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rLAMMPS lammps
bond_quartic.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: Chris Lorenz and Mark Stevens (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "bond_quartic.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
BondQuartic
::
BondQuartic
(
LAMMPS
*
lmp
)
:
Bond
(
lmp
)
{
TWO_1_3
=
pow
(
2.0
,(
1.0
/
3.0
));
}
/* ---------------------------------------------------------------------- */
BondQuartic
::~
BondQuartic
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
k
);
memory
->
destroy
(
b1
);
memory
->
destroy
(
b2
);
memory
->
destroy
(
rc
);
memory
->
destroy
(
u0
);
}
}
/* ---------------------------------------------------------------------- */
void
BondQuartic
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
n
,
m
,
type
,
itype
,
jtype
;
double
delx
,
dely
,
delz
,
ebond
,
fbond
,
evdwl
,
fpair
;
double
r
,
rsq
,
dr
,
r2
,
ra
,
rb
,
sr2
,
sr6
;
ebond
=
evdwl
=
sr6
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
// insure pair->ev_tally() will use 1-4 virial contribution
if
(
vflag_global
==
2
)
force
->
pair
->
vflag_either
=
force
->
pair
->
vflag_global
=
1
;
double
**
cutsq
=
force
->
pair
->
cutsq
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
**
bondlist
=
neighbor
->
bondlist
;
int
nbondlist
=
neighbor
->
nbondlist
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
for
(
n
=
0
;
n
<
nbondlist
;
n
++
)
{
// skip bond if already broken
if
(
bondlist
[
n
][
2
]
<=
0
)
continue
;
i1
=
bondlist
[
n
][
0
];
i2
=
bondlist
[
n
][
1
];
type
=
bondlist
[
n
][
2
];
delx
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
dely
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
delz
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
// if bond breaks, set type to 0
// both in temporary bondlist and permanent bond_type
// if this proc owns both atoms,
// negate bond_type twice if other atom stores it
// if other proc owns 2nd atom, other proc will also break bond
if
(
rsq
>
rc
[
type
]
*
rc
[
type
])
{
bondlist
[
n
][
2
]
=
0
;
for
(
m
=
0
;
m
<
atom
->
num_bond
[
i1
];
m
++
)
if
(
atom
->
bond_atom
[
i1
][
m
]
==
atom
->
tag
[
i2
])
atom
->
bond_type
[
i1
][
m
]
=
0
;
if
(
i2
<
atom
->
nlocal
)
for
(
m
=
0
;
m
<
atom
->
num_bond
[
i2
];
m
++
)
if
(
atom
->
bond_atom
[
i2
][
m
]
==
atom
->
tag
[
i1
])
atom
->
bond_type
[
i2
][
m
]
=
0
;
continue
;
}
// quartic bond
// 1st portion is from quartic term
// 2nd portion is from LJ term cut at 2^(1/6) with eps = sigma = 1.0
r
=
sqrt
(
rsq
);
dr
=
r
-
rc
[
type
];
r2
=
dr
*
dr
;
ra
=
dr
-
b1
[
type
];
rb
=
dr
-
b2
[
type
];
fbond
=
-
k
[
type
]
/
r
*
(
r2
*
(
ra
+
rb
)
+
2.0
*
dr
*
ra
*
rb
);
if
(
rsq
<
TWO_1_3
)
{
sr2
=
1.0
/
rsq
;
sr6
=
sr2
*
sr2
*
sr2
;
fbond
+=
48.0
*
sr6
*
(
sr6
-
0.5
)
/
rsq
;
}
if
(
eflag
)
{
ebond
=
k
[
type
]
*
r2
*
ra
*
rb
+
u0
[
type
];
if
(
rsq
<
TWO_1_3
)
ebond
+=
4.0
*
sr6
*
(
sr6
-
1.0
)
+
1.0
;
}
// apply force to each of 2 atoms
if
(
newton_bond
||
i1
<
nlocal
)
{
f
[
i1
][
0
]
+=
delx
*
fbond
;
f
[
i1
][
1
]
+=
dely
*
fbond
;
f
[
i1
][
2
]
+=
delz
*
fbond
;
}
if
(
newton_bond
||
i2
<
nlocal
)
{
f
[
i2
][
0
]
-=
delx
*
fbond
;
f
[
i2
][
1
]
-=
dely
*
fbond
;
f
[
i2
][
2
]
-=
delz
*
fbond
;
}
if
(
evflag
)
ev_tally
(
i1
,
i2
,
nlocal
,
newton_bond
,
ebond
,
fbond
,
delx
,
dely
,
delz
);
// subtract out pairwise contribution from 2 atoms via pair->single()
// required since special_bond = 1,1,1
// tally energy/virial in pair, using newton_bond as newton flag
itype
=
atom
->
type
[
i1
];
jtype
=
atom
->
type
[
i2
];
if
(
rsq
<
cutsq
[
itype
][
jtype
])
{
evdwl
=
-
force
->
pair
->
single
(
i1
,
i2
,
itype
,
jtype
,
rsq
,
1.0
,
1.0
,
fpair
);
fpair
=
-
fpair
;
if
(
newton_bond
||
i1
<
nlocal
)
{
f
[
i1
][
0
]
+=
delx
*
fpair
;
f
[
i1
][
1
]
+=
dely
*
fpair
;
f
[
i1
][
2
]
+=
delz
*
fpair
;
}
if
(
newton_bond
||
i2
<
nlocal
)
{
f
[
i2
][
0
]
-=
delx
*
fpair
;
f
[
i2
][
1
]
-=
dely
*
fpair
;
f
[
i2
][
2
]
-=
delz
*
fpair
;
}
if
(
evflag
)
force
->
pair
->
ev_tally
(
i1
,
i2
,
nlocal
,
newton_bond
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
/* ---------------------------------------------------------------------- */
void
BondQuartic
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
nbondtypes
;
memory
->
create
(
k
,
n
+
1
,
"bond:k"
);
memory
->
create
(
b1
,
n
+
1
,
"bond:b1"
);
memory
->
create
(
b2
,
n
+
1
,
"bond:b2"
);
memory
->
create
(
rc
,
n
+
1
,
"bond:rc"
