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  * \todo Rename the directory, source and test files to
  47  * interactive_md, and prefer type names like
  48  * InteractiveMDSession. Avoid ambiguity with IMDModule.
  49  */
  50
  51 /*! \libinternal \file
  52  *
  53  * \brief This file declares the class that coordinates with VMD via
  54  * the Interactive Molecular Dynamics protocol, along with supporting
  55  * free functions.
  56  *
  57  * \author Martin Hoefling, Carsten Kutzner <ckutzne@gwdg.de>
  58  *
  59  * \inlibraryapi
  60  * \ingroup module_imd
  61  */
  62
  63 #ifndef GMX_IMD_IMD_H
  64 #define GMX_IMD_IMD_H
  65
  66 #include <memory>
  67
  68 #include "gromacs/math/vectypes.h"
  69 #include "gromacs/utility/basedefinitions.h"
  70 #include "gromacs/utility/classhelpers.h"
  71
  72 struct gmx_domdec_t;
  73 struct gmx_enerdata_t;
  74 struct gmx_mtop_t;
  75 struct gmx_multisim_t;
  76 struct gmx_output_env_t;
  77 struct gmx_wallcycle;
  78 struct t_commrec;
  79 struct t_filenm;
  80 struct t_IMD;
  81 struct t_inputrec;
  82 class t_state;
  83
  84 namespace gmx
  85 {
  86 enum class StartingBehavior;
  87 class IMDModule;
  88 class ImdSession;
  89 class InteractiveMolecularDynamics;
  90 class MDLogger;
  91 struct ImdOptions;
  92 struct MdrunOptions;
  93
  94 /*! \brief
  95  * Creates a module for interactive molecular dynamics.
  96  */
  97 std::unique_ptr<IMDModule> createInteractiveMolecularDynamicsModule();
  98
  99 static const char IMDstr[] = "IMD:"; /**< Tag output from the IMD module with this string. */
 100
 101 /*! \brief Writes out the group of atoms selected for interactive manipulation.
 102  *
 103  * Called by grompp.
 104  * The resulting file has to be read in by VMD if one wants it to connect to mdrun.
 105  *
 106  * \param bIMD    Only springs into action if bIMD is TRUE. Otherwise returns directly.
 107  * \param ir      Structure containing MD input parameters, among those
 108  *                the IMD data structure.
 109  * \param state   The current state of the MD system.
 110  * \param sys     The global, complete system topology.
 111  * \param nfile   Number of files.
 112  * \param fnm     Filename struct.
 113  */
 114 void write_IMDgroup_to_file(bool bIMD, t_inputrec *ir, const t_state *state,
 115                             const gmx_mtop_t *sys, int nfile, const t_filenm fnm[]);
 116
 117
 118 /*! \brief Makes and returns an initialized IMD session, which may be inactive.
 119  *
 120  * This function is called before the main MD loop over time steps.
 121  *
 122  * \param ir           The inputrec structure containing the MD input parameters
 123  * \param cr           Information structure for MPI communication.
 124  * \param wcycle       Count wallcycles of IMD routines for diagnostic output.
 125  * \param enerd        Contains the GROMACS energies for the different interaction types.
 126  * \param ms           Handler for multi-simulations.
 127  * \param top_global   The topology of the whole system.
 128  * \param mdlog        Logger
 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 options      Options for interactive MD.
 134  * \param startingBehavior  Describes whether this is a restart appending to output files
 135  */
 136 std::unique_ptr<ImdSession>
 137 makeImdSession(const t_inputrec       *ir,
 138                const t_commrec        *cr,
 139                gmx_wallcycle          *wcycle,
 140                gmx_enerdata_t         *enerd,
 141                const gmx_multisim_t   *ms,
 142                const gmx_mtop_t       *top_global,
 143                const MDLogger         &mdlog,
 144                const rvec              x[],
 145                int                     nfile,
 146                const t_filenm          fnm[],
 147                const gmx_output_env_t *oenv,
 148                const ImdOptions       &options,
 149                StartingBehavior        startingBehavior);
 150
 151 class ImdSession
 152 {
 153     private:
 154         //! Private constructor, to force the use of makeImdSession()
 155         ImdSession(const MDLogger &mdlog);
 156     public:
 157         ~ImdSession();
 158
 159         /*! \brief Make a selection of the home atoms for the IMD group.
 160          *
 161          * Should be called at every domain decomposition.
 162          * Each node checks which of the atoms from "ind" are local and puts its local
 163          * atom numbers into the "ind_local" array. Furthermore, in "xa_ind" it is
 164          * stored at which position each local atom belongs in the assembled/collective
 165          * array, so that on the master node all positions can be merged into the
 166          * assembled array correctly.
 167          *
 168          * \param dd          Structure containing domain decomposition data.
 169          */
 170         void dd_make_local_IMD_atoms(const gmx_domdec_t *dd);
 171
 172         /*! \brief Prepare to do IMD if required in this time step
 173          * Also checks for new IMD connection and syncs the nodes.
 174          *
 175          * \param step         The time step.
 176          * \param bNS          Is this a neighbor searching step?
 177          * \param box          The simulation box.
 178          * \param x            The local atomic positions on this node.
 179          * \param t            The time.
 180          *
 181          * \returns            Whether or not we have to do IMD communication at this step.
 182          */
 183         bool run(int64_t      step,
 184                  bool         bNS,
 185                  const matrix box,
 186                  const rvec   x[],
 187                  double       t);
 188
 189         /*! \brief Add external forces from a running interactive molecular dynamics session.
 190          *
 191          * \param f            The forces.
 192          */
 193         void applyForces(rvec *f);
 194
 195         /*! \brief Copy energies and convert to float from enerdata to the IMD energy record.
 196          *
 197          * We do no conversion, so units in client are SI!
 198          *
 199          * \param step             The time step.
 200          * \param bHaveNewEnergies Only copy energies if we have done global summing of them before.
 201          */
 202         void fillEnergyRecord(int64_t step,
 203                               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,
 215                                                            int64_t step,
 216                                                            bool    bHaveNewEnergies);
 217
 218     private:
 219         //! Implementation type.
 220         class Impl;
 221         //! Implementation object.
 222         PrivateImplPointer<Impl> impl_;
 223
 224     public:
 225         // Befriend the factory function.
 226         friend std::unique_ptr<ImdSession>
 227         makeImdSession(const t_inputrec       *ir,
 228                        const t_commrec        *cr,
 229                        gmx_wallcycle          *wcycle,
 230                        gmx_enerdata_t         *enerd,
 231                        const gmx_multisim_t   *ms,
 232                        const gmx_mtop_t       *top_global,
 233                        const MDLogger         &mdlog,
 234                        const rvec              x[],
 235                        int                     nfile,
 236                        const t_filenm          fnm[],
 237                        const gmx_output_env_t *oenv,
 238                        const ImdOptions       &options,
 239                        StartingBehavior        startingBehavior);
 240 };
 241
 242 } // namespace gmx
 243
 244 #endif