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rLAMMPS lammps
pair_lj_gromacs.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 author: Mark Stevens (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_gromacs.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PairLJGromacs
::
PairLJGromacs
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
PairLJGromacs
::~
PairLJGromacs
()
{
if
(
allocated
)
{
memory
->
destroy_2d_int_array
(
setflag
);
memory
->
destroy_2d_double_array
(
cutsq
);
memory
->
destroy_2d_double_array
(
cut
);
memory
->
destroy_2d_double_array
(
cut_inner
);
memory
->
destroy_2d_double_array
(
cut_inner_sq
);
memory
->
destroy_2d_double_array
(
epsilon
);
memory
->
destroy_2d_double_array
(
sigma
);
memory
->
destroy_2d_double_array
(
lj1
);
memory
->
destroy_2d_double_array
(
lj2
);
memory
->
destroy_2d_double_array
(
lj3
);
memory
->
destroy_2d_double_array
(
lj4
);
memory
->
destroy_2d_double_array
(
ljsw1
);
memory
->
destroy_2d_double_array
(
ljsw2
);
memory
->
destroy_2d_double_array
(
ljsw3
);
memory
->
destroy_2d_double_array
(
ljsw4
);
memory
->
destroy_2d_double_array
(
ljsw5
);
}
}
/* ---------------------------------------------------------------------- */
void
PairLJGromacs
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
fpair
;
double
rsq
,
r2inv
,
r6inv
,
forcelj
,
factor_lj
;
double
r
,
t
,
fswitch
,
eswitch
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
evdwl
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
double
*
special_lj
=
force
->
special_lj
;
int
newton_pair
=
force
->
newton_pair
;
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
];
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
];
if
(
j
<
nall
)
factor_lj
=
1.0
;
else
{
factor_lj
=
special_lj
[
j
/
nall
];
j
%=
nall
;
}
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
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
if
(
rsq
>
cut_inner_sq
[
itype
][
jtype
])
{
r
=
sqrt
(
rsq
);
t
=
r
-
cut_inner
[
itype
][
jtype
];
fswitch
=
r
*
t
*
t
*
(
ljsw1
[
itype
][
jtype
]
+
ljsw2
[
itype
][
jtype
]
*
t
);
forcelj
+=
fswitch
;
}
fpair
=
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
)
{
evdwl
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
]);
if
(
rsq
>
cut_inner_sq
[
itype
][
jtype
])
{
eswitch
=
t
*
t
*
t
*
(
ljsw3
[
itype
][
jtype
]
+
ljsw4
[
itype
][
jtype
]
*
t
)
+
ljsw5
[
itype
][
jtype
];
evdwl
+=
eswitch
;
}
evdwl
*=
factor_lj
;
}
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
if
(
vflag_fdotr
)
virial_compute
();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairLJGromacs
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
setflag
=
memory
->
create_2d_int_array
(
n
+
1
,
n
+
1
,
"pair:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
cutsq
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cutsq"
);
cut
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cut"
);
cut_inner
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cut_inner"
);
cut_inner_sq
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cut_inner_sq"
);
epsilon
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:epsilon"
);
sigma
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:sigma"
);
lj1
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj1"
);
lj2
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj2"
);
lj3
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj3"
);
lj4
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj4"
);
ljsw1
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:ljsw1"
