src/gromacs/imd/imd.h

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  35
  36 /*! \libinternal
  37  * \defgroup module_imd Interactive molecular dynamics (IMD)
  38  * \ingroup group_mdrun
  39  *
  40  * \brief
  41  * Allows mdrun to interface with VMD via the interactive molecular dynamics
  42  * (IMD) protocol.
  43  *
  44  * \author Martin Hoefling, Carsten Kutzner <ckutzne@gwdg.de>
  45  *
  46  */
  47
  48 /*! \libinternal \file
  49  *
  50  * \brief
  51  * This file contains datatypes and function declarations necessary for mdrun
  52  * to interface with VMD via the interactive molecular dynamics protocol.
  53  *
  54  * \author Martin Hoefling, Carsten Kutzner <ckutzne@gwdg.de>
  55  *
  56  * \inlibraryapi
  57  * \ingroup module_imd
  58  */
  59
  60 #ifndef GMX_IMD_IMD_H
  61 #define GMX_IMD_IMD_H
  62
  63 #include "config.h"
  64
  65 #include "gromacs/math/vectypes.h"
  66 #include "gromacs/timing/wallcycle.h"
  67
  68 #if GMX_NATIVE_WINDOWS
  69 #include <Windows.h>
  70 #define NOFLAGS 0
  71 #endif
  72
  73 struct gmx_domdec_t;
  74 struct gmx_enerdata_t;
  75 struct gmx_mtop_t;
  76 struct gmx_output_env_t;
  77 struct t_filenm;
  78 struct t_gmx_IMD;
  79 struct t_IMD;
  80 struct t_inputrec;
  81 struct t_state;
  82
  83 static const char IMDstr[] = "IMD:";  /**< Tag output from the IMD module with this string. */
  84
  85 /*! \brief Writes out the group of atoms selected for interactive manipulation.
  86  *
  87  * Called by grompp.
  88  * The resulting file has to be read in by VMD if one wants it to connect to mdrun.
  89  *
  90  * \param bIMD    Only springs into action if bIMD is TRUE. Otherwise returns directly.
  91  * \param ir      Structure containing MD input parameters, among those
  92  *                the IMD data structure.
  93  * \param state   The current state of the MD system.
  94  * \param sys     The global, complete system topology.
  95  * \param nfile   Number of files.
  96  * \param fnm     Filename struct.
  97  */
  98 void write_IMDgroup_to_file(gmx_bool bIMD, t_inputrec *ir, t_state *state,
  99                             gmx_mtop_t *sys, int nfile, const t_filenm fnm[]);
 100
 101
 102 /*! \brief Make a selection of the home atoms for the IMD group.
 103  *
 104  * Should be called at every domain decomposition.
 105  * Each node checks which of the atoms from "ind" are local and puts its local
 106  * atom numbers into the "ind_local" array. Furthermore, in "xa_ind" it is
 107  * stored at which position each local atom belongs in the assembled/collective
 108  * array, so that on the master node all positions can be merged into the
 109  * assembled array correctly.
 110  *
 111  * \param bIMD    Only springs into action if bIMD is TRUE. Otherwise returns directly.
 112  * \param dd      Structure containing domain decomposition data.
 113  * \param imd     The IMD group of atoms.
 114  */
 115 void dd_make_local_IMD_atoms(gmx_bool bIMD, gmx_domdec_t *dd, t_IMD *imd);
 116
 117
 118 /*! \brief Initializes (or disables) IMD.
 119  *
 120  * This function is called before the main MD loop over time steps,
 121  * and it must be called prior to any call to dd_partition_system if in parallel.
 122  *
 123  * \param ir           The inputrec structure containing the MD input parameters
 124  *                     including a pointer to the IMD data structure.
 125  * \param cr           Information structure for MPI communication.
 126  * \param top_global   The topology of the whole system.
 127  * \param fplog        General output file, normally md.log.
 128  * \param defnstimd    Default IMD update (=communication) frequency.
 129  * \param x            The starting positions of the atoms.
 130  * \param nfile        Number of files.
 131  * \param fnm          Struct containing file names etc.
 132  * \param oenv         Output options.
 133  * \param imdport      Port to use for IMD connections.
 134  * \param Flags        Flags passed over from main, used to determine
 135  *                     whether or not we are appending.
