Tasks.cpp File Reference

#include "Tasks.h"
#include <Core/Log.h>
#include <Core/ModuleManager.h>
#include <Swoose/QMMM/QmRegionSelection/QmRegionSelector.h>
#include <Swoose/StructurePreparation/StructureProcessor.h>
#include <Swoose/Utilities/CalculatorOptions.h>
#include <Swoose/Utilities/SettingsNames.h>
#include <Utils/GeometryOptimization/QmmmGeometryOptimizer.h>
#include <Utils/IO/ChemicalFileFormats/ChemicalFileHandler.h>
#include <Utils/IO/ChemicalFileFormats/XyzStreamHandler.h>
#include <Utils/IO/FilesystemHelpers.h>
#include <Utils/IO/FormattedIOUtils.h>
#include <Utils/IO/MolecularTrajectoryIO.h>
#include <Utils/IO/NativeFilenames.h>
#include <Utils/MolecularDynamics/MolecularDynamics.h>
#include <Utils/Optimizer/GradientBased/Bfgs.h>
#include <Utils/Optimizer/GradientBased/GradientBasedCheck.h>
#include <boost/filesystem.hpp>
#include <ctime>

Include dependency graph for Tasks.cpp:

Functions
void	Scine::Swoose::Tasks::runPDBPreparationTask (StructurePreparation::StructureProcessor processor, const std::string &structureFile, const std::string &mode, Core::Log &log)
	Prepares the PDB file for a subsequent parametrization.
void	Scine::Swoose::Tasks::runMMCalculationTask (Core::Calculator &calculator, const std::string &structureFile, Utils::PropertyList properties, Core::Log &log)
	Performs a SFAM or GAFF molecular mechanics calculation.
void	Scine::Swoose::Tasks::runQmmmCalculationTask (Core::Calculator &calculator, const std::string &structureFile, Utils::PropertyList properties, Core::Log &log, const YAML::Node &yamlNode)
	Performs a QM/MM calculation (with SFAM or GAFF as MM).
void	Scine::Swoose::Tasks::runSFAMParametrizationTask (Core::MMParametrizer &parametrizer, const std::string &structureFile, Core::Log &log)
	Performs the parametrization of the SFAM molecular mechanics model.
void	Scine::Swoose::Tasks::runMDSimulationTask (Utils::MolecularDynamics &md, const std::string &structureFile, Core::Log &log)
	Performs an MD simulation.
void	Scine::Swoose::Tasks::runMMOptimizationTask (Core::Calculator &calculator, Utils::GeometryOptimizerBase &optimizer, const std::string &structureFile, Core::Log &log, const YAML::Node &yamlNode)
	Performs SFAM structure optimization task.
template<class OptimizerType >
void	Scine::Swoose::Tasks::runQmmmOptimizationTask (Core::Calculator &calculator, Utils::QmmmGeometryOptimizer< OptimizerType > &optimizer, const std::string &structureFile, Core::Log &log, const YAML::Node &yamlNode)
	Performs a QM/MM structure optimization (with SFAM or GAFF as MM).
void	Scine::Swoose::Tasks::runQmRegionSelectionTask (const std::string &structureFile, Core::Log &log, YAML::Node &yamlNode, std::string yamlSettingsPath)
	Performs the selection of the QM region.
template void	Scine::Swoose::Tasks::runQmmmOptimizationTask< Utils::Bfgs > (Core::Calculator &calculator, Utils::QmmmGeometryOptimizer< Utils::Bfgs > &optimizer, const std::string &structureFile, Core::Log &log, const YAML::Node &yamlNode)

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.