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pair_lj_cut_tip4p_cut_omp.cpp
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rLAMMPS lammps
pair_lj_cut_tip4p_cut_omp.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
This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "math.h"
#include "pair_lj_cut_tip4p_cut_omp.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "error.h"
#include "memory.h"
#include "neigh_list.h"
#include "suffix.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
/* ---------------------------------------------------------------------- */
PairLJCutTIP4PCutOMP
::
PairLJCutTIP4PCutOMP
(
LAMMPS
*
lmp
)
:
PairLJCutTIP4PCut
(
lmp
),
ThrOMP
(
lmp
,
THR_PAIR
)
{
suffix_flag
|=
Suffix
::
OMP
;
respa_enable
=
0
;
newsite_thr
=
NULL
;
hneigh_thr
=
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
;
}
/* ---------------------------------------------------------------------- */
PairLJCutTIP4PCutOMP
::~
PairLJCutTIP4PCutOMP
()
{
memory
->
destroy
(
hneigh_thr
);
memory
->
destroy
(
newsite_thr
);
}
/* ---------------------------------------------------------------------- */
void
PairLJCutTIP4PCutOMP
::
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_thr & newsite_thr if necessary
// initialize hneigh_thr[0] to -1 on steps when reneighboring occurred
// initialize hneigh_thr[2] to 0 every step
if
(
atom
->
nmax
>
nmax
)
{
nmax
=
atom
->
nmax
;
memory
->
destroy
(
hneigh_thr
);
memory
->
create
(
hneigh_thr
,
nmax
,
"pair:hneigh_thr"
);
memory
->
destroy
(
newsite_thr
);
memory
->
create
(
newsite_thr
,
nmax
,
"pair:newsite_thr"
);
}
int
i
;
// tag entire list as completely invalid after a neighbor
// list update, since that can change the order of atoms.
if
(
neighbor
->
ago
==
0
)
for
(
i
=
0
;
i
<
nall
;
i
++
)
hneigh_thr
[
i
].
a
=
-
1
;
// indicate that the coordinates for the M point need to
// be updated. this needs to be done in every step.
for
(
i
=
0
;
i
<
nall
;
i
++
)
hneigh_thr
[
i
].
t
=
0
;
const
int
nthreads
=
comm
->
nthreads
;
const
int
inum
=
list
->
inum
;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int
ifrom
,
ito
,
tid
;
loop_setup_thr
(
ifrom
,
ito
,
tid
,
inum
,
nthreads
);
ThrData
*
thr
=
fix
->
get_thr
(
tid
);
ev_setup_thr
(
eflag
,
vflag
,
nall
,
eatom
,
vatom
,
thr
);
if
(
evflag
)
{
if
(
eflag
)
{
if
(
vflag
)
eval
<
1
,
1
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
1
,
0
>
(
ifrom
,
ito
,
thr
);
}
else
{
if
(
vflag
)
eval
<
1
,
0
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
}
else
eval
<
0
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
reduce_thr
(
this
,
eflag
,
vflag
,
thr
);
}
// end of omp parallel region
}
/* ---------------------------------------------------------------------- */
template
<
int
EVFLAG
,
int
EFLAG
,
int
VFLAG
>
void
PairLJCutTIP4PCutOMP
::
eval
(
int
iifrom
,
int
iito
,
ThrData
*
const
thr
)
{
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
;
double
r
,
rsq
,
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
cforce
;
double
factor_coul
,
factor_lj
;
double
v
[
6
],
xH1
[
3
],
xH2
[
3
];
double
fdx
,
fdy
,
fdz
,
fOx
,
fOy
,
fOz
,
fHx
,
fHy
,
fHz
;
dbl3_t
x1
,
x2
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
int
i
,
j
,
ii
,
jj
,
jnum
,
itype
,
jtype
,
key
;
int
n
,
vlist
[
6
];
int
iH1
,
iH2
,
jH1
,
jH2
;
evdwl
=
ecoul
=
0.0
;
const
dbl3_t
*
_noalias
const
x
=
(
dbl3_t
*
)
atom
->
x
[
0
];
dbl3_t
*
_noalias
const
f
=
(
dbl3_t
*
)
thr
->
get_f
()[
0
];
const
double
*
_noalias
const
q
=
atom
->
q
;
const
int
*
_noalias
const
type
=
atom
->
type
;
const
int
nlocal
=
atom
->
nlocal
;
const
double
*
_noalias
const
special_coul
=
force
->
special_coul
;
const
double
*
_noalias
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
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// loop over neighbors of my atoms
for
(
ii
=
iifrom
;
ii
<
iito
;
++
ii
)
{
i
=
ilist
[
ii
];
qtmp
=
q
[
i
];
xtmp
=
x
[
i
].
