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pair_lj_coul.cpp
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rLAMMPS lammps
pair_lj_coul.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: Pieter J. in 't Veld (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "math_vector.h"
#include "pair_lj_coul.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "kspace.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#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
/* ---------------------------------------------------------------------- */
PairLJCoul
::
PairLJCoul
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
respa_enable
=
1
;
ftable
=
NULL
;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
#define PAIR_ILLEGAL "Illegal pair_style lj/coul command"
#define PAIR_CUTOFF "Only one cut-off allowed when requesting all long"
#define PAIR_MISSING "Cut-offs missing in pair_style lj/coul"
#define PAIR_COUL_CUT "Coulombic cut not supported in pair_style lj/coul"
#define PAIR_LARGEST "Using largest cut-off for lj/coul long long"
#define PAIR_MIX "Mixing forced for lj coefficients"
void
PairLJCoul
::
options
(
char
**
arg
,
int
order
)
{
char
*
option
[]
=
{
"long"
,
"cut"
,
"off"
,
NULL
};
int
i
;
if
(
!*
arg
)
error
->
all
(
FLERR
,
PAIR_ILLEGAL
);
for
(
i
=
0
;
option
[
i
]
&&
strcmp
(
arg
[
0
],
option
[
i
]);
++
i
);
switch
(
i
)
{
default
:
error
->
all
(
FLERR
,
PAIR_ILLEGAL
);
case
0
:
ewald_order
|=
1
<<
order
;
break
;
// set kspace r^-order
case
2
:
ewald_off
|=
1
<<
order
;
// turn r^-order off
case
1
:
break
;
}
}
void
PairLJCoul
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
3
&&
narg
!=
4
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
ewald_off
=
0
;
ewald_order
=
0
;
options
(
arg
,
6
);
options
(
++
arg
,
1
);
if
(
!
comm
->
me
&&
ewald_order
&
(
1
<<
6
))
error
->
warning
(
FLERR
,
PAIR_MIX
);
if
(
!
comm
->
me
&&
ewald_order
==
((
1
<<
1
)
|
(
1
<<
6
)))
error
->
warning
(
FLERR
,
PAIR_LARGEST
);
if
(
!*
(
++
arg
))
error
->
all
(
FLERR
,
PAIR_MISSING
);
if
(
!
((
ewald_order
^
ewald_off
)
&
(
1
<<
1
)))
error
->
all
(
FLERR
,
PAIR_COUL_CUT
);
cut_lj_global
=
force
->
numeric
(
*
(
arg
++
));
if
(
*
arg
&&
(
ewald_order
&
0x42
==
0x42
))
error
->
all
(
FLERR
,
PAIR_CUTOFF
);
if
(
narg
==
4
)
cut_coul
=
force
->
numeric
(
*
arg
);
else
cut_coul
=
cut_lj_global
;
if
(
allocated
)
{
// reset explicit cuts
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
;
}
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJCoul
::~
PairLJCoul
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cut_lj_read
);
memory
->
destroy
(
cut_lj
);
memory
->
destroy
(
cut_ljsq
);
memory
->
destroy
(
epsilon_read
);
memory
->
destroy
(
epsilon
);
memory
->
destroy
(
sigma_read
);
memory
->
destroy
(
sigma
);
memory
->
destroy
(
lj1
);
memory
->
destroy
(
lj2
);
memory
->
destroy
(
lj3
);
memory
->
destroy
(
lj4
);
memory
->
destroy
(
offset
);
}
if
(
ftable
)
free_tables
();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairLJCoul
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
memory
->
create
(
setflag
,
n
+
1
,
n
+
1
,
"pair:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
memory
->
create
(
cutsq
,
n
+
1
,
n
+
1
,
"pair:cutsq"
);
memory
->
create
(
cut_lj_read
,
n
+
1
,
n
+
1
,
"pair:cut_lj_read"
);
memory
->
create
(
cut_lj
,
n
+
1
,
n
+
1
,
"pair:cut_lj"
);
memory
->
create
(
cut_ljsq
,
n
+
1
,
n
+
1
,
"pair:cut_ljsq"
);
memory
->
create
(
epsilon_read
,
n
+
1
,
n
+
1
,
"pair:epsilon_read"
);
memory
->
create
(
epsilon
,
n
+
1
,
n
+
1
,
"pair:epsilon"
);
memory
->
create
(
sigma_read
,
n
+
1
,
n
+
1
,
"pair:sigma_read"
);
memory
->
create
(
sigma
,
n
+
1
,
n
+
1
,
"pair:sigma"
);
memory
->
create
(
lj1
,
n
+
1
,
n
+
1
,
"pair:lj1"
);
memory
->
create
(
lj2
,
n
+
1
,
n
+
1
,
"pair:lj2"
);
memory
->
create
(
lj3
,
n
+
1
,
n
+
1
,
"pair:lj3"
);
memory
->
create
(
lj4
,
n
+
1
,
n
+
1
,
"pair:lj4"
);
memory
->
create
(
offset
,
n
+
1
,
n
+
1
,
"pair:offset"
);
}
/* ----------------------------------------------------------------------
extract protected data from object
------------------------------------------------------------------------- */
void
*
PairLJCoul
::
extract
(
char
*
id
,
int
&
dim
)
{
char
*
ids
[]
=
{
"B"
,
"sigma"
,
"epsilon"
,
"ewald_order"
,
"ewald_cut"
,
"ewald_mix"
,
"cut_coul"
,
NULL
};
void
*
ptrs
[]
=
{
lj4
,
sigma
,
epsilon
,
&
ewald_order
,
&
cut_coul
,
&
mix_flag
,
&
cut_coul
,
NULL
};
int
i
;
for
(
i
=
0
;
ids
[
i
]
&&
strcmp
(
ids
[
i
],
id
);
++
i
);
if
(
i
<=
2
)
dim
=
2
;
else
dim
=
0
;
return
ptrs
[
i
];
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairLJCoul
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
4
||
narg
>
5
)
error
->
all
(
FLERR
,
"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_read
[
i
][
j
]
=
epsilon_one
;
sigma_read
[
i
][
j
]
=
sigma_one
;
cut_lj_read
[
i
][
j
]
=
cut_lj_one
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairLJCoul
::
init_style
()
{
char
*
style1
[]
=
{
"ewald"
,
"ewald/n"
,
"pppm"
,
NULL
};
char
*
style6
[]
=
{
"ewald/n"
,
NULL
};
int
i
;
// require an atom style with charge defined
if
(
!
