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pair_lj_charmm_coul_long_soft.cpp
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Sun, Oct 13, 22:51
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rLAMMPS lammps
pair_lj_charmm_coul_long_soft.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)
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_charmm_coul_long_soft.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 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
/* ---------------------------------------------------------------------- */
PairLJCharmmCoulLongSoft
::
PairLJCharmmCoulLongSoft
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
respa_enable
=
1
;
ewaldflag
=
pppmflag
=
1
;
implicit
=
0
;
mix_flag
=
ARITHMETIC
;
writedata
=
1
;
}
/* ---------------------------------------------------------------------- */
PairLJCharmmCoulLongSoft
::~
PairLJCharmmCoulLongSoft
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
epsilon
);
memory
->
destroy
(
sigma
);
memory
->
destroy
(
lambda
);
memory
->
destroy
(
eps14
);
memory
->
destroy
(
sigma14
);
memory
->
destroy
(
lj1
);
memory
->
destroy
(
lj2
);
memory
->
destroy
(
lj3
);
memory
->
destroy
(
lj4
);
memory
->
destroy
(
lj14_1
);
memory
->
destroy
(
lj14_2
);
memory
->
destroy
(
lj14_3
);
memory
->
destroy
(
lj14_4
);
}
}
/* ---------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
,
fpair
;
double
r
,
rsq
,
forcecoul
,
forcelj
,
factor_coul
,
factor_lj
;
double
grij
,
expm2
,
prefactor
,
t
,
erfc
;
double
philj
,
switch1
,
switch2
;
double
denc
,
denlj
,
r4sig6
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
evdwl
=
ecoul
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
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
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// loop over neighbors of my atoms
for
(
ii
=
0
;
ii
<
inum
;
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
];
factor_lj
=
special_lj
[
sbmask
(
j
)];
factor_coul
=
special_coul
[
sbmask
(
j
)];
j
&=
NEIGHMASK
;
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
<
cut_bothsq
)
{
if
(
rsq
<
cut_coulsq
)
{
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
;
denc
=
sqrt
(
lj4
[
itype
][
jtype
]
+
rsq
);
prefactor
=
qqrd2e
*
lj1
[
itype
][
jtype
]
*
qtmp
*
q
[
j
]
/
(
denc
*
denc
*
denc
);
forcecoul
=
prefactor
*
(
erfc
+
EWALD_F
*
grij
*
expm2
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
forcecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
)
{
r4sig6
=
rsq
*
rsq
/
lj2
[
itype
][
jtype
];
denlj
=
lj3
[
itype
][
jtype
]
+
rsq
*
r4sig6
;
forcelj
=
lj1
[
itype
][
jtype
]
*
epsilon
[
itype
][
jtype
]
*
(
48.0
*
r4sig6
/
(
denlj
*
denlj
*
denlj
)
-
24.0
*
r4sig6
/
(
denlj
*
denlj
));
if
(
rsq
>
cut_lj_innersq
)
{
switch1
=
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
+
2.0
*
rsq
-
3.0
*
cut_lj_innersq
)
/
denom_lj
;
switch2
=
12.0
*
(
cut_ljsq
-
rsq
)
*
(
rsq
-
cut_lj_innersq
)
/
denom_lj
;
philj
=
lj1
[
itype
][
jtype
]
*
4.0
*
epsilon
[
itype
][
jtype
]
*
(
1.0
/
(
denlj
*
denlj
)
-
1.0
/
denlj
);
forcelj
=
forcelj
*
switch1
+
philj
*
switch2
;
}
}
else
forcelj
=
0.0
;
fpair
=
forcecoul
+
factor_lj
*
forcelj
;
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
)
{
prefactor
=
qqrd2e
*
lj1
[
itype
][
jtype
]
*
qtmp
*
q
[
j
]
/
denc
;
ecoul
=
prefactor
