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pair_lj_cut_coul_long_omp.cpp
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text/x-c++
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rLAMMPS lammps
pair_lj_cut_coul_long_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
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_cut_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongOMP
::
PairLJCutCoulLongOMP
(
LAMMPS
*
lmp
)
:
PairOMP
(
lmp
)
{
respa_enable
=
1
;
ftable
=
NULL
;
}
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongOMP
::~
PairLJCutCoulLongOMP
()
{
if
(
allocated
)
{
memory
->
destroy_2d_int_array
(
setflag
);
memory
->
destroy_2d_double_array
(
cutsq
);
memory
->
destroy_2d_double_array
(
cut_lj
);
memory
->
destroy_2d_double_array
(
cut_ljsq
);
memory
->
destroy_2d_double_array
(
epsilon
);
memory
->
destroy_2d_double_array
(
sigma
);
memory
->
destroy_2d_double_array
(
lj1
);
memory
->
destroy_2d_double_array
(
lj2
);
memory
->
destroy_2d_double_array
(
lj3
);
memory
->
destroy_2d_double_array
(
lj4
);
memory
->
destroy_2d_double_array
(
offset
);
}
if
(
ftable
)
free_tables
();
}
/* ---------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
{
ev_setup
(
eflag
,
vflag
);
ev_setup_thr
(
eflag
,
vflag
);
}
else
evflag
=
vflag_fdotr
=
0
;
if
(
evflag
)
{
if
(
eflag
)
{
if
(
force
->
newton_pair
)
return
eval
<
1
,
1
,
1
>
();
else
return
eval
<
1
,
1
,
0
>
();
}
else
{
if
(
force
->
newton_pair
)
return
eval
<
1
,
0
,
1
>
();
else
return
eval
<
1
,
0
,
0
>
();
}
}
else
{
if
(
force
->
newton_pair
)
return
eval
<
0
,
0
,
1
>
();
else
return
eval
<
0
,
0
,
0
>
();
}
}
template
<
int
EVFLAG
,
int
EFLAG
,
int
NEWTON_PAIR
>
void
PairLJCutCoulLongOMP
::
eval
()
{
#if defined(_OPENMP)
#pragma omp parallel default(shared)
#endif
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
,
itable
,
tid
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
,
fpair
;
double
fraction
,
table
;
double
r
,
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
factor_coul
,
factor_lj
;
double
grij
,
expm2
,
prefactor
,
t
,
erfc
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
rsq
;
evdwl
=
ecoul
=
0.0
;
const
int
nlocal
=
atom
->
nlocal
;
const
int
nall
=
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
*
q
=
atom
->
q
;
int
*
type
=
atom
->
type
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
double
qqrd2e
=
force
->
qqrd2e
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// loop over neighbors of my atoms
int
iifrom
,
iito
;
f
=
loop_setup_thr
(
f
,
iifrom
,
iito
,
tid
,
inum
,
nall
,
nthreads
);
for
(
ii
=
iifrom
;
ii
<
iito
;
++
ii
)
{
i
=
ilist
[
ii
];
qtmp
=
q
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
itype
=
type
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
if
(
j
<
nall
)
factor_coul
=
factor_lj
=
1.0
;
else
{
factor_coul
=
special_coul
[
j
/
nall
];
factor_lj
=
special_lj
[
j
/
nall
];
j
%=
nall
;
}
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
jtype
=
type
[
j
];
if
(
rsq
<
cutsq
[
itype
][
jtype
])
{
r2inv
=
1.0
/
rsq
;
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
r
=
sqrt
(
rsq
);
grij
=
g_ewald
*
r
;
expm2
=
exp
(
-
grij
*
grij
);
t
=
1.0
/
(
1.0
+
EWALD_P
*
grij
);
erfc
=
t
*
(
A1
+
t
*
(
A2
+
t
*
(
A3
+
t
*
(
A4
+
t
*
A5
))))
*
expm2
;
prefactor
=
qqrd2e
*
qtmp
*
q
[
j
]
/
r
;
forcecoul
=
prefactor
*
(
erfc
+
EWALD_F
*
grij
*
expm2
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
{
union_int_float_t
rsq_lookup
;
rsq_lookup
.
f
=
rsq
;
itable
=
rsq_lookup
.
i
&
ncoulmask
;
itable
>>=
ncoulshiftbits
;
fraction
=
(
rsq_lookup
.
f
-
rtable
[
itable
])
*
drtable
[
itable
];
table
=
ftable
[
itable
]
+
fraction
*
dftable
[
itable
];
forcecoul
=
qtmp
*
q
[
j
]
*
table
;
if
(
factor_coul
<
1.0
)
{
table
=
ctable
[
itable
]
+
fraction
*
dctable
[
itable
];
prefactor
=
qtmp
*
q
[
j
]
*
table
;
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
}
}
else
forcecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
}
else
forcelj
=
0.0
;
fpair
=
(
forcecoul
+
factor_lj
*
forcelj
)
*
r2inv
;
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
if
(
NEWTON_PAIR
||
j
<
nlocal
)
{
f
[
j
][
0
]
-=
delx
*
fpair
;
f
[
j
][
1
]
-=
dely
*
fpair
;
f
[
j
][
2
]
-=
delz
*
fpair
;
}
if
(
EFLAG
)
{
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
ecoul
=
prefactor
*
erfc
;
else
{
table
=
etable
[
itable
]
+
fraction
*
detable
[
itable
];
ecoul
=
qtmp
*
q
[
j
]
*
table
;
}
if
(
factor_coul
<
1.0
)
ecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
ecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
evdwl
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
evdwl
*=
factor_lj
;
}
else
evdwl
=
0.0
;
}
if
(
EVFLAG
)
ev_tally_thr
(
i
,
j
,
nlocal
,
NEWTON_PAIR
,
evdwl
,
ecoul
,
fpair
,
delx
,
dely
,
delz
,
tid
);
}
}
}
// reduce per thread forces into global force array.
