libgromacs-dev 5.1.2-1ubuntu1 / usr / include / gromacs / legacyheaders / types / state.h

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * 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
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */
#ifndef _state_h_
#define _state_h_


#include "gromacs/legacyheaders/types/simple.h"
#include "gromacs/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    *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_ */