src/gromacs/essentialdynamics/edsam.h

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  37 /*! \libinternal \file
  38  *
  39  * \brief
  40  * Declares functions to calculate both essential dynamics constraints
  41  * as well as flooding potentials and forces.
  42  *
  43  * \authors Bert de Groot <bgroot@gwdg.de>, Oliver Lange <oliver.lange@tum.de>,
  44  * Carsten Kutzner <ckutzne@gwdg.de>
  45  *
  46  * \inlibraryapi
  47  */
  48 #ifndef GMX_ESSENTIALDYNAMICS_EDSAM_H
  49 #define GMX_ESSENTIALDYNAMICS_EDSAM_H
  50
  51 #include "gromacs/math/vectypes.h"
  52 #include "gromacs/utility/basedefinitions.h"
  53
  54
  55 /*! \brief Abstract type for essential dynamics
  56  *
  57  * The main type is defined only in edsam.c
  58  */
  59 typedef struct gmx_edsam *gmx_edsam_t;
  60
  61 struct edsamhistory_t;
  62 struct gmx_domdec_t;
  63 struct gmx_mtop_t;
  64 struct gmx_output_env_t;
  65 struct t_commrec;
  66 struct t_filenm;
  67 struct t_inputrec;
  68
  69 /*! \brief Applies essential dynamics constrains as defined in the .edi input file.
  70  *
  71  * \param ir                MD input parameter record.
  72  * \param step              Number of the time step.
  73  * \param cr                Data needed for MPI communication.
  74  * \param xs                The local positions on this processor.
  75  * \param v                 The local velocities.
  76  * \param box               The simulation box.
  77  * \param ed                The essential dynamics data.
  78  */
  79 void do_edsam(const t_inputrec *ir, gmx_int64_t step,
  80               t_commrec *cr, rvec xs[], rvec v[], matrix box, gmx_edsam_t ed);
  81
  82
  83 /*! \brief Reads in the .edi file containing the essential dynamics (ED) and flooding data.
  84  *
  85  * This function opens the ED input and output files, reads in all datasets it finds
  86  * in the input file, and cross-checks whether the .edi file information is consistent
  87  * with the ED data found in the checkpoint file (if present).
  88  * gmx make_edi can be used to create an .edi input file.
  89  *
  90  * \param natoms            Number of atoms of the whole MD system.
  91  * \param oh                Observables history, contains ED observables history
  92  * \param nfile             Number of entries (files) in the fnm structure.
  93  * \param fnm               The filenames struct; it contains also the names of the
  94  *                          essential dynamics and flooding in + output files.
  95  * \param Flags             Flags passed over from main, used to determine
  96  *                          whether we are appending.
  97  * \param oenv              Needed to open the output xvgr file.
  98  * \param cr                Data needed for MPI communication.
  99  * \returns                 Pointer to the initialized essential dynamics / flooding data.
 100  */
 101 gmx_edsam_t ed_open(int natoms, struct ObservablesHistory *oh, int nfile, const t_filenm fnm[],
 102                     unsigned long Flags, const gmx_output_env_t *oenv, t_commrec *cr);
 103
 104 /*! \brief Initializes the essential dynamics and flooding module.
 105  *
 106  * \param mtop              Molecular topology.
 107  * \param ir                MD input parameter record.
 108  * \param cr                Data needed for MPI communication.
 109  * \param ed                The essential dynamics data.
 110  * \param x                 Positions of the whole MD system.
 111  * \param box               The simulation box.
 112  * \param EDstate           ED data stored in the checkpoint file.
 113  */
 114 void init_edsam(const gmx_mtop_t *mtop, const t_inputrec *ir, t_commrec *cr,
 115                 gmx_edsam_t ed, rvec x[], matrix box, edsamhistory_t *EDstate);
 116
 117
 118 /*! \brief Make a selection of the home atoms for the ED groups.
 119  *
 120  * Should be called at every domain decomposition.
 121  *
 122  * \param dd                Domain decomposition data.
 123  * \param ed                Essential dynamics and flooding data.
 124  */
 125 void dd_make_local_ed_indices(gmx_domdec_t *dd, gmx_edsam_t ed);
 126
 127
 128 /*! \brief Evaluate the flooding potential(s) and forces as requested in the .edi input file.
 129  *
 130  * \param cr                Data needed for MPI communication.
 131  * \param ir                MD input parameter record.
 132  * \param x                 Positions on the local processor.
 133  * \param force             Forcefield forces to which the flooding forces are added.
 134  * \param ed                The essential dynamics data.
 135  * \param box               The simulation box.
 136  * \param step              Number of the time step.
 137  * \param bNS               Are we in a neighbor searching step?
 138  */
 139 void do_flood(t_commrec *cr, const t_inputrec *ir, rvec x[], rvec force[], gmx_edsam_t ed,
 140               matrix box, gmx_int64_t step, gmx_bool bNS);
 141
 142 /*! \brief Clean up
 143  *
 144  * \param ed                The essential dynamics data
 145  */
 146 void done_ed(gmx_edsam_t *ed);
 147
 148 #endif