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rLAMMPS lammps
pair_comb_omp.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include "pair_comb_omp.h"
#include "atom.h"
#include "comm.h"
#include "group.h"
#include "force.h"
#include "memory.h"
#include "my_page.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "suffix.h"
using
namespace
LAMMPS_NS
;
#define MAXNEIGH 24
/* ---------------------------------------------------------------------- */
PairCombOMP
::
PairCombOMP
(
LAMMPS
*
lmp
)
:
PairComb
(
lmp
),
ThrOMP
(
lmp
,
THR_PAIR
)
{
suffix_flag
|=
Suffix
::
OMP
;
respa_enable
=
0
;
}
/* ---------------------------------------------------------------------- */
void
PairCombOMP
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
{
ev_setup
(
eflag
,
vflag
);
}
else
evflag
=
vflag_fdotr
=
vflag_atom
=
0
;
const
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
const
int
inum
=
list
->
inum
;
// Build short range neighbor list
Short_neigh_thr
();
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int
ifrom
,
ito
,
tid
;
loop_setup_thr
(
ifrom
,
ito
,
tid
,
inum
,
nthreads
);
ThrData
*
thr
=
fix
->
get_thr
(
tid
);
thr
->
timer
(
Timer
::
START
);
ev_setup_thr
(
eflag
,
vflag
,
nall
,
eatom
,
vatom
,
thr
);
if
(
evflag
)
{
if
(
eflag
)
{
if
(
vflag_atom
)
eval
<
1
,
1
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
1
,
0
>
(
ifrom
,
ito
,
thr
);
}
else
{
if
(
vflag_atom
)
eval
<
1
,
0
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
}
else
eval
<
0
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
thr
->
timer
(
Timer
::
PAIR
);
reduce_thr
(
this
,
eflag
,
vflag
,
thr
);
}
// end of omp parallel region
}
template
<
int
EVFLAG
,
int
EFLAG
,
int
VFLAG_ATOM
>
void
PairCombOMP
::
eval
(
int
iifrom
,
int
iito
,
ThrData
*
const
thr
)
{
int
i
,
j
,
k
,
ii
,
jj
,
kk
,
jnum
,
iparam_i
;
tagint
itag
,
jtag
;
int
itype
,
jtype
,
ktype
,
iparam_ij
,
iparam_ijk
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
,
fpair
;
double
rsq
,
rsq1
,
rsq2
;
double
delr1
[
3
],
delr2
[
3
],
fi
[
3
],
fj
[
3
],
fk
[
3
];
double
zeta_ij
,
prefactor
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
int
mr1
,
mr2
,
mr3
;
int
rsc
,
inty
;
double
elp_ij
,
filp
[
3
],
fjlp
[
3
],
fklp
[
3
];
double
iq
,
jq
;
double
yaself
;
double
potal
,
fac11
,
fac11e
;
double
vionij
,
fvionij
,
sr1
,
sr2
,
sr3
,
Eov
,
Fov
;
int
sht_jnum
,
*
sht_jlist
,
nj
;
evdwl
=
ecoul
=
0.0
;
const
double
*
const
*
const
x
=
atom
->
x
;
double
*
const
*
const
f
=
thr
->
get_f
();
const
double
*
const
q
=
atom
->
q
;
const
tagint
*
const
tag
=
atom
->
tag
;
const
int
*
const
type
=
atom
->
type
;
const
int
nlocal
=
atom
->
nlocal
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
yaself
=
vionij
=
fvionij
=
Eov
=
Fov
=
0.0
;
double
fxtmp
,
fytmp
,
fztmp
;
double
fjxtmp
,
fjytmp
,
fjztmp
;
// self energy correction term: potal
potal_calc
(
potal
