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pair_tri_lj.cpp
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rLAMMPS lammps
pair_tri_lj.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_tri_lj.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_tri.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 20
/* ---------------------------------------------------------------------- */
PairTriLJ
::
PairTriLJ
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
avec
=
(
AtomVecTri
*
)
atom
->
style_match
(
"tri"
);
if
(
!
avec
)
error
->
all
(
FLERR
,
"Pair tri/lj requires atom style tri"
);
dmax
=
nmax
=
0
;
discrete
=
NULL
;
dnum
=
dfirst
=
NULL
;
single_enable
=
0
;
restartinfo
=
0
;
}
/* ---------------------------------------------------------------------- */
PairTriLJ
::~
PairTriLJ
()
{
memory
->
sfree
(
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
PairTriLJ
::
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
,
term1
,
term2
,
sig
,
sig3
,
forcelj
;
double
dxi
,
dxj
,
dyi
,
dyj
,
dzi
,
dzj
;
double
xi
[
3
],
xj
[
3
],
fi
[
3
],
fj
[
3
],
ti
[
3
],
tj
[
3
],
p
[
3
][
3
];
double
dc1
[
3
],
dc2
[
3
],
dc3
[
3
];
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
evdwl
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
AtomVecTri
::
Bonus
*
bonus
=
avec
->
bonus
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
**
torque
=
atom
->
torque
;
int
*
tri
=
atom
->
tri
;
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
;
// tri/tri interactions = NxN particles
// c1,c2,c3 = corner pts of triangle I or J
evdwl
=
0.0
;
if
(
tri
[
i
]
>=
0
&&
tri
[
j
]
>=
0
)
{
if
(
dnum
[
i
]
==
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c1
,
dc1
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c2
,
dc2
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c3
,
dc3
);
dfirst
[
i
]
=
ndiscrete
;
discretize
(
i
,
sigma
[
itype
][
itype
],
dc1
,
dc2
,
dc3
);
dnum
[
i
]
=
ndiscrete
-
dfirst
[
i
];
}
npi
=
dnum
[
i
];
ifirst
=
dfirst
[
i
];
if
(
dnum
[
j
]
==
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
j
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
j
]].
c1
,
dc1
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
j
]].
c2
,
dc2
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
j
]].
c3
,
dc3
);
dfirst
[
j
]
=
ndiscrete
;
discretize
(
j
,
sigma
[
jtype
][
jtype
],
dc1
,
dc2
,
dc3
);
dnum
[
j
]
=
ndiscrete
-
dfirst
[
j
];
}
npj
=
dnum
[
j
];
jfirst
=
dfirst
[
j
];
for
(
ni
=
0
;
ni
<
npi
;
ni
++
)
{
dxi
=
discrete
[
ifirst
+
ni
].
dx
;
dyi
=
discrete
[
ifirst
+
ni
].
dy
;
dzi
=
discrete
[
ifirst
+
ni
].
dz
;
for
(
nj
=
0
;
nj
<
npj
;
nj
++
)
{
dxj
=
discrete
[
jfirst
+
nj
].
dx
;
dyj
=
discrete
[
jfirst
+
nj
].
dy
;
dzj
=
discrete
[
jfirst
+
nj
].
dz
;
xi
[
0
]
=
x
[
i
][
0
]
+
dxi
;
xi
[
1
]
=
x
[
i
][
1
]
+
dyi
;
xi
[
2
]
=
x
[
i
][
2
]
+
dzi
;
xj
[
0
]
=
x
[
j
][
0
]
+
dxj
;
xj
[
1
]
=
x
[
j
][
1
]
+
dyj
;
xj
[
2
]
=
x
[
j
][
2
]
+
dzj
;
delx
=
xi
[
0
]
-
xj
[
0
];
dely
=
xi
[
1
]
-
xj
[
1
];
delz
=
xi
[
2
]
-
xj
[
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
sig
=
0.5
*
(
discrete
[
ifirst
+
ni
].
sigma
+
discrete
[
jfirst
+
nj
].
