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pair_lj_cut_tip4p_cut.cpp
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rLAMMPS lammps
pair_lj_cut_tip4p_cut.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: Pavel Elkind (Gothenburg University)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "pair_lj_cut_tip4p_cut.h"
#include "atom.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "domain.h"
#include "angle.h"
#include "bond.h"
#include "comm.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
/* ---------------------------------------------------------------------- */
PairLJCutTIP4PCut
::
PairLJCutTIP4PCut
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
single_enable
=
0
;
writedata
=
1
;
nmax
=
0
;
hneigh
=
NULL
;
newsite
=
NULL
;
// TIP4P cannot compute virial as F dot r
// due to finding bonded H atoms which are not near O atom
no_virial_fdotr_compute
=
1
;
}
/* ---------------------------------------------------------------------- */
PairLJCutTIP4PCut
::~
PairLJCutTIP4PCut
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cut_lj
);
memory
->
destroy
(
cut_ljsq
);
memory
->
destroy
(
epsilon
);
memory
->
destroy
(
sigma
);
memory
->
destroy
(
lj1
);
memory
->
destroy
(
lj2
);
memory
->
destroy
(
lj3
);
memory
->
destroy
(
lj4
);
memory
->
destroy
(
offset
);
}
memory
->
destroy
(
hneigh
);
memory
->
destroy
(
newsite
);
}
/* ---------------------------------------------------------------------- */
void
PairLJCutTIP4PCut
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
;
double
rsq
,
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
factor_lj
,
factor_coul
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
int
key
;
int
n
,
vlist
[
6
];
int
iH1
,
iH2
,
jH1
,
jH2
;
double
cforce
;
double
fO
[
3
],
fH
[
3
],
fd
[
3
],
v
[
6
],
xH1
[
3
],
xH2
[
3
];
double
*
x1
,
*
x2
;
evdwl
=
ecoul
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
// reallocate hneigh & newsite if necessary
// initialize hneigh[0] to -1 on steps when reneighboring occurred
// initialize hneigh[2] to 0 every step
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
if
(
atom
->
nmax
>
nmax
)
{
nmax
=
atom
->
nmax
;
memory
->
destroy
(
hneigh
);
memory
->
create
(
hneigh
,
nmax
,
3
,
"pair:hneigh"
);
memory
->
destroy
(
newsite
);
memory
->
create
(
newsite
,
nmax
,
3
,
"pair:newsite"
);
}
if
(
neighbor
->
ago
==
0
)
for
(
i
=
0
;
i
<
nall
;
i
++
)
hneigh
[
i
][
0
]
=
-
1
;
for
(
i
=
0
;
i
<
nall
;
i
++
)
hneigh
[
i
][
2
]
=
0
;
double
**
f
=
atom
->
f
;
double
**
x
=
atom
->
x
;
double
*
q
=
atom
->
q
;
tagint
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
double
*
special_lj
=
force
->
special_lj
;
double
*
special_coul
=
force
->
special_coul
;
