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state.h

added needed variables to df_history_t structure - Christopher Mirabzadeh, 11/02/2015 11:10 PM

 
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/*
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 * This file is part of the GROMACS molecular simulation package.
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 *
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 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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 * Copyright (c) 2001-2004, The GROMACS development team.
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 * Copyright (c) 2013,2014, by the GROMACS development team, led by
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 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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 * and including many others, as listed in the AUTHORS file in the
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 * top-level source directory and at http://www.gromacs.org.
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 *
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 * GROMACS is free software; you can redistribute it and/or
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 * modify it under the terms of the GNU Lesser General Public License
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 * as published by the Free Software Foundation; either version 2.1
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 * of the License, or (at your option) any later version.
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 *
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 * GROMACS is distributed in the hope that it will be useful,
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 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
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 * Lesser General Public License for more details.
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 *
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 * You should have received a copy of the GNU Lesser General Public
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 * License along with GROMACS; if not, see
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 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
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 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
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 *
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 * If you want to redistribute modifications to GROMACS, please
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 * consider that scientific software is very special. Version
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 * control is crucial - bugs must be traceable. We will be happy to
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 * consider code for inclusion in the official distribution, but
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 * derived work must not be called official GROMACS. Details are found
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 * in the README & COPYING files - if they are missing, get the
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 * official version at http://www.gromacs.org.
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 *
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 * To help us fund GROMACS development, we humbly ask that you cite
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 * the research papers on the package. Check out http://www.gromacs.org.
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 */
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#ifndef _state_h_
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#define _state_h_
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#include "simple.h"
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#include "../../swap/enums.h"
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#ifdef __cplusplus
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extern "C" {
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#endif
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/*
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 * The t_state struct should contain all the (possibly) non-static
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 * information required to define the state of the system.
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 * Currently the random seeds for SD and BD are missing.
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 */
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/* These enums are used in flags as (1<<est...).
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 * The order of these enums should not be changed,
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 * since that affects the checkpoint (.cpt) file format.
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 */
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enum {
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    estLAMBDA,
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    estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI,  estTC_INT,
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    estX,   estV,       estSDX,  estCGP,       estLD_RNG, estLD_RNGI,
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    estDISRE_INITF, estDISRE_RM3TAV,
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    estORIRE_INITF, estORIRE_DTAV,
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    estSVIR_PREV, estNH_VXI, estVETA, estVOL0, estNHPRES_XI, estNHPRES_VXI, estFVIR_PREV,
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    estFEPSTATE, estMC_RNG, estMC_RNGI,
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    estNR
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};
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#define EST_DISTR(e) (!(((e) >= estLAMBDA && (e) <= estTC_INT) || ((e) >= estSVIR_PREV && (e) <= estMC_RNGI)))
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/* The names of the state entries, defined in src/gmxlib/checkpoint.c */
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extern const char *est_names[estNR];
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typedef struct
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{
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    real  disre_initf;  /* The scaling factor for initializing the time av. */
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    int   ndisrepairs;  /* The number of distance restraints                */
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    real *disre_rm3tav; /* The r^-3 time averaged pair distances            */
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    real  orire_initf;  /* The scaling factor for initializing the time av. */
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    int   norire_Dtav;  /* The number of matrix element in dtav (npair*5)   */
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    real *orire_Dtav;   /* The time averaged orientation tensors            */
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} history_t;
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/* Struct used for checkpointing only.
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 * This struct would not be required with unlimited precision.
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 * But because of limited precision, the COM motion removal implementation
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 * can cause the kinetic energy in the MD loop to differ by a few bits from
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 * the kinetic energy one would determine from state.v.
