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fix_wall_region.cpp
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rLAMMPS lammps
fix_wall_region.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 "stdlib.h"
#include "string.h"
#include "fix_wall_region.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "region.h"
#include "lattice.h"
#include "update.h"
#include "output.h"
#include "respa.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
enum
{
LJ93
,
LJ126
,
COLLOID
,
HARMONIC
};
/* ---------------------------------------------------------------------- */
FixWallRegion
::
FixWallRegion
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
8
)
error
->
all
(
"Illegal fix wall/region command"
);
scalar_flag
=
1
;
vector_flag
=
1
;
size_vector
=
3
;
global_freq
=
1
;
extscalar
=
1
;
extvector
=
1
;
// parse args
iregion
=
domain
->
find_region
(
arg
[
3
]);
if
(
iregion
==
-
1
)
error
->
all
(
"Fix wall/region region ID does not exist"
);
if
(
strcmp
(
arg
[
4
],
"lj93"
)
==
0
)
style
=
LJ93
;
else
if
(
strcmp
(
arg
[
4
],
"lj126"
)
==
0
)
style
=
LJ126
;
else
if
(
strcmp
(
arg
[
4
],
"colloid"
)
==
0
)
style
=
COLLOID
;
else
if
(
strcmp
(
arg
[
4
],
"harmonic"
)
==
0
)
style
=
HARMONIC
;
else
error
->
all
(
"Illegal fix wall/region command"
);
epsilon
=
atof
(
arg
[
5
]);
sigma
=
atof
(
arg
[
6
]);
cutoff
=
atof
(
arg
[
7
]);
if
(
cutoff
<=
0.0
)
error
->
all
(
"Fix wall/region cutoff <= 0.0"
);
eflag
=
0
;
ewall
[
0
]
=
ewall
[
1
]
=
ewall
[
2
]
=
ewall
[
3
]
=
0.0
;
}
/* ---------------------------------------------------------------------- */
int
FixWallRegion
::
setmask
()
{
int
mask
=
0
;
mask
|=
POST_FORCE
;
mask
|=
THERMO_ENERGY
;
mask
|=
POST_FORCE_RESPA
;
mask
|=
MIN_POST_FORCE
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixWallRegion
::
init
()
{
// error checks for style COLLOID
// insure all particle shapes are spherical
// can be polydisperse
// insure all particles in group are extended particles
if
(
style
==
COLLOID
)
{
if
(
!
atom
->
avec
->
shape_type
)
error
->
all
(
"Fix wall/region colloid requires atom attribute shape"
);
if
(
atom
->
radius_flag
)
error
->
all
(
"Fix wall/region colloid cannot be used with "
"atom attribute diameter"
);
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
if
((
atom
->
shape
[
i
][
0
]
!=
atom
->
shape
[
i
][
1
])
||
(
atom
->
shape
[
i
][
0
]
!=
atom
->
shape
[
i
][
2
])
||
(
atom
->
shape
[
i
][
1
]
!=
atom
->
shape
[
i
][
2
]))
error
->
all
(
"Fix wall/region colloid requires spherical particles"
);
double
**
shape
=
atom
->
shape
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
flag
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
if
(
atom
->
shape
[
type
[
i
]][
0
]
==
0.0
)
flag
=
1
;
int
flagall
;
MPI_Allreduce
(
&
flag
,
&
flagall
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
if
(
flagall
)
error
->
all
(
"Fix wall/region colloid requires extended particles"
);
}
// setup coefficients for each style
if
(
style
==
LJ93
)
{
coeff1
=
6.0
/
5.0
*
epsilon
*
pow
(
sigma
,
9.0
);
coeff2
=
3.0
*
epsilon
*
pow
(
sigma
,
3.0
);
coeff3
=
2.0
