src/gromacs/mdtypes/state.h

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  37
  38 /*! \file
  39  *
  40  * \brief
  41  * This file contains the definition of the microstate of the simulated system
  42  *
  43  * History of observables that needs to be checkpointed should be stored
  44  * in ObservablesHistory.
  45  * The state of the mdrun machinery that needs to be checkpointed is also
  46  * stored elsewhere.
  47  *
  48  * \author Berk Hess
  49  *
  50  * \inlibraryapi
  51  * \ingroup module_mdtypes
  52  */
  53
  54 #ifndef GMX_MDTYPES_STATE_H
  55 #define GMX_MDTYPES_STATE_H
  56
  57 #include <array>
  58 #include <vector>
  59
  60 #include "gromacs/math/paddedvector.h"
  61 #include "gromacs/math/vectypes.h"
  62 #include "gromacs/mdtypes/md_enums.h"
  63 #include "gromacs/utility/basedefinitions.h"
  64 #include "gromacs/utility/real.h"
  65
  66 struct t_inputrec;
  67
  68 /*
  69  * The t_state struct should contain all the (possibly) non-static
  70  * information required to define the state of the system.
  71  * Currently the random seeds for SD and BD are missing.
  72  */
  73
  74 /* \brief Enum for all entries in \p t_state
  75  *
  76  * These enums are used in flags as (1<<est...).
  77  * The order of these enums should not be changed,
  78  * since that affects the checkpoint (.cpt) file format.
  79  */
  80 enum {
  81     estLAMBDA,
  82     estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI,  estTHERM_INT,
  83     estX,   estV,       estSDX_NOTSUPPORTED,  estCGP,
  84     estLD_RNG_NOTSUPPORTED, estLD_RNGI_NOTSUPPORTED,
  85     estDISRE_INITF, estDISRE_RM3TAV,
  86     estORIRE_INITF, estORIRE_DTAV,
  87     estSVIR_PREV, estNH_VXI, estVETA, estVOL0, estNHPRES_XI, estNHPRES_VXI, estFVIR_PREV,
  88     estFEPSTATE, estMC_RNG_NOTSUPPORTED, estMC_RNGI_NOTSUPPORTED,
  89     estBAROS_INT,
  90     estNR
  91 };
  92
  93 //! \brief The names of the state entries, defined in src/gmxlib/checkpoint.c
  94 extern const char *est_names[estNR];
  95
  96 /*! \libinternal \brief History information for NMR distance and orientation restraints
  97  *
  98  * Often this is only used for reporting observables, and thus should not
  99  * actually be part of the microstate. But with time-dependent restraining
 100  * they are actually part of the (non-Markovian) microstate.
 101  * \todo Rename this with a more descriptive name.
 102  */
 103 class history_t
 104 {
 105     public:
 106         //! Constructor
 107         history_t();
 108
 109         real  disre_initf;  //!< The scaling factor for initializing the time av.
 110         int   ndisrepairs;  //!< The number of distance restraints
 111         real *disre_rm3tav; //!< The r^-3 time averaged pair distances
 112         real  orire_initf;  //!< The scaling factor for initializing the time av.
 113         int   norire_Dtav;  //!< The number of matrix element in dtav (npair*5)
 114         real *orire_Dtav;   //!< The time averaged orientation tensors
 115 };
 116
 117 /*! \libinternal \brief Struct used for checkpointing only
 118  *
 119  * This struct would not be required with unlimited precision.
 120  * But because of limited precision, the COM motion removal implementation
 121  * can cause the kinetic energy in the MD loop to differ by a few bits from
 122  * the kinetic energy one would determine from state.v.
