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pair_lj_long_tip4p_long.cpp
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rLAMMPS lammps
pair_lj_long_tip4p_long.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 authors: Amalie Frischknecht and Ahmed Ismail (SNL)
Rolf Isele-Holder (Aachen University)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_lj_long_tip4p_long.h"
#include "angle.h"
#include "atom.h"
#include "bond.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "kspace.h"
#include "update.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
/* ---------------------------------------------------------------------- */
PairLJLongTIP4PLong
::
PairLJLongTIP4PLong
(
LAMMPS
*
lmp
)
:
PairLJLongCoulLong
(
lmp
)
{
dispersionflag
=
tip4pflag
=
1
;
single_enable
=
0
;
respa_enable
=
1
;
nmax
=
0
;
hneigh
=
NULL
;
newsite
=
NULL
;
// TIP4P cannot compute virial as F dot r
// due to find_M() finding bonded H atoms which are not near O atom
no_virial_fdotr_compute
=
1
;
}
/* ---------------------------------------------------------------------- */
PairLJLongTIP4PLong
::~
PairLJLongTIP4PLong
()
{
memory
->
destroy
(
hneigh
);
memory
->
destroy
(
newsite
);
}
/* ---------------------------------------------------------------------- */
void
PairLJLongTIP4PLong
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
,
itable
;
int
n
,
vlist
[
6
];
int
key
;
int
iH1
,
iH2
,
jH1
,
jH2
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
;
double
fraction
,
table
;
double
r
,
r2inv
,
forcecoul
,
forcelj
,
cforce
;
double
factor_coul
;
double
grij
,
expm2
,
prefactor
,
t
,
erfc
;
double
fO
[
3
],
fH
[
3
],
fd
[
3
],
v
[
6
],
xH1
[
3
],
xH2
[
3
];
// f1[3];
double
*
x1
,
*
x2
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
rsq
;
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_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
int
newton_pair
=
force
->
newton_pair
;
double
qqrd2e
=
force
->
qqrd2e
;
double
cut_coulsqplus
=
(
cut_coul
+
2.0
*
qdist
)
*
(
cut_coul
+
2.0
*
qdist
);
int
order1
=
ewald_order
&
(
1
<<
1
),
order6
=
ewald_order
&
(
1
<<
6
);
int
ni
;
double
*
lj1i
,
*
lj2i
,
*
lj3i
,
*
lj4i
,
*
offseti
;
double
g2
=
g_ewald_6
*
g_ewald_6
,
g6
=
g2
*
g2
*
g2
,
g8
=
g6
*
g2
;
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
];
offseti
=
offset
[
itype
];
lj1i
=
lj1
[
itype
];
lj2i
=
lj2
[
itype
];
lj3i
=
lj3
[
itype
];
lj4i
=
lj4
[
itype
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
ni
=
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_ljsq
[
itype
][
jtype
])
{
// lj
r2inv
=
1.0
/
rsq
;
if
(
order6
)
{
// long-range lj
if
(
!
ndisptablebits
||
rsq
<=
tabinnerdispsq
)
{
register
double
rn
=
r2inv
*
r2inv
*
r2inv
;
register
double
x2
=
g2
*
rsq
,
a2
=
1.0
/
x2
;
x2
=
a2
*
exp
(
-
x2
)
*
lj4i
[
jtype
];
if
(
ni
==
0
)
{
forcelj
=
(
rn
*=
rn
)
*
lj1i
[
jtype
]
-
g8
*
(((
6.0
*
a2
+
6.0
)
*
a2
+
3.0
)
*
a2
+
1.0
)
*
x2
*
rsq
;
if
(
eflag
)
evdwl
=
rn
*
lj3i
[
jtype
]
-
g6
*
((
a2
+
1.0
)
*
a2
+
0.5
)
*
x2
;
}
else
{
// special case
register
double
f
=
special_lj
[
ni
],
t
=
rn
*
(
1.0
-
f
);
forcelj
=
f
*
(
rn
*=
rn
)
*
lj1i
[
jtype
]
-
g8
*
(((
6.0
*
a2
+
6.0
)
*
a2
+
3.0
)
*
a2
+
1.0
)
*
x2
*
rsq
+
t
*
lj2i
[
jtype
];
if
(
eflag
)
evdwl
=
f
*
rn
*
lj3i
[
jtype
]
-
g6
*
((
a2
+
1.0
)
*
a2
+
0.5
)
*
x2
+
t
*
lj4i
[
jtype
];
}
}
else
{
// table real space
register
union_int_float_t
disp_t
;
disp_t
.
