src/gromacs/mdtypes/state.h

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  37 #ifndef GMX_MDTYPES_STATE_H
  38 #define GMX_MDTYPES_STATE_H
  39
  40 #include <memory>
  41 #include <vector>
  42
  43 #include "gromacs/math/vectypes.h"
  44 #include "gromacs/mdtypes/md_enums.h"
  45 #include "gromacs/utility/basedefinitions.h"
  46 #include "gromacs/utility/real.h"
  47
  48 struct energyhistory_t;
  49
  50 /*
  51  * The t_state struct should contain all the (possibly) non-static
  52  * information required to define the state of the system.
  53  * Currently the random seeds for SD and BD are missing.
  54  */
  55
  56 /* These enums are used in flags as (1<<est...).
  57  * The order of these enums should not be changed,
  58  * since that affects the checkpoint (.cpt) file format.
  59  */
  60 enum {
  61     estLAMBDA,
  62     estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI,  estTC_INT,
  63     estX,   estV,       est_SDX_NOTSUPPORTED,  estCGP,
  64     estLD_RNG, estLD_RNGI,
  65     estDISRE_INITF, estDISRE_RM3TAV,
  66     estORIRE_INITF, estORIRE_DTAV,
  67     estSVIR_PREV, estNH_VXI, estVETA, estVOL0, estNHPRES_XI, estNHPRES_VXI, estFVIR_PREV,
  68     estFEPSTATE, estMC_RNG, estMC_RNGI,
  69     estNR
  70 };
  71
  72 #define EST_DISTR(e) (!(((e) >= estLAMBDA && (e) <= estTC_INT) || ((e) >= estSVIR_PREV && (e) <= estMC_RNGI)))
  73
  74 /* The names of the state entries, defined in src/gmxlib/checkpoint.c */
  75 extern const char *est_names[estNR];
  76
  77 /* This vector is not padded yet, padding will be added soon */
  78 typedef std::vector<gmx::RVec> PaddedRVecVector;
  79
  80 typedef std::shared_ptr<energyhistory_t> EnerHistPtr;
  81
  82 typedef struct history_t
  83 {
  84     real  disre_initf;  /* The scaling factor for initializing the time av. */
  85     int   ndisrepairs;  /* The number of distance restraints                */
  86     real *disre_rm3tav; /* The r^-3 time averaged pair distances            */
  87     real  orire_initf;  /* The scaling factor for initializing the time av. */
  88     int   norire_Dtav;  /* The number of matrix element in dtav (npair*5)   */
  89     real *orire_Dtav;   /* The time averaged orientation tensors            */
  90 } history_t;
  91
  92 /* Struct used for checkpointing only.
  93  * This struct would not be required with unlimited precision.
  94  * But because of limited precision, the COM motion removal implementation
  95  * can cause the kinetic energy in the MD loop to differ by a few bits from
  96  * the kinetic energy one would determine from state.v.
  97  */
  98 typedef struct ekinstate_t
  99 {
 100     gmx_bool             bUpToDate;
 101     int                  ekin_n;
 102     tensor              *ekinh;
 103     tensor              *ekinf;
 104     tensor              *ekinh_old;
 105     tensor               ekin_total;
 106     std::vector<double>  ekinscalef_nhc;
 107     std::vector<double>  ekinscaleh_nhc;
 108     std::vector<double>  vscale_nhc;
 109     real                 dekindl;
 110     real                 mvcos;
 111 } ekinstate_t;
 112
 113 typedef struct df_history_t
 114 {
 115     int      nlambda;        /* total number of lambda states - for history*/
 116
 117     gmx_bool bEquil;         /* Have we reached equilibration */
 118     int     *n_at_lam;       /* number of points observed at each lambda */
 119     real    *wl_histo;       /* histogram for WL flatness determination */
 120     real     wl_delta;       /* current wang-landau delta */
 121
 122     real    *sum_weights;    /* weights of the states */
 123     real    *sum_dg;         /* free energies of the states -- not actually used for weighting, but informational */
 124     real    *sum_minvar;     /* corrections to weights for minimum variance */
 125     real    *sum_variance;   /* variances of the states */
 126
 127     real   **accum_p;        /* accumulated bennett weights for n+1 */
 128     real   **accum_m;        /* accumulated bennett weights for n-1 */
 129     real   **accum_p2;       /* accumulated squared bennett weights for n+1 */
 130     real   **accum_m2;       /* accumulated squared bennett weights for n-1 */
 131
 132     real   **Tij;            /* transition matrix */
 133     real   **Tij_empirical;  /* Empirical transition matrix */
 134
 135 } df_history_t;
 136
 137 typedef struct edsamstate_t
 138 {
 139     /* If one uses essential dynamics or flooding on a group of atoms from
 140      * more than one molecule, we cannot make this group whole with
 141      * do_pbc_first_mtop(). We assume that the ED group has the correct PBC
 142      * representation at the beginning of the simulation and keep track
 143      * of the shifts to always get it into that representation.
