Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F85077605
pair_lj_cut_coul_long_tip4p_omp.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Sep 26, 15:28
Size
14 KB
Mime Type
text/x-c++
Expires
Sat, Sep 28, 15:28 (2 d)
Engine
blob
Format
Raw Data
Handle
21126005
Attached To
rLAMMPS lammps
pair_lj_cut_coul_long_tip4p_omp.cpp
View Options
/* ----------------------------------------------------------------------
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_coul_long_tip4p_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
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongTIP4POMP
::
PairLJCutCoulLongTIP4POMP
(
LAMMPS
*
lmp
)
:
PairLJCutCoulLongTIP4P
(
lmp
),
ThrOMP
(
lmp
,
THR_PAIR
)
{
suffix_flag
|=
Suffix
::
OMP
;
respa_enable
=
0
;
// 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
;
// for caching m-shift corrected positions
maxmpos
=
0
;
h1idx
=
h2idx
=
NULL
;
mpos
=
NULL
;
}
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongTIP4POMP
::~
PairLJCutCoulLongTIP4POMP
()
{
memory
->
destroy
(
h1idx
);
memory
->
destroy
(
h2idx
);
memory
->
destroy
(
mpos
);
}
/* ---------------------------------------------------------------------- */
void
PairLJCutCoulLongTIP4POMP
::
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 per-atom arrays, if necessary
if
(
nall
>
maxmpos
)
{
maxmpos
=
nall
;
memory
->
grow
(
mpos
,
maxmpos
,
3
,
"pair:mpos"
);
memory
->
grow
(
h1idx
,
maxmpos
,
"pair:h1idx"
);
memory
->
grow
(
h2idx
,
maxmpos
,
"pair:h2idx"
);
}
// cache corrected M positions in mpos[]
const
double
*
const
*
const
x
=
atom
->
x
;
const
int
*
const
type
=
atom
->
type
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
type
[
i
]
==
typeO
)
{
find_M
(
i
,
h1idx
[
i
],
h2idx
[
i
],
mpos
[
i
]);
}
else
{
mpos
[
i
][
0
]
=
x
[
i
][
0
];
mpos
[
i
][
1
]
=
x
[
i
][
1
];
mpos
[
i
][
2
]
=
x
[
i
][
2
];
}
}
for
(
int
i
=
nlocal
;
i
<
nall
;
i
++
)
{
if
(
type
[
i
]
==
typeO
)
{
find_M_permissive
(
i
,
h1idx
[
i
],
h2idx
[
i
],
mpos
[
i
]);
}
else
{
mpos
[
i
][
0
]
=
x
[
i
][
0
];
mpos
[
i
][
1
]
=
x
[
i
][
1
];
mpos
[
i
][
2
]
=
x
[
i
][
2
];
}
}
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
(
!
ncoultablebits
)
{
if
(
evflag
)
{
if
(
eflag
)
{
if
(
vflag
)
eval
<
1
,
1
,
1
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
1
,
1
,
0
>
(
ifrom
,
ito
,
thr
);
}
else
{
if
(
vflag
)
eval
<
1
,
1
,
0
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
1
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
}
else
eval
<
1
,
0
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
else
{
if
(
evflag
)
{
if
(
eflag
)
{
if
(
vflag
)
eval
<
0
,
1
,
1
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
0
,
1
,
1
,
0
>
(
ifrom
,
ito
,
thr
);
}
else
{
if
(
vflag
)
eval
<
0
,
1
,
0
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
0
,
1
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
}
else
eval
<
0
,
0
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
reduce_thr
(
this
,
eflag
,
vflag
,
thr
);
}
// end of omp parallel region
}
/* ---------------------------------------------------------------------- */
template
<
int
CTABLE
,
int
EVFLAG
,
int
EFLAG
,
int
VFLAG
>
void
PairLJCutCoulLongTIP4POMP
::
eval
(
int
iifrom
,
int
iito
,
ThrData
*
const
thr
)
{
int
i
,
j
,
ii
,
jj
,
jnum
,
itype
,
jtype
,
itable
;
int
n
,
vlist
[
6
];
int
iH1
,
iH2
,
jH1
,
jH2
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
;
double
fraction
,
table
;
double
delxOM
,
delyOM
,
delzOM
;
double
r
,
rsq
,
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
cforce
