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Molecular Dynamics in the Open
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LennardJonesAdapter.hpp
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/*
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* Copyright (c) 2004-present, The University of Notre Dame. All rights
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* reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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*
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* 3. Neither the name of the copyright holder nor the names of its
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* contributors may be used to endorse or promote products derived from
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* this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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*
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
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* research, please cite the appropriate papers when you publish your
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* work. Good starting points are:
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*
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
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* [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
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* [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
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* [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
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* [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
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* [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
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*/
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#ifndef TYPES_LENNARDJONESADAPTER_HPP
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#define TYPES_LENNARDJONESADAPTER_HPP
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#include "types/AtomType.hpp"
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#include "
utils/GenericData.hpp
"
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using namespace
std;
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namespace
OpenMD
{
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string
const
LJtypeID =
"LJ"
;
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struct
LJAtypeParameters
{
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RealType sigma;
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RealType epsilon;
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bool
isSoft;
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};
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struct
LJAtypeParameters
{
…
};
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using
LJAtypeData
=
SimpleTypeData<LJAtypeParameters>
;
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class
LennardJonesAdapter
{
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public
:
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LennardJonesAdapter
(
AtomType
* AT) { at_ = AT; };
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void
makeLennardJones(RealType sigma, RealType epsilon,
bool
isSoft);
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bool
isLennardJones();
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RealType getSigma();
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RealType getEpsilon();
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bool
isSoft();
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private
:
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AtomType
* at_;
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LJAtypeParameters
getLJParam();
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};
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class
LennardJonesAdapter
{
…
};
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}
// namespace OpenMD
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#endif
GenericData.hpp
OpenMD::AtomType
AtomType is what OpenMD looks to for unchanging data about an atom.
Definition
AtomType.hpp:66
OpenMD::LennardJonesAdapter
Definition
LennardJonesAdapter.hpp:63
OpenMD::SimpleTypeData
SimpleTypeData class is a POD repository class.
Definition
GenericData.hpp:107
OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
Definition
ActionCorrFunc.cpp:60
OpenMD::LJAtypeParameters
Definition
LennardJonesAdapter.hpp:56
types
LennardJonesAdapter.hpp
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