*
erfc
;
if
(
factor_coul
<
1.0
)
ecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
ecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
)
{
evdwl
=
lj1
[
itype
][
jtype
]
*
4.0
*
epsilon
[
itype
][
jtype
]
*
(
1.0
/
(
denlj
*
denlj
)
-
1.0
/
denlj
);
if
(
rsq
>
cut_lj_innersq
)
{
switch1
=
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
+
2.0
*
rsq
-
3.0
*
cut_lj_innersq
)
/
denom_lj
;
evdwl
*=
switch1
;
}
evdwl
*=
factor_lj
;
}
else
evdwl
=
0.0
;
}
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
ecoul
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ---------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
compute_inner
()
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
fpair
;
double
rsq
,
forcecoul
,
forcelj
,
factor_coul
,
factor_lj
;
double
rsw
;
double
denc
,
denlj
,
r4sig6
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
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
;
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
for
(
ii
=
0
;
ii
<
inum
;
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
];
factor_lj
=
special_lj
[
sbmask
(
j
)];
factor_coul
=
special_coul
[
sbmask
(
j
)];
j
&=
NEIGHMASK
;
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
)
{
jtype
=
type
[
j
];
denc
=
sqrt
(
lj4
[
itype
][
jtype
]
+
rsq
);
forcecoul
=
qqrd2e
*
lj1
[
itype
][
jtype
]
*
qtmp
*
q
[
j
]
/
(
denc
*
denc
*
denc
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
forcecoul
;
r4sig6
=
rsq
*
rsq
/
lj2
[
itype
][
jtype
];
denlj
=
lj3
[
itype
][
jtype
]
+
rsq
*
r4sig6
;
forcelj
=
lj1
[
itype
][
jtype
]
*
epsilon
[
itype
][
jtype
]
*
(
48.0
*
r4sig6
/
(
denlj
*
denlj
*
denlj
)
-
24.0
*
r4sig6
/
(
denlj
*
denlj
));
fpair
=
forcecoul
+
factor_lj
*
forcelj
;
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
;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
compute_middle
()
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
fpair
;
double
rsq
,
forcecoul
,
forcelj
,
factor_coul
,
factor_lj
;
double
philj
,
switch1
,
switch2
;
double
rsw
;
double
denc
,
denlj
,
r4sig6
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
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
;
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
for
(
ii
=
0
;
ii
<
inum
;
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
];
factor_lj
=
special_lj
[
sbmask
(
j
)];
factor_coul
=
special_coul
[
sbmask
(
j
)];
j
&=
NEIGHMASK
;
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
)
{
jtype
=
type
[
j
];
denc
=
sqrt
(
lj4
[
itype
][
jtype
]
+
rsq
);
forcecoul
=
qqrd2e
*
lj1
[
itype
][
jtype
]
*
qtmp
*
q
[
j
]
/
(
denc
*
denc
*
denc
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
forcecoul
;
r4sig6
=
rsq
*
rsq
/
lj2
[
itype
][
jtype
];
denlj
=
lj3
[
itype
][
jtype
]
+
rsq
*
r4sig6
;
forcelj
=
lj1
[
itype
][
jtype
]
*
epsilon
[
itype
][
jtype
]
*
(
48.0
*
r4sig6
/
(
denlj
*
denlj
*
denlj
)
-
24.0
*
r4sig6
/
(
denlj
*
denlj
));
if
(
rsq
>
cut_lj_innersq
)
{
switch1
=
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
+
2.0
*
rsq
-
3.0
*
cut_lj_innersq
)
/
denom_lj
;
switch2
=
12.0
*
(
cut_ljsq
-
rsq
)
*
(
rsq
-
cut_lj_innersq
)
/
denom_lj
;
philj
=
lj1
[
itype
][
jtype
]
*
4.0
*
epsilon
[
itype
][
jtype
]
*
(
1.0
/
(
denlj
*
denlj
)
-
1.0
/
denlj
);
forcelj
=
forcelj
*
switch1
+
philj
*
switch2
;
}
fpair
=
forcecoul
