include/pull_rotation.h

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  38
  39 /*! \file pull_rotation.h
  40  *
  41  *  @brief Enforced rotation of protein parts or other groups of particles.
  42  *
  43  *  This file contains routines that are used to enforce rotational motion
  44  *  upon a subgroup of particles.
  45  *
  46  */
  47
  48 #ifndef _pull_rotation_h
  49 #define _pull_rotation_h
  50 #include "visibility.h"
  51 #include "vec.h"
  52 #include "typedefs.h"
  53
  54
  55 #ifdef __cplusplus
  56 extern "C" {
  57 #endif
  58
  59
  60 /*! \brief Initialize the enforced rotation groups.
  61  *
  62  * This routine does the memory allocation for various helper arrays, opens
  63  * the output files etc.
  64  *
  65  * \param fplog             General output file, normally md.log.
  66  * \param ir                Struct containing MD input parameters, among those
  67  *                          also the enforced rotation parameters.
  68  * \param nfile             Number of entries in the fnm structure.
  69  * \param fnm               The filenames struct containing also the names
  70  *                          of the rotation output files.
  71  * \param cr                Pointer to MPI communication data.
  72  * \param x                 The positions of all MD particles.
  73  * \param box               The simulation box.
  74  * \param mtop              Molecular topology.
  75  * \param oenv              Needed to open the rotation output xvgr file.
  76  * \param Flags             Flags passed over from main, used to determine
  77  *                          whether or not we are doing a rerun.
  78  */
  79 GMX_LIBMD_EXPORT
  80 extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
  81                      t_commrec *cr, rvec *x, matrix box, gmx_mtop_t *mtop, const output_env_t oenv,
  82                      gmx_bool bVerbose, unsigned long Flags);
  83
  84
  85 /*! \brief Make a selection of the home atoms for all enforced rotation groups.
  86  *
  87  * This routine is similar to dd_make_local_pull_groups, but works only with
  88  * domain decomposition. It should be called at every domain decomposition.
  89  *
  90  * \param dd                Structure containing domain decomposition data.
  91  * \param rot               Pointer to all the enforced rotation data.
  92  */
  93 extern void dd_make_local_rotation_groups(gmx_domdec_t *dd, t_rot *rot);
  94
  95
  96 /*! \brief Calculation of the enforced rotation potential.
  97  *
  98  * This is the main enforced rotation module which is called during every time
  99  * step. Here the rotation potential as well as the resulting forces are
 100  * calculated.
 101  *
 102  * \param cr                Pointer to MPI communication data.
 103  * \param ir                Struct containing MD input parameters, among those
 104  * \param box               Simulation box, needed to make group whole.
 105  * \param x                 The positions of all the local particles.
 106  * \param t                 Time.
 107  * \param step              The time step.
 108  * \param wcycle            During the potential calculation the wallcycles are
 109  *                          counted. Later they enter the dynamic load balancing.
 110  * \param bNS               After domain decomposition / neighborsearching several
 111  *                          local arrays have to be updated (masses, shifts)
 112  */
 113 extern void do_rotation(t_commrec *cr, t_inputrec *ir, matrix box, rvec x[], real t,
 114                         gmx_large_int_t step, gmx_wallcycle_t wcycle, gmx_bool bNS);
 115
 116
 117 /*! \brief Add the enforced rotation forces to the official force array.
 118  *
 119  * Adds the forces from enforced rotation potential to the local forces and
 120  * sums up the contributions to the rotation potential from all the nodes. Since
 121  * this needs communication, this routine should be called after the SR forces
 122  * have been evaluated (in order not to spoil cycle counts).
 123  * This routine also outputs data to the various rotation output files (e.g.
 124  * the potential, the angle of the group, torques and more).
 125  *
 126  * \param rot               Pointer to all the enforced rotation data.
 127  * \param f                 The local forces to which the rotational forces have
 128  *                          to be added.
 129  * \param cr                Pointer to MPI communication data.
 130  * \param step              The time step, used for output.
 131  * \param t                 Time, used for output.
 132  */
 133 extern real add_rot_forces(t_rot *rot, rvec f[], t_commrec *cr, gmx_large_int_t step, real t);
 134
 135
 136 /*! \brief Close the enforced rotation output files.
 137  *
 138  * \param rot               Pointer to all the enforced rotation data.
 139  */
 140 GMX_LIBMD_EXPORT
 141 extern void finish_rot(t_rot *rot);
 142
 143
 144 #ifdef __cplusplus
 145 }
 146 #endif
 147
 148
 149 #endif