);
ljsw2
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:ljsw2"
);
ljsw3
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:ljsw3"
);
ljsw4
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:ljsw4"
);
ljsw5
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:ljsw5"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairLJGromacs
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
2
)
error
->
all
(
"Illegal pair_style command"
);
cut_inner_global
=
force
->
numeric
(
arg
[
0
]);
cut_global
=
force
->
numeric
(
arg
[
1
]);
if
(
cut_inner_global
<=
0.0
||
cut_inner_global
>
cut_global
)
error
->
all
(
"Illegal pair_style command"
);
// 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_inner
[
i
][
j
]
=
cut_inner_global
;
cut
[
i
][
j
]
=
cut_global
;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairLJGromacs
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
4
&&
narg
!=
6
)
error
->
all
(
"Incorrect args for pair coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
,
jlo
,
jhi
;
force
->
bounds
(
arg
[
0
],
atom
->
ntypes
,
ilo
,
ihi
);
force
->
bounds
(
arg
[
1
],
atom
->
ntypes
,
jlo
,
jhi
);
double
epsilon_one
=
force
->
numeric
(
arg
[
2
]);
double
sigma_one
=
force
->
numeric
(
arg
[
3
]);
double
cut_inner_one
=
cut_inner_global
;
double
cut_one
=
cut_global
;
if
(
narg
==
6
)
{
cut_inner_one
=
force
->
numeric
(
arg
[
4
]);
cut_one
=
force
->
numeric
(
arg
[
5
]);
}
if
(
cut_inner_one
<=
0.0
||
cut_inner_one
>
cut_one
)
error
->
all
(
"Incorrect args for pair coefficients"
);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
for
(
int
j
=
MAX
(
jlo
,
i
);
j
<=
jhi
;
j
++
)
{
epsilon
[
i
][
j
]
=
epsilon_one
;
sigma
[
i
][
j
]
=
sigma_one
;
cut_inner
[
i
][
j
]
=
cut_inner_one
;
cut
[
i
][
j
]
=
cut_one
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairLJGromacs
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
{
epsilon
[
i
][
j
]
=
mix_energy
(
epsilon
[
i
][
i
],
epsilon
[
j
][
j
],
sigma
[
i
][
i
],
sigma
[
j
][
j
]);
sigma
[
i
][
j
]
=
mix_distance
(
sigma
[
i
][
i
],
sigma
[
j
][
j
]);
cut_inner
[
i
][
j
]
=
mix_distance
(
cut_inner
[
i
][
i
],
cut_inner
[
j
][
j
]);
cut
[
i
][
j
]
=
mix_distance
(
cut
[
i
][
i
],
cut
[
j
][
j
]);
}
cut_inner_sq
[
i
][
j
]
=
cut_inner
[
i
][
j
]
*
cut_inner
[
i
][
j
];
lj1
[
i
][
j
]
=
48.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
12.0
);
lj2
[
i
][
j
]
=
24.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
6.0
);
lj3
[
i
][
j
]
=
4.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
12.0
);
lj4
[
i
][
j
]
=
4.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
6.0
);
double
r6inv
=
1.0
/
pow
(
cut
[
i
][
j
],
6.0
);
double
r8inv
=
1.0
/
pow
(
cut
[
i
][
j
],
8.0
);
double
t
=
cut
[
i
][
j
]
-
cut_inner
[
i
][
j
];
double
t2inv
=
1.0
/
(
t
*
t
);
double
t3inv
=
t2inv
/
t
;
double
t3
=
1.0
/
t3inv
;
double
a6
=
(
7.0
*
cut_inner
[
i
][
j
]
-
10.0
*
cut
[
i
][
j
])
*
r8inv
*
t2inv
;
double
b6
=
(
9.0
*
cut
[
i
][
j
]
-
7.0
*
cut_inner
[
i
][
j
])
*
r8inv
*
t3inv
;
double
a12
=
(
13.0
*
cut_inner
[
i
][
j
]
-
16.0
*
cut
[
i
][
j
])
*
r6inv
*
r8inv
*
t2inv
;
double
b12
=
(
15.0
*
cut
[
i
][
j
]
-
13.0
*
cut_inner
[
i
][
j
])
*
r6inv
*
r8inv
*
t3inv
;
double
c6
=
r6inv
-
t3
*
(
6.0
*
a6
/
3.0
+
6.0
*
b6
*
t
/
4.0
);
double
c12
=
r6inv
*
r6inv
-
t3
*
(
12.0
*
a12
/
3.0
+
12.0
*
b12
*
t
/
4.0
);
ljsw1
[
i
][
j
]
=
lj1
[
i
][
j
]
*
a12
-
lj2
[
i
][
j
]
*
a6
;
ljsw2
[
i
][
j
]
=
lj1
[
i
][
j
]
*
b12
-
lj2
[
i
][
j
]
*
