QmmmHelpers.h

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#ifndef SWOOSE_QMMM_QMMMHELPERS_H
#define SWOOSE_QMMM_QMMMHELPERS_H

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

namespace Scine {

namespace Utils {
class Atom;
class AtomCollection;
using PositionCollection = Eigen::Matrix<double, Eigen::Dynamic, 3, Eigen::RowMajor>;
} // namespace Utils

namespace Qmmm {
namespace QmmmHelpers {

struct ChargeRedistributionResult {
  std::vector<double> atomicCharges;
  std::vector<double> auxiliaryCharges;
  Utils::PositionCollection positionsOfAuxiliaryCharges;
};

std::vector<double> writeChargesAndPositionsAsList(const Utils::AtomCollection& structure,
                                                   const ChargeRedistributionResult& chargeRedistributionResult,
                                                   const std::vector<int>& listOfQmAtoms);

void writePointChargesFile(const Utils::PositionCollection& positions,
                           const ChargeRedistributionResult& chargeRedistributionResult,
                           const std::vector<int>& listOfQmAtoms, const std::string& filename, bool writeTurbomoleFormat);

Utils::AtomCollection 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);

void checkValidityOfQmRegion(const std::vector<int>& listOfQmAtoms, const Utils::AtomCollection& structure);

void addAllLinkAtoms(Utils::AtomCollection& qmRegion, const Utils::AtomCollection& fullStructure,
                     const std::vector<std::list<int>>& listsOfNeighbors, const std::vector<int>& listOfQmAtoms,
                     std::vector<int>& mmBoundaryAtoms);

void addOneLinkAtom(Utils::AtomCollection& qmRegion, const Utils::Atom& qmAtom, const Utils::Atom& mmAtom);

ChargeRedistributionResult 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);

} // namespace QmmmHelpers
} // namespace Qmmm
} // namespace Scine

#endif // SWOOSE_QMMM_QMMMHELPERS_H