Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F88613980
atom_vec_ellipsoid.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
Sat, Oct 19, 18:31
Size
38 KB
Mime Type
text/x-c
Expires
Mon, Oct 21, 18:31 (2 d)
Engine
blob
Format
Raw Data
Handle
21256075
Attached To
rLAMMPS lammps
atom_vec_ellipsoid.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include <stdlib.h>
#include "atom_vec_ellipsoid.h"
#include "math_extra.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
/* ---------------------------------------------------------------------- */
AtomVecEllipsoid
::
AtomVecEllipsoid
(
LAMMPS
*
lmp
)
:
AtomVec
(
lmp
)
{
molecular
=
0
;
comm_x_only
=
comm_f_only
=
0
;
size_forward
=
7
;
size_reverse
=
6
;
size_border
=
14
;
size_velocity
=
6
;
size_data_atom
=
7
;
size_data_vel
=
7
;
size_data_bonus
=
8
;
xcol_data
=
5
;
atom
->
ellipsoid_flag
=
1
;
atom
->
rmass_flag
=
atom
->
angmom_flag
=
atom
->
torque_flag
=
1
;
nlocal_bonus
=
nghost_bonus
=
nmax_bonus
=
0
;
bonus
=
NULL
;
}
/* ---------------------------------------------------------------------- */
AtomVecEllipsoid
::~
AtomVecEllipsoid
()
{
memory
->
sfree
(
bonus
);
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
grow
(
int
n
)
{
if
(
n
==
0
)
grow_nmax
();
else
nmax
=
n
;
atom
->
nmax
=
nmax
;
if
(
nmax
<
0
)
error
->
one
(
FLERR
,
"Per-processor system is too big"
);
tag
=
memory
->
grow
(
atom
->
tag
,
nmax
,
"atom:tag"
);
type
=
memory
->
grow
(
atom
->
type
,
nmax
,
"atom:type"
);
mask
=
memory
->
grow
(
atom
->
mask
,
nmax
,
"atom:mask"
);
image
=
memory
->
grow
(
atom
->
image
,
nmax
,
"atom:image"
);
x
=
memory
->
grow
(
atom
->
x
,
nmax
,
3
,
"atom:x"
);
v
=
memory
->
grow
(
atom
->
v
,
nmax
,
3
,
"atom:v"
);
f
=
memory
->
grow
(
atom
->
f
,
nmax
*
comm
->
nthreads
,
3
,
"atom:f"
);
rmass
=
memory
->
grow
(
atom
->
rmass
,
nmax
,
"atom:rmass"
);
angmom
=
memory
->
grow
(
atom
->
angmom
,
nmax
,
3
,
"atom:angmom"
);
torque
=
memory
->
grow
(
atom
->
torque
,
nmax
*
comm
->
nthreads
,
3
,
"atom:torque"
);
ellipsoid
=
memory
->
grow
(
atom
->
ellipsoid
,
nmax
,
"atom:ellipsoid"
);
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
grow_arrays
(
nmax
);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
grow_reset
()
{
tag
=
atom
->
tag
;
type
=
atom
->
type
;
mask
=
atom
->
mask
;
image
=
atom
->
image
;
x
=
atom
->
x
;
v
=
atom
->
v
;
f
=
atom
->
f
;
rmass
=
atom
->
rmass
;
angmom
=
atom
->
angmom
;
torque
=
atom
->
torque
;
ellipsoid
=
atom
->
ellipsoid
;
}
/* ----------------------------------------------------------------------
grow bonus data structure
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
grow_bonus
()
{
nmax_bonus
=
grow_nmax_bonus
(
nmax_bonus
);
if
(
nmax_bonus
<
0
)
error
->
one
(
FLERR
,
"Per-processor system is too big"
);
bonus
=
(
Bonus
*
)
memory
->
srealloc
(
bonus
,
nmax_bonus
*
sizeof
(
Bonus
),
"atom:bonus"
);
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
copy
(
int
i
,
int
j
,
int
delflag
)
{
tag
[
j
]
=
tag
[
i
];
type
[
j
]
=
type
[
i
];
mask
[
j
]
=
mask
[
i
];
image
[
j
]
=
image
[
i
];
x
[
j
][
0
]
=
x
[
i
][
0
];
x
[
j
][
1
]
=
x
[
i
][
1
];
x
[
j
][
2
]
=
x
[
i
][
2
];
v
[
j
][
0
]
=
v
[
i
][
0
];
v
[
j
][
1
]
=
v
[
i
][
1
];
v
[
j
][
2
]
=
v
[
i
][
2
];
rmass
[
j
]
=
rmass
[
i
];
angmom
[
j
][
0
]
=
angmom
[
i
][
0
];
angmom
[
j
][
1
]
=
angmom
[
i
][
1
];
angmom
[
j
][
2
]
=
angmom
[
i
][
2
];
// if deleting atom J via delflag and J has bonus data, then delete it
if
(
delflag
&&
ellipsoid
[
j
]
>=
0
)
{
copy_bonus
(
nlocal_bonus
-
1
,
ellipsoid
[
j
]);
nlocal_bonus
--
;
}
// if atom I has bonus data, reset I's bonus.ilocal to loc J
// do NOT do this if self-copy (I=J) since I's bonus data is already deleted
if
(
ellipsoid
[
i
]
>=
0
&&
i
!=
j
)
bonus
[
ellipsoid
[
i
]].