f
=
rsq
;
register
const
int
disp_k
=
(
disp_t
.
i
&
ndispmask
)
>>
ndispshiftbits
;
register
double
f_disp
=
(
rsq
-
rdisptable
[
disp_k
])
*
drdisptable
[
disp_k
];
register
double
rn
=
r2inv
*
r2inv
*
r2inv
;
if
(
ni
==
0
)
{
forcelj
=
(
rn
*=
rn
)
*
lj1i
[
jtype
]
-
(
fdisptable
[
disp_k
]
+
f_disp
*
dfdisptable
[
disp_k
])
*
lj4i
[
jtype
];
if
(
eflag
)
evdwl
=
rn
*
lj3i
[
jtype
]
-
(
edisptable
[
disp_k
]
+
f_disp
*
dedisptable
[
disp_k
])
*
lj4i
[
jtype
];
}
else
{
// special case
register
double
f
=
special_lj
[
ni
],
t
=
rn
*
(
1.0
-
f
);
forcelj
=
f
*
(
rn
*=
rn
)
*
lj1i
[
jtype
]
-
(
fdisptable
[
disp_k
]
+
f_disp
*
dfdisptable
[
disp_k
])
*
lj4i
[
jtype
]
+
t
*
lj2i
[
jtype
];
if
(
eflag
)
evdwl
=
f
*
rn
*
lj3i
[
jtype
]
-
(
edisptable
[
disp_k
]
+
f_disp
*
dedisptable
[
disp_k
])
*
lj4i
[
jtype
]
+
t
*
lj4i
[
jtype
];
}
}
}
else
{
// cut lj
register
double
rn
=
r2inv
*
r2inv
*
r2inv
;
if
(
ni
==
0
)
{
forcelj
=
rn
*
(
rn
*
lj1i
[
jtype
]
-
lj2i
[
jtype
]);
if
(
eflag
)
evdwl
=
rn
*
(
rn
*
lj3i
[
jtype
]
-
lj4i
[
jtype
])
-
offseti
[
jtype
];
}
else
{
// special case
register
double
f
=
special_lj
[
ni
];
forcelj
=
f
*
rn
*
(
rn
*
lj1i
[
jtype
]
-
lj2i
[
jtype
]);
if
(
eflag
)
evdwl
=
f
*
(
rn
*
(
rn
*
lj3i
[
jtype
]
-
lj4i
[
jtype
])
-
offseti
[
jtype
]);
}
}
forcelj
*=
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
(
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)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if
(
rsq
<
cut_coulsqplus
)
{
if
(
itype
==
typeO
||
jtype
==
typeO
)
{
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
;
}
// test current rsq against cutoff and compute Coulombic force
if
(
rsq
<
cut_coulsq
&&
order1
)
{
r2inv
=
1.0
/
rsq
;
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
r
=
sqrt
(
rsq
);
grij
=
g_ewald
*
r
;
expm2
=
exp
(
-
grij
*
grij
);
t
=
1.0
/
(
1.0
+
EWALD_P
*
grij
);
erfc
=
t
*
(
A1
+
t
*
(
A2
+
t
*
(
A3
+
t
*
(
A4
+
t
*
A5
))))
*
expm2
;
prefactor
=
qqrd2e
*
qtmp
*
q
[
j
]
/
r
;
forcecoul
=
prefactor
*
(
erfc
+
EWALD_F
*
grij
*
expm2
);
if
(
factor_coul
<
1.0
)
{
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
}
else
{
union_int_float_t
rsq_lookup
;
rsq_lookup
.
f
=
rsq
;
itable
=
rsq_lookup
.
i
&
ncoulmask
;
itable
>>=
ncoulshiftbits
;
fraction
=
(
rsq_lookup
.
