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rLAMMPS lammps
angle_sdk.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Variant of the harmonic angle potential for use with the
lj/sdk potential for coarse grained MD simulations.
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "angle_sdk.h"
#include "atom.h"
#include "neighbor.h"
#include "pair.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "lj_sdk_common.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
using
namespace
LJSDKParms
;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
AngleSDK
::
AngleSDK
(
LAMMPS
*
lmp
)
:
Angle
(
lmp
)
{
repflag
=
0
;}
/* ---------------------------------------------------------------------- */
AngleSDK
::~
AngleSDK
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
k
);
memory
->
destroy
(
theta0
);
memory
->
destroy
(
repscale
);
allocated
=
0
;
}
}
/* ---------------------------------------------------------------------- */
void
AngleSDK
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
i3
,
n
,
type
;
double
delx1
,
dely1
,
delz1
,
delx2
,
dely2
,
delz2
,
delx3
,
dely3
,
delz3
;
double
eangle
,
f1
[
3
],
f3
[
3
],
e13
,
f13
;
double
dtheta
,
tk
;
double
rsq1
,
rsq2
,
rsq3
,
r1
,
r2
,
c
,
s
,
a
,
a11
,
a12
,
a22
;
eangle
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
**
anglelist
=
neighbor
->
anglelist
;
int
nanglelist
=
neighbor
->
nanglelist
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
for
(
n
=
0
;
n
<
nanglelist
;
n
++
)
{
i1
=
anglelist
[
n
][
0
];
i2
=
anglelist
[
n
][
1
];
i3
=
anglelist
[
n
][
2
];
type
=
anglelist
[
n
][
3
];
// 1st bond
delx1
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
dely1
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
delz1
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
rsq1
=
delx1
*
delx1
+
dely1
*
dely1
+
delz1
*
delz1
;
r1
=
sqrt
(
rsq1
);
// 2nd bond
delx2
=
x
[
i3
][
0
]
-
x
[
i2
][
0
];
dely2
=
x
[
i3
][
1
]
-
x
[
i2
][
1
];
delz2
=
x
[
i3
][
2
]
-
x
[
i2
][
2
];
rsq2
=
delx2
*
delx2
+
dely2
*
dely2
+
delz2
*
delz2
;
r2
=
sqrt
(
rsq2
);
// angle (cos and sin)
c
=
delx1
*
delx2
+
dely1
*
dely2
+
delz1
*
delz2
;
c
/=
r1
*
r2
;
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
s
=
sqrt
(
1.0
-
c
*
c
);
if
(
s
<
SMALL
)
s
=
SMALL
;
s
=
1.0
/
s
;
// 1-3 LJ interaction.
// we only want to use the repulsive part,
// and it can be scaled (or off).
// so this has to be done here and not in the
// general non-bonded code.
f13
=
e13
=
delx3
=
dely3
=
delz3
=
0.0
;
if
(
repflag
)
{
delx3
=
x
[
i1
][
0
]
-
x
[
i3
][
0
];
dely3
=
x
[
i1
][
1
]
-
x
[
i3
][
1
];
delz3
=
x
[
i1
][
2
]
-
x
[
i3
][
2
];
rsq3
=
delx3
*
delx3
+
dely3
*
dely3
+
delz3
*
delz3
;
const
int
type1
=
atom
->
type
[
i1
];
const
int
type3
=
atom
->
type
[
i3
];
f13
=
0.0
;
e13
=
0.0
;
if
(
rsq3
<
rminsq
[
type1
][
type3
])
{
const
int
ljt
=
lj_type
[
type1
][
type3
];
const
double
r2inv
=
1.0
/
rsq3
;
if
(
ljt
==
LJ12_4
)
{
const
double
r4inv
=
r2inv
*
r2inv
;
f13
=
r4inv
*
(
lj1
[
type1
][
type3
]
*
r4inv
*
r4inv
-
lj2
[
type1
][
type3
]);
if
(
eflag
)
e13
=
r4inv
*
(
lj3
[
type1
][
type3
]
*
r4inv
*
r4inv
-
lj4
[
type1
][
type3
]);
}
else
if
(
ljt
==
LJ9_6
)
{
const
double
r3inv
=
r2inv
*
sqrt
(
r2inv
);
const
double
r6inv
=
r3inv
*
r3inv
;
f13
=
r6inv
*
(
lj1
[
type1
][
type3
]
*
r3inv
-
lj2
[
type1
][
type3
]);
if
(
eflag
)
e13
=
r6inv
*
(
lj3
[
type1
][
type3
]
*
r3inv
-
lj4
[
type1
][
type3
]);
}
else
if
(
ljt
==
LJ12_6
)
{
const
double
r6inv
=
r2inv
*
r2inv
*
r2inv
;
f13
=
r6inv
*
(
lj1
[
type1
][
type3
]
*
r6inv
-
lj2
[
type1
][
type3
]);
if
(
eflag
)
e13
=
r6inv
*
(
lj3
[
type1
][
type3
]
*
r6inv
-
lj4
[
type1
][
type3
]);
}
// make sure energy is 0.0 at the cutoff.
