qmmmoptions.cpp File Reference

#include "gmxpre.h"
#include "qmmmoptions.h"
#include <map>
#include "gromacs/fileio/warninp.h"
#include "gromacs/mdrunutility/mdmodulesnotifiers.h"
#include "gromacs/mdtypes/imdpoptionprovider_helpers.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/optionsection.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/topology/embedded_system_preprocessing.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textreader.h"
#include "gromacs/utility/vec.h"
#include "qmmm.h"
#include "qmmminputgenerator.h"

Include dependency graph for qmmmoptions.cpp:

Description

Implements QMMMOptions class.

Author

Dmitry Morozov dmitr.nosp@m.y.mo.nosp@m.rozov.nosp@m.@jyu.nosp@m..fi

Christian Blau blau@.nosp@m.kth..nosp@m.se

Functions
std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::moduleName ()
	Helper function to make a std::string containing the module name.
std::tuple< std::vector< int > , std::vector< real > , std::vector < LinkFrontierAtom > >	gmx::anonymous_namespace{qmmmoptions.cpp}::preprocessTopology (gmx_mtop_t *mtop, ArrayRef< const Index > qmIndices, real qmC, const MDLogger &logger, WarningHandler *wi)
	Helper function to preprocess topology for QMMM.

Variables
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_activeTag_ = "active"
	Following Tags denotes names of parameters from .mdp file. More...
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_qmGroupTag_ = "qmgroup"
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_qmChargeTag_ = "qmcharge"
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_qmMultTag_ = "qmmultiplicity"
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_qmMethodTag_ = "qmmethod"
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_qmUserInputFileNameTag_ = "qmfilenames"
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_atomNumbersTag_ = "atomnumbers"
	This tags for parameters which will be generated during grompp and stored into *.tpr file via KVT.
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_mmGroupTag_ = "mmgroup"
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_qmLinkTag_ = "qmlink"
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_mmLinkTag_ = "mmlink"
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_qmInputTag_ = "qminput"
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_qmPdbTag_ = "qmpdb"
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_qmBoxTag_ = "qmbox"
const std::string	gmx::anonymous_namespace{qmmmoptions.cpp}::c_qmTransTag_ = "qmtrans"