src/gromacs/mdlib/update.h

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  37 #ifndef GMX_MDLIB_UPDATE_H
  38 #define GMX_MDLIB_UPDATE_H
  39
  40 #include "gromacs/math/paddedvector.h"
  41 #include "gromacs/math/vectypes.h"
  42 #include "gromacs/mdtypes/md_enums.h"
  43 #include "gromacs/timing/wallcycle.h"
  44 #include "gromacs/utility/arrayref.h"
  45 #include "gromacs/utility/basedefinitions.h"
  46 #include "gromacs/utility/classhelpers.h"
  47 #include "gromacs/utility/real.h"
  48
  49 class ekinstate_t;
  50 struct gmx_ekindata_t;
  51 struct gmx_enerdata_t;
  52 struct t_extmass;
  53 struct t_fcdata;
  54 struct t_graph;
  55 struct t_grpopts;
  56 struct t_inputrec;
  57 struct t_mdatoms;
  58 struct t_nrnb;
  59 class t_state;
  60
  61 /* Abstract type for update */
  62 struct gmx_stochd_t;
  63
  64 namespace gmx
  65 {
  66 class BoxDeformation;
  67 class Constraints;
  68
  69
  70 /*! \libinternal
  71  * \brief Contains data for update phase */
  72 class Update
  73 {
  74 public:
  75     //! Constructor
  76     Update(const t_inputrec* ir, BoxDeformation* boxDeformation);
  77     ~Update();
  78     // TODO Get rid of getters when more free functions are incorporated as member methods
  79     //! Returns handle to stochd_t struct
  80     gmx_stochd_t* sd() const;
  81     //! Returns pointer to PaddedVector xp
  82     PaddedVector<gmx::RVec>* xp();
  83     //! Returns handle to box deformation class
  84     BoxDeformation* deform() const;
  85     //! Resizes xp
  86     void setNumAtoms(int nAtoms);
  87
  88 private:
  89     //! Implementation type.
  90     class Impl;
  91     //! Implementation object.
  92     PrivateImplPointer<Impl> impl_;
  93 };
  94
  95 }; // namespace gmx
  96
  97 /* Update pre-computed constants that depend on the reference
  98  * temperature for coupling.
  99  *
 100  * This could change e.g. in simulated annealing. */
 101 void update_temperature_constants(gmx_stochd_t* sd, const t_inputrec* ir);
 102
 103 /* Update the size of per-atom arrays (e.g. after DD re-partitioning,
 104    which might increase the number of home atoms). */
 105
 106 void update_tcouple(int64_t           step,
 107                     const t_inputrec* inputrec,
 108                     t_state*          state,
 109                     gmx_ekindata_t*   ekind,
 110                     const t_extmass*  MassQ,
 111                     const t_mdatoms*  md);
 112
 113 /* Update Parrinello-Rahman, to be called before the coordinate update */
 114 void update_pcouple_before_coordinates(FILE*             fplog,
 115                                        int64_t           step,
 116                                        const t_inputrec* inputrec,
 117                                        t_state*          state,
 118                                        matrix            parrinellorahmanMu,
 119                                        matrix            M,
 120                                        gmx_bool          bInitStep);
 121
 122 /* Update the box, to be called after the coordinate update.
 123  * For Berendsen P-coupling, also calculates the scaling factor
 124  * and scales the coordinates.
 125  * When the deform option is used, scales coordinates and box here.
