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 <cstdio>
  66
  67 #include "gromacs/math/vectypes.h"
  68 #include "gromacs/utility/basedefinitions.h"
  69
  70
  71 #if GMX_NATIVE_WINDOWS
  72 #include <Windows.h>
  73 #define NOFLAGS 0
  74 #endif
  75
  76 struct gmx_domdec_t;
  77 struct gmx_enerdata_t;
  78 struct gmx_mtop_t;
  79 struct gmx_multisim_t;
  80 struct gmx_output_env_t;
  81 struct gmx_wallcycle;
  82 struct MdrunOptions;
  83 struct t_commrec;
  84 struct t_filenm;
  85 struct t_gmx_IMD;
  86 struct t_IMD;
  87 struct t_inputrec;
  88 class t_state;
  89
  90 static const char IMDstr[] = "IMD:";  /**< Tag output from the IMD module with this string. */
  91
  92 /*! \brief Writes out the group of atoms selected for interactive manipulation.
  93  *
  94  * Called by grompp.
  95  * The resulting file has to be read in by VMD if one wants it to connect to mdrun.
  96  *
  97  * \param bIMD    Only springs into action if bIMD is TRUE. Otherwise returns directly.
  98  * \param ir      Structure containing MD input parameters, among those
  99  *                the IMD data structure.
 100  * \param state   The current state of the MD system.
 101  * \param sys     The global, complete system topology.
 102  * \param nfile   Number of files.
 103  * \param fnm     Filename struct.
 104  */
 105 void write_IMDgroup_to_file(gmx_bool bIMD, t_inputrec *ir, const t_state *state,
 106                             const gmx_mtop_t *sys, int nfile, const t_filenm fnm[]);
 107
 108
 109 /*! \brief Make a selection of the home atoms for the IMD group.
 110  *
 111  * Should be called at every domain decomposition.
 112  * Each node checks which of the atoms from "ind" are local and puts its local
 113  * atom numbers into the "ind_local" array. Furthermore, in "xa_ind" it is
 114  * stored at which position each local atom belongs in the assembled/collective
 115  * array, so that on the master node all positions can be merged into the
 116  * assembled array correctly.
 117  *
 118  * \param bIMD    Only springs into action if bIMD is TRUE. Otherwise returns directly.
 119  * \param dd      Structure containing domain decomposition data.
 120  * \param imd     The IMD group of atoms.
 121  */
 122 void dd_make_local_IMD_atoms(gmx_bool bIMD, const gmx_domdec_t *dd, t_IMD *imd);
 123
 124
 125 /*! \brief Initializes (or disables) IMD.
 126  *
 127  * This function is called before the main MD loop over time steps.
 128  *
 129  * \param ir           The inputrec structure containing the MD input parameters
 130  *                     including a pointer to the IMD data structure.
 131  * \param cr           Information structure for MPI communication.
 132  * \param ms           Handler for multi-simulations.
 133  * \param top_global   The topology of the whole system.
 134  * \param fplog        General output file, normally md.log.
 135  * \param defnstimd    Default IMD update (=communication) frequency.
 136  * \param x            The starting positions of the atoms.
 137  * \param nfile        Number of files.
 138  * \param fnm          Struct containing file names etc.
 139  * \param oenv         Output options.
 140  * \param mdrunOptions Options for mdrun.
 141  */
 142 void init_IMD(t_inputrec *ir, const t_commrec *cr,
 143               const gmx_multisim_t *ms,
 144               const gmx_mtop_t *top_global,
 145               FILE *fplog, int defnstimd, const rvec x[],
 146               int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv,
 147               const MdrunOptions &mdrunOptions);
 148
 149
 150 /*! \brief IMD required in this time step?
 151  * Also checks for new IMD connection and syncs the nodes.
 152  *
 153  * \param bIMD         Only springs into action if bIMD is TRUE. Otherwise returns directly.
 154  * \param step         The time step.
 155  * \param cr           Information structure for MPI communication.
