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compute_property_atom.cpp
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Mon, Oct 14, 00:57
Size
48 KB
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text/x-c
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Wed, Oct 16, 00:57 (1 d, 23 h)
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blob
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rLAMMPS lammps
compute_property_atom.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 <string.h>
#include "compute_property_atom.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "atom_vec_body.h"
#include "update.h"
#include "domain.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputePropertyAtom
::
ComputePropertyAtom
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
),
index
(
NULL
),
pack_choice
(
NULL
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Illegal compute property/atom command"
);
peratom_flag
=
1
;
nvalues
=
narg
-
3
;
if
(
nvalues
==
1
)
size_peratom_cols
=
0
;
else
size_peratom_cols
=
nvalues
;
// parse input values
// customize a new keyword by adding to if statement
pack_choice
=
new
FnPtrPack
[
nvalues
];
index
=
new
int
[
nvalues
];
int
i
;
for
(
int
iarg
=
3
;
iarg
<
narg
;
iarg
++
)
{
i
=
iarg
-
3
;
if
(
strcmp
(
arg
[
iarg
],
"id"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_id
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"mol"
)
==
0
)
{
if
(
!
atom
->
molecule_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_molecule
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"proc"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_proc
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"type"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_type
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"mass"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_mass
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"x"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_x
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"y"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_y
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"z"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_z
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"xs"
)
==
0
)
{
if
(
domain
->
triclinic
)
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_xs_triclinic
;
else
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_xs
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"ys"
)
==
0
)
{
if
(
domain
->
triclinic
)
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_ys_triclinic
;
else
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_ys
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"zs"
)
==
0
)
{
if
(
domain
->
triclinic
)
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_zs_triclinic
;
else
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_zs
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"xu"
)
==
0
)
{
if
(
domain
->
triclinic
)
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_xu_triclinic
;
else
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_xu
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"yu"
)
==
0
)
{
if
(
domain
->
triclinic
)
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_yu_triclinic
;
else
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_yu
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"zu"
)
==
0
)
{
if
(
domain
->
triclinic
)
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_zu_triclinic
;
else
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_zu
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"ix"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_ix
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"iy"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_iy
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"iz"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_iz
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"vx"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_vx
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"vy"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_vy
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"vz"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_vz
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"fx"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_fx
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"fy"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_fy
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"fz"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_fz
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"q"
)
==
0
)
{
if
(
!
atom
->
q_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_q
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"mux"
)
==
0
)
{
if
(
!
atom
->
mu_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_mux
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"muy"
)
==
0
)
{
if
(
!
atom
->
mu_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_muy
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"muz"
)
==
0
)
{
if
(
!
atom
->
mu_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_muz
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"mu"
)
==
0
)
{
if
(
!
atom
->
mu_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_mu
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"radius"
)
==
0
)
{
if
(
!
atom
->
radius_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_radius
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"diameter"
)
==
0
)
{
if
(
!
atom
->
radius_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_diameter
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"omegax"
)
==
0
)
{
if
(
!
atom
->
omega_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_omegax
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"omegay"
)
==
0
)
{
if
(
!
atom
->
omega_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_omegay
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"omegaz"
)
==
0
)
{
if
(
!
atom
->
omega_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_omegaz
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"angmomx"
)
==
0
)
{
if
(
!
atom
->
angmom_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_angmomx
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"angmomy"
)
==
0
)
{
if
(
!
atom
->
angmom_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_angmomy
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"angmomz"
)
==
0
)
{
if
(
!
atom
->
angmom_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_angmomz
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"shapex"
)
==
0
)
{
avec_ellipsoid
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
if
(
!
avec_ellipsoid
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_shapex
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"shapey"
)
==
0
)
{
avec_ellipsoid
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
if
(
!
avec_ellipsoid
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_shapey
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"shapez"
)
==
0
)
{
avec_ellipsoid
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
if
(
!
avec_ellipsoid
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_shapez
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"quatw"
)
==
0
)
{
avec_ellipsoid
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
avec_body
=
(
AtomVecBody
*
)
atom
->
style_match
(
"body"
);
if
(
!
avec_ellipsoid
&&
!
avec_body
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_quatw
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"quati"
)
==
0
)
{
avec_ellipsoid
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
avec_body
=
(
AtomVecBody
*
)
atom
->
style_match
(
"body"
);
if
(
!
avec_ellipsoid
&&
!