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
];
if
(
itype
==
typeO
)
{
if
(
hneigh
[
i
][
0
]
<
0
)
{
hneigh
[
i
][
0
]
=
iH1
=
atom
->
map
(
tag
[
i
]
+
1
);
hneigh
[
i
][
1
]
=
iH2
=
atom
->
map
(
tag
[
i
]
+
2
);
hneigh
[
i
][
2
]
=
1
;
if
(
iH1
==
-
1
||
iH2
==
-
1
)
error
->
one
(
FLERR
,
"TIP4P hydrogen is missing"
);
if
(
atom
->
type
[
iH1
]
!=
typeH
||
atom
->
type
[
iH2
]
!=
typeH
)
error
->
one
(
FLERR
,
"TIP4P hydrogen has incorrect atom type"
);
compute_newsite
(
x
[
i
],
x
[
iH1
],
x
[
iH2
],
newsite
[
i
]);
}
else
{
iH1
=
hneigh
[
i
][
0
];
iH2
=
hneigh
[
i
][
1
];
if
(
hneigh
[
i
][
2
]
==
0
)
{
hneigh
[
i
][
2
]
=
1
;
compute_newsite
(
x
[
i
],
x
[
iH1
],
x
[
iH2
],
newsite
[
i
]);
}
}
x1
=
newsite
[
i
];
}
else
x1
=
x
[
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
];
// LJ interaction based on true rsq
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
forcelj
*=
factor_lj
*
r2inv
;
f
[
i
][
0
]
+=
delx
*
forcelj
;
f
[
i
][
1
]
+=
dely
*
forcelj
;
f
[
i
][
2
]
+=
delz
*
forcelj
;
f
[
j
][
0
]
-=
delx
*
forcelj
;
f
[
j
][
1
]
-=
dely
*
forcelj
;
f
[
j
][
2
]
-=
delz
*
forcelj
;
if
(
eflag
)
{
evdwl
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
evdwl
*=
factor_lj
;
}
else
evdwl
=
0.0
;
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
0.0
,
forcelj
,
delx
,
dely
,
delz
);
}
// adjust rsq and delxyz for off-site O charge(s) if necessary
// but only if they are within reach
if
(
rsq
<
cut_coulsqplus
)
{
if
(
itype
==
typeO
||
jtype
==
typeO
)
{
// if atom J = water O, set x2 = offset charge site
// else x2 = x of atom J
if
(
jtype
==
typeO
)
{
if
(
hneigh
[
j
][
0
]
<
0
)
{
hneigh
[
j
][
0
]
=
jH1
=
atom
->
map
(
tag
[
j
]
+
1
);
hneigh
[
j
][
1
]
=
jH2
=
atom
->
map
(
tag
[
j
]
+
2
);
hneigh
[
j
][
2
]
=
1
;
if
(
jH1
==
-
1
||
jH2
==
-
1
)
error
->
one
(
FLERR
,
"TIP4P hydrogen is missing"
);
if
(
atom
->
type
[
jH1
]
!=
typeH
||
atom
->
type
[
jH2
]
!=
typeH
)
error
->
one
(
FLERR
,
"TIP4P hydrogen has incorrect atom type"
);
compute_newsite
(
x
[
j
],
x
[
jH1
],
x
[
jH2
],
newsite
[
j
]);
}
else
{
jH1
=
hneigh
[
j
][
0
];
jH2
=
hneigh
[
j
][
1
];
if
(
hneigh
[
j
][
2
]
==
0
)
{
hneigh
[
j
][
2
]
=
1
;
compute_newsite
(
x
[
j
],
x
[
jH1
],
x
[
jH2
],
newsite
[
j
]);
}
}
x2
=
newsite
[
j
];
}
else
x2
=
x
[
j
];
delx
=
x1
[
0
]
-
x2
[
0
];
dely
=
x1
[
1
]
-
x2
[
1
];
delz
=
x1
[
2
]
-
x2
[
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
}
// Coulombic interaction based on modified rsq
if
(
rsq
<
cut_coulsq
)
{
r2inv
=
1.0
/
rsq
;
forcecoul
=
qqrd2e
*
qtmp
*
q
[
j
]
*
sqrt
(
r2inv
);
cforce
=
factor_coul
*
forcecoul
*
r2inv
;
// if i,j are not O atoms, force is applied directly;
// if i or j are O atoms, force is on fictitious atom & partitioned