if
(
eflag
)
e13
-=
emin
[
type1
][
type3
];
f13
*=
r2inv
;
}
}
// force & energy
dtheta
=
acos
(
c
)
-
theta0
[
type
];
tk
=
k
[
type
]
*
dtheta
;
if
(
eflag
)
eangle
=
tk
*
dtheta
;
a
=
-
2.0
*
tk
*
s
;
a11
=
a
*
c
/
rsq1
;
a12
=
-
a
/
(
r1
*
r2
);
a22
=
a
*
c
/
rsq2
;
f1
[
0
]
=
a11
*
delx1
+
a12
*
delx2
;
f1
[
1
]
=
a11
*
dely1
+
a12
*
dely2
;
f1
[
2
]
=
a11
*
delz1
+
a12
*
delz2
;
f3
[
0
]
=
a22
*
delx2
+
a12
*
delx1
;
f3
[
1
]
=
a22
*
dely2
+
a12
*
dely1
;
f3
[
2
]
=
a22
*
delz2
+
a12
*
delz1
;
// apply force to each of the 3 atoms
if
(
newton_bond
||
i1
<
nlocal
)
{
f
[
i1
][
0
]
+=
f1
[
0
]
+
f13
*
delx3
;
f
[
i1
][
1
]
+=
f1
[
1
]
+
f13
*
dely3
;
f
[
i1
][
2
]
+=
f1
[
2
]
+
f13
*
delz3
;
}
if
(
newton_bond
||
i2
<
nlocal
)
{
f
[
i2
][
0
]
-=
f1
[
0
]
+
f3
[
0
];
f
[
i2
][
1
]
-=
f1
[
1
]
+
f3
[
1
];
f
[
i2
][
2
]
-=
f1
[
2
]
+
f3
[
2
];
}
if
(
newton_bond
||
i3
<
nlocal
)
{
f
[
i3
][
0
]
+=
f3
[
0
]
-
f13
*
delx3
;
f
[
i3
][
1
]
+=
f3
[
1
]
-
f13
*
dely3
;
f
[
i3
][
2
]
+=
f3
[
2
]
-
f13
*
delz3
;
}
if
(
evflag
)
{
ev_tally
(
i1
,
i2
,
i3
,
nlocal
,
newton_bond
,
eangle
,
f1
,
f3
,
delx1
,
dely1
,
delz1
,
delx2
,
dely2
,
delz2
);
if
(
repflag
)
ev_tally13
(
i1
,
i3
,
nlocal
,
newton_bond
,
e13
,
f13
,
delx3
,
dely3
,
delz3
);
}
}
}
/* ---------------------------------------------------------------------- */
void
AngleSDK
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
nangletypes
;
memory
->
create
(
k
,
n
+
1
,
"angle:k"
);
memory
->
create
(
theta0
,
n
+
1
,
"angle:theta0"
);
memory
->
create
(
repscale
,
n
+
1
,
"angle:repscale"
);
memory
->
create
(
setflag
,
n
+
1
,
"angle:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void
AngleSDK
::
coeff
(
int
narg
,
char
**
arg
)
{
if
((
narg
<
3
)
||
(
narg
>
6
))
error
->
all
(
FLERR
,
"Incorrect args for angle coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
nangletypes
,
ilo
,
ihi
);
double
k_one
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
double
theta0_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
repscale_one
=
1.0
;
// backward compatibility with old cg/cmm style input:
// this had <lj_type> <epsilon> <sigma>
// if epsilon is set to 0.0 we accept it as repscale 0.0
// otherwise assume repscale 1.0, since we were using
// epsilon to turn repulsion on or off.