avec_body
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_quati
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"quatj"
)
==
0
)
{
avec_ellipsoid
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
avec_body
=
(
AtomVecBody
*
)
atom
->
style_match
(
"body"
);
if
(
!
avec_ellipsoid
&&
!
avec_body
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_quatj
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"quatk"
)
==
0
)
{
avec_ellipsoid
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
avec_body
=
(
AtomVecBody
*
)
atom
->
style_match
(
"body"
);
if
(
!
avec_ellipsoid
&&
!
avec_body
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_quatk
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"tqx"
)
==
0
)
{
if
(
!
atom
->
torque_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_tqx
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"tqy"
)
==
0
)
{
if
(
!
atom
->
torque_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_tqy
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"tqz"
)
==
0
)
{
if
(
!
atom
->
torque_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_tqz
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"end1x"
)
==
0
)
{
avec_line
=
(
AtomVecLine
*
)
atom
->
style_match
(
"line"
);
if
(
!
avec_line
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_end1x
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"end1y"
)
==
0
)
{
avec_line
=
(
AtomVecLine
*
)
atom
->
style_match
(
"line"
);
if
(
!
avec_line
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_end1y
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"end1z"
)
==
0
)
{
avec_line
=
(
AtomVecLine
*
)
atom
->
style_match
(
"line"
);
if
(
!
avec_line
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_end1z
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"end2x"
)
==
0
)
{
avec_line
=
(
AtomVecLine
*
)
atom
->
style_match
(
"line"
);
if
(
!
avec_line
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_end2x
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"end2y"
)
==
0
)
{
avec_line
=
(
AtomVecLine
*
)
atom
->
style_match
(
"line"
);
if
(
!
avec_line
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_end2y
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"end2z"
)
==
0
)
{
avec_line
=
(
AtomVecLine
*
)
atom
->
style_match
(
"line"
);
if
(
!
avec_line
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_end2z
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"corner1x"
)
==
0
)
{
avec_tri
=
(
AtomVecTri
*
)
atom
->
style_match
(
"tri"
);
if
(
!
avec_tri
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_corner1x
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"corner1y"
)
==
0
)
{
avec_tri
=
(
AtomVecTri
*
)
atom
->
style_match
(
"tri"
);
if
(
!
avec_tri
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_corner1y
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"corner1z"
)
==
0
)
{
avec_tri
=
(
AtomVecTri
*
)
atom
->
style_match
(
"tri"
);
if
(
!
avec_tri
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_corner1z
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"corner2x"
)
==
0
)
{
avec_tri
=
(
AtomVecTri
*
)
atom
->
style_match
(
"tri"
);
if
(
!
avec_tri
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_corner2x
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"corner2y"
)
==
0
)
{
avec_tri
=
(
AtomVecTri
*
)
atom
->
style_match
(
"tri"
);
if
(
!
avec_tri
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_corner2y
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"corner2z"
)
==
0
)
{
avec_tri
=
(
AtomVecTri
*
)
atom
->
style_match
(
"tri"
);
if
(
!
avec_tri
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_corner2z
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"corner3x"
)
==
0
)
{
avec_tri
=
(
AtomVecTri
*
)
atom
->
style_match
(
"tri"
);
if
(
!
avec_tri
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_corner3x
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"corner3y"
)
==
0
)
{
avec_tri
=
(
AtomVecTri
*
)
atom
->
style_match
(
"tri"
);
if
(
!
avec_tri
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_corner3y
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"corner3z"
)
==
0
)
{
avec_tri
=
(
AtomVecTri
*
)
atom
->
style_match
(
"tri"
);
if
(
!
avec_tri
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_corner3z
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"nbonds"
)
==
0
)
{
if
(
!
