Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F68443528
body_nparticle.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Jun 27, 10:22
Size
7 KB
Mime Type
text/x-c
Expires
Sat, Jun 29, 10:22 (2 d)
Engine
blob
Format
Raw Data
Handle
18529973
Attached To
rLAMMPS lammps
body_nparticle.cpp
View Options
/* ----------------------------------------------------------------------
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 <stdlib.h>
#include "body_nparticle.h"
#include "math_extra.h"
#include "atom_vec_body.h"
#include "atom.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define EPSILON 1.0e-7
enum
{
SPHERE
,
LINE
,
TRI
};
// also in DumpImage
/* ---------------------------------------------------------------------- */
BodyNparticle
::
BodyNparticle
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Body
(
lmp
,
narg
,
arg
),
imflag
(
NULL
),
imdata
(
NULL
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Invalid body nparticle command"
);
int
nmin
=
force
->
inumeric
(
FLERR
,
arg
[
1
]);
int
nmax
=
force
->
inumeric
(
FLERR
,
arg
[
2
]);
if
(
nmin
<=
0
||
nmin
>
nmax
)
error
->
all
(
FLERR
,
"Invalid body nparticle command"
);
size_forward
=
0
;
size_border
=
1
+
3
*
nmax
;
// NOTE: need to set appropriate nnbin param for dcp
icp
=
new
MyPoolChunk
<
int
>
(
1
,
1
);
dcp
=
new
MyPoolChunk
<
double
>
(
3
*
nmin
,
3
*
nmax
);
memory
->
create
(
imflag
,
nmax
,
"body/nparticle:imflag"
);
memory
->
create
(
imdata
,
nmax
,
4
,
"body/nparticle:imdata"
);
}
/* ---------------------------------------------------------------------- */
BodyNparticle
::~
BodyNparticle
()
{
delete
icp
;
delete
dcp
;
memory
->
destroy
(
imflag
);
memory
->
destroy
(
imdata
);
}
/* ---------------------------------------------------------------------- */
int
BodyNparticle
::
nsub
(
AtomVecBody
::
Bonus
*
bonus
)
{
return
bonus
->
ivalue
[
0
];
}
/* ---------------------------------------------------------------------- */
double
*
BodyNparticle
::
coords
(
AtomVecBody
::
Bonus
*
bonus
)
{
return
bonus
->
dvalue
;
}
/* ---------------------------------------------------------------------- */
int
BodyNparticle
::
pack_border_body
(
AtomVecBody
::
Bonus
*
bonus
,
double
*
buf
)
{
int
nsub
=
bonus
->
ivalue
[
0
];
buf
[
0
]
=
nsub
;
memcpy
(
&
buf
[
1
],
bonus
->
dvalue
,
3
*
nsub
*
sizeof
(
double
));
return
1
+
3
*
nsub
;
}
/* ---------------------------------------------------------------------- */
int
BodyNparticle
::
unpack_border_body
(
AtomVecBody
::
Bonus
*
bonus
,
double
*
buf
)
{
int
nsub
=
static_cast
<
int
>
(
buf
[
0
]);
bonus
->
ivalue
[
0
]
=
nsub
;
memcpy
(
bonus
->
dvalue
,
&
buf
[
1
],
3
*
nsub
*
sizeof
(
double
));
return
1
+
3
*
nsub
;
}
/* ----------------------------------------------------------------------
populate bonus data structure with data file values
------------------------------------------------------------------------- */
void
BodyNparticle
::
data_body
(
int
ibonus
,
int
ninteger
,
int
ndouble
,
int
*
ifile
,
double
*
dfile
)
{
AtomVecBody
::
Bonus
*
bonus
=
&
avec
->
bonus
[
ibonus
];
// set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles
if
(
ninteger
!=
1
)
error
->
one
(
FLERR
,
"Incorrect # of integer values in "
"Bodies section of data file"
);
int
nsub
=
ifile
[
0
];
if
(
nsub
<
1
)
error
->
one
(
FLERR
,
"Incorrect integer value in "
"Bodies section of data file"
);
if
(
ndouble
!=
6
+
3
*
nsub
)
error
->
one
(
FLERR
,
"Incorrect # of floating-point values in "
"Bodies section of data file"
);
bonus
->
ninteger
=
1
;
bonus
->
ivalue
=
icp
->
get
(
bonus
->
iindex
);
bonus
->
ivalue
[
0
]
=
nsub
;
bonus
->
ndouble
=
3
*
nsub
;
bonus
->
dvalue
=
dcp
->
get
(
bonus
->
ndouble
,
bonus
->
dindex
);
// diagonalize inertia tensor
double
tensor
[
3
][
3
];
tensor
[
0
][
0
]
=
dfile
[
0
];
tensor
[
1
][
1
]
=
dfile
[
1
];
tensor
[
2
][
2
]
=
dfile
[
2
];
tensor
[
0
][
1
]
=
tensor
[
1
][
0
]
=
dfile
[
3
];
tensor
[
0
][
2
]
=
tensor
[
2
][
0
]
=
dfile
[
4
];
tensor
[
1
][
2
]
=
tensor
[
2
][
1
]
=
dfile
[
5
];
double
*
inertia
=
bonus
->
inertia
;
double
evectors
[
3
][
3
];
int
ierror
=
MathExtra
::
jacobi
(
tensor
,