// force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
// f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
// preserves total force and torque on water molecule
// virial = sum(r x F) where each water's atoms are near xi and xj
// vlist stores 2,4,6 atoms whose forces contribute to virial
n
=
0
;
key
=
0
;
if
(
itype
!=
typeO
)
{
f
[
i
][
0
]
+=
delx
*
cforce
;
f
[
i
][
1
]
+=
dely
*
cforce
;
f
[
i
][
2
]
+=
delz
*
cforce
;
if
(
vflag
)
{
v
[
0
]
=
x
[
i
][
0
]
*
delx
*
cforce
;
v
[
1
]
=
x
[
i
][
1
]
*
dely
*
cforce
;
v
[
2
]
=
x
[
i
][
2
]
*
delz
*
cforce
;
v
[
3
]
=
x
[
i
][
0
]
*
dely
*
cforce
;
v
[
4
]
=
x
[
i
][
0
]
*
delz
*
cforce
;
v
[
5
]
=
x
[
i
][
1
]
*
delz
*
cforce
;
}
vlist
[
n
++
]
=
i
;
}
else
{
key
++
;
fd
[
0
]
=
delx
*
cforce
;
fd
[
1
]
=
dely
*
cforce
;
fd
[
2
]
=
delz
*
cforce
;
fO
[
0
]
=
fd
[
0
]
*
(
1.0
-
alpha
);
fO
[
1
]
=
fd
[
1
]
*
(
1.0
-
alpha
);
fO
[
2
]
=
fd
[
2
]
*
(
1.0
-
alpha
);
fH
[
0
]
=
0.5
*
alpha
*
fd
[
0
];
fH
[
1
]
=
0.5
*
alpha
*
fd
[
1
];
fH
[
2
]
=
0.5
*
alpha
*
fd
[
2
];
f
[
i
][
0
]
+=
fO
[
0
];
f
[
i
][
1
]
+=
fO
[
1
];
f
[
i
][
2
]
+=
fO
[
2
];
f
[
iH1
][
0
]
+=
fH
[
0
];
f
[
iH1
][
1
]
+=
fH
[
1
];
f
[
iH1
][
2
]
+=
fH
[
2
];
f
[
iH2
][
0
]
+=
fH
[
0
];
f
[
iH2
][
1
]
+=
fH
[
1
];
f
[
iH2
][
2
]
+=
fH
[
2
];
if
(
vflag
)
{
domain
->
closest_image
(
x
[
i
],
x
[
iH1
],
xH1
);
domain
->
closest_image
(
x
[
i
],
x
[
iH2
],
xH2
);
v
[
0
]
=
x
[
i
][
0
]
*
fO
[
0
]
+
xH1
[
0
]
*
fH
[
0
]
+
xH2
[
0
]
*
fH
[
0
];
v
[
1
]
=
x
[
i
][
1
]
*
fO
[
1
]
+
xH1
[
1
]
*
fH
[
1
]
+
xH2
[
1
]
*
fH
[
1
];
v
[
2
]
=
x
[
i
][
2
]
*
fO
[
2
]
+
xH1
[
2
]
*
fH
[
2
]
+
xH2
[
2
]
*
fH
[
2
];
v
[
3
]
=
x
[
i
][
0
]
*
fO
[
1
]
+
xH1
[
0
]
*
fH
[
1
]
+
xH2
[
0
]
*
fH
[
1
];
v
[
4
]
=
x
[
i
][
0
]
*
fO
[
2
]
+
xH1
[
0
]
*
fH
[
2
]
+
xH2
[
0
]
*
fH
[
2
];
v
[
5
]
=
x
[
i
][
1
]
*
fO
[
2
]
+
xH1
[
1
]
*
fH
[
2
]
+
xH2
[
1
]
*
fH
[
2
];
}
vlist
[
n
++
]
=
i
;
vlist
[
n
++
]
=
iH1
;
vlist
[
n
++
]
=
iH2
;
}
if
(
jtype
!=
typeO
)
{
f
[
j
][
0
]
-=
delx
*
cforce
;
f
[
j
][
1
]
-=
dely
*
cforce
;
f
[
j
][
2
]
-=
delz
*
cforce
;
if
(
vflag
)
{
v
[
0
]
-=
x
[
j
][
0
]
*
delx
*
cforce
;
v
[
1
]
-=
x
[
j
][
1
]
*
dely
*
cforce
;
v
[
2
]
-=
x
[
j
][
2
]
*
delz
*
cforce
;
v
[
3
]
-=
x
[
j
][
0
]
*
dely
*
cforce
;
v
[
4
]
-=
x
[
j
][
0
]
*
delz
*
cforce
;
v
[
5
]
-=
x
[
j
][
1
]
*
delz
*
cforce
;
}
vlist
[
n
++
]
=
j
;
}
else
{
key
+=
2
;
fd
[
0
]
=
-
delx
*
cforce
;
fd
[
1
]
=
-
dely
*
cforce
;
fd
[
2
]
=
-
delz
*
cforce
;
fO
[
0
]
=
fd
[
0
]
*
(
1
-
alpha
);
fO
[
1
]
=
fd
[
1
]
*
(
1
-
alpha
);
fO
[
2
]
=
fd
[
2
]
*
(
1
-
alpha
);
fH
[
0
]
=
0.5
*
alpha
*
fd
[
0
];
fH
[
1
]
=
0.5
*
alpha
*
fd
[
1
];
fH
[
2
]
=
0.5
*
alpha
*
fd
[
2
