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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/fileio/filenm.h"
54 #include "gromacs/legacyheaders/typedefs.h"
63 /*! \brief Get the value for pull coord coord_ind.
65 * \param[in,out] pull The pull struct.
66 * \param[in] coord_ind Number of the pull coordinate.
67 * \param[in] pbc Information structure about periodicity.
68 * \param[out] value The value of the pull coordinate.
70 void get_pull_coord_value(struct pull_t *pull,
72 const struct t_pbc *pbc,
76 /*! \brief Set the all the pull forces to zero.
78 * \param pull The pull group.
80 void clear_pull_forces(struct pull_t *pull);
83 /*! \brief Determine the COM pull forces and add them to f, return the potential
85 * \param[in,out] pull The pull struct.
86 * \param[in] md All atoms.
87 * \param[in] pbc Information struct about periodicity.
88 * \param[in] cr Struct for communication info.
90 * \param[in] lambda The value of lambda in FEP calculations.
91 * \param[in] x Positions.
92 * \param[in] f Forces.
93 * \param[in,out] vir The virial, which, if != NULL, gets a pull correction.
94 * \param[out] dvdlambda Pull contribution to dV/d(lambda).
96 * \returns The pull potential energy.
98 real pull_potential(struct pull_t *pull, t_mdatoms *md, struct t_pbc *pbc,
99 t_commrec *cr, double t, real lambda,
100 rvec *x, rvec *f, tensor vir, real *dvdlambda);
103 /*! \brief Constrain the coordinates xp in the directions in x
104 * and also constrain v when v != NULL.
106 * \param[in,out] pull The pull data.
107 * \param[in] md All atoms.
108 * \param[in] pbc Information struct about periodicity.
109 * \param[in] cr Struct for communication info.
110 * \param[in] dt The time step length.
111 * \param[in] t The time.
112 * \param[in] x Positions.
113 * \param[in,out] xp Updated x, can be NULL.
114 * \param[in,out] v Velocities, which may get a pull correction.
115 * \param[in,out] vir The virial, which, if != NULL, gets a pull correction.
117 void pull_constraint(struct pull_t *pull, t_mdatoms *md, struct t_pbc *pbc,
118 t_commrec *cr, double dt, double t,
119 rvec *x, rvec *xp, rvec *v, tensor vir);
122 /*! \brief Make a selection of the home atoms for all pull groups.
123 * Should be called at every domain decomposition.
125 * \param cr Structure for communication info.
126 * \param pull The pull group.
127 * \param md All atoms.
129 void dd_make_local_pull_groups(t_commrec *cr,
130 struct pull_t *pull, t_mdatoms *md);
133 /*! \brief Allocate, initialize and return a pull work struct.
135 * \param fplog General output file, normally md.log.
136 * \param pull_params The pull input parameters containing all pull settings.
137 * \param ir The inputrec.
138 * \param nfile Number of files.
139 * \param fnm Standard filename struct.
140 * \param mtop The topology of the whole system.
141 * \param cr Struct for communication info.
142 * \param oenv Output options.
143 * \param lambda FEP lambda.
144 * \param bOutFile Open output files?
145 * \param Flags Flags passed over from main, used to determine
146 * whether or not we are appending.
148 struct pull_t *init_pull(FILE *fplog,
149 const pull_params_t *pull_params,
150 const t_inputrec *ir,
152 const t_filenm fnm[],
155 const output_env_t oenv,
158 unsigned long Flags);
161 /*! \brief Close the pull output files.
163 * \param pull The pull group.
165 void finish_pull(struct pull_t *pull);
168 /*! \brief Print the pull output (x and/or f)
170 * \param pull The pull data structure.
171 * \param step Time step number.
174 void pull_print_output(struct pull_t *pull, gmx_int64_t step, double time);
177 /*! \brief Calculates centers of mass all pull groups.
179 * \param[in] cr Struct for communication info.
180 * \param[in] pull The pull data structure.
181 * \param[in] md All atoms.
182 * \param[in] pbc Information struct about periodicity.
183 * \param[in] t Time, only used for cylinder ref.
184 * \param[in] x The local positions.
185 * \param[in,out] xp Updated x, can be NULL.
188 void pull_calc_coms(t_commrec *cr,
197 /*! \brief Returns if we have pull coordinates with potential pulling.
199 * \param[in] pull The pull data structure.
201 gmx_bool pull_have_potential(const struct pull_t *pull);
204 /*! \brief Returns if we have pull coordinates with constraint pulling.
206 * \param[in] pull The pull data structure.
208 gmx_bool pull_have_constraint(const struct pull_t *pull);