/
15.0
*
epsilon
*
pow
(
sigma
,
9.0
);
coeff4
=
epsilon
*
pow
(
sigma
,
3.0
);
double
rinv
=
1.0
/
cutoff
;
double
r2inv
=
rinv
*
rinv
;
double
r4inv
=
r2inv
*
r2inv
;
offset
=
coeff3
*
r4inv
*
r4inv
*
rinv
-
coeff4
*
r2inv
*
rinv
;
}
else
if
(
style
==
LJ126
)
{
coeff1
=
48.0
*
epsilon
*
pow
(
sigma
,
12.0
);
coeff2
=
24.0
*
epsilon
*
pow
(
sigma
,
6.0
);
coeff3
=
4.0
*
epsilon
*
pow
(
sigma
,
12.0
);
coeff4
=
4.0
*
epsilon
*
pow
(
sigma
,
6.0
);
double
r2inv
=
1.0
/
(
cutoff
*
cutoff
);
double
r6inv
=
r2inv
*
r2inv
*
r2inv
;
offset
=
r6inv
*
(
coeff3
*
r6inv
-
coeff4
);
}
else
if
(
style
==
COLLOID
)
{
coeff1
=
-
4.0
/
315.0
*
epsilon
*
pow
(
sigma
,
6.0
);
coeff2
=
-
2.0
/
3.0
*
epsilon
;
coeff3
=
epsilon
*
pow
(
sigma
,
6.0
)
/
7560.0
;
coeff4
=
epsilon
/
6.0
;
double
rinv
=
1.0
/
cutoff
;
double
r2inv
=
rinv
*
rinv
;
double
r4inv
=
r2inv
*
r2inv
;
offset
=
coeff3
*
r4inv
*
r4inv
*
rinv
-
coeff4
*
r2inv
*
rinv
;
}
if
(
strcmp
(
update
->
integrate_style
,
"respa"
)
==
0
)
nlevels_respa
=
((
Respa
*
)
update
->
integrate
)
->
nlevels
;
}
/* ---------------------------------------------------------------------- */
void
FixWallRegion
::
setup
(
int
vflag
)
{
if
(
strcmp
(
update
->
integrate_style
,
"verlet"
)
==
0
)
post_force
(
vflag
);
else
{
((
Respa
*
)
update
->
integrate
)
->
copy_flevel_f
(
nlevels_respa
-
1
);
post_force_respa
(
vflag
,
nlevels_respa
-
1
,
0
);
((
Respa
*
)
update
->
integrate
)
->
copy_f_flevel
(
nlevels_respa
-
1
);
}
}
/* ---------------------------------------------------------------------- */
void
FixWallRegion
::
min_setup
(
int
vflag
)
{
post_force
(
vflag
);
}
/* ---------------------------------------------------------------------- */
void
FixWallRegion
::
post_force
(
int
vflag
)
{
int
i
,
m
,
n
;
double
fx
,
fy
,
fz
,
tooclose
;
eflag
=
0
;
ewall
[
0
]
=
ewall
[
1
]
=
ewall
[
2
]
=
ewall
[
3
]
=
0.0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
**
shape
=
atom
->
shape
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
Region
*
region
=
domain
->
regions
[
iregion
];
int
onflag
=
0
;
// region->match() insures particle is in region or on surface, else error
// if returned contact dist r = 0, is on surface, also an error
// in COLLOID case, r <= shape radius is an error
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
if
(
!
region
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
{
onflag
=
1
;
continue
;
}
if
(
style
==
COLLOID
)
tooclose
=
shape
[
type
[
i
]][
0
];
else
tooclose
=
0.0
;
n
=
region
->
surface
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
],
cutoff
);
for
(
m
=
0
;
m
<
n
;
m
++
)
{
if
(
region
->
contact
[
m
].
r
<=
tooclose
)
{
onflag
=
1
;
continue
;
}
if
(
style
==
LJ93
)
lj93
(
region
->
contact
[
m
].
r
);
else
if
(
style
==
LJ126
)
lj126
(
region
->
contact
[
m
].
r
);
else
if
(
style
==
COLLOID
)
colloid
(
region
->
contact
[
m
].
r
,
shape
[
type
[
i
]][
0
]);
else
harmonic
(
region
->
contact
[
m
].
r
);
ewall
[
0
]
+=
eng
;
fx
=
fwall
*
region
->
contact
[
m
].
delx
;
fy
=
fwall
*
region
->
contact
[
m
].
dely
;
fz
=
fwall
*
region
->
contact
[
m
].