force_reduce_thr
(
atom
->
f
,
nall
,
nthreads
,
tid
);
}
ev_reduce_thr
();
if
(
vflag_fdotr
)
virial_compute
();
}
/* ---------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
compute_inner
()
{
if
(
force
->
newton_pair
)
return
eval_inner
<
1
>
();
else
return
eval_inner
<
0
>
();
}
template
<
int
NEWTON_PAIR
>
void
PairLJCutCoulLongOMP
::
eval_inner
()
{
#if defined(_OPENMP)
#pragma omp parallel default(shared)
#endif
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
,
tid
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
fpair
;
double
rsq
,
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
factor_coul
,
factor_lj
;
double
rsw
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
const
int
nlocal
=
atom
->
nlocal
;
const
int
nall
=
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
*
q
=
atom
->
q
;
int
*
type
=
atom
->
type
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
double
qqrd2e
=
force
->
qqrd2e
;
inum
=
listinner
->
inum
;
ilist
=
listinner
->
ilist
;
numneigh
=
listinner
->
numneigh
;
firstneigh
=
listinner
->
firstneigh
;
double
cut_out_on
=
cut_respa
[
0
];
double
cut_out_off
=
cut_respa
[
1
];
double
cut_out_diff
=
cut_out_off
-
cut_out_on
;
double
cut_out_on_sq
=
cut_out_on
*
cut_out_on
;
double
cut_out_off_sq
=
cut_out_off
*
cut_out_off
;
// loop over neighbors of my atoms
int
iifrom
,
iito
;
f
=
loop_setup_thr
(
f
,
iifrom
,
iito
,
tid
,
inum
,
nall
,
nthreads
);
for
(
ii
=
iifrom
;
ii
<
iito
;
++
ii
)
{
i
=
ilist
[
ii
];
qtmp
=
q
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
itype
=
type
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
if
(
j
<
nall
)
factor_coul
=
factor_lj
=
1.0
;
else
{
factor_coul
=
special_coul
[
j
/
nall
];
factor_lj
=
special_lj
[
j
/
nall
];
j
%=
nall
;
}
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
if
(
rsq
<
cut_out_off_sq
)
{
r2inv
=
1.0
/
rsq
;
forcecoul
=
qqrd2e
*
qtmp
*
q
[
j
]
*
sqrt
(
r2inv
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
forcecoul
;
jtype
=
type
[
j
];
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
}
else
forcelj
=
0.0
;
fpair
=
(
forcecoul
+
factor_lj
*
forcelj
)
*
r2inv
;
if
(
rsq
>
cut_out_on_sq
)
{
rsw
=
(
sqrt
(
rsq
)
-
cut_out_on
)
/
cut_out_diff
;
fpair
*=
1.0
+
rsw
*
rsw
*
(
2.0
*
rsw
-
3.0
);
}
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
if
(
NEWTON_PAIR
||
j
<
nlocal
)
{
f
[
j
][
0
]
-=
delx
*
fpair
;
f
[
j
][
1
]
-=
dely
*
fpair
;
f
[
j
][
2
]
-=
delz
*
fpair
;
}
}
}
}
// reduce per thread forces into global force array.
