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bond.cpp
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Created
Sat, Aug 17, 12:59
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5 KB
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text/x-c
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Mon, Aug 19, 12:59 (2 d)
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blob
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19953245
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rLAMMPS lammps
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 "string.h"
#include "bond.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "suffix.h"
#include "atom_masks.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* -----------------------------------------------------------------------
set bond contribution to Vdwl energy to 0.0
a particular bond style can override this
------------------------------------------------------------------------- */
Bond
::
Bond
(
LAMMPS
*
lmp
)
:
Pointers
(
lmp
)
{
energy
=
0.0
;
allocated
=
0
;
suffix_flag
=
Suffix
::
NONE
;
maxeatom
=
maxvatom
=
0
;
eatom
=
NULL
;
vatom
=
NULL
;
datamask
=
ALL_MASK
;
datamask_ext
=
ALL_MASK
;
}
/* ---------------------------------------------------------------------- */
Bond
::~
Bond
()
{
memory
->
destroy
(
eatom
);
memory
->
destroy
(
vatom
);
}
/* ----------------------------------------------------------------------
check if all coeffs are set
------------------------------------------------------------------------- */
void
Bond
::
init
()
{
if
(
!
allocated
)
error
->
all
(
FLERR
,
"Bond coeffs are not set"
);
for
(
int
i
=
1
;
i
<=
atom
->
nbondtypes
;
i
++
)
if
(
setflag
[
i
]
==
0
)
error
->
all
(
FLERR
,
"All bond coeffs are not set"
);
init_style
();
}
/* ----------------------------------------------------------------------
setup for energy, virial computation
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
------------------------------------------------------------------------- */
void
Bond
::
ev_setup
(
int
eflag
,
int
vflag
)
{
int
i
,
n
;
evflag
=
1
;
eflag_either
=
eflag
;
eflag_global
=
eflag
%
2
;
eflag_atom
=
eflag
/
2
;
vflag_either
=
vflag
;
vflag_global
=
vflag
%
4
;
vflag_atom
=
vflag
/
4
;
// reallocate per-atom arrays if necessary
if
(
eflag_atom
&&
atom
->
nmax
>
maxeatom
)
{
maxeatom
=
atom
->
nmax
;
memory
->
destroy
(
eatom
);
memory
->
create
(
eatom
,
comm
->
nthreads
*
maxeatom
,
"bond:eatom"
);
}
if
(
vflag_atom
&&
atom
->
nmax
>
maxvatom
)
{
maxvatom
=
atom
->
nmax
;
memory
->
destroy
(
vatom
);
memory
->
create
(
vatom
,
comm
->
nthreads
*
maxvatom
,
6
,
"bond:vatom"
);
}
// zero accumulators
if
(
eflag_global
)
energy
=
0.0
;
if
(
vflag_global
)
for
(
i
=
0
;
i
<
6
;
i
++
)
virial
[
i
]
=
0.0
;
if
(
eflag_atom
)
{
n
=
atom
->
nlocal
;
