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36 /*! \libinternal \file
40 * This file contains datatypes for the mdp options used by the pull code.
45 * \ingroup module_mdtypes
48 #ifndef GMX_MDTYPES_PULL_PARAMS_H
49 #define GMX_MDTYPES_PULL_PARAMS_H
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"
62 /*! \brief Struct that defines a pull group */
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 */
71 /*! Maximum number of pull groups that can be used in a pull coordinate */
72 static constexpr int c_pullCoordNgroupMax = 6;
74 /*! \brief Struct that defines a pull coordinate */
77 //! The pull type: umbrella, constraint, ...
78 PullingAlgorithm eType = PullingAlgorithm::Umbrella;
79 //! Name of the module providing the external potential, only used with eType==epullEXTERNAL
80 std::string externalPotentialProvider;
82 PullGroupGeometry eGeom = PullGroupGeometry::Distance;
83 //! Mathematical expression evaluated by the pull code for transformation coordinates.
84 std::string expression;
85 //! The finite difference to use in numerical derivation of mathematical expressions
87 //! The number of groups, depends on eGeom
89 /*! \brief The pull groups:
91 * indices into the group arrays in pull_t and pull_params_t,
92 * ngroup indices are used
94 std::array<int, c_pullCoordNgroupMax> group;
95 //! Used to select components for constraint
96 gmx::IVec dim = { 0, 0, 0 };
97 //! The origin for the absolute reference
98 gmx::RVec origin = { 0, 0, 0 };
99 //! The pull vector, direction or position
100 gmx::RVec vec = { 0, 0, 0 };
101 //! Set init based on the initial structure
103 //! Initial reference displacement (nm) or (deg)
105 //! Rate of motion (nm/ps) or (deg/ps)
107 /*! \brief Force constant
109 * For umbrella pull type this is (kJ/(mol nm^2) or kJ/(mol rad^2).
110 * For constant force pull type it is kJ/(mol nm) or kJ/(mol rad).
113 //! Force constant for state B
115 //! The index of this coordinate in the list of coordinates
119 /*! \brief Struct containing all pull parameters */
122 //! Number of pull groups
124 //! Number of pull coordinates
126 //! Radius of cylinder for dynamic COM (nm)
127 real cylinder_r = 0.0;
128 //! Absolute tolerance for constraints in (nm)
129 real constr_tol = 0.0;
130 //! Print coordinates of COM for each coord
131 bool bPrintCOM = false;
132 //! Print the reference value for each coord
133 bool bPrintRefValue = false;
134 //! Print cartesian components for each coord with geometry=distance
135 bool bPrintComp = false;
136 //! Use the COM of each group from the previous step as reference
137 bool bSetPbcRefToPrevStepCOM = false;
138 //! Output interval for pull x
140 //! Output interval for pull f
142 //! Write the average coordinate during the output interval
143 bool bXOutAverage = false;
144 //! Write the average force during the output interval
145 bool bFOutAverage = false;
146 //! groups to pull/restrain/etc/
147 std::vector<t_pull_group> group;
148 //! the pull coordinates
149 std::vector<t_pull_coord> coord;
154 #endif /* GMX_MDTYPES_PULL_PARAMS_H */