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atom_vec_body.cpp
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Sat, Jul 6, 08:52
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Mon, Jul 8, 08:52 (1 d, 23 h)
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rLAMMPS lammps
atom_vec_body.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 "atom_vec_body.h"
#include "style_body.h"
#include "body.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "force.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 10000
#define DELTA_BONUS 10000
/* ---------------------------------------------------------------------- */
AtomVecBody
::
AtomVecBody
(
LAMMPS
*
lmp
)
:
AtomVec
(
lmp
)
{
molecular
=
0
;
// size_forward and size_border set in settings(), via Body class
comm_x_only
=
comm_f_only
=
0
;
size_forward
=
0
;
size_reverse
=
6
;
size_border
=
0
;
size_velocity
=
6
;
size_data_atom
=
7
;
size_data_vel
=
7
;
xcol_data
=
5
;
atom
->
body_flag
=
1
;
atom
->
rmass_flag
=
1
;
atom
->
angmom_flag
=
atom
->
torque_flag
=
1
;
nlocal_bonus
=
nghost_bonus
=
nmax_bonus
=
0
;
bonus
=
NULL
;
bptr
=
NULL
;
nargcopy
=
0
;
argcopy
=
NULL
;
copyflag
=
1
;
if
(
sizeof
(
double
)
==
sizeof
(
int
))
intdoubleratio
=
1
;
else
if
(
sizeof
(
double
)
==
2
*
sizeof
(
int
))
intdoubleratio
=
2
;
else
error
->
all
(
FLERR
,
"Internal error in atom_style body"
);
}
/* ---------------------------------------------------------------------- */
AtomVecBody
::~
AtomVecBody
()
{
int
nall
=
nlocal_bonus
+
nghost_bonus
;
for
(
int
i
=
0
;
i
<
nall
;
i
++
)
{
icp
->
put
(
bonus
[
i
].
iindex
);
dcp
->
put
(
bonus
[
i
].
dindex
);
}
memory
->
sfree
(
bonus
);
delete
bptr
;
for
(
int
i
=
0
;
i
<
nargcopy
;
i
++
)
delete
[]
argcopy
[
i
];
delete
[]
argcopy
;
}
/* ----------------------------------------------------------------------
process additional args
instantiate Body class
set size_forward and size_border to max sizes
------------------------------------------------------------------------- */
void
AtomVecBody
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
1
)
error
->
all
(
FLERR
,
"Invalid atom_style body command"
);
if
(
0
)
bptr
=
NULL
;
#define BODY_CLASS
#define BodyStyle(key,Class) \
else if (strcmp(arg[0],#key) == 0) bptr = new Class(lmp,narg,arg);
#include "style_body.h"
#undef BodyStyle
#undef BODY_CLASS
else
error
->
all
(
FLERR
,
"Invalid body style"
);
bptr
->
avec
=
this
;
icp
=
bptr
->
icp
;
dcp
=
bptr
->
dcp
;
// max size of forward/border comm
// 7,16 are packed in pack_comm/pack_border
// bptr values = max number of additional ivalues/dvalues from Body class
size_forward
=
7
+
bptr
->
size_forward
;
size_border
=
16
+
bptr
->
size_border
;
// make copy of args if called externally, so can write to restart file
// make no copy of args if called from read_restart()
if
(
copyflag
)
{
nargcopy
=
narg
;
argcopy
=
new
char
*
[
nargcopy
];
for
(
int
i
=
0
;
i
<
nargcopy
;
i
++
)
{
int
n
=
strlen
(
arg
[
i
])
+
1
;
argcopy
[
i
]
=
new
char
[
n
];
strcpy
(
argcopy
[
i
],
arg
[
i
]);
}
}
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void
AtomVecBody
::
grow
(
int
n
)
{
if
(
n
==
0
)
nmax
+=
DELTA
;
else
nmax
=
n
;
atom
->
nmax
=
nmax
;
if
(
nmax
<
0
||
nmax
>
MAXSMALLINT
)
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"
);
body
=
memory
->
grow
(
atom
->
body
,
nmax
,
"atom:body"
);
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
AtomVecBody
::
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
;
body
=
atom
->
body
;
}
/* ----------------------------------------------------------------------
grow bonus data structure
------------------------------------------------------------------------- */
void
AtomVecBody
::
grow_bonus
()
{
nmax_bonus
+=
DELTA_BONUS
;
if
(
nmax_bonus
<
0
||
nmax_bonus
>
MAXSMALLINT
)
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
if delflag and atom J has bonus data, then delete it
------------------------------------------------------------------------- */
void
AtomVecBody
::
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
&&
body
[
j
]
>=
0
)
{
icp
->
put
(
bonus
[
body
[
j
]].
