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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
54 #include "../fileio/filenm.h"
61 /*! \brief Get the distance to the reference and deviation for pull coord coord_ind.
63 * \param[in] pull The pull group.
64 * \param[in] coord_ind Number of the pull coordinate.
65 * \param[in] pbc Information structure about periodicity.
67 * \param[out] dr The pull coordinate difference vector.
68 * \param[out] dev The deviation from the reference distance.
70 void get_pull_coord_distance(const t_pull *pull,
72 const t_pbc *pbc, double t,
73 dvec dr, double *dev);
76 /*! \brief Set the all the pull forces to zero.
78 * \param pull The pull group.
80 void clear_pull_forces(t_pull *pull);
83 /*! \brief Determine the COM pull forces and add them to f, return the potential
85 * \param[in] ePull Enum defining the type of pulling: umbrella, const force, ...
86 * \param[in] pull The pull group.
87 * \param[in] md All atoms.
88 * \param[in] pbc Information struct about periodicity.
89 * \param[in] cr Struct for communication info.
91 * \param[in] lambda The value of lambda in FEP calculations.
92 * \param[in] x Positions.
93 * \param[in] f Forces.
94 * \param[in,out] vir The virial, which, if != NULL, gets a pull correction.
95 * \param[out] dvdlambda Pull contribution to dV/d(lambda).
97 * \returns The pull potential energy.
99 real pull_potential(int ePull, t_pull *pull, t_mdatoms *md, t_pbc *pbc,
100 t_commrec *cr, double t, real lambda,
101 rvec *x, rvec *f, tensor vir, real *dvdlambda);
104 /*! \brief Constrain the coordinates xp in the directions in x
105 * and also constrain v when v != NULL.
107 * \param[in] pull The pull group.
108 * \param[in] md All atoms.
109 * \param[in] pbc Information struct about periodicity.
110 * \param[in] cr Struct for communication info.
111 * \param[in] dt The time step length.
112 * \param[in] t The time.
113 * \param[in] x Positions.
114 * \param[in,out] xp Updated x, can be NULL.
115 * \param[in,out] v Velocities, which may get a pull correction.
116 * \param[in,out] vir The virial, which, if != NULL, gets a pull correction.
118 void pull_constraint(t_pull *pull, t_mdatoms *md, t_pbc *pbc,
119 t_commrec *cr, double dt, double t,
120 rvec *x, rvec *xp, rvec *v, tensor vir);
123 /*! \brief Make a selection of the home atoms for all pull groups.
124 * Should be called at every domain decomposition.
126 * \param dd Structure containing domain decomposition data.
127 * \param pull The pull group.
128 * \param md All atoms.
130 void dd_make_local_pull_groups(gmx_domdec_t *dd,
131 t_pull *pull, t_mdatoms *md);
134 /*! \brief Get memory and initialize the fields of pull that still need it, and
135 * do runtype specific initialization.
137 * \param fplog General output file, normally md.log.
138 * \param ir The inputrec.
139 * \param nfile Number of files.
140 * \param fnm Standard filename struct.
141 * \param mtop The topology of the whole system.
142 * \param cr Struct for communication info.
143 * \param oenv Output options.
144 * \param lambda FEP lambda.
145 * \param bOutFile Open output files?
146 * \param Flags Flags passed over from main, used to determine
147 * whether or not we are appending.
149 void init_pull(FILE *fplog,
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(t_pull *pull);
168 /*! \brief Print the pull output (x and/or f)
170 * \param pull The pull group.
171 * \param step Time step number.
174 void pull_print_output(t_pull *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 group.
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,