];
f
[
j
][
0
]
+=
fO
[
0
];
f
[
j
][
1
]
+=
fO
[
1
];
f
[
j
][
2
]
+=
fO
[
2
];
f
[
jH1
][
0
]
+=
fH
[
0
];
f
[
jH1
][
1
]
+=
fH
[
1
];
f
[
jH1
][
2
]
+=
fH
[
2
];
f
[
jH2
][
0
]
+=
fH
[
0
];
f
[
jH2
][
1
]
+=
fH
[
1
];
f
[
jH2
][
2
]
+=
fH
[
2
];
if
(
vflag
)
{
domain
->
closest_image
(
x
[
j
],
x
[
jH1
],
xH1
);
domain
->
closest_image
(
x
[
j
],
x
[
jH2
],
xH2
);
v
[
0
]
+=
x
[
j
][
0
]
*
fO
[
0
]
+
xH1
[
0
]
*
fH
[
0
]
+
xH2
[
0
]
*
fH
[
0
];
v
[
1
]
+=
x
[
j
][
1
]
*
fO
[
1
]
+
xH1
[
1
]
*
fH
[
1
]
+
xH2
[
1
]
*
fH
[
1
];
v
[
2
]
+=
x
[
j
][
2
]
*
fO
[
2
]
+
xH1
[
2
]
*
fH
[
2
]
+
xH2
[
2
]
*
fH
[
2
];
v
[
3
]
+=
x
[
j
][
0
]
*
fO
[
1
]
+
xH1
[
0
]
*
fH
[
1
]
+
xH2
[
0
]
*
fH
[
1
];
v
[
4
]
+=
x
[
j
][
0
]
*
fO
[
2
]
+
xH1
[
0
]
*
fH
[
2
]
+
xH2
[
0
]
*
fH
[
2
];
v
[
5
]
+=
x
[
j
][
1
]
*
fO
[
2
]
+
xH1
[
1
]
*
fH
[
2
]
+
xH2
[
1
]
*
fH
[
2
];
}
vlist
[
n
++
]
=
j
;
vlist
[
n
++
]
=
jH1
;
vlist
[
n
++
]
=
jH2
;
}
if
(
eflag
)
{
ecoul
=
qqrd2e
*
qtmp
*
q
[
j
]
*
sqrt
(
r2inv
);
ecoul
*=
factor_coul
;
}
else
ecoul
=
0.0
;
if
(
evflag
)
ev_tally_tip4p
(
key
,
vlist
,
v
,
ecoul
,
alpha
);
}
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairLJCutTIP4PCut
::
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
,
n
+
1
,
n
+
1
,
"pair:cut_lj"
);
memory
->
create
(
cut_ljsq
,
n
+
1
,
n
+
1
,
"pair:cut_ljsq"
);
memory
->
create
(
epsilon
,
n
+
1
,
n
+
1
,
"pair:epsilon"
);
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"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairLJCutTIP4PCut
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
6
||
narg
>
7
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
typeO
=
force
->
inumeric
(
FLERR
,
arg
[
0
]);
typeH
=
force
->
inumeric
(
FLERR
,
arg
[
1
]);
typeB
=
force
->
inumeric
(
FLERR
,
arg
[
2
]);
typeA
=
force
->
inumeric
(
FLERR
,
arg
[
3
]);
qdist
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
cut_lj_global
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
if
(
narg
==
6
)
cut_coul
=
cut_lj_global
;
else
cut_coul
=
force
->
numeric
(
FLERR
,
arg
[
6
]);
cut_coulsq
=
cut_coul
*
cut_coul
;
cut_coulsqplus
=
(
cut_coul
+
2.0
*
qdist
)
*
(
cut_coul
+
2.0
*
qdist
);
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
PairLJCutTIP4PCut
::
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
(
FLERR
,
arg
[
2
]);
double
sigma_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
cut_lj_one
=
cut_lj_global
;
if
(
narg
==
5
)
cut_lj_one
=
force
->
numeric
(
FLERR
,
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
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairLJCutTIP4PCut
::
init_style
()
{
if
(
atom
->
tag_enable
==
0
)
error
->
all
(
FLERR
,
"Pair style lj/cut/tip4p/cut requires atom IDs"