ilocal
=
j
;
ellipsoid
[
j
]
=
ellipsoid
[
i
];
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
copy_arrays
(
i
,
j
,
delflag
);
}
/* ----------------------------------------------------------------------
copy bonus data from I to J, effectively deleting the J entry
also reset ellipsoid that points to I to now point to J
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
copy_bonus
(
int
i
,
int
j
)
{
ellipsoid
[
bonus
[
i
].
ilocal
]
=
j
;
memcpy
(
&
bonus
[
j
],
&
bonus
[
i
],
sizeof
(
Bonus
));
}
/* ----------------------------------------------------------------------
clear ghost info in bonus data
called before ghosts are recommunicated in comm and irregular
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
clear_bonus
()
{
nghost_bonus
=
0
;
}
/* ----------------------------------------------------------------------
set shape values in bonus data for particle I
oriented aligned with xyz axes
this may create or delete entry in bonus data
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
set_shape
(
int
i
,
double
shapex
,
double
shapey
,
double
shapez
)
{
if
(
ellipsoid
[
i
]
<
0
)
{
if
(
shapex
==
0.0
&&
shapey
==
0.0
&&
shapez
==
0.0
)
return
;
if
(
nlocal_bonus
==
nmax_bonus
)
grow_bonus
();
double
*
shape
=
bonus
[
nlocal_bonus
].
shape
;
double
*
quat
=
bonus
[
nlocal_bonus
].
quat
;
shape
[
0
]
=
shapex
;
shape
[
1
]
=
shapey
;
shape
[
2
]
=
shapez
;
quat
[
0
]
=
1.0
;
quat
[
1
]
=
0.0
;
quat
[
2
]
=
0.0
;
quat
[
3
]
=
0.0
;
bonus
[
nlocal_bonus
].
ilocal
=
i
;
ellipsoid
[
i
]
=
nlocal_bonus
++
;
}
else
if
(
shapex
==
0.0
&&
shapey
==
0.0
&&
shapez
==
0.0
)
{
copy_bonus
(
nlocal_bonus
-
1
,
ellipsoid
[
i
]);
nlocal_bonus
--
;
ellipsoid
[
i
]
=
-
1
;
}
else
{
double
*
shape
=
bonus
[
ellipsoid
[
i
]].
shape
;
shape
[
0
]
=
shapex
;
shape
[
1
]
=
shapey
;
shape
[
2
]
=
shapez
;
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_comm
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
double
dx
,
dy
,
dz
;
double
*
quat
;
m
=
0
;
if
(
pbc_flag
==
0
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
];
buf
[
m
++
]
=
x
[
j
][
1
];
buf
[
m
++
]
=
x
[
j
][
2
];
if
(
ellipsoid
[
j
]
>=
0
)
{
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
}
}
else
{
if
(
domain
->
triclinic
==
0
)
{
dx
=
pbc
[
0
]
*
domain
->
xprd
;
dy
=
pbc
[
1
]
*
domain
->
yprd
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
else
{
dx
=
pbc
[
0
]
*
domain
->
xprd
+
pbc
[
5
]
*
domain
->
xy
+
pbc
[
4
]
*
domain
->
xz
;
dy
=
pbc
[
1
]
*
domain
->
yprd
+
pbc
[
3
]
*
domain
->
yz
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
if
(
ellipsoid
[
j
]
>=
0
)
{
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_comm_vel
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
double
dx
,
dy
,
dz
,
dvx
,
dvy
,
dvz
;
double
*
quat
;
m
=
0
;
if
(
pbc_flag
==
0
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
];
buf
[
m
++
]
=
x
[
j
][
1
];
buf
[
m
++
]
=
x
[
j
][
2
];
if
(
ellipsoid
[
j
]
>=
0
)
{
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
buf
[
m
++
]
=
angmom
[
j
][
0
];
buf
[
m
++
]
=
angmom
[
j
][
1
];
buf
[
m
++
]
=
angmom
[
j
][
2
];
}
}
else
{
if
(
domain
->
triclinic
==
0
)
{
dx
=
pbc
[
0
]
*
domain
->
xprd
;
dy
=
pbc
[
1
]
*
domain
->
yprd
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
else
{
dx
=
pbc
[
0
]
*
domain
->
xprd
+
pbc
[
5
]
*
domain
->
xy
+
pbc
[
4
]
*
domain
->
xz
;
dy
=
pbc
[
1
]
*
domain
->
yprd
+
pbc
[
3
]
*
domain
->
yz
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
if
(
!
deform_vremap
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
if
(
ellipsoid
[
j
]
>=
0
)
{
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
buf
[
m
++
]
=
angmom
[
j
][
0
];
buf
[
m
++
]
=
angmom
[
j
][
1
];
buf
[
m
++
]
=
angmom
[
j
][
2
];
}
}
else
{
dvx
=
pbc
[
0
]
*
h_rate
[
0
]
+
pbc
[
5
]
*
h_rate
[
5
]
+
pbc
[
4
]
*
h_rate
[
4
];
dvy
=
pbc
[
1
]
*
h_rate
[
1
]
+
pbc
[
3
]
*
h_rate
[
3
];
dvz
=
pbc
[
2
]
*
h_rate
[
2
];
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
if
(
ellipsoid
[
j
]
>=
0
)
{
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
if
(
mask
[
i
]
&
deform_groupbit
)
{
buf
[
m
++
]
=
v
[
j
][
0
]
+
dvx
;
buf
[
m
++
]
=
v
[
j
][
1
]
+
dvy
;
buf
[
m
++
]
=
v
[
j
][
2
]
+
dvz
;
}
else
{
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
}
buf
[
m
++
]
=
angmom
[
j
][
0
];
buf
[
m
++
]
=
angmom
[
j
][
1
];
buf
[
m
++
]
=
angmom
[
j
][
2
];
}
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_comm_hybrid
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
double
*
quat
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
if
(
ellipsoid
[
j
]
>=
0
)
{
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
unpack_comm
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
double
*
quat
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
x
[
i
][
0
]
=
buf
[
m
++
];
x
[
i
][
1
]
=
buf
[
m
++
];
x
[
i
][
2
]
=
buf
[
m
++
];
if
(
ellipsoid
[
i
]
>=
0
)
{
quat
=
bonus
[
ellipsoid
[
i
]].