,
fac11
,
fac11e
);
// loop over full neighbor list of my atoms
for
(
ii
=
iifrom
;
ii
<
iito
;
++
ii
)
{
i
=
ilist
[
ii
];
itag
=
tag
[
i
];
itype
=
map
[
type
[
i
]];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
fxtmp
=
fytmp
=
fztmp
=
0.0
;
iq
=
q
[
i
];
NCo
[
i
]
=
0
;
nj
=
0
;
iparam_i
=
elem2param
[
itype
][
itype
][
itype
];
// self energy, only on i atom
yaself
=
self
(
&
params
[
iparam_i
],
iq
,
potal
);
if
(
EVFLAG
)
ev_tally_thr
(
this
,
i
,
i
,
nlocal
,
0
,
yaself
,
0.0
,
0.0
,
0.0
,
0.0
,
0.0
,
thr
);
// two-body interactions (long and short repulsive)
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
sht_jlist
=
sht_first
[
i
];
sht_jnum
=
sht_num
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
jtag
=
tag
[
j
];
if
(
itag
>
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
0
)
continue
;
}
else
if
(
itag
<
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
1
)
continue
;
}
else
{
if
(
x
[
j
][
2
]
<
ztmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
<
ytmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
==
ytmp
&&
x
[
j
][
0
]
<
xtmp
)
continue
;
}
// Qj calculates 2-body Coulombic
jtype
=
map
[
type
[
j
]];
jq
=
q
[
j
];
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
iparam_ij
=
elem2param
[
itype
][
jtype
][
jtype
];
// long range q-dependent
if
(
rsq
>
params
[
iparam_ij
].
lcutsq
)
continue
;
inty
=
intype
[
itype
][
jtype
];
// polynomial three-point interpolation
tri_point
(
rsq
,
mr1
,
mr2
,
mr3
,
sr1
,
sr2
,
sr3
,
itype
);
// 1/r energy and forces
direct
(
inty
,
mr1
,
mr2
,
mr3
,
rsq
,
sr1
,
sr2
,
sr3
,
iq
,
jq
,
potal
,
fac11
,
fac11e
,
vionij
,
fvionij
);
// field correction to self energy
field
(
&
params
[
iparam_ij
],
rsq
,
iq
,
jq
,
vionij
,
fvionij
);
// polarization field
// sums up long range forces
fxtmp
+=
delx
*
fvionij
;
fytmp
+=
dely
*
fvionij
;
fztmp
+=
delz
*
fvionij
;
f
[
j
][
0
]
-=
delx
*
fvionij
;
f
[
j
][
1
]
-=
dely
*
fvionij
;
f
[
j
][
2
]
-=
delz
*
fvionij
;
if
(
EVFLAG
)
ev_tally_thr
(
this
,
i
,
j
,
nlocal
,
/* newton_pair */
1
,
0.0
,
vionij
,
fvionij
,
delx
,
dely
,
delz
,
thr
);
// short range q-independent
if
(
rsq
>
params
[
iparam_ij
].
cutsq
)
continue
;
repulsive
(
&
params
[
iparam_ij
],
rsq
,
fpair
,
EFLAG
,
evdwl
,
iq
,
jq
);
// repulsion is pure two-body, sums up pair repulsive forces
fxtmp
+=
delx
*
fpair
;
fytmp
+=
dely
*
fpair
;
fztmp
+=
delz
*
fpair
;
f
[
j
][
0
]
-=
delx
*
fpair
;
f
[
j
][
1
]
-=
dely
*
fpair
;
f
[
j
][
2
]
-=
delz
*
fpair
;
if
(
EVFLAG
)
ev_tally_thr
(
this
,
i
,
j
,
nlocal
,
/* newton_pair */
1
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
,
thr
);
}
// accumulate coordination number information
if
(
cor_flag
)
{
int
numcoor
=
0
;
for
(
jj
=
0
;
jj
<
sht_jnum
;
jj
++
)
{
j
=
sht_jlist
[
jj
];
jtype
=
map
[
type
[
j
]];
iparam_ij
=
elem2param
[
itype
][
jtype
][
jtype
];
if
(
params
[
iparam_ij
].
