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fix_shear_history.cpp
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Sun, Aug 25, 21:42
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8 KB
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text/x-c
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Tue, Aug 27, 21:42 (2 d)
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blob
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20163436
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rLAMMPS lammps
fix_shear_history.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 "stdio.h"
#include "fix_shear_history.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "force.h"
#include "pair.h"
#include "update.h"
#include "modify.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define MAXTOUCH 15
/* ---------------------------------------------------------------------- */
FixShearHistory
::
FixShearHistory
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
restart_peratom
=
1
;
// perform initial allocation of atom-based arrays
// register with atom class
npartner
=
NULL
;
partner
=
NULL
;
shearpartner
=
NULL
;
grow_arrays
(
atom
->
nmax
);
atom
->
add_callback
(
0
);
atom
->
add_callback
(
1
);
// initialize npartner to 0 so neighbor list creation is OK the 1st time
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
npartner
[
i
]
=
0
;
}
/* ---------------------------------------------------------------------- */
FixShearHistory
::~
FixShearHistory
()
{
// unregister this fix so atom class doesn't invoke it any more
atom
->
delete_callback
(
id
,
0
);
atom
->
delete_callback
(
id
,
1
);
// delete locally stored arrays
memory
->
sfree
(
npartner
);
memory
->
destroy_2d_int_array
(
partner
);
memory
->
destroy_3d_double_array
(
shearpartner
);
}
/* ---------------------------------------------------------------------- */
int
FixShearHistory
::
setmask
()
{
int
mask
=
0
;
mask
|=
PRE_EXCHANGE
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixShearHistory
::
init
()
{
if
(
atom
->
tag_enable
==
0
)
error
->
all
(
"Pair style granular with history requires atoms have IDs"
);
}
/* ----------------------------------------------------------------------
copy shear partner info from neighbor lists to atom arrays
so can be exchanged with atoms
------------------------------------------------------------------------- */
void
FixShearHistory
::
pre_exchange
()
{
int
i
,
j
,
ii
,
jj
,
m
,
inum
,
jnum
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
int
*
touch
,
**
firsttouch
;
double
*
shear
,
*
allshear
,
**
firstshear
;
// zero npartners for all current atoms
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
npartner
[
i
]
=
0
;
// copy shear info from neighbor list atoms to atom arrays
int
*
tag
=
atom
->
tag
;
NeighList
*
list
=
pair
->
list
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
firsttouch
=
list
->
listgranhistory
->
firstneigh
;
firstshear
=
list
->
listgranhistory
->
firstdouble
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
jlist
=
firstneigh
[
i
];
allshear
=
firstshear
[
i
];
jnum
=
numneigh
[
i
];
touch
=
firsttouch
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
if
(
touch
[
jj
])
{
shear
=
&
allshear
[
3
*
jj
];
j
=
jlist
[
jj
];
if
(
npartner
[
i
]
<
MAXTOUCH
)
{
m
=
npartner
[
i
];
partner
[
i
][
m
]
=
tag
[
j
];
shearpartner
[
i
][
m
][
0
]
=
shear
[
0
];
shearpartner
[
i
][
m
][
1
]
=
shear
[
1
];
shearpartner
[
i
][
m
][
2
]
=
shear
[
2
];
}
npartner
[
i
]
++
;
if
(
j
<
nlocal
)
{
if
(
npartner
[
j
]
<
MAXTOUCH
)
{
m
=
npartner
[
j
];
partner
[
j
][
m
]
=
tag
[
i
];
shearpartner
[
j
][
m
][
0
]
=
-
shear
[
0
];
shearpartner
[
j
][
m
][
1
]
=
-
shear
[
1
];
shearpartner
[
j
][
m
][
2
]
=
-
shear
[
2
];
}
npartner
