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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 */
60 int nat
; /**< Number of atoms in the pull group */
61 int *ind
; /**< The global atoms numbers */
62 int nweight
; /**< The number of weights (0 or nat) */
63 real
*weight
; /**< Weights (use all 1 when weight==NULL) */
64 int pbcatom
; /**< The reference atom for pbc (global number) */
67 /*! Maximum number of pull groups that can be used in a pull coordinate */
68 static const int c_pullCoordNgroupMax
= 6;
70 /*! \brief Struct that defines a pull coordinate */
72 int eType
; /**< The pull type: umbrella, constraint, ... */
73 int eGeom
; /**< The pull geometry */
74 int ngroup
; /**< The number of groups, depends on eGeom */
75 int group
[c_pullCoordNgroupMax
]; /**< The pull groups: indices into the group arrays in pull_t and pull_params_t, ngroup indices are used */
76 ivec dim
; /**< Used to select components for constraint */
77 rvec origin
; /**< The origin for the absolute reference */
78 rvec vec
; /**< The pull vector, direction or position */
79 gmx_bool bStart
; /**< Set init based on the initial structure */
80 real init
; /**< Initial reference displacement (nm) or (deg) */
81 real rate
; /**< Rate of motion (nm/ps) or (deg/ps) */
82 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 */
83 real kB
; /**< Force constant for state B */
86 /*! \brief Struct containing all pull parameters */
87 typedef struct pull_params_t
{
88 int ngroup
; /**< Number of pull groups */
89 int ncoord
; /**< Number of pull coordinates */
90 real cylinder_r
; /**< Radius of cylinder for dynamic COM (nm) */
91 real constr_tol
; /**< Absolute tolerance for constraints in (nm) */
92 gmx_bool bPrintCOM
; /**< Print coordinates of COM for each coord */
93 gmx_bool bPrintRefValue
; /**< Print the reference value for each coord */
94 gmx_bool bPrintComp
; /**< Print cartesian components for each coord with geometry=distance */
95 int nstxout
; /**< Output interval for pull x */
96 int nstfout
; /**< Output interval for pull f */
98 t_pull_group
*group
; /**< groups to pull/restrain/etc/ */
99 t_pull_coord
*coord
; /**< the pull coordinates */
104 #endif /* GMX_MDTYPES_PULL_PARAMS_H */