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rLAMMPS lammps
atom_vec_peri.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
#include "float.h"
#include "stdlib.h"
#include "string.h"
#include "atom_vec_peri.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
static
const
char
cite_peri_package
[]
=
"PERI package for Peridynamics:
\n\n
"
"@Article{Parks08,
\n
"
" author = {M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling},
\n
"
" title = {Implementing peridynamics within a molecular dynamics code},
\n
"
" journal = {Comp.~Phys.~Comm.},
\n
"
" year = 2008,
\n
"
" volume = 179,
\n
"
" pages = {777--783}
\n
"
"}
\n\n
"
;
/* ---------------------------------------------------------------------- */
AtomVecPeri
::
AtomVecPeri
(
LAMMPS
*
lmp
)
:
AtomVec
(
lmp
)
{
if
(
lmp
->
citeme
)
lmp
->
citeme
->
add
(
cite_peri_package
);
molecular
=
0
;
comm_x_only
=
0
;
comm_f_only
=
1
;
size_forward
=
4
;
size_reverse
=
3
;
size_border
=
11
;
size_velocity
=
3
;
size_data_atom
=
7
;
size_data_vel
=
4
;
xcol_data
=
5
;
atom
->
peri_flag
=
1
;
atom
->
vfrac_flag
=
atom
->
rmass_flag
=
1
;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void
AtomVecPeri
::
grow
(
int
n
)
{
if
(
n
==
0
)
grow_nmax
();
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"
);
vfrac
=
memory
->
grow
(
atom
->
vfrac
,
nmax
,
"atom:vfrac"
);
rmass
=
memory
->
grow
(
atom
->
rmass
,
nmax
,
"atom:rmass"
);
s0
=
memory
->
grow
(
atom
->
s0
,
nmax
,
"atom:s0"
);
x0
=
memory
->
grow
(
atom
->
x0
,
nmax
,
3
,
"atom:x0"
);
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
AtomVecPeri
::
grow_reset
()
{
tag
=
atom
->
tag
;
type
=
atom
->
type
;
mask
=
atom
->
mask
;
image
=
atom
->
image
;
x
=
atom
->
x
;
v
=
atom
->
v
;
f
=
atom
->
f
;
vfrac
=
atom
->
vfrac
;
rmass
=
atom
->
rmass
;
s0
=
atom
->
s0
;
x0
=
atom
->
x0
;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void
AtomVecPeri
::
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
];
vfrac
[
j
]
=
vfrac
[
i
];
rmass
[
j
]
=
rmass
[
i
];
s0
[
j
]
=
s0
[
i
];
x0
[
j
][
0
]
=
x0
[
i
][
0
];
x0
[
j
][
1
]
=
x0
[
i
][
1
];
x0
[
j
][
2
]
=
x0
[
i
][
2
];
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
copy_arrays
(
i
,
j
,
delflag
);
}
/* ---------------------------------------------------------------------- */
int
AtomVecPeri
::
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
];
buf
[
m
++
]
=
s0
[
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
]
*
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
;
buf
[
m
++
]
=
s0
[
j
];
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecPeri
::
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
++
]
=
s0
[
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
]
*
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
++
]
=
s0
[
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
++
]
=
s0
[
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
AtomVecPeri
::
pack_comm_hybrid
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
s0
[
j
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecPeri
::
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
++
];
s0
[
i
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
void
AtomVecPeri
::
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
++
];
s0
[
i
]
=
buf
[
m
++
];
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecPeri
::
unpack_comm_hybrid
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
s0
[
i
]
=
buf
[
m
++
];
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecPeri
::
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
AtomVecPeri
::
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
AtomVecPeri
::
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
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
buf
[
m
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
s0
[
j
];
buf
[
m
++
]
=
x0
[
j
][
0
];
buf
[
m
++
]
=
x0
[
j
][
1
];
buf
[
m
++
]
=
x0
[
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
];
}
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
buf
[
m
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
buf
[
m
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
s0
[
j
];
buf
[
m
++
]
=
x0
[
j
][
0
];
buf
[
m
++
]
=
x0
[
j
][
1
];
buf
[
m
++
]
=
x0
[
j
][
2
];
}
}
if
(
atom
->
nextra_border
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_border
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_border
[
iextra
]]
->
pack_border
(
n
,
list
,
&
buf
[
m
]);
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecPeri
::
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
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
buf
[
m
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
s0
[
j
];
buf
[
m
++
]
=
x0
[
j
][
0
];
buf
[
m
++
]
=
x0
[
j
][
1
];
buf
[
m
++
]
=
x0
[
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
];
dy
=
pbc
[
1
];
dz
=
pbc
[
2
];
}
if
(
!
