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rLAMMPS lammps
atom_vec_bond.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "atom_vec_bond.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecBond
::
AtomVecBond
(
LAMMPS
*
lmp
)
:
AtomVec
(
lmp
)
{
molecular
=
1
;
bonds_allow
=
1
;
mass_type
=
1
;
comm_x_only
=
comm_f_only
=
1
;
size_forward
=
3
;
size_reverse
=
3
;
size_border
=
7
;
size_velocity
=
3
;
size_data_atom
=
6
;
size_data_vel
=
4
;
xcol_data
=
4
;
atom
->
molecule_flag
=
1
;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void
AtomVecBond
::
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"
);
molecule
=
memory
->
grow
(
atom
->
molecule
,
nmax
,
"atom:molecule"
);
nspecial
=
memory
->
grow
(
atom
->
nspecial
,
nmax
,
3
,
"atom:nspecial"
);
special
=
memory
->
grow
(
atom
->
special
,
nmax
,
atom
->
maxspecial
,
"atom:special"
);
num_bond
=
memory
->
grow
(
atom
->
num_bond
,
nmax
,
"atom:num_bond"
);
bond_type
=
memory
->
grow
(
atom
->
bond_type
,
nmax
,
atom
->
bond_per_atom
,
"atom:bond_type"
);
bond_atom
=
memory
->
grow
(
atom
->
bond_atom
,
nmax
,
atom
->
bond_per_atom
,
"atom:bond_atom"
);
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
AtomVecBond
::
grow_reset
()
{
tag
=
atom
->
tag
;
type
=
atom
->
type
;
mask
=
atom
->
mask
;
image
=
atom
->
image
;
x
=
atom
->
x
;
v
=
atom
->
v
;
f
=
atom
->
f
;
molecule
=
atom
->
molecule
;
nspecial
=
atom
->
nspecial
;
special
=
atom
->
special
;
num_bond
=
atom
->
num_bond
;
bond_type
=
atom
->
bond_type
;
bond_atom
=
atom
->
bond_atom
;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void
AtomVecBond
::
copy
(
int
i
,
int
j
,
int
delflag
)
{
int
k
;
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
];
molecule
[
j
]
=
molecule
[
i
];
num_bond
[
j
]
=
num_bond
[
i
];
for
(
k
=
0
;
k
<
num_bond
[
j
];
k
++
)
{
bond_type
[
j
][
k
]
=
bond_type
[
i
][
k
];
bond_atom
[
j
][
k
]
=
bond_atom
[
i
][
k
];
}
nspecial
[
j
][
0
]
=
nspecial
[
i
][
0
];
nspecial
[
j
][
1
]
=
nspecial
[
i
][
1
];
nspecial
[
j
][
2
]
=
nspecial
[
i
][
2
];
for
(
k
=
0
;
k
<
nspecial
[
j
][
2
];
k
++
)
special
[
j
][
k
]
=
special
[
i
][
k
];
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
copy_arrays
(
i
,
j
);
}
/* ---------------------------------------------------------------------- */
int
AtomVecBond
::
pack_comm
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
double
dx
,
dy
,
dz
;
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
];
}
}
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
;
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecBond
::
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
;
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
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
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
;
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
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
(
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
];
}
}
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecBond
::
unpack_comm
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
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
++
];
}
}
/* ---------------------------------------------------------------------- */
void
AtomVecBond
::
unpack_comm_vel
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
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
++
];
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecBond
::
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
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecBond
::
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
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecBond
::
pack_border
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
double
dx
,
dy
,
dz
;
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
];
buf
[
m
++
]
=
molecule
[
j
];
}
}
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
];
buf
[
m
++
]
=
molecule
[
j
];
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecBond
::
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
;
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
];
buf
[
m
++
]
=
molecule
[
j
];
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
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
];
buf
[
m
++
]
=
molecule
[
j
];
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
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
];
buf
[
m
++
]
=
molecule
[
j
];
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
];
}
}
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecBond
::
pack_border_hybrid
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
molecule
[
j
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecBond
::
unpack_border
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
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