atom
->
q_flag
&&
(
ewald_order
&
(
1
<<
1
)))
error
->
all
(
FLERR
,
"Invoking coulombic in pair style lj/coul requires atom attribute q"
);
// request regular or rRESPA neighbor lists
int
irequest
;
if
(
update
->
whichflag
==
0
&&
strstr
(
update
->
integrate_style
,
"respa"
))
{
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
(
strstr
(
update
->
integrate_style
,
"respa"
)
&&
((
Respa
*
)
update
->
integrate
)
->
level_inner
>=
0
)
cut_respa
=
((
Respa
*
)
update
->
integrate
)
->
cutoff
;
else
cut_respa
=
NULL
;
// ensure use of KSpace long-range solver, set g_ewald
if
(
ewald_order
&
(
1
<<
1
))
{
// r^-1 kspace
if
(
force
->
kspace
==
NULL
)
error
->
all
(
FLERR
,
"Pair style is incompatible with KSpace style"
);
for
(
i
=
0
;
style1
[
i
]
&&
strcmp
(
force
->
kspace_style
,
style1
[
i
]);
++
i
);
if
(
!
style1
[
i
])
error
->
all
(
FLERR
,
"Pair style is incompatible with KSpace style"
);
}
if
(
ewald_order
&
(
1
<<
6
))
{
// r^-6 kspace
if
(
force
->
kspace
==
NULL
)
error
->
all
(
FLERR
,
"Pair style is incompatible with KSpace style"
);
for
(
i
=
0
;
style6
[
i
]
&&
strcmp
(
force
->
kspace_style
,
style6
[
i
]);
++
i
);
if
(
!
style6
[
i
])
error
->
all
(
FLERR
,
"Pair style is incompatible with KSpace style"
);
}
if
(
force
->
kspace
)
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
PairLJCoul
::
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
PairLJCoul
::
init_one
(
int
i
,
int
j
)
{
if
((
ewald_order
&
(
1
<<
6
))
||
(
setflag
[
i
][
j
]
==
0
))
{
epsilon
[
i
][
j
]
=
mix_energy
(
epsilon_read
[
i
][
i
],
epsilon_read
[
j
][
j
],
sigma_read
[
i
][
i
],
sigma_read
[
j
][
j
]);
sigma
[
i
][
j
]
=
mix_distance
(
sigma_read
[
i
][
i
],
sigma_read
[
j
][
j
]);
if
(
ewald_order
&
(
1
<<
6
))
cut_lj
[
i
][
j
]
=
cut_lj_global
;
else
cut_lj
[
i
][
j
]
=
mix_distance
(
cut_lj_read
[
i
][
i
],
cut_lj_read
[
j
][
j
]);
}
else
{
sigma
[
i
][
j
]
=
sigma_read
[
i
][
j
];
epsilon
[
i
][
j
]
=
epsilon_read
[
i
][
j
];
cut_lj
[
i
][
j
]
=
cut_lj_read
[
i
][
j
];
}
double
cut
=
MAX
(
cut_lj
[
i
][
j
],
cut_coul
);
cutsq
[
i
][
j
]
=
cut
*
cut
;
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
);
// check interior rRESPA cutoff
if
(
cut_respa
&&
MIN
(
cut_lj
[
i
][
j
],
cut_coul
)
<
cut_respa
[
3
])
error
->
all
(
FLERR
,
"Pair cutoff < Respa interior cutoff"
);
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
;
cutsq
[
j
][
i
]
=
cutsq
[
i
][
j
];
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
];
return
cut
;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJCoul
::
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_read
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
sigma_read
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut_lj_read
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJCoul
::
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_read
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
sigma_read
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut_lj_read
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
MPI_Bcast
(
&
epsilon_read
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma_read
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut_lj_read
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJCoul
::
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
);
fwrite
(
&
ewald_order
,
sizeof
(
int
),
1
