src/gromacs/imd/imd.h

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  36
  37 /*! \libinternal
  38  * \defgroup module_imd Interactive molecular dynamics (IMD)
  39  * \ingroup group_mdrun
  40  *
  41  * \brief
  42  * Allows mdrun to interface with VMD via the interactive molecular dynamics
  43  * (IMD) protocol.
  44  *
  45  * \author Martin Hoefling, Carsten Kutzner <ckutzne@gwdg.de>
  46  *
  47  * \todo Rename the directory, source and test files to
  48  * interactive_md, and prefer type names like
  49  * InteractiveMDSession. Avoid ambiguity with IMDModule.
  50  */
  51
  52 /*! \libinternal \file
  53  *
  54  * \brief This file declares the class that coordinates with VMD via
  55  * the Interactive Molecular Dynamics protocol, along with supporting
  56  * free functions.
  57  *
  58  * \author Martin Hoefling, Carsten Kutzner <ckutzne@gwdg.de>
  59  *
  60  * \inlibraryapi
  61  * \ingroup module_imd
  62  */
  63
  64 #ifndef GMX_IMD_IMD_H
  65 #define GMX_IMD_IMD_H
  66
  67 #include <memory>
  68
  69 #include "gromacs/math/vectypes.h"
  70 #include "gromacs/utility/basedefinitions.h"
  71 #include "gromacs/utility/classhelpers.h"
  72
  73 struct gmx_domdec_t;
  74 struct gmx_enerdata_t;
  75 struct gmx_mtop_t;
  76 struct gmx_multisim_t;
  77 struct gmx_output_env_t;
  78 struct gmx_wallcycle;
  79 struct t_commrec;
  80 struct t_filenm;
  81 struct t_IMD;
  82 struct t_inputrec;
  83 class t_state;
  84
  85 namespace gmx
  86 {
  87 enum class StartingBehavior;
  88 class IMDModule;
  89 class ImdSession;
  90 class InteractiveMolecularDynamics;
  91 class MDLogger;
  92 struct ImdOptions;
  93 struct MdrunOptions;
  94
  95 /*! \brief
  96  * Creates a module for interactive molecular dynamics.
  97  */
  98 std::unique_ptr<IMDModule> createInteractiveMolecularDynamicsModule();
  99
 100 static const char IMDstr[] = "IMD:"; /**< Tag output from the IMD module with this string. */
 101
 102 /*! \brief Writes out the group of atoms selected for interactive manipulation.
 103  *
 104  * Called by grompp.
 105  * The resulting file has to be read in by VMD if one wants it to connect to mdrun.
 106  *
 107  * \param bIMD    Only springs into action if bIMD is TRUE. Otherwise returns directly.
 108  * \param ir      Structure containing MD input parameters, among those
 109  *                the IMD data structure.
 110  * \param state   The current state of the MD system.
 111  * \param sys     The global, complete system topology.
 112  * \param nfile   Number of files.
 113  * \param fnm     Filename struct.
 114  */
 115 void write_IMDgroup_to_file(bool              bIMD,
 116                             t_inputrec*       ir,
 117                             const t_state*    state,
 118                             const gmx_mtop_t* sys,
 119                             int               nfile,
 120                             const t_filenm    fnm[]);
 121
 122
 123 /*! \brief Makes and returns an initialized IMD session, which may be inactive.
 124  *
 125  * This function is called before the main MD loop over time steps.
 126  *
 127  * \param ir           The inputrec structure containing the MD input parameters
 128  * \param cr           Information structure for MPI communication.
 129  * \param wcycle       Count wallcycles of IMD routines for diagnostic output.
 130  * \param enerd        Contains the GROMACS energies for the different interaction types.
 131  * \param ms           Handler for multi-simulations.
 132  * \param top_global   The topology of the whole system.
 133  * \param mdlog        Logger
 134  * \param x            The starting positions of the atoms.
 135  * \param nfile        Number of files.
 136  * \param fnm          Struct containing file names etc.
 137  * \param oenv         Output options.
 138  * \param options      Options for interactive MD.