hfocor
>
0.0
)
{
delr1
[
0
]
=
x
[
j
][
0
]
-
xtmp
;
delr1
[
1
]
=
x
[
j
][
1
]
-
ytmp
;
delr1
[
2
]
=
x
[
j
][
2
]
-
ztmp
;
rsq1
=
vec3_dot
(
delr1
,
delr1
);
if
(
rsq1
>
params
[
iparam_ij
].
cutsq
)
continue
;
++
numcoor
;
}
}
NCo
[
i
]
=
numcoor
;
}
// three-body interactions
// half i-j loop
for
(
jj
=
0
;
jj
<
sht_jnum
;
jj
++
)
{
j
=
sht_jlist
[
jj
];
jtype
=
map
[
type
[
j
]];
iparam_ij
=
elem2param
[
itype
][
jtype
][
jtype
];
// this Qj for q-dependent BSi
jq
=
q
[
j
];
delr1
[
0
]
=
x
[
j
][
0
]
-
xtmp
;
delr1
[
1
]
=
x
[
j
][
1
]
-
ytmp
;
delr1
[
2
]
=
x
[
j
][
2
]
-
ztmp
;
rsq1
=
vec3_dot
(
delr1
,
delr1
);
if
(
rsq1
>
params
[
iparam_ij
].
cutsq
)
continue
;
nj
++
;
// accumulate bondorder zeta for each i-j interaction via loop over k
fjxtmp
=
fjytmp
=
fjztmp
=
0.0
;
zeta_ij
=
0.0
;
cuo_flag1
=
0
;
cuo_flag2
=
0
;
for
(
kk
=
0
;
kk
<
sht_jnum
;
kk
++
)
{
k
=
sht_jlist
[
kk
];
if
(
j
==
k
)
continue
;
ktype
=
map
[
type
[
k
]];
iparam_ijk
=
elem2param
[
itype
][
jtype
][
ktype
];
delr2
[
0
]
=
x
[
k
][
0
]
-
xtmp
;
delr2
[
1
]
=
x
[
k
][
1
]
-
ytmp
;
delr2
[
2
]
=
x
[
k
][
2
]
-
ztmp
;
rsq2
=
vec3_dot
(
delr2
,
delr2
);
if
(
rsq2
>
params
[
iparam_ijk
].
cutsq
)
continue
;
zeta_ij
+=
zeta
(
&
params
[
iparam_ijk
],
rsq1
,
rsq2
,
delr1
,
delr2
);
if
(
params
[
iparam_ijk
].
hfocor
==
-
2.0
)
cuo_flag1
=
1
;
if
(
params
[
iparam_ijk
].
hfocor
==
-
1.0
)
cuo_flag2
=
1
;
}
if
(
cuo_flag1
&&
cuo_flag2
)
cuo_flag
=
1
;
else
cuo_flag
=
0
;
force_zeta
(
&
params
[
iparam_ij
],
EFLAG
,
i
,
nj
,
rsq1
,
zeta_ij
,
iq
,
jq
,
fpair
,
prefactor
,
evdwl
);
// over-coordination correction for HfO2
if
(
cor_flag
&&
NCo
[
i
]
!=
0
)
Over_cor
(
&
params
[
iparam_ij
],
rsq1
,
NCo
[
i
],
Eov
,
Fov
);
evdwl
+=
Eov
;
fpair
+=
Fov
;
fxtmp
+=
delr1
[
0
]
*
fpair
;
fytmp
+=
delr1
[
1
]
*
fpair
;
fztmp
+=
delr1
[
2
]
*
fpair
;
fjxtmp
-=
delr1
[
0
]
*
fpair
;
fjytmp
-=
delr1
[
1
]
*
fpair
;
fjztmp
-=
delr1
[
2
]
*
fpair
;
if
(
EVFLAG
)
ev_tally_thr
(
this
,
i
,
j
,
nlocal
,
/* newton_pair */
1
,
evdwl
,
0.0
,
-
fpair
,
-
delr1
[
0
],
-
delr1
[
1
],
-
delr1
[
2
],
thr
);
// attractive term via loop over k (3-body forces)
for
(
kk
=
0
;
kk
<
sht_jnum
;
kk
++
)
{
k
=
sht_jlist
[
kk
];
if
(
j
==
k
)
continue
;
ktype
=
map
[
type
[
k
]];
iparam_ijk
=
elem2param
[
itype
][
jtype
][
ktype
];
delr2
[
0
]
=
x
[
k
][
0
]
-
xtmp
;
delr2
[
1
]
=
x
[
k
][
1
]
-
ytmp
;
delr2
[
2
]
=
x
[
k
][
2
]
-
ztmp
;
rsq2
=
vec3_dot
(
delr2
,
delr2
);
if
(
rsq2
>
params
[
iparam_ijk
].