delz
;
f
[
i
][
0
]
+=
fx
;
f
[
i
][
1
]
+=
fy
;
f
[
i
][
2
]
+=
fz
;
ewall
[
1
]
-=
fx
;
ewall
[
2
]
-=
fy
;
ewall
[
3
]
-=
fz
;
}
}
if
(
onflag
)
error
->
one
(
"Particle on or inside fix wall/region surface"
);
}
/* ---------------------------------------------------------------------- */
void
FixWallRegion
::
post_force_respa
(
int
vflag
,
int
ilevel
,
int
iloop
)
{
if
(
ilevel
==
nlevels_respa
-
1
)
post_force
(
vflag
);
}
/* ---------------------------------------------------------------------- */
void
FixWallRegion
::
min_post_force
(
int
vflag
)
{
post_force
(
vflag
);
}
/* ----------------------------------------------------------------------
energy of wall interaction
------------------------------------------------------------------------- */
double
FixWallRegion
::
compute_scalar
()
{
// only sum across procs one time
if
(
eflag
==
0
)
{
MPI_Allreduce
(
ewall
,
ewall_all
,
4
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
eflag
=
1
;
}
return
ewall_all
[
0
];
}
/* ----------------------------------------------------------------------
components of force on wall
------------------------------------------------------------------------- */
double
FixWallRegion
::
compute_vector
(
int
n
)
{
// only sum across procs one time
if
(
eflag
==
0
)
{
MPI_Allreduce
(
ewall
,
ewall_all
,
4
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
eflag
=
1
;
}
return
ewall_all
[
n
+
1
];
}
/* ----------------------------------------------------------------------
LJ 9/3 interaction for particle with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void
FixWallRegion
::
lj93
(
double
r
)
{
double
rinv
=
1.0
/
r
;
double
r2inv
=
rinv
*
rinv
;
double
r4inv
=
r2inv
*
r2inv
;
double
r10inv
=
r4inv
*
r4inv
*
r2inv
;
fwall
=
coeff1
*
r10inv
-
coeff2
*
r4inv
;
eng
=
coeff3
*
r4inv
*
r4inv
*
rinv
-
coeff4
*
r2inv
*
rinv
-
offset
;
}
/* ----------------------------------------------------------------------
LJ 12/6 interaction for particle with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void
FixWallRegion
::
lj126
(
double
r
)
{
double
rinv
=
1.0
/
r
;
double
r2inv
=
rinv
*
rinv
;
double
r6inv
=
r2inv
*
r2inv
*
r2inv
;
fwall
=
r6inv
*
(
coeff1
*
r6inv
-
coeff2
)
*
rinv
;
eng
=
r6inv
*
(
coeff3
*
r6inv
-
coeff4
)
-
offset
;
}
/* ----------------------------------------------------------------------
colloid interaction for finite-size particle of rad with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void
FixWallRegion
::
colloid
(
double
r
,
double
rad
)
{
double
new_coeff2
=
coeff2
*
rad
*
rad
*
rad
;
double
diam
=
2.0
*
rad
;
double
rad2
=
rad
*
rad
;
double
rad4
=
rad2
*
rad2
;
double
rad8
=
rad4
*
rad4
;
double
delta2
=
rad2
-
r
*
r
;
double
rinv
=
1.0
/
delta2
;
double
r2inv
=
rinv
*
rinv
;
double
r4inv
=
r2inv
*
r2inv
;
double
r8inv
=
r4inv
*
r4inv
;
fwall
=
coeff1
*
(
rad8
*
rad
+
27.0
*
rad4
*
rad2
*
rad
*
pow
(
r
,
2.0
)
+
63.0
*
rad4
*
rad
*
pow
(
r
,
4.0
)
+
21.0
*
rad2
*
rad
*
pow
(
r
,
6.0
))
*
r8inv
-
new_coeff2
*
r2inv
;
double
r2
=
0.5
*
diam
-
r
;
double
rinv2
=
1.0
/
r2
;
double
r2inv2
=
rinv2
*
rinv2
;
double
r4inv2
=
r2inv2
*
r2inv2
;
double
r6inv2
=
r4inv2
*
r2inv2
;
double
r3
=
r
+
0.5
*
diam
;
double
rinv3
=
1.0
/
r3
;
double
r2inv3
=
rinv3
*
rinv3
;
double
r4inv3
=
r2inv3
*
r2inv3
;
double
r6inv3
=
r4inv3
*
r2inv3
;
eng
=
coeff3
*
((
-
3.5
*
diam
+
r
)
*
r4inv2
*
r2inv2
*
rinv2
+
(
3.5
*
diam
+
r
)
*
r4inv3
*
r2inv3
*
rinv3
)
-
coeff4
*
((
-
diam
*
r
+
r2
*
r3
*
(
log
(
-
r2
)
-
log
(
r3
)))
*
(
-
rinv2
)
*
rinv3
)
-
offset
;
}
/* ----------------------------------------------------------------------
harmonic interaction for particle with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void
FixWallRegion
::
harmonic
(
double
r
)
{
fwall
=
2.0
*
epsilon
*
r
;
eng
=
epsilon
*
r
*
r
-
offset
;
}
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