atom
->
molecule_flag
)
error
->
all
(
FLERR
,
"Compute property/atom for "
"atom property that isn't allocated"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_nbonds
;
}
else
if
(
strstr
(
arg
[
iarg
],
"i_"
)
==
arg
[
iarg
])
{
int
flag
;
index
[
i
]
=
atom
->
find_custom
(
&
arg
[
iarg
][
2
],
flag
);
if
(
index
[
i
]
<
0
||
flag
!=
0
)
error
->
all
(
FLERR
,
"Compute property/atom integer "
"vector does not exist"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_iname
;
}
else
if
(
strstr
(
arg
[
iarg
],
"d_"
)
==
arg
[
iarg
])
{
int
flag
;
index
[
i
]
=
atom
->
find_custom
(
&
arg
[
iarg
][
2
],
flag
);
if
(
index
[
i
]
<
0
||
flag
!=
1
)
error
->
all
(
FLERR
,
"Compute property/atom floating point "
"vector does not exist"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_dname
;
// check if atom style recognizes keyword
}
else
{
index
[
i
]
=
atom
->
avec
->
property_atom
(
arg
[
iarg
]);
if
(
index
[
i
]
<
0
)
error
->
all
(
FLERR
,
"Invalid keyword in compute property/atom command"
);
pack_choice
[
i
]
=
&
ComputePropertyAtom
::
pack_property_atom
;
}
}
nmax
=
0
;
}
/* ---------------------------------------------------------------------- */
ComputePropertyAtom
::~
ComputePropertyAtom
()
{
delete
[]
pack_choice
;
delete
[]
index
;
memory
->
destroy
(
vector
);
memory
->
destroy
(
array
);
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
init
()
{
avec_ellipsoid
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
avec_line
=
(
AtomVecLine
*
)
atom
->
style_match
(
"line"
);
avec_tri
=
(
AtomVecTri
*
)
atom
->
style_match
(
"tri"
);
avec_body
=
(
AtomVecBody
*
)
atom
->
style_match
(
"body"
);
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
compute_peratom
()
{
invoked_peratom
=
update
->
ntimestep
;
// grow vector or array if necessary
if
(
atom
->
nmax
>
nmax
)
{
nmax
=
atom
->
nmax
;
if
(
nvalues
==
1
)
{
memory
->
destroy
(
vector
);
memory
->
create
(
vector
,
nmax
,
"property/atom:vector"
);
vector_atom
=
vector
;
}
else
{
memory
->
destroy
(
array
);
memory
->
create
(
array
,
nmax
,
nvalues
,
"property/atom:array"
);
array_atom
=
array
;
}
}
// fill vector or array with per-atom values
if
(
nvalues
==
1
)
{
buf
=
vector
;
(
this
->*
pack_choice
[
0
])(
0
);
}
else
{
if
(
nmax
)
buf
=
&
array
[
0
][
0
];
else
buf
=
NULL
;
for
(
int
n
=
0
;
n
<
nvalues
;
n
++
)
(
this
->*
pack_choice
[
n
])(
n
);
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double
ComputePropertyAtom
::
memory_usage
()
{
double
bytes
=
nmax
*
nvalues
*
sizeof
(
double
);
return
bytes
;
}
/* ----------------------------------------------------------------------
one method for every keyword compute property/atom can output
the atom property is packed into buf starting at n with stride nvalues
customize a new keyword by adding a method
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_id
(
int
n
)
{
tagint
*
tag
=
atom
->
tag
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
tag
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_molecule
(
int
n
)
{
tagint
*
molecule
=
atom
->
molecule
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
molecule
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_proc
(
int
n
)
{
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
me
=
comm
->
me
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
me
;
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_type
(
int
n
)
{
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
type
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_mass
(
int
n
)
{
int
*
type
=
atom
->
type
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
rmass
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
rmass
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
else
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
mass
[
type
[
i
]];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_x
(
int
n
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
x
[
i
][
0
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_y
(
int
n
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
x
[
i
][
1
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_z
(
int
n
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
x
[
i
][
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_xs
(
int
n
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
boxxlo
=
domain
->
boxlo
[
0
];
double
invxprd
=
1.0
/
domain
->
xprd
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
(
x
[
i
][
0
]
-
boxxlo
)
*
invxprd
;
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_ys
(
int
n
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
boxylo
=
domain
->
boxlo
[
1
];
double
invyprd
=
1.0
/
domain
->
yprd
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
(
x
[
i
][
1
]
-
boxylo
)
*
invyprd
;
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_zs
(
int
n
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
boxzlo
=
domain
->
boxlo
[
2
];
double
invzprd
=
1.0
/
domain
->
zprd
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
(
x
[
i
][
2
]
-
boxzlo
)
*
invzprd
;
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_xs_triclinic
(
int
n
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
*
boxlo
=
domain
->
boxlo
;
double
*
h_inv
=
domain
->
h_inv
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
h_inv
[
0
]
*
(
x
[
i
][
0
]
-
boxlo
[
0
])
+
h_inv
[
5
]
*
(
x
[
i
][
1
]
-
boxlo
[
1
])
+
h_inv
[
4
]
*
(
x
[
i
][
2
]
-
boxlo
[
2
]);
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_ys_triclinic
(
int
n
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
*
boxlo
=
domain
->
boxlo
;
double
*
h_inv
=
domain
->
h_inv
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
h_inv
[
1
]
*
(
x
[
i
][
1
]
-
boxlo
[
1
])
+
h_inv
[
3
]
*
(
x
[
i
][
2
]
-
boxlo
[
2
]);
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_zs_triclinic
(
int
n
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
*
boxlo
=
domain
->
boxlo
;
double
*
h_inv
=
domain
->
h_inv
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
h_inv
[
2
]
*
(
x
[
i
][
2
]
-
boxlo
[
2
]);
