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32 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
35 /*! \file pull_rotation.h
37 * @brief Enforced rotation of protein parts or other groups of particles.
39 * This file contains routines that are used to enforce rotational motion
40 * upon a subgroup of particles.
44 #ifndef _pull_rotation_h
45 #define _pull_rotation_h
46 #include "visibility.h"
56 /*! \brief Initialize the enforced rotation groups.
58 * This routine does the memory allocation for various helper arrays, opens
59 * the output files etc.
61 * \param fplog General output file, normally md.log.
62 * \param ir Struct containing MD input parameters, among those
63 * also the enforced rotation parameters.
64 * \param nfile Number of entries in the fnm structure.
65 * \param fnm The filenames struct containing also the names
66 * of the rotation output files.
67 * \param cr Pointer to MPI communication data.
68 * \param x The positions of all MD particles.
69 * \param mtop Molecular topology.
70 * \param oenv Needed to open the rotation output xvgr file.
71 * \param Flags Flags passed over from main, used to determine
72 * whether or not we are doing a rerun.
75 extern void init_rot(FILE *fplog,t_inputrec *ir,int nfile,const t_filenm fnm[],
76 t_commrec *cr, rvec *x, matrix box, gmx_mtop_t *mtop, const output_env_t oenv,
77 gmx_bool bVerbose, unsigned long Flags);
80 /*! \brief Make a selection of the home atoms for all enforced rotation groups.
82 * This routine is similar to dd_make_local_pull_groups, but works only with
83 * domain decomposition. It should be called at every domain decomposition.
85 * \param dd Structure containing domain decomposition data.
86 * \param rot Pointer to all the enforced rotation data.
88 extern void dd_make_local_rotation_groups(gmx_domdec_t *dd,t_rot *rot);
91 /*! \brief Calculation of the enforced rotation potential.
93 * This is the main enforced rotation module which is called during every time
94 * step. Here the rotation potential as well as the resulting forces are
97 * \param cr Pointer to MPI communication data.
98 * \param ir Struct containing MD input parameters, among those
99 * \param box Simulation box, needed to make group whole.
100 * \param x The positions of all the local particles.
102 * \param step The time step.
103 * \param wcycle During the potential calculation the wallcycles are
104 * counted. Later they enter the dynamic load balancing.
105 * \param bNS After domain decomposition / neighborsearching several
106 * local arrays have to be updated (masses, shifts)
108 extern void do_rotation(t_commrec *cr,t_inputrec *ir,matrix box,rvec x[],real t,
109 gmx_large_int_t step,gmx_wallcycle_t wcycle,gmx_bool bNS);
112 /*! \brief Add the enforced rotation forces to the official force array.
114 * Adds the forces from enforced rotation potential to the local forces and
115 * sums up the contributions to the rotation potential from all the nodes. Since
116 * this needs communication, this routine should be called after the SR forces
117 * have been evaluated (in order not to spoil cycle counts).
118 * This routine also outputs data to the various rotation output files (e.g.
119 * the potential, the angle of the group, torques and more).
121 * \param rot Pointer to all the enforced rotation data.
122 * \param f The local forces to which the rotational forces have
124 * \param cr Pointer to MPI communication data.
125 * \param step The time step, used for output.
126 * \param t Time, used for output.
128 extern real add_rot_forces(t_rot *rot, rvec f[], t_commrec *cr, gmx_large_int_t step, real t);
131 /*! \brief Close the enforced rotation output files.
133 * \param fplog General output file, normally md.log.
134 * \param rot Pointer to all the enforced rotation data.
137 extern void finish_rot(FILE *fplog,t_rot *rot);