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dihedral.cpp
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Created
Fri, Sep 6, 21:21
Size
7 KB
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text/x-c
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Sun, Sep 8, 21:21 (1 d, 23 h)
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blob
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rLAMMPS lammps
dihedral.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 "dihedral.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "pair.h"
#include "suffix.h"
#include "atom_masks.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ----------------------------------------------------------------------
set dihedral contribution to Vdwl and Coulombic energy to 0.0
DihedralCharmm will override this
------------------------------------------------------------------------- */
Dihedral
::
Dihedral
(
LAMMPS
*
lmp
)
:
Pointers
(
lmp
)
{
energy
=
0.0
;
writedata
=
0
;
allocated
=
0
;
maxeatom
=
maxvatom
=
0
;
eatom
=
NULL
;
vatom
=
NULL
;
setflag
=
NULL
;
datamask
=
ALL_MASK
;
datamask_ext
=
ALL_MASK
;
execution_space
=
Host
;
datamask_read
=
ALL_MASK
;
datamask_modify
=
ALL_MASK
;
copymode
=
0
;
}
/* ---------------------------------------------------------------------- */
Dihedral
::~
Dihedral
()
{
if
(
copymode
)
return
;
memory
->
destroy
(
eatom
);
memory
->
destroy
(
vatom
);
}
/* ----------------------------------------------------------------------
check if all coeffs are set
------------------------------------------------------------------------- */
void
Dihedral
::
init
()
{
if
(
!
allocated
&&
atom
->
ndihedraltypes
)
error
->
all
(
FLERR
,
"Dihedral coeffs are not set"
);
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
if
(
setflag
[
i
]
==
0
)
error
->
all
(
FLERR
,
"All dihedral 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
Dihedral
::
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
,
"dihedral:eatom"
);
}
if
(
vflag_atom
&&
atom
->
nmax
>
maxvatom
)
{
maxvatom
=
atom
->
nmax
;
memory
->
destroy
(
vatom
);
memory
->
create
(
vatom
,
comm
->
nthreads
*
maxvatom
,
6
,
"dihedral: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
virial = r1F1 + r2F2 + r3F3 + r4F4 = (r1-r2) F1 + (r3-r2) F3 + (r4-r2) F4
= (r1-r2) F1 + (r3-r2) F3 + (r4-r3 + r3-r2) F4
= vb1*f1 + vb2*f3 + (vb3+vb2)*f4
------------------------------------------------------------------------- */
void
Dihedral
::
ev_tally
(
int
i1
,
int
i2
,
int
i3
,
int
i4
,
int
nlocal
,
int
newton_bond
,
double
edihedral
,
double
*
f1
,
double
*
f3
,
double
*
f4
,
double
vb1x
,
double
vb1y
,
double
vb1z
,
double
vb2x
,
double
vb2y
,
double
vb2z
,
double
vb3x
,
double
vb3y
,
double
vb3z
)
{
double
edihedralquarter
,
v
[
6
];
if
(
eflag_either
)
{
if
(
eflag_global
)
{
if
(
newton_bond
)
energy
+=
edihedral
;
else
{
edihedralquarter
=
0.25
*
edihedral
;
if
(
i1
<
nlocal
)
energy
+=
edihedralquarter
;
if
(
i2
<
nlocal
)
energy
+=
edihedralquarter
;
if
(
i3
<
nlocal
)
energy
+=
edihedralquarter
;
if
(
i4
<
nlocal
)
energy
+=
edihedralquarter
;
}
}
if
(
