src/gromacs/pulling/pull_rotation.h

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  37
  38 /*! \libinternal \file
  39  *
  40  * \brief
  41  * Declares functions to enforce rotational motion upon a group of particles.
  42  *
  43  * \author Carsten Kutzner <ckutzne@gwdg.de>
  44  *
  45  * \inlibraryapi
  46  */
  47
  48 #ifndef GMX_PULLING_PULL_ROTATION_H
  49 #define GMX_PULLING_PULL_ROTATION_H
  50
  51 #include <stdio.h>
  52
  53 #include "gromacs/math/vectypes.h"
  54 #include "gromacs/utility/basedefinitions.h"
  55
  56 struct gmx_domdec_t;
  57 struct gmx_mtop_t;
  58 struct gmx_output_env_t;
  59 struct t_commrec;
  60 struct t_filenm;
  61 struct t_inputrec;
  62 struct t_rot;
  63
  64 #ifdef __cplusplus
  65 extern "C" {
  66 #endif
  67
  68
  69 /*! \brief Initializes the enforced rotation groups.
  70  *
  71  * This routine does the memory allocation for various helper arrays, opens
  72  * the output files etc.
  73  *
  74  * \param fplog    General output file, normally md.log.
  75  * \param ir       Struct containing MD input parameters, among those
  76  *                 also the enforced rotation parameters.
  77  * \param nfile    Number of entries in the fnm structure.
  78  * \param fnm      The filenames struct containing also the names
  79  *                 of the rotation output files.
  80  * \param cr       Pointer to MPI communication data.
  81  * \param x        The positions of all MD particles.
  82  * \param box      The simulation box.
  83  * \param mtop     Molecular topology.
  84  * \param oenv     Needed to open the rotation output xvgr file.
  85  * \param bVerbose Whether to print extra status information.
  86  * \param Flags    Flags passed over from main, used to determine
  87  *                 whether or not we are doing a rerun.
  88  */
  89 extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
  90                      struct t_commrec *cr, rvec *x, matrix box, gmx_mtop_t *mtop, const gmx_output_env_t *oenv,
  91                      gmx_bool bVerbose, unsigned long Flags);
  92
  93
  94 /*! \brief Make a selection of the home atoms for all enforced rotation groups.
  95  *
  96  * This routine is similar to \ref dd_make_local_pull_groups, but works only with
  97  * domain decomposition. It should be called at every domain decomposition.
  98  *
  99  * \param dd      Structure containing domain decomposition data.
 100  * \param rot     Pointer to all the enforced rotation data.
 101  */
 102 extern void dd_make_local_rotation_groups(struct gmx_domdec_t *dd, t_rot *rot);
 103
 104
 105 /*! \brief Calculates the enforced rotation potential(s).
 106  *
 107  * This is the main enforced rotation module which is called during every time
 108  * step. Here the rotation potential as well as the resulting forces are
 109  * calculated.
 110  *
 111  * \param cr      Pointer to MPI communication data.
 112  * \param ir      Struct containing MD input parameters, among those
 113  * \param box     Simulation box, needed to make group whole.
 114  * \param x       The positions of all the local particles.
 115  * \param t       Time.
 116  * \param step    The time step.
 117  * \param bNS     After domain decomposition / neighbor searching several
 118  *                local arrays have to be updated (masses, shifts)
 119  */
 120 extern void do_rotation(struct t_commrec *cr, t_inputrec *ir, matrix box, rvec x[], real t,
 121                         gmx_int64_t step, gmx_bool bNS);
 122
 123
 124 /*! \brief Add the enforced rotation forces to the official force array.
 125  *
 126  * Adds the forces from enforced rotation potential to the local forces and
 127  * sums up the contributions to the rotation potential from all the nodes. Since
 128  * this needs communication, this routine should be called after the short range
 129  * forces have been evaluated (in order not to spoil cycle counts).
 130  * This routine also outputs data to the rotation output files (e.g.
 131  * the potential, the angle of the group(s), and torques).
 132  *
 133  * \param rot     Pointer to all the enforced rotation data.
 134  * \param f       The local forces to which the rotational forces have
 135  *                to be added.
 136  * \param cr      Pointer to MPI communication data.
 137  * \param step    The time step, used for output.
 138  * \param t       Time, used for output.
 139  * \returns       The potential energy of the rotation potentials.
 140  */
 141 extern real add_rot_forces(t_rot *rot, rvec f[], struct t_commrec *cr, gmx_int64_t step, real t);
 142
 143
 144 /*! \brief Close the enforced rotation output files.
 145  *
 146  * \param rot     Pointer to all the enforced rotation data.
 147  */
 148 extern void finish_rot(t_rot *rot);
 149
 150
 151 #ifdef __cplusplus
 152 }
 153 #endif
 154
 155
 156 #endif