f
-
rtable
[
itable
])
*
drtable
[
itable
];
table
=
ftable
[
itable
]
+
fraction
*
dftable
[
itable
];
forcecoul
=
qtmp
*
q
[
j
]
*
table
;
if
(
factor_coul
<
1.0
)
{
table
=
ctable
[
itable
]
+
fraction
*
dctable
[
itable
];
prefactor
=
qtmp
*
q
[
j
]
*
table
;
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
}
cforce
=
forcecoul
*
r2inv
;
//if (evflag) ev_tally(i,j,nlocal,newton_pair,
// evdwl,0.0,cforce,delx,dely,delz);
// 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
+=
1
;
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
[
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
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
ecoul
=
prefactor
*
erfc
;
else
{
table
=
etable
[
itable
]
+
fraction
*
detable
[
itable
];
ecoul
=
qtmp
*
q
[
j
]
*
table
;
}
if
(
factor_coul
<
1.0
)
ecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
ecoul
=
0.0
;
if
(
evflag
)
ev_tally_tip4p
(
key
,
vlist
,
v
,
ecoul
,
alpha
);
}
}
}
}
}
/* --------------------------------------------------------------------- */
void
PairLJLongTIP4PLong
::
compute_inner
()
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
int
iH1
,
iH2
,
jH1
,
jH2
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
;
double
r2inv
,
forcecoul
,
forcelj
,
cforce
;
double
fO
[
3
],
fH
[
3
],
fd
[
3
];
// f1[3];
double
*
x1
,
*
x2
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
rsq
,
qri
;
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
;
// 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
;
// atom->nmax > nmax will occur during setup
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_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
double
qqrd2e
=
force
->
qqrd2e
;
double
cut_coulsqplus
=
(
cut_coul
+
2.0
*
qdist
)
*
(
cut_coul
+
2.0
*
qdist
);
int
order1
=
ewald_order
&
(
1
<<
1
);
int
ni
;
double
*
lj1i
,
*
lj2i
;
inum
=
listinner
->
inum
;
ilist
=
listinner
->
ilist
;
numneigh
=
listinner
->
numneigh
;
firstneigh
=
listinner
->
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
&&
order1
)
{
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
];
lj1i
=
lj1
[
itype
];
lj2i
=
lj2
[
itype
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
ni
=
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_ljsq
[
itype
][
jtype
]
&&
rsq
<
cut_out_off_sq
)
{
// lj
r2inv
=
1.0
/
rsq
;
register
double
rn
=
r2inv
*
r2inv
*
r2inv
;
if
(
ni
==
0
)
forcelj
=
rn
*
(
rn
*
lj1i
[
jtype
]
-
lj2i
[
jtype
]);
else
{
// special case
register
double
f
=
special_lj
[
ni
];
forcelj
=
f
*
rn
*
(
rn
*
lj1i
[
jtype
]
-
lj2i
[
jtype
]);
}
if
(
rsq
>
cut_out_on_sq
)
{
// switching
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_out_on
)
/
cut_out_diff
;
forcelj
*=
1.0
+
rsw
*
rsw
*
(
2.0
*
rsw
-
3.0
);
}
forcelj
*=
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
;
}
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if
(
rsq
<
cut_coulsqplus
&&
order1
)
{
if
(
itype
==
typeO
||
jtype
==
typeO
)
{
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
;
}
// test current rsq against cutoff and compute Coulombic force
if
(
rsq
<
cut_coulsq
&&
rsq
<
cut_out_off_sq
)
{
r2inv
=
1.0
/
rsq
;
qri
=
qqrd2e
*
qtmp
;
if
(
ni
==
0
)
forcecoul
=
qri
*
q
[
j
]
*
sqrt
(
r2inv
);
else
{
forcecoul
=
qri
*
q
[
j
]
*
sqrt
(
r2inv
)
*
special_coul
[
ni
];
}
if
(
rsq
>
cut_out_on_sq
)
{
// switching
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_out_on
)
/
cut_out_diff
;
forcecoul
*=
1.0
+
rsw
*
rsw
*
(
2.0
*
rsw
-
3.0
);
}
cforce
=
forcecoul
*
r2inv
;
//if (evflag) ev_tally(i,j,nlocal,newton_pair,
// evdwl,0.0,cforce,delx,dely,delz);
