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pair_lj_cut_tip4p_long_opt.cpp
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rLAMMPS lammps
pair_lj_cut_tip4p_long_opt.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
OPT version: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include "pair_lj_cut_tip4p_long_opt.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "error.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.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
/* ---------------------------------------------------------------------- */
PairLJCutTIP4PLongOpt
::
PairLJCutTIP4PLongOpt
(
LAMMPS
*
lmp
)
:
PairLJCutTIP4PLong
(
lmp
)
{
single_enable
=
0
;
respa_enable
=
0
;
// 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
;
}
/* ---------------------------------------------------------------------- */
void
PairLJCutTIP4PLongOpt
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
const
int
nlocal
=
atom
->
nlocal
;
const
int
nall
=
nlocal
+
atom
->
nghost
;
// reallocate hneigh & newsite if necessary
// initialize hneigh[0] to -1 on steps when reneighboring occurred
// initialize hneigh[2] to 0 every step
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"
);
}
int
i
;
if
(
neighbor
->
ago
==
0
)
for
(
i
=
0
;
i
<
nall
;
i
++
)
hneigh
[
i
][
0
]
=
-
1
;
for
(
i
=
0
;
i
<
nall
;
i
++
)
hneigh
[
i
][
2
]
=
0
;
if
(
!
ncoultablebits
)
{
if
(
evflag
)
{
if
(
eflag
)
{
if
(
vflag
)
return
eval
<
1
,
1
,
1
,
1
>
();
else
return
eval
<
1
,
1
,
1
,
0
>
();
}
else
{
if
(
vflag
)
return
eval
<
1
,
1
,
0
,
1
>
();
else
return
eval
<
1
,
1
,
0
,
0
>
();
}
}
else
return
eval
<
1
,
0
,
0
,
0
>
();
}
else
{
if
(
evflag
)
{
if
(
eflag
)
{
if
(
vflag
)
return
eval
<
0
,
1
,
1
,
1
>
();
else
return
eval
<
0
,
1
,
1
,
0
>
();
}
else
{
if
(
vflag
)
return
eval
<
0
,
1
,
0
,
1
>
();
else
return
eval
<
0
,
1
,
0
,
0
>
();
}
}
else
return
eval
<
0
,
0
,
0
,
0
>
();
}
}
/* ---------------------------------------------------------------------- */
template
<
const
int
CTABLE
,
const
int
EVFLAG
,
const
int
EFLAG
,
const
int
VFLAG
>
void
PairLJCutTIP4PLongOpt
::
eval
()
{
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
;
double
fraction
,
table
;
double
r
,
rsq
,
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
cforce
;
double
factor_coul
,
factor_lj
;
double
grij
,
expm2
,
prefactor
,
t
,
erfc
;
double
v
[
6
],
xH1
[
3
],
xH2
[
3
];
double
fdx
,
fdy
,
fdz
,
fOx
,
fOy
,
fOz
,
fHx
,
fHy
,
fHz
;
const
double
*
x1
,
*
x2
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
,
itable
,
key
;
int
n
,
vlist
[
6
];
int
iH1
,
iH2
,
jH1
,
jH2
;
evdwl
=
ecoul
=
0.0
;
const
double
*
const
*
const
x
=
atom
->
x
;
double
*
const
*
const
f
=
atom
->
f
;
const
double
*
const
q
=
atom
->
q
;
const
tagint
*
const
tag
=
atom
->
tag
;
const
int
*
const
type
=
atom
->
type
;
const
int
nlocal
=
atom
->
nlocal
;
const
double
*
const
special_coul
=
force
->
special_coul
;
const
double
*
const
special_lj
=
force
->
special_lj
;
const
double
qqrd2e
=
force
->
qqrd2e
;
const
double
cut_coulsqplus
=
(
cut_coul
+
2.0
*
qdist
)
*
(
cut_coul
+
2.0
*
qdist
);
double
fxtmp
,
fytmp
,
fztmp
;
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 atom I = water O, set x1 = offset charge site
// else x1 = x of atom 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_opt
(
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_opt
(
x
[
i
],
x
[
iH1
],
x
[
iH2
],
newsite
[
i
]);
}
}
x1
=
newsite
[
i
];
}
else
x1
=
x
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
fxtmp
=
fytmp
=
fztmp
=
0.0
;
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
;
fxtmp
+=
delx
*
forcelj
;
fytmp
+=
dely
*
forcelj
;
fztmp
+=
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 = */
1
