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37 * Declares structers and types needed to evaluate forces and energies for QM/MM
39 * \author Dmitry Morozov <dmitry.morozov@jyu.fi>
40 * \author Christian Blau <blau@kth.se>
41 * \ingroup module_applied_forces
43 #ifndef GMX_APPLIED_FORCES_QMMMTYPES_H
44 #define GMX_APPLIED_FORCES_QMMMTYPES_H
50 #include "gromacs/math/vectypes.h"
51 #include "gromacs/utility/classhelpers.h"
52 #include "gromacs/utility/enumerationhelpers.h"
53 #include "gromacs/utility/real.h"
59 * \brief Helper structure with indexes of broken bonds between QM and MM
60 * Used to determine and store pair of QM and MM atoms between which chemical bond is broken
64 //! Global index of QM atom at Frontier
66 //! Global index of MM atom at Frontier
70 /*! \brief Enumerator for supported QM methods
71 * Also could be INPUT which means external input file provided
72 * with the name determined by QMMMParameters::qminputfilename_
74 enum class QMMMQMMethod
76 PBE, //!< DFT with PBE functional
77 BLYP, //!< DFT with BLYP functional
78 INPUT, //!< User provides suitable input file for QM package
82 //! The names of the supported QM methods
83 static const EnumerationArray<QMMMQMMethod, const char*> c_qmmmQMMethodNames = {
84 { "PBE", "BLYP", "INPUT" }
87 //! symbols of the elements in periodic table
88 const std::vector<std::string> periodic_system = {
89 "X ", "H ", "He ", "Li ", "Be ", "B ", "C ", "N ", "O ", "F ", "Ne ", "Na ", "Mg ",
90 "Al ", "Si ", "P ", "S ", "Cl ", "Ar ", "K ", "Ca ", "Sc ", "Ti ", "V ", "Cr ", "Mn ",
91 "Fe ", "Co ", "Ni ", "Cu ", "Zn ", "Ga ", "Ge ", "As ", "Se ", "Br ", "Kr "
95 * \brief Holding all parameters needed for QM/MM simulation.
96 * Also used for setting all default parameter values.
100 //! Indicate if QM/MM is active (default false)
101 bool active_ = false;
102 //! Indices of the atoms that are part of the QM region (default whole System)
103 std::vector<index> qmIndices_;
104 //! Indices of the atoms that are part of the MM region (default no MM atoms)
105 std::vector<index> mmIndices_;
106 //! Vector with pairs of indicies defining broken bonds in QMMM (default determined from topology)
107 std::vector<LinkFrontier> link_;
108 //! Vector with atomic numbers of all atoms in the system (default determined from topology)
109 std::vector<int> atomNumbers_;
110 //! Total charge of QM system (default 0)
112 //! Total multiplicity of QM system (default 1)
114 //! Method used for QM calculation (default DFT with PBE functional)
115 QMMMQMMethod qmMethod_ = QMMMQMMethod::PBE;
116 //! String containing name of the input file for CP2K (default "topol-qmmm.inp")
117 std::string qmInputFileName_ = "topol-qmmm.inp";
118 //! String containing name of the PDB file for CP2K input (default "topol-qmmm.pdb")
119 std::string qmPdbFileName_ = "topol-qmmm.pdb";
120 //! String containing whole CP2K input which can be stored inside *.tpr
121 std::string qmInput_;
122 //! String containing PDB file for CP2K input which can be stored inside *.tpr
124 //! Matrix that contains vectors defining QM box
126 //! Matrix that contains vectors defining QM box
129 //! Constructor with default initializers for arrays
131 qmBox_{ { 0.0, 0.0, 0.0 }, { 0.0, 0.0, 0.0 }, { 0.0, 0.0, 0.0 } }, qmTrans_{ 0.0, 0.0, 0.0 }
135 GMX_DISALLOW_COPY_AND_ASSIGN(QMMMParameters);
140 #endif // GMX_APPLIED_FORCES_QMMMTYPES_H