 126  */
 127 void update_pcouple_after_coordinates(FILE*             fplog,
 128                                       int64_t           step,
 129                                       const t_inputrec* inputrec,
 130                                       const t_mdatoms*  md,
 131                                       const matrix      pressure,
 132                                       const matrix      forceVirial,
 133                                       const matrix      constraintVirial,
 134                                       matrix            pressureCouplingMu,
 135                                       t_state*          state,
 136                                       t_nrnb*           nrnb,
 137                                       gmx::Update*      upd,
 138                                       bool              scaleCoordinates);
 139
 140 void update_coords(int64_t           step,
 141                    const t_inputrec* inputrec, /* input record and box stuff    */
 142                    const t_mdatoms*  md,
 143                    t_state*          state,
 144                    gmx::ArrayRefWithPadding<const gmx::RVec> f, /* forces on home particles */
 145                    const t_fcdata*                           fcd,
 146                    const gmx_ekindata_t*                     ekind,
 147                    const matrix                              M,
 148                    gmx::Update*                              upd,
 149                    int                                       bUpdatePart,
 150                    const t_commrec* cr, /* these shouldn't be here -- need to think about it */
 151                    const gmx::Constraints* constr);
 152
 153 /* Return TRUE if OK, FALSE in case of Shake Error */
 154
 155 extern gmx_bool update_randomize_velocities(const t_inputrec*        ir,
 156                                             int64_t                  step,
 157                                             const t_commrec*         cr,
 158                                             const t_mdatoms*         md,
 159                                             gmx::ArrayRef<gmx::RVec> v,
 160                                             const gmx::Update*       upd,
 161                                             const gmx::Constraints*  constr);
 162
 163 void constrain_velocities(int64_t step,
 164                           real* dvdlambda, /* the contribution to be added to the bonded interactions */
 165                           t_state*          state,
 166                           tensor            vir_part,
 167                           gmx::Constraints* constr,
 168                           gmx_bool          bCalcVir,
 169                           bool              do_log,
 170                           bool              do_ene);
 171
 172 void constrain_coordinates(int64_t step,
 173                            real* dvdlambda, /* the contribution to be added to the bonded interactions */
 174                            t_state*          state,
 175                            tensor            vir_part,
 176                            gmx::Update*      upd,
 177                            gmx::Constraints* constr,
 178                            gmx_bool          bCalcVir,
 179                            bool              do_log,
 180                            bool              do_ene);
 181
 182 void update_sd_second_half(int64_t step,
 183                            real* dvdlambda, /* the contribution to be added to the bonded interactions */
 184                            const t_inputrec* inputrec, /* input record and box stuff */
 185                            const t_mdatoms*  md,
 186                            t_state*          state,
 187                            const t_commrec*  cr,
 188                            t_nrnb*           nrnb,
 189                            gmx_wallcycle_t   wcycle,
 190                            gmx::Update*      upd,
 191                            gmx::Constraints* constr,
 192                            bool              do_log,
 193                            bool              do_ene);
 194
 195 void finish_update(const t_inputrec*       inputrec,
 196                    const t_mdatoms*        md,
 197                    t_state*                state,
 198                    const t_graph*          graph,
 199                    t_nrnb*                 nrnb,
 200                    gmx_wallcycle_t         wcycle,
 201                    gmx::Update*            upd,
 202                    const gmx::Constraints* constr);
 203
 204 /* Return TRUE if OK, FALSE in case of Shake Error */
 205
 206 void calc_ke_part(const rvec*      x,
 207                   const rvec*      v,
 208                   const matrix     box,
 209                   const t_grpopts* opts,
 210                   const t_mdatoms* md,
 211                   gmx_ekindata_t*  ekind,
 212                   t_nrnb*          nrnb,
 213                   gmx_bool         bEkinAveVel);
 214 /*
 215  * Compute the partial kinetic energy for home particles;
 216  * will be accumulated in the calling routine.
 217  * The tensor is
 218  *
 219  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 220  *
 221  *     use v[i] = v[i] - u[i] when calculating temperature
 222  *
 223  * u must be accumulated already.
 224  *
 225  * Now also computes the contribution of the kinetic energy to the
 226  * free energy
 227  *
 228  */
 229
 230
 231 void init_ekinstate(ekinstate_t* ekinstate, const t_inputrec* ir);
 232
 233 void update_ekinstate(ekinstate_t* ekinstate, const gmx_ekindata_t* ekind);
 234
 235 /*! \brief Restores data from \p ekinstate to \p ekind, then broadcasts it
 236    to the rest of the simulation */
 237 void restore_ekinstate_from_state(const t_commrec* cr, gmx_ekindata_t* ekind, const ekinstate_t* ekinstate);
 238
 239 void berendsen_tcoupl(const t_inputrec*    ir,
 240                       gmx_ekindata_t*      ekind,
 241                       real                 dt,
 242                       std::vector<double>& therm_integral); //NOLINT(google-runtime-references)
 243
 244 void andersen_tcoupl(const t_inputrec*         ir,
 245                      int64_t                   step,
 246                      const t_commrec*          cr,
 247                      const t_mdatoms*          md,
 248                      gmx::ArrayRef<gmx::RVec>  v,
 249                      real                      rate,
 250                      const std::vector<bool>&  randomize,
 251                      gmx::ArrayRef<const real> boltzfac);
 252
 253 void nosehoover_tcoupl(const t_grpopts*      opts,
 254                        const gmx_ekindata_t* ekind,
 255                        real                  dt,
 256                        double                xi[],
 257                        double                vxi[],
 258                        const t_extmass*      MassQ);
 259
 260 void trotter_update(const t_inputrec*               ir,
 261                     int64_t                         step,
 262                     gmx_ekindata_t*                 ekind,
 263                     const gmx_enerdata_t*           enerd,
 264                     t_state*                        state,
 265                     const tensor                    vir,
 266                     const t_mdatoms*                md,
 267                     const t_extmass*                MassQ,
 268                     gmx::ArrayRef<std::vector<int>> trotter_seqlist,
 269                     int                             trotter_seqno);
 270
 271 std::array<std::vector<int>, ettTSEQMAX>
 272 init_npt_vars(const t_inputrec* ir, t_state* state, t_extmass* Mass, gmx_bool bTrotter);
 273
 274 real NPT_energy(const t_inputrec* ir, const t_state* state, const t_extmass* MassQ);
 275 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 276
 277 void vrescale_tcoupl(const t_inputrec* ir, int64_t step, gmx_ekindata_t* ekind, real dt, double therm_integral[]);
 278 /* Compute temperature scaling. For V-rescale it is done in update. */
 279
 280 void rescale_velocities(const gmx_ekindata_t* ekind, const t_mdatoms* mdatoms, int start, int end, rvec v[]);
 281 /* Rescale the velocities with the scaling factor in ekind */
 282
 283 //! Check whether we do simulated annealing.