// 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
if
(
itype
!=
typeO
)
{
f
[
i
][
0
]
+=
delx
*
cforce
;
f
[
i
][
1
]
+=
dely
*
cforce
;
f
[
i
][
2
]
+=
delz
*
cforce
;
}
else
{
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
[
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
(
jtype
!=
typeO
)
{
f
[
j
][
0
]
-=
delx
*
cforce
;
f
[
j
][
1
]
-=
dely
*
cforce
;
f
[
j
][
2
]
-=
delz
*
cforce
;
}
else
{
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
];
}
}
}
}
}
}
/* --------------------------------------------------------------------- */
void
PairLJLongTIP4PLong
::
compute_middle
()
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
int
iH1
,
iH2
,
jH1
,
jH2
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
;
double
r2inv
,
forcecoul
,
forcelj
,
cforce
;
double
fO
[
3
],
fH
[
3
],
fd
[
3
];
double
*
x1
,
*
x2
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
rsq
,
qri
;
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
;
// reallocate hneigh & newsite if necessary
// initialize hneigh[0] to -1 on steps when reneighboring occurred
// initialize hneigh[2] to 0 every step
double
**
f
=
atom
->
f
;
double
**
x
=
atom
->
x
;
double
*
q
=
atom
->
q
;
tagint
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
double
qqrd2e
=
force
->
qqrd2e
;
double
cut_coulsqplus
=
(
cut_coul
+
2.0
*
qdist
)
*
(
cut_coul
+
2.0
*
qdist
);
int
order1
=
ewald_order
&
(
1
<<
1
);
int
ni
;
double
*
lj1i
,
*
lj2i
;
inum
=
listmiddle
->
inum
;
ilist
=
listmiddle
->
ilist
;
numneigh
=
listmiddle
->
numneigh
;
firstneigh
=
listmiddle
->
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
&&
order1
)
{
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
];
lj1i
=
lj1
[
itype
];
lj2i
=
lj2
[
itype
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
ni
=
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_ljsq
[
itype
][
jtype
]
&&
rsq
>=
cut_in_off_sq
&&
rsq
<=
cut_out_off_sq
)
{
// lj
r2inv
=
1.0
/
rsq
;
register
double
rn
=
r2inv
*
r2inv
*
r2inv
;
if
(
ni
==
0
)
forcelj
=
rn
*
(
rn
*
lj1i
[
jtype
]
-
lj2i
[
jtype
]);
else
{
// special case
register
double
f
=
special_lj
[
ni
];
forcelj
=
f
*
rn
*
(
rn
*
lj1i
[
jtype
]
-
lj2i
[
jtype
]);
}
if
(
rsq
<
cut_in_on_sq
)
{
// switching
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_in_off
)
/
cut_in_diff
;
forcelj
*=
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
if
(
rsq
>
cut_out_on_sq
)
{
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_out_on
)
/
cut_out_diff
;
forcelj
*=
1.0
+
rsw
*
rsw
*
(
2.0
*
rsw
-
3.0
);
}
forcelj
*=
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
;
}
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if
(
rsq
<
cut_coulsqplus
&&
order1
)
{
if
(
itype
==
typeO
||
jtype
==
typeO
)
{
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
;
}
// test current rsq against cutoff and compute Coulombic force
if
(
rsq
<
cut_coulsq
&&
rsq
>=
cut_in_off_sq
&&
rsq
<=
cut_out_off_sq
)
{
r2inv
=
1.0
/
rsq
;
qri
=
qqrd2e
*
qtmp
;
if
(
ni
==
0
)
forcecoul
=
qri
*
q
[
j
]
*
sqrt
(
r2inv
);
else
{
forcecoul
=
qri
*
q
[
j
]
*
sqrt
(
r2inv
)
*
special_coul
[
ni
];
}
if
(
rsq
<
cut_in_on_sq
)
{
// switching
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_in_off
)
/
cut_in_diff
;
forcecoul
*=
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
if
(
rsq
>
cut_out_on_sq
)
{
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_out_on
)
/
cut_out_diff
;
forcecoul
*=
1.0
+
rsw
*
rsw
*
(
2.0
*
rsw
-
3.0
);
}
cforce
=
forcecoul
*
r2inv
;
//if (evflag) ev_tally(i,j,nlocal,newton_pair,
// evdwl,0.0,cforce,delx,dely,delz);