force_reduce_thr
(
atom
->
f
,
nall
,
nthreads
,
tid
);
}
}
/* ---------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
compute_middle
()
{
if
(
force
->
newton_pair
)
return
eval_middle
<
1
>
();
else
return
eval_middle
<
0
>
();
}
template
<
int
NEWTON_PAIR
>
void
PairLJCutCoulLongOMP
::
eval_middle
()
{
#if defined(_OPENMP)
#pragma omp parallel default(shared)
#endif
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
,
tid
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
fpair
;
double
rsq
,
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
factor_coul
,
factor_lj
;
double
rsw
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
const
int
nlocal
=
atom
->
nlocal
;
const
int
nall
=
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
*
q
=
atom
->
q
;
int
*
type
=
atom
->
type
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
double
qqrd2e
=
force
->
qqrd2e
;
inum
=
listmiddle
->
inum
;
ilist
=
listmiddle
->
ilist
;
numneigh
=
listmiddle
->
numneigh
;
firstneigh
=
listmiddle
->
firstneigh
;
double
cut_in_off
=
cut_respa
[
0
];
double
cut_in_on
=
cut_respa
[
1
];
double
cut_out_on
=
cut_respa
[
2
];
double
cut_out_off
=
cut_respa
[
3
];
double
cut_in_diff
=
cut_in_on
-
cut_in_off
;
double
cut_out_diff
=
cut_out_off
-
cut_out_on
;
double
cut_in_off_sq
=
cut_in_off
*
cut_in_off
;
double
cut_in_on_sq
=
cut_in_on
*
cut_in_on
;
double
cut_out_on_sq
=
cut_out_on
*
cut_out_on
;
double
cut_out_off_sq
=
cut_out_off
*
cut_out_off
;
// loop over neighbors of my atoms
int
iifrom
,
iito
;
f
=
loop_setup_thr
(
f
,
iifrom
,
iito
,
tid
,
inum
,
nall
,
nthreads
);
for
(
ii
=
iifrom
;
ii
<
iito
;
++
ii
)
{
i
=
ilist
[
ii
];
qtmp
=
q
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
itype
=
type
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
if
(
j
<
nall
)
factor_coul
=
factor_lj
=
1.0
;
else
{
factor_coul
=
special_coul
[
j
/
nall
];
factor_lj
=
special_lj
[
j
/
nall
];
j
%=
nall
;
}
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
if
(
rsq
<
cut_out_off_sq
&&
rsq
>
cut_in_off_sq
)
{
r2inv
=
1.0
/
rsq
;
forcecoul
=
qqrd2e
*
qtmp
*
q
[
j
]
*
sqrt
(
r2inv
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
forcecoul
;
jtype
=
type
[
j
];
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
}
else
forcelj
=
0.0
;
fpair
=
(
forcecoul
+
factor_lj
*
forcelj
)
*
r2inv
;
if
(
rsq
<
cut_in_on_sq
)
{
rsw
=
(
sqrt
(
rsq
)
-
cut_in_off
)
/
cut_in_diff
;
fpair
*=
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
if
(
rsq
>
cut_out_on_sq
)
{
rsw
=
(
sqrt
(
rsq
)
-
cut_out_on
)
/
cut_out_diff
;
fpair
*=
1.0
+
rsw
*
rsw
*
(
2.0
*
rsw
-
3.0
);
}
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
if
(
NEWTON_PAIR
||
j
<
nlocal
)
{
f
[
j
][
0
]
-=
delx
*
fpair
;
f
[
j
][
1
]
-=
dely
*
fpair
;
f
[
j
][
2
]
-=
delz
*
fpair
;
}
}
}
}
// reduce per thread forces into global force array.
force_reduce_thr
(
atom
->
f
,
nall
,
nthreads
,
tid
);
}
}
/* ---------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
compute_outer
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
{
ev_setup
(
eflag
,
vflag
);
ev_setup_thr
(
eflag
,
vflag
);
}
else
evflag
=
vflag_fdotr
=
0
;
if
(
evflag
)
{
if
(
eflag
)
{
if
(
vflag
)
{
if
(
force
->
newton_pair
)
return
eval_outer
<
1
,
1
,
1
,
1
>
();
else
return
eval_outer
<
1
,
1
,
1
,
0
>
();
}
else
{
if
(
force
->
newton_pair
)
return
eval_outer
<
1
,
1
,
0
,
1
>
();
else
return
eval_outer
<
1
,
1
,
0
,
0
>
();
}
}
else
{
if
(
vflag
)
{
if
(
force
->
newton_pair
)
return
eval_outer
<
1
,
0
,
1
,
1
>
();
else
return
eval_outer
<
1
,
0
,
1
,
0
>
();
}
else
{
if
(
force
->
newton_pair
)
return
eval_outer
<
1
,
0
,
0
,
1
>
();
else
return
eval_outer
<
1
,
0
,
0
,
0
>
();
}
}
}
else
{
if
(
force
->
newton_pair
)
return
eval_outer
<
0
,
0
,
0
,
1
>
();
else
return
eval_outer
<
0
,
0
,
0
,
0
>
();
}
}
template
<
int
EVFLAG
,
int
EFLAG
,
int
VFLAG
,
int
NEWTON_PAIR
>
void
PairLJCutCoulLongOMP
::
eval_outer
()
{
#if defined(_OPENMP)
#pragma omp parallel default(shared)
#endif
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
,
itable
,
tid
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
,
fpair
;
double
fraction
,
table
;
double
r
,
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
factor_coul
,
factor_lj
;
double
grij
,
expm2
,
prefactor
,
t
,
erfc
;
double
rsw
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
rsq
;
evdwl
=
ecoul
=
0.0
;
const
int
nlocal
=
atom
->
nlocal
;
const
int
nall
=
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
*
q
=
atom
->
q
;
int
*
type
=
atom
->
type
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
double
qqrd2e
=
force
->
qqrd2e
;
inum
=
listouter
->
inum
;
ilist
=
listouter
->
ilist
;
numneigh
=
listouter
->
numneigh
;
firstneigh
=
listouter
->
firstneigh
;
double
cut_in_off
=
cut_respa
[
2
];
double
cut_in_on
=
cut_respa
[
3
];
double
cut_in_diff
=
cut_in_on
-
cut_in_off
;
double
cut_in_off_sq
=
cut_in_off
*
cut_in_off
;
double
cut_in_on_sq
=
cut_in_on
*
cut_in_on
;
// loop over neighbors of my atoms
int
iifrom
,
iito
;
f
=
loop_setup_thr
(
f
,
iifrom
,
iito
,
tid
,
inum
,
nall
,
nthreads
);
for
(
ii
=
iifrom
;
ii
<
iito
;
++
ii
)
{
i
=
ilist
[
ii
];
qtmp
=
q
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
itype
=
type
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
if
(
j
<
nall
)
factor_coul
=
factor_lj
=
1.0
;
else
{
factor_coul
=
special_coul
[
j
/
nall
];
factor_lj
=
special_lj
[
j
/
nall
];
j
%=
nall
;
}
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
jtype
=
type
[
j
];
if
(
rsq
<
cutsq
[
itype
][
jtype
])
{
r2inv
=
1.0
/
rsq
;
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
r
=
sqrt
(
rsq
);
grij
=
g_ewald
*
r
;
expm2
=
exp
(
-
grij
*
grij
);
t
=
1.0
/
(
1.0
+
EWALD_P
*
grij
);
erfc
=
t
*
(
A1
+
t
*
(
A2
+
t
*
(
A3
+
t
*
(
A4
+
t
*
A5
))))
*
expm2
;
prefactor
=
qqrd2e
*
qtmp
*
q
[
j
]
/
r
;
forcecoul
=
prefactor
*
(
erfc
+
EWALD_F
*
grij
*
expm2
-
1.0
);
if
(
rsq
>
cut_in_off_sq
)
{
if
(
rsq
<
cut_in_on_sq
)
{
rsw
=
(
r
-
cut_in_off
)
/
cut_in_diff
;
forcecoul
+=
prefactor
*
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
*
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
else
{
forcecoul
+=
prefactor
;
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
}
}
else
{
union_int_float_t
rsq_lookup
;
rsq_lookup
.