sigma
);
sig3
=
sig
*
sig
*
sig
;
term2
=
24.0
*
epsilon
[
itype
][
jtype
]
*
sig3
*
sig3
;
term1
=
2.0
*
term2
*
sig3
*
sig3
;
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
term1
*
r6inv
-
term2
);
fpair
=
forcelj
*
r2inv
;
if
(
eflag
)
evdwl
+=
r6inv
*
(
term1
/
12.0
*
r6inv
-
term2
/
6.0
);
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
]
=
dyi
*
fi
[
2
]
-
dzi
*
fi
[
1
];
ti
[
1
]
=
dzi
*
fi
[
0
]
-
dxi
*
fi
[
2
];
ti
[
2
]
=
dxi
*
fi
[
1
]
-
dyi
*
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
]
=
dyj
*
fj
[
2
]
-
dzj
*
fj
[
1
];
tj
[
1
]
=
dzj
*
fj
[
0
]
-
dxj
*
fj
[
2
];
tj
[
2
]
=
dxj
*
fj
[
1
]
-
dyj
*
fj
[
0
];
torque
[
j
][
0
]
+=
tj
[
0
];
torque
[
j
][
1
]
+=
tj
[
1
];
torque
[
j
][
2
]
+=
tj
[
2
];
}
}
}
// tri/particle interaction = Nx1 particles
// c1,c2,c3 = corner pts of triangle I
}
else
if
(
tri
[
i
]
>=
0
)
{
if
(
dnum
[
i
]
==
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c1
,
dc1
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c2
,
dc2
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c3
,
dc3
);
dfirst
[
i
]
=
ndiscrete
;
discretize
(
i
,
sigma
[
itype
][
itype
],
dc1
,
dc2
,
dc3
);
dnum
[
i
]
=
ndiscrete
-
dfirst
[
i
];
}
npi
=
dnum
[
i
];
ifirst
=
dfirst
[
i
];
for
(
ni
=
0
;
ni
<
npi
;
ni
++
)
{
dxi
=
discrete
[
ifirst
+
ni
].
dx
;
dyi
=
discrete
[
ifirst
+
ni
].
dy
;
dzi
=
discrete
[
ifirst
+
ni
].
dz
;
xi
[
0
]
=
x
[
i
][
0
]
+
dxi
;
xi
[
1
]
=
x
[
i
][
1
]
+
dyi
;
xi
[
2
]
=
x
[
i
][
2
]
+
dzi
;
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
;
sig
=
0.5
*
(
discrete
[
ifirst
+
ni
].
sigma
+
sigma
[
jtype
][
jtype
]);
sig3
=
sig
*
sig
*
sig
;
term2
=
24.0
*
epsilon
[
itype
][
jtype
]
*
sig3
*
sig3
;
term1
=
2.0
*
term2
*
sig3
*
sig3
;
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
term1
*
r6inv
-
term2
);
fpair
=
forcelj
*
r2inv
;
if
(
eflag
)
evdwl
+=
r6inv
*
(
term1
/
12.0
*
r6inv
-
term2
/
6.0
);
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
]
=
dyi
*
fi
[
2
]
-
dzi
*
fi
[
1
];
ti
[
1
]
=
dzi
*
fi
[
0
]
-
dxi
*
fi
[
2
];
ti
[
2
]
=
dxi
*
fi
[
1
]
-
dyi
*
fi
[
0
];
torque
[
i
][
2
]
+=
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/tri interaction = Nx1 particles
// c1,c2,c3 = corner pts of triangle J
}
else
if
(
tri
[
j
]
>=
0
)
{
if
(
dnum
[
j
]
==
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
j
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
j
]].
c1
,
dc1
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
j
]].
c2
,
dc2
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
j
]].
c3
,
dc3
);
dfirst
[
j
]
=
ndiscrete
;
discretize
(
j
,
sigma
[
jtype
][
jtype
],
dc1
,
dc2
,
dc3
);
dnum
[
j
]
=
ndiscrete
-
dfirst
[
j
];
}
npj
=
dnum
[
j
];
jfirst
=
dfirst
[
j
];
for
(
nj
=
0
;
nj
<
npj
;
nj
++
)
{
dxj
=
discrete
[
jfirst
+
nj
].
dx
;
dyj
=
discrete
[
jfirst
+
nj
].
dy
;
dzj
=
discrete
[
jfirst
+
nj
].