iindex
);
dcp
->
put
(
bonus
[
body
[
j
]].
dindex
);
copy_bonus
(
nlocal_bonus
-
1
,
body
[
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
(
body
[
i
]
>=
0
&&
i
!=
j
)
bonus
[
body
[
i
]].
ilocal
=
j
;
body
[
j
]
=
body
[
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 body that points to I to now point to J
------------------------------------------------------------------------- */
void
AtomVecBody
::
copy_bonus
(
int
i
,
int
j
)
{
body
[
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
AtomVecBody
::
clear_bonus
()
{
int
nall
=
nlocal_bonus
+
nghost_bonus
;
for
(
int
i
=
nlocal_bonus
;
i
<
nall
;
i
++
)
{
icp
->
put
(
bonus
[
i
].
iindex
);
dcp
->
put
(
bonus
[
i
].
dindex
);
}
nghost_bonus
=
0
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecBody
::
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
(
body
[
j
]
>=
0
)
{
quat
=
bonus
[
body
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
m
+=
bptr
->
pack_comm_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
}
}
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
(
body
[
j
]
>=
0
)
{
quat
=
bonus
[
body
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
m
+=
bptr
->
pack_comm_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecBody
::
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
(
body
[
j
]
>=
0
)
{
quat
=
bonus
[
body
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
m
+=
bptr
->
pack_comm_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
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
(
body
[
j
]
>=
0
)
{
quat
=
bonus
[
body
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
m
+=
bptr
->
pack_comm_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
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
(
body
[
j
]
>=
0
)
{
quat
=
bonus
[
body
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
m
+=
bptr
->
pack_comm_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
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
AtomVecBody
::
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
(
body
[
j
]
>=
0
)
{
quat
=
bonus
[
body
[
j
]].
quat
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
m
+=
bptr
->
pack_comm_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecBody
::
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
(
body
[
i
]
>=
0
)
{
quat
=
bonus
[
body
[
i
]].
quat
;
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
m
+=
bptr
->
unpack_comm_body
(
&
bonus
[
body
[
i
]],
&
buf
[
m
]);
}
}
}
/* ---------------------------------------------------------------------- */
void
AtomVecBody
::
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
(
body
[
i
]
>=
0
)
{
quat
=
bonus
[
body
[
i
]].
quat
;
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
m
+=
bptr
->
unpack_comm_body
(
&
bonus
[
body
[
i
]],
&
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
AtomVecBody
::
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
(
body
[
i
]
>=
0
)
{
quat
=
bonus
[
body
[
i
]].
quat
;
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
m
+=
bptr
->
unpack_comm_body
(
&
bonus
[
body
[
i
]],
&
buf
[
m
]);
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecBody
::
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
AtomVecBody
::
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
AtomVecBody
::
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
AtomVecBody
::
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
AtomVecBody
::
pack_border
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
double
dx
,
dy
,
dz
;
double
*
quat
,
*
c1
,
*
c2
,
*
c3
,
*
inertia
;
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
++
]
=
tag
[
j
];
buf
[
m
++
]
=
type
[
j
];
buf
[
m
++
]
=
mask
[
j
];
if
(
body
[
j
]
<
0
)
buf
[
m
++
]
=
0
;
else
{
buf
[
m
++
]
=
1
;
quat
=
bonus
[
body
[
j
]].
quat
;
inertia
=
bonus
[
body
[
j
]].
inertia
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
buf
[
m
++
]
=
inertia
[
0
];
buf
[
m
++
]
=
inertia
[
1
];
buf
[
m
++
]
=
inertia
[
2
];
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ninteger
;
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ndouble
;
m
+=
bptr
->
pack_border_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
}
}
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
++
]
=
tag
[
j
];
buf
[
m
++
]
=
type
[
j
];
buf
[
m
++
]
=
mask
[
j
];
if
(
body
[
j
]
<
0
)
buf
[
m
++
]
=
0
;
else
{
buf
[
m
++
]
=
1
;
quat
=
bonus
[
body
[
j
]].