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 */
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typedef struct
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{
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    gmx_bool     bUpToDate;
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    int          ekin_n;
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    tensor      *ekinh;
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    tensor      *ekinf;
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    tensor      *ekinh_old;
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    tensor       ekin_total;
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    double      *ekinscalef_nhc;
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    double      *ekinscaleh_nhc;
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    double      *vscale_nhc;
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    real         dekindl;
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    real         mvcos;
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} ekinstate_t;
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/* energy history for delta_h histograms */
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typedef struct
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{
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    int      nndh;             /* the number of energy difference lists */
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    int     *ndh;              /* the number in each energy difference list */
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    real   **dh;               /* the energy difference lists */
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    double   start_time;       /* the start time of these energy diff blocks */
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    double   start_lambda;     /* lambda at start time */
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    gmx_bool start_lambda_set; /* whether the lambda value is set. Here
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                                  For backward-compatibility. */
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} delta_h_history_t;
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typedef struct
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{
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    int      nlambda;        /* total number of lambda states - for history*/
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    gmx_bool bEquil;         /* Have we reached equilibration */
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    int     *n_at_lam;       /* number of points observed at each lambda */
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    real    *wl_histo;       /* histogram for WL flatness determination */
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    real     wl_delta;       /* current wang-landau delta */
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    real    *dfavg;          /* used to update the free energy estimate for AIM */
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    real    *sum_dvdl;       /* used to update the sum of the derivative of the potential energy term at lambda */
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    real    *store_fepot;    /* store the potential energy at lambda */
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    int     *aim_at_lam;      /* number of points observed at each lambda after chosen*/
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    int     *laccept;        /* track lambda acceptance */
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    real    *sum_weights;    /* weights of the states */
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    real    *sum_dg;         /* free energies of the states -- not actually used for weighting, but informational */
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    real    *sum_minvar;     /* corrections to weights for minimum variance */
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    real    *sum_variance;   /* variances of the states */
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    real   **accum_p;        /* accumulated bennett weights for n+1 */
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    real   **accum_m;        /* accumulated bennett weights for n-1 */
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    real   **accum_p2;       /* accumulated squared bennett weights for n+1 */
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    real   **accum_m2;       /* accumulated squared bennett weights for n-1 */
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    real   **Tij;            /* transition matrix */
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    real   **Tij_empirical;  /* Empirical transition matrix */
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} df_history_t;
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typedef struct
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{
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    gmx_int64_t        nsteps;       /* The number of steps in the history            */
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    gmx_int64_t        nsum;         /* The nr. of steps in the ener_ave and ener_sum */
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    double         *   ener_ave;     /* Energy term history sum to get fluctuations   */
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    double         *   ener_sum;     /* Energy term history sum to get fluctuations   */
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    int                nener;        /* Number of energy terms in two previous arrays */
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    gmx_int64_t        nsteps_sim;   /* The number of steps in ener_sum_sim      */
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    gmx_int64_t        nsum_sim;     /* The number of frames in ener_sum_sim     */
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    double         *   ener_sum_sim; /* Energy term history sum of the whole sim      */
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    delta_h_history_t *dht;          /* The BAR energy differences */
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}
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energyhistory_t;
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typedef struct
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{
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    /* If one uses essential dynamics or flooding on a group of atoms from
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     * more than one molecule, we cannot make this group whole with
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     * do_pbc_first_mtop(). We assume that the ED group has the correct PBC
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     * representation at the beginning of the simulation and keep track
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     * of the shifts to always get it into that representation.
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     * For proper restarts from a checkpoint we store the positions of the
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     * reference group at the time of checkpoint writing */
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    gmx_bool      bFromCpt;     /* Did we start from a checkpoint file?       */
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    int           nED;          /* No. of ED/Flooding data sets, if <1 no ED  */
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    int          *nref;         /* No. of atoms in i'th reference structure   */
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    int          *nav;          /* Same for average structure                 */
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    rvec        **old_sref;     /* Positions of the reference atoms
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                                   at the last time step (with correct PBC
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                                   representation)                            */
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    rvec        **old_sref_p;   /* Pointer to these positions                 */
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    rvec        **old_sav;      /* Same for the average positions             */
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    rvec        **old_sav_p;
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}
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edsamstate_t;
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typedef struct
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{
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    int        eSwapCoords;                         /* Swapping along x, y, or z-direction?      */
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    int        nat_req[eCompNR][eIonNR];            /* Requested ion numbers per type an comp.   */
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    int       *nat_req_p[eCompNR][eIonNR];          /* Pointer to this data (for .cpt writing)   */
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    int        nAverage;                            /* Use average over this many swap attempt
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                                                       steps when determining the ion counts     */
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    int        inflow_netto[eCompNR][eIonNR];       /* Flux determined from the # of swaps       */