+
factor_lj
*
forcelj
;
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
;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
compute_outer
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
,
fpair
;
double
r
,
rsq
,
forcecoul
,
forcelj
,
factor_coul
,
factor_lj
;
double
grij
,
expm2
,
fprefactor
,
eprefactor
,
t
,
erfc
;
double
philj
,
switch1
,
switch2
;
double
rsw
;
double
denc
,
denlj
,
r4sig6
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
evdwl
=
ecoul
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
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
;
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
for
(
ii
=
0
;
ii
<
inum
;
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
];
factor_lj
=
special_lj
[
sbmask
(
j
)];
factor_coul
=
special_coul
[
sbmask
(
j
)];
j
&=
NEIGHMASK
;
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_bothsq
)
{
jtype
=
type
[
j
];
if
(
rsq
<
cut_coulsq
)
{
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
;
denc
=
sqrt
(
lj4
[
itype
][
jtype
]
+
rsq
);
fprefactor
=
qqrd2e
*
lj1
[
itype
][
jtype
]
*
qtmp
*
q
[
j
]
/
(
denc
*
denc
*
denc
);
forcecoul
=
fprefactor
*
(
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
+=
fprefactor
*
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
fprefactor
*
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
else
{
forcecoul
+=
fprefactor
;
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
fprefactor
;
}
}
}
else
forcecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
&&
rsq
>
cut_in_off_sq
)
{
r4sig6
=
rsq
*
rsq
/
lj2
[
itype
][
jtype
];
denlj
=
lj3
[
itype
][
jtype
]
+
rsq
*
r4sig6
;
forcelj
=
lj1
[
itype
][
jtype
]
*
epsilon
[
itype
][
jtype
]
*
(
48.0
*
r4sig6
/
(
denlj
*
denlj
*
denlj
)
-
24.0
*
r4sig6
/
(
denlj
*
denlj
));
if
(
rsq
>
cut_lj_innersq
)
{
switch1
=
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
+
2.0
*
rsq
-
3.0
*
cut_lj_innersq
)
/
denom_lj
;
switch2
=
12.0
*
(
cut_ljsq
-
rsq
)
*
(
rsq
-
cut_lj_innersq
)
/
denom_lj
;
philj
=
lj1
[
itype
][
jtype
]
*
4.0
*
epsilon
[
itype
][
jtype
]
*
(
1.0
/
(
denlj
*
denlj
)
-
1.0
/
denlj
);
forcelj
=
forcelj
*
switch1
+
philj
*
switch2
;
}
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
;
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
)
{
eprefactor
=
qqrd2e
*
lj1
[
itype
][
jtype
]
*
qtmp
*
q
[
j
]
/
denc
;
ecoul
=
eprefactor
*
erfc
;
if
(
factor_coul
<
1.0
)
ecoul
-=
(
1.0
-
factor_coul
)
*
eprefactor
;
}
else
ecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
)
{
r4sig6
=
rsq
*
rsq
/
lj2
[
itype
][
jtype
];
denlj
=
lj3
[
itype
][
jtype
]
+
rsq
*
r4sig6
;
evdwl
=
lj1
[
itype
][
jtype
]
*
4.0
*
epsilon
[
itype
][
jtype
]
*
(
1.0
/
(
denlj
*
denlj
)
-
1.0
/
denlj
);
if
(
rsq
>
cut_lj_innersq
)
{
switch1
=
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
+
2.0
*
rsq
-
3.0
*
cut_lj_innersq
)
/
denom_lj
;
evdwl
*=
switch1
;
}
evdwl
*=
factor_lj
;
}
else
evdwl
=
0.0
;
}
if
(
vflag
)
{
if
(
rsq
<
cut_coulsq
)
{
forcecoul
=
fprefactor
*
(
erfc
+
EWALD_F
*
grij
*
expm2
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
fprefactor
;
}
else
forcecoul
=
0.0
;
if
(
rsq
<=
cut_in_off_sq
)
{
r4sig6
=
rsq
*
rsq
/
lj2
[
itype
][
jtype
];
denlj
=
lj3
[
itype
][
jtype
]
+
rsq
*
r4sig6
;
forcelj
=
lj1
[
itype
][
jtype
]
*
epsilon
[
itype
][
jtype
]
*
(
48.0
*