 123  */
 124 class ekinstate_t
 125 {
 126     public:
 127         ekinstate_t();
 128
 129         gmx_bool             bUpToDate;      //!< Test if all data is up to date
 130         int                  ekin_n;         //!< The number of tensors
 131         tensor              *ekinh;          //!< Half step Ekin, size \p ekin_n
 132         tensor              *ekinf;          //!< Full step Ekin, size \p ekin_n
 133         tensor              *ekinh_old;      //!< Half step Ekin of the previous step, size \p ekin_n
 134         tensor               ekin_total;     //!< Total kinetic energy
 135         std::vector<double>  ekinscalef_nhc; //!< Nose-Hoover Ekin scaling factors for full step Ekin
 136         std::vector<double>  ekinscaleh_nhc; //!< Nose-Hoover Ekin scaling factors for half step Ekin
 137         std::vector<double>  vscale_nhc;     //!< Nose-Hoover velocity scaling factors
 138         real                 dekindl;        //!< dEkin/dlambda, with free-energy
 139         real                 mvcos;          //!< Cosine(z) component of the momentum, for viscosity calculations
 140 };
 141
 142 /*! \brief Free-energy sampling history struct
 143  *
 144  * \todo Split out into microstate and observables history.
 145  */
 146 typedef struct df_history_t
 147 {
 148     int      nlambda;        //!< total number of lambda states - for history
 149
 150     gmx_bool bEquil;         //!< Have we reached equilibration
 151     int     *n_at_lam;       //!< number of points observed at each lambda
 152     real    *wl_histo;       //!< histogram for WL flatness determination
 153     real     wl_delta;       //!< current wang-landau delta
 154
 155     real    *sum_weights;    //!< weights of the states
 156     real    *sum_dg;         //!< free energies of the states -- not actually used for weighting, but informational
 157     real    *sum_minvar;     //!< corrections to weights for minimum variance
 158     real    *sum_variance;   //!< variances of the states
 159
 160     real   **accum_p;        //!< accumulated bennett weights for n+1
 161     real   **accum_m;        //!< accumulated bennett weights for n-1
 162     real   **accum_p2;       //!< accumulated squared bennett weights for n+1
 163     real   **accum_m2;       //!< accumulated squared bennett weights for n-1
 164
 165     real   **Tij;            //!< transition matrix
 166     real   **Tij_empirical;  //!< Empirical transition matrix
 167
 168 } df_history_t;
 169
 170
 171 /*! \brief The microstate of the system
 172  *
 173  * The global state will contain complete data for all used entries.
 174  * The local state with domain decomposition will have partial entries
 175  * for which \p stateEntryIsAtomProperty() is true. Some entries that
 176  * are used in the global state might not be present in the local state.
 177  * \todo Move pure observables history to ObservablesHistory.
 178  */
 179 class t_state
 180 {
 181     public:
 182         //! Constructor
 183         t_state();
 184
 185         // All things public
 186         int                      natoms;          //!< Number of atoms, local + non-local; this is the size of \p x, \p v and \p cg_p, when used
 187         int                      ngtc;            //!< The number of temperature coupling groups
 188         int                      nnhpres;         //!< The NH-chain length for the MTTK barostat
 189         int                      nhchainlength;   //!< The NH-chain length for temperature coupling
 190         int                      flags;           //!< Set of bit-flags telling which entries are present, see enum at the top of the file
 191         int                      fep_state;       //!< indicates which of the alchemical states we are in
 192         std::array<real, efptNR> lambda;          //!< Free-energy lambda vector
 193         matrix                   box;             //!< Matrix of box vectors
 194         matrix                   box_rel;         //!< Relative box vectors to preserve box shape
 195         matrix                   boxv;            //!< Box velocities for Parrinello-Rahman P-coupling
 196         matrix                   pres_prev;       //!< Pressure of the previous step for pcoupl
 197         matrix                   svir_prev;       //!< Shake virial for previous step for pcoupl
