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body_nparticle.cpp
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Tue, Aug 20, 16:52
Size
7 KB
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text/x-c
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Thu, Aug 22, 16:52 (1 d, 23 h)
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blob
Format
Raw Data
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20039485
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rLAMMPS lammps
body_nparticle.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 <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
;
}
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