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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
51 #include "gromacs/math/vectypes.h"
52 #include "gromacs/mdtypes/md_enums.h"
53 #include "gromacs/utility/basedefinitions.h"
54 #include "gromacs/utility/real.h"
58 /*! \brief Struct that defines a pull group */
61 int nat; /**< Number of atoms in the pull group */
62 int* ind; /**< The global atoms numbers */
63 int nweight; /**< The number of weights (0 or nat) */
64 real* weight; /**< Weights (use all 1 when weight==NULL) */
65 int pbcatom; /**< The reference atom for pbc (global number) */
66 int pbcatom_input; /**< The reference atom for pbc (global number) as specified in the input parameters */
69 /*! Maximum number of pull groups that can be used in a pull coordinate */
70 static const int c_pullCoordNgroupMax = 6;
72 /*! \brief Struct that defines a pull coordinate */
75 int eType; /**< The pull type: umbrella, constraint, ... */
76 char* externalPotentialProvider; /**< Name of the module providing the external potential, only used with eType==epullEXTERNAL */
77 int eGeom; /**< The pull geometry */
78 int ngroup; /**< The number of groups, depends on eGeom */
79 int group[c_pullCoordNgroupMax]; /**< The pull groups: indices into the group arrays in pull_t and pull_params_t, ngroup indices are used */
80 ivec dim; /**< Used to select components for constraint */
81 rvec origin; /**< The origin for the absolute reference */
82 rvec vec; /**< The pull vector, direction or position */
83 gmx_bool bStart; /**< Set init based on the initial structure */
84 real init; /**< Initial reference displacement (nm) or (deg) */
85 real rate; /**< Rate of motion (nm/ps) or (deg/ps) */
86 real k; /**< Force constant (kJ/(mol nm^2) or kJ/(mol rad^2) for umbrella pull type, or kJ/(mol nm) or kJ/(mol rad) for constant force pull type */
87 real kB; /**< Force constant for state B */
90 /*! \brief Struct containing all pull parameters */
91 typedef struct pull_params_t
93 int ngroup; /**< Number of pull groups */
94 int ncoord; /**< Number of pull coordinates */
95 real cylinder_r; /**< Radius of cylinder for dynamic COM (nm) */
96 real constr_tol; /**< Absolute tolerance for constraints in (nm) */
97 gmx_bool bPrintCOM; /**< Print coordinates of COM for each coord */
98 gmx_bool bPrintRefValue; /**< Print the reference value for each coord */
99 gmx_bool bPrintComp; /**< Print cartesian components for each coord with geometry=distance */
100 gmx_bool bSetPbcRefToPrevStepCOM; /**< Use the COM of each group from the previous step as reference */
101 int nstxout; /**< Output interval for pull x */
102 int nstfout; /**< Output interval for pull f */
103 bool bXOutAverage; /**< Write the average coordinate during the output interval */
104 bool bFOutAverage; /**< Write the average force during the output interval */
106 t_pull_group* group; /**< groups to pull/restrain/etc/ */
107 t_pull_coord* coord; /**< the pull coordinates */
112 #endif /* GMX_MDTYPES_PULL_PARAMS_H */