r4sig6
/
(
denlj
*
denlj
*
denlj
)
-
24.0
*
r4sig6
/
(
denlj
*
denlj
));
if
(
rsq
>
cut_lj_innersq
)
{
switch1
=
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
+
2.0
*
rsq
-
3.0
*
cut_lj_innersq
)
/
denom_lj
;
switch2
=
12.0
*
(
cut_ljsq
-
rsq
)
*
(
rsq
-
cut_lj_innersq
)
/
denom_lj
;
philj
=
lj1
[
itype
][
jtype
]
*
4.0
*
epsilon
[
itype
][
jtype
]
*
(
1.0
/
(
denlj
*
denlj
)
-
1.0
/
denlj
);
forcelj
=
forcelj
*
switch1
+
philj
*
switch2
;
}
}
else
if
(
rsq
<=
cut_in_on_sq
)
{
r4sig6
=
rsq
*
rsq
/
lj2
[
itype
][
jtype
];
denlj
=
lj3
[
itype
][
jtype
]
+
rsq
*
r4sig6
;
forcelj
=
lj1
[
itype
][
jtype
]
*
epsilon
[
itype
][
jtype
]
*
(
48.0
*
r4sig6
/
(
denlj
*
denlj
*
denlj
)
-
24.0
*
r4sig6
/
(
denlj
*
denlj
));
if
(
rsq
>
cut_lj_innersq
)
{
switch1
=
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
+
2.0
*
rsq
-
3.0
*
cut_lj_innersq
)
/
denom_lj
;
switch2
=
12.0
*
(
cut_ljsq
-
rsq
)
*
(
rsq
-
cut_lj_innersq
)
/
denom_lj
;
philj
=
lj1
[
itype
][
jtype
]
*
4.0
*
epsilon
[
itype
][
jtype
]
*
(
1.0
/
(
denlj
*
denlj
)
-
1.0
/
denlj
);
forcelj
=
forcelj
*
switch1
+
philj
*
switch2
;
}
}
fpair
=
forcecoul
+
factor_lj
*
forcelj
;
}
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
ecoul
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
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
(
epsilon
,
n
+
1
,
n
+
1
,
"pair:epsilon"
);
memory
->
create
(
sigma
,
n
+
1
,
n
+
1
,
"pair:sigma"
);
memory
->
create
(
lambda
,
n
+
1
,
n
+
1
,
"pair:lambda"
);
memory
->
create
(
eps14
,
n
+
1
,
n
+
1
,
"pair:eps14"
);
memory
->
create
(
sigma14
,
n
+
1
,
n
+
1
,
"pair:sigma14"
);
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
(
lj14_1
,
n
+
1
,
n
+
1
,
"pair:lj14_1"
);
memory
->
create
(
lj14_2
,
n
+
1
,
n
+
1
,
"pair:lj14_2"
);
memory
->
create
(
lj14_3
,
n
+
1
,
n
+
1
,
"pair:lj14_3"
);
memory
->
create
(
lj14_4
,
n
+
1
,
n
+
1
,
"pair:lj14_4"
);
}
/* ----------------------------------------------------------------------
global settings
unlike other pair styles,
there are no individual pair settings that these override
------------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
5
&&
narg
!=
6
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
nlambda
=
force
->
numeric
(
FLERR
,
arg
[
0
]);
alphalj
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
alphac
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
cut_lj_inner
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
cut_lj
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
if
(
narg
==
5
)
cut_coul
=
cut_lj
;
else
cut_coul
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
5
&&
narg
!=
7
)
error
->
all
(
FLERR
,
"Illegal pair_coeff command"
);
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
(
FLERR
,
arg
[
2
]);
double
sigma_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
lambda_one
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
double
eps14_one
=
epsilon_one
;
double
sigma14_one
=
sigma_one
;
if
(
narg
==
7
)
{
eps14_one
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
sigma14_one
=
force
->
numeric
(
FLERR
,
arg
[
6
]);
}
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
;
lambda
[
i
][
j
]
=
lambda_one
;
eps14
[
i
][
j
]
=
eps14_one
;
sigma14
[
i
][
j
]
=
sigma14_one
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
init_style
()
{
if
(
!