// 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
if
(
itype
!=
typeO
)
{
f
[
i
][
0
]
+=
delx
*
cforce
;
f
[
i
][
1
]
+=
dely
*
cforce
;
f
[
i
][
2
]
+=
delz
*
cforce
;
}
else
{
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
[
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
(
jtype
!=
typeO
)
{
f
[
j
][
0
]
-=
delx
*
cforce
;
f
[
j
][
1
]
-=
dely
*
cforce
;
f
[
j
][
2
]
-=
delz
*
cforce
;
}
else
{
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
];
}
}
}
}
}
}
/* --------------------------------------------------------------------- */
void
PairLJLongTIP4PLong
::
compute_outer
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
int
n
,
vlist
[
6
];
int
key
;
int
iH1
,
iH2
,
jH1
,
jH2
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
;
double
r2inv
,
forcecoul
,
forcelj
,
cforce
,
respa_coul
,
respa_lj
,
frespa
,
fvirial
;
double
fO
[
3
],
fH
[
3
],
fd
[
3
],
v
[
6
],
xH1
[
3
],
xH2
[
3
];
// f1[3];
double
*
x1
,
*
x2
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
rsq
,
qri
;
int
respa_flag
;
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_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
int
newton_pair
=
force
->
newton_pair
;
double
qqrd2e
=
force
->
qqrd2e
;
double
cut_coulsqplus
=
(
cut_coul
+
2.0
*
qdist
)
*
(
cut_coul
+
2.0
*
qdist
);
int
order1
=
ewald_order
&
(
1
<<
1
),
order6
=
ewald_order
&
(
1
<<
6
);
int
ni
;
double
*
lj1i
,
*
lj2i
,
*
lj3i
,
*
lj4i
,
*
offseti
;
double
g2
=
g_ewald_6
*
g_ewald_6
,
g6
=
g2
*
g2
*
g2
,
g8
=
g6
*
g2
;
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
;
inum
=
listouter
->
inum
;
ilist
=
listouter
->
ilist
;
numneigh
=
listouter
->
numneigh
;
firstneigh
=
listouter
->
firstneigh
;
// loop over neighbors of my atoms
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
qtmp
=
q
[
i
];
qri
=
qtmp
*
qqrd2e
;
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
];
offseti
=
offset
[
itype
];
lj1i
=
lj1
[
itype
];
lj2i
=
lj2
[
itype
];
lj3i
=
lj3
[
itype
];
lj4i
=
lj4
[
itype
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
ni
=
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
];
respa_coul
=
0
;
respa_lj
=
0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
// lj
frespa
=
1.0
;
// check whether and how to compute respa corrections
respa_flag
=
rsq
<
cut_in_on_sq
?
1
:
0
;
if
(
respa_flag
&&
(
rsq
>
cut_in_off_sq
))
{
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_in_off
)
/
cut_in_diff
;
frespa
=
1
-
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
r2inv
=
1.0
/
rsq
;
register
double
rn
=
r2inv
*
r2inv
*
r2inv
;
if
(
respa_flag
)
respa_lj
=
ni
==
0
?
// correct for respa
frespa
*
rn
*
(
rn
*
lj1i
[
jtype
]
-
lj2i
[
jtype
])
:
frespa
*
rn
*
(
rn
*
lj1i
[
jtype
]
-
lj2i
[
jtype
])
*
special_lj
[
ni
];
if
(
order6
)
{
// long-range form
if
(
!
ndisptablebits
||
rsq
<=
tabinnerdispsq
)
{
register
double
x2
=
g2
*
rsq
,
a2
=
1.0
/
x2
;
x2
=
a2
*
exp
(
-
x2
)
*
lj4i
[
jtype
];
if
(
ni
==
0
)
{
forcelj
=
(
rn
*=
rn
)
*
lj1i
[
jtype
]
-
g8
*
(((
6.0
*
a2
+
6.0
)
*
a2
+
3.0
)
*
a2
+
1.0
)
*
x2
*
rsq
-
respa_lj
;
if
(
eflag
)
evdwl
=
rn
*
lj3i
[
jtype
]
-
g6
*
((
a2
+
1.0
)
*
a2
+
0.5
)
*
x2
;
}
else
{
// correct for special
register
double
f
=
special_lj
[
ni
],
t
=
rn
*
(
1.0
-
f
);
forcelj
=
f
*
(
rn
*=
rn
)
*
lj1i
[
jtype
]
-
g8
*
(((
6.0
*
a2
+
6.0
)
*
a2
+
3.0
)
*
a2
+
1.0
)
*
x2
*
rsq
+
t
*
lj2i
[
jtype
]
-
respa_lj
;
if
(
eflag
)
evdwl
=
f
*
rn
*
lj3i
[
jtype
]
-
g6
*
((
a2
+
1.0
)
*
a2
+
0.5
)
*
x2
+
t
*
lj4i
[
jtype
];
}
}
else
{
// table real space
register
union_int_float_t
disp_t
;
disp_t
.
