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atom_vec_tdpd.cpp
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rLAMMPS lammps
atom_vec_tdpd.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 <string.h>
#include <stdlib.h>
#include "atom_vec_tdpd.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include "input.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
AtomVecTDPD
::
AtomVecTDPD
(
LAMMPS
*
lmp
)
:
AtomVec
(
lmp
)
{
if
(
strcmp
(
update
->
unit_style
,
"lj"
)
!=
0
)
error
->
all
(
FLERR
,
"Atom style edpd requires lj units"
);
molecular
=
0
;
mass_type
=
1
;
forceclearflag
=
1
;
comm_x_only
=
comm_f_only
=
0
;
comm
->
ghost_velocity
=
1
;
cc_species
=
0
;
// for now, reset in process_args()
size_forward
=
3
+
cc_species
+
3
;
//vest[3]
size_reverse
=
3
+
cc_species
;
size_border
=
6
+
cc_species
+
3
;
//vest[3]
size_velocity
=
3
;
// for data_atom, we read id + type + xyz[3] + cc[i] where i=1,cc_species
size_data_atom
=
5
+
cc_species
;
size_data_vel
=
4
;
xcol_data
=
3
;
atom
->
tdpd_flag
=
1
;
atom
->
vest_flag
=
1
;
}
/* ----------------------------------------------------------------------
process additional args
single arg = number of cc_species
------------------------------------------------------------------------- */
void
AtomVecTDPD
::
process_args
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
1
)
error
->
all
(
FLERR
,
"Invalid atom_style tdpd command"
);
atom
->
cc_species
=
force
->
inumeric
(
FLERR
,
arg
[
0
]);
cc_species
=
atom
->
cc_species
;
// reset sizes that depend on cc_species
size_forward
=
3
+
cc_species
+
3
;
size_reverse
=
3
+
cc_species
;
size_border
=
6
+
cc_species
+
3
;
size_data_atom
=
5
+
cc_species
;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void
AtomVecTDPD
::
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"
);
cc
=
memory
->
grow
(
atom
->
cc
,
nmax
*
comm
->
nthreads
,
cc_species
,
"atom:cc"
);
cc_flux
=
memory
->
grow
(
atom
->
cc_flux
,
nmax
*
comm
->
nthreads
,
cc_species
,
"atom:cc_flux"
);
vest
=
memory
->
grow
(
atom
->
vest
,
nmax
,
3
,
"atom:vest"
);
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
AtomVecTDPD
::
grow_reset
()
{
tag
=
atom
->
tag
;
type
=
atom
->
type
;
mask
=
atom
->
mask
;
image
=
atom
->
image
;
x
=
atom
->
x
;
v
=
atom
->
v
;
f
=
atom
->
f
;
cc
=
atom
->
cc
;
cc_flux
=
atom
->
cc_flux
;
vest
=
atom
->
vest
;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void
AtomVecTDPD
::
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
];
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
cc
[
j
][
k
]
=
cc
[
i
][
k
];
vest
[
j
][
0
]
=
vest
[
i
][
0
];
vest
[
j
][
1
]
=
vest
[
i
][
1
];
vest
[
j
][
2
]
=
vest
[
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
);
}
void
AtomVecTDPD
::
force_clear
(
int
n
,
size_t
nbytes
)
{
memset
(
&
cc_flux
[
n
][
0
],
0
,
cc_species
*
nbytes
);
}
/* ---------------------------------------------------------------------- */
int
AtomVecTDPD
::
pack_comm
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
k
,
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
];
for
(
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
j
][
k
];
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
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
;
for
(
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
j
][
k
];
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
j
][
2
];
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecTDPD
::
pack_comm_vel
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
k
,
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
];
for
(
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
j
][
k
];
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
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
];
for
(
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
j
][
k
];
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
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
];
}
for
(
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
j
][
k
];
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
j
][
2
];
}
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecTDPD
::
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
++
];
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
cc
[
i
][
k
]
=
buf
[
m
++
];
vest
[
i
][
0
]
=
buf
[
m
++
];
vest
[
i
][
1
]
=
buf
[
m
++
];
vest
[
i
][
2
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
void
AtomVecTDPD
::
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
++
];
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
cc
[
i
][
k
]
=
buf
[
m
++
];
vest
[
i
][
0
]
=
buf
[
m
++
];
vest
[
i
][
1
]
=
buf
[
m
++
];
vest
[
i
][
2
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecTDPD
::
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
];
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc_flux
[
i
][
k
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecTDPD
::
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
++
];
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
cc_flux
[
j
][
k
]
+=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecTDPD
::
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
;
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
j
][
k
];
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
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
;