quat
;
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
}
}
}
/* ---------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
unpack_comm_vel
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
double
*
quat
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
x
[
i
][
0
]
=
buf
[
m
++
];
x
[
i
][
1
]
=
buf
[
m
++
];
x
[
i
][
2
]
=
buf
[
m
++
];
if
(
ellipsoid
[
i
]
>=
0
)
{
quat
=
bonus
[
ellipsoid
[
i
]].
quat
;
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
}
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
angmom
[
i
][
0
]
=
buf
[
m
++
];
angmom
[
i
][
1
]
=
buf
[
m
++
];
angmom
[
i
][
2
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
unpack_comm_hybrid
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
double
*
quat
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
if
(
ellipsoid
[
i
]
>=
0
)
{
quat
=
bonus
[
ellipsoid
[
i
]].
quat
;
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_reverse
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
buf
[
m
++
]
=
f
[
i
][
0
];
buf
[
m
++
]
=
f
[
i
][
1
];
buf
[
m
++
]
=
f
[
i
][
2
];
buf
[
m
++
]
=
torque
[
i
][
0
];
buf
[
m
++
]
=
torque
[
i
][
1
];
buf
[
m
++
]
=
torque
[
i
][
2
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_reverse_hybrid
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
buf
[
m
++
]
=
torque
[
i
][
0
];
buf
[
m
++
]
=
torque
[
i
][
1
];
buf
[
m
++
]
=
torque
[
i
][
2
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
unpack_reverse
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
f
[
j
][
0
]
+=
buf
[
m
++
];
f
[
j
][
1
]
+=
buf
[
m
++
];
f
[
j
][
2
]
+=
buf
[
m
++
];
torque
[
j
][
0
]
+=
buf
[
m
++
];
torque
[
j
][
1
]
+=
buf
[
m
++
];
torque
[
j
][
2
]
+=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
unpack_reverse_hybrid
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
torque
[
j
][
0
]
+=
buf
[
m
++
];
torque
[
j
][
1
]
+=
buf
[
m
++
];
torque
[
j
][
2
]
+=
buf
[
m
++
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_border
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
double
dx
,
dy
,
dz
;
double
*
shape
,
*
quat
;
m
=
0
;
if
(
pbc_flag
==
0
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
];
buf
[
m
++
]
=
x
[
j
][
1
];
buf
[
m
++
]
=
x
[
j
][
2
];
buf
[
m
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
if
(
ellipsoid
[
j
]
<
0
)
buf
[
m
++
]
=
ubuf
(
0
).
d
;
else
{
buf
[
m
++
]
=
ubuf
(
1
).
d
;
shape
=
bonus
[
ellipsoid
[
j
]].
shape
;
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
shape
[
0
];
buf
[
m
++
]
=
shape
[
1
];
buf
[
m
++
]
=
shape
[
2
];
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
}
}
else
{
if
(
domain
->
triclinic
==
0
)
{
dx
=
pbc
[
0
]
*
domain
->
xprd
;
dy
=
pbc
[
1
]
*
domain
->
yprd
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
else
{
dx
=
pbc
[
0
];
dy
=
pbc
[
1
];
dz
=
pbc
[
2
];
}
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
buf
[
m
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
if
(
ellipsoid
[
j
]
<
0
)
buf
[
m
++
]
=
ubuf
(
0
).
d
;
else
{
buf
[
m
++
]
=
ubuf
(
1
).
d
;
shape
=
bonus
[
ellipsoid
[
j
]].
shape
;
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
shape
[
0
];
buf
[
m
++
]
=
shape
[
1
];
buf
[
m
++
]
=
shape
[
2
];
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
}
}
if
(
atom
->
nextra_border
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_border
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_border
[
iextra
]]
->
pack_border
(
n
,
list
,
&
buf
[
m
]);
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_border_vel
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
double
dx
,
dy
,
dz
,
dvx
,
dvy
,
dvz
;
double
*
shape
,
*
quat
;
m
=
0
;
if
(
pbc_flag
==
0
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
];
buf
[
m
++
]
=
x
[
j
][
1
];
buf
[
m
++
]
=
x
[
j
][
2
];
buf
[
m
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
if
(
ellipsoid
[
j
]
<
0
)
buf
[
m
++
]
=
ubuf
(
0
).
d
;
else
{
buf
[
m
++
]
=
ubuf
(
1
).
d
;
shape
=
bonus
[
ellipsoid
[
j
]].
shape
;
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
shape
[
0
];
buf
[
m
++
]
=
shape
[
1
];
buf
[
m
++
]
=
shape
[
2
];
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
buf
[
m
++
]
=
angmom
[
j
][
0
];
buf
[
m
++
]
=
angmom
[
j
][
1
];
buf
[
m
++
]
=
angmom
[
j
][
2
];
}
}
else
{
if
(
domain
->
triclinic
==
0
)
{
dx
=
pbc
[
0
]
*
domain
->
xprd
;
dy
=
pbc
[
1
]
*
domain
->
yprd
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
else
{
dx
=
pbc
[
0
];
dy
=
pbc
[
1
];
dz
=
pbc
[
2
];
}
if
(
!
