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compute_improper_local.cpp
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Wed, Sep 4, 03:44
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7 KB
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text/x-c
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Fri, Sep 6, 03:44 (2 d)
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rLAMMPS lammps
compute_improper_local.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 "compute_improper_local.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "update.h"
#include "domain.h"
#include "force.h"
#include "improper.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
#define DELTA 10000
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
ComputeImproperLocal
::
ComputeImproperLocal
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
),
vector
(
NULL
),
array
(
NULL
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Illegal compute improper/local command"
);
if
(
atom
->
avec
->
impropers_allow
==
0
)
error
->
all
(
FLERR
,
"Compute improper/local used when impropers are not allowed"
);
local_flag
=
1
;
nvalues
=
narg
-
3
;
if
(
nvalues
==
1
)
size_local_cols
=
0
;
else
size_local_cols
=
nvalues
;
cflag
=
-
1
;
nvalues
=
0
;
for
(
int
iarg
=
3
;
iarg
<
narg
;
iarg
++
)
{
if
(
strcmp
(
arg
[
iarg
],
"chi"
)
==
0
)
cflag
=
nvalues
++
;
else
error
->
all
(
FLERR
,
"Invalid keyword in compute improper/local command"
);
}
nmax
=
0
;
}
/* ---------------------------------------------------------------------- */
ComputeImproperLocal
::~
ComputeImproperLocal
()
{
memory
->
destroy
(
vector
);
memory
->
destroy
(
array
);
}
/* ---------------------------------------------------------------------- */
void
ComputeImproperLocal
::
init
()
{
if
(
force
->
improper
==
NULL
)
error
->
all
(
FLERR
,
"No improper style is defined for compute improper/local"
);
// do initial memory allocation so that memory_usage() is correct
ncount
=
compute_impropers
(
0
);
if
(
ncount
>
nmax
)
reallocate
(
ncount
);
size_local_rows
=
ncount
;
}
/* ---------------------------------------------------------------------- */
void
ComputeImproperLocal
::
compute_local
()
{
invoked_local
=
update
->
ntimestep
;
// count local entries and compute improper info
ncount
=
compute_impropers
(
0
);
if
(
ncount
>
nmax
)
reallocate
(
ncount
);
size_local_rows
=
ncount
;
ncount
=
compute_impropers
(
1
);
}
/* ----------------------------------------------------------------------
count impropers on this proc
only count if 2nd atom is the one storing the improper
all atoms in interaction must be in group
all atoms in interaction must be known to proc
if flag is set, compute requested info about improper
------------------------------------------------------------------------- */
int
ComputeImproperLocal
::
compute_impropers
(
int
flag
)
{
int
i
,
m
,
n
,
ni
,
atom1
,
atom2
,
atom3
,
atom4
,
imol
,
iatom
;
tagint
tagprev
;
double
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
;
double
ss1
,
ss2
,
ss3
,
r1
,
r2
,
r3
,
c0
,
c1
,
c2
,
s1
,
s2
;
double
s12
,
c
;
double
*
cbuf
;
double
**
x
=
atom
->
x
;
tagint
*
tag
=
atom
->
tag
;
int
*
num_improper
=
atom
->
num_improper
;
tagint
**
improper_atom1
=
atom
->
improper_atom1
;
tagint
**
improper_atom2
=
atom
->
improper_atom2
;
tagint
**
improper_atom3
=
atom
->
improper_atom3
;
tagint
**
improper_atom4
=
atom
->
improper_atom4
;
int
*
mask
=
atom
->
mask
;
int
*
molindex
=
atom
->
molindex
;
int
*
molatom
=
atom
->
molatom
;
Molecule
**
onemols
=
atom
->
avec
->
onemols
;
int
nlocal
=
atom
->
nlocal
;
int
molecular
=
atom
->
molecular
;
if
(
flag
)
{
if
(
nvalues
==
1
)
{
if
(
cflag
>=
0
)
cbuf
=
vector
;
}
else
{
if
(
cflag
>=
0
&&
array
)
cbuf
=
&
array
[
0
][
cflag
];
else
cbuf
=
NULL
;
}
}
m
=
n
=
0
;
for
(
atom2
=
0
;
atom2
<
nlocal
;
atom2
++
)
{
if
(
!