f
=
rsq
;
register
const
int
disp_k
=
(
disp_t
.
i
&
ndispmask
)
>>
ndispshiftbits
;
register
double
f_disp
=
(
rsq
-
rdisptable
[
disp_k
])
*
drdisptable
[
disp_k
];
if
(
ni
==
0
)
{
forcelj
=
(
rn
*=
rn
)
*
lj1i
[
jtype
]
-
(
fdisptable
[
disp_k
]
+
f_disp
*
dfdisptable
[
disp_k
])
*
lj4i
[
jtype
]
-
respa_lj
;
if
(
eflag
)
evdwl
=
rn
*
lj3i
[
jtype
]
-
(
edisptable
[
disp_k
]
+
f_disp
*
dedisptable
[
disp_k
])
*
lj4i
[
jtype
];
}
else
{
// special case
register
double
f
=
special_lj
[
ni
],
t
=
rn
*
(
1.0
-
f
);
forcelj
=
f
*
(
rn
*=
rn
)
*
lj1i
[
jtype
]
-
(
fdisptable
[
disp_k
]
+
f_disp
*
dfdisptable
[
disp_k
])
*
lj4i
[
jtype
]
+
t
*
lj2i
[
jtype
]
-
respa_lj
;
if
(
eflag
)
evdwl
=
f
*
rn
*
lj3i
[
jtype
]
-
(
edisptable
[
disp_k
]
+
f_disp
*
dedisptable
[
disp_k
])
*
lj4i
[
jtype
]
+
t
*
lj4i
[
jtype
];
}
}
}
else
{
// cut form
if
(
ni
==
0
)
{
forcelj
=
rn
*
(
rn
*
lj1i
[
jtype
]
-
lj2i
[
jtype
])
-
respa_lj
;
if
(
eflag
)
evdwl
=
rn
*
(
rn
*
lj3i
[
jtype
]
-
lj4i
[
jtype
])
-
offseti
[
jtype
];
}
else
{
// correct for special
register
double
f
=
special_lj
[
ni
];
forcelj
=
f
*
rn
*
(
rn
*
lj1i
[
jtype
]
-
lj2i
[
jtype
])
-
respa_lj
;
if
(
eflag
)
evdwl
=
f
*
(
rn
*
(
rn
*
lj3i
[
jtype
]
-
lj4i
[
jtype
])
-
offseti
[
jtype
]);
}
}
forcelj
*=
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
(
evflag
)
{
fvirial
=
forcelj
+
respa_lj
*
r2inv
;
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
0.0
,
fvirial
,
delx
,
dely
,
delz
);
}
}
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if
(
rsq
<
cut_coulsqplus
)
{
if
(
itype
==
typeO
||
jtype
==
typeO
)
{
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
;
}
// test current rsq against cutoff and compute Coulombic force
if
((
rsq
<
cut_coulsq
)
&&
order1
)
{
frespa
=
1.0
;
// check whether and how to compute respa corrections
respa_flag
=
rsq
<
cut_in_on_sq
?
1
:
0
;
if
(
respa_flag
&&
(
rsq
>
cut_in_off_sq
))
{
register
double
rsw
=
(
sqrt
(
rsq
)
-
cut_in_off
)
/
cut_in_diff
;
frespa
=
1
-
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
r2inv
=
1.0
/
rsq
;
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
);
forcecoul
=
(
t
*=
((((
t
*
A5
+
A4
)
*
t
+
A3
)
*
t
+
A2
)
*
t
+
A1
)
*
s
/
x
)
+
EWALD_F
*
s
-
respa_coul
;
if
(
eflag
)
ecoul
=
t
;
}
else
{
// correct for special
r
=
s
*
(
1.0
-
special_coul
[
ni
])
/
r
;
s
*=
g_ewald
*
exp
(
-
x
*
x
);
forcecoul
=
(
t
*=
((((
t
*
A5
+
A4
)
*
t
+
A3
)
*
t
+
A2
)
*
t
+
A1
)
*
s
/
x
)
+
EWALD_F
*
s
-
r
-
respa_coul
;
if
(
eflag
)
ecoul
=
t
-
r
;
}
}
// table real space
else
{
if
(
respa_flag
)
{
register
double
r
=
sqrt
(
rsq
),
s
=
qri
*
q
[
j
];
respa_coul
=
ni
==
0
?