x
;
ytmp
=
x
[
i
].
y
;
ztmp
=
x
[
i
].
z
;
itype
=
type
[
i
];
// if atom I = water O, set x1 = offset charge site
// else x1 = x of atom I
// NOTE: to make this part thread safe, we need to
// make sure that the hneigh_thr[][] entries only get
// updated, when all data is in place. worst case,
// some calculation is repeated, but since the results
// will be the same, there is no race condition.
if
(
itype
==
typeO
)
{
if
(
hneigh_thr
[
i
].
a
<
0
)
{
iH1
=
atom
->
map
(
atom
->
tag
[
i
]
+
1
);
iH2
=
atom
->
map
(
atom
->
tag
[
i
]
+
2
);
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_thr
(
x
[
i
],
x
[
iH1
],
x
[
iH2
],
newsite_thr
[
i
]);
hneigh_thr
[
i
].
t
=
1
;
hneigh_thr
[
i
].
b
=
iH2
;
hneigh_thr
[
i
].
a
=
iH1
;
}
else
{
iH1
=
hneigh_thr
[
i
].
a
;
iH2
=
hneigh_thr
[
i
].
b
;
if
(
hneigh_thr
[
i
].
t
==
0
)
{
compute_newsite_thr
(
x
[
i
],
x
[
iH1
],
x
[
iH2
],
newsite_thr
[
i
]);
hneigh_thr
[
i
].
t
=
1
;
}
}
x1
=
newsite_thr
[
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
].
x
;
dely
=
ytmp
-
x
[
j
].
y
;
delz
=
ztmp
-
x
[
j
].
z
;
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
].
x
-=
delx
*
forcelj
;
f
[
j
].
y
-=
dely
*
forcelj
;
f
[
j
].
z
-=
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_thr
(
this
,
i
,
j
,
nlocal
,
/* newton_pair = */
1
,
evdwl
,
0.0
,
forcelj
,
delx
,
dely
,
delz
,
thr
);
}
// adjust rsq and delxyz for off-site O charge(s) if necessary
// but only if they are within reach
// NOTE: to make this part thread safe, we need to
// make sure that the hneigh_thr[][] entries only get
// updated, when all data is in place. worst case,
// some calculation is repeated, but since the results
// will be the same, there is no race condition.
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_thr
[
j
].
a
<
0
)
{
jH1
=
atom
->
map
(
atom
->
tag
[
j
]
+
1
);
jH2
=
atom
->
map
(
atom
->
tag
[
j
]
+
2
);
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_thr
(
x
[
j
],
x
[
jH1
],
x
[
jH2
],
newsite_thr
[
j
]);
hneigh_thr
[
j
].
t
=
1
;
hneigh_thr
[
j
].
b
=
jH2
;
hneigh_thr
[
j
].
a
=
jH1
;
}
else
{
jH1
=
hneigh_thr
[
j
].
a
;
jH2
=
hneigh_thr
[
j
].
b
;
if
(
hneigh_thr
[
j
].
t
==
0
)
{
compute_newsite_thr
(
x
[
j
],
x
[
jH1
],
x
[
jH2
],
newsite_thr
[
j
]);
hneigh_thr
[
j
].
t
=
1
;
}
}
x2
=
newsite_thr
[
j
];
}
else
x2
=
x
[
j
];
delx
=
x1
.
