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pair_body.cpp
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rLAMMPS lammps
pair_body.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.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_body.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_body.h"
#include "body_nparticle.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
PairBody
::
PairBody
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
dmax
=
nmax
=
0
;
discrete
=
NULL
;
dnum
=
dfirst
=
NULL
;
single_enable
=
0
;
restartinfo
=
0
;
}
/* ---------------------------------------------------------------------- */
PairBody
::~
PairBody
()
{
memory
->
destroy
(
discrete
);
memory
->
destroy
(
dnum
);
memory
->
destroy
(
dfirst
);
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cut
);
memory
->
destroy
(
epsilon
);
memory
->
destroy
(
sigma
);
memory
->
destroy
(
lj1
);
memory
->
destroy
(
lj2
);
memory
->
destroy
(
lj3
);
memory
->
destroy
(
lj4
);
}
}
/* ---------------------------------------------------------------------- */
void
PairBody
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
int
ni
,
nj
,
npi
,
npj
,
ifirst
,
jfirst
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
fpair
;
double
rsq
,
r2inv
,
r6inv
,
forcelj
;
double
xi
[
3
],
xj
[
3
],
fi
[
3
],
fj
[
3
],
ti
[
3
],
tj
[
3
];
double
*
dxi
,
*
dxj
;
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
;
double
**
torque
=
atom
->
torque
;
int
*
body
=
atom
->
body
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
int
newton_pair
=
force
->
newton_pair
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// grow discrete list if necessary and initialize
if
(
nall
>
nmax
)
{
nmax
=
nall
;
memory
->
destroy
(
dnum
);
memory
->
destroy
(
dfirst
);
memory
->
create
(
dnum
,
nall
,
"pair:dnum"
);
memory
->
create
(
dfirst
,
nall
,
"pair:dfirst"
);
}
for
(
i
=
0
;
i
<
nall
;
i
++
)
dnum
[
i
]
=
0
;
ndiscrete
=
0
;
// 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
];
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
];
if
(
rsq
>=
cutsq
[
itype
][
jtype
])
continue
;
// body/body interactions = NxM sub-particles
evdwl
=
0.0
;
if
(
body
[
i
]
>=
0
&&
body
[
j
]
>=
0
)
{
if
(
dnum
[
i
]
==
0
)
body2space
(
i
);
npi
=
dnum
[
i
];
ifirst
=
dfirst
[
i
];
if
(
dnum
[
j
]
==
0
)
body2space
(
j
);
npj
=
dnum
[
j
];
jfirst
=
dfirst
[
j
];
for
(
ni
=
0
;
ni
<
npi
;
ni
++
)
{
dxi
=
discrete
[
ifirst
+
ni
];
for
(
nj
=
0
;
nj
<
npj
;
nj
++
)
{
dxj
=
discrete
[
jfirst
+
nj
];
xi
[
0
]
=
x
[
i
][
0
]
+
dxi
[
0
];
xi
[
1
]
=
x
[
i
][
1
]
+
dxi
[
1
];
xi
[
2
]
=
x
[
i
][
2
]
+
dxi
[
2
];
xj
[
0
]
=
x
[
j
][
0
]
+
dxj
[
0
];
xj
[
1
]
=
x
[
j
][
1
]
+
dxj
[
1
];
xj
[
2
]
=
x
[
j
][
2
]
+
dxj
[
2
];
delx
=
xi
[
0
]
-
xj
[
0
];
dely
=
xi
[
1
]
-
xj
[
1
];
delz
=
xi
[
2
]
-
xj
[
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
fpair
=
forcelj
*
r2inv
;
if
(
eflag
)
evdwl
+=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
]);
fi
[
0
]
=
delx
*
fpair
;
fi
[
1
]
=
dely
*
fpair
;
fi
[
2
]
=
delz
*
fpair
;
f
[
i
][
0
]
+=
fi
[
0
];
f
[
i
][
1
]
+=
fi
[
1
];
f
[
i
][
2
]
+=
fi
[
2
];
ti
[
0
]
=
dxi
[
1
]
*
fi
[
2
]
-
dxi
[
2
]
*
fi
[
1
];
ti
[
1
]
=
dxi
[
2
]
*
fi
[
0
]
-
dxi
[
0
]
*
fi
[
2
];
ti
[
2
]
=
dxi
[
0
]
*
fi
[
1
]
-
dxi
[
1
]
*
fi
[
0
