GROMACS

/*

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 *

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 * Copyright (c) 2001-2004, The GROMACS development team.

 * Copyright (c) 2013,2014, by the GROMACS development team, led by

 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,

 * and including many others, as listed in the AUTHORS file in the

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#ifndef _state_h_

#define _state_h_

#include "simple.h"

#include "../../swap/enums.h"

#ifdef __cplusplus

extern "C" {

#endif

/*

 * The t_state struct should contain all the (possibly) non-static

 * information required to define the state of the system.

 * Currently the random seeds for SD and BD are missing.

 */

/* These enums are used in flags as (1<<est...).

 * The order of these enums should not be changed,

 * since that affects the checkpoint (.cpt) file format.

 */

enum {

    estLAMBDA,

    estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI,  estTC_INT,

    estX,   estV,       estSDX,  estCGP,       estLD_RNG, estLD_RNGI,

    estDISRE_INITF, estDISRE_RM3TAV,

    estORIRE_INITF, estORIRE_DTAV,

    estSVIR_PREV, estNH_VXI, estVETA, estVOL0, estNHPRES_XI, estNHPRES_VXI, estFVIR_PREV,

    estFEPSTATE, estMC_RNG, estMC_RNGI,

    estNR

};

#define EST_DISTR(e) (!(((e) >= estLAMBDA && (e) <= estTC_INT) || ((e) >= estSVIR_PREV && (e) <= estMC_RNGI)))

/* The names of the state entries, defined in src/gmxlib/checkpoint.c */

extern const char *est_names[estNR];

typedef struct

{

    real  disre_initf;  /* The scaling factor for initializing the time av. */

    int   ndisrepairs;  /* The number of distance restraints                */

    real *disre_rm3tav; /* The r^-3 time averaged pair distances            */

    real  orire_initf;  /* The scaling factor for initializing the time av. */

    int   norire_Dtav;  /* The number of matrix element in dtav (npair*5)   */

    real *orire_Dtav;   /* The time averaged orientation tensors            */

} history_t;

/* Struct used for checkpointing only.

 * This struct would not be required with unlimited precision.

 * But because of limited precision, the COM motion removal implementation

 * can cause the kinetic energy in the MD loop to differ by a few bits from

 * the kinetic energy one would determine from state.v.

 */

typedef struct

{

    gmx_bool     bUpToDate;

    int          ekin_n;

    tensor      *ekinh;

    tensor      *ekinf;

    tensor      *ekinh_old;

    tensor       ekin_total;

    double      *ekinscalef_nhc;

    double      *ekinscaleh_nhc;

    double      *vscale_nhc;

    real         dekindl;

    real         mvcos;

} ekinstate_t;

/* energy history for delta_h histograms */

typedef struct

{

    int      nndh;             /* the number of energy difference lists */

    int     *ndh;              /* the number in each energy difference list */

    real   **dh;               /* the energy difference lists */

    double   start_time;       /* the start time of these energy diff blocks */

    double   start_lambda;     /* lambda at start time */

    gmx_bool start_lambda_set; /* whether the lambda value is set. Here

                                  For backward-compatibility. */

} delta_h_history_t;

typedef struct

{

    int      nlambda;        /* total number of lambda states - for history*/

    gmx_bool bEquil;         /* Have we reached equilibration */

    int     *n_at_lam;       /* number of points observed at each lambda */

    real    *wl_histo;       /* histogram for WL flatness determination */

    real     wl_delta;       /* current wang-landau delta */

    real    *dfavg;          /* used to update the free energy estimate for AIM */

    real    *sum_dvdl;       /* used to update the sum of the derivative of the potential energy term at lambda */

    real    *store_fepot;    /* store the potential energy at lambda */

    int     *aim_at_lam;      /* number of points observed at each lambda after chosen*/

    int     *laccept;        /* track lambda acceptance */

    real    *sum_weights;    /* weights of the states */

    real    *sum_dg;         /* free energies of the states -- not actually used for weighting, but informational */

    real    *sum_minvar;     /* corrections to weights for minimum variance */

    real    *sum_variance;   /* variances of the states */

    real   **accum_p;        /* accumulated bennett weights for n+1 */

    real   **accum_m;        /* accumulated bennett weights for n-1 */

    real   **accum_p2;       /* accumulated squared bennett weights for n+1 */

    real   **accum_m2;       /* accumulated squared bennett weights for n-1 */

    real   **Tij;            /* transition matrix */

    real   **Tij_empirical;  /* Empirical transition matrix */

} df_history_t;

typedef struct

{

    gmx_int64_t        nsteps;       /* The number of steps in the history            */

    gmx_int64_t        nsum;         /* The nr. of steps in the ener_ave and ener_sum */

    double         *   ener_ave;     /* Energy term history sum to get fluctuations   */

    double         *   ener_sum;     /* Energy term history sum to get fluctuations   */

    int                nener;        /* Number of energy terms in two previous arrays */

    gmx_int64_t        nsteps_sim;   /* The number of steps in ener_sum_sim      */

    gmx_int64_t        nsum_sim;     /* The number of frames in ener_sum_sim     */

    double         *   ener_sum_sim; /* Energy term history sum of the whole sim      */

    delta_h_history_t *dht;          /* The BAR energy differences */

}

energyhistory_t;

typedef struct

{

    /* If one uses essential dynamics or flooding on a group of atoms from

     * more than one molecule, we cannot make this group whole with

     * do_pbc_first_mtop(). We assume that the ED group has the correct PBC

     * representation at the beginning of the simulation and keep track

     * of the shifts to always get it into that representation.