deform_vremap
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
buf
[
m
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
buf
[
m
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
s0
[
j
];
buf
[
m
++
]
=
x0
[
j
][
0
];
buf
[
m
++
]
=
x0
[
j
][
1
];
buf
[
m
++
]
=
x0
[
j
][
2
];
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
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
buf
[
m
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
s0
[
j
];
buf
[
m
++
]
=
x0
[
j
][
0
];
buf
[
m
++
]
=
x0
[
j
][
1
];
buf
[
m
++
]
=
x0
[
j
][
2
];
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
];
}
}
}
}
if
(
atom
->
nextra_border
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_border
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_border
[
iextra
]]
->
pack_border
(
n
,
list
,
&
buf
[
m
]);
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecPeri
::
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
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
s0
[
j
];
buf
[
m
++
]
=
x0
[
j
][
0
];
buf
[
m
++
]
=
x0
[
j
][
1
];
buf
[
m
++
]
=
x0
[
j
][
2
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecPeri
::
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
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
type
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
mask
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
vfrac
[
i
]
=
buf
[
m
++
];
s0
[
i
]
=
buf
[
m
++
];
x0
[
i
][
0
]
=
buf
[
m
++
];
x0
[
i
][
1
]
=
buf
[
m
++
];
x0
[
i
][
2
]
=
buf
[
m
++
];
}
if
(
atom
->
nextra_border
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_border
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_border
[
iextra
]]
->
unpack_border
(
n
,
first
,
&
buf
[
m
]);
}
/* ---------------------------------------------------------------------- */
void
AtomVecPeri
::
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
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
type
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
mask
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
vfrac
[
i
]
=
buf
[
m
++
];
s0
[
i
]
=
buf
[
m
++
];
x0
[
i
][
0
]
=
buf
[
m
++
];
x0
[
i
][
1
]
=
buf
[
m
++
];
x0
[
i
][
2
]
=
buf
[
m
++
];
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
}
if
(
atom
->
nextra_border
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_border
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_border
[
iextra
]]
->
unpack_border
(
n
,
first
,
&
buf
[
m
]);
}
/* ---------------------------------------------------------------------- */
int
AtomVecPeri
::
unpack_border_hybrid
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
vfrac
[
i
]
=
buf
[
m
++
];
s0
[
i
]
=
buf
[
m
++
];
x0
[
i
][
0
]
=
buf
[
m
++
];
x0
[
i
][
1
]
=
buf
[
m
++
];
x0
[
i
][
2
]
=
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
AtomVecPeri
::
pack_exchange
(
int
i
,
double
*
buf
)
{
int
m
=
1
;
buf
[
m
++
]
=
x
[
i
][
0
];
buf
[
m
++
]
=
x
[
i
][
1
];
buf
[
m
++
]
=
x
[
i
][
2
];
buf
[
m
++
]
=
v
[
i
][
0
];
buf
[
m
++
]
=
v
[
i
][
1
];
buf
[
m
++
]
=
v
[
i
][
2
];
buf
[
m
++
]
=
ubuf
(
tag
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
image
[
i
]).
d
;
buf
[
m
++
]
=
vfrac
[
i
];
buf
[
m
++
]
=
rmass
[
i
];
buf
[
m
++
]
=
s0
[
i
];
buf
[
m
++
]
=
x0
[
i
][
0
];
buf
[
m
++
]
=
x0
[
i
][
1
];
buf
[
m
++
]
=
x0
[
i
][
2
];
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
AtomVecPeri
::
unpack_exchange
(
double
*
buf
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
int
m
=
1
;
x
[
nlocal
][
0
]
=
buf
[
m
++
];
x
[
nlocal
][
1
]
=
buf
[
m
++
];
x
[
nlocal
][
2
]
=
buf
[
m
++
];
v
[
nlocal
][
0
]
=
buf
[
m
++
];
v
[
nlocal
][
1
]
=
buf
[
m
++
];
v
[
nlocal
][
2
]
=
buf
[
m
++
];
tag
[
nlocal
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
type
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
mask
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
image
[
nlocal
]
=
(
imageint
)
ubuf
(
buf
[
m
++
]).