quat
;
inertia
=
bonus
[
body
[
j
]].
inertia
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
buf
[
m
++
]
=
inertia
[
0
];
buf
[
m
++
]
=
inertia
[
1
];
buf
[
m
++
]
=
inertia
[
2
];
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ninteger
;
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ndouble
;
m
+=
bptr
->
pack_border_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecBody
::
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
*
quat
,
*
c1
,
*
c2
,
*
c3
,
*
inertia
;
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
++
]
=
tag
[
j
];
buf
[
m
++
]
=
type
[
j
];
buf
[
m
++
]
=
mask
[
j
];
if
(
body
[
j
]
<
0
)
buf
[
m
++
]
=
0
;
else
{
buf
[
m
++
]
=
1
;
quat
=
bonus
[
body
[
j
]].
quat
;
inertia
=
bonus
[
body
[
j
]].
inertia
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
buf
[
m
++
]
=
inertia
[
0
];
buf
[
m
++
]
=
inertia
[
1
];
buf
[
m
++
]
=
inertia
[
2
];
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ninteger
;
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ndouble
;
m
+=
bptr
->
pack_border_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
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
++
]
=
tag
[
j
];
buf
[
m
++
]
=
type
[
j
];
buf
[
m
++
]
=
mask
[
j
];
if
(
body
[
j
]
<
0
)
buf
[
m
++
]
=
0
;
else
{
buf
[
m
++
]
=
1
;
quat
=
bonus
[
body
[
j
]].
quat
;
inertia
=
bonus
[
body
[
j
]].
inertia
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
buf
[
m
++
]
=
inertia
[
0
];
buf
[
m
++
]
=
inertia
[
1
];
buf
[
m
++
]
=
inertia
[
2
];
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ninteger
;
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ndouble
;
m
+=
bptr
->
pack_border_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
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
++
]
=
tag
[
j
];
buf
[
m
++
]
=
type
[
j
];
buf
[
m
++
]
=
mask
[
j
];
if
(
body
[
j
]
<
0
)
buf
[
m
++
]
=
0
;
else
{
buf
[
m
++
]
=
1
;
quat
=
bonus
[
body
[
j
]].
quat
;
inertia
=
bonus
[
body
[
j
]].
inertia
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
buf
[
m
++
]
=
inertia
[
0
];
buf
[
m
++
]
=
inertia
[
1
];
buf
[
m
++
]
=
inertia
[
2
];
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ninteger
;
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ndouble
;
m
+=
bptr
->
pack_border_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
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
AtomVecBody
::
pack_border_hybrid
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
double
*
quat
,
*
c1
,
*
c2
,
*
c3
,
*
inertia
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
if
(
body
[
j
]
<
0
)
buf
[
m
++
]
=
0
;
else
{
buf
[
m
++
]
=
1
;
quat
=
bonus
[
body
[
j
]].
quat
;
inertia
=
bonus
[
body
[
j
]].
inertia
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
buf
[
m
++
]
=
inertia
[
0
];
buf
[
m
++
]
=
inertia
[
1
];
buf
[
m
++
]
=
inertia
[
2
];
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ninteger
;
buf
[
m
++
]
=
bonus
[
body
[
j
]].
ndouble
;
m
+=
bptr
->
pack_border_body
(
&
bonus
[
body
[
j
]],
&
buf
[
m
]);
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecBody
::
unpack_border
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
j
,
m
,
last
;
double
*
quat
,
*
c1
,
*
c2
,
*
c3
,
*
inertia
;
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
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
type
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
mask
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
body
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
if
(
body
[
i
]
==
0
)
body
[
i
]
=
-
1
;
else
{
j
=
nlocal_bonus
+
nghost_bonus
;
if
(
j
==
nmax_bonus
)
grow_bonus
();
quat
=
bonus
[
j
].
quat
;
inertia
=
bonus
[
j
].
inertia
;
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
inertia
[
0
]
=
buf
[
m
++
];
inertia
[
1
]
=
buf
[
m
++
];
inertia
[
2
]
=
buf
[
m
++
];
bonus
[
j
].
ninteger
=
static_cast
<
int
>
(
buf
[
m
++
]);
bonus
[
j
].
ndouble
=
static_cast
<
int
>
(
buf
[
m
++
]);
bonus
[
j
].
ivalue
=
icp
->
get
(
bonus
[
j
].
