src/gromacs/mdtypes/state.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #ifndef GMX_MDTYPES_STATE_H
  38 #define GMX_MDTYPES_STATE_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #include "gromacs/mdtypes/md_enums.h"
  42 #include "gromacs/utility/basedefinitions.h"
  43 #include "gromacs/utility/real.h"
  44
  45 struct energyhistory_t;
  46
  47 /*
  48  * The t_state struct should contain all the (possibly) non-static
  49  * information required to define the state of the system.
  50  * Currently the random seeds for SD and BD are missing.
  51  */
  52
  53 /* These enums are used in flags as (1<<est...).
  54  * The order of these enums should not be changed,
  55  * since that affects the checkpoint (.cpt) file format.
  56  */
  57 enum {
  58     estLAMBDA,
  59     estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI,  estTC_INT,
  60     estX,   estV,       est_SDX_NOTSUPPORTED,  estCGP,
  61     estLD_RNG, estLD_RNGI,
  62     estDISRE_INITF, estDISRE_RM3TAV,
  63     estORIRE_INITF, estORIRE_DTAV,
  64     estSVIR_PREV, estNH_VXI, estVETA, estVOL0, estNHPRES_XI, estNHPRES_VXI, estFVIR_PREV,
  65     estFEPSTATE, estMC_RNG, estMC_RNGI,
  66     estNR
  67 };
  68
  69 #define EST_DISTR(e) (!(((e) >= estLAMBDA && (e) <= estTC_INT) || ((e) >= estSVIR_PREV && (e) <= estMC_RNGI)))
  70
  71 /* The names of the state entries, defined in src/gmxlib/checkpoint.c */
  72 extern const char *est_names[estNR];
  73
  74 typedef struct history_t
  75 {
  76     real  disre_initf;  /* The scaling factor for initializing the time av. */
  77     int   ndisrepairs;  /* The number of distance restraints                */
  78     real *disre_rm3tav; /* The r^-3 time averaged pair distances            */
  79     real  orire_initf;  /* The scaling factor for initializing the time av. */
  80     int   norire_Dtav;  /* The number of matrix element in dtav (npair*5)   */
  81     real *orire_Dtav;   /* The time averaged orientation tensors            */
  82 } history_t;
  83
  84 /* Struct used for checkpointing only.
  85  * This struct would not be required with unlimited precision.
  86  * But because of limited precision, the COM motion removal implementation
  87  * can cause the kinetic energy in the MD loop to differ by a few bits from
  88  * the kinetic energy one would determine from state.v.
  89  */
  90 typedef struct ekinstate_t
  91 {
  92     gmx_bool     bUpToDate;
  93     int          ekin_n;
  94     tensor      *ekinh;
  95     tensor      *ekinf;
  96     tensor      *ekinh_old;
  97     tensor       ekin_total;
  98     double      *ekinscalef_nhc;
  99     double      *ekinscaleh_nhc;
 100     double      *vscale_nhc;
 101     real         dekindl;
 102     real         mvcos;
 103 } ekinstate_t;
 104
 105 typedef struct df_history_t
 106 {
 107     int      nlambda;        /* total number of lambda states - for history*/
 108
 109     gmx_bool bEquil;         /* Have we reached equilibration */
 110     int     *n_at_lam;       /* number of points observed at each lambda */
 111     real    *wl_histo;       /* histogram for WL flatness determination */
 112     real     wl_delta;       /* current wang-landau delta */
 113
 114     real    *sum_weights;    /* weights of the states */
 115     real    *sum_dg;         /* free energies of the states -- not actually used for weighting, but informational */
 116     real    *sum_minvar;     /* corrections to weights for minimum variance */
 117     real    *sum_variance;   /* variances of the states */
 118
 119     real   **accum_p;        /* accumulated bennett weights for n+1 */
 120     real   **accum_m;        /* accumulated bennett weights for n-1 */
 121     real   **accum_p2;       /* accumulated squared bennett weights for n+1 */
 122     real   **accum_m2;       /* accumulated squared bennett weights for n-1 */
 123
 124     real   **Tij;            /* transition matrix */
 125     real   **Tij_empirical;  /* Empirical transition matrix */
 126
 127 } df_history_t;
 128
 129 typedef struct edsamstate_t
 130 {
 131     /* If one uses essential dynamics or flooding on a group of atoms from
 132      * more than one molecule, we cannot make this group whole with
 133      * do_pbc_first_mtop(). We assume that the ED group has the correct PBC
 134      * representation at the beginning of the simulation and keep track
 135      * of the shifts to always get it into that representation.