frespa
*
s
/
r
:
frespa
*
s
/
r
*
special_coul
[
ni
];
}
register
union_int_float_t
t
;
t
.
f
=
rsq
;
register
const
int
k
=
(
t
.
i
&
ncoulmask
)
>>
ncoulshiftbits
;
register
double
f
=
(
t
.
f
-
rtable
[
k
])
*
drtable
[
k
],
qiqj
=
qtmp
*
q
[
j
];
if
(
ni
==
0
)
{
forcecoul
=
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
]);
forcecoul
=
qiqj
*
(
ftable
[
k
]
+
f
*
dftable
[
k
]
-
t
.
f
);
if
(
eflag
)
{
t
.
f
=
(
1.0
-
special_coul
[
ni
])
*
(
ptable
[
k
]
+
f
*
dptable
[
k
]);
ecoul
=
qiqj
*
(
etable
[
k
]
+
f
*
detable
[
k
]
-
t
.
f
);
}
}
}
cforce
=
forcecoul
*
r2inv
;
fvirial
=
(
forcecoul
+
respa_coul
)
*
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
*
fvirial
;
v
[
1
]
=
x
[
i
][
1
]
*
dely
*
fvirial
;
v
[
2
]
=
x
[
i
][
2
]
*
delz
*
fvirial
;
v
[
3
]
=
x
[
i
][
0
]
*
dely
*
fvirial
;
v
[
4
]
=
x
[
i
][
0
]
*
delz
*
fvirial
;
v
[
5
]
=
x
[
i
][
1
]
*
delz
*
fvirial
;
}
vlist
[
n
++
]
=
i
;
}
else
{
key
+=
1
;
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
[
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
)
{
fd
[
0
]
=
delx
*
fvirial
;
fd
[
1
]
=
dely
*
fvirial
;
fd
[
2
]
=
delz
*
fvirial
;
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
];
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
*
fvirial
;
v
[
1
]
-=
x
[
j
][
1
]
*
dely
*
fvirial
;
v
[
2
]
-=
x
[
j
][
2
]
*
delz
*
fvirial
;
v
[
3
]
-=
x
[
j
][
0
]
*
dely
*
fvirial
;
v
[
4
]
-=
x
[
j
][
0
]
*
delz
*
fvirial
;
v
[
5
]
-=
x
[
j
][
1
]
*
delz
*
fvirial
;
}
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
)
{
fd
[
0
]
=
-
delx
*
fvirial
;
fd
[
1
]
=
-
dely
*
fvirial
;
fd
[
2
]
=
-
delz
*
fvirial
;
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
];
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
(
evflag
)
ev_tally_tip4p
(
key
,
vlist
,
v
,
ecoul
,
alpha
);
}
}
}
}
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairLJLongTIP4PLong
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
8
||
narg
>
9
)
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
,
"Mixing forced for lj coefficients"
);
if
(
!
comm
->
me
&&
ewald_order
==
((
1
<<
1
)
|
(
1
<<
6
)))
error
->
warning
(
FLERR
,
"Using largest cutoff for pair_style lj/long/tip4p/long"
);
if
(
!