ninteger
,
bonus
[
j
].
iindex
);
bonus
[
j
].
dvalue
=
dcp
->
get
(
bonus
[
j
].
ndouble
,
bonus
[
j
].
dindex
);
m
+=
bptr
->
unpack_border_body
(
&
bonus
[
j
],
&
buf
[
m
]);
bonus
[
j
].
ilocal
=
i
;
body
[
i
]
=
j
;
nghost_bonus
++
;
}
}
}
/* ---------------------------------------------------------------------- */
void
AtomVecBody
::
unpack_border_vel
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
j
,
m
,
last
;
double
*
quat
,
*
c1
,
*
c2
,
*
c3
,
*
inertia
;
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
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
type
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
mask
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
body
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
if
(
body
[
i
]
==
0
)
body
[
i
]
=
-
1
;
else
{
j
=
nlocal_bonus
+
nghost_bonus
;
if
(
j
==
nmax_bonus
)
grow_bonus
();
quat
=
bonus
[
j
].
quat
;
inertia
=
bonus
[
j
].
inertia
;
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
inertia
[
0
]
=
buf
[
m
++
];
inertia
[
1
]
=
buf
[
m
++
];
inertia
[
2
]
=
buf
[
m
++
];
bonus
[
j
].
ninteger
=
static_cast
<
int
>
(
buf
[
m
++
]);
bonus
[
j
].
ndouble
=
static_cast
<
int
>
(
buf
[
m
++
]);
bonus
[
j
].
ivalue
=
icp
->
get
(
bonus
[
j
].
ninteger
,
bonus
[
j
].
iindex
);
bonus
[
j
].
dvalue
=
dcp
->
get
(
bonus
[
j
].
ndouble
,
bonus
[
j
].
dindex
);
m
+=
bptr
->
unpack_border_body
(
&
bonus
[
j
],
&
buf
[
m
]);
bonus
[
j
].
ilocal
=
i
;
body
[
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
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecBody
::
unpack_border_hybrid
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
j
,
m
,
last
;
double
*
quat
,
*
c1
,
*
c2
,
*
c3
,
*
inertia
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
body
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
if
(
body
[
i
]
==
0
)
body
[
i
]
=
-
1
;
else
{
j
=
nlocal_bonus
+
nghost_bonus
;
if
(
j
==
nmax_bonus
)
grow_bonus
();
quat
=
bonus
[
j
].
quat
;
inertia
=
bonus
[
j
].
inertia
;
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
inertia
[
0
]
=
buf
[
m
++
];
inertia
[
1
]
=
buf
[
m
++
];
inertia
[
2
]
=
buf
[
m
++
];
bonus
[
j
].
ninteger
=
static_cast
<
int
>
(
buf
[
m
++
]);
bonus
[
j
].
ndouble
=
static_cast
<
int
>
(
buf
[
m
++
]);
bonus
[
j
].
ivalue
=
icp
->
get
(
bonus
[
j
].
ninteger
,
bonus
[
j
].
iindex
);
bonus
[
j
].
dvalue
=
dcp
->
get
(
bonus
[
j
].
ndouble
,
bonus
[
j
].
dindex
);
m
+=
bptr
->
unpack_border_body
(
&
bonus
[
j
],
&
buf
[
m
]);
bonus
[
j
].
ilocal
=
i
;
body
[
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
AtomVecBody
::
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
++
]
=
tag
[
i
];
buf
[
m
++
]
=
type
[
i
];
buf
[
m
++
]
=
mask
[
i
];
*
((
tagint
*
)
&
buf
[
m
++
])
=
image
[
i
];
buf
[
m
++
]
=
rmass
[
i
];
buf
[
m
++
]
=
angmom
[
i
][
0
];
buf
[
m
++
]
=
angmom
[
i
][
1
];
buf
[
m
++
]
=
angmom
[
i
][
2
];
if
(
body
[
i
]
<
0
)
buf
[
m
++
]
=
0
;
else
{
buf
[
m
++
]
=
1
;
int
j
=
body
[
i
];
double
*
quat
=
bonus
[
j
].
quat
;
double
*
inertia
=
bonus
[
j
].
inertia
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
buf
[
m
++
]
=
inertia
[
0
];
buf
[
m
++
]
=
inertia
[
1
];
buf
[
m
++
]
=
inertia
[
2
];
buf
[
m
++
]
=
bonus
[
j
].