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJCoul
::
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
);
fread
(
&
ewald_order
,
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
);
MPI_Bcast
(
&
ewald_order
,
1
,
MPI_INT
,
0
,
world
);
}
/* ----------------------------------------------------------------------
compute pair interactions
------------------------------------------------------------------------- */
void
PairLJCoul
::
compute
(
int
eflag
,
int
vflag
)
{
double
evdwl
,
ecoul
,
fpair
;
evdwl
=
ecoul
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
double
**
x
=
atom
->
x
,
*
x0
=
x
[
0
];
double
**
f
=
atom
->
f
,
*
f0
=
f
[
0
],
*
fi
=
f0
;
double
*
q
=
atom
->
q
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
int
newton_pair
=
force
->
newton_pair
;
double
qqrd2e
=
force
->
qqrd2e
;
int
i
,
j
,
order1
=
ewald_order
&
(
1
<<
1
),
order6
=
ewald_order
&
(
1
<<
6
);
int
*
ineigh
,
*
ineighn
,
*
jneigh
,
*
jneighn
,
typei
,
typej
,
ni
;
double
qi
,
qri
,
*
cutsqi
,
*
cut_ljsqi
,
*
lj1i
,
*
lj2i
,
*
lj3i
,
*
lj4i
,
*
offseti
;
double
rsq
,
r2inv
,
force_coul
,
force_lj
;
double
g2
=
g_ewald
*
g_ewald
,
g6
=
g2
*
g2
*
g2
,
g8
=
g6
*
g2
;
vector
xi
,
d
;
ineighn
=
(
ineigh
=
list
->
ilist
)
+
list
->
inum
;
for
(;
ineigh
<
ineighn
;
++
ineigh
)
{
// loop over my atoms
i
=
*
ineigh
;
fi
=
f0
+
3
*
i
;
if
(
order1
)
qri
=
(
qi
=
q
[
i
])
*
qqrd2e
;
// initialize constants
offseti
=
offset
[
typei
=
type
[
i
]];
lj1i
=
lj1
[
typei
];
lj2i
=
lj2
[
typei
];
lj3i
=
lj3
[
typei
];
lj4i
=
lj4
[
typei
];
cutsqi
=
cutsq
[
typei
];
cut_ljsqi
=
cut_ljsq
[
typei
];
memcpy
(
xi
,
x0
+
(
i
+
(
i
<<
1
)),
sizeof
(
vector
));
jneighn
=
(
jneigh
=
list
->
firstneigh
[
i
])
+
list
->
numneigh
[
i
];
for
(;
jneigh
<
jneighn
;
++
jneigh
)
{
// loop over neighbors
j
=
*
jneigh
;
ni
=
sbmask
(
j
);
j
&=
NEIGHMASK
;
{
register
double
*
xj
=
x0
+
(
j
+
(
j
<<
1
));
d
[
0
]
=
xi
[
0
]
-
xj
[
0
];
// pair vector
d
[
1
]
=
xi
[
1
]
-
xj
[
1
];
d
[
2
]
=
xi
[
2
]
-
xj
[
2
];
}
if
((
rsq
=
vec_dot
(
d
,
d
))
>=
cutsqi
[
typej
=
type
[
j
]])
continue
;
r2inv
=
1.0
/
rsq
;
if
(
order1
&&
(
rsq
<
cut_coulsq
))
{
// coulombic
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
// series real space
register
double
r
=
sqrt
(
rsq
),
x
=
g_ewald
*
r
;
register
double
s
=
qri
*
q
[
j
],
t
=
1.0
/
(
1.0
+
EWALD_P
*
x
);
if
(
ni
==
0
)
{
s
*=
g_ewald
*
exp
(
-
x
*
x
);
force_coul
=
(
t
*=
((((
t
*
A5
+
A4
)
*
t
+
A3
)
*
t
+
A2
)
*
t
+
A1
)
*
s
/
x
)
+
EWALD_F
*
s
;
if
(
eflag
)
ecoul
=
t
;
}
else
{
// special case
r
=
s
*
(
1.0
-
special_coul
[
ni
])
/
r
;
s
*=
g_ewald
*
exp
(
-
x
*
x
);
force_coul
=
(
t
*=
((((
t
*
A5
+
A4
)
*
t
+
A3
)
*
t
+
A2
)
*
t
+
A1
)
*
s
/
x
)
+
EWALD_F
*
s
-
r
;
if
(
eflag
)
ecoul
=
t
-
r
;
}
}
// table real space
else
{
register
union_int_float_t
t
;
t
.
f
=
rsq
;
register
const
int
k
=
(
t
.
i
&
ncoulmask
)
>>
ncoulshiftbits
;
register
double
f
=
(
rsq
-
rtable
[
k
])
*
drtable
[
k
],
qiqj
=
qi
*
q
[
j
];
if
(
ni
==
0
)
{
force_coul
=
qiqj
*
(
ftable
[
k
]
+
f
*
dftable
[
k
]);
if
(
eflag
)
ecoul
=
qiqj
*
(
etable
[
k
]
+
f
*
detable
[
k
]);
}
else
{
// special case
t
.
f
=
(
1.0
-
special_coul
[
ni
])
*
(
ctable
[
k
]
+
f
*
dctable
[
k
]);
force_coul
=
qiqj
*
(
ftable
[
k
]
+
f
*
dftable
[
k
]
-
t
.
f
);
if
(
eflag
)
ecoul
=
qiqj
*
(
etable
[
k
]
+
f
*
detable
[
k
]
-
t
.
