include/types/state.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
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  35 #ifndef _state_h_
  36 #define _state_h_
  37
  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 /*
  43  * The t_state struct should contain all the (possibly) non-static
  44  * information required to define the state of the system.
  45  * Currently the random seeds for SD and BD are missing.
  46  */
  47
  48 /* These enums are used in flags as (1<<est...).
  49  * The order of these enums should not be changed,
  50  * since that affects the checkpoint (.cpt) file format.
  51  */
  52 enum { estLAMBDA,
  53        estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI,  estTC_INT,
  54        estX,   estV,       estSDX,  estCGP,       estLD_RNG, estLD_RNGI,
  55        estDISRE_INITF, estDISRE_RM3TAV,
  56        estORIRE_INITF, estORIRE_DTAV,
  57        estNR };
  58
  59 /* The names of the state entries, defined in src/gmxib/checkpoint.c */
  60 extern const char *est_names[estNR];
  61
  62 typedef struct
  63 {
  64   real disre_initf;    /* The scaling factor for initializing the time av. */
  65   int  ndisrepairs;    /* The number of distance restraints                */
  66   real *disre_rm3tav;  /* The r^-3 time averaged pair distances            */
  67   real orire_initf;    /* The scaling factor for initializing the time av. */
  68   int  norire_Dtav;    /* The number of matrix element in dtav (npair*5)   */
  69   real *orire_Dtav;    /* The time averaged orientation tensors            */
  70 } history_t;
  71
  72 /* Struct used for checkpointing only.
  73  * This struct would not be required with unlimited precision.
  74  * But because of limited precision, the COM motion removal implementation
  75  * can cause the kinetic energy in the MD loop to differ by a few bits from
  76  * the kinetic energy one would determine from state.v.
  77  */
  78 typedef struct
  79 {
  80   bool     bUpToDate;
  81   int      ekinh_n;
  82   tensor * ekinh;
  83   real     dekindl;
  84   real     mvcos;
  85 } ekinstate_t;
  86
  87 typedef struct
  88 {
  89   gmx_large_int_t nsteps;       /* The number of steps in the history            */
  90   gmx_large_int_t nsum;         /* The nr. of steps in the ener_ave and ener_sum */
  91   double *   ener_ave;     /* Energy term history sum to get fluctuations   */
  92   double *   ener_sum;     /* Energy term history sum to get fluctuations   */
  93   int        nener;        /* Number of energy terms in two previous arrays */
  94   gmx_large_int_t nsteps_sim;   /* The number of steps in ener_sum_sim           */
  95   gmx_large_int_t nsum_sim;     /* The number of frames in ener_sum_sim          */
  96   double *   ener_sum_sim; /* Energy term history sum of the whole sim      */
  97 }
  98 energyhistory_t;
  99
 100 typedef struct
 101 {
 102   int           natoms;
 103   int           ngtc;
 104   int           nrng;
 105   int           nrngi;
 106   int           flags;  /* Flags telling which entries are present      */
 107   real          lambda; /* the free energy switching parameter          */
 108   matrix            box;    /* box vector coordinates                           */
 109   matrix        box_rel; /* Relitaive box vectors to preserve shape     */
 110   matrix            boxv;   /* box velocitites for Parrinello-Rahman pcoupl */
 111   matrix        pres_prev; /* Pressure of the previous step for pcoupl  */
 112   real          *nosehoover_xi;  /* for Nose-Hoover tcoupl (ngtc)       */
 113   double        *therm_integral; /* for N-H/V-rescale tcoupl (ngtc)     */
 114   int           nalloc; /* Allocation size for x, v and sd_x when !=NULL*/
 115   rvec          *x;     /* the coordinates (natoms)                     */
 116   rvec          *v;     /* the velocities (natoms)                      */
 117   rvec          *sd_X;  /* random part of the x update for stoch. dyn.  */
 118   rvec          *cg_p;  /* p vector for conjugate gradient minimization */
 119
 120   unsigned int  *ld_rng;  /* RNG random state                           */
 121   int           *ld_rngi; /* RNG index                                  */
 122
 123   history_t     hist;   /* Time history for restraints                  */
 124
 125   ekinstate_t   ekinstate; /* The state of the kinetic energy data      */
 126
 127   energyhistory_t  enerhist; /* Energy history for statistics           */
 128
 129   int           ddp_count; /* The DD partitioning count for this state  */
 130   int           ddp_count_cg_gl; /* The DD part. count for index_gl     */
 131   int           ncg_gl; /* The number of local charge groups            */
 132   int           *cg_gl; /* The global cg number of the local cgs        */
 133   int           cg_gl_nalloc; /* Allocation size of cg_gl;              */
 134 } t_state;
 135
 136 #endif /* _state_h_ */