[
j
]
++
;
}
}
}
}
// test for too many touching neighbors
int
flag
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
npartner
[
i
]
>=
MAXTOUCH
)
flag
=
1
;
int
flag_all
;
MPI_Allreduce
(
&
flag
,
&
flag_all
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
if
(
flag_all
)
error
->
all
(
"Too many touching neighbors - boost MAXTOUCH"
);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double
FixShearHistory
::
memory_usage
()
{
int
nmax
=
atom
->
nmax
;
double
bytes
=
nmax
*
sizeof
(
int
);
bytes
+=
nmax
*
MAXTOUCH
*
sizeof
(
int
);
bytes
+=
nmax
*
MAXTOUCH
*
3
*
sizeof
(
double
);
return
bytes
;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void
FixShearHistory
::
grow_arrays
(
int
nmax
)
{
npartner
=
(
int
*
)
memory
->
srealloc
(
npartner
,
nmax
*
sizeof
(
int
),
"shear_history:npartner"
);
partner
=
memory
->
grow_2d_int_array
(
partner
,
nmax
,
MAXTOUCH
,
"shear_history:partner"
);
shearpartner
=
memory
->
grow_3d_double_array
(
shearpartner
,
nmax
,
MAXTOUCH
,
3
,
"shear_history:shearpartner"
);
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void
FixShearHistory
::
copy_arrays
(
int
i
,
int
j
)
{
npartner
[
j
]
=
npartner
[
i
];
for
(
int
m
=
0
;
m
<
npartner
[
j
];
m
++
)
{
partner
[
j
][
m
]
=
partner
[
i
][
m
];
shearpartner
[
j
][
m
][
0
]
=
shearpartner
[
i
][
m
][
0
];
shearpartner
[
j
][
m
][
1
]
=
shearpartner
[
i
][
m
][
1
];
shearpartner
[
j
][
m
][
2
]
=
shearpartner
[
i
][
m
][
2
];
}
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int
FixShearHistory
::
pack_exchange
(
int
i
,
double
*
buf
)
{
int
m
=
0
;
buf
[
m
++
]
=
npartner
[
i
];
for
(
int
n
=
0
;
n
<
npartner
[
i
];
n
++
)
{
buf
[
m
++
]
=
partner
[
i
][
n
];
buf
[
m
++
]
=
shearpartner
[
i
][
n
][
0
];
buf
[
m
++
]
=
shearpartner
[
i
][
n
][
1
];
buf
[
m
++
]
=
shearpartner
[
i
][
n
][
2
];
}
return
m
;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int
FixShearHistory
::
unpack_exchange
(
int
nlocal
,
double
*
buf
)
{
int
m
=
0
;
npartner
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
for
(
int
n
=
0
;
n
<
npartner
[
nlocal
];
n
++
)
{
partner
[
nlocal
][
n
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
shearpartner
[
nlocal
][
n
][
0
]
=
buf
[
m
++
];
shearpartner
[
nlocal
][
n
][
1
]
=
buf
[
m
++
];
shearpartner
[
nlocal
][
n
][
2
]
=
buf
[
m
++
];
}
return
m
;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int
FixShearHistory
::
pack_restart
(
int
i
,
double
*
buf
)
{
int
m
=
0
;
buf
[
m
++
]
=
4
*
npartner
[
i
]
+
2
;
buf
[
m
++
]
=
npartner
[
i
];
for
(
int
n
=
0
;
n
<
npartner
[
i
];
n
++
)
{
buf
[
m
++
]
=
partner
[
i
][
n
];
buf
[
m
++
]
=
shearpartner
[
i
][
n
][
0
];
buf
[
m
++
]
=
shearpartner
[
i
][
n
][
1
];
buf
[
m
++
]
=
shearpartner
[
i
][
n
][
2
];
}
return
m
;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void
FixShearHistory
::
unpack_restart
(
int
nlocal
,
int
nth
)
{
double
**
extra
=
atom
->
extra
;
// skip to Nth set of extra values
int
m
=
0
;
for
(
int
i
=
0
;
i
<
nth
;
i
++
)
m
+=
static_cast
<
int
>
(
extra
[
nlocal
][
m
]);
m
++
;
npartner
[
nlocal
]
=
static_cast
<
int
>
(
extra
[
nlocal
][
m
++
]);
for
(
int
n
=
0
;
n
<
npartner
[
nlocal
];
n
++
)
{
partner
[
nlocal
][
n
]
=
static_cast
<
int
>
(
extra
[
nlocal
][
m
++
]);
shearpartner
[
nlocal
][
n
][
0
]
=
extra
[
nlocal
][
m
++
];
shearpartner
[
nlocal
][
n
][
1
]
=
extra
[
nlocal
][
m
++
];
shearpartner
[
nlocal
][
n
][
2
]
=
extra
[
nlocal
][
m
++
];
}
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int
FixShearHistory
::
maxsize_restart
()
{
return
4
*
MAXTOUCH
+
2
;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int
FixShearHistory
::
size_restart
(
int
nlocal
)
{
return
4
*
npartner
[
nlocal
]
+
2
;
}
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