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compute_dihedral_local.cpp
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Sat, Aug 31, 08:29
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Mon, Sep 2, 08:29 (1 d, 23 h)
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rLAMMPS lammps
compute_dihedral_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_dihedral_local.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "update.h"
#include "domain.h"
#include "force.h"
#include "dihedral.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
/* ---------------------------------------------------------------------- */
ComputeDihedralLocal
::
ComputeDihedralLocal
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
),
vlocal
(
NULL
),
alocal
(
NULL
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Illegal compute dihedral/local command"
);
if
(
atom
->
avec
->
dihedrals_allow
==
0
)
error
->
all
(
FLERR
,
"Compute dihedral/local used when dihedrals are not allowed"
);
local_flag
=
1
;
nvalues
=
narg
-
3
;
if
(
nvalues
==
1
)
size_local_cols
=
0
;
else
size_local_cols
=
nvalues
;
pflag
=
-
1
;
nvalues
=
0
;
for
(
int
iarg
=
3
;
iarg
<
narg
;
iarg
++
)
{
if
(
strcmp
(
arg
[
iarg
],
"phi"
)
==
0
)
pflag
=
nvalues
++
;
else
error
->
all
(
FLERR
,
"Invalid keyword in compute dihedral/local command"
);
}
nmax
=
0
;
vlocal
=
NULL
;
alocal
=
NULL
;
}
/* ---------------------------------------------------------------------- */
ComputeDihedralLocal
::~
ComputeDihedralLocal
()
{
memory
->
destroy
(
vlocal
);
memory
->
destroy
(
alocal
);
}
/* ---------------------------------------------------------------------- */
void
ComputeDihedralLocal
::
init
()
{
if
(
force
->
dihedral
==
NULL
)
error
->
all
(
FLERR
,
"No dihedral style is defined for compute dihedral/local"
);
// do initial memory allocation so that memory_usage() is correct
ncount
=
compute_dihedrals
(
0
);
if
(
ncount
>
nmax
)
reallocate
(
ncount
);
size_local_rows
=
ncount
;
}
/* ---------------------------------------------------------------------- */
void
ComputeDihedralLocal
::
compute_local
()
{
invoked_local
=
update
->
ntimestep
;
// count local entries and compute dihedral info
ncount
=
compute_dihedrals
(
0
);
if
(
ncount
>
nmax
)
reallocate
(
ncount
);
size_local_rows
=
ncount
;
ncount
=
compute_dihedrals
(
1
);
}
/* ----------------------------------------------------------------------
count dihedrals on this proc
only count if 2nd atom is the one storing the dihedral
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 dihedral
------------------------------------------------------------------------- */
int
ComputeDihedralLocal
::
compute_dihedrals
(
int
flag
)
{
int
i
,
m
,
n
,
nd
,
atom1
,
atom2
,
atom3
,
atom4
,
imol
,
iatom
;
tagint
tagprev
;
double
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
,
vb2xm
,
vb2ym
,
vb2zm
;
double
ax
,
ay
,
az
,
bx
,
by
,
bz
,
rasq
,
rbsq
,
rgsq
,
rg
,
ra2inv
,
rb2inv
,
rabinv
;
double
s
,
c
;
double
*
pbuf
;
double
**
x
=
atom
->
x
;
tagint
*
tag
=
atom
->
tag
;
int
*
num_dihedral
=
atom
->
num_dihedral
;
tagint
**
dihedral_atom1
=
atom
->
dihedral_atom1
;
tagint
**
dihedral_atom2
=
atom
->
dihedral_atom2
;
tagint
**
dihedral_atom3
=
atom
->
dihedral_atom3
;
tagint
**
dihedral_atom4
=
atom
->
dihedral_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
(
pflag
>=
0
)
pbuf
=
vlocal
;
}
else
{
if
(
pflag
>=
0
&&
alocal
)
pbuf
=
&
alocal
[
0
][
pflag
];
else
pbuf
=
NULL
;
}
}
m
=
n
=
0
;
for
(
atom2
=
0
;
atom2
<
nlocal
;
atom2
++
)
{
if
(
!