);
if
(
!
force
->
newton_pair
)
error
->
all
(
FLERR
,
"Pair style lj/cut/tip4p/cut requires newton pair on"
);
if
(
!
atom
->
q_flag
)
error
->
all
(
FLERR
,
"Pair style lj/cut/tip4p/cut requires atom attribute q"
);
if
(
force
->
bond
==
NULL
)
error
->
all
(
FLERR
,
"Must use a bond style with TIP4P potential"
);
if
(
force
->
angle
==
NULL
)
error
->
all
(
FLERR
,
"Must use an angle style with TIP4P potential"
);
neighbor
->
request
(
this
,
instance_me
);
// set alpha parameter
double
theta
=
force
->
angle
->
equilibrium_angle
(
typeA
);
double
blen
=
force
->
bond
->
equilibrium_distance
(
typeB
);
alpha
=
qdist
/
(
cos
(
0.5
*
theta
)
*
blen
);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairLJCutTIP4PCut
::
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
]);
}
// include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P
double
cut
=
MAX
(
cut_lj
[
i
][
j
],
cut_coul
+
2.0
*
qdist
);
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
];
// 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
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
*
MY_PI
*
all
[
0
]
*
all
[
1
]
*
epsilon
[
i
][
j
]
*
sig6
*
(
sig6
-
3.0
*
rc6
)
/
(
9.0
*
rc9
);
ptail_ij
=
16.0
*
MY_PI
*
all
[
0
]
*
all
[
1
]
*
epsilon
[
i
][
j
]
*
sig6
*
(
2.0
*
sig6
-
3.0
*
rc6
)
/
(
9.0
*
rc9
);
}
// check that LJ epsilon = 0.0 for water H
// set LJ cutoff to 0.0 for any interaction involving water H
// so LJ term isn't calculated in compute()
if
((
i
==
typeH
&&
epsilon
[
i
][
i
]
!=
0.0
)
||
(
j
==
typeH
&&
epsilon
[
j
][
j
]
!=
0.0
))
error
->
all
(
FLERR
,
"Water H epsilon must be 0.0 for "
"pair style lj/cut/tip4p/cut"
);
if
(
i
==
typeH
||
j
==
typeH
)
cut_ljsq
[
j
][
i
]
=
cut_ljsq
[
i
][
j
]
=
0.0
;
return
cut
;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJCutTIP4PCut
::
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
PairLJCutTIP4PCut
::
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
PairLJCutTIP4PCut
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
typeO
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
typeH
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
typeB
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
typeA
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
qdist
,
sizeof
(
double
),
1
,
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
(
&
tail_flag
,
sizeof
(
int
),
1
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJCutTIP4PCut
::
read_restart_settings
(
FILE
*
fp
)
{
if
(
comm
->
me
==
0
)
{
fread
(
&
typeO
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
typeH
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
typeB
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
typeA