atom
->
q_flag
)
error
->
all
(
FLERR
,
"Pair style lj/charmm/coul/long/soft requires atom attribute q"
);
// request regular or rRESPA neighbor lists
int
irequest
;
if
(
update
->
whichflag
==
1
&&
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
,
instance_me
);
else
if
(
respa
==
1
)
{
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
id
=
1
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
respainner
=
1
;
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
id
=
3
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
respaouter
=
1
;
}
else
{
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
id
=
1
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
respainner
=
1
;
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
id
=
2
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
respamiddle
=
1
;
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
id
=
3
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
respaouter
=
1
;
}
}
else
irequest
=
neighbor
->
request
(
this
,
instance_me
);
// require cut_lj_inner < cut_lj
if
(
cut_lj_inner
>=
cut_lj
)
error
->
all
(
FLERR
,
"Pair inner cutoff >= Pair outer cutoff"
);
cut_lj_innersq
=
cut_lj_inner
*
cut_lj_inner
;
cut_ljsq
=
cut_lj
*
cut_lj
;
cut_coulsq
=
cut_coul
*
cut_coul
;
cut_bothsq
=
MAX
(
cut_ljsq
,
cut_coulsq
);
denom_lj
=
(
cut_ljsq
-
cut_lj_innersq
)
*
(
cut_ljsq
-
cut_lj_innersq
)
*
(
cut_ljsq
-
cut_lj_innersq
);
// set & error check interior rRESPA cutoffs
if
(
strstr
(
update
->
integrate_style
,
"respa"
)
&&
((
Respa
*
)
update
->
integrate
)
->
level_inner
>=
0
)
{
cut_respa
=
((
Respa
*
)
update
->
integrate
)
->
cutoff
;
if
(
MIN
(
cut_lj
,
cut_coul
)
<
cut_respa
[
3
])
error
->
all
(
FLERR
,
"Pair cutoff < Respa interior cutoff"
);
if
(
cut_lj_inner
<
cut_respa
[
1
])
error
->
all
(
FLERR
,
"Pair inner cutoff < Respa interior cutoff"
);
}
else
cut_respa
=
NULL
;
// insure use of KSpace long-range solver, set g_ewald
if
(
force
->
kspace
==
NULL
)
error
->
all
(
FLERR
,
"Pair style requires a KSpace style"
);
g_ewald
=
force
->
kspace
->
g_ewald
;
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
regular or rRESPA
------------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
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
PairLJCharmmCoulLongSoft
::
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
]);
if
(
lambda
[
i
][
i
]
!=
lambda
[
j
][
j
])
error
->
all
(
FLERR
,
"Pair lj/charmm/coul/long/soft different lambda values in mix"
);
lambda
[
i
][
j
]
=
lambda
[
i
][
i
];
eps14
[
i
][
j
]
=
mix_energy
(
eps14
[
i
][
i
],
eps14
[
j
][
j
],
sigma14
[
i
][
i
],
sigma14
[
j
][
j
]);
sigma14
[
i
][
j
]
=
mix_distance
(
sigma14
[
i
][
i
],
sigma14
[
j
][
j
]);
}
double
cut
=
MAX
(
cut_lj
,
cut_coul
);
lj1
[
i
][
j
]
=
pow
(
lambda
[
i
][
j
],
nlambda
);
lj2
[
i
][
j
]
=
pow
(
sigma
[
i
][
j
],
6.0
);
lj3
[
i
][
j
]
=
alphalj
*
(
1.0
-
lambda
[
i
][
j
])
*
(
1.0
-
lambda
[
i
][
j
]);
lj4
[
i
][
j
]
=
alphac
*
(
1.0
-
lambda
[
i
][
j
])
*
(
1.0
-
lambda
[