x
-
x2
.
x
;
dely
=
x1
.
y
-
x2
.
y
;
delz
=
x1
.
z
-
x2
.
z
;
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
}
// Coulombic interaction based on modified rsq
if
(
rsq
<
cut_coulsq
)
{
r
=
sqrt
(
rsq
);
r2inv
=
1.0
/
rsq
;
forcecoul
=
qqrd2e
*
qtmp
*
q
[
j
]
/
r
;
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
if
(
EVFLAG
)
{
n
=
0
;
key
=
0
;
}
if
(
itype
!=
typeO
)
{
fxtmp
+=
delx
*
cforce
;
fytmp
+=
dely
*
cforce
;
fztmp
+=
delz
*
cforce
;
if
(
VFLAG
)
{
v
[
0
]
=
x
[
i
].
x
*
delx
*
cforce
;
v
[
1
]
=
x
[
i
].
y
*
dely
*
cforce
;
v
[
2
]
=
x
[
i
].
z
*
delz
*
cforce
;
v
[
3
]
=
x
[
i
].
x
*
dely
*
cforce
;
v
[
4
]
=
x
[
i
].
x
*
delz
*
cforce
;
v
[
5
]
=
x
[
i
].
y
*
delz
*
cforce
;
}
if
(
EVFLAG
)
vlist
[
n
++
]
=
i
;
}
else
{
if
(
EVFLAG
)
key
++
;
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
].
x
+=
fHx
;
f
[
iH1
].
y
+=
fHy
;
f
[
iH1
].
z
+=
fHz
;
f
[
iH2
].
x
+=
fHx
;
f
[
iH2
].
y
+=
fHy
;
f
[
iH2
].
z
+=
fHz
;
if
(
VFLAG
)
{
domain
->
closest_image
(
&
x
[
i
].
x
,
&
x
[
iH1
].
x
,
xH1
);
domain
->
closest_image
(
&
x
[
i
].
x
,
&
x
[
iH2
].
x
,
xH2
);
v
[
0
]
=
x
[
i
].
x
*
fOx
+
xH1
[
0
]
*
fHx
+
xH2
[
0
]
*
fHx
;
v
[
1
]
=
x
[
i
].
y
*
fOy
+
xH1
[
1
]
*
fHy
+
xH2
[
1
]
*
fHy
;
v
[
2
]
=
x
[
i
].
z
*
fOz
+
xH1
[
2
]
*
fHz
+
xH2
[
2
]
*
fHz
;
v
[
3
]
=
x
[
i
].
x
*
fOy
+
xH1
[
0
]
*
fHy
+
xH2
[
0
]
*
fHy
;
v
[
4
]
=
x
[
i
].
x
*
fOz
+
xH1
[
0
]
*
fHz
+
xH2
[
0
]
*
fHz
;
v
[
5
]
=
x
[
i
].
y
*
fOz
+
xH1
[
1
]
*
fHz
+
xH2
[
1
]
*
fHz
;
}
if
(
EVFLAG
)
{
vlist
[
n
++
]
=
i
;
vlist
[
n
++
]
=
iH1
;
vlist
[
n
++
]
=
iH2
;
}
}
if
(
jtype
!=
typeO
)
{
f
[
j
].
x
-=
delx
*
cforce
;
f
[
j
].
y
-=
dely
*
cforce
;
f
[
j
].
z
-=
delz
*
cforce
;
if
(
VFLAG
)
{
v
[
0
]
-=
x
[
j
].
x
*
delx
*
cforce
;
v
[
1
]
-=
x
[
j
].
y
*
dely
*
cforce
;
v
[
2
]
-=
x
[
j
].
z
*
delz
*
cforce
;
v
[
3
]
-=
x
[
j
].
x
*
dely
*
cforce
;
v
[
4
]
-=
x
[
j
].
x
*
delz
*
cforce
;
v
[
5
]
-=
x
[
j
].
y
*
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
].
x
+=
fOx
;
f
[
j
].
