src/gromacs/mdlib/update.h

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  38 #ifndef GMX_MDLIB_UPDATE_H
  39 #define GMX_MDLIB_UPDATE_H
  40
  41 #include "gromacs/math/paddedvector.h"
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/mdtypes/md_enums.h"
  44 #include "gromacs/timing/wallcycle.h"
  45 #include "gromacs/utility/arrayref.h"
  46 #include "gromacs/utility/basedefinitions.h"
  47 #include "gromacs/utility/classhelpers.h"
  48 #include "gromacs/utility/real.h"
  49
  50 class ekinstate_t;
  51 struct gmx_ekindata_t;
  52 struct gmx_enerdata_t;
  53 enum class PbcType;
  54 struct t_fcdata;
  55 struct t_graph;
  56 struct t_grpopts;
  57 struct t_inputrec;
  58 struct t_mdatoms;
  59 struct t_nrnb;
  60 class t_state;
  61
  62 namespace gmx
  63 {
  64 class BoxDeformation;
  65 class Constraints;
  66
  67
  68 /*! \libinternal
  69  * \brief Contains data for update phase */
  70 class Update
  71 {
  72 public:
  73     /*! \brief Constructor
  74      *
  75      * \param[in] inputRecord     Input record, used to construct SD object.
  76      * \param[in] boxDeformation  Periodic box deformation object.
  77      */
  78     Update(const t_inputrec& inputRecord, BoxDeformation* boxDeformation);
  79     //! Destructor
  80     ~Update();
  81     /*! \brief Get the pointer to updated coordinates
  82      *
  83      * Update saves the updated coordinates into separate buffer, so that constraints will have
  84      * access to both updated and not update coordinates. For that, update owns a separate buffer.
  85      * See finish_update(...) for details.
  86      *
  87      * \returns The pointer to the intermediate coordinates buffer.
  88      */
  89     PaddedVector<gmx::RVec>* xp();
  90     /*!\brief Getter to local copy of box deformation class.
  91      *
  92      * \returns handle to box deformation class
  93      */
  94     BoxDeformation* deform() const;
  95     /*! \brief Resizes buffer that stores intermediate coordinates.
  96      *
  97      * \param[in] numAtoms  Updated number of atoms.
  98      */
  99     void setNumAtoms(int numAtoms);
 100
 101     /*! \brief Perform numerical integration step.
 102      *
 103      * Selects the appropriate integrator, based on the input record and performs a numerical integration step.
 104      *
 105      * \param[in]  inputRecord      Input record.
 106      * \param[in]  step             Current timestep.
 107      * \param[in]  md               MD atoms data.
 108      * \param[in]  state            System state object.
 109      * \param[in]  f                Buffer with atomic forces for home particles.
 110      * \param[in]  fcdata           Force calculation data to update distance and orientation restraints.
 111      * \param[in]  ekind            Kinetic energy data (for temperature coupling, energy groups, etc.).
 112      * \param[in]  M                Parrinello-Rahman velocity scaling matrix.
 113      * \param[in]  updatePart       What should be updated, coordinates or velocities. This enum only used in VV integrator.
 114      * \param[in]  cr               Comunication record  (Old comment: these shouldn't be here -- need to think about it).
 115      * \param[in]  haveConstraints  If the system has constraints.
 116      */
 117     void update_coords(const t_inputrec&                                inputRecord,
 118                        int64_t                                          step,
 119                        const t_mdatoms*                                 md,
 120                        t_state*                                         state,
 121                        const gmx::ArrayRefWithPadding<const gmx::RVec>& f,
 122                        const t_fcdata&                                  fcdata,
 123                        const gmx_ekindata_t*                            ekind,
 124                        const matrix                                     M,
 125                        int                                              updatePart,
 126                        const t_commrec*                                 cr,
 127                        bool                                             haveConstraints);
 128
 129     /*! \brief Finalize the coordinate update.
 130      *
 131      * Copy the updated coordinates to the main coordinates buffer for the atoms that are not frozen.
 132      *
 133      * \param[in]  inputRecord      Input record.
 134      * \param[in]  md               MD atoms data.
 135      * \param[in]  state            System state object.
 136      * \param[in]  wcycle           Wall-clock cycle counter.