 156  * \param bNS          Is this a neighbor searching step?
 157  * \param box          The simulation box.
 158  * \param x            The local atomic positions on this node.
 159  * \param ir           The inputrec structure containing the MD input parameters
 160  *                     including a pointer to the IMD data structure.
 161  * \param t            The time.
 162  * \param wcycle       Count wallcycles of IMD routines for diagnostic output.
 163  *
 164  * \returns            Whether or not we have to do IMD communication at this step.
 165  */
 166 gmx_bool do_IMD(gmx_bool bIMD, int64_t step, const t_commrec *cr,
 167                 gmx_bool bNS,
 168                 const matrix box, const rvec x[], t_inputrec *ir, double t,
 169                 gmx_wallcycle *wcycle);
 170
 171
 172 /*! \brief Get the IMD update frequency.
 173  *
 174  * \param IMDsetup     Opaque pointer to IMD private data.
 175  *
 176  * \returns            The current IMD update/communication frequency
 177  */
 178 int IMD_get_step(t_gmx_IMD *IMDsetup);
 179
 180
 181 /*! \brief Add external forces from a running interactive molecular dynamics session.
 182  *
 183  * \param bIMD         Returns directly if bIMD is FALSE.
 184  * \param imd          The IMD data structure.
 185  * \param cr           Information structure for MPI communication.
 186  * \param f            The forces.
 187  * \param wcycle       Count wallcycles of IMD routines for diagnostic output.
 188  */
 189 void IMD_apply_forces(gmx_bool bIMD, t_IMD *imd,
 190                       const t_commrec *cr, rvec *f,
 191                       gmx_wallcycle *wcycle);
 192
 193
 194 /*! \brief Copy energies and convert to float from enerdata to the IMD energy record.
 195  *
 196  * We do no conversion, so units in client are SI!
 197  *
 198  * \param bIMD             Only springs into action if bIMD is TRUE. Otherwise returns directly.
 199  * \param imd              The IMD data structure.
 200  * \param enerd            Contains the GROMACS energies for the different interaction types.
 201  * \param step             The time step.
 202  * \param bHaveNewEnergies Only copy energies if we have done global summing of them before.
 203  *
 204  */
 205 void IMD_fill_energy_record(gmx_bool bIMD, t_IMD *imd, const gmx_enerdata_t *enerd,
 206                             int64_t step, gmx_bool bHaveNewEnergies);
 207
 208
 209 /*! \brief Send positions and energies to the client.
 210  *
 211  * \param imd              The IMD data structure.
 212  */
 213 void IMD_send_positions(t_IMD *imd);
 214
 215
 216 /*! \brief Calls IMD_prepare_energies() and then IMD_send_positions().
 217  *
 218  * \param bIMD             Returns directly if bIMD is FALSE.
 219  * \param bIMDstep         If true, transfer the positions. Otherwise just update the time step and potentially the energy record.
 220  * \param imd              The IMD data structure.
 221  * \param enerd            Contains the GROMACS energies for the different interaction types.
 222  * \param step             The time step.
 223  * \param bHaveNewEnergies Only update the energy record if we have done global summing of the energies.
 224  * \param wcycle           Count wallcycles of IMD routines for diagnostic output.
 225  *
 226  */
 227 void IMD_prep_energies_send_positions(gmx_bool bIMD, gmx_bool bIMDstep,
 228                                       t_IMD *imd, const gmx_enerdata_t *enerd,
 229                                       int64_t step, gmx_bool bHaveNewEnergies,
 230                                       gmx_wallcycle *wcycle);
 231
 232 /*! \brief Finalize IMD and do some cleaning up.
 233  *
 234  * Currently, IMD finalize closes the force output file.
 235  *
 236  * \param bIMD         Returns directly if bIMD is FALSE.
 237  * \param imd          The IMD data structure.
 238  */
 239 void IMD_finalize(gmx_bool bIMD, t_IMD *imd);
 240
 241 #endif