cutsq
)
continue
;
for
(
rsc
=
0
;
rsc
<
3
;
rsc
++
)
fi
[
rsc
]
=
fj
[
rsc
]
=
fk
[
rsc
]
=
0.0
;
attractive
(
&
params
[
iparam_ijk
],
prefactor
,
rsq1
,
rsq2
,
delr1
,
delr2
,
fi
,
fj
,
fk
);
// 3-body LP and BB correction and forces
elp_ij
=
elp
(
&
params
[
iparam_ijk
],
rsq1
,
rsq2
,
delr1
,
delr2
);
flp
(
&
params
[
iparam_ijk
],
rsq1
,
rsq2
,
delr1
,
delr2
,
filp
,
fjlp
,
fklp
);
fxtmp
+=
fi
[
0
]
+
filp
[
0
];
fytmp
+=
fi
[
1
]
+
filp
[
1
];
fztmp
+=
fi
[
2
]
+
filp
[
2
];
fjxtmp
+=
fj
[
0
]
+
fjlp
[
0
];
fjytmp
+=
fj
[
1
]
+
fjlp
[
1
];
fjztmp
+=
fj
[
2
]
+
fjlp
[
2
];
f
[
k
][
0
]
+=
fk
[
0
]
+
fklp
[
0
];
f
[
k
][
1
]
+=
fk
[
1
]
+
fklp
[
1
];
f
[
k
][
2
]
+=
fk
[
2
]
+
fklp
[
2
];
if
(
EVFLAG
)
ev_tally_thr
(
this
,
i
,
j
,
nlocal
,
/* newton_pair */
1
,
elp_ij
,
0.0
,
0.0
,
0.0
,
0.0
,
0.0
,
thr
);
if
(
VFLAG_ATOM
)
v_tally3_thr
(
i
,
j
,
k
,
fj
,
fk
,
delr1
,
delr2
,
thr
);
}
f
[
j
][
0
]
+=
fjxtmp
;
f
[
j
][
1
]
+=
fjytmp
;
f
[
j
][
2
]
+=
fjztmp
;
}
f
[
i
][
0
]
+=
fxtmp
;
f
[
i
][
1
]
+=
fytmp
;
f
[
i
][
2
]
+=
fztmp
;
if
(
cuo_flag
)
params
[
iparam_i
].