dz
;
xi
[
0
]
=
x
[
i
][
0
];
xi
[
1
]
=
x
[
i
][
1
];
xi
[
2
]
=
x
[
i
][
2
];
xj
[
0
]
=
x
[
j
][
0
]
+
dxj
;
xj
[
1
]
=
x
[
j
][
1
]
+
dyj
;
xj
[
2
]
=
x
[
j
][
2
]
+
dzj
;
delx
=
xi
[
0
]
-
xj
[
0
];
dely
=
xi
[
1
]
-
xj
[
1
];
delz
=
xi
[
2
]
-
xj
[
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
sig
=
0.5
*
(
sigma
[
itype
][
itype
]
+
discrete
[
jfirst
+
nj
].
sigma
);
sig3
=
sig
*
sig
*
sig
;
term2
=
24.0
*
epsilon
[
itype
][
jtype
]
*
sig3
*
sig3
;
term1
=
2.0
*
term2
*
sig3
*
sig3
;
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
term1
*
r6inv
-
term2
);
fpair
=
forcelj
*
r2inv
;
if
(
eflag
)
evdwl
+=
r6inv
*
(
term1
/
12.0
*
r6inv
-
term2
/
6.0
);
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
]
=
dyj
*
fj
[
2
]
-
dzj
*
fj
[
1
];
tj
[
1
]
=
dzj
*
fj
[
0
]
-
dxj
*
fj
[
2
];
tj
[
2
]
=
dxj
*
fj
[
1
]
-
dyj
*
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
PairTriLJ
::
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
PairTriLJ
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
1
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
cut_global
=
force
->
numeric
(
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
PairTriLJ
::
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
(
arg
[
2
]);
double
sigma_one
=
force
->
numeric
(
arg
[
3
]);
double
cut_one
=
cut_global
;
if
(
narg
==
5
)
cut_one
=
force
->
numeric
(
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 for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairTriLJ
::
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
];
}
/* ----------------------------------------------------------------------
recursively discretize triangle I with displaced corners c1,c2,c3
into N sub-tris no more than sigma in size
recurse by making 2 tris via bisecting longest side
store new discrete particles in Discrete list
------------------------------------------------------------------------- */
void
PairTriLJ
::
discretize
(
int
i
,
double
sigma
,
double
*
c1
,
double
*
c2
,
double
*
c3
)
{
double
c1c2
[
3
],
c2c3
[
3
],
c1c3
[
3
];
double
centroid
[
3
],
dc1
[
3
],
dc2
[
3
],
dc3
[
3
];
centroid
[
0
]
=
(
c1
[
0
]
+
c2
[
0
]
+
c3
[
0
])
/
3.0
;
centroid
[
1
]
=
(
c1
[
1
]
+
c2
[
1
]
+
c3
[
1
])
/
3.0
;
centroid
[
2
]
=
(
c1
[
2
]
+
c2
[
2
]
+
c3
[
2
])
/
3.0
;
MathExtra
::
sub3
(
c1
,
centroid
,
dc1
);
MathExtra
::
sub3
(
c2
,
centroid
,
dc2
);
MathExtra
::
sub3
(
c3
,
centroid
,
dc3
);
double
sigmasq
=
0.25
*
sigma
*
sigma
;
double
len1sq
=
MathExtra
::
lensq3
(
dc1
);
double
len2sq
=
MathExtra
::
lensq3
(
dc2
);
double
len3sq
=
MathExtra
::
lensq3
(
dc3
);
// if sigma sphere overlaps all corner points, add particle at centroid
if
(
len1sq
<=
sigmasq
&&
len2sq
<=
sigmasq
&
len3sq
<=
sigmasq
)
{
if
(
ndiscrete
==
dmax
)
{
dmax
+=
DELTA
;
discrete
=
(
Discrete
*
)
memory
->
srealloc
(
discrete
,
dmax
*
sizeof
(
Discrete
),
"pair:discrete"
);
}
discrete
[
ndiscrete
].
dx
=
centroid
[
0
];
discrete
[
ndiscrete
].
dy
=
centroid
[
1
];
discrete
[
ndiscrete
].
dz
=
centroid
[
2
];
sigmasq
=
MAX
(
len1sq
,
len2sq
);
sigmasq
=
MAX
(
sigmasq
,
len3sq
);
discrete
[
ndiscrete
].