 136  */
 137 void init_IMD(t_inputrec *ir, t_commrec *cr, gmx_mtop_t *top_global,
 138               FILE *fplog, int defnstimd, rvec x[],
 139               int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv,
 140               int imdport, unsigned long  Flags);
 141
 142
 143 /*! \brief IMD required in this time step?
 144  * Also checks for new IMD connection and syncs the nodes.
 145  *
 146  * \param bIMD         Only springs into action if bIMD is TRUE. Otherwise returns directly.
 147  * \param step         The time step.
 148  * \param cr           Information structure for MPI communication.
 149  * \param bNS          Is this a neighbor searching step?
 150  * \param box          The simulation box.
 151  * \param x            The local atomic positions on this node.
 152  * \param ir           The inputrec structure containing the MD input parameters
 153  *                     including a pointer to the IMD data structure.
 154  * \param t            The time.
 155  * \param wcycle       Count wallcycles of IMD routines for diagnostic output.
 156  *
 157  * \returns            Whether or not we have to do IMD communication at this step.
 158  */
 159 gmx_bool do_IMD(gmx_bool bIMD, gmx_int64_t step, t_commrec *cr,
 160                 gmx_bool bNS,
 161                 matrix box, rvec x[], t_inputrec *ir, double t,
 162                 gmx_wallcycle_t wcycle);
 163
 164
 165 /*! \brief Get the IMD update frequency.
 166  *
 167  * \param IMDsetup     Opaque pointer to IMD private data.
 168  *
 169  * \returns            The current IMD update/communication frequency
 170  */
 171 int IMD_get_step(t_gmx_IMD *IMDsetup);
 172
 173
 174 /*! \brief Add external forces from a running interactive molecular dynamics session.
 175  *
 176  * \param bIMD         Returns directly if bIMD is FALSE.
 177  * \param imd          The IMD data structure.
 178  * \param cr           Information structure for MPI communication.
 179  * \param f            The forces.
 180  * \param wcycle       Count wallcycles of IMD routines for diagnostic output.
 181  */
 182 void IMD_apply_forces(gmx_bool bIMD, t_IMD *imd,
 183                       t_commrec *cr, rvec *f,
 184                       gmx_wallcycle_t wcycle);
 185
 186
 187 /*! \brief Copy energies and convert to float from enerdata to the IMD energy record.
 188  *
 189  * We do no conversion, so units in client are SI!
 190  *
 191  * \param bIMD             Only springs into action if bIMD is TRUE. Otherwise returns directly.
 192  * \param imd              The IMD data structure.
 193  * \param enerd            Contains the GROMACS energies for the different interaction types.
 194  * \param step             The time step.
 195  * \param bHaveNewEnergies Only copy energies if we have done global summing of them before.
 196  *
 197  */
 198 void IMD_fill_energy_record(gmx_bool bIMD, t_IMD *imd, gmx_enerdata_t *enerd,
 199                             gmx_int64_t step, gmx_bool bHaveNewEnergies);
 200
 201
 202 /*! \brief Send positions and energies to the client.
 203  *
 204  * \param imd              The IMD data structure.
 205  */
 206 void IMD_send_positions(t_IMD *imd);
 207
 208
 209 /*! \brief Calls IMD_prepare_energies() and then IMD_send_positions().
 210  *
 211  * \param bIMD             Returns directly if bIMD is FALSE.
 212  * \param bIMDstep         If true, transfer the positions. Otherwise just update the time step and potentially the energy record.
 213  * \param imd              The IMD data structure.
 214  * \param enerd            Contains the GROMACS energies for the different interaction types.
 215  * \param step             The time step.
 216  * \param bHaveNewEnergies Only update the energy record if we have done global summing of the energies.
 217  * \param wcycle           Count wallcycles of IMD routines for diagnostic output.
 218  *
 219  */
 220 void IMD_prep_energies_send_positions(gmx_bool bIMD, gmx_bool bIMDstep,
 221                                       t_IMD *imd, gmx_enerdata_t *enerd,
 222                                       gmx_int64_t step, gmx_bool bHaveNewEnergies,
 223                                       gmx_wallcycle_t wcycle);
 224
 225 /*! \brief Finalize IMD and do some cleaning up.
 226  *
 227  * Currently, IMD finalize closes the force output file.
 228  *
 229  * \param bIMD         Returns directly if bIMD is FALSE.
 230  * \param imd          The IMD data structure.
 231  */
 232 void IMD_finalize(gmx_bool bIMD, t_IMD *imd);
 233
 234 #endif