include/types/state.h

   1 /*
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  38 #ifndef _state_h_
  39 #define _state_h_
  40
  41
  42 #include "simple.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 /*
  49  * The t_state struct should contain all the (possibly) non-static
  50  * information required to define the state of the system.
  51  * Currently the random seeds for SD and BD are missing.
  52  */
  53
  54 /* for now, define the length of the NH chains here */
  55 #define NHCHAINLENGTH 10
  56 #define MAXLAMBDAS 1024
  57
  58 /* These enums are used in flags as (1<<est...).
  59  * The order of these enums should not be changed,
  60  * since that affects the checkpoint (.cpt) file format.
  61  */
  62 enum {
  63     estLAMBDA,
  64     estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI,  estTC_INT,
  65     estX,   estV,       estSDX,  estCGP,       estLD_RNG, estLD_RNGI,
  66     estDISRE_INITF, estDISRE_RM3TAV,
  67     estORIRE_INITF, estORIRE_DTAV,
  68     estSVIR_PREV, estNH_VXI, estVETA, estVOL0, estNHPRES_XI, estNHPRES_VXI, estFVIR_PREV,
  69     estFEPSTATE, estMC_RNG, estMC_RNGI,
  70     estNR
  71 };
  72
  73 #define EST_DISTR(e) (!(((e) >= estLAMBDA && (e) <= estTC_INT) || ((e) >= estSVIR_PREV && (e) <= estMC_RNGI)))
  74
  75 /* The names of the state entries, defined in src/gmxlib/checkpoint.c */
  76 extern const char *est_names[estNR];
  77
  78 typedef struct
  79 {
  80     real  disre_initf;  /* The scaling factor for initializing the time av. */
  81     int   ndisrepairs;  /* The number of distance restraints                */
  82     real *disre_rm3tav; /* The r^-3 time averaged pair distances            */
  83     real  orire_initf;  /* The scaling factor for initializing the time av. */
  84     int   norire_Dtav;  /* The number of matrix element in dtav (npair*5)   */
  85     real *orire_Dtav;   /* The time averaged orientation tensors            */
  86 } history_t;
  87
  88 /* Struct used for checkpointing only.
  89  * This struct would not be required with unlimited precision.
  90  * But because of limited precision, the COM motion removal implementation
  91  * can cause the kinetic energy in the MD loop to differ by a few bits from
  92  * the kinetic energy one would determine from state.v.
  93  */
  94 typedef struct
  95 {
  96     gmx_bool     bUpToDate;
  97     int          ekin_n;
  98     tensor      *ekinh;
  99     tensor      *ekinf;
 100     tensor      *ekinh_old;
 101     tensor       ekin_total;
 102     double      *ekinscalef_nhc;
 103     double      *ekinscaleh_nhc;
 104     double      *vscale_nhc;
 105     real         dekindl;
 106     real         mvcos;
 107 } ekinstate_t;
 108
 109 /* energy history for delta_h histograms */
 110 typedef struct
 111 {
 112     int      nndh;             /* the number of energy difference lists */
 113     int     *ndh;              /* the number in each energy difference list */
 114     real   **dh;               /* the energy difference lists */
 115
 116     double   start_time;       /* the start time of these energy diff blocks */
 117     double   start_lambda;     /* lambda at start time */
 118
 119     gmx_bool start_lambda_set; /* whether the lambda value is set. Here
 120                                   For backward-compatibility. */
 121 } delta_h_history_t;
 122
 123 typedef struct
 124 {
 125     int      nlambda;        /* total number of lambda states - for history*/
 126
 127     gmx_bool bEquil;         /* reached equilibration */
 128     int     *n_at_lam;       /* number of points observed at each lambda */
 129     real    *wl_histo;       /* histogram for WL flatness determination */
 130     real     wl_delta;       /* current wang-landau delta */
 131
 132     real    *sum_weights;    /* weights of the states */
 133     real    *sum_dg;         /* free energies of the states -- not actually used for weighting, but informational */
 134     real    *sum_minvar;     /* corrections to weights for minimum variance */
 135     real    *sum_variance;   /* variances of the states */
 136
 137     real   **accum_p;        /* accumulated bennett weights for n+1 */
 138     real   **accum_m;        /* accumulated bennett weights for n-1 */
 139     real   **accum_p2;       /* accumulated squared bennett weights for n+1 */
 140     real   **accum_m2;       /* accumulated squared bennett weights for n-1 */
 141
 142     real   **Tij;            /* transition matrix */
 143     real   **Tij_empirical;  /* Empirical transition matrix */
 144 } df_history_t;
 145
 146 typedef struct
 147 {
 148     gmx_large_int_t    nsteps;       /* The number of steps in the history            */
 149     gmx_large_int_t    nsum;         /* The nr. of steps in the ener_ave and ener_sum */
 150     double         *   ener_ave;     /* Energy term history sum to get fluctuations   */
 151     double         *   ener_sum;     /* Energy term history sum to get fluctuations   */
 152     int                nener;        /* Number of energy terms in two previous arrays */
 153     gmx_large_int_t    nsteps_sim;   /* The number of steps in ener_sum_sim      */
 154     gmx_large_int_t    nsum_sim;     /* The number of frames in ener_sum_sim     */
 155     double         *   ener_sum_sim; /* Energy term history sum of the whole sim      */
 156
 157     delta_h_history_t *dht;          /* The BAR energy differences */
 158 }
 159 energyhistory_t;
 160
 161 typedef struct
 162 {
 163     /* If one uses essential dynamics or flooding on a group of atoms from
 164      * more than one molecule, we cannot make this group whole with
 165      * do_pbc_first_mtop(). We assume that the ED group has the correct PBC
 166      * representation at the beginning of the simulation and keep track
 167      * of the shifts to always get it into that representation.