 136      * For proper restarts from a checkpoint we store the positions of the
 137      * reference group at the time of checkpoint writing */
 138     gmx_bool      bFromCpt;     /* Did we start from a checkpoint file?       */
 139     int           nED;          /* No. of ED/Flooding data sets, if <1 no ED  */
 140     int          *nref;         /* No. of atoms in i'th reference structure   */
 141     int          *nav;          /* Same for average structure                 */
 142     rvec        **old_sref;     /* Positions of the reference atoms
 143                                    at the last time step (with correct PBC
 144                                    representation)                            */
 145     rvec        **old_sref_p;   /* Pointer to these positions                 */
 146     rvec        **old_sav;      /* Same for the average positions             */
 147     rvec        **old_sav_p;
 148 }
 149 edsamstate_t;
 150
 151 typedef struct swapstateIons_t
 152 {
 153     int  nMolReq[eCompNR];                  /* Requested # of molecules per compartment      */
 154     int *nMolReq_p[eCompNR];                /* Pointer to this data (for .cpt writing)       */
 155     int  inflow_net[eCompNR];               /* Flux determined from the # of swaps           */
 156     int *inflow_net_p[eCompNR];             /* Pointer to this data                          */
 157     int *nMolPast[eCompNR];                 /* Array with nAverage entries for history       */
 158     int *nMolPast_p[eCompNR];               /* Pointer points to the first entry only        */
 159     /*                                                                                       */
 160     /* Channel flux detection, this is counting only and has no influence on whether swaps   */
 161     /* are performed or not:                                                                 */
 162     int            fluxfromAtoB[eCompNR];   /* Flux determined from the split cylinders      */
 163     int           *fluxfromAtoB_p[eCompNR]; /* Pointer to this data                          */
 164     int            nMol;                    /* # of molecules, size of the following arrays  */
 165     unsigned char *comp_from;               /* Ion came from which compartment?              */
 166     unsigned char *channel_label;           /* Through which channel did this ion pass?      */
 167 } swapstateIons_t;
 168
 169 typedef struct swapstate_t
 170 {
 171     int  eSwapCoords;                       /* Swapping along x, y, or z-direction?          */
 172     int  nIonTypes;                         /* Number of ion types, this is the size of      */
 173                                             /* the following arrays                          */
 174     int  nAverage;                          /* Use average over this many swap attempt       */
 175                                             /* steps when determining the ion counts         */
 176     int  fluxleak;                          /* Ions not going through any channel (bad!)     */
 177     int *fluxleak_p;                        /* Pointer to this data                          */
 178     /*                                                                                       */
 179     /* To also make multimeric channel proteins whole, we save the last whole configuration  */
 180     /* of the channels in the checkpoint file. If we have no checkpoint file, we assume      */
 181     /* that the starting configuration has the correct PBC representation after making the   */
 182     /* individual molecules whole                                                            */
 183     gmx_bool         bFromCpt;                 /* Did we start from a checkpoint file?       */
 184     int              nat[eChanNR];             /* Size of xc_old_whole, i.e. the number of   */
 185                                                /* atoms in each channel                      */
 186     rvec            *xc_old_whole[eChanNR];    /* Last known whole positions of the two      */
 187                                                /* channels (important for multimeric ch.!)   */
 188     rvec           **xc_old_whole_p[eChanNR];  /* Pointer to these positions                 */
 189     swapstateIons_t *ionType;
 190 }
 191 swapstate_t;
 192
 193