deform_vremap
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
buf
[
m
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
if
(
ellipsoid
[
j
]
<
0
)
buf
[
m
++
]
=
ubuf
(
0
).
d
;
else
{
buf
[
m
++
]
=
ubuf
(
1
).
d
;
shape
=
bonus
[
ellipsoid
[
j
]].
shape
;
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
shape
[
0
];
buf
[
m
++
]
=
shape
[
1
];
buf
[
m
++
]
=
shape
[
2
];
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
buf
[
m
++
]
=
angmom
[
j
][
0
];
buf
[
m
++
]
=
angmom
[
j
][
1
];
buf
[
m
++
]
=
angmom
[
j
][
2
];
}
}
else
{
dvx
=
pbc
[
0
]
*
h_rate
[
0
]
+
pbc
[
5
]
*
h_rate
[
5
]
+
pbc
[
4
]
*
h_rate
[
4
];
dvy
=
pbc
[
1
]
*
h_rate
[
1
]
+
pbc
[
3
]
*
h_rate
[
3
];
dvz
=
pbc
[
2
]
*
h_rate
[
2
];
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
buf
[
m
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
if
(
ellipsoid
[
j
]
<
0
)
buf
[
m
++
]
=
ubuf
(
0
).
d
;
else
{
buf
[
m
++
]
=
ubuf
(
1
).
d
;
shape
=
bonus
[
ellipsoid
[
j
]].
shape
;
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
shape
[
0
];
buf
[
m
++
]
=
shape
[
1
];
buf
[
m
++
]
=
shape
[
2
];
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
if
(
mask
[
i
]
&
deform_groupbit
)
{
buf
[
m
++
]
=
v
[
j
][
0
]
+
dvx
;
buf
[
m
++
]
=
v
[
j
][
1
]
+
dvy
;
buf
[
m
++
]
=
v
[
j
][
2
]
+
dvz
;
}
else
{
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
}
buf
[
m
++
]
=
angmom
[
j
][
0
];
buf
[
m
++
]
=
angmom
[
j
][
1
];
buf
[
m
++
]
=
angmom
[
j
][
2
];
}
}
}
if
(
atom
->
nextra_border
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_border
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_border
[
iextra
]]
->
pack_border
(
n
,
list
,
&
buf
[
m
]);
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_border_hybrid
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
double
*
shape
,
*
quat
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
if
(
ellipsoid
[
j
]
<
0
)
buf
[
m
++
]
=
ubuf
(
0
).
d
;
else
{
buf
[
m
++
]
=
ubuf
(
1
).
d
;
shape
=
bonus
[
ellipsoid
[
j
]].
shape
;
quat
=
bonus
[
ellipsoid
[
j
]].
quat
;
buf
[
m
++
]
=
shape
[
0
];
buf
[
m
++
]
=
shape
[
1
];
buf
[
m
++
]
=
shape
[
2
];
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
unpack_border
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
j
,
m
,
last
;
double
*
shape
,
*
quat
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
if
(
i
==
nmax
)
grow
(
0
);
x
[
i
][
0
]
=
buf
[
m
++
];
x
[
i
][
1
]
=
buf
[
m
++
];
x
[
i
][
2
]
=
buf
[
m
++
];
tag
[
i
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
type
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
mask
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
ellipsoid
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
if
(
ellipsoid
[
i
]
==
0
)
ellipsoid
[
i
]
=
-
1
;
else
{
j
=
nlocal_bonus
+
nghost_bonus
;
if
(
j
==
nmax_bonus
)
grow_bonus
();
shape
=
bonus
[
j
].
shape
;
quat
=
bonus
[
j
].
quat
;
shape
[
0
]
=
buf
[
m
++
];
shape
[
1
]
=
buf
[
m
++
];
shape
[
2
]
=
buf
[
m
++
];
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
bonus
[
j
].
ilocal
=
i
;
ellipsoid
[
i
]
=
j
;
nghost_bonus
++
;
}
}
if
(
atom
->
nextra_border
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_border
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_border
[
iextra
]]
->
unpack_border
(
n
,
first
,
&
buf
[
m
]);
}
/* ---------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
unpack_border_vel
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
j
,
m
,
last
;
double
*
shape
,
*
quat
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
if
(
i
==
nmax
)
grow
(
0
);
x
[
i
][
0
]
=
buf
[
m
++
];
x
[
i
][
1
]
=
buf
[
m
++
];
x
[
i
][
2
]
=
buf
[
m
++
];
tag
[
i
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
type
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
mask
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
ellipsoid
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
if
(
ellipsoid
[
i
]
==
0
)
ellipsoid
[
i
]
=
-
1
;
else
{
j
=
nlocal_bonus
+
nghost_bonus
;
if
(
j
==
nmax_bonus
)
grow_bonus
();
shape
=
bonus
[
j
].
shape
;
quat
=
bonus
[
j
].
quat
;
shape
[
0
]
=
buf
[
m
++
];
shape
[
1
]
=
buf
[
m
++
];
shape
[
2
]
=
buf
[
m
++
];
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
bonus
[
j
].