y
+=
fOy
;
f
[
j
].
z
+=
fOz
;
f
[
jH1
].
x
+=
fHx
;
f
[
jH1
].
y
+=
fHy
;
f
[
jH1
].
z
+=
fHz
;
f
[
jH2
].
x
+=
fHx
;
f
[
jH2
].
y
+=
fHy
;
f
[
jH2
].
z
+=
fHz
;
if
(
VFLAG
)
{
domain
->
closest_image
(
&
x
[
j
].
x
,
&
x
[
jH1
].
x
,
xH1
);
domain
->
closest_image
(
&
x
[
j
].
x
,
&
x
[
jH2
].
x
,
xH2
);
v
[
0
]
+=
x
[
j
].
x
*
fOx
+
xH1
[
0
]
*
fHx
+
xH2
[
0
]
*
fHx
;
v
[
1
]
+=
x
[
j
].
y
*
fOy
+
xH1
[
1
]
*
fHy
+
xH2
[
1
]
*
fHy
;
v
[
2
]
+=
x
[
j
].
z
*
fOz
+
xH1
[
2
]
*
fHz
+
xH2
[
2
]
*
fHz
;
v
[
3
]
+=
x
[
j
].
x
*
fOy
+
xH1
[
0
]
*
fHy
+
xH2
[
0
]
*
fHy
;
v
[
4
]
+=
x
[
j
].
x
*
fOz
+
xH1
[
0
]
*
fHz
+
xH2
[
0
]
*
fHz
;
v
[
5
]
+=
x
[
j
].
y
*
fOz
+
xH1
[
1
]
*
fHz
+
xH2
[
1
]
*
fHz
;
}
if
(
EVFLAG
)
{
vlist
[
n
++
]
=
j
;
vlist
[
n
++
]
=
jH1
;
vlist
[
n
++
]
=
jH2
;
}
}
if
(
EFLAG
)
{
ecoul
=
qqrd2e
*
qtmp
*
q
[
j
]
/
r
;
ecoul
*=
factor_coul
;
}
else
ecoul
=
0.0
;
if
(
EVFLAG
)
ev_tally_list_thr
(
this
,
key
,
vlist
,
v
,
ecoul
,
alpha
,
thr
);
}
}
}
f
[
i
].
x
+=
fxtmp
;
f
[
i
].
y
+=
fytmp
;
f
[
i
].
z
+=
fztmp
;
}
}
/* ----------------------------------------------------------------------
compute position xM of fictitious charge site for O atom and 2 H atoms
return it as xM
------------------------------------------------------------------------- */
void
PairLJCutTIP4PCutOMP
::
compute_newsite_thr
(
const
dbl3_t
&
xO
,
const
dbl3_t
&
xH1
,
const
dbl3_t
&
xH2
,
dbl3_t
&
xM
)
const
{
double
delx1
=
xH1
.
x
-
xO
.
x
;
double
dely1
=
xH1
.
y
-
xO
.
y
;
double
delz1
=
xH1
.
z
-
xO
.
z
;
domain
->
minimum_image
(
delx1
,
dely1
,
delz1
);
double
delx2
=
xH2
.
x
-
xO
.
x
;
double
dely2
=
xH2
.
y
-
xO
.
y
;
double
delz2
=
xH2
.
z
-
xO
.
z
;
domain
->
minimum_image
(
delx2
,
dely2
,
delz2
);
const
double
prefac
=
alpha
*
0.5
;
xM
.
x
=
xO
.
x
+
prefac
*
(
delx1
+
delx2
);
xM
.
y
=
xO
.
y
+
prefac
*
(
dely1
+
dely2
);
xM
.
z
=
xO
.
z
+
prefac
*
(
delz1
+
delz2
);
}
/* ---------------------------------------------------------------------- */
double
PairLJCutTIP4PCutOMP
::
memory_usage
()
{
double
bytes
=
memory_usage_thr
();
bytes
+=
PairLJCutTIP4PCut
::
memory_usage
();
return
bytes
;
}
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