];
torque
[
i
][
0
]
+=
ti
[
0
];
torque
[
i
][
1
]
+=
ti
[
1
];
torque
[
i
][
2
]
+=
ti
[
2
];
if
(
newton_pair
||
j
<
nlocal
)
{
fj
[
0
]
=
-
delx
*
fpair
;
fj
[
1
]
=
-
dely
*
fpair
;
fj
[
2
]
=
-
delz
*
fpair
;
f
[
j
][
0
]
+=
fj
[
0
];
f
[
j
][
1
]
+=
fj
[
1
];
f
[
j
][
2
]
+=
fj
[
2
];
tj
[
0
]
=
dxj
[
1
]
*
fj
[
2
]
-
dxj
[
2
]
*
fj
[
1
];
tj
[
1
]
=
dxj
[
2
]
*
fj
[
0
]
-
dxj
[
0
]
*
fj
[
2
];
tj
[
2
]
=
dxj
[
0
]
*
fj
[
1
]
-
dxj
[
1
]
*
fj
[
0
];
torque
[
j
][
0
]
+=
tj
[
0
];
torque
[
j
][
1
]
+=
tj
[
1
];
torque
[
j
][
2
]
+=
tj
[
2
];
}
}
}
// body/particle interaction = Nx1 sub-particles
}
else
if
(
body
[
i
]
>=
0
)
{
if
(
dnum
[
i
]
==
0
)
body2space
(
i
);
npi
=
dnum
[
i
];
ifirst
=
dfirst
[
i
];
for
(
ni
=
0
;
ni
<
npi
;
ni
++
)
{
dxi
=
discrete
[
ifirst
+
ni
];
xi
[
0
]
=
x
[
i
][
0
]
+
dxi
[
0
];
xi
[
1
]
=
x
[
i
][
1
]
+
dxi
[
1
];
xi
[
2
]
=
x
[
i
][
2
]
+
dxi
[
2
];
xj
[
0
]
=
x
[
j
][
0
];
xj
[
1
]
=
x
[
j
][
1
];
xj
[
2
]
=
x
[
j
][
2
];
delx
=
xi
[
0
]
-
xj
[
0
];
dely
=
xi
[
1
]
-
xj
[
1
];
delz
=
xi
[
2
]
-
xj
[
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
fpair
=
forcelj
*
r2inv
;
if
(
eflag
)
evdwl
+=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
]);
fi
[
0
]
=
delx
*
fpair
;
fi
[
1
]
=
dely
*
fpair
;
fi
[
2
]
=
delz
*
fpair
;
f
[
i
][
0
]
+=
fi
[
0
];
f
[
i
][
1
]
+=
fi
[
1
];
f
[
i
][
2
]
+=
fi
[
2
];
ti
[
0
]
=
dxi
[
1
]
*
fi
[
2
]
-
dxi
[
2
]
*
fi
[
1
];
ti
[
1
]
=
dxi
[
2
]
*
fi
[
0
]
-
dxi
[
0
]
*
fi
[
2
];
ti
[
2
]
=
dxi
[
0
]
*
fi
[
1
]
-
dxi
[
1
]
*
fi
[
0
];
torque
[
i
][
0
]
+=
ti
[
0
];
torque
[
i
][
1
]
+=
ti
[
1
];
torque
[
i
][
2
]
+=
ti
[
2
];
if
(
newton_pair
||
j
<
nlocal
)
{
fj
[
0
]
=
-
delx
*
fpair
;
fj
[
1
]
=
-
dely
*
fpair
;
fj
[
2
]
=
-
delz
*
fpair
;
f
[
j
][
0
]
+=
fj
[
0
];
f
[
j
][
1
]
+=
fj
[
1
];
f
[
j
][
2
]
+=
fj
[
2
];
}
}
// particle/body interaction = Nx1 sub-particles
}
else
if
(
body
[
j
]
>=
0
)
{
if
(
dnum
[
j
]
==
0
)
body2space
(
j
);
npj
=
dnum
[
j
];
jfirst
=
dfirst
[
j
];
for
(
nj
=
0
;
nj
<
npj
;
nj
++
)
{
dxj
=
discrete
[
jfirst
+
nj
];
xi
[
0
]
=
x
[
i
][
0
];
xi
[
1
]
=
x
[
i
][
1
];
xi
[
2
]
=
x
[
i
][
2
];
xj
[
0
]
=
x
[
j
][
0
]
+
dxj
[
0
];
xj
[
1
]
=
x
[
j
][
1
]
+
dxj
[
1
];
xj
[
2
]
=
x
[
j
][
2
]
+
dxj
[
2
];
delx
=
xi
[
0
]
-
xj
[
0
];
dely
=
xi
[
1
]
-
xj
[
1
];
delz
=
xi
[
2
]
-
xj
[
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
fpair
=
forcelj
*
r2inv
;
if
(
eflag
)
evdwl
+=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
]);
fi
[
0
]
=
delx
*
fpair
;
fi
[
1
]
=
dely
*
fpair
;
fi
[
2
]
=
delz
*
fpair
;
f
[
i
][
0
]
+=
fi
[
0
];
f
[
i
][
1
]
+=
fi
[
1
];
f
[
i
][
2
]
+=
fi
[
2
];
if
(
newton_pair
||
j
<
nlocal
)
{
fj
[
0
]
=
-
delx
*
fpair
;
fj
[
1
]
=
-
dely
*
fpair
;
fj
[
2
]
=
-
delz
*
fpair
;
f
[
j
][
0
]
+=
fj
[
0
];
f
[
j
][
1
]
+=
fj
[
1
];
f
[
j
][
2
]
+=
fj
[
2
];
tj
[
0
]
=
dxj
[
1
]
*
fj
[
2
]
-
dxj
[
2
]
*
fj
[
1
];
tj
[
1
]
=
dxj
[
2
]
*
fj
[
0
]
-
dxj
[
0
]
*
fj
[
2
];
tj
[
2
]
=
dxj
[
0
]
*
fj
[
1
]
-
dxj
[
1
]
*
fj
[
0
];
torque
[
j
][
0
]
+=
tj
[
0
];
torque
[
j
][
1
]
+=
tj
[
1
];
torque
[
j
][
2
]
+=
tj
[
2
];
}
}
// particle/particle interaction = 1x1 particles
}
else
{
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
fpair
=
forcelj
*
r2inv
;
if
(
eflag
)
evdwl
+=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