if
(
narg
==
6
)
{
repscale_one
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
if
(
repscale_one
>
0.0
)
repscale_one
=
1.0
;
}
else
if
(
narg
==
4
)
repscale_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
else
if
(
narg
==
3
)
repscale_one
=
1.0
;
else
error
->
all
(
FLERR
,
"Incorrect args for angle coefficients"
);
// convert theta0 from degrees to radians and store coefficients
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
k
[
i
]
=
k_one
;
theta0
[
i
]
=
theta0_one
/
180.0
*
MY_PI
;
repscale
[
i
]
=
repscale_one
;
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for angle coefficients"
);
}
/* ----------------------------------------------------------------------
error check and initialize all values needed for force computation
------------------------------------------------------------------------- */
void
AngleSDK
::
init_style
()
{
// make sure we use an SDK pair_style and that we need the 1-3 repulsion
repflag
=
0
;
for
(
int
i
=
1
;
i
<=
atom
->
nangletypes
;
i
++
)
if
(
repscale
[
i
]
>
0.0
)
repflag
=
1
;
// set up pointers to access SDK LJ parameters for 1-3 interactions
if
(
repflag
)
{
int
itmp
;
if
(
force
->
pair
==
NULL
)
error
->
all
(
FLERR
,
"Angle style SDK requires use of a compatible with Pair style"
);
lj1
=
(
double
**
)
force
->
pair
->
extract
(
"lj1"
,
itmp
);
lj2
=
(
double
**
)
force
->
pair
->
extract
(
"lj2"
,
itmp
);
lj3
=
(
double
**
)
force
->
pair
->
extract
(
"lj3"
,
itmp
);
lj4
=
(
double
**
)
force
->
pair
->
extract
(
"lj4"
,
itmp
);
lj_type
=
(
int
**
)
force
->
pair
->
extract
(
"lj_type"
,
itmp
);
rminsq
=
(
double
**
)
force
->
pair
->
extract
(
"rminsq"
,
itmp
);
emin
=
(
double
**
)
force
->
pair
->
extract
(
"emin"
,
itmp
);
if
(
!
lj1
||
!
lj2
||
!
lj3
||
!
lj4
||
!
lj_type
||
!
rminsq
||
!
emin
)
error
->
all
(
FLERR
,
"Angle style SDK is incompatible with Pair style"
);
}
}
/* ---------------------------------------------------------------------- */
double
AngleSDK
::
equilibrium_angle
(
int
i
)
{
return
theta0
[
i
];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
AngleSDK
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
theta0
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
repscale
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
AngleSDK
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
theta0
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
repscale
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
MPI_Bcast
(
&
k
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
theta0
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
repscale
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
nangletypes
;
i
++
)
setflag
[
i
]
=
1
;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void
AngleSDK
::
write_data
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
nangletypes
;
i
++
)
fprintf
(
fp
,
"%d %g %g
\n
"
,
i
,
k
[
i
],
theta0
[
i
]
/
MY_PI
*
180.0
);
}
/* ---------------------------------------------------------------------- */
void
AngleSDK
::
ev_tally13
(
int
i
,
int
j
,
int
nlocal
,
int
newton_bond
,
double
evdwl
,
double
fpair
,
double
delx
,
double
dely
,
double
delz
)
{
double
v
[
6
];
if
(
eflag_either
)
{
if
(
eflag_global
)
{
if
(
newton_bond
)
{
energy
+=
evdwl
;
}
else
{
if
(
i
<
nlocal
)
energy
+=
0.5
*
evdwl
;
if
(
j
<
nlocal
)
energy
+=
0.5
*
evdwl
;
}
}
if
(
eflag_atom
)
{
if
(
newton_bond
||
i
<
nlocal
)
eatom
[
i
]
+=
0.5
*
evdwl
;
if
(
newton_bond
||
j
<
nlocal
)
eatom
[
j
]
+=
