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pair_gran_hooke.cpp
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rLAMMPS lammps
pair_gran_hooke.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: Leo Silbert (SNL), Gary Grest (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <string.h>
#include "pair_gran_hooke.h"
#include "atom.h"
#include "force.h"
#include "fix.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "comm.h"
#include "memory.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairGranHooke
::
PairGranHooke
(
LAMMPS
*
lmp
)
:
PairGranHookeHistory
(
lmp
)
{
no_virial_fdotr_compute
=
0
;
history
=
0
;
}
/* ---------------------------------------------------------------------- */
void
PairGranHooke
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
fx
,
fy
,
fz
;
double
radi
,
radj
,
radsum
,
rsq
,
r
,
rinv
,
rsqinv
;
double
vr1
,
vr2
,
vr3
,
vnnr
,
vn1
,
vn2
,
vn3
,
vt1
,
vt2
,
vt3
;
double
wr1
,
wr2
,
wr3
;
double
vtr1
,
vtr2
,
vtr3
,
vrel
;
double
mi
,
mj
,
meff
,
damp
,
ccel
,
tor1
,
tor2
,
tor3
;
double
fn
,
fs
,
ft
,
fs1
,
fs2
,
fs3
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
// update rigid body info for owned & ghost atoms if using FixRigid masses
// body[i] = which body atom I is in, -1 if none
// mass_body = mass of each rigid body
if
(
fix_rigid
&&
neighbor
->
ago
==
0
)
{
int
tmp
;
int
*
body
=
(
int
*
)
fix_rigid
->
extract
(
"body"
,
tmp
);
double
*
mass_body
=
(
double
*
)
fix_rigid
->
extract
(
"masstotal"
,
tmp
);
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy
(
mass_rigid
);
nmax
=
atom
->
nmax
;
memory
->
create
(
mass_rigid
,
nmax
,
"pair:mass_rigid"
);
}
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
body
[
i
]
>=
0
)
mass_rigid
[
i
]
=
mass_body
[
body
[
i
]];
else
mass_rigid
[
i
]
=
0.0
;
comm
->
forward_comm_pair
(
this
);
}
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
**
omega
=
atom
->
omega
;
double
**
torque
=
atom
->
torque
;
double
*
radius
=
atom
->
radius
;
double
*
rmass
=
atom
->
rmass
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
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
];
radi
=
radius
[
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
;
radj
=
radius
[
j
];
radsum
=
radi
+
radj
;
if
(
rsq
<
radsum
*
radsum
)
{
r
=
sqrt
(
rsq
);
rinv
=
1.0
/
r
;
rsqinv
=
1.0
/
rsq
;
// relative translational velocity
vr1
=
v
[
i
][
0
]
-
v
[
j
][
0
];
vr2
=
v
[
i
][
1
]
-
v
[
j
][
1
];
vr3
=
v
[
i
][
2
]
-
v
[
j
][
2
];
// normal component
vnnr
=
vr1
*
delx
+
vr2
*
dely
+
vr3
*
delz
;
vn1
=
delx
*
vnnr
*
rsqinv
;
vn2
=
dely
*
vnnr
*
rsqinv
;
vn3
=
delz
*
vnnr
*