f
=
rsq
;
itable
=
rsq_lookup
.
i
&
ncoulmask
;
itable
>>=
ncoulshiftbits
;
fraction
=
(
rsq_lookup
.
f
-
rtable
[
itable
])
*
drtable
[
itable
];
table
=
ftable
[
itable
]
+
fraction
*
dftable
[
itable
];
forcecoul
=
qtmp
*
q
[
j
]
*
table
;
if
(
factor_coul
<
1.0
)
{
table
=
ctable
[
itable
]
+
fraction
*
dctable
[
itable
];
prefactor
=
qtmp
*
q
[
j
]
*
table
;
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
}
}
else
forcecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
]
&&
rsq
>
cut_in_off_sq
)
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
if
(
rsq
<
cut_in_on_sq
)
{
rsw
=
(
sqrt
(
rsq
)
-
cut_in_off
)
/
cut_in_diff
;
forcelj
*=
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
}
else
forcelj
=
0.0
;
fpair
=
(
forcecoul
+
forcelj
)
*
r2inv
;
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
if
(
NEWTON_PAIR
||
j
<
nlocal
)
{
f
[
j
][
0
]
-=
delx
*
fpair
;
f
[
j
][
1
]
-=
dely
*
fpair
;
f
[
j
][
2
]
-=
delz
*
fpair
;
}
if
(
EFLAG
)
{
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
ecoul
=
prefactor
*
erfc
;
if
(
factor_coul
<
1.0
)
ecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
{
table
=
etable
[
itable
]
+
fraction
*
detable
[
itable
];
ecoul
=
qtmp
*
q
[
j
]
*
table
;
if
(
factor_coul
<
1.0
)
{
table
=
ptable
[
itable
]
+
fraction
*
dptable
[
itable
];
prefactor
=
qtmp
*
q
[
j
]
*
table
;
ecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
}
}
else
ecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
evdwl
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
evdwl
*=
factor_lj
;
}
else
evdwl
=
0.0
;
}
if
(
VFLAG
)
{
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
forcecoul
=
prefactor
*
(
erfc
+
EWALD_F
*
grij
*
expm2
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
{
table
=
vtable
[
itable
]
+
fraction
*
dvtable
[
itable
];
forcecoul
=
qtmp
*
q
[
j
]
*
table
;
if
(
factor_coul
<
1.0
)
{
table
=
ptable
[
itable
]
+
fraction
*
dptable
[
itable
];
prefactor
=
qtmp
*
q
[
j
]
*
table
;
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
}
}
else
forcecoul
=
0.0
;
if
(
rsq
<=
cut_in_off_sq
)
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
}
else
if
(
rsq
<=
cut_in_on_sq
)
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
fpair
=
(
forcecoul
+
factor_lj
*
forcelj
)
*
r2inv
;
fpair
=
(
forcecoul
+
factor_lj
*
forcelj
)
*
r2inv
;
}
if
(
EVFLAG
)
ev_tally_thr
(
i
,
j
,
nlocal
,
NEWTON_PAIR
,
evdwl
,
ecoul
,
fpair
,
delx
,
dely
,
delz
,
tid
);
}
}
}
// reduce per thread forces into global force array.
