File BSplineInterpolationTask.h

Copyright

This code is licensed under the 3-clause BSD license.

Copyright ETH Zurich, Laboratory for Physical Chemistry, Reiher Group.

See LICENSE.txt for details.

namespace Scine

namespace Readuct

class BSplineInterpolationTask : public Scine::Readuct::Task

Public Functions

BSplineInterpolationTask(std::vector<std::string> input, std::vector<std::string> output)

std::string name() const

virtual bool run(std::map<std::string, std::shared_ptr<Core::Calculator>> &systems, const YAML::Node &taskSettings) const

Private Functions

ElementaryStepOptimization::ReactionProfile interpolateElementaryStep(const Utils::AtomCollection &start, Utils::AtomCollection end, Utils::MolecularTrajectory trajectoryGuess = Utils::MolecularTrajectory()) const

ElementaryStepOptimization::ReactionProfile optimizeElementaryStep(ElementaryStepOptimization::ReactionProfile interpolatedProfile, std::shared_ptr<Core::Calculator> calculator, YAML::Node &settingsCopy) const

std::vector<Utils::AtomCollection> extractTransitionStateGuessStructure(ElementaryStepOptimization::ReactionProfile profile, std::shared_ptr<Core::Calculator> calculator, boost::filesystem::path dir) const

void writeTangentToFile(const Eigen::VectorXd &tangent, const boost::filesystem::path &generalOutputDir) const

Utils::MolecularTrajectory convertProfileToTrajectory(ElementaryStepOptimization::ReactionProfile profile) const

Utils::MolecularTrajectory discretizeSpline(const Utils::ElementTypeCollection &elements, const Utils::BSplines::BSpline &spline, int numberPoints) const

void writeTrajectory(Utils::MolecularTrajectory trajectory, std::string filepath) const

Utils::MolecularTrajectory readTrajectory(std::string filepath) const

void getInitialValues(int &maxEnergyIndex, std::vector<double> &coordinates, std::vector<double> &energies, std::shared_ptr<Core::Calculator> calculator, const ElementaryStepOptimization::ReactionProfile &profile) const

double pointDistance(const std::vector<double> &coordinates, int maxEnergyIndex) const

std::vector<double> getNewCoordinates(const std::vector<double> &oldCoordinates, int maxEnergyIndex) const

std::vector<double> getNewEnergies(const std::vector<double> &oldEnergies, const std::vector<double> &coordinates, int maxEnergyIndex, std::shared_ptr<Core::Calculator> calculator, const Utils::BSplines::MolecularSpline &spline) const

int getIndexForMaxEnergyAndCheckValidity(const std::vector<double> &energies) const

Private Members

bool alignStructuresBeforeInterpolation_ = true

int numberControlPointsForInterpolation_ = 5

int numberStructuresForMolecularTrajectory_ = 10

bool optimize_ = true

std::string optimizer_ = "lbfgs"

bool extractTsGuess_ = false

bool extractTsGuessNeighbours_ = false

bool extractTangent_ = false

std::string tangentFileName_ = ""

double coordinateThresholdForMaximumExtraction_ = 1e-3