include/pull_rotation.h

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  34
  35 /*! \file pull_rotation.h
  36  *
  37  *  @brief Enforced rotation of protein parts or other groups of particles.
  38  *
  39  *  This file contains routines that are used to enforce rotational motion
  40  *  upon a subgroup of particles.
  41  *
  42  */
  43
  44 #ifndef _rotation_h
  45 #define _rotation_h
  46
  47 #ifdef HAVE_CONFIG_H
  48   #include <config.h>
  49 #endif
  50
  51 #include "vec.h"
  52 #include "typedefs.h"
  53
  54
  55 /*! \brief Initialize the enforced rotation groups.
  56  *
  57  * This routine does the memory allocation for various helper arrays, opens
  58  * the output files etc.
  59  *
  60  * \param fplog             General output file, normally md.log.
  61  * \param ir                Struct containing MD input parameters, among those
  62  *                          also the enforced rotation parameters.
  63  * \param nfile             Number of entries in the fnm structure.
  64  * \param fnm               The filenames struct containing also the names
  65  *                          of the rotation output files.
  66  * \param cr                Pointer to MPI communication data.
  67  * \param x                 The positions of all MD particles.
  68  * \param mtop              Molecular topology.
  69  * \param oenv              Needed to open the rotation output xvgr file.
  70  * \param Flags             Flags passed over from main, used to determine
  71  *                          whether or not we are doing a rerun.
  72  */
  73 extern void init_rot(FILE *fplog,t_inputrec *ir,int nfile,const t_filenm fnm[],
  74         t_commrec *cr, rvec *x, gmx_mtop_t *mtop, const output_env_t oenv,
  75         unsigned long Flags);
  76
  77
  78 /*! \brief Calculation of the enforced rotation potential.
  79  *
  80  * This is the main enforced rotation module which is called during every time
  81  * step. Here the rotation potential as well as the resulting forces are
  82  * calculated.
  83  *
  84  * \param cr                Pointer to MPI communication data.
  85  * \param ir                Struct containing MD input parameters, among those
  86  * \param box               Simulation box, needed to make group whole.
  87  * \param x                 The positions of all the local particles.
  88  * \param t                 Time.
  89  * \param step              The time step.
  90  * \param wcycle            During the potential calculation the wallcycles are
  91  *                          counted. Later they enter the dynamic load balancing.
  92  * \param bNS               After domain decomposition / neighborsearching several
  93  *                          local arrays have to be updated (masses, shifts)
  94  */
  95 extern void do_rotation(t_commrec *cr,t_inputrec *ir,matrix box,rvec x[],real t,
  96         int step,gmx_wallcycle_t wcycle,bool bNS);
  97
  98
  99 /*! \brief Add the enforced rotation forces to the official force array.
 100  *
 101  * Adds the forces from enforced rotation potential to the local forces and
 102  * sums up the contributions to the rotation potential from all the nodes. Since
 103  * this needs communication, this routine should be called after the SR forces
 104  * have been evaluated (in order not to spoil cycle counts).
 105  * This routine also outputs data to the various rotation output files (e.g.
 106  * the potential, the angle of the group, torques and more).
 107  *
 108  * \param rot               Pointer to all the enforced rotation data.
 109  * \param f                 The local forces to which the rotational forces have
 110  *                          to be added.
 111  * \param cr                Pointer to MPI communication data.
 112  * \param step              The time step, used for output.
 113  * \param t                 Time, used for output.
 114  */
 115 extern real add_rot_forces(t_rot *rot, rvec f[], t_commrec *cr, int step, real t);
 116
 117
 118 /*! \brief Close the enforced rotation output files.
 119  *
 120  * \param fplog             General output file, normally md.log.
 121  * \param rot               Pointer to all the enforced rotation data.
 122  */
 123 extern void finish_rot(FILE *fplog,t_rot *rot);
 124
 125
 126 #endif