 194 typedef struct t_state
 195 {
 196     int                     natoms;
 197     int                     ngtc;
 198     int                     nnhpres;
 199     int                     nhchainlength;   /* number of nose-hoover chains               */
 200     int                     flags;           /* Flags telling which entries are present      */
 201     int                     fep_state;       /* indicates which of the alchemical states we are in                 */
 202     real                   *lambda;          /* lambda vector                               */
 203     matrix                  box;             /* box vector coordinates                         */
 204     matrix                  box_rel;         /* Relitaive box vectors to preserve shape        */
 205     matrix                  boxv;            /* box velocitites for Parrinello-Rahman pcoupl */
 206     matrix                  pres_prev;       /* Pressure of the previous step for pcoupl  */
 207     matrix                  svir_prev;       /* Shake virial for previous step for pcoupl */
 208     matrix                  fvir_prev;       /* Force virial of the previous step for pcoupl  */
 209     double                 *nosehoover_xi;   /* for Nose-Hoover tcoupl (ngtc)       */
 210     double                 *nosehoover_vxi;  /* for N-H tcoupl (ngtc)               */
 211     double                 *nhpres_xi;       /* for Nose-Hoover pcoupl for barostat     */
 212     double                 *nhpres_vxi;      /* for Nose-Hoover pcoupl for barostat     */
 213     double                 *therm_integral;  /* for N-H/V-rescale tcoupl (ngtc)     */
 214     real                    veta;            /* trotter based isotropic P-coupling             */
 215     real                    vol0;            /* initial volume,required for computing NPT conserverd quantity */
 216     int                     nalloc;          /* Allocation size for x and v when !=NULL*/
 217     rvec                   *x;               /* the coordinates (natoms)                     */
 218     rvec                   *v;               /* the velocities (natoms)                      */
 219     rvec                   *cg_p;            /* p vector for conjugate gradient minimization */
 220
 221     history_t               hist;            /* Time history for restraints                  */
 222
 223     ekinstate_t             ekinstate;       /* The state of the kinetic energy data      */
 224
 225     struct energyhistory_t *enerhist;        /* Energy history for statistics           */
 226     swapstate_t             swapstate;       /* Position swapping                       */
 227     df_history_t            dfhist;          /*Free energy history for free energy analysis  */
 228     edsamstate_t            edsamstate;      /* Essential dynamics / flooding history */
 229
 230     int                     ddp_count;       /* The DD partitioning count for this state  */
 231     int                     ddp_count_cg_gl; /* The DD part. count for index_gl     */
 232     int                     ncg_gl;          /* The number of local charge groups            */
 233     int                    *cg_gl;           /* The global cg number of the local cgs        */
 234     int                     cg_gl_nalloc;    /* Allocation size of cg_gl;              */
 235 } t_state;
 236
 237 typedef struct t_extmass
 238 {
 239     double *Qinv;  /* inverse mass of thermostat -- computed from inputs, but a good place to store */
 240     double *QPinv; /* inverse mass of thermostat for barostat -- computed from inputs, but a good place to store */
 241     double  Winv;  /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */
 242     tensor  Winvm; /* inverse pressure mass tensor, computed       */
 243 } t_extmass;
 244
 245
 246 typedef struct
 247 {
 248     real    veta;
 249     double  rscale;
 250     double  vscale;
 251     double  rvscale;
 252     double  alpha;
 253     double *vscale_nhc;
 254 } t_vetavars;
 255
 256 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength);
 257
 258 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda);
 259
 260 t_state *serial_init_local_state(t_state *state_global);
 261
 262 void done_state(t_state *state);
 263
 264 void comp_state(const t_state *st1, const t_state *st2, gmx_bool bRMSD, real ftol, real abstol);
 265
 266 #endif