;
double
factor_coul
,
factor_lj
;
double
grij
,
expm2
,
prefactor
,
t
,
erfc
,
ddotf
;
double
v
[
6
],
xH1
[
3
],
xH2
[
3
];
double
fdx
,
fdy
,
fdz
,
f1x
,
f1y
,
f1z
,
fOx
,
fOy
,
fOz
,
fHx
,
fHy
,
fHz
;
double
*
x1
,
*
x2
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
evdwl
=
ecoul
=
0.0
;
const
double
*
const
*
const
x
=
atom
->
x
;
double
*
const
*
const
f
=
thr
->
get_f
();
const
double
*
const
q
=
atom
->
q
;
const
int
*
const
type
=
atom
->
type
;
const
int
nlocal
=
atom
->
nlocal
;
const
int
tid
=
thr
->
get_tid
();
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
;
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
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
itype
=
type
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
fxtmp
=
fytmp
=
fztmp
=
0.0
;
x1
=
mpos
[
i
];
iH1
=
h1idx
[
i
];
iH2
=
h2idx
[
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
;
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_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),
// but only if they are within reach
if
(
rsq
<
cut_coulsqplus
)
{
if
(
itype
==
typeO
||
jtype
==
typeO
)
{
x2
=
mpos
[
j
];
jH1
=
h1idx
[
j
];
jH2
=
h2idx
[
j
];
if
(
check_error_thr
((
jtype
==
typeO
&&
(
jH1
<
0
||
jH2
<
0
)),
tid
,
FLERR
,
"TIP4P hydrogen is missing"
))
return
;
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
n
=
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
;
vlist
[
n
++
]
=
i
;
}
}
else
{
fdx
=
delx
*
cforce
;
fdy
=
dely
*
cforce
;
fdz
=
delz
*
cforce
;
delxOM
=
x
[
i
][
0
]
-
x1
[
0
];
delyOM
=
x
[
i
][
1
]
-
x1
[
1
];
delzOM
=
x
[
i
][
2
]
-
x1
[
2
];
ddotf
=
(
delxOM
*
fdx
+
delyOM
*
fdy
+
delzOM
*
fdz
)
/
(
qdist
*
qdist
);
f1x
=
alpha
*
(
fdx
-
ddotf
*
delxOM
);
f1y
=
alpha
*
(
fdy
-
ddotf
*
delyOM
);
f1z
=
alpha
*
(
fdz
-
ddotf
*
delzOM
);
fOx
=
fdx
-
f1x
;
fOy
=
fdy
-
f1y
;
fOz
=
fdz
-
f1z
;
fHx
=
0.5
*
f1x
;
fHy
=
0.5
*
f1y
;
fHz
=
0.5
*
f1z
;
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
;
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
{
fdx
=
-
delx
*
cforce
;
fdy
=
-
dely
*
cforce
;
fdz
=
-
delz
*
cforce
;
delxOM
=
x
[
j
][
0
]
-
x2
[
0
];
delyOM
=
x
[
j
][
1
]
-
x2
[
1
];
delzOM
=
x
[
j
][
2
]
-
x2
[
2
];
ddotf
=
(
delxOM
*
fdx
+
delyOM
*
fdy
+
delzOM
*
fdz
)
/
(
qdist
*
qdist
);
f1x
=
alpha
*
(
fdx
-
ddotf
*
delxOM
);
f1y
=
alpha
*
(
fdy
-
ddotf
*
delyOM
);
f1z
=
alpha
*
(
fdz
-
ddotf
*
delzOM
);
fOx
=
fdx
-
f1x
;
fOy
=
fdy
-
f1y
;
fOz
=
fdz
-
f1z
;
fHx
=
0.5
*
f1x
;
fHy
=
0.5
*
f1y
;
fHz
=
0.5
*
f1z
;
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
;
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_list_thr
(
this
,
n
,
vlist
,
ecoul
,
v
,
thr
);
}
}
}
f
[
i
][
0
]
+=
fxtmp
;
f
[
i
][
1
]
+=
fytmp
;
f
[
i
][
2
]
+=
fztmp
;
}
}
/* ---------------------------------------------------------------------- */
void
PairLJCutCoulLongTIP4POMP
::
find_M_permissive
(
int
i
,
int
&
iH1
,
int
&
iH2
,
double
*
xM
)
{
// test that O is correctly bonded to 2 succesive H atoms
iH1
=
atom
->
map
(
atom
->
tag
[
i
]
+
1
);
iH2
=
atom
->
map
(
atom
->
tag
[
i
]
+
2
);
if
(
iH1
==
-
1
||
iH2
==
-
1
)
return
;
else
find_M
(
i
,
iH1
,
iH2
,
xM
);
}
/* ---------------------------------------------------------------------- */
double
PairLJCutCoulLongTIP4POMP
::
memory_usage
()
{
double
bytes
=
memory_usage_thr
();
bytes
+=
PairLJCutCoulLongTIP4P
::
memory_usage
();
bytes
+=
2
*
maxmpos
*
sizeof
(
int
);
bytes
+=
3
*
maxmpos
*
sizeof
(
double
);
bytes
+=
maxmpos
*
sizeof
(
double
*
);
return
bytes
;
}
Event Timeline
Log In to Comment