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38 /*! \libinternal \file
42 * This file contains datatypes and function declarations necessary
43 for mdrun to interface with the pull code.
50 #ifndef GMX_PULLING_PULL_H
51 #define GMX_PULLING_PULL_H
53 #include "gromacs/legacyheaders/typedefs.h"
54 #include "../fileio/filenm.h"
62 /*! \brief Get the distance to the reference and deviation for pull coord coord_ind.
64 * \param[in] pull The pull group.
65 * \param[in] coord_ind Number of the pull coordinate.
66 * \param[in] pbc Information structure about periodicity.
68 * \param[out] dr The pull coordinate difference vector.
69 * \param[out] dev The deviation from the reference distance.
71 void get_pull_coord_distance(const t_pull *pull,
73 const struct t_pbc *pbc, double t,
74 dvec dr, double *dev);
77 /*! \brief Set the all the pull forces to zero.
79 * \param pull The pull group.
81 void clear_pull_forces(t_pull *pull);
84 /*! \brief Determine the COM pull forces and add them to f, return the potential
86 * \param[in] ePull Enum defining the type of pulling: umbrella, const force, ...
87 * \param[in] pull The pull group.
88 * \param[in] md All atoms.
89 * \param[in] pbc Information struct about periodicity.
90 * \param[in] cr Struct for communication info.
92 * \param[in] lambda The value of lambda in FEP calculations.
93 * \param[in] x Positions.
94 * \param[in] f Forces.
95 * \param[in,out] vir The virial, which, if != NULL, gets a pull correction.
96 * \param[out] dvdlambda Pull contribution to dV/d(lambda).
98 * \returns The pull potential energy.
100 real pull_potential(int ePull, t_pull *pull, t_mdatoms *md, struct t_pbc *pbc,
101 t_commrec *cr, double t, real lambda,
102 rvec *x, rvec *f, tensor vir, real *dvdlambda);
105 /*! \brief Constrain the coordinates xp in the directions in x
106 * and also constrain v when v != NULL.
108 * \param[in] pull The pull group.
109 * \param[in] md All atoms.
110 * \param[in] pbc Information struct about periodicity.
111 * \param[in] cr Struct for communication info.
112 * \param[in] dt The time step length.
113 * \param[in] t The time.
114 * \param[in] x Positions.
115 * \param[in,out] xp Updated x, can be NULL.
116 * \param[in,out] v Velocities, which may get a pull correction.
117 * \param[in,out] vir The virial, which, if != NULL, gets a pull correction.
119 void pull_constraint(t_pull *pull, t_mdatoms *md, struct t_pbc *pbc,
120 t_commrec *cr, double dt, double t,
121 rvec *x, rvec *xp, rvec *v, tensor vir);
124 /*! \brief Make a selection of the home atoms for all pull groups.
125 * Should be called at every domain decomposition.
127 * \param dd Structure containing domain decomposition data.
128 * \param pull The pull group.
129 * \param md All atoms.
131 void dd_make_local_pull_groups(gmx_domdec_t *dd,
132 t_pull *pull, t_mdatoms *md);
135 /*! \brief Get memory and initialize the fields of pull that still need it, and
136 * do runtype specific initialization.
138 * \param fplog General output file, normally md.log.
139 * \param ir The inputrec.
140 * \param nfile Number of files.
141 * \param fnm Standard filename struct.
142 * \param mtop The topology of the whole system.
143 * \param cr Struct for communication info.
144 * \param oenv Output options.
145 * \param lambda FEP lambda.
146 * \param bOutFile Open output files?
147 * \param Flags Flags passed over from main, used to determine
148 * whether or not we are appending.
150 void init_pull(FILE *fplog,
153 const t_filenm fnm[],
156 const output_env_t oenv,
159 unsigned long Flags);
162 /*! \brief Close the pull output files.
164 * \param pull The pull group.
166 void finish_pull(t_pull *pull);
169 /*! \brief Print the pull output (x and/or f)
171 * \param pull The pull group.
172 * \param step Time step number.
175 void pull_print_output(t_pull *pull, gmx_int64_t step, double time);
178 /*! \brief Calculates centers of mass all pull groups.
180 * \param[in] cr Struct for communication info.
181 * \param[in] pull The pull group.
182 * \param[in] md All atoms.
183 * \param[in] pbc Information struct about periodicity.
184 * \param[in] t Time, only used for cylinder ref.
185 * \param[in] x The local positions.
186 * \param[in,out] xp Updated x, can be NULL.
189 void pull_calc_coms(t_commrec *cr,