src/gromacs/mdtypes/state.h

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  38
  39 /*! \file
  40  *
  41  * \brief
  42  * This file contains the definition of the microstate of the simulated system
  43  *
  44  * History of observables that needs to be checkpointed should be stored
  45  * in ObservablesHistory.
  46  * The state of the mdrun machinery that needs to be checkpointed is also
  47  * stored elsewhere.
  48  *
  49  * \author Berk Hess
  50  *
  51  * \inlibraryapi
  52  * \ingroup module_mdtypes
  53  */
  54
  55 #ifndef GMX_MDTYPES_STATE_H
  56 #define GMX_MDTYPES_STATE_H
  57
  58 #include <array>
  59 #include <memory>
  60 #include <vector>
  61
  62 #include "gromacs/gpu_utils/hostallocator.h"
  63 #include "gromacs/math/paddedvector.h"
  64 #include "gromacs/math/vectypes.h"
  65 #include "gromacs/mdtypes/md_enums.h"
  66 #include "gromacs/utility/arrayref.h"
  67 #include "gromacs/utility/basedefinitions.h"
  68 #include "gromacs/utility/real.h"
  69
  70 struct t_inputrec;
  71
  72 namespace gmx
  73 {
  74 struct AwhHistory;
  75 }
  76
  77 //! Convenience alias for until all is moved in the gmx namespace
  78 template<class T>
  79 using PaddedHostVector = gmx::PaddedHostVector<T>;
  80
  81 /*
  82  * The t_state struct should contain all the (possibly) non-static
  83  * information required to define the state of the system.
  84  * Currently the random seeds for SD and BD are missing.
  85  */
  86
  87 /* \brief Enum for all entries in \p t_state
  88  *
  89  * These enums are used in flags as (1<<est...).
  90  * The order of these enums should not be changed,
  91  * since that affects the checkpoint (.cpt) file format.
  92  */
  93 enum
  94 {
  95     estLAMBDA,
  96     estBOX,
  97     estBOX_REL,
  98     estBOXV,
  99     estPRES_PREV,
 100     estNH_XI,
 101     estTHERM_INT,
 102     estX,
 103     estV,
 104     estSDX_NOTSUPPORTED,
 105     estCGP,
 106     estLD_RNG_NOTSUPPORTED,
 107     estLD_RNGI_NOTSUPPORTED,
 108     estDISRE_INITF,
 109     estDISRE_RM3TAV,
 110     estORIRE_INITF,
 111     estORIRE_DTAV,
 112     estSVIR_PREV,
 113     estNH_VXI,
 114     estVETA,
 115     estVOL0,
 116     estNHPRES_XI,
 117     estNHPRES_VXI,
 118     estFVIR_PREV,
 119     estFEPSTATE,
 120     estMC_RNG_NOTSUPPORTED,
 121     estMC_RNGI_NOTSUPPORTED,
 122     estBAROS_INT,
 123     estPULLCOMPREVSTEP,
 124     estNR
 125 };
 126
 127 //! \brief The names of the state entries, defined in src/gmxlib/checkpoint.c
 128 extern const char* est_names[estNR];
 129
 130 /*! \libinternal \brief History information for NMR distance and orientation restraints
 131  *
 132  * Often this is only used for reporting observables, and thus should not
 133  * actually be part of the microstate. But with time-dependent restraining
 134  * they are actually part of the (non-Markovian) microstate.
 135  * \todo Rename this with a more descriptive name.
 136  */
 137 class history_t
 138 {
 139 public:
 140     history_t();
 141
 142     real  disre_initf;  //!< The scaling factor for initializing the time av.
 143     int   ndisrepairs;  //!< The number of distance restraints
 144     real* disre_rm3tav; //!< The r^-3 time averaged pair distances
 145     real  orire_initf;  //!< The scaling factor for initializing the time av.
 146     int   norire_Dtav;  //!< The number of matrix element in dtav (npair*5)
 147     real* orire_Dtav;   //!< The time averaged orientation tensors
 148 };
 149
 150 /*! \libinternal \brief Struct used for checkpointing only
 151  *
 152  * This struct would not be required with unlimited precision.
 153  * But because of limited precision, the COM motion removal implementation
 154  * can cause the kinetic energy in the MD loop to differ by a few bits from
 155  * the kinetic energy one would determine from state.v.