force_reduce_thr
(
atom
->
f
,
nall
,
nthreads
,
tid
);
}
// reduce per thread accumulators
ev_reduce_thr
();
if
(
vflag_fdotr
)
virial_compute
();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
setflag
=
memory
->
create_2d_int_array
(
n
+
1
,
n
+
1
,
"pair:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
cutsq
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cutsq"
);
cut_lj
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cut_lj"
);
cut_ljsq
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cut_ljsq"
);
epsilon
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:epsilon"
);
sigma
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:sigma"
);
lj1
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj1"
);
lj2
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj2"
);
lj3
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj3"
);
lj4
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj4"
);
offset
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:offset"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
1
||
narg
>
2
)
error
->
all
(
"Illegal pair_style command"
);
cut_lj_global
=
force
->
numeric
(
arg
[
0
]);
if
(
narg
==
1
)
cut_coul
=
cut_lj_global
;
else
cut_coul
=
force
->
numeric
(
arg
[
1
]);
// reset cutoffs that have been explicitly set
if
(
allocated
)
{
int
i
,
j
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
+
1
;
j
<=
atom
->
ntypes
;
j
++
)
if
(
setflag
[
i
][
j
])
cut_lj
[
i
][
j
]
=
cut_lj_global
;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
4
||
narg
>
5
)
error
->
all
(
"Incorrect args for pair coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
,
jlo
,
jhi
;
force
->
bounds
(
arg
[
0
],
atom
->
ntypes
,
ilo
,
ihi
);
force
->
bounds
(
arg
[
1
],
atom
->
ntypes
,
jlo
,
jhi
);
double
epsilon_one
=
force
->
numeric
(
arg
[
2
]);
double
sigma_one
=
force
->
numeric
(
arg
[
3
]);
double
cut_lj_one
=
cut_lj_global
;
if
(
narg
==
5
)
cut_lj_one
=
force
->
numeric
(
arg
[
4
]);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
for
(
int
j
=
MAX
(
jlo
,
i
);
j
<=
jhi
;
j
++
)
{
epsilon
[
i
][
j
]
=
epsilon_one
;
sigma
[
i
][
j
]
=
sigma_one
;
cut_lj
[
i
][
j
]
=
cut_lj_one
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
init_style
()
{
if
(
!
atom
->
q_flag
)
error
->
all
(
"Pair style lj/cut/coul/long requires atom attribute q"
);
// request regular or rRESPA neighbor lists
int
irequest
;
if
(
update
->
whichflag
==
1
&&
strcmp
(
update
->
integrate_style
,
"respa"
)
==
0
)
{
int
respa
=
0
;
if
(((
Respa
*
)
update
->
integrate
)
->
level_inner
>=
0
)
respa
=
1
;
if
(((
Respa
*
)
update
->
integrate
)
->
level_middle
>=
0
)
respa
=
2
;
if
(
respa
==
0
)
irequest
=
neighbor
->
request
(
this
);
else
if
(
respa
==
1
)
{
irequest
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest
]
->
id
=
1
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
respainner
=
1
;
irequest
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest
]
->
id
=
3
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
respaouter
=
1
;
}
else
{
irequest
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest
]
->
id
=
1
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
respainner
=
1
;
irequest
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest
]
->
id
=
2
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
respamiddle
=
1
;
irequest
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest
]
->
id
=
3
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
respaouter
=
1
;
}
}
else
irequest
=
neighbor
->
request
(
this
);
cut_coulsq
=
cut_coul
*
cut_coul
;
// set rRESPA cutoffs
if
(
strcmp
(
update
->
integrate_style
,
"respa"
)
==
0
&&
((
Respa
*
)
update
->
integrate
)
->
level_inner
>=
0
)
cut_respa
=
((
Respa
*
)
update
->
integrate
)
->
cutoff
;
else
cut_respa
=
NULL
;
// insure use of KSpace long-range solver, set g_ewald
if
(
force
->
kspace
==
NULL
)
error
->
all
(
"Pair style is incompatible with KSpace style"
);
g_ewald
=
force
->
kspace
->
g_ewald
;
// setup force tables
if
(
ncoultablebits
)
init_tables
();
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
regular or rRESPA
------------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
if
(
id
==
0
)
list
=
ptr
;
else
if
(
id
==
1
)
listinner
=
ptr
;
else
if
(
id
==
2
)
listmiddle
=
ptr
;
else
if
(
id
==
3
)
listouter
=
ptr
;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairLJCutCoulLongOMP
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
{
epsilon
[
i
][
j
]
=
mix_energy
(
epsilon
[
i
][
i
],
epsilon
[
j
][
j
],
sigma
[
i
][
i
],
sigma
[
j
][
j
]);
sigma
[
i
][
j
]
=
mix_distance
(
sigma