ninteger
;
buf
[
m
++
]
=
bonus
[
j
].
ndouble
;
memcpy
(
&
buf
[
m
],
bonus
[
j
].
ivalue
,
bonus
[
j
].
ninteger
*
sizeof
(
int
));
if
(
intdoubleratio
==
1
)
m
+=
bonus
[
j
].
ninteger
;
else
m
+=
(
bonus
[
j
].
ninteger
+
1
)
/
2
;
memcpy
(
&
buf
[
m
],
bonus
[
j
].
dvalue
,
bonus
[
j
].
ndouble
*
sizeof
(
double
));
m
+=
bonus
[
j
].
ndouble
;
}
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
AtomVecBody
::
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
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
type
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
mask
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
image
[
nlocal
]
=
*
((
tagint
*
)
&
buf
[
m
++
]);
rmass
[
nlocal
]
=
buf
[
m
++
];
angmom
[
nlocal
][
0
]
=
buf
[
m
++
];
angmom
[
nlocal
][
1
]
=
buf
[
m
++
];
angmom
[
nlocal
][
2
]
=
buf
[
m
++
];
body
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
if
(
body
[
nlocal
]
==
0
)
body
[
nlocal
]
=
-
1
;
else
{
if
(
nlocal_bonus
==
nmax_bonus
)
grow_bonus
();
double
*
quat
=
bonus
[
nlocal_bonus
].
quat
;
double
*
inertia
=
bonus
[
nlocal_bonus
].
inertia
;
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
inertia
[
0
]
=
buf
[
m
++
];
inertia
[
1
]
=
buf
[
m
++
];
inertia
[
2
]
=
buf
[
m
++
];
bonus
[
nlocal_bonus
].
ninteger
=
static_cast
<
int
>
(
buf
[
m
++
]);
bonus
[
nlocal_bonus
].
ndouble
=
static_cast
<
int
>
(
buf
[
m
++
]);
bonus
[
nlocal_bonus
].
ivalue
=
icp
->
get
(
bonus
[
nlocal_bonus
].
ninteger
,
bonus
[
nlocal_bonus
].
iindex
);
bonus
[
nlocal_bonus
].
dvalue
=
dcp
->
get
(
bonus
[
nlocal_bonus
].
ndouble
,
bonus
[
nlocal_bonus
].
dindex
);
memcpy
(
bonus
[
nlocal_bonus
].
ivalue
,
&
buf
[
m
],
bonus
[
nlocal_bonus
].
ninteger
*
sizeof
(
int
));
if
(
intdoubleratio
==
1
)
m
+=
bonus
[
nlocal_bonus
].
ninteger
;
else
m
+=
(
bonus
[
nlocal_bonus
].
ninteger
+
1
)
/
2
;
memcpy
(
bonus
[
nlocal_bonus
].
dvalue
,
&
buf
[
m
],
bonus
[
nlocal_bonus
].
ndouble
*
sizeof
(
double
));
m
+=
bonus
[
nlocal_bonus
].
ndouble
;
bonus
[
nlocal_bonus
].
ilocal
=
nlocal
;
body
[
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
AtomVecBody
::
size_restart
()
{
int
i
;
int
n
=
0
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
body
[
i
]
>=
0
)
{
n
+=
25
;
if
(
intdoubleratio
==
1
)
n
+=
bonus
[
body
[
i
]].
ninteger
;
else
n
+=
(
bonus
[
body
[
i
]].
ninteger
+
1
)
/
2
;
n
+=
bonus
[
body
[
i
]].
ndouble
;
}
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 extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int
AtomVecBody
::
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
++
]
=
tag
[
i
];
buf
[
m
++
]
=
type
[
i
];
buf
[
m
++
]
=
mask
[
i
];
*
((
tagint
*
)
&
buf
[
m
++
])
=
image
[
i
];
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
(
body
[
i
]
<
0
)
buf
[
m
++
]
=
0
;
else
{
buf
[
m
++
]
=
1
;
int
j
=
body
[
i
];
double
*
quat
=
bonus
[
j
].
quat
;
double
*
inertia
=
bonus
[
j
].
inertia
;
buf
[
m
++
]
=
quat
[
0
];
buf
[
m
++
]
=
quat
[
1
];
buf
[
m
++
]
=
quat
[
2
];
buf
[
m
++
]
=
quat
[
3
];
buf
[
m
++
]
=
inertia
[
0
];
buf
[
m
++
]
=
inertia
[
1
];
buf
[
m
++
]
=
inertia
[
2
];
buf
[
m
++
]
=
bonus
[
j
].