 284 bool doSimulatedAnnealing(const t_inputrec* ir);
 285
 286 //! Initialize simulated annealing.
 287 bool initSimulatedAnnealing(t_inputrec* ir, gmx::Update* upd);
 288
 289 // TODO: This is the only function in update.h altering the inputrec
 290 void update_annealing_target_temp(t_inputrec* ir, real t, gmx::Update* upd);
 291 /* Set reference temp for simulated annealing at time t*/
 292
 293 real calc_temp(real ekin, real nrdf);
 294 /* Calculate the temperature */
 295
 296 real calc_pres(int ePBC, int nwall, const matrix box, const tensor ekin, const tensor vir, tensor pres);
 297 /* Calculate the pressure tensor, returns the scalar pressure.
 298  * The unit of pressure is bar.
 299  */
 300
 301 void parrinellorahman_pcoupl(FILE*             fplog,
 302                              int64_t           step,
 303                              const t_inputrec* ir,
 304                              real              dt,
 305                              const tensor      pres,
 306                              const tensor      box,
 307                              tensor            box_rel,
 308                              tensor            boxv,
 309                              tensor            M,
 310                              matrix            mu,
 311                              gmx_bool          bFirstStep);
 312
 313 void berendsen_pcoupl(FILE*             fplog,
 314                       int64_t           step,
 315                       const t_inputrec* ir,
 316                       real              dt,
 317                       const tensor      pres,
 318                       const matrix      box,
 319                       const matrix      force_vir,
 320                       const matrix      constraint_vir,
 321                       matrix            mu,
 322                       double*           baros_integral);
 323
 324 void berendsen_pscale(const t_inputrec*    ir,
 325                       const matrix         mu,
 326                       matrix               box,
 327                       matrix               box_rel,
 328                       int                  start,
 329                       int                  nr_atoms,
 330                       rvec                 x[],
 331                       const unsigned short cFREEZE[],
 332                       t_nrnb*              nrnb,
 333                       bool                 scaleCoordinates);
 334
 335 void pleaseCiteCouplingAlgorithms(FILE* fplog, const t_inputrec& ir);
 336
 337 /*! \brief Computes the atom range for a thread to operate on, ensuring SIMD aligned ranges
 338  *
 339  * \param[in]  numThreads   The number of threads to divide atoms over
 340  * \param[in]  threadIndex  The thread to get the range for
 341  * \param[in]  numAtoms     The total number of atoms (on this rank)
 342  * \param[out] startAtom    The start of the atom range
 343  * \param[out] endAtom      The end of the atom range, note that this is in general not a multiple of the SIMD width
 344  */
 345 void getThreadAtomRange(int numThreads, int threadIndex, int numAtoms, int* startAtom, int* endAtom);
 346
 347 /*! \brief Generate a new kinetic energy for the v-rescale thermostat
 348  *
 349  * Generates a new value for the kinetic energy, according to
 350  * Bussi et al JCP (2007), Eq. (A7)
 351  *
 352  * This is used by update_tcoupl(), and by the VRescaleThermostat of the modular
 353  * simulator.
 354  * TODO: Move this to the VRescaleThermostat once the modular simulator becomes
 355  *       the default code path.
 356  *
 357  * @param kk     present value of the kinetic energy of the atoms to be thermalized (in arbitrary units)
 358  * @param sigma  target average value of the kinetic energy (ndeg k_b T/2)  (in the same units as kk)
 359  * @param ndeg   number of degrees of freedom of the atoms to be thermalized
 360  * @param taut   relaxation time of the thermostat, in units of 'how often this routine is called'
 361  * @param step   the time step this routine is called on
 362  * @param seed   the random number generator seed
 363  * @return  the new kinetic energy
 364  */
 365 real vrescale_resamplekin(real kk, real sigma, real ndeg, real taut, int64_t step, int64_t seed);
 366
 367 #endif