i
][
j
]);
// 1-4 interactions unaffected (they're part of the dihedral term)
lj14_1
[
i
][
j
]
=
48.0
*
eps14
[
i
][
j
]
*
pow
(
sigma14
[
i
][
j
],
12.0
);
lj14_2
[
i
][
j
]
=
24.0
*
eps14
[
i
][
j
]
*
pow
(
sigma14
[
i
][
j
],
6.0
);
lj14_3
[
i
][
j
]
=
4.0
*
eps14
[
i
][
j
]
*
pow
(
sigma14
[
i
][
j
],
12.0
);
lj14_4
[
i
][
j
]
=
4.0
*
eps14
[
i
][
j
]
*
pow
(
sigma14
[
i
][
j
],
6.0
);
epsilon
[
j
][
i
]
=
epsilon
[
i
][
j
];
sigma
[
j
][
i
]
=
sigma
[
i
][
j
];
lambda
[
j
][
i
]
=
lambda
[
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
];
lj14_1
[
j
][
i
]
=
lj14_1
[
i
][
j
];
lj14_2
[
j
][
i
]
=
lj14_2
[
i
][
j
];
lj14_3
[
j
][
i
]
=
lj14_3
[
i
][
j
];
lj14_4
[
j
][
i
]
=
lj14_4
[
i
][
j
];
return
cut
;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
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
(
&
lambda
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
eps14
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
sigma14
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
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
(
&
lambda
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
eps14
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
sigma14
[
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
(
&
lambda
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
eps14
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma14
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
nlambda
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
alphalj
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
alphac
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut_lj_inner
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut_lj
,
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
PairLJCharmmCoulLongSoft
::
read_restart_settings
(
FILE
*
fp
)
{
if
(
comm
->
me
==
0
)
{
fread
(
&
nlambda
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
alphalj
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
alphac
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut_lj_inner
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut_lj
,
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
(
&
nlambda
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
alphalj
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
alphac
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut_lj_inner
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut_lj
,
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
);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
write_data
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
fprintf
(
fp
,
"%d %g %g %g %g %g
\n
"
,
i
,
epsilon
[
i
][
i
],
sigma
[
i
][
i
],
lambda
[
i
][
i
],
eps14
[
i
][
i
],
sigma14
[
i
][
i
]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void
PairLJCharmmCoulLongSoft
::
write_data_all
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
int
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
fprintf
(
fp
,
"%d %d %g %g %g %g %g
\n
"
,
i
,
j
,