 168      * For proper restarts from a checkpoint we store the positions of the
 169      * reference group at the time of checkpoint writing */
 170     gmx_bool      bFromCpt;     /* Did we start from a checkpoint file?       */
 171     int           nED;          /* No. of ED/Flooding data sets, if <1 no ED  */
 172     int          *nref;         /* No. of atoms in i'th reference structure   */
 173     int          *nav;          /* Same for average structure                 */
 174     rvec        **old_sref;     /* Positions of the reference atoms
 175                                    at the last time step (with correct PBC
 176                                    representation)                            */
 177     rvec        **old_sref_p;   /* Pointer to these positions                 */
 178     rvec        **old_sav;      /* Same for the average positions             */
 179     rvec        **old_sav_p;
 180 }
 181 edsamstate_t;
 182
 183 typedef struct
 184 {
 185     int              natoms;
 186     int              ngtc;
 187     int              nnhpres;
 188     int              nhchainlength; /* number of nose-hoover chains               */
 189     int              nrng;
 190     int              nrngi;
 191     int              flags;           /* Flags telling which entries are present      */
 192     int              fep_state;       /* indicates which of the alchemical states we are in                 */
 193     real            *lambda;          /* lambda vector                               */
 194     matrix           box;             /* box vector coordinates                         */
 195     matrix           box_rel;         /* Relitaive box vectors to preserve shape        */
 196     matrix           boxv;            /* box velocitites for Parrinello-Rahman pcoupl */
 197     matrix           pres_prev;       /* Pressure of the previous step for pcoupl  */
 198     matrix           svir_prev;       /* Shake virial for previous step for pcoupl */
 199     matrix           fvir_prev;       /* Force virial of the previous step for pcoupl  */
 200     double          *nosehoover_xi;   /* for Nose-Hoover tcoupl (ngtc)       */
 201     double          *nosehoover_vxi;  /* for N-H tcoupl (ngtc)               */
 202     double          *nhpres_xi;       /* for Nose-Hoover pcoupl for barostat     */
 203     double          *nhpres_vxi;      /* for Nose-Hoover pcoupl for barostat     */
 204     double          *therm_integral;  /* for N-H/V-rescale tcoupl (ngtc)     */
 205     real             veta;            /* trotter based isotropic P-coupling             */
 206     real             vol0;            /* initial volume,required for computing NPT conserverd quantity */
 207     int              nalloc;          /* Allocation size for x, v and sd_x when !=NULL*/
 208     rvec            *x;               /* the coordinates (natoms)                     */
 209     rvec            *v;               /* the velocities (natoms)                      */
 210     rvec            *sd_X;            /* random part of the x update for stoch. dyn.  */
 211     rvec            *cg_p;            /* p vector for conjugate gradient minimization */
 212
 213     unsigned int    *ld_rng;          /* RNG random state                           */
 214     int             *ld_rngi;         /* RNG index                                  */
 215
 216     int              nmcrng;          /* number of RNG states                       */
 217     unsigned int    *mc_rng;          /* lambda MC RNG random state                 */
 218     int             *mc_rngi;         /* lambda MC RNG index                        */
 219
 220     history_t        hist;            /* Time history for restraints                  */
 221
 222     ekinstate_t      ekinstate;       /* The state of the kinetic energy data      */
 223
 224     energyhistory_t  enerhist;        /* Energy history for statistics           */
 225     df_history_t     dfhist;          /*Free energy history for free energy analysis  */
 226     edsamstate_t     edsamstate;      /* Essential dynamics / flooding history */
 227
 228     int              ddp_count;       /* The DD partitioning count for this state  */
 229     int              ddp_count_cg_gl; /* The DD part. count for index_gl     */
 230     int              ncg_gl;          /* The number of local charge groups            */
 231     int             *cg_gl;           /* The global cg number of the local cgs        */
 232     int              cg_gl_nalloc;    /* Allocation size of cg_gl;              */
 233 } t_state;
 234
 235 typedef struct
 236 {
 237     double *Qinv;  /* inverse mass of thermostat -- computed from inputs, but a good place to store */
 238     double *QPinv; /* inverse mass of thermostat for barostat -- computed from inputs, but a good place to store */
 239     double  Winv;  /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */
 240     tensor  Winvm; /* inverse pressure mass tensor, computed       */
 241 } t_extmass;
 242
 243
 244 typedef struct
 245 {
 246     real    veta;
 247     double  rscale;
 248     double  vscale;
 249     double  rvscale;
 250     double  alpha;
 251     double *vscale_nhc;
 252 } t_vetavars;
 253
 254 #ifdef __cplusplus
 255 }
 256 #endif
 257
 258
 259 #endif /* _state_h_ */