ilocal
=
i
;
ellipsoid
[
i
]
=
j
;
nghost_bonus
++
;
}
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
angmom
[
i
][
0
]
=
buf
[
m
++
];
angmom
[
i
][
1
]
=
buf
[
m
++
];
angmom
[
i
][
2
]
=
buf
[
m
++
];
}
if
(
atom
->
nextra_border
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_border
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_border
[
iextra
]]
->
unpack_border
(
n
,
first
,
&
buf
[
m
]);
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
unpack_border_hybrid
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
j
,
m
,
last
;
double
*
shape
,
*
quat
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
ellipsoid
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
if
(
ellipsoid
[
i
]
==
0
)
ellipsoid
[
i
]
=
-
1
;
else
{
j
=
nlocal_bonus
+
nghost_bonus
;
if
(
j
==
nmax_bonus
)
grow_bonus
();
shape
=
bonus
[
j
].
shape
;
quat
=
bonus
[
j
].
quat
;
shape
[
0
]
=
buf
[
m
++
];
shape
[
1
]
=
buf
[
m
++
];
shape
[
2
]
=
buf
[
m
++
];
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
bonus
[
j
].
ilocal
=
i
;
ellipsoid
[
i
]
=
j
;
nghost_bonus
++
;
}
}
return
m
;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_exchange
(
int
i
,
double
*
buf
)
{
int
m
=
1
;
buf
[
m
++
]
=
x
[
i
][
0
];
buf
[
m
++
]
=
x
[
i
][
1
];
buf
[
m
++
]
=
x
[
i
][
2
];
buf
[
m
++
]
=
v
[
i
][
0
];
buf
[
m
++
]
=
v
[
i
][
1
];
buf
[
m
++
]
=
v
[
i
][
2
];
buf
[
m
++
]
=
ubuf
(
tag
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
image
[
i
]).
d
;
buf
[
m
++
]
=
rmass
[
i
];
buf
[
m
++
]
=
angmom
[
i
][
0
];
buf
[
m
++
]
=
angmom
[
i
][
1
];
buf
[
m
++
]
=
angmom
[
i
][
2
];
if
(
ellipsoid
[
i
]
<
0
)
buf
[
m
++
]
=
ubuf
(
0
).
d
;
else
{
buf
[
m
++
]
=
ubuf
(
1
).
d
;
int
j
=
ellipsoid
[
i
];
double
*
shape
=
bonus
[
j
].
shape
;
double
*
quat
=
bonus
[
j
].
quat
;
buf
[
m
++
]
=
shape
[
0
];
buf
[
m
++
]
=
shape
[
1
];
buf
[
m
++
]
=
shape
[
2
];
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
}
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
pack_exchange
(
i
,
&
buf
[
m
]);
buf
[
0
]
=
m
;
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
unpack_exchange
(
double
*
buf
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
int
m
=
1
;
x
[
nlocal
][
0
]
=
buf
[
m
++
];
x
[
nlocal
][
1
]
=
buf
[
m
++
];
x
[
nlocal
][
2
]
=
buf
[
m
++
];
v
[
nlocal
][
0
]
=
buf
[
m
++
];
v
[
nlocal
][
1
]
=
buf
[
m
++
];
v
[
nlocal
][
2
]
=
buf
[
m
++
];
tag
[
nlocal
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
type
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
mask
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
image
[
nlocal
]
=
(
imageint
)
ubuf
(
buf
[
m
++
]).
i
;
rmass
[
nlocal
]
=
buf
[
m
++
];
angmom
[
nlocal
][
0
]
=
buf
[
m
++
];
angmom
[
nlocal
][
1
]
=
buf
[
m
++
];
angmom
[
nlocal
][
2
]
=
buf
[
m
++
];
ellipsoid
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
if
(
ellipsoid
[
nlocal
]
==
0
)
ellipsoid
[
nlocal
]
=
-
1
;
else
{
if
(
nlocal_bonus
==
nmax_bonus
)
grow_bonus
();
double
*
shape
=
bonus
[
nlocal_bonus
].
shape
;
double
*
quat
=
bonus
[
nlocal_bonus
].
quat
;
shape
[
0
]
=
buf
[
m
++
];
shape
[
1
]
=
buf
[
m
++
];
shape
[
2
]
=
buf
[
m
++
];
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
bonus
[
nlocal_bonus
].
ilocal
=
nlocal
;
ellipsoid
[
nlocal
]
=
nlocal_bonus
++
;
}
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
unpack_exchange
(
nlocal
,
&
buf
[
m
]);
atom
->
nlocal
++
;
return
m
;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
size_restart
()
{
int
i
;
int
n
=
0
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
ellipsoid
[
i
]
>=
0
)
n
+=
23
;
else
n
+=
16
;
if
(
atom
->
nextra_restart
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_restart
;
iextra
++
)
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
n
+=
modify
->
fix
[
atom
->
extra_restart
[
iextra
]]
->
size_restart
(
i
);
return
n
;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including bonus data
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_restart
(
int
i
,
double
*
buf
)
{
int
m
=
1
;
buf
[
m
++
]
=
x
[
i
][
0
];
buf
[
m
++
]
=
x
[
i
][
1
];
buf
[
m
++
]
=
x
[
i
][
2
];
buf
[
m
++
]
=
ubuf
(
tag
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
image
[
i
]).
d
;
buf
[
m
++
]
=
v
[
i
][
0
];
buf
[
m
++
]
=
v
[
i
][
1
];
buf
[
m
++
]
=
v
[
i
][
2
];
buf
[
m
++
]
=
rmass
[
i
];
buf
[
m
++
]
=
angmom
[
i
][
0
];
buf
[
m
++
]
=
angmom
[
i
][
1
];
buf
[
m
++
]
=
angmom
[
i
][
2
];
if
(
ellipsoid
[
i
]
<
0
)
buf
[
m
++
]
=
ubuf
(
0
).