b6
;
ljsw3
[
i
][
j
]
=
-
lj3
[
i
][
j
]
*
12.0
*
a12
/
3.0
+
lj4
[
i
][
j
]
*
6.0
*
a6
/
3.0
;
ljsw4
[
i
][
j
]
=
-
lj3
[
i
][
j
]
*
12.0
*
b12
/
4.0
+
lj4
[
i
][
j
]
*
6.0
*
b6
/
4.0
;
ljsw5
[
i
][
j
]
=
-
lj3
[
i
][
j
]
*
c12
+
lj4
[
i
][
j
]
*
c6
;
cut_inner
[
j
][
i
]
=
cut_inner
[
i
][
j
];
cut_inner_sq
[
j
][
i
]
=
cut_inner_sq
[
i
][
j
];
lj1
[
j
][
i
]
=
lj1
[
i
][
j
];
lj2
[
j
][
i
]
=
lj2
[
i
][
j
];
lj3
[
j
][
i
]
=
lj3
[
i
][
j
];
lj4
[
j
][
i
]
=
lj4
[
i
][
j
];
ljsw1
[
j
][
i
]
=
ljsw1
[
i
][
j
];
ljsw2
[
j
][
i
]
=
ljsw2
[
i
][
j
];
ljsw3
[
j
][
i
]
=
ljsw3
[
i
][
j
];
ljsw4
[
j
][
i
]
=
ljsw4
[
i
][
j
];
ljsw5
[
j
][
i
]
=
ljsw5
[
i
][
j
];
return
cut
[
i
][
j
];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJGromacs
::
write_restart
(
FILE
*
fp
)
{
write_restart_settings
(
fp
);
int
i
,
j
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
{
fwrite
(
&
setflag
[
i
][
j
],
sizeof
(
int
),
1
,
fp
);
if
(
setflag
[
i
][
j
])
{
fwrite
(
&
epsilon
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
sigma
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut_inner
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJGromacs
::
read_restart
(
FILE
*
fp
)
{
read_restart_settings
(
fp
);
allocate
();
int
i
,
j
;
int
me
=
comm
->
me
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
{
if
(
me
==
0
)
fread
(
&
setflag
[
i
][
j
],
sizeof
(
int
),
1
,
fp
);
MPI_Bcast
(
&
setflag
[
i
][
j
],
1
,
MPI_INT
,
0
,
world
);
if
(
setflag
[
i
][
j
])
{
if
(
me
==
0
)
{
fread
(
&
epsilon
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
sigma
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut_inner
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
MPI_Bcast
(
&
epsilon
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut_inner
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJGromacs
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
cut_inner_global
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut_global
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
offset_flag
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJGromacs
::
read_restart_settings
(
FILE
*
fp
)
{
int
me
=
comm
->
me
;
if
(
me
==
0
)
{
fread
(
&
cut_inner_global
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut_global
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
offset_flag
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
}
MPI_Bcast
(
&
cut_inner_global
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut_global
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
offset_flag
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
mix_flag
,
1
,
MPI_INT
,
0
,
world
);
}
/* ---------------------------------------------------------------------- */
double
PairLJGromacs
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r2inv
,
r6inv
,
forcelj
,
philj
;
double
r
,
t
,
fswitch
,
phiswitch
;
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
if
(
rsq
>
cut_inner_sq
[
itype
][
jtype
])
{
r
=
sqrt
(
rsq
);
t
=
r
-
cut_inner
[
itype
][
jtype
];
fswitch
=
r
*
t
*
t
*
(
ljsw1
[
itype
][
jtype
]
+
ljsw2
[
itype
][
jtype
]
*
t
);
forcelj
+=
fswitch
;
}
fforce
=
factor_lj
*
forcelj
*
r2inv
;
philj
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
]);
if
(
rsq
>
cut_inner_sq
[
itype
][
jtype
])
{
phiswitch
=
t
*
t
*
t
*
(
ljsw3
[
itype
][
jtype
]
+
ljsw4
[
itype
][
jtype
]
*
t
)
+
ljsw5
[
itype
][
jtype
];
philj
+=
phiswitch
;
}
return
factor_lj
*
philj
;
}
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