 198         matrix                   fvir_prev;       //!< Force virial of the previous step for pcoupl
 199         std::vector<double>      nosehoover_xi;   //!< Nose-Hoover coordinates (ngtc)
 200         std::vector<double>      nosehoover_vxi;  //!< Nose-Hoover velocities (ngtc)
 201         std::vector<double>      nhpres_xi;       //!< Pressure Nose-Hoover coordinates
 202         std::vector<double>      nhpres_vxi;      //!< Pressure Nose-Hoover velocities
 203         std::vector<double>      therm_integral;  //!< Work exterted N-H/V-rescale T-coupling (ngtc)
 204         double                   baros_integral;  //!< For Berendsen P-coupling conserved quantity
 205         real                     veta;            //!< Trotter based isotropic P-coupling
 206         real                     vol0;            //!< Initial volume,required for computing MTTK conserved quantity
 207         PaddedRVecVector         x;               //!< The coordinates (natoms)
 208         PaddedRVecVector         v;               //!< The velocities (natoms)
 209         PaddedRVecVector         cg_p;            //!< p vector for conjugate gradient minimization
 210
 211         ekinstate_t              ekinstate;       //!< The state of the kinetic energy
 212
 213         /* History for special algorithms, should be moved to a history struct */
 214         history_t                hist;            //!< Time history for restraints
 215         df_history_t            *dfhist;          //!< Free-energy history for free energy analysis
 216
 217         int                      ddp_count;       //!< The DD partitioning count for this state
 218         int                      ddp_count_cg_gl; //!< The DD partitioning count for index_gl
 219         std::vector<int>         cg_gl;           //!< The global cg number of the local cgs
 220 };
 221
 222 #ifndef DOXYGEN
 223 /* We don't document the structs below, as they don't belong here.
 224  * TODO: Move the next two structs out of state.h.
 225  */
 226
 227 typedef struct t_extmass
 228 {
 229     double *Qinv;  /* inverse mass of thermostat -- computed from inputs, but a good place to store */
 230     double *QPinv; /* inverse mass of thermostat for barostat -- computed from inputs, but a good place to store */
 231     double  Winv;  /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */
 232     tensor  Winvm; /* inverse pressure mass tensor, computed       */
 233 } t_extmass;
 234
 235
 236 typedef struct
 237 {
 238     real    veta;
 239     double  rscale;
 240     double  vscale;
 241     double  rvscale;
 242     double  alpha;
 243     double *vscale_nhc;
 244 } t_vetavars;
 245
 246 #endif // DOXYGEN
 247
 248 //! Resizes the T- and P-coupling state variables
 249 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength);
 250
 251 //! Change the number of atoms represented by this state, allocating memory as needed.
 252 void state_change_natoms(t_state *state, int natoms);
 253
 254 //! Allocates memory for free-energy history
 255 void init_dfhist_state(t_state *state, int dfhistNumLambda);
 256
 257 /*! \brief Compares two states, write the differences to stdout */
 258 void comp_state(const t_state *st1, const t_state *st2, gmx_bool bRMSD, real ftol, real abstol);
 259
 260 /*! \brief Allocates an rvec pointer and copy the contents of v to it */
 261 rvec *getRvecArrayFromPaddedRVecVector(const PaddedRVecVector *v,
 262                                        unsigned int            n);
 263
 264 /*! \brief Determine the relative box components
 265  *
 266  * Set box_rel e.g. used in mdrun state, used to preserve the box shape
 267  * \param[in]    ir      Input record
 268  * \param[inout] state   State
 269  */
 270 void set_box_rel(const t_inputrec *ir, t_state *state);
 271
 272 /*! \brief Make sure the relative box shape remains the same
 273  *
 274  * This function ensures that the relative box dimensions are
 275  * preserved, which otherwise might diffuse away due to rounding
 276  * errors in pressure coupling or the deform option.
 277  *
 278  * \param[in]    ir      Input record
 279  * \param[in]    box_rel Relative box dimensions
 280  * \param[inout] box     The corrected actual box dimensions
 281  */
 282 void preserve_box_shape(const t_inputrec *ir, matrix box_rel, matrix box);
 283
 284 #endif