QmmmHelpers.h File Reference

#include <Eigen/Core>
#include <list>
#include <vector>

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Classes
struct	Scine::Qmmm::QmmmHelpers::ChargeRedistributionResult
	A small container for the result of a charge redistribution, containing the new atomic charges, the auxiliary virtual charges that are not placed on atoms as well as their positions. More...

Typedefs
using	Scine::Utils::PositionCollection = Eigen::Matrix< double, Eigen::Dynamic, 3, Eigen::RowMajor >

Functions
std::vector< double >	Scine::Qmmm::QmmmHelpers::writeChargesAndPositionsAsList (const Utils::AtomCollection &structure, const ChargeRedistributionResult &chargeRedistributionResult, const std::vector< int > &listOfQmAtoms)
void	Scine::Qmmm::QmmmHelpers::writePointChargesFile (const Utils::PositionCollection &positions, const ChargeRedistributionResult &chargeRedistributionResult, const std::vector< int > &listOfQmAtoms, const std::string &filename, bool writeTurbomoleFormat)
	Writes the point charges of the MM region to a file needed by ORCA. More...
Utils::AtomCollection	Scine::Qmmm::QmmmHelpers::createQmRegion (const std::vector< int > &listOfQmAtoms, const Utils::AtomCollection &structure, const std::vector< std::list< int >> &listsOfNeighbors, const std::string &xyzFilename, std::vector< int > &mmBoundaryAtoms)
	Creates the QM region from the whole structure. More...
void	Scine::Qmmm::QmmmHelpers::checkValidityOfQmRegion (const std::vector< int > &listOfQmAtoms, const Utils::AtomCollection &structure)
	Checks the validity of the selected QM region. More...
void	Scine::Qmmm::QmmmHelpers::addAllLinkAtoms (Utils::AtomCollection &qmRegion, const Utils::AtomCollection &fullStructure, const std::vector< std::list< int >> &listsOfNeighbors, const std::vector< int > &listOfQmAtoms, std::vector< int > &mmBoundaryAtoms)
	Adds the link atoms to the QM region. More...
void	Scine::Qmmm::QmmmHelpers::addOneLinkAtom (Utils::AtomCollection &qmRegion, const Utils::Atom &qmAtom, const Utils::Atom &mmAtom)
	Adds a single link atom where a bond between two given atoms exists in the full molecular structure. More...
ChargeRedistributionResult	Scine::Qmmm::QmmmHelpers::getRedistributedCharges (std::vector< double > charges, const Utils::PositionCollection &positions, const std::vector< int > &mmBoundaryAtoms, const std::vector< std::list< int >> &listsOfNeighbors, const std::vector< int > &listOfQmAtoms, const std::string &scheme)
	Performs a charge redistribution, so that the MM atoms close to the QM-MM boundary carry no charge. More...

Detailed Description

Copyright

This code is licensed under the 3-clause BSD license.
Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
See LICENSE.txt for details.