cutsq
*=
0.65
;
}
cuo_flag
=
0
;
}
/* ---------------------------------------------------------------------- */
double
PairCombOMP
::
yasu_char
(
double
*
qf_fix
,
int
&
igroup
)
{
int
ii
;
double
potal
,
fac11
,
fac11e
;
const
double
*
const
*
const
x
=
atom
->
x
;
const
double
*
const
q
=
atom
->
q
;
const
int
*
const
type
=
atom
->
type
;
const
tagint
*
const
tag
=
atom
->
tag
;
const
int
inum
=
list
->
inum
;
const
int
*
const
ilist
=
list
->
ilist
;
const
int
*
const
numneigh
=
list
->
numneigh
;
const
int
*
const
*
const
firstneigh
=
list
->
firstneigh
;
const
int
*
const
mask
=
atom
->
mask
;
const
int
groupbit
=
group
->
bitmask
[
igroup
];
qf
=
qf_fix
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
const
int
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
qf
[
i
]
=
0.0
;
}
// communicating charge force to all nodes, first forward then reverse
comm
->
forward_comm_pair
(
this
);
// self energy correction term: potal
potal_calc
(
potal
,
fac11
,
fac11e
);
// loop over full neighbor list of my atoms
#if defined(_OPENMP)
#pragma omp parallel for private(ii) default(none) shared(potal,fac11e)
#endif
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
double
fqi
,
fqj
,
fqij
,
fqji
,
fqjj
,
delr1
[
3
];
double
sr1
,
sr2
,
sr3
;
int
mr1
,
mr2
,
mr3
;
const
int
i
=
ilist
[
ii
];
const
tagint
itag
=
tag
[
i
];
int
nj
=
0
;
if
(
mask
[
i
]
&
groupbit
)
{
fqi
=
fqj
=
fqij
=
fqji
=
fqjj
=
0.0
;
// should not be needed.
int
itype
=
map
[
type
[
i
]];
const
double
xtmp
=
x
[
i
][
0
];
const
double
ytmp
=
x
[
i
][
1
];
const
double
ztmp
=
x
[
i
][
2
];
const
double
iq
=
q
[
i
];
const
int
iparam_i
=
elem2param
[
itype
][
itype
][
itype
];
// charge force from self energy
fqi
=
qfo_self
(
&
params
[
iparam_i
],
iq
,
potal
);
// two-body interactions
const
int
*
const
jlist
=
firstneigh
[
i
];
const
int
jnum
=
numneigh
[
i
];
for
(
int
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
const
int
j
=
jlist
[
jj
]
&
NEIGHMASK
;
const
tagint
jtag
=
tag
[
j
];
if
(
itag
>
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
0
)
continue
;
}
else
if
(
itag
<
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
1
)
continue
;
}
else
{
if
(
x
[
j
][
2
]
<
ytmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
<
ytmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
==
ytmp
&&
x
[
j
][
0
]
<
xtmp
)
continue
;
}
const
int
jtype
=
map
[
type
[
j
]];
double
jq
=
q
[
j
];
delr1
[
0
]
=
x
[
j
][
0
]
-
xtmp
;
delr1
[
1
]
=
x
[
j
][
1
]
-
ytmp
;
delr1
[
2
]
=
x
[
j
][
2
]
-
ztmp
;
double
rsq1
=
vec3_dot
(
delr1
,
delr1
);
const
int
iparam_ij
=
elem2param
[
itype
][
jtype
][
jtype
];
// long range q-dependent
if
(
rsq1
>
params
[
iparam_ij
].
lcutsq
)
continue
;
const
int
inty
=
intype
[
itype
][
jtype
];
// polynomial three-point interpolation
tri_point
(
rsq1
,
mr1
,
mr2
,
mr3
,
sr1
,
sr2
,
sr3
,
itype
);
// 1/r charge forces
qfo_direct
(
inty
,
mr1
,
mr2
,
mr3
,
rsq1
,
sr1
,
sr2
,
sr3
,
fac11e
,
fqij
);
// field correction to self energy and charge force
qfo_field
(
&
params
[
iparam_ij
],
rsq1
,
iq
,
jq
,
fqji
,
fqjj
);
fqi
+=
jq
*
fqij
+
fqji
;
#if defined(_OPENMP)
#pragma omp atomic
#endif
qf
[
j
]
+=
(
iq
*
fqij
+
fqjj
);
}
// three-body interactions
for
(
int
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
const
int
j
=
jlist
[
jj
]
&
NEIGHMASK
;
const
int
jtype
=
map
[
type
[
j
]];
const
double
jq
=
q
[
j
];
delr1
[
0
]
=
x
[
j
][
0
]
-
xtmp
;
delr1
[
1
]
=
x
[
j
][
1
]
-
ytmp
;
delr1
[
2
]
=
x
[
j
][
2
]
-
ztmp
;
double
rsq1
=
vec3_dot
(
delr1
,
delr1
);
const
int
iparam_ij
=
elem2param
[
itype
][
jtype
][
jtype
];
if
(
rsq1
>
params
[
iparam_ij
].
