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pair_lj_cut_coul_msm.cpp
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rLAMMPS lammps
pair_lj_cut_coul_msm.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: Stan Moore (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_cut_coul_msm.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 "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
/* ---------------------------------------------------------------------- */
PairLJCutCoulMSM
::
PairLJCutCoulMSM
(
LAMMPS
*
lmp
)
:
PairLJCutCoulLong
(
lmp
)
{
ewaldflag
=
pppmflag
=
0
;
msmflag
=
1
;
}
/* ---------------------------------------------------------------------- */
void
PairLJCutCoulMSM
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
ii
,
j
,
jj
,
inum
,
jnum
,
itype
,
jtype
,
itable
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
,
fpair
;
double
fraction
,
table
;
double
r
,
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
factor_coul
,
factor_lj
;
double
egamma
,
fgamma
,
prefactor
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
rsq
;
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
<
cutsq
[
itype
][
jtype
])
{
r2inv
=
1.0
/
rsq
;
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
r
=
sqrt
(
rsq
);
prefactor
=
qqrd2e
*
qtmp
*
q
[
j
]
/
r
;
egamma
=
1.0
-
(
r
/
cut_coul
)
*
force
->
kspace
->
gamma
(
r
/
cut_coul
);
fgamma
=
1.0
+
(
rsq
/
cut_coulsq
)
*
force
->
kspace
->
dgamma
(
r
/
cut_coul
);
forcecoul
=
prefactor
*
fgamma
;
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
;
}
}
}
else
forcecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
}
else
forcelj
=
0.0
;
fpair
=
(
forcecoul
+
factor_lj
*
forcelj
)
*
r2inv
;
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
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
ecoul
=
prefactor
*
egamma
;
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
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
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
,
ecoul
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ---------------------------------------------------------------------- */
void
PairLJCutCoulMSM
::
compute_outer
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
,
itable
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
,
fpair
;
double
fraction
,
table
;
double
r
,
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
factor_coul
,
factor_lj
;
double
egamma
,
fgamma
,
prefactor
;
double
rsw
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
rsq
;
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
;
jtype
=
type
[
j
];
if
(
rsq
<
cutsq
[
itype
][
jtype
])
{
r2inv
=
1.0
/
rsq
;
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
r
=
sqrt
(
rsq
);
prefactor
=
qqrd2e
*
qtmp
*
q
[
j
]
/
r
;
egamma
=
1.0
-
(
r
/
cut_coul
)
*
force
->
kspace
->
gamma
(
r
/
cut_coul
);
fgamma
=
1.0
+
(
rsq
/
cut_coulsq
)
*
force
->
kspace
->
dgamma
(
r
/
cut_coul
);
forcecoul
=
prefactor
*
(
fgamma
-
1.0
);
if
(
rsq
>
cut_in_off_sq
)
{
if
(
rsq
<
cut_in_on_sq
)
{
rsw
=
(
r
-
cut_in_off
)
/
cut_in_diff
;
forcecoul
+=
prefactor
*
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
*
rsw
*
rsw
*
(
3.0
-
2.0
*
rsw
);
}
else
{
forcecoul
+=
prefactor
;
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
;
}
}
}
else
forcecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
]
&&
rsq
>
cut_in_off_sq
)
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
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
)
*
r2inv
;
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
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
ecoul
=
prefactor
*
egamma
;
if
(
factor_coul
<
1.0
)
ecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
{
table
=
etable
[
itable
]
+
fraction
*
detable
[
itable
];
ecoul
=
qtmp
*
q
[
j
]
*
table
;
if
(
factor_coul
<
1.0
)
{
table
=
ptable
[
itable
]
+
fraction
*
dptable
[
itable
];
prefactor
=
qtmp
*
q
[
j
]
*
table
;
ecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
}
}
else
ecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
evdwl
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
evdwl
*=
factor_lj
;
}
else
evdwl
=
0.0
;
}
if
(
vflag
)
{
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
forcecoul
=
prefactor
*
fgamma
;
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
{
table
=
vtable
[
itable
]
+
fraction
*
dvtable
[
itable
];
forcecoul
=
qtmp
*
q
[
j
]
*
table
;
if
(
factor_coul
<
1.0
)
{
table
=
ptable
[
itable
]
+
fraction
*
dptable
[
itable
];
prefactor
=
qtmp
*
q
[
j
]
*
table
;
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
}
}
else
forcecoul
=
0.0
;
if
(
rsq
<=
cut_in_off_sq
)
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
}
else
if
(
rsq
<=
cut_in_on_sq
)
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
fpair
=
(
forcecoul
+
factor_lj
*
forcelj
)
*
r2inv
;
}
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
ecoul
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
}
/* ---------------------------------------------------------------------- */
double
PairLJCutCoulMSM
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r2inv
,
r6inv
,
r
,
egamma
,
fgamma
,
prefactor
;
double
fraction
,
table
,
forcecoul
,
forcelj
,
phicoul
,
philj
;
int
itable
;
r2inv
=
1.0
/
rsq
;
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
{
r
=
sqrt
(
rsq
);
prefactor
=
force
->
qqrd2e
*
atom
->
q
[
i
]
*
atom
->
q
[
j
]
/
r
;
egamma
=
1.0
-
(
r
/
cut_coul
)
*
force
->
kspace
->
gamma
(
r
/
cut_coul
);
fgamma
=
1.0
+
(
rsq
/
cut_coulsq
)
*
force
->
kspace
->
dgamma
(
r
/
cut_coul
);
forcecoul
=
prefactor
*
fgamma
;
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
{
union_int_float_t
rsq_lookup_single
;
rsq_lookup_single
.
f
=
rsq
;
itable
=
rsq_lookup_single
.
i
&
ncoulmask
;
itable
>>=
ncoulshiftbits
;
fraction
=
(
rsq_lookup_single
.
f
-
rtable
[
itable
])
*
drtable
[
itable
];
table
=
ftable
[
itable
]
+
fraction
*
dftable
[
itable
];
forcecoul
=
atom
->
q
[
i
]
*
atom
->
q
[
j
]
*
table
;
if
(
factor_coul
<
1.0
)
{
table
=
ctable
[
itable
]
+
fraction
*
dctable
[
itable
];
prefactor
=
atom
->
q
[
i
]
*
atom
->
q
[
j
]
*
table
;
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
}
}
else
forcecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
}
else
forcelj
=
0.0
;
fforce
=
(
forcecoul
+
factor_lj
*
forcelj
)
*
r2inv
;
double
eng
=
0.0
;
if
(
rsq
<
cut_coulsq
)
{
if
(
!
ncoultablebits
||
rsq
<=
tabinnersq
)
phicoul
=
prefactor
*
egamma
;
else
{
table
=
etable
[
itable
]
+
fraction
*
detable
[
itable
];
phicoul
=
atom
->
q
[
i
]
*
atom
->
q
[
j
]
*
table
;
}
if
(
factor_coul
<
1.0
)
phicoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
eng
+=
phicoul
;
}
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
philj
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
eng
+=
factor_lj
*
philj
;
}
return
eng
;
}
/* ---------------------------------------------------------------------- */
void
*
PairLJCutCoulMSM
::
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
;
return
NULL
;
}
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