0.5
*
evdwl
;
}
}
if
(
vflag_either
)
{
v
[
0
]
=
delx
*
delx
*
fpair
;
v
[
1
]
=
dely
*
dely
*
fpair
;
v
[
2
]
=
delz
*
delz
*
fpair
;
v
[
3
]
=
delx
*
dely
*
fpair
;
v
[
4
]
=
delx
*
delz
*
fpair
;
v
[
5
]
=
dely
*
delz
*
fpair
;
if
(
vflag_global
)
{
if
(
newton_bond
)
{
virial
[
0
]
+=
v
[
0
];
virial
[
1
]
+=
v
[
1
];
virial
[
2
]
+=
v
[
2
];
virial
[
3
]
+=
v
[
3
];
virial
[
4
]
+=
v
[
4
];
virial
[
5
]
+=
v
[
5
];
}
else
{
if
(
i
<
nlocal
)
{
virial
[
0
]
+=
0.5
*
v
[
0
];
virial
[
1
]
+=
0.5
*
v
[
1
];
virial
[
2
]
+=
0.5
*
v
[
2
];
virial
[
3
]
+=
0.5
*
v
[
3
];
virial
[
4
]
+=
0.5
*
v
[
4
];
virial
[
5
]
+=
0.5
*
v
[
5
];
}
if
(
j
<
nlocal
)
{
virial
[
0
]
+=
0.5
*
v
[
0
];
virial
[
1
]
+=
0.5
*
v
[
1
];
virial
[
2
]
+=
0.5
*
v
[
2
];
virial
[
3
]
+=
0.5
*
v
[
3
];
virial
[
4
]
+=
0.5
*
v
[
4
];
virial
[
5
]
+=
0.5
*
v
[
5
];
}
}
}
if
(
vflag_atom
)
{
if
(
newton_bond
||
i
<
nlocal
)
{
vatom
[
i
][
0
]
+=
0.5
*
v
[
0
];
vatom
[
i
][
1
]
+=
0.5
*
v
[
1
];
vatom
[
i
][
2
]
+=
0.5
*
v
[
2
];
vatom
[
i
][
3
]
+=
0.5
*
v
[
3
];
vatom
[
i
][
4
]
+=
0.5
*
v
[
4
];
vatom
[
i
][
5
]
+=
0.5
*
v
[
5
];
}
if
(
newton_bond
||
j
<
nlocal
)
{
vatom
[
j
][
0
]
+=
0.5
*
v
[
0
];
vatom
[
j
][
1
]
+=
0.5
*
v
[
1
];
vatom
[
j
][
2
]
+=
0.5
*
v
[
2
];
vatom
[
j
][
3
]
+=
0.5
*
v
[
3
];
vatom
[
j
][
4
]
+=
0.5
*
v
[
4
];
vatom
[
j
][
5
]
+=
0.5
*
v
[
5
];
}
}
}
}
/* ---------------------------------------------------------------------- */
double
AngleSDK
::
single
(
int
type
,
int
i1
,
int
i2
,
int
i3
)
{
double
**
x
=
atom
->
x
;
double
delx1
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
double
dely1
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
double
delz1
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
domain
->
minimum_image
(
delx1
,
dely1
,
delz1
);
double
r1
=
sqrt
(
delx1
*
delx1
+
dely1
*
dely1
+
delz1
*
delz1
);
double
delx2
=
x
[
i3
][
0
]
-
x
[
i2
][
0
];
double
dely2
=
x
[
i3
][
1
]
-
x
[
i2
][
1
];
double
delz2
=
x
[
i3
][
2
]
-
x
[
i2
][
2
];
domain
->
minimum_image
(
delx2
,
dely2
,
delz2
);
double
r2
=
sqrt
(
delx2
*
delx2
+
dely2
*
dely2
+
delz2
*
delz2
);
double
c
=
delx1
*
delx2
+
dely1
*
dely2
+
delz1
*
delz2
;
c
/=
r1
*
r2
;
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
double
e13
=
0.0
;
if
(
repflag
)
{
// 1-3 LJ interaction.
double
delx3
=
x
[
i1
][
0
]
-
x
[
i3
][
0
];
double
dely3
=
x
[
i1
][
1
]
-
x
[
i3
][
1
];
double
delz3
=
x
[
i1
][
2
]
-
x
[
i3
][
2
];
domain
->
minimum_image
(
delx3
,
dely3
,
delz3
);
const
int
type1
=
atom
->
type
[
i1
];
const
int
type3
=
atom
->
type
[
i3
];
const
double
rsq3
=
delx3
*
delx3
+
dely3
*
dely3
+
delz3
*
delz3
;
if
(
rsq3
<
rminsq
[
type1
][
type3
])
{
const
int
ljt
=
lj_type
[
type1
][
type3
];
const
double
r2inv
=
1.0
/
rsq3
;
if
(
ljt
==
LJ12_4
)
{
const
double
r4inv
=
r2inv
*
r2inv
;
e13
=
r4inv
*
(
lj3
[
type1
][
type3
]
*
r4inv
*
r4inv
-
lj4
[
type1
][
type3
]);
}
else
if
(
ljt
==
LJ9_6
)
{
const
double
r3inv
=
r2inv
*
sqrt
(
r2inv
);
const
double
r6inv
=
r3inv
*
r3inv
;
e13
=
r6inv
*
(
lj3
[
type1
][
type3
]
*
r3inv
-
lj4
[
type1
][
type3
]);
}
else
if
(
ljt
==
LJ12_6
)
{
const
double
r6inv
=
r2inv
*
r2inv
*
r2inv
;
e13
=
r6inv
*
(
lj3
[
type1
][
type3
]
*
r6inv
-
lj4
[
type1
][
type3
]);
}
// make sure energy is 0.0 at the cutoff.
e13
-=
emin
[
type1
][
type3
];
}
}
double
dtheta
=
acos
(
c
)
-
theta0
[
type
];
double
tk
=
k
[
type
]
*
dtheta
;
return
tk
*
dtheta
+
e13
;
}
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