[
i
][
i
],
sigma
[
j
][
j
]);
cut_lj
[
i
][
j
]
=
mix_distance
(
cut_lj
[
i
][
i
],
cut_lj
[
j
][
j
]);
}
double
cut
=
MAX
(
cut_lj
[
i
][
j
],
cut_coul
);
cut_ljsq
[
i
][
j
]
=
cut_lj
[
i
][
j
]
*
cut_lj
[
i
][
j
];
lj1
[
i
][
j
]
=
48.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
12.0
);
lj2
[
i
][
j
]
=
24.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
6.0
);
lj3
[
i
][
j
]
=
4.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
12.0
);
lj4
[
i
][
j
]
=
4.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
6.0
);
if
(
offset_flag
)
{
double
ratio
=
sigma
[
i
][
j
]
/
cut_lj
[
i
][
j
];
offset
[
i
][
j
]
=
4.0
*
epsilon
[
i
][
j
]
*
(
pow
(
ratio
,
12.0
)
-
pow
(
ratio
,
6.0
));
}
else
offset
[
i
][
j
]
=
0.0
;
cut_ljsq
[
j
][
i
]
=
cut_ljsq
[
i
][
j
];
lj1
[
j
][
i
]
=
lj1
[
i
][
j
];
lj2
[
j
][
i
]
=
lj2
[
i
][
j
];
lj3
[
j
][
i
]
=
lj3
[
i
][
j
];
lj4
[
j
][
i
]
=
lj4
[
i
][
j
];
offset
[
j
][
i
]
=
offset
[
i
][
j
];
// check interior rRESPA cutoff
if
(
cut_respa
&&
MIN
(
cut_lj
[
i
][
j
],
cut_coul
)
<
cut_respa
[
3
])
error
->
all
(
"Pair cutoff < Respa interior cutoff"
);
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if
(
tail_flag
)
{
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
double
count
[
2
],
all
[
2
];
count
[
0
]
=
count
[
1
]
=
0.0
;
for
(
int
k
=
0
;
k
<
nlocal
;
k
++
)
{
if
(
type
[
k
]
==
i
)
count
[
0
]
+=
1.0
;
if
(
type
[
k
]
==
j
)
count
[
1
]
+=
1.0
;
}
MPI_Allreduce
(
count
,
all
,
2
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
double
PI
=
4.0
*
atan
(
1.0
);
double
sig2
=
sigma
[
i
][
j
]
*
sigma
[
i
][
j
];
double
sig6
=
sig2
*
sig2
*
sig2
;
double
rc3
=
cut_lj
[
i
][
j
]
*
cut_lj
[
i
][
j
]
*
cut_lj
[
i
][
j
];
double
rc6
=
rc3
*
rc3
;
double
rc9
=
rc3
*
rc6
;
etail_ij
=
8.0
*
PI
*
all
[
0
]
*
all
[
1
]
*
epsilon
[
i
][
j
]
*
sig6
*
(
sig6
-
3.0
*
rc6
)
/
(
9.0
*
rc9
);
ptail_ij
=
16.0
*
PI
*
all
[
0
]
*
all
[
1
]
*
epsilon
[
i
][
j
]
*
sig6
*
(
2.0
*
sig6
-
3.0
*
rc6
)
/
(
9.0
*
rc9
);
}
return
cut
;
}
/* ----------------------------------------------------------------------
setup force tables used in compute routines
------------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
init_tables
()
{
int
masklo
,
maskhi
;
double
r
,
grij
,
expm2
,
derfc
,
rsw
;
double
qqrd2e
=
force
->
qqrd2e
;
tabinnersq
=
tabinner
*
tabinner
;
init_bitmap
(
tabinner
,
cut_coul
,
ncoultablebits
,
masklo
,
maskhi
,
ncoulmask
,
ncoulshiftbits
);
int
ntable
=
1
;
for
(
int
i
=
0
;
i
<
ncoultablebits
;
i
++
)
ntable
*=
2
;
// linear lookup tables of length N = 2^ncoultablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
if
(
ftable
)
free_tables
();
rtable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:rtable"
);
ftable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:ftable"
);
ctable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:ctable"
);
etable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:etable"
);
drtable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:drtable"
);
dftable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:dftable"
);
dctable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:dctable"
);
detable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:detable"
);
if
(
cut_respa
==
NULL
)
{
vtable
=
ptable
=
dvtable
=
dptable
=
NULL
;
}
else
{
vtable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:vtable"
);
ptable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:ptable"
);
dvtable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:dvtable"
);
dptable
=
(
double
*
)
memory
->
smalloc
(
ntable
*
sizeof
(
double
),
"pair:dptable"
);
}
union_int_float_t
rsq_lookup
;
union_int_float_t
minrsq_lookup
;
int
itablemin
;
minrsq_lookup
.
i
=
0
<<
ncoulshiftbits
;
minrsq_lookup
.
i
|=
maskhi
;
for
(
int
i
=
0
;
i
<
ntable
;
i
++
)
{
rsq_lookup
.
i
=
i
<<
ncoulshiftbits
;
rsq_lookup
.
i
|=
masklo
;
if
(
rsq_lookup
.
f
<
tabinnersq
)
{
rsq_lookup
.
i
=
i
<<
ncoulshiftbits
;
rsq_lookup
.
i
|=
maskhi
;
}
r
=
sqrtf
(
rsq_lookup
.
f
);
grij
=
g_ewald
*
r
;
expm2
=
exp
(
-
grij
*
grij
);
derfc
=
erfc
(
grij
);
if
(
cut_respa
==
NULL
)
{
rtable
[
i
]
=
rsq_lookup
.
f
;
ftable
[
i
]
=
qqrd2e
/
r
*
(
derfc
+
EWALD_F
*
grij
*
expm2
);
ctable
[
i
]
=
qqrd2e
/
r
;
etable
[
i
]
=
qqrd2e
/
r
*
derfc
;
}
else
{
rtable
[
i
]
=
rsq_lookup
.
f
;
ftable
[
i
]
=
qqrd2e
/
r
*
(
derfc
+
EWALD_F
*
grij
*
expm2
-
1.0
);
ctable
[
i
]
=
0.0
;
etable
[
i
]
=
qqrd2e
/
r
*
derfc
;
ptable
[
i
]
=
qqrd2e
/
r
;
vtable
[
i
]
=
qqrd2e
/
r
*
(
derfc
+
EWALD_F
*
grij
*
expm2
);
if
(
rsq_lookup
.
f
>
cut_respa
[
2
]
*
cut_respa
[
2
])
{
if
(
rsq_lookup
.