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    int       *inflow_netto_p[eCompNR][eIonNR];     /* Pointer to this data                      */
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    int       *nat_past[eCompNR][eIonNR];           /* Array with nAverage entries for history   */
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    int       *nat_past_p[eCompNR][eIonNR];         /* Pointer points to the first entry only    */
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    /* Channel flux detection, this is counting only and has no influence on whether swaps
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     * are performed or not: */
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    int            fluxfromAtoB[eCompNR][eIonNR];   /* Flux determined from the split cylinders  */
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    int           *fluxfromAtoB_p[eCompNR][eIonNR]; /* Pointer to this data                      */
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    int           *fluxleak;                        /* Flux not going through any channel        */
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    int            nions;                           /* Size of the following arrays              */
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    unsigned char *comp_from;                       /* Ion came from which compartment?          */
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    unsigned char *channel_label;                   /* Through which channel did this ion pass?  */
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    /* To also make multimeric channel proteins whole, we save the last whole configuration of
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     * the channels in the checkpoint file. If we have no checkpoint file, we assume that the
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     * starting configuration hast the correct PBC representation after making the individual
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     * molecules whole */
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    gmx_bool    bFromCpt;                           /* Did we started from a checkpoint file?    */
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    int         nat[eChanNR];                       /* Size of xc_old_whole, i.e. the number of
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                                                       atoms in each channel                     */
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    rvec       *xc_old_whole[eChanNR];              /* Last known whole positions of the two
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                                                       channels (important for multimeric ch.!)  */
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    rvec      **xc_old_whole_p[eChanNR];            /* Pointer to these positions                */
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}
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swapstate_t;
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typedef struct
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{
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    int              natoms;
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    int              ngtc;
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    int              nnhpres;
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    int              nhchainlength;   /* number of nose-hoover chains               */
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    int              flags;           /* Flags telling which entries are present      */
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    int              fep_state;       /* indicates which of the alchemical states we are in                 */
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    real            *lambda;          /* lambda vector                               */
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    matrix           box;             /* box vector coordinates                         */
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    matrix           box_rel;         /* Relitaive box vectors to preserve shape        */
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    matrix           boxv;            /* box velocitites for Parrinello-Rahman pcoupl */
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    matrix           pres_prev;       /* Pressure of the previous step for pcoupl  */
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    matrix           svir_prev;       /* Shake virial for previous step for pcoupl */
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    matrix           fvir_prev;       /* Force virial of the previous step for pcoupl  */
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    double          *nosehoover_xi;   /* for Nose-Hoover tcoupl (ngtc)       */
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    double          *nosehoover_vxi;  /* for N-H tcoupl (ngtc)               */
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    double          *nhpres_xi;       /* for Nose-Hoover pcoupl for barostat     */
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    double          *nhpres_vxi;      /* for Nose-Hoover pcoupl for barostat     */
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    double          *therm_integral;  /* for N-H/V-rescale tcoupl (ngtc)     */
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    real             veta;            /* trotter based isotropic P-coupling             */
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    real             vol0;            /* initial volume,required for computing NPT conserverd quantity */
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    int              nalloc;          /* Allocation size for x, v and sd_x when !=NULL*/
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    rvec            *x;               /* the coordinates (natoms)                     */
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    rvec            *v;               /* the velocities (natoms)                      */
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    rvec            *sd_X;            /* random part of the x update for stoch. dyn.  */
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    rvec            *cg_p;            /* p vector for conjugate gradient minimization */
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    history_t        hist;            /* Time history for restraints                  */
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    ekinstate_t      ekinstate;       /* The state of the kinetic energy data      */
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    energyhistory_t  enerhist;        /* Energy history for statistics           */
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    swapstate_t      swapstate;       /* Position swapping                       */
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    df_history_t     dfhist;          /*Free energy history for free energy analysis  */
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    edsamstate_t     edsamstate;      /* Essential dynamics / flooding history */
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    int              ddp_count;       /* The DD partitioning count for this state  */
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    int              ddp_count_cg_gl; /* The DD part. count for index_gl     */
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    int              ncg_gl;          /* The number of local charge groups            */
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    int             *cg_gl;           /* The global cg number of the local cgs        */
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    int              cg_gl_nalloc;    /* Allocation size of cg_gl;              */
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} t_state;
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typedef struct
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{
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    double *Qinv;  /* inverse mass of thermostat -- computed from inputs, but a good place to store */
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    double *QPinv; /* inverse mass of thermostat for barostat -- computed from inputs, but a good place to store */
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    double  Winv;  /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */
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    tensor  Winvm; /* inverse pressure mass tensor, computed       */
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} t_extmass;
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typedef struct
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{
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    real    veta;
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    double  rscale;
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    double  vscale;
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    double  rvscale;
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    double  alpha;
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    double *vscale_nhc;
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} t_vetavars;
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#ifdef __cplusplus
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}
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#endif
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#endif /* _state_h_ */