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bond_oxdna2_fene.cpp
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Created
Tue, Oct 15, 13:54
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1 KB
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text/x-c
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Thu, Oct 17, 13:54 (1 d, 23 h)
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rLAMMPS lammps
bond_oxdna2_fene.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "bond_oxdna2_fene.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
BondOxdna2Fene
::
BondOxdna2Fene
(
LAMMPS
*
lmp
)
:
BondOxdnaFene
(
lmp
)
{
}
/* ---------------------------------------------------------------------- */
BondOxdna2Fene
::~
BondOxdna2Fene
()
{
}
/* ----------------------------------------------------------------------
compute vector COM-sugar-phosphate backbone interaction site in oxDNA2
------------------------------------------------------------------------- */
void
BondOxdna2Fene
::
compute_interaction_sites
(
double
e1
[
3
],
double
e2
[
3
],
double
r
[
3
])
{
double
d_cs_x
=-
0.34
,
d_cs_y
=+
0.3408
;
r
[
0
]
=
d_cs_x
*
e1
[
0
]
+
d_cs_y
*
e2
[
0
];
r
[
1
]
=
d_cs_x
*
e1
[
1
]
+
d_cs_y
*
e2
[
1
];
r
[
2
]
=
d_cs_x
*
e1
[
2
]
+
d_cs_y
*
e2
[
2
];
}
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