epsilon
[
i
][
j
],
sigma
[
i
][
j
],
lambda
[
i
][
j
],
eps14
[
i
][
j
],
sigma14
[
i
][
j
]);
}
/* ---------------------------------------------------------------------- */
double
PairLJCharmmCoulLongSoft
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r
,
grij
,
expm2
,
t
,
erfc
,
prefactor
;
double
switch1
,
switch2
,
forcecoul
,
forcelj
,
phicoul
,
philj
;
double
denc
,
denlj
,
r4sig6
;
if
(
rsq
<
cut_coulsq
)
{
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
;
denc
=
sqrt
(
lj4
[
itype
][
jtype
]
+
rsq
);
prefactor
=
force
->
qqrd2e
*
lj1
[
itype
][
jtype
]
*
atom
->
q
[
i
]
*
atom
->
q
[
j
]
/
(
denc
*
denc
*
denc
);
forcecoul
=
prefactor
*
(
erfc
+
EWALD_F
*
grij
*
expm2
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
forcecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
)
{
r4sig6
=
rsq
*
rsq
/
lj2
[
itype
][
jtype
];
denlj
=
lj3
[
itype
][
jtype
]
+
rsq
*
r4sig6
;
forcelj
=
lj1
[
itype
][
jtype
]
*
epsilon
[
itype
][
jtype
]
*
(
48.0
*
r4sig6
/
(
denlj
*
denlj
*
denlj
)
-
24.0
*
r4sig6
/
(
denlj
*
denlj
));
if
(
rsq
>
cut_lj_innersq
)
{
switch1
=
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
+
2.0
*
rsq
-
3.0
*
cut_lj_innersq
)
/
denom_lj
;
switch2
=
12.0
*
(
cut_ljsq
-
rsq
)
*
(
rsq
-
cut_lj_innersq
)
/
denom_lj
;
philj
=
lj1
[
itype
][
jtype
]
*
4.0
*
epsilon
[
itype
][
jtype
]
*
(
1.0
/
(
denlj
*
denlj
)
-
1.0
/
denlj
);
forcelj
=
forcelj
*
switch1
+
philj
*
switch2
;
}
}
else
forcelj
=
0.0
;
fforce
=
forcecoul
+
factor_lj
*
forcelj
;
double
eng
=
0.0
;
if
(
rsq
<
cut_coulsq
)
{
prefactor
=
force
->
qqrd2e
*
lj1
[
itype
][
jtype
]
*
atom
->
q
[
i
]
*
atom
->
q
[
j
]
/
denc
;
phicoul
=
prefactor
*
erfc
;
if
(
factor_coul
<
1.0
)
phicoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
eng
+=
phicoul
;
}
if
(
rsq
<
cut_ljsq
)
{
philj
=
lj1
[
itype
][
jtype
]
*
4.0
*
epsilon
[
itype
][
jtype
]
*
(
1.0
/
(
denlj
*
denlj
)
-
1.0
/
denlj
)
-
offset
[
itype
][
jtype
];
if
(
rsq
>
cut_lj_innersq
)
{
switch1
=
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
-
rsq
)
*
(
cut_ljsq
+
2.0
*
rsq
-
3.0
*
cut_lj_innersq
)
/
denom_lj
;
philj
*=
switch1
;
}
eng
+=
factor_lj
*
philj
;
}
return
eng
;
}
/* ---------------------------------------------------------------------- */
void
*
PairLJCharmmCoulLongSoft
::
extract
(
const
char
*
str
,
int
&
dim
)
{
dim
=
2
;
if
(
strcmp
(
str
,
"lj14_1"
)
==
0
)
return
(
void
*
)
lj14_1
;
if
(
strcmp
(
str
,
"lj14_2"
)
==
0
)
return
(
void
*
)
lj14_2
;
if
(
strcmp
(
str
,
"lj14_3"
)
==
0
)
return
(
void
*
)
lj14_3
;
if
(
strcmp
(
str
,
"lj14_4"
)
==
0
)
return
(
void
*
)
lj14_4
;
if
(
strcmp
(
str
,
"epsilon"
)
==
0
)
return
(
void
*
)
epsilon
;
if
(
strcmp
(
str
,
"sigma"
)
==
0
)
return
(
void
*
)
sigma
;
if
(
strcmp
(
str
,
"lambda"
)
==
0
)
return
(
void
*
)
lambda
;
dim
=
0
;
if
(
strcmp
(
str
,
"implicit"
)
==
0
)
return
(
void
*
)
&
implicit
;
if
(
strcmp
(
str
,
"cut_coul"
)
==
0
)
return
(
void
*
)
&
cut_coul
;
return
NULL
;
}
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