((
ewald_order
^
ewald_off
)
&
(
1
<<
1
)))
error
->
all
(
FLERR
,
"Coulomb cut not supported in pair_style lj/long/tip4p/long"
);
typeO
=
force
->
inumeric
(
FLERR
,
arg
[
1
]);
typeH
=
force
->
inumeric
(
FLERR
,
arg
[
2
]);
typeB
=
force
->
inumeric
(
FLERR
,
arg
[
3
]);
typeA
=
force
->
inumeric
(
FLERR
,
arg
[
4
]);
qdist
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
cut_lj_global
=
force
->
numeric
(
FLERR
,
arg
[
6
]);
if
(
narg
==
8
)
cut_coul
=
cut_lj_global
;
else
cut_coul
=
force
->
numeric
(
FLERR
,
arg
[
7
]);
// reset cutoffs that have been explicitly set
if
(
allocated
)
{
int
i
,
j
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
+
1
;
j
<=
atom
->
ntypes
;
j
++
)
if
(
setflag
[
i
][
j
])
cut_lj
[
i
][
j
]
=
cut_lj_global
;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairLJLongTIP4PLong
::
init_style
()
{
if
(
atom
->
tag_enable
==
0
)
error
->
all
(
FLERR
,
"Pair style lj/long/tip4p/long requires atom IDs"
);
if
(
!
force
->
newton_pair
)
error
->
all
(
FLERR
,
"Pair style lj/long/tip4p/long requires newton pair on"
);
if
(
!
atom
->
q_flag
)
error
->
all
(
FLERR
,
"Pair style lj/long/tip4p/long 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"
);
PairLJLongCoulLong
::
init_style
();
// 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
PairLJLongTIP4PLong
::
init_one
(
int
i
,
int
j
)
{
double
cut
=
PairLJLongCoulLong
::
init_one
(
i
,
j
);
// 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
))
error
->
all
(
FLERR
,
"Water H epsilon must be 0.0 for "
"pair style lj/long/tip4p/long"
);
if
(
i
==
typeH
||
j
==
typeH
)
cut_ljsq
[
j
][
i
]
=
cut_ljsq
[
i
][
j
]
=
0.0
;
return
cut
;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJLongTIP4PLong
::
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
(
&
ncoultablebits
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
tabinner
,
sizeof
(
double
),
1
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJLongTIP4PLong
::
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
(
&
ncoultablebits
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
tabinner
,
sizeof
(
double
),
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
(
&
ncoultablebits
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
tabinner
,
1
,
MPI_DOUBLE
,
0
,
world
);
}
/* ----------------------------------------------------------------------
compute position xM of fictitious charge site for O atom and 2 H atoms
return it as xM
------------------------------------------------------------------------- */
void
PairLJLongTIP4PLong
::
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
*
PairLJLongTIP4PLong
::
extract
(
const
char
*
str
,
int
&
dim
)
{
dim
=
0
;
if
(
strcmp
(
str
,
"qdist"
)
==
0
)
return
(
void
*
)
&
qdist
;
if
(
strcmp
(
str
,
"typeO"
)
==
0
)
return
(
void
*
)
&
typeO
;
if
(
strcmp
(
str
,
"typeH"
)
==
0
)
return
(
void
*
)
&
typeH
;
if
(
strcmp
(
str
,
"typeA"
)
==
0
)
return
(
void
*
)
&
typeA
;
if
(
strcmp
(
str
,
"typeB"
)
==
0
)
return
(
void
*
)
&
typeB
;
if
(
strcmp
(
str
,
"cut_coul"
)
==
0
)
return
(
void
*
)
&
cut_coul
;
const
char
*
ids
[]
=
{
"B"
,
"sigma"
,
"epsilon"
,
"ewald_order"
,
"ewald_cut"
,
"cut_coul"
,
"ewald_mix"
,
"cut_LJ"
,
NULL
};
void
*
ptrs
[]
=
{
lj4
,
sigma
,
epsilon
,
&
ewald_order
,
&
cut_coul
,
&
cut_coul
,
&
mix_flag
,
&
cut_lj_global
,
NULL
};
int
i
;
i
=
0
;
while
(
ids
[
i
]
!=
NULL
)
{
if
(
i
<=
2
)
dim
=
2
;
else
dim
=
0
;
if
(
strcmp
(
ids
[
i
],
str
)
==
0
)
return
ptrs
[
i
];
++
i
;
}
return
NULL
;
}
/* ----------------------------------------------------------------------
memory usage of hneigh
------------------------------------------------------------------------- */
double
PairLJLongTIP4PLong
::
memory_usage
()
{
double
bytes
=
maxeatom
*
sizeof
(
double
);
bytes
+=
maxvatom
*
6
*
sizeof
(
double
);
bytes
+=
2
*
nmax
*
sizeof
(
double
);
return
bytes
;
}
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