i
;
vfrac
[
nlocal
]
=
buf
[
m
++
];
rmass
[
nlocal
]
=
buf
[
m
++
];
s0
[
nlocal
]
=
buf
[
m
++
];
x0
[
nlocal
][
0
]
=
buf
[
m
++
];
x0
[
nlocal
][
1
]
=
buf
[
m
++
];
x0
[
nlocal
][
2
]
=
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
AtomVecPeri
::
size_restart
()
{
int
i
;
int
nlocal
=
atom
->
nlocal
;
int
n
=
17
*
nlocal
;
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
AtomVecPeri
::
pack_restart
(
int
i
,
double
*
buf
)
{
int
m
=
1
;
buf
[
m
++
]
=
x
[
i
][
0
];
buf
[
m
++
]
=
x
[
i
][
1
];
buf
[
m
++
]
=
x
[
i
][
2
];
buf
[
m
++
]
=
ubuf
(
tag
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
image
[
i
]).
d
;
buf
[
m
++
]
=
v
[
i
][
0
];
buf
[
m
++
]
=
v
[
i
][
1
];
buf
[
m
++
]
=
v
[
i
][
2
];
buf
[
m
++
]
=
vfrac
[
i
];
buf
[
m
++
]
=
rmass
[
i
];
buf
[
m
++
]
=
s0
[
i
];
buf
[
m
++
]
=
x0
[
i
][
0
];
buf
[
m
++
]
=
x0
[
i
][
1
];
buf
[
m
++
]
=
x0
[
i
][
2
];
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
AtomVecPeri
::
unpack_restart
(
double
*
buf
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
{
grow
(
0
);
if
(
atom
->
nextra_store
)
memory
->
grow
(
atom
->
extra
,
nmax
,
atom
->
nextra_store
,
"atom:extra"
);
}
int
m
=
1
;
x
[
nlocal
][
0
]
=
buf
[
m
++
];
x
[
nlocal
][
1
]
=
buf
[
m
++
];
x
[
nlocal
][
2
]
=
buf
[
m
++
];
tag
[
nlocal
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
type
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
mask
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
image
[
nlocal
]
=
(
imageint
)
ubuf
(
buf
[
m
++
]).
i
;
v
[
nlocal
][
0
]
=
buf
[
m
++
];
v
[
nlocal
][
1
]
=
buf
[
m
++
];
v
[
nlocal
][
2
]
=
buf
[
m
++
];
vfrac
[
nlocal
]
=
buf
[
m
++
];
rmass
[
nlocal
]
=
buf
[
m
++
];
s0
[
nlocal
]
=
buf
[
m
++
];
x0
[
nlocal
][
0
]
=
buf
[
m
++
];
x0
[
nlocal
][
1
]
=
buf
[
m
++
];
x0
[
nlocal
][
2
]
=
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
AtomVecPeri
::
create_atom
(
int
itype
,
double
*
coord
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
tag
[
nlocal
]
=
0
;
type
[
nlocal
]
=
itype
;
x
[
nlocal
][
0
]
=
coord
[
0
];
x
[
nlocal
][
1
]
=
coord
[
1
];
x
[
nlocal
][
2
]
=
coord
[
2
];
mask
[
nlocal
]
=
1
;
image
[
nlocal
]
=
((
imageint
)
IMGMAX
<<
IMG2BITS
)
|
((
imageint
)
IMGMAX
<<
IMGBITS
)
|
IMGMAX
;
v
[
nlocal
][
0
]
=
0.0
;
v
[
nlocal
][
1
]
=
0.0
;
v
[
nlocal
][
2
]
=
0.0
;
vfrac
[
nlocal
]
=
1.0
;
rmass
[
nlocal
]
=
1.0
;
s0
[
nlocal
]
=
DBL_MAX
;
x0
[
nlocal
][
0
]
=
coord
[
0
];
x0
[
nlocal
][
1
]
=
coord
[
1
];
x0
[
nlocal
][
2
]
=
coord
[
2
];
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void
AtomVecPeri
::
data_atom
(
double
*
coord
,
imageint
imagetmp
,
char
**
values
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
tag
[
nlocal
]
=
ATOTAGINT
(
values
[
0
]);
type
[
nlocal
]
=
atoi
(
values
[
1
]);
if
(
type
[
nlocal
]
<=
0
||
type
[
nlocal
]
>
atom
->
ntypes
)
error
->
one
(
FLERR
,
"Invalid atom type in Atoms section of data file"
);
vfrac
[
nlocal
]
=
atof
(
values
[
2
]);
rmass
[
nlocal
]
=
atof
(
values
[
3
]);
if
(
rmass
[
nlocal
]
<=
0.0
)
error
->
one
(
FLERR
,
"Invalid mass value"
);
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
;
s0
[
nlocal
]
=
DBL_MAX
;
x0
[
nlocal
][
0
]
=
coord
[
0
];
x0
[
nlocal
][
1
]
=
coord
[
1
];
x0
[
nlocal
][
2
]
=
coord
[
2
];
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int
AtomVecPeri
::
data_atom_hybrid
(
int
nlocal
,
char
**
values
)
{
vfrac
[
nlocal
]
=
atof
(
values
[
0
]);
rmass
[
nlocal
]
=
atof
(
values
[
1
]);
if
(
rmass
[
nlocal
]
<=
0.0
)
error
->
one
(
FLERR
,
"Invalid mass value"
);
s0
[
nlocal
]
=
DBL_MAX
;
x0
[
nlocal
][
0
]
=
x
[
nlocal
][
0
];
x0
[
nlocal
][
1
]
=
x
[
nlocal
][
1
];
x0
[
nlocal
][
2
]
=
x
[
nlocal
][
2
];
return
2
;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void
AtomVecPeri
::
pack_data
(
double
**
buf
)
{
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
buf
[
i
][
0
]
=
ubuf
(
tag
[
i
]).