sigma
=
2.0
*
sqrt
(
sigmasq
);
ndiscrete
++
;
return
;
}
// else break triangle into 2 sub-triangles and recurse
double
c12
[
3
],
c23
[
3
],
c13
[
3
],
mid
[
3
];
MathExtra
::
sub3
(
c2
,
c3
,
c23
);
len1sq
=
MathExtra
::
lensq3
(
c23
);
MathExtra
::
sub3
(
c1
,
c3
,
c13
);
len2sq
=
MathExtra
::
lensq3
(
c13
);
MathExtra
::
sub3
(
c1
,
c2
,
c12
);
len3sq
=
MathExtra
::
lensq3
(
c12
);
double
maxsq
=
MAX
(
len1sq
,
len2sq
);
maxsq
=
MAX
(
maxsq
,
len3sq
);
if
(
len1sq
==
maxsq
)
{
MathExtra
::
add3
(
c2
,
c3
,
mid
);
MathExtra
::
scale3
(
0.5
,
mid
);
discretize
(
i
,
sigma
,
c1
,
c2
,
mid
);
discretize
(
i
,
sigma
,
c1
,
c3
,
mid
);
}
else
if
(
len2sq
==
maxsq
)
{
MathExtra
::
add3
(
c1
,
c3
,
mid
);
MathExtra
::
scale3
(
0.5
,
mid
);
discretize
(
i
,
sigma
,
c2
,
c1
,
mid
);
discretize
(
i
,
sigma
,
c2
,
c3
,
mid
);
}
else
{
MathExtra
::
add3
(
c1
,
c2
,
mid
);
MathExtra
::
scale3
(
0.5
,
mid
);
discretize
(
i
,
sigma
,
c3
,
c1
,
mid
);
discretize
(
i
,
sigma
,
c3
,
c2
,
mid
);
}
}
/* ----------------------------------------------------------------------
recursively discretize triangle I with displaced corners c1,c2,c3
into N sub-tris no more than sigma in size
recurse by making 6 tris via centroid
store new discrete particles in Discrete list
------------------------------------------------------------------------- */
/*
void PairTriLJ::discretize(int i, double sigma,
double *c1, double *c2, double *c3)
{
double centroid[3],dc1[3],dc2[3],dc3[3];
centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0;
centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0;
centroid[2] = (c1[2] + c2[2] + c3[2]) / 3.0;
MathExtra::sub3(c1,centroid,dc1);
MathExtra::sub3(c2,centroid,dc2);
MathExtra::sub3(c3,centroid,dc3);
double sigmasq = 0.25 * sigma*sigma;
double len1sq = MathExtra::lensq3(dc1);
double len2sq = MathExtra::lensq3(dc2);
double len3sq = MathExtra::lensq3(dc3);
// if sigma sphere overlaps all corner points, add particle at centroid
if (len1sq <= sigmasq && len2sq <= sigmasq & len3sq <= sigmasq) {
if (ndiscrete == dmax) {
dmax += DELTA;
discrete = (Discrete *)
memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
}
discrete[ndiscrete].dx = centroid[0];
discrete[ndiscrete].dy = centroid[1];
discrete[ndiscrete].dz = centroid[2];
sigmasq = MAX(len1sq,len2sq);
sigmasq = MAX(sigmasq,len3sq);
discrete[ndiscrete].sigma = 2.0 * sqrt(sigmasq);
ndiscrete++;
return;
}
// else break triangle into 6 sub-triangles and recurse
double c1c2mid[3],c2c3mid[3],c1c3mid[3];
MathExtra::add3(c1,c2,c1c2mid);
MathExtra::scale3(0.5,c1c2mid);
MathExtra::add3(c2,c3,c2c3mid);
MathExtra::scale3(0.5,c2c3mid);
MathExtra::add3(c1,c3,c1c3mid);
MathExtra::scale3(0.5,c1c3mid);
discretize(i,sigma,c1,c1c2mid,centroid);
discretize(i,sigma,c1,c1c3mid,centroid);
discretize(i,sigma,c2,c2c3mid,centroid);
discretize(i,sigma,c2,c1c2mid,centroid);
discretize(i,sigma,c3,c1c3mid,centroid);
discretize(i,sigma,c3,c2c3mid,centroid);
}
*/
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