,
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_opt
(
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_opt
(
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
/
rsq
;
if
(
CTABLE
||
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 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
(
EVFLAG
)
{
n
=
0
;
key
=
0
;
}
if
(
itype
!=
typeO
)
{
fxtmp
+=
delx
*
cforce
;
fytmp
+=
dely
*
cforce
;
fztmp
+=
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
;
}
if
(
EVFLAG
)
vlist
[
n
++
]
=
i
;
}
else
{
if
(
EVFLAG
)
key
+=
1
;
fdx
=
delx
*
cforce
;
fdy
=
dely
*
cforce
;
fdz
=
delz
*
cforce
;
fOx
=
fdx
*
(
1
-
alpha
);
fOy
=
fdy
*
(
1
-
alpha
);
fOz
=
fdz
*
(
1
-
alpha
);
fHx
=
0.5
*
alpha
*
fdx
;
fHy
=
0.5
*
alpha
*
fdy
;
fHz
=
0.5
*
alpha
*
fdz
;
fxtmp
+=
fOx
;
fytmp
+=
fOy
;
fztmp
+=
fOz
;
f
[
iH1
][
0
]
+=
fHx
;
f
[
iH1
][
1
]
+=
fHy
;
f
[
iH1
][
2
]
+=
fHz
;
f
[
iH2
][
0
]
+=
fHx
;
f
[
iH2
][
1
]
+=
fHy
;
f
[
iH2
][
2
]
+=
fHz
;
if
(
VFLAG
)
{
domain
->
closest_image
(
x
[
i
],
x
[
iH1
],
xH1
);
domain
->
closest_image
(
x
[
i
],
x
[
iH2
],
xH2
);
v
[
0
]
=
x
[
i
][
0
]
*
fOx
+
xH1
[
0
]
*
fHx
+
xH2
[
0
]
*
fHx
;
v
[
1
]
=
x
[
i
][
1
]
*
fOy
+
xH1
[
1
]
*
fHy
+
xH2
[
1
]
*
fHy
;
v
[
2
]
=
x
[
i
][
2
]
*
fOz
+
xH1
[
2
]
*
fHz
+
xH2
[
2
]
*
fHz
;
v
[
3
]
=
x
[
i
][
0
]
*
fOy
+
xH1
[
0
]
*
fHy
+
xH2
[
0
]
*
fHy
;
v
[
4
]
=
x
[
i
][
0
]
*
fOz
+
xH1
[
0
]
*
fHz
+
xH2
[
0
]
*
fHz
;
v
[
5
]
=
x
[
i
][
1
]
*
fOz
+
xH1
[
1
]
*
fHz
+
xH2
[
1
]
*
fHz
;
}
if
(
EVFLAG
)
{
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
;
}
if
(
EVFLAG
)
vlist
[
n
++
]
=
j
;
}
else
{
if
(
EVFLAG
)
key
+=
2
;
fdx
=
-
delx
*
cforce
;
fdy
=
-
dely
*
cforce
;
fdz
=
-
delz
*
cforce
;
fOx
=
fdx
*
(
1
-
alpha
);
fOy
=
fdy
*
(
1
-
alpha
);
fOz
=
fdz
*
(
1
-
alpha
);
fHx
=
0.5
*
alpha
*
fdx
;
fHy
=
0.5
*
alpha
*
fdy
;
fHz
=
0.5
*
alpha
*
fdz
;
f
[
j
][
0
]
+=
fOx
;
f
[
j
][
1
]
+=
fOy
;
f
[
j
][
2
]
+=
fOz
;
f
[
jH1
][
0
]
+=
fHx
;
f
[
jH1
][
1
]
+=
fHy
;
f
[
jH1
][
2
]
+=
fHz
;
f
[
jH2
][
0
]
+=
fHx
;
f
[
jH2
][
1
]
+=
fHy
;
f
[
jH2
][
2
]
+=
fHz
;
if
(
VFLAG
)
{
domain
->
closest_image
(
x
[
j
],
x
[
jH1
],
xH1
);
domain
->
closest_image
(
x
[
j
],
x
[
jH2
],
xH2
);
v
[
0
]
+=
x
[
j
][
0
]
*
fOx
+
xH1
[
0
]
*
fHx
+
xH2
[
0
]
*
fHx
;
v
[
1
]
+=
x
[
j
][
1
]
*
fOy
+
xH1
[
1
]
*
fHy
+
xH2
[
1
]
*
fHy
;
v
[
2
]
+=
x
[
j
][
2
]
*
fOz
+
xH1
[
2
]
*
fHz
+
xH2
[
2
]
*
fHz
;
v
[
3
]
+=
x
[
j
][
0
]
*
fOy
+
xH1
[
0
]
*
fHy
+
xH2
[
0
]
*
fHy
;
v
[
4
]
+=
x
[
j
][
0
]
*
fOz
+
xH1
[
0
]
*
fHz
+
xH2
[
0
]
*
fHz
;
v
[
5
]
+=
x
[
j
][
1
]
*
fOz
+
xH1
[
1
]
*
fHz
+
xH2
[
1
]
*
fHz
;
}
if
(
EVFLAG
)
{
vlist
[
n
++
]
=
j
;
vlist
[
n
++
]
=
jH1
;
vlist
[
n
++
]
=
jH2
;
}
}
if
(
EFLAG
)
{
if
(
CTABLE
||
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
);
}
}
}
f
[
i
][
0
]
+=
fxtmp
;
f
[
i
][
1
]
+=
fytmp
;
f
[
i
][
2
]
+=
fztmp
;
}
}
/* ----------------------------------------------------------------------
compute position xM of fictitious charge site for O atom and 2 H atoms
return it as xM
------------------------------------------------------------------------- */
void
PairLJCutTIP4PLongOpt
::
compute_newsite_opt
(
const
double
*
xO
,
const
double
*
xH1
,
const
double
*
xH2
,
double
*
xM
)
const
{
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
);
const
double
prefac
=
alpha
*
0.5
;
xM
[
0
]
=
xO
[
0
]
+
prefac
*
(
delx1
+
delx2
);
xM
[
1
]
=
xO
[
1
]
+
prefac
*
(
dely1
+
dely2
);
xM
[
2
]
=
xO
[
2
]
+
prefac
*
(
delz1
+
delz2
);
}
/* ---------------------------------------------------------------------- */
double
PairLJCutTIP4PLongOpt
::
memory_usage
()
{
double
bytes
=
PairLJCutTIP4PLong
::
memory_usage
();
return
bytes
;
}
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