inertia
,
evectors
);
if
(
ierror
)
error
->
one
(
FLERR
,
"Insufficient Jacobi rotations for body nparticle"
);
// if any principal moment < scaled EPSILON, set to 0.0
double
max
;
max
=
MAX
(
inertia
[
0
],
inertia
[
1
]);
max
=
MAX
(
max
,
inertia
[
2
]);
if
(
inertia
[
0
]
<
EPSILON
*
max
)
inertia
[
0
]
=
0.0
;
if
(
inertia
[
1
]
<
EPSILON
*
max
)
inertia
[
1
]
=
0.0
;
if
(
inertia
[
2
]
<
EPSILON
*
max
)
inertia
[
2
]
=
0.0
;
// exyz_space = principal axes in space frame
double
ex_space
[
3
],
ey_space
[
3
],
ez_space
[
3
];
ex_space
[
0
]
=
evectors
[
0
][
0
];
ex_space
[
1
]
=
evectors
[
1
][
0
];
ex_space
[
2
]
=
evectors
[
2
][
0
];
ey_space
[
0
]
=
evectors
[
0
][
1
];
ey_space
[
1
]
=
evectors
[
1
][
1
];
ey_space
[
2
]
=
evectors
[
2
][
1
];
ez_space
[
0
]
=
evectors
[
0
][
2
];
ez_space
[
1
]
=
evectors
[
1
][
2
];
ez_space
[
2
]
=
evectors
[
2
][
2
];
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd vector if needed
double
cross
[
3
];
MathExtra
::
cross3
(
ex_space
,
ey_space
,
cross
);
if
(
MathExtra
::
dot3
(
cross
,
ez_space
)
<
0.0
)
MathExtra
::
negate3
(
ez_space
);
// create initial quaternion
MathExtra
::
exyz_to_q
(
ex_space
,
ey_space
,
ez_space
,
bonus
->
quat
);
// bonus->dvalue = sub-particle displacements in body frame
double
delta
[
3
];
int
j
=
6
;
int
k
=
0
;
for
(
int
i
=
0
;
i
<
nsub
;
i
++
)
{
delta
[
0
]
=
dfile
[
j
];
delta
[
1
]
=
dfile
[
j
+
1
];
delta
[
2
]
=
dfile
[
j
+
2
];
MathExtra
::
transpose_matvec
(
ex_space
,
ey_space
,
ez_space
,
delta
,
&
bonus
->
dvalue
[
k
]);
j
+=
3
;
k
+=
3
;
}
}
/* ----------------------------------------------------------------------
return radius of body particle defined by ifile/dfile params
params are ordered as in data file
called by Molecule class which needs single body size
------------------------------------------------------------------------- */
double
BodyNparticle
::
radius_body
(
int
ninteger
,
int
ndouble
,
int
*
ifile
,
double
*
dfile
)
{
int
nsub
=
ifile
[
0
];
if
(
nsub
<
1
)
error
->
one
(
FLERR
,
"Incorrect integer value in "
"Bodies section of data file"
);
if
(
ndouble
!=
6
+
3
*
nsub
)
error
->
one
(
FLERR
,
"Incorrect # of floating-point values in "
"Bodies section of data file"
);
// sub-particle coords are relative to body center at (0,0,0)
// offset = 6 for sub-particle coords
double
onerad
;
double
maxrad
=
0.0
;
double
delta
[
3
];
int
offset
=
6
;
for
(
int
i
=
0
;
i
<
nsub
;
i
++
)
{
delta
[
0
]
=
dfile
[
offset
];
delta
[
1
]
=
dfile
[
offset
+
1
];
delta
[
2
]
=
dfile
[
offset
+
2
];
offset
+=
3
;
onerad
=
MathExtra
::
len3
(
delta
);
maxrad
=
MAX
(
maxrad
,
onerad
);
}
return
maxrad
;
}
/* ---------------------------------------------------------------------- */
int
BodyNparticle
::
noutcol
()
{
return
3
;
}
/* ---------------------------------------------------------------------- */
int
BodyNparticle
::
noutrow
(
int
ibonus
)
{
return
avec
->
bonus
[
ibonus
].
ivalue
[
0
];
}
/* ---------------------------------------------------------------------- */
void
BodyNparticle
::
output
(
int
ibonus
,
int
m
,
double
*
values
)
{
AtomVecBody
::
Bonus
*
bonus
=
&
avec
->
bonus
[
ibonus
];
double
p
[
3
][
3
];
MathExtra
::
quat_to_mat
(
bonus
->
quat
,
p
);
MathExtra
::
matvec
(
p
,
&
bonus
->
dvalue
[
3
*
m
],
values
);
double
*
x
=
atom
->
x
[
bonus
->
ilocal
];
values
[
0
]
+=
x
[
0
];
values
[
1
]
+=
x
[
1
];
values
[
2
]
+=
x
[
2
];
}
/* ---------------------------------------------------------------------- */
int
BodyNparticle
::
image
(
int
ibonus
,
double
flag1
,
double
flag2
,
int
*&
ivec
,
double
**&
darray
)
{
double
p
[
3
][
3
];
double
*
x
;
AtomVecBody
::
Bonus
*
bonus
=
&
avec
->
bonus
[
ibonus
];
int
n
=
bonus
->
ivalue
[
0
];
for
(
int
i
=
0
;
i
<
n
;
i
++
)
{
imflag
[
i
]
=
SPHERE
;
MathExtra
::
quat_to_mat
(
bonus
->
quat
,
p
);
MathExtra
::
matvec
(
p
,
&
bonus
->
dvalue
[
3
*
i
],
imdata
[
i
]);
x
=
atom
->
x
[
bonus
->
ilocal
];
imdata
[
i
][
0
]
+=
x
[
0
];
imdata
[
i
][
1
]
+=
x
[
1
];
imdata
[
i
][
2
]
+=
x
[
2
];
imdata
[
i
][
3
]
=
flag1
;
}
ivec
=
imflag
;
darray
=
imdata
;
return
n
;
}
Event Timeline
Log In to Comment