ninteger
;
buf
[
m
++
]
=
bonus
[
j
].
ndouble
;
memcpy
(
&
buf
[
m
],
bonus
[
j
].
ivalue
,
bonus
[
j
].
ninteger
*
sizeof
(
int
));
if
(
intdoubleratio
==
1
)
m
+=
bonus
[
j
].
ninteger
;
else
m
+=
(
bonus
[
j
].
ninteger
+
1
)
/
2
;
memcpy
(
&
buf
[
m
],
bonus
[
j
].
dvalue
,
bonus
[
j
].
ndouble
*
sizeof
(
double
));
m
+=
bonus
[
j
].
ndouble
;
}
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 extra quantities
------------------------------------------------------------------------- */
int
AtomVecBody
::
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
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
type
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
mask
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
image
[
nlocal
]
=
*
((
tagint
*
)
&
buf
[
m
++
]);
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
++
];
body
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
if
(
body
[
nlocal
]
==
0
)
body
[
nlocal
]
=
-
1
;
else
{
if
(
nlocal_bonus
==
nmax_bonus
)
grow_bonus
();
double
*
quat
=
bonus
[
nlocal_bonus
].
quat
;
double
*
inertia
=
bonus
[
nlocal_bonus
].
inertia
;
quat
[
0
]
=
buf
[
m
++
];
quat
[
1
]
=
buf
[
m
++
];
quat
[
2
]
=
buf
[
m
++
];
quat
[
3
]
=
buf
[
m
++
];
inertia
[
0
]
=
buf
[
m
++
];
inertia
[
1
]
=
buf
[
m
++
];
inertia
[
2
]
=
buf
[
m
++
];
bonus
[
nlocal_bonus
].
ninteger
=
static_cast
<
int
>
(
buf
[
m
++
]);
bonus
[
nlocal_bonus
].
ndouble
=
static_cast
<
int
>
(
buf
[
m
++
]);
bonus
[
nlocal_bonus
].
ivalue
=
icp
->
get
(
bonus
[
nlocal_bonus
].
ninteger
,
bonus
[
nlocal_bonus
].
iindex
);
bonus
[
nlocal_bonus
].
dvalue
=
dcp
->
get
(
bonus
[
nlocal_bonus
].
ndouble
,
bonus
[
nlocal_bonus
].
dindex
);
memcpy
(
bonus
[
nlocal_bonus
].
ivalue
,
&
buf
[
m
],
bonus
[
nlocal_bonus
].
ninteger
*
sizeof
(
int
));
if
(
intdoubleratio
==
1
)
m
+=
bonus
[
nlocal_bonus
].
ninteger
;
else
m
+=
(
bonus
[
nlocal_bonus
].
ninteger
+
1
)
/
2
;
memcpy
(
bonus
[
nlocal_bonus
].
dvalue
,
&
buf
[
m
],
bonus
[
nlocal_bonus
].
ndouble
*
sizeof
(
double
));
m
+=
bonus
[
nlocal_bonus
].
ndouble
;
bonus
[
nlocal_bonus
].