d
;
buf
[
i
][
1
]
=
ubuf
(
type
[
i
]).
d
;
buf
[
i
][
2
]
=
vfrac
[
i
];
buf
[
i
][
3
]
=
rmass
[
i
];
buf
[
i
][
4
]
=
x
[
i
][
0
];
buf
[
i
][
5
]
=
x
[
i
][
1
];
buf
[
i
][
6
]
=
x
[
i
][
2
];
buf
[
i
][
7
]
=
ubuf
((
image
[
i
]
&
IMGMASK
)
-
IMGMAX
).
d
;
buf
[
i
][
8
]
=
ubuf
((
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
).
d
;
buf
[
i
][
9
]
=
ubuf
((
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
).
d
;
}
}
/* ----------------------------------------------------------------------
pack hybrid atom info for data file
------------------------------------------------------------------------- */
int
AtomVecPeri
::
pack_data_hybrid
(
int
i
,
double
*
buf
)
{
buf
[
0
]
=
vfrac
[
i
];
buf
[
1
]
=
rmass
[
i
];
return
2
;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void
AtomVecPeri
::
write_data
(
FILE
*
fp
,
int
n
,
double
**
buf
)
{
for
(
int
i
=
0
;
i
<
n
;
i
++
)
fprintf
(
fp
,
TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d
\n
"
,
(
tagint
)
ubuf
(
buf
[
i
][
0
]).
i
,(
int
)
ubuf
(
buf
[
i
][
1
]).
i
,
buf
[
i
][
2
],
buf
[
i
][
3
],
buf
[
i
][
4
],
buf
[
i
][
5
],
buf
[
i
][
6
],
(
int
)
ubuf
(
buf
[
i
][
7
]).
i
,(
int
)
ubuf
(
buf
[
i
][
8
]).
i
,
(
int
)
ubuf
(
buf
[
i
][
9
]).
i
);
}
/* ----------------------------------------------------------------------
write hybrid atom info to data file
------------------------------------------------------------------------- */
int
AtomVecPeri
::
write_data_hybrid
(
FILE
*
fp
,
double
*
buf
)
{
fprintf
(
fp
,
" %-1.16e %-1.16e"
,
buf
[
0
],
buf
[
1
]);
return
2
;
}
/* ----------------------------------------------------------------------
assign an index to named atom property and return index
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int
AtomVecPeri
::
property_atom
(
char
*
name
)
{
if
(
strcmp
(
name
,
"vfrac"
)
==
0
)
return
0
;
if
(
strcmp
(
name
,
"s0"
)
==
0
)
return
1
;
return
-
1
;
}
/* ----------------------------------------------------------------------
pack per-atom data into buf for ComputePropertyAtom
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void
AtomVecPeri
::
pack_property_atom
(
int
index
,
double
*
buf
,
int
nvalues
,
int
groupbit
)
{
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
n
=
0
;
if
(
index
==
0
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
vfrac
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
else
if
(
index
==
1
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
buf
[
n
]
=
s0
[
i
];
else
buf
[
n
]
=
0.0
;
n
+=
nvalues
;
}
}
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint
AtomVecPeri
::
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
(
"vfrac"
))
bytes
+=
memory
->
usage
(
vfrac
,
nmax
);
if
(
atom
->
memcheck
(
"rmass"
))
bytes
+=
memory
->
usage
(
rmass
,
nmax
);
if
(
atom
->
memcheck
(
"s0"
))
bytes
+=
memory
->
usage
(
s0
,
nmax
);
if
(
atom
->
memcheck
(
"x0"
))
bytes
+=
memory
->
usage
(
x0
,
nmax
,
3
);
return
bytes
;
}
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