);
memory
->
create
(
u0
,
n
+
1
,
"bond:u0"
);
memory
->
create
(
setflag
,
n
+
1
,
"bond:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void
BondQuartic
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
6
)
error
->
all
(
FLERR
,
"Incorrect args for bond coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
nbondtypes
,
ilo
,
ihi
);
double
k_one
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
double
b1_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
b2_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
rc_one
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
double
u0_one
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
k
[
i
]
=
k_one
;
b1
[
i
]
=
b1_one
;
b2
[
i
]
=
b2_one
;
rc
[
i
]
=
rc_one
;
u0
[
i
]
=
u0_one
;
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for bond coefficients"
);
}
/* ----------------------------------------------------------------------
check if pair defined and special_bond settings are valid
------------------------------------------------------------------------- */
void
BondQuartic
::
init_style
()
{
if
(
force
->
pair
==
NULL
||
force
->
pair
->
single_enable
==
0
)
error
->
all
(
FLERR
,
"Pair style does not support bond_style quartic"
);
if
(
force
->
angle
||
force
->
dihedral
||
force
->
improper
)
error
->
all
(
FLERR
,
"Bond style quartic cannot be used with 3,4-body interactions"
);
if
(
atom
->
molecular
==
2
)
error
->
all
(
FLERR
,
"Bond style quartic cannot be used with atom style template"
);
// special bonds must be 1 1 1
if
(
force
->
special_lj
[
1
]
!=
1.0
||
force
->
special_lj
[
2
]
!=
1.0
||
force
->
special_lj
[
3
]
!=
1.0
)
error
->
all
(
FLERR
,
"Bond style quartic requires special_bonds = 1,1,1"
);
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */
double
BondQuartic
::
equilibrium_distance
(
int
i
)
{
return
0.97
;
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
BondQuartic
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fwrite
(
&
b1
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fwrite
(
&
b2
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fwrite
(
&
rc
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fwrite
(
&
u0
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
BondQuartic
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fread
(
&
b1
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fread
(
&
b2
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fread
(
&
rc
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fread
(
&
u0
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
}
MPI_Bcast
(
&
k
[
1
],
atom
->
nbondtypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
b1
[
1
],
atom
->
nbondtypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
b2
[
1
],
atom
->
nbondtypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rc
[
1
],
atom
->
nbondtypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
u0
[
1
],
atom
->
nbondtypes
,
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
nbondtypes
;
i
++
)
setflag
[
i
]
=
1
;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void
BondQuartic
::
write_data
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
nbondtypes
;
i
++
)
fprintf
(
fp
,
"%d %g %g %g %g %g
\n
"
,
i
,
k
[
i
],
b1
[
i
],
b2
[
i
],
rc
[
i
],
u0
[
i
]);
}
/* ---------------------------------------------------------------------- */
double
BondQuartic
::
single
(
int
type
,
double
rsq
,
int
i
,
int
j
,
double
&
fforce
)
{
double
r
,
dr
,
r2
,
ra
,
rb
,
sr2
,
sr6
;
if
(
type
<=
0
)
return
0.0
;
double
eng
=
0.0
;
// subtract out pairwise contribution from 2 atoms via pair->single()
// required since special_bond = 1,1,1
int
itype
=
atom
->
type
[
i
];
int
jtype
=
atom
->
type
[
j
];
if
(
rsq
<
force
->
pair
->
cutsq
[
itype
][
jtype
])
{
double
tmp
;
eng
=
-
force
->
pair
->
single
(
i
,
j
,
itype
,
jtype
,
rsq
,
1.0
,
1.0
,
tmp
);
}
// quartic bond
// 1st portion is from quartic term
// 2nd portion is from LJ term cut at 2^(1/6) with eps = sigma = 1.0
r
=
sqrt
(
rsq
);
dr
=
r
-
rc
[
type
];
r2
=
dr
*
dr
;
ra
=
dr
-
b1
[
type
];
rb
=
dr
-
b2
[
type
];
eng
+=
k
[
type
]
*
r2
*
ra
*
rb
+
u0
[
type
];
fforce
=
-
k
[
type
]
/
r
*
(
r2
*
(
ra
+
rb
)
+
2.0
*
dr
*
ra
*
rb
);
if
(
rsq
<
TWO_1_3
)
{
sr2
=
1.0
/
rsq
;
sr6
=
sr2
*
sr2
*
sr2
;
eng
+=
4.0
*
sr6
*
(
sr6
-
1.0
)
+
1.0
;
fforce
+=
48.0
*
sr6
*
(
sr6
-
0.5
)
/
rsq
;
}
return
eng
;
}
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