ilocal
=
nlocal
;
body
[
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
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecBody
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
nargcopy
,
sizeof
(
int
),
1
,
fp
);
for
(
int
i
=
0
;
i
<
nargcopy
;
i
++
)
{
int
n
=
strlen
(
argcopy
[
i
])
+
1
;
fwrite
(
&
n
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
argcopy
[
i
],
sizeof
(
char
),
n
,
fp
);
}
}
/* ---------------------------------------------------------------------- */
void
AtomVecBody
::
read_restart_settings
(
FILE
*
fp
)
{
int
n
;
int
me
=
comm
->
me
;
if
(
me
==
0
)
fread
(
&
nargcopy
,
sizeof
(
int
),
1
,
fp
);
MPI_Bcast
(
&
nargcopy
,
1
,
MPI_INT
,
0
,
world
);
argcopy
=
new
char
*
[
nargcopy
];
for
(
int
i
=
0
;
i
<
nargcopy
;
i
++
)
{
if
(
me
==
0
)
fread
(
&
n
,
sizeof
(
int
),
1
,
fp
);
MPI_Bcast
(
&
n
,
1
,
MPI_INT
,
0
,
world
);
argcopy
[
i
]
=
new
char
[
n
];
if
(
me
==
0
)
fread
(
argcopy
[
i
],
sizeof
(
char
),
n
,
fp
);
MPI_Bcast
(
argcopy
[
i
],
n
,
MPI_CHAR
,
0
,
world
);
}
copyflag
=
0
;
settings
(
nargcopy
,
argcopy
);
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void
AtomVecBody
::
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
]
=
((
tagint
)
IMGMAX
<<
IMG2BITS
)
|
((
tagint
)
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
;
body
[
nlocal
]
=
-
1
;
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void
AtomVecBody
::
data_atom
(
double
*
coord
,
tagint
imagetmp
,
char
**
values
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
tag
[
nlocal
]
=
atoi
(
values
[
0
]);
if
(
tag
[
nlocal
]
<=
0
)
error
->
one
(
FLERR
,
"Invalid atom ID in Atoms section of data file"
);
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"
);
body
[
nlocal
]
=
atoi
(
values
[
2
]);
if
(
body
[
nlocal
]
==
0
)
body
[
nlocal
]
=
-
1
;
else
if
(
body
[
nlocal
]
==
1
)
body
[
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
AtomVecBody
::
data_atom_hybrid
(
int
nlocal
,
char
**
values
)
{
body
[
nlocal
]
=
atoi
(
values
[
0
]);
if
(
body
[
nlocal
]
==
0
)
body
[
nlocal
]
=
-
1
;
else
if
(
body
[
nlocal
]
==
1
)
body
[
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 body from Bodies section of data file
------------------------------------------------------------------------- */
void
AtomVecBody
::
data_body
(
int
m
,
int
ninteger
,
int
ndouble
,
char
**
ivalues
,
char
**
dvalues
)
{
if
(
body
[
m
])
error
->
one
(
FLERR
,
"Assigning body parameters to non-body atom"
);
if
(
nlocal_bonus
==
nmax_bonus
)
grow_bonus
();
bptr
->
data_body
(
nlocal_bonus
,
ninteger
,
ndouble
,
ivalues
,
dvalues
);
bonus
[
nlocal_bonus
].
ilocal
=
m
;
body
[
m
]
=
nlocal_bonus
++
;
}
/* ----------------------------------------------------------------------
unpack one tri from Velocities section of data file
------------------------------------------------------------------------- */
void
AtomVecBody
::
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 body in Velocities section of data file
------------------------------------------------------------------------- */
int
AtomVecBody
::
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
;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint
AtomVecBody
::
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
(
"body"
))
bytes
+=
memory
->
usage
(
body
,
nmax
);
bytes
+=
nmax_bonus
*
sizeof
(
Bonus
);
bytes
+=
icp
->
size
+
dcp
->
size
;
int
nall
=
nlocal_bonus
+
nghost_bonus
;
for
(
int
i
=
0
;
i
<
nall
;
i
++
)
{
bytes
+=
bonus
[
i
].
ninteger
*
sizeof
(
int
);
bytes
+=
bonus
[
i
].
ndouble
*
sizeof
(
double
);
}
return
bytes
;
}
/* ----------------------------------------------------------------------
debug method for sanity checking of own/bonus data pointers
------------------------------------------------------------------------- */
/*
void AtomVecBody::check(int flag)
{
for (int i = 0; i < atom->nlocal; i++) {
if (atom->body[i] >= 0 && atom->body[i] >= nlocal_bonus) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD AAA");
}
}
for (int i = atom->nlocal; i < atom->nlocal+atom->nghost; i++) {
if (atom->body[i] >= 0 &&
(atom->body[i] < nlocal_bonus ||
atom->body[i] >= nlocal_bonus+nghost_bonus)) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD BBB");
}
}
for (int i = 0; i < nlocal_bonus; i++) {
if (bonus[i].ilocal < 0 || bonus[i].ilocal >= atom->nlocal) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD CCC");
}
}
for (int i = 0; i < nlocal_bonus; i++) {
if (atom->body[bonus[i].ilocal] != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD DDD");
}
}
for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
if (bonus[i].ilocal < atom->nlocal ||
bonus[i].ilocal >= atom->nlocal+atom->nghost) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD EEE");
}
}
for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
if (atom->body[bonus[i].ilocal] != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD FFF");
}
}
}
*/
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