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_xu
(
int
n
)
{
double
**
x
=
atom
->
x
;
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
xprd
=
domain
->
xprd
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
x
[
i
][
0
]
+
((
image
[
i
]
&
IMGMASK
)
-
IMGMAX
)
*
xprd
;
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_yu
(
int
n
)
{
double
**
x
=
atom
->
x
;
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
yprd
=
domain
->
yprd
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
x
[
i
][
1
]
+
((
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
)
*
yprd
;
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_zu
(
int
n
)
{
double
**
x
=
atom
->
x
;
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
zprd
=
domain
->
zprd
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
x
[
i
][
2
]
+
((
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
)
*
zprd
;
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_xu_triclinic
(
int
n
)
{
double
**
x
=
atom
->
x
;
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
*
h
=
domain
->
h
;
int
xbox
,
ybox
,
zbox
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
xbox
=
(
image
[
i
]
&
IMGMASK
)
-
IMGMAX
;
ybox
=
(
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
;
zbox
=
(
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
;
buf
[
n
]
=
x
[
i
][
0
]
+
h
[
0
]
*
xbox
+
h
[
5
]
*
ybox
+
h
[
4
]
*
zbox
;
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_yu_triclinic
(
int
n
)
{
double
**
x
=
atom
->
x
;
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
*
h
=
domain
->
h
;
int
ybox
,
zbox
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
ybox
=
(
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
;
zbox
=
(
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
;
buf
[
n
]
=
x
[
i
][
1
]
+
h
[
1
]
*
ybox
+
h
[
3
]
*
zbox
;
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_zu_triclinic
(
int
n
)
{
double
**
x
=
atom
->
x
;
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
*
h
=
domain
->
h
;
int
zbox
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
zbox
=
(
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
;
buf
[
n
]
=
x
[
i
][
2
]
+
h
[
2
]
*
zbox
;
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_ix
(
int
n
)
{
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
(
image
[
i
]
&
IMGMASK
)
-
IMGMAX
;
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_iy
(
int
n
)
{
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
(
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
;
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_iz
(
int
n
)
{
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
(
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
;
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_vx
(
int
n
)
{
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
v
[
i
][
0
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_vy
(
int
n
)
{
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
v
[
i
][
1
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_vz
(
int
n
)
{
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
v
[
i
][
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_fx
(
int
n
)
{
double
**
f
=
atom
->
f
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
f
[
i
][
0
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_fy
(
int
n
)
{
double
**
f
=
atom
->
f
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
f
[
i
][
1
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_fz
(
int
n
)
{
double
**
f
=
atom
->
f
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
f
[
i
][
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_q
(
int
n
)
{
double
*
q
=
atom
->
q
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
q
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_mux
(
int
n
)
{
double
**
mu
=
atom
->
mu
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
mu
[
i
][
0
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_muy
(
int
n
)
{
double
**
mu
=
atom
->
mu
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
mu
[
i
][
1
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_muz
(
int
n
)
{
double
**
mu
=
atom
->
mu
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
mu
[
i
][
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_mu
(
int
n
)
{
double
**
mu
=
atom
->
mu
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
mu
[
i
][
3
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_radius
(
int
n
)
{
double
*
radius
=
atom
->
radius
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
radius
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_diameter
(
int
n
)
{
double
*
radius
=
atom
->
radius
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
2.0
*
radius
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_omegax
(
int
n
)
{
double
**
omega
=
atom
->
omega
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
omega
[
i
][
0
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_omegay
(
int
n
)
{
double
**
omega
=
atom
->
omega
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
omega
[
i
][
1
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_omegaz
(
int
n
)
{
double
**
omega
=
atom
->
omega
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
omega
[
i
][
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_angmomx
(
int
n
)
{
double
**
angmom
=
atom
->
angmom
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
angmom
[
i
][
0
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_angmomy
(
int
n
)
{
double
**
angmom
=
atom
->
angmom
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
angmom
[
i
][
1
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_angmomz
(
int
n
)
{
double
**
angmom
=
atom
->
angmom
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
angmom
[
i
][
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_shapex
(
int
n
)
{
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec_ellipsoid
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
ellipsoid
[
i
]
>=
0
)
buf
[
n
]
=
bonus
[
ellipsoid
[
i
]].