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
j
][
k
];
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
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
AtomVecTDPD
::
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
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
j
][
k
];
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
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
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
j
][
k
];
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
j
][
2
];
}
}
else
{
dvx
=
pbc
[
0
]
*
h_rate
[
0
]
+
pbc
[
5
]
*
h_rate
[
5
]
+
pbc
[
4
]
*
h_rate
[
4
];
dvy
=
pbc
[
1
]
*
h_rate
[
1
]
+
pbc
[
3
]
*
h_rate
[
3
];
dvz
=
pbc
[
2
]
*
h_rate
[
2
];
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
buf
[
m
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
if
(
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
];
}
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
j
][
k
];
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
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
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecTDPD
::
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
;
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
cc
[
i
][
k
]
=
buf
[
m
++
];
vest
[
i
][
0
]
=
buf
[
m
++
];
vest
[
i
][
1
]
=
buf
[
m
++
];
vest
[
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
AtomVecTDPD
::
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
;
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
cc
[
i
][
k
]
=
buf
[
m
++
];
vest
[
i
][
0
]
=
buf
[
m
++
];
vest
[
i
][
1
]
=
buf
[
m
++
];
vest
[
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
]);
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int
AtomVecTDPD
::
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
;
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
i
][
k
];
buf
[
m
++
]
=
vest
[
i
][
0
];
buf
[
m
++
]
=
vest
[
i
][
1
];
buf
[
m
++
]
=
vest
[
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
AtomVecTDPD
::
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
;
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
cc
[
nlocal
][
k
]
=
buf
[
m
++
];
vest
[
nlocal
][
0
]
=
buf
[
m
++
];
vest
[
nlocal
][
1
]
=
buf
[
m
++
];
vest
[
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
AtomVecTDPD
::
size_restart
()
{
int
i
;
int
nlocal
=
atom
->
nlocal
;
int
n
=
(
11
+
cc_species
+
3
)
*
nlocal
;
// 11 + cc[i] + vest[3]
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
AtomVecTDPD
::
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
];
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
m
++
]
=
cc
[
i
][
k
];
buf
[
m
++
]
=
vest
[
i
][
0
];
buf
[
m
++
]
=
vest
[
i
][
1
];
buf
[
m
++
]
=
vest
[
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
AtomVecTDPD
::
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
++
];
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
cc
[
nlocal
][
k
]
=
buf
[
m
++
];
vest
[
nlocal
][
0
]
=
buf
[
m
++
];
vest
[
nlocal
][
1
]
=
buf
[
m
++
];
vest
[
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
AtomVecTDPD
::
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
;
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
cc
[
nlocal
][
k
]
=
0.0
;
vest
[
nlocal
][
0
]
=
0.0
;
vest
[
nlocal
][
1
]
=
0.0
;
vest
[
nlocal
][
2
]
=
0.0
;
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void
AtomVecTDPD
::
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"
);
x
[
nlocal
][
0
]
=
coord
[
0
];
x
[
nlocal
][
1
]
=
coord
[
1
];
x
[
nlocal
][
2
]
=
coord
[
2
];
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
cc
[
nlocal
][
k
]
=
atof
(
values
[
5
+
k
]
);
image
[
nlocal
]
=
imagetmp
;
mask
[
nlocal
]
=
1
;
v
[
nlocal
][
0
]
=
0.0
;
v
[
nlocal
][
1
]
=
0.0
;
v
[
nlocal
][
2
]
=
0.0
;
vest
[
nlocal
][
0
]
=
0.0
;
vest
[
nlocal
][
1
]
=
0.0
;
vest
[
nlocal
][
2
]
=
0.0
;
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void
AtomVecTDPD
::
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
]
=
x
[
i
][
0
];
buf
[
i
][
3
]
=
x
[
i
][
1
];
buf
[
i
][
4
]
=
x
[
i
][
2
];
buf
[
i
][
5
]
=
ubuf
((
image
[
i
]
&
IMGMASK
)
-
IMGMAX
).
d
;
buf
[
i
][
6
]
=
ubuf
((
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
).
d
;
buf
[
i
][
7
]
=
ubuf
((
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
).
d
;
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
buf
[
i
][
8
+
k
]
=
cc
[
i
][
k
];
}
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void
AtomVecTDPD
::
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 %d %d %d"
,
(
tagint
)
ubuf
(
buf
[
i
][
0
]).
i
,(
int
)
ubuf
(
buf
[
i
][
1
]).
i
,
buf
[
i
][
2
],
buf
[
i
][
3
],
buf
[
i
][
4
],
(
int
)
ubuf
(
buf
[
i
][
5
]).
i
,(
int
)
ubuf
(
buf
[
i
][
6
]).
i
,
(
int
)
ubuf
(
buf
[
i
][
7
]).
i
);
for
(
int
k
=
0
;
k
<
cc_species
;
k
++
)
fprintf
(
fp
,
" %-1.16e"
,
buf
[
i
][
8
+
k
]);
fprintf
(
fp
,
"
\n
"
);
}
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint
AtomVecTDPD
::
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
(
"cc"
))
bytes
+=
memory
->
usage
(
cc
,
nmax
*
comm
->
nthreads
,
cc_species
);
if
(
atom
->
memcheck
(
"cc_flux"
))
bytes
+=
memory
->
usage
(
cc_flux
,
nmax
*
comm
->
nthreads
,
cc_species
);
if
(
atom
->
memcheck
(
"vest"
))
bytes
+=
memory
->
usage
(
vest
,
nmax
);
return
bytes
;
}
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