(
mask
[
atom2
]
&
groupbit
))
continue
;
if
(
molecular
==
1
)
nd
=
num_dihedral
[
atom2
];
else
{
if
(
molindex
[
atom2
]
<
0
)
continue
;
imol
=
molindex
[
atom2
];
iatom
=
molatom
[
atom2
];
nd
=
onemols
[
imol
]
->
num_dihedral
[
iatom
];
}
for
(
i
=
0
;
i
<
nd
;
i
++
)
{
if
(
molecular
==
1
)
{
if
(
tag
[
atom2
]
!=
dihedral_atom2
[
atom2
][
i
])
continue
;
atom1
=
atom
->
map
(
dihedral_atom1
[
atom2
][
i
]);
atom3
=
atom
->
map
(
dihedral_atom3
[
atom2
][
i
]);
atom4
=
atom
->
map
(
dihedral_atom4
[
atom2
][
i
]);
}
else
{
if
(
tag
[
atom2
]
!=
onemols
[
imol
]
->
dihedral_atom2
[
atom2
][
i
])
continue
;
tagprev
=
tag
[
atom2
]
-
iatom
-
1
;
atom1
=
atom
->
map
(
onemols
[
imol
]
->
dihedral_atom1
[
atom2
][
i
]
+
tagprev
);
atom3
=
atom
->
map
(
onemols
[
imol
]
->
dihedral_atom3
[
atom2
][
i
]
+
tagprev
);
atom4
=
atom
->
map
(
onemols
[
imol
]
->
dihedral_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
)
{
// phi calculation from dihedral style harmonic
if
(
pflag
>=
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
);
vb2xm
=
-
vb2x
;
vb2ym
=
-
vb2y
;
vb2zm
=
-
vb2z
;
domain
->
minimum_image
(
vb2xm
,
vb2ym
,
vb2zm
);
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
);
ax
=
vb1y
*
vb2zm
-
vb1z
*
vb2ym
;
ay
=
vb1z
*
vb2xm
-
vb1x
*
vb2zm
;
az
=
vb1x
*
vb2ym
-
vb1y
*
vb2xm
;
bx
=
vb3y
*
vb2zm
-
vb3z
*
vb2ym
;
by
=
vb3z
*
vb2xm
-
vb3x
*
vb2zm
;
bz
=
vb3x
*
vb2ym
-
vb3y
*
vb2xm
;
rasq
=
ax
*
ax
+
ay
*
ay
+
az
*
az
;
rbsq
=
bx
*
bx
+
by
*
by
+
bz
*
bz
;
rgsq
=
vb2xm
*
vb2xm
+
vb2ym
*
vb2ym
+
vb2zm
*
vb2zm
;
rg
=
sqrt
(
rgsq
);
ra2inv
=
rb2inv
=
0.0
;
if
(
rasq
>
0
)
ra2inv
=
1.0
/
rasq
;
if
(
rbsq
>
0
)
rb2inv
=
1.0
/
rbsq
;
rabinv
=
sqrt
(
ra2inv
*
rb2inv
);
c
=
(
ax
*
bx
+
ay
*
by
+
az
*
bz
)
*
rabinv
;
s
=
rg
*
rabinv
*
(
ax
*
vb3x
+
ay
*
vb3y
+
az
*
vb3z
);
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
pbuf
[
n
]
=
180.0
*
atan2
(
s
,
c
)
/
MY_PI
;
}
n
+=
nvalues
;
}
m
++
;
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
ComputeDihedralLocal
::
reallocate
(
int
n
)
{
// grow vector_local or array_local
while
(
nmax
<
n
)
nmax
+=
DELTA
;
if
(
nvalues
==
1
)
{
memory
->
destroy
(
vlocal
);
memory
->
create
(
vlocal
,
nmax
,
"dihedral/local:vector_local"
);
vector_local
=
vlocal
;
}
else
{
memory
->
destroy
(
alocal
);
memory
->
create
(
alocal
,
nmax
,
nvalues
,
"dihedral/local:array_local"
);
array_local
=
alocal
;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputeDihedralLocal
::
memory_usage
()
{
double
bytes
=
nmax
*
nvalues
*
sizeof
(
double
);
return
bytes
;
}
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