f
<
cut_respa
[
3
]
*
cut_respa
[
3
])
{
rsw
=
(
r
-
cut_respa
[
2
])
/
(
cut_respa
[
3
]
-
cut_respa
[
2
]);
ftable
[
i
]
+=
qqrd2e
/
r
*
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
ctable
[
i
]
=
qqrd2e
/
r
*
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
else
{
ftable
[
i
]
=
qqrd2e
/
r
*
(
derfc
+
EWALD_F
*
grij
*
expm2
);
ctable
[
i
]
=
qqrd2e
/
r
;
}
}
}
minrsq_lookup
.
f
=
MIN
(
minrsq_lookup
.
f
,
rsq_lookup
.
f
);
}
tabinnersq
=
minrsq_lookup
.
f
;
int
ntablem1
=
ntable
-
1
;
for
(
int
i
=
0
;
i
<
ntablem1
;
i
++
)
{
drtable
[
i
]
=
1.0
/
(
rtable
[
i
+
1
]
-
rtable
[
i
]);
dftable
[
i
]
=
ftable
[
i
+
1
]
-
ftable
[
i
];
dctable
[
i
]
=
ctable
[
i
+
1
]
-
ctable
[
i
];
detable
[
i
]
=
etable
[
i
+
1
]
-
etable
[
i
];
}
if
(
cut_respa
)
{
for
(
int
i
=
0
;
i
<
ntablem1
;
i
++
)
{
dvtable
[
i
]
=
vtable
[
i
+
1
]
-
vtable
[
i
];
dptable
[
i
]
=
ptable
[
i
+
1
]
-
ptable
[
i
];
}
}
// get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
drtable
[
ntablem1
]
=
1.0
/
(
rtable
[
0
]
-
rtable
[
ntablem1
]);
dftable
[
ntablem1
]
=
ftable
[
0
]
-
ftable
[
ntablem1
];
dctable
[
ntablem1
]
=
ctable
[
0
]
-
ctable
[
ntablem1
];
detable
[
ntablem1
]
=
etable
[
0
]
-
etable
[
ntablem1
];
if
(
cut_respa
)
{
dvtable
[
ntablem1
]
=
vtable
[
0
]
-
vtable
[
ntablem1
];
dptable
[
ntablem1
]
=
ptable
[
0
]
-
ptable
[
ntablem1
];
}
// get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
// if so, compute deltas between rsq and cut*cut
double
f_tmp
,
c_tmp
,
e_tmp
,
p_tmp
,
v_tmp
;
itablemin
=
minrsq_lookup
.
i
&
ncoulmask
;
itablemin
>>=
ncoulshiftbits
;
int
itablemax
=
itablemin
-
1
;
if
(
itablemin
==
0
)
itablemax
=
ntablem1
;
rsq_lookup
.
i
=
itablemax
<<
ncoulshiftbits
;
rsq_lookup
.
i
|=
maskhi
;
if
(
rsq_lookup
.
f
<
cut_coulsq
)
{
rsq_lookup
.
f
=
cut_coulsq
;
r
=
sqrtf
(
rsq_lookup
.
f
);
grij
=
g_ewald
*
r
;
expm2
=
exp
(
-
grij
*
grij
);
derfc
=
erfc
(
grij
);
if
(
cut_respa
==
NULL
)
{
f_tmp
=
qqrd2e
/
r
*
(
derfc
+
EWALD_F
*
grij
*
expm2
);
c_tmp
=
qqrd2e
/
r
;
e_tmp
=
qqrd2e
/
r
*
derfc
;
}
else
{
f_tmp
=
qqrd2e
/
r
*
(
derfc
+
EWALD_F
*
grij
*
expm2
-
1.0
);
c_tmp
=
0.0
;
e_tmp
=
qqrd2e
/
r
*
derfc
;
p_tmp
=
qqrd2e
/
r
;
v_tmp
=
qqrd2e
/
r
*
(
derfc
+
EWALD_F
*
grij
*
expm2
);
if
(
rsq_lookup
.
f
>
cut_respa
[
2
]
*
cut_respa
[
2
])
{
if
(
rsq_lookup
.
f
<
cut_respa
[
3
]
*
cut_respa
[
3
])
{
rsw
=
(
r
-
cut_respa
[
2
])
/
(
cut_respa
[
3
]
-
cut_respa
[
2
]);
f_tmp
+=
qqrd2e
/
r
*
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
c_tmp
=
qqrd2e
/
r
*
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
else
{
f_tmp
=
qqrd2e
/
r
*
(
derfc
+
EWALD_F
*
grij
*
expm2
);
c_tmp
=
qqrd2e
/
r
;
}
}
}
drtable
[
itablemax
]
=
1.0
/
(
rsq_lookup
.