 156  */
 157 class ekinstate_t
 158 {
 159 public:
 160     ekinstate_t();
 161
 162     gmx_bool            bUpToDate;      //!< Test if all data is up to date
 163     int                 ekin_n;         //!< The number of tensors
 164     tensor*             ekinh;          //!< Half step Ekin, size \p ekin_n
 165     tensor*             ekinf;          //!< Full step Ekin, size \p ekin_n
 166     tensor*             ekinh_old;      //!< Half step Ekin of the previous step, size \p ekin_n
 167     tensor              ekin_total;     //!< Total kinetic energy
 168     std::vector<double> ekinscalef_nhc; //!< Nose-Hoover Ekin scaling factors for full step Ekin
 169     std::vector<double> ekinscaleh_nhc; //!< Nose-Hoover Ekin scaling factors for half step Ekin
 170     std::vector<double> vscale_nhc;     //!< Nose-Hoover velocity scaling factors
 171     real                dekindl;        //!< dEkin/dlambda, with free-energy
 172     real                mvcos; //!< Cosine(z) component of the momentum, for viscosity calculations
 173     /*! \brief Whether KE terms have been read from the checkpoint.
 174      *
 175      * Only used for managing whether the call to compute_globals
 176      * before we enter the MD loop should compute these quantities
 177      * fresh, or not. */
 178     bool hasReadEkinState;
 179 };
 180
 181 /*! \brief Free-energy sampling history struct
 182  *
 183  * \todo Split out into microstate and observables history.
 184  */
 185 typedef struct df_history_t
 186 {
 187     int nlambda; //!< total number of lambda states - for history
 188
 189     gmx_bool bEquil;   //!< Have we reached equilibration
 190     int*     n_at_lam; //!< number of points observed at each lambda
 191     real*    wl_histo; //!< histogram for WL flatness determination
 192     real     wl_delta; //!< current wang-landau delta
 193
 194     real* sum_weights; //!< weights of the states
 195     real* sum_dg; //!< free energies of the states -- not actually used for weighting, but informational
 196     real* sum_minvar;   //!< corrections to weights for minimum variance
 197     real* sum_variance; //!< variances of the states
 198
 199     real** accum_p;  //!< accumulated bennett weights for n+1
 200     real** accum_m;  //!< accumulated bennett weights for n-1
 201     real** accum_p2; //!< accumulated squared bennett weights for n+1
 202     real** accum_m2; //!< accumulated squared bennett weights for n-1
 203
 204     real** Tij;           //!< transition matrix
 205     real** Tij_empirical; //!< Empirical transition matrix
 206
 207 } df_history_t;
 208
 209
 210 /*! \brief The microstate of the system
 211  *
 212  * The global state will contain complete data for all used entries.
 213  * The local state with domain decomposition will have partial entries
 214  * for which \p stateEntryIsAtomProperty() is true. Some entries that
 215  * are used in the global state might not be present in the local state.
 216  * \todo Move pure observables history to ObservablesHistory.
 217  */
 218 class t_state
 219 {
 220 public:
 221     t_state();
 222
 223     // All things public
 224     int natoms; //!< Number of atoms, local + non-local; this is the size of \p x, \p v and \p cg_p, when used
 225     int ngtc;          //!< The number of temperature coupling groups
 226     int nnhpres;       //!< The NH-chain length for the MTTK barostat
 227     int nhchainlength; //!< The NH-chain length for temperature coupling
 228     int flags; //!< Set of bit-flags telling which entries are present, see enum at the top of the file
 229     int                      fep_state;      //!< indicates which of the alchemical states we are in
 230     std::array<real, efptNR> lambda;         //!< Free-energy lambda vector
 231     matrix                   box;            //!< Matrix of box vectors
 232     matrix                   box_rel;        //!< Relative box vectors to preserve box shape
 233     matrix                   boxv;           //!< Box velocities for Parrinello-Rahman P-coupling
 234     matrix                   pres_prev;      //!< Pressure of the previous step for pcoupl
 235     matrix                   svir_prev;      //!< Shake virial for previous step for pcoupl
 236     matrix                   fvir_prev;      //!< Force virial of the previous step for pcoupl
 237     std::vector<double>      nosehoover_xi;  //!< Nose-Hoover coordinates (ngtc)
 238     std::vector<double>      nosehoover_vxi; //!< Nose-Hoover velocities (ngtc)
 239     std::vector<double>      nhpres_xi;      //!< Pressure Nose-Hoover coordinates
 240     std::vector<double>      nhpres_vxi;     //!< Pressure Nose-Hoover velocities
 241     std::vector<double>      therm_integral; //!< Work exterted N-H/V-rescale T-coupling (ngtc)
 242     double                   baros_integral; //!< For Berendsen P-coupling conserved quantity
 243     real                     veta;           //!< Trotter based isotropic P-coupling
 244     real vol0; //!< Initial volume,required for computing MTTK conserved quantity
 245     PaddedHostVector<gmx::RVec> x;    //!< The coordinates (natoms)
 246     PaddedHostVector<gmx::RVec> v;    //!< The velocities (natoms)
 247     PaddedHostVector<gmx::RVec> cg_p; //!< p vector for conjugate gradient minimization
 248
 249     ekinstate_t ekinstate; //!< The state of the kinetic energy
 250
 251     /* History for special algorithms, should be moved to a history struct */
 252     history_t                        hist;       //!< Time history for restraints
 253     df_history_t*                    dfhist;     //!< Free-energy history for free energy analysis
 254     std::shared_ptr<gmx::AwhHistory> awhHistory; //!< Accelerated weight histogram history
 255
 256     int              ddp_count;       //!< The DD partitioning count for this state
 257     int              ddp_count_cg_gl; //!< The DD partitioning count for index_gl
 258     std::vector<int> cg_gl;           //!< The global cg number of the local cgs
 259
 260     std::vector<double> pull_com_prev_step; //!< The COM of the previous step of each pull group
 261 };
 262
 263 #ifndef DOXYGEN
 264 /* We don't document the structs below, as they don't belong here.
