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Molecular Dynamics in the Open
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InversionTypesSectionParser.hpp
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/*
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* modification, are permitted provided that the following conditions are met:
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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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* 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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* 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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* 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 IO_INVERSIONTYPESSECTIONPARSER_HPP
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#define IO_INVERSIONTYPESSECTIONPARSER_HPP
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#include "io/ForceFieldOptions.hpp"
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#include "io/SectionParser.hpp"
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namespace
OpenMD
{
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/**
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* @class InversionTypesSectionParser InversionTypesSectionParser.hpp
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* "io/InversionTypesSectionParser.hpp"
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*/
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class
InversionTypesSectionParser
:
public
SectionParser
{
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public
:
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InversionTypesSectionParser
(
ForceFieldOptions
& options);
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private
:
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// Inversion types vary by force field: In this description,
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// I is the central atom, while J, K, and L are atoms directly
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// bonded to I (but not to each other):
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// Amber uses a special bond (IL) as the hinge between the planes
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// IJL and IKL (the central atom I & peripheral atom L are common
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// in both planes). It then applies a cosine series much like
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// other torsional forms.
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// Gromacs & Charmm use an improper torsion that is harmonic
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// in the angle between the IJK and JKL planes (Central atom is I, but
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// this atom appears in only one of the plane definitions.
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// MM2 and Tripos use a planarity definition of the central atom (I)
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// distance from the plane made by the other three atoms (JKL).
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// The Dreiding force field uses a complicated umbrella inversion
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// form.
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void
parseLine(
ForceField
& ff,
const
std::string& line,
int
lineNo);
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};
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}
// namespace OpenMD
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#endif
// IO_INVERSIONTYPESSECTIONPARSER_HPP
OpenMD::ForceField
Definition
ForceField.hpp:74
OpenMD::ForceFieldOptions
Definition
ForceFieldOptions.hpp:56
OpenMD::InversionTypesSectionParser
"io/InversionTypesSectionParser.hpp"
Definition
InversionTypesSectionParser.hpp:57
OpenMD::SectionParser
Definition
SectionParser.hpp:61
OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
Definition
ActionCorrFunc.cpp:60
io
InversionTypesSectionParser.hpp
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