shape
[
0
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_shapey
(
int
n
)
{
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec_ellipsoid
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
ellipsoid
[
i
]
>=
0
)
buf
[
n
]
=
bonus
[
ellipsoid
[
i
]].
shape
[
1
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_shapez
(
int
n
)
{
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec_ellipsoid
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
ellipsoid
[
i
]
>=
0
)
buf
[
n
]
=
bonus
[
ellipsoid
[
i
]].
shape
[
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_quatw
(
int
n
)
{
if
(
avec_ellipsoid
)
{
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec_ellipsoid
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
ellipsoid
[
i
]
>=
0
)
buf
[
n
]
=
bonus
[
ellipsoid
[
i
]].
quat
[
0
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
else
{
AtomVecBody
::
Bonus
*
bonus
=
avec_body
->
bonus
;
int
*
body
=
atom
->
body
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
body
[
i
]
>=
0
)
buf
[
n
]
=
bonus
[
body
[
i
]].
quat
[
0
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_quati
(
int
n
)
{
if
(
avec_ellipsoid
)
{
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec_ellipsoid
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
ellipsoid
[
i
]
>=
0
)
buf
[
n
]
=
bonus
[
ellipsoid
[
i
]].
quat
[
1
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
else
{
AtomVecBody
::
Bonus
*
bonus
=
avec_body
->
bonus
;
int
*
body
=
atom
->
body
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
body
[
i
]
>=
0
)
buf
[
n
]
=
bonus
[
body
[
i
]].
quat
[
1
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_quatj
(
int
n
)
{
if
(
avec_ellipsoid
)
{
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec_ellipsoid
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
ellipsoid
[
i
]
>=
0
)
buf
[
n
]
=
bonus
[
ellipsoid
[
i
]].
quat
[
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
else
{
AtomVecBody
::
Bonus
*
bonus
=
avec_body
->
bonus
;
int
*
body
=
atom
->
body
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
body
[
i
]
>=
0
)
buf
[
n
]
=
bonus
[
body
[
i
]].
quat
[
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_quatk
(
int
n
)
{
if
(
avec_ellipsoid
)
{
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec_ellipsoid
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
ellipsoid
[
i
]
>=
0
)
buf
[
n
]
=
bonus
[
ellipsoid
[
i
]].
quat
[
3
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
else
{
AtomVecBody
::
Bonus
*
bonus
=
avec_body
->
bonus
;
int
*
body
=
atom
->
body
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
body
[
i
]
>=
0
)
buf
[
n
]
=
bonus
[
body
[
i
]].
quat
[
3
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_tqx
(
int
n
)
{
double
**
torque
=
atom
->
torque
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
torque
[
i
][
0
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_tqy
(
int
n
)
{
double
**
torque
=
atom
->
torque
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
torque
[
i
][
1
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_tqz
(
int
n
)
{
double
**
torque
=
atom
->
torque
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
torque
[
i
][
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_end1x
(
int
n
)
{
AtomVecLine
::
Bonus
*
bonus
=
avec_line
->
bonus
;
int
*
line
=
atom
->
line
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
line
[
i
]
>=
0
)
buf
[
n
]
=
x
[
i
][
0
]
-
0.5
*
bonus
[
line
[
i
]].
length
*
cos
(
bonus
[
line
[
i
]].
theta
);
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_end1y
(
int
n
)
{
AtomVecLine
::
Bonus
*
bonus
=
avec_line
->
bonus
;
int
*
line
=
atom
->
line
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
line
[
i
]
>=
0
)
buf
[
n
]
=
x
[
i
][
1
]
-
0.5
*
bonus
[
line
[
i
]].
length
*
sin
(
bonus
[
line
[
i
]].
theta
);
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_end1z
(
int
n
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
x
[
i
][
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_end2x
(
int
n
)
{
AtomVecLine
::
Bonus
*
bonus
=
avec_line
->
bonus
;
int
*
line
=
atom
->
line
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
line
[
i
]
>=
0
)
buf
[
n
]
=
x
[
i
][
0
]
+
0.5
*
bonus
[
line
[
i
]].