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
qdist
,
sizeof
(
double
),
1
,
fp
);
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
(
&
tail_flag
,
sizeof
(
int
),
1
,
fp
);
}
MPI_Bcast
(
&
typeO
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
typeH
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
typeB
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
typeA
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
qdist
,
1
,
MPI_DOUBLE
,
0
,
world
);
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
(
&
tail_flag
,
1
,
MPI_INT
,
0
,
world
);
cut_coulsq
=
cut_coul
*
cut_coul
;
cut_coulsqplus
=
(
cut_coul
+
2.0
*
qdist
)
*
(
cut_coul
+
2.0
*
qdist
);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void
PairLJCutTIP4PCut
::
write_data
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
fprintf
(
fp
,
"%d %g %g
\n
"
,
i
,
epsilon
[
i
][
i
],
sigma
[
i
][
i
]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void
PairLJCutTIP4PCut
::
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
\n
"
,
i
,
j
,
epsilon
[
i
][
j
],
sigma
[
i
][
j
],
cut_lj
[
i
][
j
]);
}
/* ----------------------------------------------------------------------
compute position xM of fictitious charge site for O atom and 2 H atoms
return it as xM
------------------------------------------------------------------------- */
void
PairLJCutTIP4PCut
::
compute_newsite
(
double
*
xO
,
double
*
xH1
,
double
*
xH2
,
double
*
xM
)
{
double
delx1
=
xH1
[
0
]
-
xO
[
0
];
double
dely1
=
xH1
[
1
]
-
xO
[
1
];
double
delz1
=
xH1
[
2
]
-
xO
[
2
];
domain
->
minimum_image
(
delx1
,
dely1
,
delz1
);
double
delx2
=
xH2
[
0
]
-
xO
[
0
];
double
dely2
=
xH2
[
1
]
-
xO
[
1
];
double
delz2
=
xH2
[
2
]
-
xO
[
2
];
domain
->
minimum_image
(
delx2
,
dely2
,
delz2
);
xM
[
0
]
=
xO
[
0
]
+
alpha
*
0.5
*
(
delx1
+
delx2
);
xM
[
1
]
=
xO
[
1
]
+
alpha
*
0.5
*
(
dely1
+
dely2
);
xM
[
2
]
=
xO
[
2
]
+
alpha
*
0.5
*
(
delz1
+
delz2
);
}
/* ---------------------------------------------------------------------- */
void
*
PairLJCutTIP4PCut
::
extract
(
const
char
*
str
,
int
&
dim
)
{
dim
=
0
;
if
(
strcmp
(
str
,
"cut_coul"
)
==
0
)
return
(
void
*
)
&
cut_coul
;
dim
=
2
;
if
(
strcmp
(
str
,
"epsilon"
)
==
0
)
return
(
void
*
)
epsilon
;
if
(
strcmp
(
str
,
"sigma"
)
==
0
)
return
(
void
*
)
sigma
;
return
NULL
;
}
/* ----------------------------------------------------------------------
memory usage of hneigh
------------------------------------------------------------------------- */
double
PairLJCutTIP4PCut
::
memory_usage
()
{
double
bytes
=
maxeatom
*
sizeof
(
double
);
bytes
+=
maxvatom
*
6
*
sizeof
(
double
);
bytes
+=
2
*
nmax
*
sizeof
(
double
);
return
bytes
;
}
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