 144      * For proper restarts from a checkpoint we store the positions of the
 145      * reference group at the time of checkpoint writing */
 146     gmx_bool      bFromCpt;     /* Did we start from a checkpoint file?       */
 147     int           nED;          /* No. of ED/Flooding data sets, if <1 no ED  */
 148     int          *nref;         /* No. of atoms in i'th reference structure   */
 149     int          *nav;          /* Same for average structure                 */
 150     rvec        **old_sref;     /* Positions of the reference atoms
 151                                    at the last time step (with correct PBC
 152                                    representation)                            */
 153     rvec        **old_sref_p;   /* Pointer to these positions                 */
 154     rvec        **old_sav;      /* Same for the average positions             */
 155     rvec        **old_sav_p;
 156 }
 157 edsamstate_t;
 158
 159 typedef struct swapstateIons_t
 160 {
 161     int  nMolReq[eCompNR];                  /* Requested # of molecules per compartment      */
 162     int *nMolReq_p[eCompNR];                /* Pointer to this data (for .cpt writing)       */
 163     int  inflow_net[eCompNR];               /* Flux determined from the # of swaps           */
 164     int *inflow_net_p[eCompNR];             /* Pointer to this data                          */
 165     int *nMolPast[eCompNR];                 /* Array with nAverage entries for history       */
 166     int *nMolPast_p[eCompNR];               /* Pointer points to the first entry only        */
 167     /*                                                                                       */
 168     /* Channel flux detection, this is counting only and has no influence on whether swaps   */
 169     /* are performed or not:                                                                 */
 170     int            fluxfromAtoB[eCompNR];   /* Flux determined from the split cylinders      */
 171     int           *fluxfromAtoB_p[eCompNR]; /* Pointer to this data                          */
 172     int            nMol;                    /* # of molecules, size of the following arrays  */
 173     unsigned char *comp_from;               /* Ion came from which compartment?              */
 174     unsigned char *channel_label;           /* Through which channel did this ion pass?      */
 175 } swapstateIons_t;
 176
 177 typedef struct swapstate_t
 178 {
 179     int  eSwapCoords;                       /* Swapping along x, y, or z-direction?          */
 180     int  nIonTypes;                         /* Number of ion types, this is the size of      */
 181                                             /* the following arrays                          */
 182     int  nAverage;                          /* Use average over this many swap attempt       */
 183                                             /* steps when determining the ion counts         */
 184     int  fluxleak;                          /* Ions not going through any channel (bad!)     */
 185     int *fluxleak_p;                        /* Pointer to this data                          */
 186     /*                                                                                       */
 187     /* To also make multimeric channel proteins whole, we save the last whole configuration  */
 188     /* of the channels in the checkpoint file. If we have no checkpoint file, we assume      */
 189     /* that the starting configuration has the correct PBC representation after making the   */
 190     /* individual molecules whole                                                            */
 191     gmx_bool         bFromCpt;                 /* Did we start from a checkpoint file?       */
 192     int              nat[eChanNR];             /* Size of xc_old_whole, i.e. the number of   */
 193                                                /* atoms in each channel                      */
 194     rvec            *xc_old_whole[eChanNR];    /* Last known whole positions of the two      */
 195                                                /* channels (important for multimeric ch.!)   */
 196     rvec           **xc_old_whole_p[eChanNR];  /* Pointer to these positions                 */