f
);
}
}
}
else
force_coul
=
ecoul
=
0.0
;
if
(
rsq
<
cut_ljsqi
[
typej
])
{
// lj
if
(
order6
)
{
// long-range lj
register
double
rn
=
r2inv
*
r2inv
*
r2inv
;
register
double
x2
=
g2
*
rsq
,
a2
=
1.0
/
x2
;
x2
=
a2
*
exp
(
-
x2
)
*
lj4i
[
typej
];
if
(
ni
==
0
)
{
force_lj
=
(
rn
*=
rn
)
*
lj1i
[
typej
]
-
g8
*
(((
6.0
*
a2
+
6.0
)
*
a2
+
3.0
)
*
a2
+
1.0
)
*
x2
*
rsq
;
if
(
eflag
)
evdwl
=
rn
*
lj3i
[
typej
]
-
g6
*
((
a2
+
1.0
)
*
a2
+
0.5
)
*
x2
;
}
else
{
// special case
register
double
f
=
special_lj
[
ni
],
t
=
rn
*
(
1.0
-
f
);
force_lj
=
f
*
(
rn
*=
rn
)
*
lj1i
[
typej
]
-
g8
*
(((
6.0
*
a2
+
6.0
)
*
a2
+
3.0
)
*
a2
+
1.0
)
*
x2
*
rsq
+
t
*
lj2i
[
typej
];
if
(
eflag
)
evdwl
=
f
*
rn
*
lj3i
[
typej
]
-
g6
*
((
a2
+
1.0
)
*
a2
+
0.5
)
*
x2
+
t
*
lj4i
[
typej
];
}
}
else
{
// cut lj
register
double
rn
=
r2inv
*
r2inv
*
r2inv
;
if
(
ni
==
0
)
{
force_lj
=
rn
*
(
rn
*
lj1i
[
typej
]
-
lj2i
[
typej
]);
if
(
eflag
)
evdwl
=
rn
*
(
rn
*
lj3i
[
typej
]
-
lj4i
[
typej
])
-
offseti
[
typej
];
}
else
{
// special case
register
double
f
=
special_lj
[
ni
];
force_lj
=
f
*
rn
*
(
rn
*
lj1i
[
typej
]
-
lj2i
[
typej
]);
if
(
eflag
)
evdwl
=
f
*
(
rn
*
(
rn
*
lj3i
[
typej
]
-
lj4i
[
typej
])
-
offseti
[
typej
]);
}
}
}
else
force_lj
=
evdwl
=
0.0
;
fpair
=
(
force_coul
+
force_lj
)
*
r2inv
;
if
(
newton_pair
||
j
<
nlocal
)
{
register
double
*
fj
=
f0
+
(
j
+
(
j
<<
1
)),
f
;
fi
[
0
]
+=
f
=
d
[
0
]
*
fpair
;
fj
[
0
]
-=
f
;
fi
[
1
]
+=
f
=
d
[
1
]
*
fpair
;
fj
[
1
]
-=
f
;
fi
[
2
]
+=
f
=
d
[
2
]
*
fpair
;
fj
[
2
]
-=
f
;
}
else
{
fi
[
0
]
+=
d
[
0
]
*
fpair
;
fi
[
1
]
+=
d
[
1
]
*
fpair
;
fi
[
2
]
+=
d
[
2
]
*
fpair
;
}
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
ecoul
,
fpair
,
d
[
0
],
d
[
1
],
d
[
2
]);
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ---------------------------------------------------------------------- */
void
PairLJCoul
::
compute_inner
()
{
double
rsq
,
r2inv
,
force_coul
,
force_lj
,
fpair
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
double
*
x0
=
atom
->
x
[
0
],
*
f0
=
atom
->
f
[
0
],
*
fi
=
f0
,
*
q
=
atom
->
q
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
int
newton_pair
=
force
->
newton_pair
;
double
qqrd2e
=
force
->
qqrd2e
;
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
;
int
*
ineigh
,
*
ineighn
,
*
jneigh
,
*
jneighn
,
typei
,
typej
,
ni
;
int
i
,
j
,
order1
=
(
ewald_order
|
(
ewald_off
^-
1
))
&
(
1
<<
1
);
double
qri
,
*
cut_ljsqi
,
*
lj1i
,
*
lj2i
;
vector
xi
,
d
;
ineighn
=
(
ineigh
=
list
->
ilist
)
+
list
->
inum
;
for
(;
ineigh
<
ineighn
;
++
ineigh
)
{
// loop over my atoms
i
=
*
ineigh
;
fi
=
f0
+
3
*
i
;
qri
=
qqrd2e
*
q
[
i
];
memcpy
(
xi
,
x0
+
(
i
+
(
i
<<
1
)),
sizeof
(
vector
));
cut_ljsqi
=
cut_ljsq
[
typei
=
type
[
i
]];
lj1i
=
lj1
[
typei
];
lj2i
=
lj2
[
typei
];
jneighn
=
(
jneigh
=
list
->
firstneigh
[
i
])
+
list
->
numneigh
[
i
];
for
(;
jneigh
<
jneighn
;
++
jneigh
)
{
// loop over neighbors
j
=
*
jneigh
;
ni
=
sbmask
(
j
);
j
&=
NEIGHMASK
;
{
register
double
*
xj
=
x0
+
(
j
+
(
j
<<
1
));
d
[
0
]
=
xi
[
0
]
-
xj
[
0
];
// pair vector
d
[
1
]
=
xi
[
1
]
-
xj
[
1
];
d
[
2
]
=
xi
[
2
]
-
xj
[
2
];
}
if
((
rsq
=
vec_dot
(
d
,
d
))
>=
cut_out_off_sq
)
continue
;
r2inv
=
1.0
/
rsq
;
if
(
order1
&&
(
rsq
<
cut_coulsq
))
// coulombic
force_coul
=
ni
==
0
?
