflag != (mask & NP_SSA)) continue;
if (bondflag != (mask & NP_BOND)) continue;
if (ompflag != (mask & NP_OMP)) continue; if (ompflag != (mask & NP_OMP)) continue;
if (intelflag != (mask & NP_INTEL)) continue; if (intelflag != (mask & NP_INTEL)) continue;

1
src/neighbor.h
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@ -267,6 +267,7 @@ namespace NeighConst {
static const int NP_TRI = 1<<19; static const int NP_TRI = 1<<19;
static const int NP_KOKKOS_DEVICE = 1<<20; static const int NP_KOKKOS_DEVICE = 1<<20;
static const int NP_KOKKOS_HOST = 1<<21; static const int NP_KOKKOS_HOST = 1<<21;
static const int NP_BOND = 1<<22;
} }
} }

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "20 Jan 2017" #define LAMMPS_VERSION "26 Jan 2017"