rsqinv
;
// tangential component
vt1
=
vr1
-
vn1
;
vt2
=
vr2
-
vn2
;
vt3
=
vr3
-
vn3
;
// relative rotational velocity
wr1
=
(
radi
*
omega
[
i
][
0
]
+
radj
*
omega
[
j
][
0
])
*
rinv
;
wr2
=
(
radi
*
omega
[
i
][
1
]
+
radj
*
omega
[
j
][
1
])
*
rinv
;
wr3
=
(
radi
*
omega
[
i
][
2
]
+
radj
*
omega
[
j
][
2
])
*
rinv
;
// meff = effective mass of pair of particles
// if I or J part of rigid body, use body mass
// if I or J is frozen, meff is other particle
mi
=
rmass
[
i
];
mj
=
rmass
[
j
];
if
(
fix_rigid
)
{
if
(
mass_rigid
[
i
]
>
0.0
)
mi
=
mass_rigid
[
i
];
if
(
mass_rigid
[
j
]
>
0.0
)
mj
=
mass_rigid
[
j
];
}
meff
=
mi
*
mj
/
(
mi
+
mj
);
if
(
mask
[
i
]
&
freeze_group_bit
)
meff
=
mj
;
if
(
mask
[
j
]
&
freeze_group_bit
)
meff
=
mi
;
// normal forces = Hookian contact + normal velocity damping
damp
=
meff
*
gamman
*
vnnr
*
rsqinv
;
ccel
=
kn
*
(
radsum
-
r
)
*
rinv
-
damp
;
// relative velocities
vtr1
=
vt1
-
(
delz
*
wr2
-
dely
*
wr3
);
vtr2
=
vt2
-
(
delx
*
wr3
-
delz
*
wr1
);
vtr3
=
vt3
-
(
dely
*
wr1
-
delx
*
wr2
);
vrel
=
vtr1
*
vtr1
+
vtr2
*
vtr2
+
vtr3
*
vtr3
;
vrel
=
sqrt
(
vrel
);
// force normalization
fn
=
xmu
*
fabs
(
ccel
*
r
);
fs
=
meff
*
gammat
*
vrel
;
if
(
vrel
!=
0.0
)
ft
=
MIN
(
fn
,
fs
)
/
vrel
;
else
ft
=
0.0
;
// tangential force due to tangential velocity damping
fs1
=
-
ft
*
vtr1
;
fs2
=
-
ft
*
vtr2
;
fs3
=
-
ft
*
vtr3
;
// forces & torques
fx
=
delx
*
ccel
+
fs1
;
fy
=
dely
*
ccel
+
fs2
;
fz
=
delz
*
ccel
+
fs3
;
f
[
i
][
0
]
+=
fx
;
f
[
i
][
1
]
+=
fy
;
f
[
i
][
2
]
+=
fz
;
tor1
=
rinv
*
(
dely
*
fs3
-
delz
*
fs2
);
tor2
=
rinv
*
(
delz
*
fs1
-
delx
*
fs3
);
tor3
=
rinv
*
(
delx
*
fs2
-
dely
*
fs1
);
torque
[
i
][
0
]
-=
radi
*
tor1
;
torque
[
i
][
1
]
-=
radi
*
tor2
;
torque
[
i
][
2
]
-=
radi
*
tor3
;
if
(
newton_pair
||
j
<
nlocal
)
{
f
[
j
][
0
]
-=
fx
;
f
[
j
][
1
]
-=
fy
;
f
[
j
][
2
]
-=
fz
;
torque
[
j
][
0
]
-=
radj
*
tor1
;
torque
[
j
][
1
]
-=
radj
*
tor2
;
torque
[
j
][
2
]
-=
radj
*
tor3
;
}
if
(
evflag
)
ev_tally_xyz
(
i
,
j
,
nlocal
,
newton_pair
,
0.0
,
0.0
,
fx
,
fy
,
fz
,
delx
,
dely
,
delz
);
}
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ---------------------------------------------------------------------- */
double
PairGranHooke
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
radi
,
radj
,
radsum
,
r
,
rinv
,
rsqinv
;
double
delx
,
dely
,
delz
;
double
vr1
,
vr2
,
vr3
,
vnnr
,
vn1
,
vn2
,
vn3
,
vt1
,
vt2
,
vt3
,
wr1
,
wr2
,
wr3
;
double
vtr1
,
vtr2
,
vtr3
,
vrel
;
double
mi
,
mj
,
meff
,
damp
,
ccel
;
double
fn
,
fs
,
ft
;
double
*
radius
=
atom
->
radius
;
radi
=
radius
[
i
];
radj
=
radius
[
j
];
radsum