qri
*
q
[
j
]
*
sqrt
(
r2inv
)
:
qri
*
q
[
j
]
*
sqrt
(
r2inv
)
*
special_coul
[
ni
];
if
(
rsq
<
cut_ljsqi
[
typej
=
type
[
j
]])
{
// lennard-jones
register
double
rn
=
r2inv
*
r2inv
*
r2inv
;
force_lj
=
ni
==
0
?
rn
*
(
rn
*
lj1i
[
typej
]
-
lj2i
[
typej
])
:
rn
*
(
rn
*
lj1i
[
typej
]
-
lj2i
[
typej
])
*
special_lj
[
ni
];
}
else
force_lj
=
0.0
;
fpair
=
(
force_coul
+
force_lj
)
*
r2inv
;
if
(
rsq
>
cut_out_on_sq
)
{
// switching
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_out_on
)
/
cut_out_diff
;
fpair
*=
1.0
+
rsw
*
rsw
*
(
2.0
*
rsw
-
3.0
);
}
if
(
newton_pair
||
j
<
nlocal
)
{
// force update
register
double
*
fj
=
f0
+
(
j
+
(
j
<<
1
)),
f
;
fi
[
0
]
+=
f
=
d
[
0
]
*
fpair
;
fj
[
0
]
-=
f
;
fi
[
1
]
+=
f
=
d
[
1
]
*
fpair
;
fj
[
1
]
-=
f
;
fi
[
2
]
+=
f
=
d
[
2
]
*
fpair
;
fj
[
2
]
-=
f
;
}
else
{
fi
[
0
]
+=
d
[
0
]
*
fpair
;
fi
[
1
]
+=
d
[
1
]
*
fpair
;
fi
[
2
]
+=
d
[
2
]
*
fpair
;
}
}
}
}
/* ---------------------------------------------------------------------- */
void
PairLJCoul
::
compute_middle
()
{
double
rsq
,
r2inv
,
force_coul
,
force_lj
,
fpair
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
double
*
x0
=
atom
->
x
[
0
],
*
f0
=
atom
->
f
[
0
],
*
fi
=
f0
,
*
q
=
atom
->
q
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
int
newton_pair
=
force
->
newton_pair
;
double
qqrd2e
=
force
->
qqrd2e
;
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
;
int
*
ineigh
,
*
ineighn
,
*
jneigh
,
*
jneighn
,
typei
,
typej
,
ni
;
int
i
,
j
,
order1
=
(
ewald_order
|
(
ewald_off
^-
1
))
&
(
1
<<
1
);
double
qri
,
*
cut_ljsqi
,
*
lj1i
,
*
lj2i
;
vector
xi
,
d
;
ineighn
=
(
ineigh
=
list
->
ilist
)
+
list
->
inum
;
for
(;
ineigh
<
ineighn
;
++
ineigh
)
{
// loop over my atoms
i
=
*
ineigh
;
fi
=
f0
+
3
*
i
;
qri
=
qqrd2e
*
q
[
i
];
memcpy
(
xi
,
x0
+
(
i
+
(
i
<<
1
)),
sizeof
(
vector
));
cut_ljsqi
=
cut_ljsq
[
typei
=
type
[
i
]];
lj1i
=
lj1
[
typei
];
lj2i
=
lj2
[
typei
];
jneighn
=
(
jneigh
=
list
->
firstneigh
[
i
])
+
list
->
numneigh
[
i
];
for
(;
jneigh
<
jneighn
;
++
jneigh
)
{
j
=
*
jneigh
;
ni
=
sbmask
(
j
);
j
&=
NEIGHMASK
;
{
register
double
*
xj
=
x0
+
(
j
+
(
j
<<
1
));
d
[
0
]
=
xi
[
0
]
-
xj
[
0
];
// pair vector
d
[
1
]
=
xi
[
1
]
-
xj
[
1
];
d
[
2
]
=
xi
[
2
]
-
xj
[
2
];
}
if
((
rsq
=
vec_dot
(
d
,
d
))
>=
cut_out_off_sq
)
continue
;
if
(
rsq
<=
cut_in_off_sq
)
continue
;
r2inv
=
1.0
/
rsq
;
if
(
order1
&&
(
rsq
<
cut_coulsq
))
// coulombic
force_coul
=
ni
==
0
?
qri
*
q
[
j
]
*
sqrt
(
r2inv
)
:
qri
*
q
[
j
]
*
sqrt
(
r2inv
)
*
special_coul
[
ni
];
if
(
rsq
<
cut_ljsqi
[
typej
=
type
[
j
]])
{
// lennard-jones
register
double
rn
=
r2inv
*
r2inv
*
r2inv
;
force_lj
=
ni
==
0
?