d
;
else
{
buf
[
m
++
]
=
ubuf
(
1
).
d
;
int
j
=
ellipsoid
[
i
];
buf
[
m
++
]
=
bonus
[
j
].
shape
[
0
];
buf
[
m
++
]
=
bonus
[
j
].
shape
[
1
];
buf
[
m
++
]
=
bonus
[
j
].
shape
[
2
];
buf
[
m
++
]
=
bonus
[
j
].
quat
[
0
];
buf
[
m
++
]
=
bonus
[
j
].
quat
[
1
];
buf
[
m
++
]
=
bonus
[
j
].
quat
[
2
];
buf
[
m
++
]
=
bonus
[
j
].
quat
[
3
];
}
if
(
atom
->
nextra_restart
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_restart
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_restart
[
iextra
]]
->
pack_restart
(
i
,
&
buf
[
m
]);
buf
[
0
]
=
m
;
return
m
;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including bonus data
------------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
unpack_restart
(
double
*
buf
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
{
grow
(
0
);
if
(
atom
->
nextra_store
)
memory
->
grow
(
atom
->
extra
,
nmax
,
atom
->
nextra_store
,
"atom:extra"
);
}
int
m
=
1
;
x
[
nlocal
][
0
]
=
buf
[
m
++
];
x
[
nlocal
][
1
]
=
buf
[
m
++
];
x
[
nlocal
][
2
]
=
buf
[
m
++
];
tag
[
nlocal
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
type
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
mask
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
image
[
nlocal
]
=
(
imageint
)
ubuf
(
buf
[
m
++
]).
i
;
v
[
nlocal
][
0
]
=
buf
[
m
++
];
v
[
nlocal
][
1
]
=
buf
[
m
++
];
v
[
nlocal
][
2
]
=
buf
[
m
++
];
rmass
[
nlocal
]
=
buf
[
m
++
];
angmom
[
nlocal
][
0
]
=
buf
[
m
++
];
angmom
[
nlocal
][
1
]
=
buf
[
m
++
];
angmom
[
nlocal
][
2
]
=
buf
[
m
++
];
ellipsoid
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
if
(
ellipsoid
[
nlocal
]
==
0
)
ellipsoid
[
nlocal
]
=
-
1
;
else
{
if
(
nlocal_bonus
==
nmax_bonus
)
grow_bonus
();
double
*
shape
=
bonus
[
nlocal_bonus
].
shape
;
double
*
quat
=
bonus
[
nlocal_bonus
].
quat
;
shape
[
0
]
=
buf
[
m
++
];
shape
[
1
]
=
buf
[
m
++
];
shape
[
2
]
=
buf
[
m
++
];
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
bonus
[
nlocal_bonus
].
ilocal
=
nlocal
;
ellipsoid
[
nlocal
]
=
nlocal_bonus
++
;
}
double
**
extra
=
atom
->
extra
;
if
(
atom
->
nextra_store
)
{
int
size
=
static_cast
<
int
>
(
buf
[
0
])
-
m
;
for
(
int
i
=
0
;
i
<
size
;
i
++
)
extra
[
nlocal
][
i
]
=
buf
[
m
++
];
}
atom
->
nlocal
++
;
return
m
;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
create_atom
(
int
itype
,
double
*
coord
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
tag
[
nlocal
]
=
0
;
type
[
nlocal
]
=
itype
;
x
[
nlocal
][
0
]
=
coord
[
0
];
x
[
nlocal
][
1
]
=
coord
[
1
];
x
[
nlocal
][
2
]
=
coord
[
2
];
mask
[
nlocal
]
=
1
;
image
[
nlocal
]
=
((
imageint
)
IMGMAX
<<
IMG2BITS
)
|
((
imageint
)
IMGMAX
<<
IMGBITS
)
|
IMGMAX
;
v
[
nlocal
][
0
]
=
0.0
;
v
[
nlocal
][
1
]
=
0.0
;
v
[
nlocal
][
2
]
=
0.0
;
rmass
[
nlocal
]
=
1.0
;
angmom
[
nlocal
][
0
]
=
0.0
;
angmom
[
nlocal
][
1
]
=
0.0
;
angmom
[
nlocal
][
2
]
=
0.0
;
ellipsoid
[
nlocal
]
=
-
1
;
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
data_atom
(
double
*
coord
,
imageint
imagetmp
,
char
**
values
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
tag
[
nlocal
]
=
ATOTAGINT
(
values
[
0
]);
type
[
nlocal
]
=
atoi
(
values
[
1
]);
if
(
type
[
nlocal
]
<=
0
||
type
[
nlocal
]
>
atom
->
ntypes
)
error
->
one
(
FLERR
,
"Invalid atom type in Atoms section of data file"
);
ellipsoid
[
nlocal
]
=
atoi
(
values
[
2
]);
if
(
ellipsoid
[
nlocal
]
==
0
)
ellipsoid
[
nlocal
]
=
-
1
;
else
if
(
ellipsoid
[
nlocal
]
==
1
)
ellipsoid
[
nlocal
]
=
0
;
else
error
->
one
(
FLERR
,
"Invalid atom type in Atoms section of data file"
);
rmass
[
nlocal
]
=
atof
(
values
[
3
]);
if
(
rmass
[
nlocal
]
<=
0.0
)
error
->
one
(
FLERR
,
"Invalid density in Atoms section of data file"