 139  * \param startingBehavior  Describes whether this is a restart appending to output files
 140  */
 141 std::unique_ptr<ImdSession> makeImdSession(const t_inputrec*       ir,
 142                                            const t_commrec*        cr,
 143                                            gmx_wallcycle*          wcycle,
 144                                            gmx_enerdata_t*         enerd,
 145                                            const gmx_multisim_t*   ms,
 146                                            const gmx_mtop_t*       top_global,
 147                                            const MDLogger&         mdlog,
 148                                            const rvec              x[],
 149                                            int                     nfile,
 150                                            const t_filenm          fnm[],
 151                                            const gmx_output_env_t* oenv,
 152                                            const ImdOptions&       options,
 153                                            StartingBehavior        startingBehavior);
 154
 155 class ImdSession
 156 {
 157 private:
 158     //! Private constructor, to force the use of makeImdSession()
 159     ImdSession(const MDLogger& mdlog);
 160
 161 public:
 162     ~ImdSession();
 163
 164     /*! \brief Make a selection of the home atoms for the IMD group.
 165      *
 166      * Should be called at every domain decomposition.
 167      * Each node checks which of the atoms from "ind" are local and puts its local
 168      * atom numbers into the "ind_local" array. Furthermore, in "xa_ind" it is
 169      * stored at which position each local atom belongs in the assembled/collective
 170      * array, so that on the master node all positions can be merged into the
 171      * assembled array correctly.
 172      *
 173      * \param dd          Structure containing domain decomposition data.
 174      */
 175     void dd_make_local_IMD_atoms(const gmx_domdec_t* dd);
 176
 177     /*! \brief Prepare to do IMD if required in this time step
 178      * Also checks for new IMD connection and syncs the nodes.
 179      *
 180      * \param step         The time step.
 181      * \param bNS          Is this a neighbor searching step?
 182      * \param box          The simulation box.
 183      * \param x            The local atomic positions on this node.
 184      * \param t            The time.
 185      *
 186      * \returns            Whether or not we have to do IMD communication at this step.
 187      */
 188     bool run(int64_t step, bool bNS, const matrix box, const rvec x[], double t);
 189
 190     /*! \brief Add external forces from a running interactive molecular dynamics session.
 191      *
 192      * \param f            The forces.
 193      */
 194     void applyForces(rvec* f);
 195
 196     /*! \brief Copy energies and convert to float from enerdata to the IMD energy record.
 197      *
 198      * We do no conversion, so units in client are SI!
 199      *
 200      * \param step             The time step.
 201      * \param bHaveNewEnergies Only copy energies if we have done global summing of them before.
 202      */
 203     void fillEnergyRecord(int64_t step, bool bHaveNewEnergies);
 204
 205     /*! \brief Send positions and energies to the client. */
 206     void sendPositionsAndEnergies();
 207
 208     /*! \brief Updates the energy record sent to VMD if needed, and sends positions and energies.
 209      *
 210      * \param bIMDstep         If true, transfer the positions. Otherwise just update the time step and potentially the energy record.
 211      * \param step             The time step.
 212      * \param bHaveNewEnergies Update the energy record if we have done global summing of the energies.
 213      */
 214     void updateEnergyRecordAndSendPositionsAndEnergies(bool bIMDstep, int64_t step, bool bHaveNewEnergies);
 215
 216 private:
 217     //! Implementation type.
 218     class Impl;
 219     //! Implementation object.
 220     PrivateImplPointer<Impl> impl_;
 221
 222 public:
 223     // Befriend the factory function.
 224     friend std::unique_ptr<ImdSession> makeImdSession(const t_inputrec*       ir,
 225                                                       const t_commrec*        cr,
 226                                                       gmx_wallcycle*          wcycle,
 227                                                       gmx_enerdata_t*         enerd,
 228                                                       const gmx_multisim_t*   ms,
 229                                                       const gmx_mtop_t*       top_global,
 230                                                       const MDLogger&         mdlog,
 231                                                       const rvec              x[],
 232                                                       int                     nfile,
 233                                                       const t_filenm          fnm[],
 234                                                       const gmx_output_env_t* oenv,
 235                                                       const ImdOptions&       options,
 236                                                       StartingBehavior        startingBehavior);
 237 };
 238
 239 } // namespace gmx
 240
 241 #endif