rn
*
(
rn
*
lj1i
[
typej
]
-
lj2i
[
typej
])
:
rn
*
(
rn
*
lj1i
[
typej
]
-
lj2i
[
typej
])
*
special_lj
[
ni
];
}
else
force_lj
=
0.0
;
fpair
=
(
force_coul
+
force_lj
)
*
r2inv
;
if
(
rsq
<
cut_in_on_sq
)
{
// switching
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_in_off
)
/
cut_in_diff
;
fpair
*=
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
if
(
rsq
>
cut_out_on_sq
)
{
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_out_on
)
/
cut_out_diff
;
fpair
*=
1.0
+
rsw
*
rsw
*
(
2.0
*
rsw
-
3.0
);
}
if
(
newton_pair
||
j
<
nlocal
)
{
// force update
register
double
*
fj
=
f0
+
(
j
+
(
j
<<
1
)),
f
;
fi
[
0
]
+=
f
=
d
[
0
]
*
fpair
;
fj
[
0
]
-=
f
;
fi
[
1
]
+=
f
=
d
[
1
]
*
fpair
;
fj
[
1
]
-=
f
;
fi
[
2
]
+=
f
=
d
[
2
]
*
fpair
;
fj
[
2
]
-=
f
;
}
else
{
fi
[
0
]
+=
d
[
0
]
*
fpair
;
fi
[
1
]
+=
d
[
1
]
*
fpair
;
fi
[
2
]
+=
d
[
2
]
*
fpair
;
}
}
}
}
/* ---------------------------------------------------------------------- */
void
PairLJCoul
::
compute_outer
(
int
eflag
,
int
vflag
)
{
double
evdwl
,
ecoul
,
fpair
;
evdwl
=
ecoul
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
double
**
x
=
atom
->
x
,
*
x0
=
x
[
0
];
double
**
f
=
atom
->
f
,
*
f0
=
f
[
0
],
*
fi
=
f0
;
double
*
q
=
atom
->
q
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
int
newton_pair
=
force
->
newton_pair
;
double
qqrd2e
=
force
->
qqrd2e
;
int
i
,
j
,
order1
=
ewald_order
&
(
1
<<
1
),
order6
=
ewald_order
&
(
1
<<
6
);
int
*
ineigh
,
*
ineighn
,
*
jneigh
,
*
jneighn
,
typei
,
typej
,
ni
,
respa_flag
;
double
qi
,
qri
,
*
cutsqi
,
*
cut_ljsqi
,
*
lj1i
,
*
lj2i
,
*
lj3i
,
*
lj4i
,
*
offseti
;
double
rsq
,
r2inv
,
force_coul
,
force_lj
;
double
g2
=
g_ewald
*
g_ewald
,
g6
=
g2
*
g2
*
g2
,
g8
=
g6
*
g2
;
double
respa_lj
,
respa_coul
,
frespa
;
vector
xi
,
d
;
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
;
ineighn
=
(
ineigh
=
list
->
ilist
)
+
list
->
inum
;
for
(;
ineigh
<
ineighn
;
++
ineigh
)
{
// loop over my atoms
i
=
*
ineigh
;
fi
=
f0
+
3
*
i
;
if
(
order1
)
qri
=
(
qi
=
q
[
i
])
*
qqrd2e
;
// initialize constants
offseti
=
offset
[
typei
=
type
[
i
]];
lj1i
=
lj1
[
typei
];
lj2i
=
lj2
[
typei
];
lj3i
=
lj3
[
typei
];
lj4i
=
lj4
[
typei
];
cutsqi
=
cutsq
[
typei
];
cut_ljsqi
=
cut_ljsq
[
typei
];
memcpy
(
xi
,
x0
+
(
i
+
(
i
<<
1
)),
sizeof
(
vector
));
jneighn
=
(
jneigh
=
list
->
firstneigh
[
i
])
+
list
->
numneigh
[
i
];
for
(;
jneigh
<
jneighn
;
++
jneigh
)
{
// loop over neighbors
j
=
*
jneigh
;
ni
=
sbmask
(
j
);
j
&=
NEIGHMASK
;
{
register
double
*
xj
=
x0
+
(
j
+
(
j
<<
1
));
d
[
0
]
=
xi
[
0
]
-
xj
[
0
];
// pair vector
d
[
1
]
=
xi
[
1
]
-
xj
[
1
];
d
[
2
]
=
xi
[
2
]
-
xj
[
2
];
}
if
((
rsq
=
vec_dot
(
d
,
d
))
>=
cutsqi
[
typej
=
type
[
j
]])
continue
;
r2inv
=
1.0
/
rsq
;
if
((
respa_flag
=
(
rsq
>
cut_in_off_sq
)
&&
(
rsq
<
cut_in_on_sq
)))
{
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_in_off
)
/
cut_in_diff
;
frespa
=
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
if
(
order1
&&
(
rsq
<
cut_coulsq
))
{
// coulombic
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
// series real space
register
double
r
=
sqrt
(
rsq
),
s
=
qri
*
q
[
j
];
if
(
respa_flag
)
// correct for respa
respa_coul
=
ni
==
0
?
frespa
*
s
/
r
:
frespa
*
s
/
r
*
special_coul
[
ni
];
register
double
x
=
g_ewald
*
r
,
t
=
1.0
/
(
1.0
+
EWALD_P
*
x
);
if
(
ni
==
0
)
{
s
*=
g_ewald
*
exp
(
-
x
*
x
);
force_coul
=
(
t
*=
((((
t
*
A5
+
A4
)
*
t
+
A3
)
*
t
+
A2
)
*
t
+
A1
)
*
s
/
x
)
+
EWALD_F
*
s
;
if
(
eflag
)
ecoul
=
t
;
}
else
{
// correct for special
r
=
s
*
(
1.0
-
special_coul
[
ni
])
/
r
;
s
*=
g_ewald
*
exp
(
-
x
*
x
);
force_coul
=
(
t
*=
((((
t
*
A5
+
A4
)
*
t
+
A3
)
*
t
+
A2
)
*
t
+
A1
)
*
s
/
x
)
+
EWALD_F
*
s
-
r
;
if
(
eflag
)
ecoul
=
t
-
r
;
}
}
// table real space
else
{
if
(
respa_flag
)
respa_coul
=
ni
==
0
?
