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
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * GRoups of Organic Molecules in ACtion for Science
  34  */
  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 /* for now, define the number of NH chains here */
  49 #define NNHCHAIN 5
  50
  51 /* These enums are used in flags as (1<<est...).
  52  * The order of these enums should not be changed,
  53  * since that affects the checkpoint (.cpt) file format.
  54  */
  55 enum { estLAMBDA,
  56        estBOX, estBOX_REL, estBOXV, estVIR_PREV, estPRES_PREV,
  57        estNH_XI,  estNH_VXI, estTC_INT, estVETA, estVOL0,
  58        estX,   estV,       estSDX,  estCGP,       estLD_RNG, estLD_RNGI,
  59        estDISRE_INITF, estDISRE_RM3TAV,
  60        estORIRE_INITF, estORIRE_DTAV,
  61        estNR };
  62
  63 /* The names of the state entries, defined in src/gmxib/checkpoint.c */
  64 extern const char *est_names[estNR];
  65
  66 typedef struct
  67 {
  68   real disre_initf;    /* The scaling factor for initializing the time av. */
  69   int  ndisrepairs;    /* The number of distance restraints                */
  70   real *disre_rm3tav;  /* The r^-3 time averaged pair distances            */
  71   real orire_initf;    /* The scaling factor for initializing the time av. */
  72   int  norire_Dtav;    /* The number of matrix element in dtav (npair*5)   */
  73   real *orire_Dtav;    /* The time averaged orientation tensors            */
  74 } history_t;
  75
  76 /* Struct used for checkpointing only.
  77  * This struct would not be required with unlimited precision.
  78  * But because of limited precision, the COM motion removal implementation
  79  * can cause the kinetic energy in the MD loop to differ by a few bits from
  80  * the kinetic energy one would determine from state.v.
  81  */
  82 typedef struct
  83 {
  84   bool     bUpToDate;
  85   int      ekinh_n;
  86   int      ekin_n;
  87   tensor * ekinh;
  88   tensor * ekin;
  89   tensor   ekin_total;
  90   real     dekindl;
  91   real     mvcos;
  92 } ekinstate_t;
  93
  94 typedef struct
  95 {
  96   gmx_large_int_t nsteps;       /* The number of steps in the history            */
  97   gmx_large_int_t nsum;         /* The nr. of steps in the ener_ave and ener_sum */
  98   double *   ener_ave;     /* Energy term history sum to get fluctuations   */
  99   double *   ener_sum;     /* Energy term history sum to get fluctuations   */
 100   int        nener;        /* Number of energy terms in two previous arrays */
 101   gmx_large_int_t nsteps_sim;   /* The number of steps in ener_sum_sim           */
 102   gmx_large_int_t nsum_sim;     /* The number of frames in ener_sum_sim          */
 103   double *   ener_sum_sim; /* Energy term history sum of the whole sim      */
 104 }
 105 energyhistory_t;
 106
 107 typedef struct
 108 {
 109   int           natoms;
 110   int           ngtc;
 111   int           nrng;
 112   int           nrngi;
 113   int           flags;  /* Flags telling which entries are present      */
 114   real          lambda; /* the free energy switching parameter          */
 115   matrix        box;    /* box vector coordinates                       */
 116   matrix        box_rel; /* Relitaive box vectors to preserve shape     */
 117   matrix        boxv;   /* box velocitites for Parrinello-Rahman pcoupl */
 118   matrix        pres_prev; /* Pressure of the previous step for pcoupl  */
 119   matrix        vir_prev; /* Pressure of the previous step for pcoupl  */
 120   double        *nosehoover_xi;  /* for Nose-Hoover tcoupl (ngtc)       */
 121   double        *nosehoover_vxi; /* for N-H tcoupl (ngtc)               */
 122   double        *therm_integral; /* for N-H/V-rescale tcoupl (ngtc)     */
 123   real          veta; /* trotter based isotropic P-coupling             */
 124   real          vol0; /* initial volume,required for computing NPT conserverd quantity */
 125   int           nalloc; /* Allocation size for x, v and sd_x when !=NULL*/
 126   rvec          *x;     /* the coordinates (natoms)                     */
 127   rvec          *v;     /* the velocities (natoms)                      */
 128   rvec          *sd_X;  /* random part of the x update for stoch. dyn.  */
 129   rvec          *cg_p;  /* p vector for conjugate gradient minimization */
 130
 131   unsigned int  *ld_rng;  /* RNG random state                           */
 132   int           *ld_rngi; /* RNG index                                  */
 133
 134   history_t     hist;   /* Time history for restraints                  */
 135
 136   ekinstate_t   ekinstate; /* The state of the kinetic energy data      */
 137
 138   energyhistory_t  enerhist; /* Energy history for statistics           */
 139
 140   int           ddp_count; /* The DD partitioning count for this state  */
 141   int           ddp_count_cg_gl; /* The DD part. count for index_gl     */
 142   int           ncg_gl; /* The number of local charge groups            */
 143   int           *cg_gl; /* The global cg number of the local cgs        */
 144   int           cg_gl_nalloc; /* Allocation size of cg_gl;              */
 145 } t_state;
 146
 147 typedef struct
 148 {
 149   double *Qinv;  /* inverse mass of thermostat -- computed from inputs, but a good place to store */
 150   double Winv;   /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */
 151   tensor Winvm;  /* inverse pressure mass tensor, computed       */
 152 } t_extmass;
 153
 154
 155 typedef struct
 156 {
 157   real veta;
 158   double rscale;
 159   double vscale;
 160   double rvscale;
 161   double alpha;
 162   double *vscale_nhc;
 163 } t_vetavars;
 164
 165
 166 #endif /* _state_h_ */