length
*
cos
(
bonus
[
line
[
i
]].
theta
);
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_end2y
(
int
n
)
{
AtomVecLine
::
Bonus
*
bonus
=
avec_line
->
bonus
;
int
*
line
=
atom
->
line
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
line
[
i
]
>=
0
)
buf
[
n
]
=
x
[
i
][
1
]
+
0.5
*
bonus
[
line
[
i
]].
length
*
sin
(
bonus
[
line
[
i
]].
theta
);
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_end2z
(
int
n
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
x
[
i
][
2
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_corner1x
(
int
n
)
{
AtomVecTri
::
Bonus
*
bonus
=
avec_tri
->
bonus
;
int
*
tri
=
atom
->
tri
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
p
[
3
][
3
],
c
[
3
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
tri
[
i
]
>=
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c1
,
c
);
buf
[
n
]
=
x
[
i
][
0
]
+
c
[
0
];
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_corner1y
(
int
n
)
{
AtomVecTri
::
Bonus
*
bonus
=
avec_tri
->
bonus
;
int
*
tri
=
atom
->
tri
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
p
[
3
][
3
],
c
[
3
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
tri
[
i
]
>=
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c1
,
c
);
buf
[
n
]
=
x
[
i
][
1
]
+
c
[
1
];
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_corner1z
(
int
n
)
{
AtomVecTri
::
Bonus
*
bonus
=
avec_tri
->
bonus
;
int
*
tri
=
atom
->
tri
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
p
[
3
][
3
],
c
[
3
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
tri
[
i
]
>=
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c1
,
c
);
buf
[
n
]
=
x
[
i
][
2
]
+
c
[
2
];
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_corner2x
(
int
n
)
{
AtomVecTri
::
Bonus
*
bonus
=
avec_tri
->
bonus
;
int
*
tri
=
atom
->
tri
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
p
[
3
][
3
],
c
[
3
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
tri
[
i
]
>=
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c2
,
c
);
buf
[
n
]
=
x
[
i
][
0
]
+
c
[
0
];
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_corner2y
(
int
n
)
{
AtomVecTri
::
Bonus
*
bonus
=
avec_tri
->
bonus
;
int
*
tri
=
atom
->
tri
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
p
[
3
][
3
],
c
[
3
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
tri
[
i
]
>=
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c2
,
c
);
buf
[
n
]
=
x
[
i
][
1
]
+
c
[
1
];
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_corner2z
(
int
n
)
{
AtomVecTri
::
Bonus
*
bonus
=
avec_tri
->
bonus
;
int
*
tri
=
atom
->
tri
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
p
[
3
][
3
],
c
[
3
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
tri
[
i
]
>=
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c2
,
c
);
buf
[
n
]
=
x
[
i
][
2
]
+
c
[
2
];
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_corner3x
(
int
n
)
{
AtomVecTri
::
Bonus
*
bonus
=
avec_tri
->
bonus
;
int
*
tri
=
atom
->
tri
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
p
[
3
][
3
],
c
[
3
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
tri
[
i
]
>=
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c3
,
c
);
buf
[
n
]
=
x
[
i
][
0
]
+
c
[
0
];
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_corner3y
(
int
n
)
{
AtomVecTri
::
Bonus
*
bonus
=
avec_tri
->
bonus
;
int
*
tri
=
atom
->
tri
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
p
[
3
][
3
],
c
[
3
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
tri
[
i
]
>=
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c3
,
c
);
buf
[
n
]
=
x
[
i
][
1
]
+
c
[
1
];
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_corner3z
(
int
n
)
{
AtomVecTri
::
Bonus
*
bonus
=
avec_tri
->
bonus
;
int
*
tri
=
atom
->
tri
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
p
[
3
][
3
],
c
[
3
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
tri
[
i
]
>=
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c3
,
c
);
buf
[
n
]
=
x
[
i
][
2
]
+
c
[
2
];
}
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_nbonds
(
int
n
)
{
int
*
num_bond
=
atom
->
num_bond
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
num_bond
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_iname
(
int
n
)
{
int
*
ivector
=
atom
->
ivector
[
index
[
n
]];
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
ivector
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_dname
(
int
n
)
{
double
*
dvector
=
atom
->
dvector
[
index
[
n
]];
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
dvector
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyAtom
::
pack_property_atom
(
int
n
)
{
atom
->
avec
->
pack_property_atom
(
index
[
n
],
&
buf
[
n
],
nvalues
,
groupbit
);
}
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