 265  * TODO: Move the next two structs out of state.h.
 266  */
 267
 268 struct t_extmass
 269 {
 270     std::vector<double> Qinv; /* inverse mass of thermostat -- computed from inputs, but a good place to store */
 271     std::vector<double> QPinv; /* inverse mass of thermostat for barostat -- computed from inputs, but a good place to store */
 272     double              Winv; /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */
 273     tensor              Winvm; /* inverse pressure mass tensor, computed       */
 274 };
 275
 276
 277 typedef struct
 278 {
 279     real    veta;
 280     double  rscale;
 281     double  vscale;
 282     double  rvscale;
 283     double  alpha;
 284     double* vscale_nhc;
 285 } t_vetavars;
 286
 287 #endif // DOXYGEN
 288
 289 //! Resizes the T- and P-coupling state variables
 290 void init_gtc_state(t_state* state, int ngtc, int nnhpres, int nhchainlength);
 291
 292 //! Change the number of atoms represented by this state, allocating memory as needed.
 293 void state_change_natoms(t_state* state, int natoms);
 294
 295 //! Allocates memory for free-energy history
 296 void init_dfhist_state(t_state* state, int dfhistNumLambda);
 297
 298 /*! \brief Compares two states, write the differences to stdout */
 299 void comp_state(const t_state* st1, const t_state* st2, gmx_bool bRMSD, real ftol, real abstol);
 300
 301 /*! \brief Allocates an rvec pointer and copy the contents of v to it */
 302 rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n);
 303
 304 /*! \brief Determine the relative box components
 305  *
 306  * Set box_rel e.g. used in mdrun state, used to preserve the box shape
 307  * \param[in]    ir      Input record
 308  * \param[inout] state   State
 309  */
 310 void set_box_rel(const t_inputrec* ir, t_state* state);
 311
 312 /*! \brief Make sure the relative box shape remains the same
 313  *
 314  * This function ensures that the relative box dimensions are
 315  * preserved, which otherwise might diffuse away due to rounding
 316  * errors in pressure coupling or the deform option.
 317  *
 318  * \param[in]    ir      Input record
 319  * \param[in]    box_rel Relative box dimensions
 320  * \param[inout] box     The corrected actual box dimensions
 321  */
 322 void preserve_box_shape(const t_inputrec* ir, matrix box_rel, matrix box);
 323
 324 /*! \brief Returns an arrayRef to the positions in \p state when \p state!=null
 325  *
 326  * When \p state=nullptr, returns an empty arrayRef.
 327  *
 328  * \note The size returned is the number of atoms, without padding.
 329  *
 330  * \param[in] state  The state, can be nullptr
 331  */
 332 static inline gmx::ArrayRef<const gmx::RVec> positionsFromStatePointer(const t_state* state)
 333 {
 334     if (state)
 335     {
 336         return gmx::makeConstArrayRef(state->x).subArray(0, state->natoms);
 337     }
 338     else
 339     {
 340         return {};
 341     }
 342 };
 343
 344 /*! \brief Fills fep_state, lambda, and lam0 if needed
 345  *
 346  * If FEP or simulated tempering is in use:
 347  *
 348  *    fills non-null lam0 with the initial lambda values, and
 349  *    on master rank fills fep_state and lambda.
 350  *
 351  * Reports the initial lambda state to the log file. */
 352 void initialize_lambdas(FILE*               fplog,
 353                         const t_inputrec&   ir,
 354                         bool                isMaster,
 355                         int*                fep_state,
 356                         gmx::ArrayRef<real> lambda,
 357                         double*             lam0);
 358
 359 #endif