]);
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
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
);
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairBody
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
memory
->
create
(
setflag
,
n
+
1
,
n
+
1
,
"pair:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
memory
->
create
(
cutsq
,
n
+
1
,
n
+
1
,
"pair:cutsq"
);
memory
->
create
(
cut
,
n
+
1
,
n
+
1
,
"pair:cut"
);
memory
->
create
(
epsilon
,
n
+
1
,
n
+
1
,
"pair:epsilon"
);
memory
->
create
(
sigma
,
n
+
1
,
n
+
1
,
"pair:sigma"
);
memory
->
create
(
lj1
,
n
+
1
,
n
+
1
,
"pair:lj1"
);
memory
->
create
(
lj2
,
n
+
1
,
n
+
1
,
"pair:lj2"
);
memory
->
create
(
lj3
,
n
+
1
,
n
+
1
,
"pair:lj3"
);
memory
->
create
(
lj4
,
n
+
1
,
n
+
1
,
"pair:lj4"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairBody
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
1
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
cut_global
=
force
->
numeric
(
FLERR
,
arg
[
0
]);
// 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
[
i
][
j
]
=
cut_global
;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairBody
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
4
||
narg
>
5
)
error
->
all
(
FLERR
,
"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
(
FLERR
,
arg
[
2
]);
double
sigma_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
cut_one
=
cut_global
;
if
(
narg
==
5
)
cut_one
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
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
[
i
][
j
]
=
cut_one
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairBody
::
init_style
()
{
avec
=
(
AtomVecBody
*
)
atom
->
style_match
(
"body"
);
if
(
!
avec
)
error
->
all
(
FLERR
,
"Pair body requires atom style body"
);
if
(
strcmp
(
avec
->
bptr
->
style
,
"nparticle"
)
!=
0
)
error
->
all
(
FLERR
,
"Pair body requires body style nparticle"
);
bptr
=
(
BodyNparticle
*
)
avec
->
bptr
;
neighbor
->
request
(
this
,
instance_me
);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairBody
::
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
[
i
][
j
]
=
mix_distance
(
cut
[
i
][
i
],
cut
[
j
][
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
);
epsilon
[
j
][
i
]
=
epsilon
[
i
][
j
];
sigma
[
j
][
i
]
=
sigma
[
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
];
return
cut
[
i
][
j
];
}
/* ----------------------------------------------------------------------
convert N sub-particles in body I to space frame using current quaternion
store sub-particle space-frame displacements from COM in discrete list
------------------------------------------------------------------------- */
void
PairBody
::
body2space
(
int
i
)
{
int
ibonus
=
atom
->
body
[
i
];
AtomVecBody
::
Bonus
*
bonus
=
&
avec
->
bonus
[
ibonus
];
int
nsub
=
bptr
->
nsub
(
bonus
);
double
*
coords
=
bptr
->
coords
(
bonus
);
dnum
[
i
]
=
nsub
;
dfirst
[
i
]
=
ndiscrete
;
if
(
ndiscrete
+
nsub
>
dmax
)
{
dmax
+=
DELTA
;
memory
->
grow
(
discrete
,
dmax
,
3
,
"pair:discrete"
);
}
double
p
[
3
][
3
];
MathExtra
::
quat_to_mat
(
bonus
->
quat
,
p
);
for
(
int
m
=
0
;
m
<
nsub
;
m
++
)
{
MathExtra
::
matvec
(
p
,
&
coords
[
3
*
m
],
discrete
[
ndiscrete
]);
ndiscrete
++
;
}
}
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