if
(
force
->
newton_bond
)
n
+=
atom
->
nghost
;
for
(
i
=
0
;
i
<
n
;
i
++
)
eatom
[
i
]
=
0.0
;
}
if
(
vflag_atom
)
{
n
=
atom
->
nlocal
;
if
(
force
->
newton_bond
)
n
+=
atom
->
nghost
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
vatom
[
i
][
0
]
=
0.0
;
vatom
[
i
][
1
]
=
0.0
;
vatom
[
i
][
2
]
=
0.0
;
vatom
[
i
][
3
]
=
0.0
;
vatom
[
i
][
4
]
=
0.0
;
vatom
[
i
][
5
]
=
0.0
;
}
}
}
/* ----------------------------------------------------------------------
tally energy and virial into global and per-atom accumulators
------------------------------------------------------------------------- */
void
Bond
::
ev_tally
(
int
i
,
int
j
,
int
nlocal
,
int
newton_bond
,
double
ebond
,
double
fbond
,
double
delx
,
double
dely
,
double
delz
)
{
double
ebondhalf
,
v
[
6
];
if
(
eflag_either
)
{
if
(
eflag_global
)
{
if
(
newton_bond
)
energy
+=
ebond
;
else
{
ebondhalf
=
0.5
*
ebond
;
if
(
i
<
nlocal
)
energy
+=
ebondhalf
;
if
(
j
<
nlocal
)
energy
+=
ebondhalf
;
}
}
if
(
eflag_atom
)
{
ebondhalf
=
0.5
*
ebond
;
if
(
newton_bond
||
i
<
nlocal
)
eatom
[
i
]
+=
ebondhalf
;
if
(
newton_bond
||
j
<
nlocal
)
eatom
[
j
]
+=
ebondhalf
;
}
}
if
(
vflag_either
)
{
v
[
0
]
=
delx
*
delx
*
fbond
;
v
[
1
]
=
dely
*
dely
*
fbond
;
v
[
2
]
=
delz
*
delz
*
fbond
;
v
[
3
]
=
delx
*
dely
*
fbond
;
v
[
4
]
=
delx
*
delz
*
fbond
;
v
[
5
]
=
dely
*
delz
*
fbond
;
if
(
vflag_global
)
{
if
(
newton_bond
)
{
virial
[
0
]
+=
v
[
0
];
virial
[
1
]
+=
v
[
1
];
virial
[
2
]
+=
v
[
2
];
virial
[
3
]
+=
v
[
3
];
virial
[
4
]
+=
v
[
4
];
virial
[
5
]
+=
v
[
5
];
}
else
{
if
(
i
<
nlocal
)
{
virial
[
0
]
+=
0.5
*
v
[
0
];
virial
[
1
]
+=
0.5
*
v
[
1
];
virial
[
2
]
+=
0.5
*
v
[
2
];
virial
[
3
]
+=
0.5
*
v
[
3
];
virial
[
4
]
+=
0.5
*
v
[
4
];
virial
[
5
]
+=
0.5
*
v
[
5
];
}
if
(
j
<
nlocal
)
{
virial
[
0
]
+=
0.5
*
v
[
0
];
virial
[
1
]
+=
0.5
*
v
[
1
];
virial
[
2
]
+=
0.5
*
v
[
2
];
virial
[
3
]
+=
0.5
*
v
[
3
];
virial
[
4
]
+=
0.5
*
v
[
4
];
virial
[
5
]
+=
0.5
*
v
[
5
];
}
}
}
if
(
vflag_atom
)
{
if
(
newton_bond
||
i
<
nlocal
)
{
vatom
[
i
][
0
]
+=
0.5
*
v
[
0
];
vatom
[
i
][
1
]
+=
0.5
*
v
[
1
];
vatom
[
i
][
2
]
+=
0.5
*
v
[
2
];
vatom
[
i
][
3
]
+=
0.5
*
v
[
3
];
vatom
[
i
][
4
]
+=
0.5
*
v
[
4
];
vatom
[
i
][
5
]
+=
0.5
*
v
[
5
];
}
if
(
newton_bond
||
j
<
nlocal
)
{
vatom
[
j
][
0
]
+=
0.5
*
v
[
0
];
vatom
[
j
][
1
]
+=
0.5
*
v
[
1
];
vatom
[
j
][
2
]
+=
0.5
*
v
[
2
];
vatom
[
j
][
3
]
+=
0.5
*
v
[
3
];
vatom
[
j
][
4
]
+=
0.5
*
v
[
4
];
vatom
[
j
][
5
]
+=
0.5
*
v
[
5
];
}
}
}
}
/* ---------------------------------------------------------------------- */
double
Bond
::
memory_usage
()
{
double
bytes
=
comm
->
nthreads
*
maxeatom
*
sizeof
(
double
);
bytes
+=
comm
->
nthreads
*
maxvatom
*
6
*
sizeof
(
double
);
return
bytes
;
}
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