// correct for respa
frespa
*
qri
*
q
[
j
]
/
sqrt
(
rsq
)
:
frespa
*
qri
*
q
[
j
]
/
sqrt
(
rsq
)
*
special_coul
[
ni
];
register
union_int_float_t
t
;
t
.
f
=
rsq
;
register
const
int
k
=
(
t
.
i
&
ncoulmask
)
>>
ncoulshiftbits
;
register
double
f
=
(
rsq
-
rtable
[
k
])
*
drtable
[
k
],
qiqj
=
qi
*
q
[
j
];
if
(
ni
==
0
)
{
force_coul
=
qiqj
*
(
ftable
[
k
]
+
f
*
dftable
[
k
]);
if
(
eflag
)
ecoul
=
qiqj
*
(
etable
[
k
]
+
f
*
detable
[
k
]);
}
else
{
// correct for special
t
.
f
=
(
1.0
-
special_coul
[
ni
])
*
(
ctable
[
k
]
+
f
*
dctable
[
k
]);
force_coul
=
qiqj
*
(
ftable
[
k
]
+
f
*
dftable
[
k
]
-
t
.
f
);
if
(
eflag
)
ecoul
=
qiqj
*
(
etable
[
k
]
+
f
*
detable
[
k
]
-
t
.
f
);
}
}
}
else
force_coul
=
respa_coul
=
ecoul
=
0.0
;
if
(
rsq
<
cut_ljsqi
[
typej
])
{
// lennard-jones
register
double
rn
=
r2inv
*
r2inv
*
r2inv
;
if
(
respa_flag
)
respa_lj
=
ni
==
0
?
// correct for respa
frespa
*
rn
*
(
rn
*
lj1i
[
typej
]
-
lj2i
[
typej
])
:
frespa
*
rn
*
(
rn
*
lj1i
[
typej
]
-
lj2i
[
typej
])
*
special_lj
[
ni
];
if
(
order6
)
{
// long-range form
register
double
x2
=
g2
*
rsq
,
a2
=
1.0
/
x2
;
x2
=
a2
*
exp
(
-
x2
)
*
lj4i
[
typej
];
if
(
ni
==
0
)
{
force_lj
=
(
rn
*=
rn
)
*
lj1i
[
typej
]
-
g8
*
(((
6.0
*
a2
+
6.0
)
*
a2
+
3.0
)
*
a2
+
1.0
)
*
x2
*
rsq
;
if
(
eflag
)
evdwl
=
rn
*
lj3i
[
typej
]
-
g6
*
((
a2
+
1.0
)
*
a2
+
0.5
)
*
x2
;
}
else
{
// correct for special
register
double
f
=
special_lj
[
ni
],
t
=
rn
*
(
1.0
-
f
);
force_lj
=
f
*
(
rn
*=
rn
)
*
lj1i
[
typej
]
-
g8
*
(((
6.0
*
a2
+
6.0
)
*
a2
+
3.0
)
*
a2
+
1.0
)
*
x2
*
rsq
+
t
*
lj2i
[
typej
];
if
(
eflag
)
evdwl
=
f
*
rn
*
lj3i
[
typej
]
-
g6
*
((
a2
+
1.0
)
*
a2
+
0.5
)
*
x2
+
t
*
lj4i
[
typej
];
}
}
else
{
// cut form
if
(
ni
==
0
)
{
force_lj
=
rn
*
(
rn
*
lj1i
[
typej
]
-
lj2i
[
typej
]);
if
(
eflag
)
evdwl
=
rn
*
(
rn
*
lj3i
[
typej
]
-
lj4i
[
typej
])
-
offseti
[
typej
];
}
else
{
// correct for special
register
double
f
=
special_lj
[
ni
];
force_lj
=
f
*
rn
*
(
rn
*
lj1i
[
typej
]
-
lj2i
[
typej
]);
if
(
eflag
)
evdwl
=
f
*
(
rn
*
(
rn
*
lj3i
[
typej
]
-
lj4i
[
typej
])
-
offseti
[
typej
]);
}
}
}
else
force_lj
=
respa_lj
=
evdwl
=
0.0
;
fpair
=
(
force_coul
+
force_lj
)
*
r2inv
;
frespa
=
fpair
-
(
respa_coul
+
respa_lj
)
*
r2inv
;
if
(
newton_pair
||
j
<
nlocal
)
{
register
double
*
fj
=
f0
+
(
j
+
(
j
<<
1
)),
f
;
fi
[
0
]
+=
f
=
d
[
0
]
*
frespa
;
fj
[
0
]
-=
f
;
fi
[
1
]
+=
f
=
d
[
1
]
*
frespa
;
fj
[
1
]
-=
f
;
fi
[
2
]
+=
f
=
d
[
2
]
*
frespa
;
fj
[
2
]
-=
f
;
}
else
{
fi
[
0
]
+=
d
[
0
]
*
frespa
;
fi
[
1
]
+=
d
[
1
]
*
frespa
;
fi
[
2
]
+=
d
[
2
]
*
frespa
;
}
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
ecoul
,
fpair
,
d
[
0
],
d
[
1
],
d
[
2
]);
}
}
}
/* ----------------------------------------------------------------------
setup force tables used in compute routines
------------------------------------------------------------------------- */
void
PairLJCoul
::
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
();
memory
->
create
(
rtable
,
ntable
,
"pair:rtable"
);
memory
->
create
(
ftable
,
ntable
,
"pair:ftable"
);
memory
->
create
(
ctable
,
ntable
,
"pair:ctable"
);
memory
->
create
(
etable
,
ntable
,
"pair:etable"
);
memory
->
create
(
drtable
,
ntable
,
"pair:drtable"
);
memory