);
x
[
nlocal
][
0
]
=
coord
[
0
];
x
[
nlocal
][
1
]
=
coord
[
1
];
x
[
nlocal
][
2
]
=
coord
[
2
];
image
[
nlocal
]
=
imagetmp
;
mask
[
nlocal
]
=
1
;
v
[
nlocal
][
0
]
=
0.0
;
v
[
nlocal
][
1
]
=
0.0
;
v
[
nlocal
][
2
]
=
0.0
;
angmom
[
nlocal
][
0
]
=
0.0
;
angmom
[
nlocal
][
1
]
=
0.0
;
angmom
[
nlocal
][
2
]
=
0.0
;
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
data_atom_hybrid
(
int
nlocal
,
char
**
values
)
{
ellipsoid
[
nlocal
]
=
atoi
(
values
[
0
]);
if
(
ellipsoid
[
nlocal
]
==
0
)
ellipsoid
[
nlocal
]
=
-
1
;
else
if
(
ellipsoid
[
nlocal
]
==
1
)
ellipsoid
[
nlocal
]
=
0
;
else
error
->
one
(
FLERR
,
"Invalid atom type in Atoms section of data file"
);
rmass
[
nlocal
]
=
atof
(
values
[
1
]);
if
(
rmass
[
nlocal
]
<=
0.0
)
error
->
one
(
FLERR
,
"Invalid density in Atoms section of data file"
);
return
2
;
}
/* ----------------------------------------------------------------------
unpack one line from Ellipsoids section of data file
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
data_atom_bonus
(
int
m
,
char
**
values
)
{
if
(
ellipsoid
[
m
])
error
->
one
(
FLERR
,
"Assigning ellipsoid parameters to non-ellipsoid atom"
);
if
(
nlocal_bonus
==
nmax_bonus
)
grow_bonus
();
double
*
shape
=
bonus
[
nlocal_bonus
].
shape
;
shape
[
0
]
=
0.5
*
atof
(
values
[
0
]);
shape
[
1
]
=
0.5
*
atof
(
values
[
1
]);
shape
[
2
]
=
0.5
*
atof
(
values
[
2
]);
if
(
shape
[
0
]
<=
0.0
||
shape
[
1
]
<=
0.0
||
shape
[
2
]
<=
0.0
)
error
->
one
(
FLERR
,
"Invalid shape in Ellipsoids section of data file"
);
double
*
quat
=
bonus
[
nlocal_bonus
].
quat
;
quat
[
0
]
=
atof
(
values
[
3
]);
quat
[
1
]
=
atof
(
values
[
4
]);
quat
[
2
]
=
atof
(
values
[
5
]);
quat
[
3
]
=
atof
(
values
[
6
]);
MathExtra
::
qnormalize
(
quat
);
// reset ellipsoid mass
// previously stored density in rmass
rmass
[
m
]
*=
4.0
*
MY_PI
/
3.0
*
shape
[
0
]
*
shape
[
1
]
*
shape
[
2
];
bonus
[
nlocal_bonus
].
ilocal
=
m
;
ellipsoid
[
m
]
=
nlocal_bonus
++
;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
data_vel
(
int
m
,
char
**
values
)
{
v
[
m
][
0
]
=
atof
(
values
[
0
]);
v
[
m
][
1
]
=
atof
(
values
[
1
]);
v
[
m
][
2
]
=
atof
(
values
[
2
]);
angmom
[
m
][
0
]
=
atof
(
values
[
3
]);
angmom
[
m
][
1
]
=
atof
(
values
[
4
]);
angmom
[
m
][
2
]
=
atof
(
values
[
5
]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
data_vel_hybrid
(
int
m
,
char
**
values
)
{
angmom
[
m
][
0
]
=
atof
(
values
[
0
]);
angmom
[
m
][
1
]
=
atof
(
values
[
1
]);
angmom
[
m
][
2
]
=
atof
(
values
[
2
]);
return
3
;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
pack_data
(
double
**
buf
)
{
double
*
shape
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
buf
[
i
][
0
]
=
ubuf
(
tag
[
i
]).
d
;
buf
[
i
][
1
]
=
ubuf
(
type
[
i
]).
d
;
if
(
ellipsoid
[
i
]
<
0
)
buf
[
i
][
2
]
=
ubuf
(
0
).
d
;
else
buf
[
i
][
2
]
=
ubuf
(
1
).
d
;
if
(
ellipsoid
[
i
]
<
0
)
buf
[
i
][
3
]
=
rmass
[
i
];
else
{
shape
=
bonus
[
ellipsoid
[
i
]].
shape
;
buf
[
i
][
3
]
=
rmass
[
i
]
/
(
4.0
*
MY_PI
/
3.0
*
shape
[
0
]
*
shape
[
1
]
*
shape
[
2
]);
}
buf
[
i
][
4
]
=
x
[
i
][
0
];
buf
[
i
][
5
]
=
x
[
i
][
1
];
buf
[
i
][
6
]
=
x
[
i
][
2
];
buf
[
i
][
7
]
=
ubuf
((
image
[
i
]
&
IMGMASK
)
-
IMGMAX
).
d
;
buf
[
i
][
8
]
=
ubuf
((
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
).
d
;
buf
[
i
][
9
]
=
ubuf
((
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
).
d
;
}
}
/* ----------------------------------------------------------------------
pack hybrid atom info for data file
------------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_data_hybrid
(
int
i
,
double
*
buf
)
{
if
(
ellipsoid
[
i
]
<
0
)
buf
[
0
]
=
ubuf
(
0
).