 197     swapstateIons_t *ionType;
 198 }
 199 swapstate_t;
 200
 201
 202 typedef struct t_state
 203 {
 204     int                     natoms;
 205     int                     ngtc;
 206     int                     nnhpres;
 207     int                     nhchainlength;   /* number of nose-hoover chains               */
 208     int                     flags;           /* Flags telling which entries are present      */
 209     int                     fep_state;       /* indicates which of the alchemical states we are in                 */
 210     std::vector<real>       lambda;          /* lambda vector                               */
 211     matrix                  box;             /* box vector coordinates                         */
 212     matrix                  box_rel;         /* Relitaive box vectors to preserve shape        */
 213     matrix                  boxv;            /* box velocitites for Parrinello-Rahman pcoupl */
 214     matrix                  pres_prev;       /* Pressure of the previous step for pcoupl  */
 215     matrix                  svir_prev;       /* Shake virial for previous step for pcoupl */
 216     matrix                  fvir_prev;       /* Force virial of the previous step for pcoupl  */
 217     std::vector<double>     nosehoover_xi;   /* for Nose-Hoover tcoupl (ngtc)       */
 218     std::vector<double>     nosehoover_vxi;  /* for N-H tcoupl (ngtc)               */
 219     std::vector<double>     nhpres_xi;       /* for Nose-Hoover pcoupl for barostat     */
 220     std::vector<double>     nhpres_vxi;      /* for Nose-Hoover pcoupl for barostat     */
 221     std::vector<double>     therm_integral;  /* for N-H/V-rescale tcoupl (ngtc)     */
 222     real                    veta;            /* trotter based isotropic P-coupling             */
 223     real                    vol0;            /* initial volume,required for computing NPT conserverd quantity */
 224     PaddedRVecVector        x;               /* the coordinates (natoms)                     */
 225     PaddedRVecVector        v;               /* the velocities (natoms)                      */
 226     PaddedRVecVector        cg_p;            /* p vector for conjugate gradient minimization */
 227
 228     history_t               hist;            /* Time history for restraints                  */
 229
 230     ekinstate_t             ekinstate;       /* The state of the kinetic energy data      */
 231
 232     EnerHistPtr             enerhist;        /* Energy history for statistics           */
 233     swapstate_t            *swapstate;       /* Position swapping                       */
 234     df_history_t           *dfhist;          /*Free energy history for free energy analysis  */
 235     edsamstate_t           *edsamstate;      /* Essential dynamics / flooding history */
 236
 237     int                     ddp_count;       /* The DD partitioning count for this state  */
 238     int                     ddp_count_cg_gl; /* The DD part. count for index_gl     */
 239     std::vector<int>        cg_gl;           /* The global cg number of the local cgs        */
 240 } t_state;
 241
 242 typedef struct t_extmass
 243 {
 244     double *Qinv;  /* inverse mass of thermostat -- computed from inputs, but a good place to store */
 245     double *QPinv; /* inverse mass of thermostat for barostat -- computed from inputs, but a good place to store */
 246     double  Winv;  /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */
 247     tensor  Winvm; /* inverse pressure mass tensor, computed       */
 248 } t_extmass;
 249
 250
 251 typedef struct
 252 {
 253     real    veta;
 254     double  rscale;
 255     double  vscale;
 256     double  rvscale;
 257     double  alpha;
 258     double *vscale_nhc;
 259 } t_vetavars;
 260
 261 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength);
 262
 263 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int dfhistNumLambda);
 264
 265 void comp_state(const t_state *st1, const t_state *st2, gmx_bool bRMSD, real ftol, real abstol);
 266
 267 /*! \brief Allocate an rvec pointer and copy the contents of v to it */
 268 rvec *getRvecArrayFromPaddedRVecVector(const PaddedRVecVector *v,
 269                                        unsigned int            n);
 270
 271 #endif