eflag_atom
)
{
edihedralquarter
=
0.25
*
edihedral
;
if
(
newton_bond
||
i1
<
nlocal
)
eatom
[
i1
]
+=
edihedralquarter
;
if
(
newton_bond
||
i2
<
nlocal
)
eatom
[
i2
]
+=
edihedralquarter
;
if
(
newton_bond
||
i3
<
nlocal
)
eatom
[
i3
]
+=
edihedralquarter
;
if
(
newton_bond
||
i4
<
nlocal
)
eatom
[
i4
]
+=
edihedralquarter
;
}
}
if
(
vflag_either
)
{
v
[
0
]
=
vb1x
*
f1
[
0
]
+
vb2x
*
f3
[
0
]
+
(
vb3x
+
vb2x
)
*
f4
[
0
];
v
[
1
]
=
vb1y
*
f1
[
1
]
+
vb2y
*
f3
[
1
]
+
(
vb3y
+
vb2y
)
*
f4
[
1
];
v
[
2
]
=
vb1z
*
f1
[
2
]
+
vb2z
*
f3
[
2
]
+
(
vb3z
+
vb2z
)
*
f4
[
2
];
v
[
3
]
=
vb1x
*
f1
[
1
]
+
vb2x
*
f3
[
1
]
+
(
vb3x
+
vb2x
)
*
f4
[
1
];
v
[
4
]
=
vb1x
*
f1
[
2
]
+
vb2x
*
f3
[
2
]
+
(
vb3x
+
vb2x
)
*
f4
[
2
];
v
[
5
]
=
vb1y
*
f1
[
2
]
+
vb2y
*
f3
[
2
]
+
(
vb3y
+
vb2y
)
*
f4
[
2
];
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
(
i1
<
nlocal
)
{
virial
[
0
]
+=
0.25
*
v
[
0
];
virial
[
1
]
+=
0.25
*
v
[
1
];
virial
[
2
]
+=
0.25
*
v
[
2
];
virial
[
3
]
+=
0.25
*
v
[
3
];
virial
[
4
]
+=
0.25
*
v
[
4
];
virial
[
5
]
+=
0.25
*
v
[
5
];
}
if
(
i2
<
nlocal
)
{
virial
[
0
]
+=
0.25
*
v
[
0
];
virial
[
1
]
+=
0.25
*
v
[
1
];
virial
[
2
]
+=
0.25
*
v
[
2
];
virial
[
3
]
+=
0.25
*
v
[
3
];
virial
[
4
]
+=
0.25
*
v
[
4
];
virial
[
5
]
+=
0.25
*
v
[
5
];
}
if
(
i3
<
nlocal
)
{
virial
[
0
]
+=
0.25
*
v
[
0
];
virial
[
1
]
+=
0.25
*
v
[
1
];
virial
[
2
]
+=
0.25
*
v
[
2
];
virial
[
3
]
+=
0.25
*
v
[
3
];
virial
[
4
]
+=
0.25
*
v
[
4
];
virial
[
5
]
+=
0.25
*
v
[
5
];
}
if
(
i4
<
nlocal
)
{
virial
[
0
]
+=
0.25
*
v
[
0
];
virial
[
1
]
+=
0.25
*
v
[
1
];
virial
[
2
]
+=
0.25
*
v
[
2
];
virial
[
3
]
+=
0.25
*
v
[
3
];
virial
[
4
]
+=
0.25
*
v
[
4
];
virial
[
5
]
+=
0.25
*
v
[
5
];
}
}
}
if
(
vflag_atom
)
{
if
(
newton_bond
||
i1
<
nlocal
)
{
vatom
[
i1
][
0
]
+=
0.25
*
v
[
0
];
vatom
[
i1
][
1
]
+=
0.25
*
v
[
1
];
vatom
[
i1
][
2
]
+=
0.25
*
v
[
2
];
vatom
[
i1
][
3
]
+=
0.25
*
v
[
3
];
vatom
[
i1
][
4
]
+=
0.25
*
v
[
4
];
vatom
[
i1
][
5
]
+=
0.25
*
v
[
5
];
}
if
(
newton_bond
||
i2
<
nlocal
)
{
vatom
[
i2
][
0
]
+=
0.25
*
v
[
0
];
vatom
[
i2
][
1
]
+=
0.25
*
v
[
1
];
vatom
[
i2
][
2
]
+=
0.25
*
v
[
2
];
vatom
[
i2
][
3
]
+=
0.25
*
v
[
3
];
vatom
[
i2
][
4
]
+=
0.25
*
v
[
4
];
vatom
[
i2
][
5
]
+=
0.25
*
v
[
5
];
}
if
(
newton_bond
||
i3
<
nlocal
)
{
vatom
[
i3
][
0
]
+=
0.25
*
v
[
0
];
vatom
[
i3
][
1
]
+=
0.25
*
v
[
1
];
vatom
[
i3
][
2
]
+=
0.25
*
v
[
2
];
vatom
[
i3
][
3
]
+=
0.25
*
v
[
3
];
vatom
[
i3
][
4
]
+=
0.25
*
v
[
4
];
vatom
[
i3
][
5
]
+=
0.25
*
v
[
5
];
}
if
(
newton_bond
||
i4
<
nlocal
)
{
vatom
[
i4
][
0
]
+=
0.25
*
v
[
0
];
vatom
[
i4
][
1
]
+=
0.25
*
v
[
1
];
vatom
[
i4
][
2
]
+=
0.25
*
v
[
2
];
vatom
[
i4
][
3
]
+=
0.25
*
v
[
3
];
vatom
[
i4
][
4
]
+=
0.25
*
v
[
4
];
vatom
[
i4
][
5
]
+=
0.25
*
v
[
5
];
}
}
}
}
/* ---------------------------------------------------------------------- */
double
Dihedral
::
memory_usage
()
{
double
bytes
=
comm
->
nthreads
*
maxeatom
*
sizeof
(
double
);
bytes
+=
comm
->
nthreads
*
maxvatom
*
6
*
sizeof
(
double
);
return
bytes
;
}
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