d
;
else
buf
[
0
]
=
ubuf
(
1
).
d
;
if
(
ellipsoid
[
i
]
<
0
)
buf
[
1
]
=
rmass
[
i
];
else
{
double
*
shape
=
bonus
[
ellipsoid
[
i
]].
shape
;
buf
[
1
]
=
rmass
[
i
]
/
(
4.0
*
MY_PI
/
3.0
*
shape
[
0
]
*
shape
[
1
]
*
shape
[
2
]);
}
return
2
;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
write_data
(
FILE
*
fp
,
int
n
,
double
**
buf
)
{
for
(
int
i
=
0
;
i
<
n
;
i
++
)
fprintf
(
fp
,
TAGINT_FORMAT
" %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d
\n
"
,
(
tagint
)
ubuf
(
buf
[
i
][
0
]).
i
,(
int
)
ubuf
(
buf
[
i
][
1
]).
i
,
(
int
)
ubuf
(
buf
[
i
][
2
]).
i
,
buf
[
i
][
3
],
buf
[
i
][
4
],
buf
[
i
][
5
],
buf
[
i
][
6
],
(
int
)
ubuf
(
buf
[
i
][
7
]).
i
,(
int
)
ubuf
(
buf
[
i
][
8
]).
i
,
(
int
)
ubuf
(
buf
[
i
][
9
]).
i
);
}
/* ----------------------------------------------------------------------
write hybrid atom info to data file
------------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
write_data_hybrid
(
FILE
*
fp
,
double
*
buf
)
{
fprintf
(
fp
,
" %d %-1.16e"
,(
int
)
ubuf
(
buf
[
0
]).
i
,
buf
[
1
]);
return
2
;
}
/* ----------------------------------------------------------------------
pack velocity info for data file
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
pack_vel
(
double
**
buf
)
{
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
buf
[
i
][
0
]
=
ubuf
(
tag
[
i
]).
d
;
buf
[
i
][
1
]
=
v
[
i
][
0
];
buf
[
i
][
2
]
=
v
[
i
][
1
];
buf
[
i
][
3
]
=
v
[
i
][
2
];
buf
[
i
][
4
]
=
angmom
[
i
][
0
];
buf
[
i
][
5
]
=
angmom
[
i
][
1
];
buf
[
i
][
6
]
=
angmom
[
i
][
2
];
}
}
/* ----------------------------------------------------------------------
pack hybrid velocity info for data file
------------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
pack_vel_hybrid
(
int
i
,
double
*
buf
)
{
buf
[
0
]
=
angmom
[
i
][
0
];
buf
[
1
]
=
angmom
[
i
][
1
];
buf
[
2
]
=
angmom
[
i
][
2
];
return
3
;
}
/* ----------------------------------------------------------------------
write velocity info to data file
------------------------------------------------------------------------- */
void
AtomVecEllipsoid
::
write_vel
(
FILE
*
fp
,
int
n
,
double
**
buf
)
{
for
(
int
i
=
0
;
i
<
n
;
i
++
)
fprintf
(
fp
,
TAGINT_FORMAT
" %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e
\n
"
,
(
tagint
)
ubuf
(
buf
[
i
][
0
]).
i
,
buf
[
i
][
1
],
buf
[
i
][
2
],
buf
[
i
][
3
],
buf
[
i
][
4
],
buf
[
i
][
5
],
buf
[
i
][
6
]);
}
/* ----------------------------------------------------------------------
write hybrid velocity info to data file
------------------------------------------------------------------------- */
int
AtomVecEllipsoid
::
write_vel_hybrid
(
FILE
*
fp
,
double
*
buf
)
{
fprintf
(
fp
,
" %-1.16e %-1.16e %-1.16e"
,
buf
[
0
],
buf
[
1
],
buf
[
2
]);
return
3
;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint
AtomVecEllipsoid
::
memory_usage
()
{
bigint
bytes
=
0
;
if
(
atom
->
memcheck
(
"tag"
))
bytes
+=
memory
->
usage
(
tag
,
nmax
);
if
(
atom
->
memcheck
(
"type"
))
bytes
+=
memory
->
usage
(
type
,
nmax
);
if
(
atom
->
memcheck
(
"mask"
))
bytes
+=
memory
->
usage
(
mask
,
nmax
);
if
(
atom
->
memcheck
(
"image"
))
bytes
+=
memory
->
usage
(
image
,
nmax
);
if
(
atom
->
memcheck
(
"x"
))
bytes
+=
memory
->
usage
(
x
,
nmax
,
3
);
if
(
atom
->
memcheck
(
"v"
))
bytes
+=
memory
->
usage
(
v
,
nmax
,
3
);
if
(
atom
->
memcheck
(
"f"
))
bytes
+=
memory
->
usage
(
f
,
nmax
*
comm
->
nthreads
,
3
);
if
(
atom
->
memcheck
(
"rmass"
))
bytes
+=
memory
->
usage
(
rmass
,
nmax
);
if
(
atom
->
memcheck
(
"angmom"
))
bytes
+=
memory
->
usage
(
angmom
,
nmax
,
3
);
if
(
atom
->
memcheck
(
"torque"
))
bytes
+=
memory
->
usage
(
torque
,
nmax
*
comm
->
nthreads
,
3
);
if
(
atom
->
memcheck
(
"ellipsoid"
))
bytes
+=
memory
->
usage
(
ellipsoid
,
nmax
);
bytes
+=
nmax_bonus
*
sizeof
(
Bonus
);
return
bytes
;
}
Event Timeline
Log In to Comment