     * For proper restarts from a checkpoint we store the positions of the

     * reference group at the time of checkpoint writing */

    gmx_bool      bFromCpt;     /* Did we start from a checkpoint file?       */

    int           nED;          /* No. of ED/Flooding data sets, if <1 no ED  */

    int          *nref;         /* No. of atoms in i'th reference structure   */

    int          *nav;          /* Same for average structure                 */

    rvec        **old_sref;     /* Positions of the reference atoms

                                   at the last time step (with correct PBC

                                   representation)                            */

    rvec        **old_sref_p;   /* Pointer to these positions                 */

    rvec        **old_sav;      /* Same for the average positions             */

    rvec        **old_sav_p;

}

edsamstate_t;

typedef struct

{

    int        eSwapCoords;                         /* Swapping along x, y, or z-direction?      */

    int        nat_req[eCompNR][eIonNR];            /* Requested ion numbers per type an comp.   */

    int       *nat_req_p[eCompNR][eIonNR];          /* Pointer to this data (for .cpt writing)   */

    int        nAverage;                            /* Use average over this many swap attempt

                                                       steps when determining the ion counts     */

    int        inflow_netto[eCompNR][eIonNR];       /* Flux determined from the # of swaps       */

    int       *inflow_netto_p[eCompNR][eIonNR];     /* Pointer to this data                      */

    int       *nat_past[eCompNR][eIonNR];           /* Array with nAverage entries for history   */

    int       *nat_past_p[eCompNR][eIonNR];         /* Pointer points to the first entry only    */

    /* Channel flux detection, this is counting only and has no influence on whether swaps

     * are performed or not: */

    int            fluxfromAtoB[eCompNR][eIonNR];   /* Flux determined from the split cylinders  */

    int           *fluxfromAtoB_p[eCompNR][eIonNR]; /* Pointer to this data                      */

    int           *fluxleak;                        /* Flux not going through any channel        */

    int            nions;                           /* Size of the following arrays              */

    unsigned char *comp_from;                       /* Ion came from which compartment?          */

    unsigned char *channel_label;                   /* Through which channel did this ion pass?  */

    /* To also make multimeric channel proteins whole, we save the last whole configuration of

     * the channels in the checkpoint file. If we have no checkpoint file, we assume that the

     * starting configuration hast the correct PBC representation after making the individual

     * molecules whole */

    gmx_bool    bFromCpt;                           /* Did we started from a checkpoint file?    */

    int         nat[eChanNR];                       /* Size of xc_old_whole, i.e. the number of

                                                       atoms in each channel                     */

    rvec       *xc_old_whole[eChanNR];              /* Last known whole positions of the two

                                                       channels (important for multimeric ch.!)  */

    rvec      **xc_old_whole_p[eChanNR];            /* Pointer to these positions                */

}

swapstate_t;

typedef struct

{

    int              natoms;

    int              ngtc;

    int              nnhpres;

    int              nhchainlength;   /* number of nose-hoover chains               */

    int              flags;           /* Flags telling which entries are present      */

    int              fep_state;       /* indicates which of the alchemical states we are in                 */

    real            *lambda;          /* lambda vector                               */

    matrix           box;             /* box vector coordinates                         */

    matrix           box_rel;         /* Relitaive box vectors to preserve shape        */

    matrix           boxv;            /* box velocitites for Parrinello-Rahman pcoupl */

    matrix           pres_prev;       /* Pressure of the previous step for pcoupl  */

    matrix           svir_prev;       /* Shake virial for previous step for pcoupl */

    matrix           fvir_prev;       /* Force virial of the previous step for pcoupl  */

    double          *nosehoover_xi;   /* for Nose-Hoover tcoupl (ngtc)       */

    double          *nosehoover_vxi;  /* for N-H tcoupl (ngtc)               */

    double          *nhpres_xi;       /* for Nose-Hoover pcoupl for barostat     */

    double          *nhpres_vxi;      /* for Nose-Hoover pcoupl for barostat     */

    double          *therm_integral;  /* for N-H/V-rescale tcoupl (ngtc)     */

    real             veta;            /* trotter based isotropic P-coupling             */

    real             vol0;            /* initial volume,required for computing NPT conserverd quantity */

    int              nalloc;          /* Allocation size for x, v and sd_x when !=NULL*/

    rvec            *x;               /* the coordinates (natoms)                     */

    rvec            *v;               /* the velocities (natoms)                      */

    rvec            *sd_X;            /* random part of the x update for stoch. dyn.  */

    rvec            *cg_p;            /* p vector for conjugate gradient minimization */

    history_t        hist;            /* Time history for restraints                  */

    ekinstate_t      ekinstate;       /* The state of the kinetic energy data      */

    energyhistory_t  enerhist;        /* Energy history for statistics           */

    swapstate_t      swapstate;       /* Position swapping                       */

    df_history_t     dfhist;          /*Free energy history for free energy analysis  */

    edsamstate_t     edsamstate;      /* Essential dynamics / flooding history */

    int              ddp_count;       /* The DD partitioning count for this state  */

    int              ddp_count_cg_gl; /* The DD part. count for index_gl     */

    int              ncg_gl;          /* The number of local charge groups            */

    int             *cg_gl;           /* The global cg number of the local cgs        */

    int              cg_gl_nalloc;    /* Allocation size of cg_gl;              */

} t_state;

typedef struct

{

    double *Qinv;  /* inverse mass of thermostat -- computed from inputs, but a good place to store */

    double *QPinv; /* inverse mass of thermostat for barostat -- computed from inputs, but a good place to store */

    double  Winv;  /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */

    tensor  Winvm; /* inverse pressure mass tensor, computed       */

} t_extmass;

typedef struct

{

    real    veta;

    double  rscale;

    double  vscale;

    double  rvscale;

    double  alpha;

    double *vscale_nhc;

} t_vetavars;

#ifdef __cplusplus

}

#endif

#endif /* _state_h_ */