 137      * \param[in]  haveConstraints  If the system has constraints.
 138      */
 139     void finish_update(const t_inputrec& inputRecord,
 140                        const t_mdatoms*  md,
 141                        t_state*          state,
 142                        gmx_wallcycle_t   wcycle,
 143                        bool              haveConstraints);
 144
 145     /*! \brief Secong part of the SD integrator.
 146      *
 147      * The first part of integration is performed in the update_coords(...) method.
 148      *
 149      * \param[in]  inputRecord  Input record.
 150      * \param[in]  step         Current timestep.
 151      * \param[in]  dvdlambda    Free energy derivative. Contribution to be added to the bonded
 152      * interactions. \param[in]  md           MD atoms data. \param[in]  state        System state
 153      * object. \param[in]  cr           Comunication record. \param[in]  nrnb         Cycle
 154      * counters. \param[in]  wcycle       Wall-clock cycle counter. \param[in]  constr Constraints
 155      * object. The constraints are applied on coordinates after update. \param[in]  do_log       If
 156      * this is logging step. \param[in]  do_ene       If this is an energy evaluation step.
 157      */
 158     void update_sd_second_half(const t_inputrec& inputRecord,
 159                                int64_t           step,
 160                                real*             dvdlambda,
 161                                const t_mdatoms*  md,
 162                                t_state*          state,
 163                                const t_commrec*  cr,
 164                                t_nrnb*           nrnb,
 165                                gmx_wallcycle_t   wcycle,
 166                                gmx::Constraints* constr,
 167                                bool              do_log,
 168                                bool              do_ene);
 169     /*! \brief Update pre-computed constants that depend on the reference temperature for coupling.
 170      *
 171      * This could change e.g. in simulated annealing.
 172      *
 173      * \param[in]  inputRecord  Input record.
 174      */
 175     void update_temperature_constants(const t_inputrec& inputRecord);
 176
 177     /*!\brief Getter for the list of the randomize groups.
 178      *
 179      *  Needed for Andersen temperature control.
 180      *
 181      * \returns Reference to the groups from the SD data object.
 182      */
 183     const std::vector<bool>& getAndersenRandomizeGroup() const;
 184     /*!\brief Getter for the list of the Boltzmann factors.
 185      *
 186      *  Needed for Andersen temperature control.
 187      *
 188      * \returns Reference to the Boltzmann factors from the SD data object.
 189      */
 190     const std::vector<real>& getBoltzmanFactor() const;
 191
 192 private:
 193     //! Implementation type.
 194     class Impl;
 195     //! Implementation object.
 196     PrivateImplPointer<Impl> impl_;
 197 };
 198
 199 }; // namespace gmx
 200
 201 /*
 202  * Compute the partial kinetic energy for home particles;
 203  * will be accumulated in the calling routine.
 204  * The tensor is
 205  *
 206  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 207  *
 208  *     use v[i] = v[i] - u[i] when calculating temperature
 209  *
 210  * u must be accumulated already.
 211  *
 212  * Now also computes the contribution of the kinetic energy to the
 213  * free energy
 214  *
 215  */
 216
 217
 218 void init_ekinstate(ekinstate_t* ekinstate, const t_inputrec* ir);
 219
 220 void update_ekinstate(ekinstate_t* ekinstate, const gmx_ekindata_t* ekind);
 221
 222 /*! \brief Restores data from \p ekinstate to \p ekind, then broadcasts it
 223    to the rest of the simulation */
 224 void restore_ekinstate_from_state(const t_commrec* cr, gmx_ekindata_t* ekind, const ekinstate_t* ekinstate);
 225
 226 /*! \brief Computes the atom range for a thread to operate on, ensuring SIMD aligned ranges
 227  *
 228  * \param[in]  numThreads   The number of threads to divide atoms over
 229  * \param[in]  threadIndex  The thread to get the range for
 230  * \param[in]  numAtoms     The total number of atoms (on this rank)
 231  * \param[out] startAtom    The start of the atom range
 232  * \param[out] endAtom      The end of the atom range, note that this is in general not a multiple of the SIMD width
 233  */
 234 void getThreadAtomRange(int numThreads, int threadIndex, int numAtoms, int* startAtom, int* endAtom);
 235
 236 #endif