cutsq
)
continue
;
nj
++
;
// charge force in Aij and Bij
qfo_short
(
&
params
[
iparam_ij
],
i
,
nj
,
rsq1
,
iq
,
jq
,
fqij
,
fqjj
);
fqi
+=
fqij
;
#if defined(_OPENMP)
#pragma omp atomic
#endif
qf
[
j
]
+=
fqjj
;
}
#if defined(_OPENMP)
#pragma omp atomic
#endif
qf
[
i
]
+=
fqi
;
}
}
comm
->
reverse_comm_pair
(
this
);
// sum charge force on each node and return it
double
eneg
=
0.0
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
const
int
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
eneg
+=
qf
[
i
];
}
double
enegtot
;
MPI_Allreduce
(
&
eneg
,
&
enegtot
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
return
enegtot
;
}
/* ---------------------------------------------------------------------- */
double
PairCombOMP
::
memory_usage
()
{
double
bytes
=
memory_usage_thr
();
bytes
+=
PairComb
::
memory_usage
();
return
bytes
;
}
/* ---------------------------------------------------------------------- */
void
PairCombOMP
::
Short_neigh_thr
()
{
if
(
atom
->
nmax
>
nmax
)
{
nmax
=
atom
->
nmax
;
memory
->
sfree
(
sht_first
);
sht_first
=
(
int
**
)
memory
->
smalloc
(
nmax
*
sizeof
(
int
*
),
"pair:sht_first"
);
memory
->
grow
(
sht_num
,
nmax
,
"pair:sht_num"
);
memory
->
grow
(
NCo
,
nmax
,
"pair:NCo"
);
memory
->
grow
(
bbij
,
nmax
,
MAXNEIGH
,
"pair:bbij"
);
}
const
int
nthreads
=
comm
->
nthreads
;
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
int
nj
,
*
neighptrj
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
int
jnum
,
i
,
j
,
ii
,
jj
;
double
xtmp
,
ytmp
,
ztmp
,
rsq
,
delrj
[
3
];
double
**
x
=
atom
->
x
;
const
int
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
#if defined(_OPENMP)
const
int
tid
=
omp_get_thread_num
();
#else
const
int
tid
=
0
;
#endif
const
int
iidelta
=
1
+
inum
/
nthreads
;
const
int
iifrom
=
tid
*
iidelta
;
const
int
iito
=
((
iifrom
+
iidelta
)
>
inum
)
?
inum
:
(
iifrom
+
iidelta
);
// each thread has its own page allocator
MyPage
<
int
>
&
ipg
=
ipage
[
tid
];
ipg
.
reset
();
// create Comb neighbor list
for
(
ii
=
iifrom
;
ii
<
iito
;
ii
++
)
{
i
=
ilist
[
ii
];
nj
=
0
;
neighptrj
=
ipg
.
vget
();
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
delrj
[
0
]
=
xtmp
-
x
[
j
][
0
];
delrj
[
1
]
=
ytmp
-
x
[
j
][
1
];
delrj
[
2
]
=
ztmp
-
x
[
j
][
2
];
rsq
=
vec3_dot
(
delrj
,
delrj
);
if
(
rsq
>
cutmin
)
continue
;
neighptrj
[
nj
++
]
=
j
;
}
sht_first
[
i
]
=
neighptrj
;
sht_num
[
i
]
=
nj
;
ipg
.
vgot
(
nj
);
if
(
ipg
.
status
())
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
}
}
}
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