(
mask
[
atom2
]
&
groupbit
))
continue
;
if
(
molecular
==
1
)
ni
=
num_improper
[
atom2
];
else
{
if
(
molindex
[
atom2
]
<
0
)
continue
;
imol
=
molindex
[
atom2
];
iatom
=
molatom
[
atom2
];
ni
=
onemols
[
imol
]
->
num_improper
[
iatom
];
}
for
(
i
=
0
;
i
<
ni
;
i
++
)
{
if
(
molecular
==
1
)
{
if
(
tag
[
atom2
]
!=
improper_atom2
[
atom2
][
i
])
continue
;
atom1
=
atom
->
map
(
improper_atom1
[
atom2
][
i
]);
atom3
=
atom
->
map
(
improper_atom3
[
atom2
][
i
]);
atom4
=
atom
->
map
(
improper_atom4
[
atom2
][
i
]);
}
else
{
if
(
tag
[
atom2
]
!=
onemols
[
imol
]
->
improper_atom2
[
atom2
][
i
])
continue
;
tagprev
=
tag
[
atom2
]
-
iatom
-
1
;
atom1
=
atom
->
map
(
onemols
[
imol
]
->
improper_atom1
[
atom2
][
i
]
+
tagprev
);
atom3
=
atom
->
map
(
onemols
[
imol
]
->
improper_atom3
[
atom2
][
i
]
+
tagprev
);
atom4
=
atom
->
map
(
onemols
[
imol
]
->
improper_atom4
[
atom2
][
i
]
+
tagprev
);
}
if
(
atom1
<
0
||
!
(
mask
[
atom1
]
&
groupbit
))
continue
;
if
(
atom3
<
0
||
!
(
mask
[
atom3
]
&
groupbit
))
continue
;
if
(
atom4
<
0
||
!
(
mask
[
atom4
]
&
groupbit
))
continue
;
if
(
flag
)
{
// chi calculation from improper style harmonic
if
(
cflag
>=
0
)
{
vb1x
=
x
[
atom1
][
0
]
-
x
[
atom2
][
0
];
vb1y
=
x
[
atom1
][
1
]
-
x
[
atom2
][
1
];
vb1z
=
x
[
atom1
][
2
]
-
x
[
atom2
][
2
];
domain
->
minimum_image
(
vb1x
,
vb1y
,
vb1z
);
vb2x
=
x
[
atom3
][
0
]
-
x
[
atom2
][
0
];
vb2y
=
x
[
atom3
][
1
]
-
x
[
atom2
][
1
];
vb2z
=
x
[
atom3
][
2
]
-
x
[
atom2
][
2
];
domain
->
minimum_image
(
vb2x
,
vb2y
,
vb2z
);
vb3x
=
x
[
atom4
][
0
]
-
x
[
atom3
][
0
];
vb3y
=
x
[
atom4
][
1
]
-
x
[
atom3
][
1
];
vb3z
=
x
[
atom4
][
2
]
-
x
[
atom3
][
2
];
domain
->
minimum_image
(
vb3x
,
vb3y
,
vb3z
);
ss1
=
1.0
/
(
vb1x
*
vb1x
+
vb1y
*
vb1y
+
vb1z
*
vb1z
);
ss2
=
1.0
/
(
vb2x
*
vb2x
+
vb2y
*
vb2y
+
vb2z
*
vb2z
);
ss3
=
1.0
/
(
vb3x
*
vb3x
+
vb3y
*
vb3y
+
vb3z
*
vb3z
);
r1
=
sqrt
(
ss1
);
r2
=
sqrt
(
ss2
);
r3
=
sqrt
(
ss3
);
c0
=
(
vb1x
*
vb3x
+
vb1y
*
vb3y
+
vb1z
*
vb3z
)
*
r1
*
r3
;
c1
=
(
vb1x
*
vb2x
+
vb1y
*
vb2y
+
vb1z
*
vb2z
)
*
r1
*
r2
;
c2
=
-
(
vb3x
*
vb2x
+
vb3y
*
vb2y
+
vb3z
*
vb2z
)
*
r3
*
r2
;
s1
=
1.0
-
c1
*
c1
;
if
(
s1
<
SMALL
)
s1
=
SMALL
;
s1
=
1.0
/
s1
;
s2
=
1.0
-
c2
*
c2
;
if
(
s2
<
SMALL
)
s2
=
SMALL
;
s2
=
1.0
/
s2
;
s12
=
sqrt
(
s1
*
s2
);
c
=
(
c1
*
c2
+
c0
)
*
s12
;
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
cbuf
[
n
]
=
180.0
*
acos
(
c
)
/
MY_PI
;
}
n
+=
nvalues
;
}
m
++
;
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
ComputeImproperLocal
::
reallocate
(
int
n
)
{
// grow vector or array and indices array
while
(
nmax
<
n
)
nmax
+=
DELTA
;
if
(
nvalues
==
1
)
{
memory
->
destroy
(
vector
);
memory
->
create
(
vector
,
nmax
,
"bond/local:vector"
);
vector_local
=
vector
;
}
else
{
memory
->
destroy
(
array
);
memory
->
create
(
array
,
nmax
,
nvalues
,
"bond/local:array"
);
array_local
=
array
;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputeImproperLocal
::
memory_usage
()
{
double
bytes
=
nmax
*
nvalues
*
sizeof
(
double
);
return
bytes
;
}
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