++
]);
molecule
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
}
}
/* ---------------------------------------------------------------------- */
void
AtomVecBond
::
unpack_border_vel
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
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
++
]);
molecule
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecBond
::
unpack_border_hybrid
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
molecule
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
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
AtomVecBond
::
pack_exchange
(
int
i
,
double
*
buf
)
{
int
k
;
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
++
]
=
molecule
[
i
];
buf
[
m
++
]
=
num_bond
[
i
];
for
(
k
=
0
;
k
<
num_bond
[
i
];
k
++
)
{
buf
[
m
++
]
=
bond_type
[
i
][
k
];
buf
[
m
++
]
=
bond_atom
[
i
][
k
];
}
buf
[
m
++
]
=
nspecial
[
i
][
0
];
buf
[
m
++
]
=
nspecial
[
i
][
1
];
buf
[
m
++
]
=
nspecial
[
i
][
2
];
for
(
k
=
0
;
k
<
nspecial
[
i
][
2
];
k
++
)
buf
[
m
++
]
=
special
[
i
][
k
];
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
AtomVecBond
::
unpack_exchange
(
double
*
buf
)
{
int
k
;
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
++
]);
molecule
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
num_bond
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
for
(
k
=
0
;
k
<
num_bond
[
nlocal
];
k
++
)
{
bond_type
[
nlocal
][
k
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
bond_atom
[
nlocal
][
k
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
}
nspecial
[
nlocal
][
0
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
nspecial
[
nlocal
][
1
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
nspecial
[
nlocal
][
2
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
for
(
k
=
0
;
k
<
nspecial
[
nlocal
][
2
];
k
++
)
special
[
nlocal
][
k
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
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
AtomVecBond
::
size_restart
()
{
int
i
;
int
nlocal
=
atom
->
nlocal
;
int
n
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
n
+=
13
+
2
*
num_bond
[
i
];
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
AtomVecBond
::
pack_restart
(
int
i
,
double
*
buf
)
{
int
k
;
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
++
]
=
molecule
[
i
];
buf
[
m
++
]
=
num_bond
[
i
];
for
(
k
=
0
;
k
<
num_bond
[
i
];
k
++
)
{
buf
[
m
++
]
=
MAX
(
bond_type
[
i
][
k
],
-
bond_type
[
i
][
k
]);
buf
[
m
++
]
=
bond_atom
[
i
][
k
];
}
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
AtomVecBond
::
unpack_restart
(
double
*
buf
)
{
int
k
;
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
++
];
molecule
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
num_bond
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
for
(
k
=
0
;
k
<
num_bond
[
nlocal
];
k
++
)
{
bond_type
[
nlocal
][
k
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
bond_atom
[
nlocal
][
k
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
}
double
**
extra
=
atom
->
extra
;
if
(
atom
->
nextra_store
)
{
int
size
=
static_cast
<
int
>
(
buf
[
0
])
-
m
;
for
(
int
i
=
0
;
i
<
size
;
i
++
)
extra
[
nlocal
][
i
]
=
buf
[
m
++
];
}
atom
->
nlocal
++
;
return
m
;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void
AtomVecBond
::
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
;
molecule
[
nlocal
]
=
0
;
num_bond
[
nlocal
]
=
0
;
nspecial
[
nlocal
][
0
]
=
nspecial
[
nlocal
][
1
]
=
nspecial
[
nlocal
][
2
]
=
0
;
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void
AtomVecBond
::
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"
);
molecule
[
nlocal
]
=
atoi
(
values
[
1
]);
type
[
nlocal
]
=
atoi
(
values
[
2
]);
if
(
type
[
nlocal
]
<=
0
||
type
[
nlocal
]
>
atom
->
ntypes
)
error
->
one
(
FLERR
,
"Invalid atom type 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
;
num_bond
[
nlocal
]
=
0
;
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int
AtomVecBond
::
data_atom_hybrid
(
int
nlocal
,
char
**
values
)
{
molecule
[
nlocal
]
=
atoi
(
values
[
0
]);
num_bond
[
nlocal
]
=
0
;
return
1
;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint
AtomVecBond
::
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
(
"molecule"
))
bytes
+=
memory
->
usage
(
molecule
,
nmax
);
if
(
atom
->
memcheck
(
"nspecial"
))
bytes
+=
memory
->
usage
(
nspecial
,
nmax
,
3
);
if
(
atom
->
memcheck
(
"special"
))
bytes
+=
memory
->
usage
(
special
,
nmax
,
atom
->
maxspecial
);
if
(
atom
->
memcheck
(
"num_bond"
))
bytes
+=
memory
->
usage
(
num_bond
,
nmax
);
if
(
atom
->
memcheck
(
"bond_type"
))
bytes
+=
memory
->
usage
(
bond_type
,
nmax
,
atom
->
bond_per_atom
);
if
(
atom
->
memcheck
(
"bond_atom"
))
bytes
+=
memory
->
usage
(
bond_atom
,
nmax
,
atom
->
bond_per_atom
);
return
bytes
;
}
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