->
create
(
dftable
,
ntable
,
"pair:dftable"
);
memory
->
create
(
dctable
,
ntable
,
"pair:dctable"
);
memory
->
create
(
detable
,
ntable
,
"pair:detable"
);
if
(
cut_respa
==
NULL
)
{
vtable
=
ptable
=
dvtable
=
dptable
=
NULL
;
}
else
{
memory
->
create
(
vtable
,
ntable
,
"pair:vtable"
);
memory
->
create
(
ptable
,
ntable
,
"pair:ptable"
);
memory
->
create
(
dvtable
,
ntable
,
"pair:dvtable"
);
memory
->
create
(
dptable
,
ntable
,
"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
];
}
}
}
/* ----------------------------------------------------------------------
free memory for tables used in pair computations
------------------------------------------------------------------------- */
void
PairLJCoul
::
free_tables
()
{
memory
->
destroy
(
rtable
);
memory
->
destroy
(
drtable
);
memory
->
destroy
(
ftable
);
memory
->
destroy
(
dftable
);
memory
->
destroy
(
ctable
);
memory
->
destroy
(
dctable
);
memory
->
destroy
(
etable
);
memory
->
destroy
(
detable
);
memory
->
destroy
(
vtable
);
memory
->
destroy
(
dvtable
);
memory
->
destroy
(
ptable
);
memory
->
destroy
(
dptable
);
}
/* ---------------------------------------------------------------------- */
double
PairLJCoul
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r2inv
,
r6inv
,
force_coul
,
force_lj
;
double
g2
=
g_ewald
*
g_ewald
,
g6
=
g2
*
g2
*
g2
,
g8
=
g6
*
g2
,
*
q
=
atom
->
q
;
double
eng
=
0.0
;
r2inv
=
1.0
/
rsq
;
if
((
ewald_order
&
2
)
&&
(
rsq
<
cut_coulsq
))
{
// coulombic
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
// series real space
register
double
r
=
sqrt
(
rsq
),
x
=
g_ewald
*
r
;
register
double
s
=
force
->
qqrd2e
*
q
[
i
]
*
q
[
j
],
t
=
1.0
/
(
1.0
+
EWALD_P
*
x
);
r
=
s
*
(
1.0
-
factor_coul
)
/
r
;
s
*=
g_ewald
*
exp
(
-
x
*
x
);
force_coul
=
(
t
*=
((((
t
*
A5
+
A4
)
*
t
+
A3
)
*
t
+
A2
)
*
t
+
A1
)
*
s
/
x
)
+
EWALD_F
*
s
-
r
;
eng
+=
t
-
r
;
}
else
{
// table real space
register
union_int_float_t
t
;
t
.
f
=
rsq
;
register
const
int
k
=
(
t
.
i
&
ncoulmask
)
>>
ncoulshiftbits
;
register
double
f
=
(
rsq
-
rtable
[
k
])
*
drtable
[
k
],
qiqj
=
q
[
i
]
*
q
[
j
];
t
.
f
=
(
1.0
-
factor_coul
)
*
(
ctable
[
k
]
+
f
*
dctable
[
k
]);
force_coul
=
qiqj
*
(
ftable
[
k
]
+
f
*
dftable
[
k
]
-
t
.
f
);
eng
+=
qiqj
*
(
etable
[
k
]
+
f
*
detable
[
k
]
-
t
.
f
);
}
}
else
force_coul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
// lennard-jones
r6inv
=
r2inv
*
r2inv
*
r2inv
;
if
(
ewald_order
&
64
)
{
// long-range
register
double
x2
=
g2
*
rsq
,
a2
=
1.0
/
x2
,
t
=
r6inv
*
(
1.0
-
factor_lj
);
x2
=
a2
*
exp
(
-
x2
)
*
lj4
[
itype
][
jtype
];
force_lj
=
factor_lj
*
(
r6inv
*=
r6inv
)
*
lj1
[
itype
][
jtype
]
-
g8
*
(((
6.0
*
a2
+
6.0
)
*
a2
+
3.0
)
*
a2
+
a2
)
*
x2
*
rsq
+
t
*
lj2
[
itype
][
jtype
];
eng
+=
factor_lj
*
r6inv
*
lj3
[
itype
][
jtype
]
-
g6
*
((
a2
+
1.0
)
*
a2
+
0.5
)
*
x2
+
t
*
lj4
[
itype
][
jtype
];
}
else
{
// cut
force_lj
=
factor_lj
*
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
eng
+=
factor_lj
*
(
r6inv
*
(
r6inv
*
lj3
[
itype
][
jtype
]
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
]);
}
}
else
force_lj
=
0.0
;
fforce
=
(
force_coul
+
force_lj
)
*
r2inv
;
return
eng
;
}
Event Timeline
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