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Check out http://www.gromacs.org. 34 */ 35 36 /*! \libinternal \file 37 * 38 * 39 * \brief 40 * This file contains datatypes for the mdp options used by the pull code. 41 * 42 * \author Berk Hess 43 * 44 * \inlibraryapi 45 * \ingroup module_mdtypes 46 */ 47 48 #ifndef GMX_MDTYPES_PULL_PARAMS_H 49 #define GMX_MDTYPES_PULL_PARAMS_H 50 51 #include <array> 52 #include <string> 53 #include <vector> 54 55 #include "gromacs/math/vectypes.h" 56 #include "gromacs/mdtypes/md_enums.h" 57 #include "gromacs/utility/basedefinitions.h" 58 #include "gromacs/utility/real.h" 59 60 /*! \cond INTERNAL */ 61 62 /*! \brief Struct that defines a pull group */ 63 struct t_pull_group 64 { 65 std::vector<int> ind; /**< The global atoms numbers */ 66 std::vector<real> weight; /**< Weights (use all 1 when weight==NULL) */ 67 int pbcatom; /**< The reference atom for pbc (global number) */ 68 int pbcatom_input; /**< The reference atom for pbc (global number) as specified in the input parameters */ 69 }; 70 71 /*! Maximum number of pull groups that can be used in a pull coordinate */ 72 static const int c_pullCoordNgroupMax = 6; 73 74 /*! \brief Struct that defines a pull coordinate */ 75 struct t_pull_coord 76 { 77 //! The pull type: umbrella, constraint, ... 78 int eType = 0; 79 //! Name of the module providing the external potential, only used with eType==epullEXTERNAL 80 std::string externalPotentialProvider; 81 //! The pull geometry 82 int eGeom = 0; 83 //! The number of groups, depends on eGeom 84 int ngroup = 0; 85 /*! \brief The pull groups: 86 * 87 * indices into the group arrays in pull_t and pull_params_t, 88 * ngroup indices are used 89 */ 90 std::array<int, c_pullCoordNgroupMax> group; 91 //! Used to select components for constraint 92 gmx::IVec dim = { 0, 0, 0 }; 93 //! The origin for the absolute reference 94 gmx::RVec origin = { 0, 0, 0 }; 95 //! The pull vector, direction or position 96 gmx::RVec vec = { 0, 0, 0 }; 97 //! Set init based on the initial structure 98 bool bStart = false; 99 //! Initial reference displacement (nm) or (deg) 100 real init = 0.0; 101 //! Rate of motion (nm/ps) or (deg/ps) 102 real rate = 0.0; 103 /*! \brief Force constant 104 * 105 * For umbrella pull type this is (kJ/(mol nm^2) or kJ/(mol rad^2). 106 * For constant force pull type it is kJ/(mol nm) or kJ/(mol rad). 107 */ 108 real k = 0.0; 109 //! Force constant for state B 110 real kB = 0.0; 111 }; 112 113 /*! \brief Struct containing all pull parameters */ 114 struct pull_params_t 115 { 116 //! Number of pull groups 117 int ngroup = 0; 118 //! Number of pull coordinates 119 int ncoord = 0; 120 //! Radius of cylinder for dynamic COM (nm) 121 real cylinder_r = 0.0; 122 //! Absolute tolerance for constraints in (nm) 123 real constr_tol = 0.0; 124 //! Print coordinates of COM for each coord 125 bool bPrintCOM = false; 126 //! Print the reference value for each coord 127 bool bPrintRefValue = false; 128 //! Print cartesian components for each coord with geometry=distance 129 bool bPrintComp = false; 130 //! Use the COM of each group from the previous step as reference 131 bool bSetPbcRefToPrevStepCOM = false; 132 //! Output interval for pull x 133 int nstxout = 0; 134 //! Output interval for pull f 135 int nstfout = 0; 136 //! Write the average coordinate during the output interval 137 bool bXOutAverage = false; 138 //! Write the average force during the output interval 139 bool bFOutAverage = false; 140 //! groups to pull/restrain/etc/ 141 std::vector<t_pull_group> group; 142 //! the pull coordinates 143 std::vector<t_pull_coord> coord; 144 }; 145 146 /*! \endcond */ 147 148 #endif /* GMX_MDTYPES_PULL_PARAMS_H */ 149