f
-
rtable
[
itablemax
]);
dftable
[
itablemax
]
=
f_tmp
-
ftable
[
itablemax
];
dctable
[
itablemax
]
=
c_tmp
-
ctable
[
itablemax
];
detable
[
itablemax
]
=
e_tmp
-
etable
[
itablemax
];
if
(
cut_respa
)
{
dvtable
[
itablemax
]
=
v_tmp
-
vtable
[
itablemax
];
dptable
[
itablemax
]
=
p_tmp
-
ptable
[
itablemax
];
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
write_restart
(
FILE
*
fp
)
{
write_restart_settings
(
fp
);
int
i
,
j
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
{
fwrite
(
&
setflag
[
i
][
j
],
sizeof
(
int
),
1
,
fp
);
if
(
setflag
[
i
][
j
])
{
fwrite
(
&
epsilon
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
sigma
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut_lj
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
read_restart
(
FILE
*
fp
)
{
read_restart_settings
(
fp
);
allocate
();
int
i
,
j
;
int
me
=
comm
->
me
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
{
if
(
me
==
0
)
fread
(
&
setflag
[
i
][
j
],
sizeof
(
int
),
1
,
fp
);
MPI_Bcast
(
&
setflag
[
i
][
j
],
1
,
MPI_INT
,
0
,
world
);
if
(
setflag
[
i
][
j
])
{
if
(
me
==
0
)
{
fread
(
&
epsilon
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
sigma
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut_lj
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
MPI_Bcast
(
&
epsilon
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut_lj
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
cut_lj_global
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut_coul
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
offset_flag
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
read_restart_settings
(
FILE
*
fp
)
{
if
(
comm
->
me
==
0
)
{
fread
(
&
cut_lj_global
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut_coul
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
offset_flag
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
}
MPI_Bcast
(
&
cut_lj_global
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut_coul
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
offset_flag
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
mix_flag
,
1
,
MPI_INT
,
0
,
world
);
}
/* ----------------------------------------------------------------------
free memory for tables used in pair computations
------------------------------------------------------------------------- */
void
PairLJCutCoulLongOMP
::
free_tables
()
{
memory
->
sfree
(
rtable
);
memory
->
sfree
(
drtable
);
memory
->
sfree
(
ftable
);
memory
->
sfree
(
dftable
);
memory
->
sfree
(
ctable
);
memory
->
sfree
(
dctable
);
memory
->
sfree
(
etable
);
memory
->
sfree
(
detable
);
memory
->
sfree
(
vtable
);
memory
->
sfree
(
dvtable
);
memory
->
sfree
(
ptable
);
memory
->
sfree
(
dptable
);
}
/* ---------------------------------------------------------------------- */
double
PairLJCutCoulLongOMP
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r2inv
,
r6inv
,
r
,
grij
,
expm2
,
t
,
erfc
,
prefactor
;
double
fraction
,
table
,
forcecoul
,
forcelj
,
phicoul
,
philj
;
int
itable
;
r2inv
=
1.0
/
rsq
;
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
r
=
sqrt
(
rsq
);
grij
=
g_ewald
*
r
;
expm2
=
exp
(
-
grij
*
grij
);
t
=
1.0
/
(
1.0
+
EWALD_P
*
grij
);
erfc
=
t
*
(
A1
+
t
*
(
A2
+
t
*
(
A3
+
t
*
(
A4
+
t
*
A5
))))
*
expm2
;
prefactor
=
force
->
qqrd2e
*
atom
->
q
[
i
]
*
atom
->
q
[
j
]
/
r
;
forcecoul
=
prefactor
*
(
erfc
+
EWALD_F
*
grij
*
expm2
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
{
union_int_float_t
rsq_lookup_single
;
rsq_lookup_single
.
f
=
rsq
;
itable
=
rsq_lookup_single
.
i
&
ncoulmask
;
itable
>>=
ncoulshiftbits
;
fraction
=
(
rsq_lookup_single
.
f
-
rtable
[
itable
])
*
drtable
[
itable
];
table
=
ftable
[
itable
]
+
fraction
*
dftable
[
itable
];
forcecoul
=
atom
->
q
[
i
]
*
atom
->
q
[
j
]
*
table
;
if
(
factor_coul
<
1.0
)
{
table
=
ctable
[
itable
]
+
fraction
*
dctable
[
itable
];
prefactor
=
atom
->
q
[
i
]
*
atom
->
q
[
j
]
*
table
;
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
}
}
else
forcecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
}
else
forcelj
=
0.0
;
fforce
=
(
forcecoul
+
factor_lj
*
forcelj
)
*
r2inv
;
double
eng
=
0.0
;
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
phicoul
=
prefactor
*
erfc
;
else
{
table
=
etable
[
itable
]
+
fraction
*
detable
[
itable
];
phicoul
=
atom
->
q
[
i
]
*
atom
->
q
[
j
]
*
table
;
}
if
(
factor_coul
<
1.0
)
phicoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
eng
+=
phicoul
;
}
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
philj
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
eng
+=
factor_lj
*
philj
;
}
return
eng
;
}
/* ---------------------------------------------------------------------- */
void
*
PairLJCutCoulLongOMP
::
extract
(
char
*
str
)
{
if
(
strcmp
(
str
,
"cut_coul"
)
==
0
)
return
(
void
*
)
&
cut_coul
;
return
NULL
;
}
/* ---------------------------------------------------------------------- */
double
PairLJCutCoulLongOMP
::
memory_usage
()
{
const
int
n
=
atom
->
ntypes
;
double
bytes
=
PairOMP
::
memory_usage
();
bytes
+=
9
*
((
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
double
)
+
(
n
+
1
)
*
sizeof
(
double
*
));
bytes
+=
1
*
((
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
int
)
+
(
n
+
1
)
*
sizeof
(
int
*
));
return
bytes
;
}
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