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compute_contact_atom.cpp
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Sat, Aug 31, 09:46
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5 KB
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text/x-c
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Mon, Sep 2, 09:46 (2 d)
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rLAMMPS lammps
compute_contact_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 <stdlib.h>
#include "compute_contact_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeContactAtom
::
ComputeContactAtom
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
),
contact
(
NULL
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Illegal compute contact/atom command"
);
peratom_flag
=
1
;
size_peratom_cols
=
0
;
comm_reverse
=
1
;
nmax
=
0
;
// error checks
if
(
!
atom
->
sphere_flag
)
error
->
all
(
FLERR
,
"Compute contact/atom requires atom style sphere"
);
}
/* ---------------------------------------------------------------------- */
ComputeContactAtom
::~
ComputeContactAtom
()
{
memory
->
destroy
(
contact
);
}
/* ---------------------------------------------------------------------- */
void
ComputeContactAtom
::
init
()
{
if
(
force
->
pair
==
NULL
)
error
->
all
(
FLERR
,
"Compute contact/atom requires a pair style be defined"
);
int
count
=
0
;
for
(
int
i
=
0
;
i
<
modify
->
ncompute
;
i
++
)
if
(
strcmp
(
modify
->
compute
[
i
]
->
style
,
"contact/atom"
)
==
0
)
count
++
;
if
(
count
>
1
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"More than one compute contact/atom"
);
// need an occasional neighbor list
int
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
size
=
1
;
neighbor
->
requests
[
irequest
]
->
pair
=
0
;
neighbor
->
requests
[
irequest
]
->
compute
=
1
;
neighbor
->
requests
[
irequest
]
->
occasional
=
1
;
}
/* ---------------------------------------------------------------------- */
void
ComputeContactAtom
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
list
=
ptr
;
}
/* ---------------------------------------------------------------------- */
void
ComputeContactAtom
::
compute_peratom
()
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
double
radi
,
radsum
,
radsumsq
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
invoked_peratom
=
update
->
ntimestep
;
// grow contact array if necessary
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy
(
contact
);
nmax
=
atom
->
nmax
;
memory
->
create
(
contact
,
nmax
,
"contact/atom:contact"
);
vector_atom
=
contact
;
}
// invoke neighbor list (will copy or build if necessary)
neighbor
->
build_one
(
list
);
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// compute number of contacts for each atom in group
// contact if distance <= sum of radii
// tally for both I and J
double
**
x
=
atom
->
x
;
double
*
radius
=
atom
->
radius
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
for
(
i
=
0
;
i
<
nall
;
i
++
)
contact
[
i
]
=
0.0
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
{
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
radi
=
radius
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
radsum
=
radi
+
radius
[
j
];
radsumsq
=
radsum
*
radsum
;
if
(
rsq
<=
radsumsq
)
{
contact
[
i
]
+=
1.0
;
contact
[
j
]
+=
1.0
;
}
}
}
}
// communicate ghost atom counts between neighbor procs if necessary
if
(
force
->
newton_pair
)
comm
->
reverse_comm_compute
(
this
);
}
/* ---------------------------------------------------------------------- */
int
ComputeContactAtom
::
pack_reverse_comm
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
buf
[
m
++
]
=
contact
[
i
];
return
m
;
}
/* ---------------------------------------------------------------------- */
void
ComputeContactAtom
::
unpack_reverse_comm
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
contact
[
j
]
+=
buf
[
m
++
];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double
ComputeContactAtom
::
memory_usage
()
{
double
bytes
=
nmax
*
sizeof
(
double
);
return
bytes
;
}
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