=
radi
+
radj
;
// zero out forces if caller requests non-touching pair outside cutoff
if
(
rsq
>=
radsum
*
radsum
)
{
fforce
=
0.0
;
for
(
int
m
=
0
;
m
<
single_extra
;
m
++
)
svector
[
m
]
=
0.0
;
return
0.0
;
}
r
=
sqrt
(
rsq
);
rinv
=
1.0
/
r
;
rsqinv
=
1.0
/
rsq
;
// relative translational velocity
double
**
v
=
atom
->
v
;
vr1
=
v
[
i
][
0
]
-
v
[
j
][
0
];
vr2
=
v
[
i
][
1
]
-
v
[
j
][
1
];
vr3
=
v
[
i
][
2
]
-
v
[
j
][
2
];
// normal component
double
**
x
=
atom
->
x
;
delx
=
x
[
i
][
0
]
-
x
[
j
][
0
];
dely
=
x
[
i
][
1
]
-
x
[
j
][
1
];
delz
=
x
[
i
][
2
]
-
x
[
j
][
2
];
vnnr
=
vr1
*
delx
+
vr2
*
dely
+
vr3
*
delz
;
vn1
=
delx
*
vnnr
*
rsqinv
;
vn2
=
dely
*
vnnr
*
rsqinv
;
vn3
=
delz
*
vnnr
*
rsqinv
;
// tangential component
vt1
=
vr1
-
vn1
;
vt2
=
vr2
-
vn2
;
vt3
=
vr3
-
vn3
;
// relative rotational velocity
double
**
omega
=
atom
->
omega
;
wr1
=
(
radi
*
omega
[
i
][
0
]
+
radj
*
omega
[
j
][
0
])
*
rinv
;
wr2
=
(
radi
*
omega
[
i
][
1
]
+
radj
*
omega
[
j
][
1
])
*
rinv
;
wr3
=
(
radi
*
omega
[
i
][
2
]
+
radj
*
omega
[
j
][
2
])
*
rinv
;
// meff = effective mass of pair of particles
// if I or J part of rigid body, use body mass
// if I or J is frozen, meff is other particle
double
*
rmass
=
atom
->
rmass
;
int
*
mask
=
atom
->
mask
;
mi
=
rmass
[
i
];
mj
=
rmass
[
j
];
if
(
fix_rigid
)
{
// NOTE: insure mass_rigid is current for owned+ghost atoms?
if
(
mass_rigid
[
i
]
>
0.0
)
mi
=
mass_rigid
[
i
];
if
(
mass_rigid
[
j
]
>
0.0
)
mj
=
mass_rigid
[
j
];
}
meff
=
mi
*
mj
/
(
mi
+
mj
);
if
(
mask
[
i
]
&
freeze_group_bit
)
meff
=
mj
;
if
(
mask
[
j
]
&
freeze_group_bit
)
meff
=
mi
;
// normal forces = Hookian contact + normal velocity damping
damp
=
meff
*
gamman
*
vnnr
*
rsqinv
;
ccel
=
kn
*
(
radsum
-
r
)
*
rinv
-
damp
;
// relative velocities
vtr1
=
vt1
-
(
delz
*
wr2
-
dely
*
wr3
);
vtr2
=
vt2
-
(
delx
*
wr3
-
delz
*
wr1
);
vtr3
=
vt3
-
(
dely
*
wr1
-
delx
*
wr2
);
vrel
=
vtr1
*
vtr1
+
vtr2
*
vtr2
+
vtr3
*
vtr3
;
vrel
=
sqrt
(
vrel
);
// force normalization
fn
=
xmu
*
fabs
(
ccel
*
r
);
fs
=
meff
*
gammat
*
vrel
;
if
(
vrel
!=
0.0
)
ft
=
MIN
(
fn
,
fs
)
/
vrel
;
else
ft
=
0.0
;
// set force and return no energy
fforce
=
ccel
;
// set single_extra quantities
svector
[
0
]
=
-
ft
*
vtr1
;
svector
[
1
]
=
-
ft
*
vtr2
;
svector
[
2
]
=
-
ft
*
vtr3
;
svector
[
3
]
=
sqrt
(
svector
[
0
]
*
svector
[
0
]
+
svector
[
1
]
*
svector
[
1
]
+
svector
[
2
]
*
svector
[
2
]);
svector
[
4
]
=
vn1
;
svector
[
5
]
=
vn2
;
svector
[
6
]
=
vn3
;
svector
[
7
]
=
vt1
;
svector
[
8
]
=
vt2
;
svector
[
9
]
=
vt3
;
return
0.0
;
}
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