include/update.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  * Gromacs Runs On Most of All Computer Systems
  34  */
  35
  36 #ifndef _update_h
  37 #define _update_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include "typedefs.h"
  44 #include "mshift.h"
  45 #include "tgroup.h"
  46 #include "network.h"
  47 #include "force.h"
  48 #include "pull.h"
  49 #include "gmx_random.h"
  50
  51 /* Abstract type for stochastic dynamics */
  52 typedef struct gmx_update *gmx_update_t;
  53
  54 /* Initialize the stochastic dynamics struct */
  55 extern gmx_update_t init_update(FILE *fplog,t_inputrec *ir);
  56
  57 /* Store the random state from sd in state */
  58 extern void get_stochd_state(gmx_update_t sd,t_state *state);
  59
  60 /* Set the random in sd from state */
  61 extern void set_stochd_state(gmx_update_t sd,t_state *state);
  62
  63 /* Store the box at step step
  64  * as a reference state for simulations with box deformation.
  65  */
  66 extern void set_deform_reference_box(gmx_update_t upd,
  67                                      gmx_large_int_t step,matrix box);
  68
  69 extern void update_extended(FILE         *fplog,
  70                    gmx_large_int_t   step,
  71                    t_inputrec   *inputrec,
  72                    t_mdatoms    *md,
  73                    t_state      *state,
  74                    gmx_ekindata_t *ekind,
  75                    matrix       pcoupl_mu,
  76                    matrix       M,
  77                    gmx_wallcycle_t wcycle,
  78                    gmx_update_t upd,
  79                    bool         bInitStep,
  80                    bool         bFirstHalf,
  81                    t_extmass    *MassQ
  82 );
  83 /* Return TRUE if OK, FALSE in case of Shake Error */
  84
  85 extern void update_coords(FILE         *fplog,
  86                           gmx_large_int_t   step,
  87                           t_inputrec   *inputrec,  /* input record and box stuff        */
  88                           t_mdatoms    *md,
  89                           t_state      *state,
  90                           rvec         *f,    /* forces on home particles */
  91                           bool         bDoLR,
  92                           rvec         *f_lr,
  93                           t_fcdata     *fcd,
  94                           gmx_ekindata_t *ekind,
  95                           matrix       M,
  96                           gmx_wallcycle_t wcycle,
  97                           gmx_update_t upd,
  98                           bool         bInitStep,
  99                           bool         bFirstHalf,
 100                           t_commrec    *cr,  /* these shouldn't be here -- need to think about it */
 101                           t_nrnb       *nrnb,
 102                           gmx_constr_t constr,
 103                           t_idef       *idef);
 104
 105 /* Return TRUE if OK, FALSE in case of Shake Error */
 106
 107 extern void update_constraints(FILE         *fplog,
 108                                gmx_large_int_t   step,
 109                                real         *dvdlambda, /* FEP stuff */
 110                                t_inputrec   *inputrec,  /* input record and box stuff   */
 111                                t_mdatoms    *md,
 112                                t_state      *state,
 113                                t_graph      *graph,
 114                                rvec         force[],    /* forces on home particles */
 115                                t_idef       *idef,
 116                                tensor       vir_part,
 117                                tensor       vir,
 118                                t_commrec    *cr,
 119                                t_nrnb       *nrnb,
 120                                gmx_wallcycle_t wcycle,
 121                                gmx_update_t upd,
 122                                gmx_constr_t constr,
 123                                bool         bInitStep,
 124                                bool         bFirstHalf,
 125                                bool         bCalcVir,
 126                                real         vetanew);
 127
 128 /* Return TRUE if OK, FALSE in case of Shake Error */
 129
 130 extern void update_box(FILE         *fplog,
 131                        gmx_large_int_t   step,
 132                        t_inputrec   *inputrec,  /* input record and box stuff   */
 133                        t_mdatoms    *md,
 134                        t_state      *state,
 135                        t_graph      *graph,
 136                        rvec         force[],    /* forces on home particles */
 137                        matrix       *scale_tot,
 138                        matrix       pcoupl_mu,
 139                        t_nrnb       *nrnb,
 140                        gmx_wallcycle_t wcycle,
 141                        gmx_update_t upd,
 142                        bool         bInitStep,
 143                        bool         bFirstHalf);
 144 /* Return TRUE if OK, FALSE in case of Shake Error */
 145
 146 extern void calc_ke_part(t_state *state,t_grpopts *opts,t_mdatoms *md,
 147                          gmx_ekindata_t *ekind,t_nrnb *nrnb,bool bFullStepV);
 148 /*
 149  * Compute the partial kinetic energy for home particles;
 150  * will be accumulated in the calling routine.
 151  * The tensor is
 152  *
 153  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 154  *
 155  *     use v[i] = v[i] - u[i] when calculating temperature
 156  *
 157  * u must be accumulated already.
 158  *
 159  * Now also computes the contribution of the kinetic energy to the
 160  * free energy
 161  *
 162  */
 163
 164 extern void
 165 init_ekinstate(ekinstate_t *ekinstate,t_inputrec *ir);
 166
 167 extern void
 168 update_ekinstate(ekinstate_t *ekinstate,gmx_ekindata_t *ekind);
 169
 170 extern void
 171 restore_ekinstate_from_state(t_commrec *cr,
 172                              gmx_ekindata_t *ekind,ekinstate_t *ekinstate);
 173
 174 extern void berendsen_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt);
 175
 176 extern void nosehoover_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
 177                               double xi[],double vxi[],t_extmass *MassQ);
 178
 179 extern t_state *init_bufstate(int size, int ntc);
 180
 181
 182 /*
 183 extern trotter_update(t_inputrec *ir,gmx_ekindata_t *ekind, gmx_enerdata_t *enerd,
 184                            t_state *state, tensor vir, t_mdatoms *md,
 185                            t_extmass *MassQ, bool bFirstHalf, bool bThermo, bool bBaro, bool bInitStep);
 186 */
 187
 188
 189 extern void trotter_update(t_inputrec *ir,gmx_ekindata_t *ekind, gmx_enerdata_t *enerd,
 190                            t_state *state, tensor vir, t_mdatoms *md,
 191                            t_extmass *MassQ, int *trotter_seq);
 192
 193 extern int **init_trotter(t_inputrec *ir, t_state *state, t_extmass *Mass);
 194
 195
 196 extern real NPT_energy(t_inputrec *ir, double *xi, double *vxi, real veta, tensor box, t_extmass *MassQ);
 197 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 198
 199 extern void NBaroT_trotter(t_grpopts *opts, real dt,
 200                            double xi[],double vxi[],real *veta, t_extmass *MassQ);
 201
 202 extern void vrescale_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
 203                             double therm_integral[],
 204                             gmx_rng_t rng);
 205 /* Compute temperature scaling. For V-rescale it is done in update. */
 206
 207 extern real vrescale_energy(t_grpopts *opts,double therm_integral[]);
 208 /* Returns the V-rescale contribution to the conserved energy */
 209
 210
 211 /* Set reference temp for simulated annealing at time t*/
 212 extern void update_annealing_target_temp(t_grpopts *opts,real t);
 213
 214 extern real calc_temp(real ekin,real nrdf);
 215 /* Calculate the temperature */
 216
 217 extern real calc_pres(int ePBC,int nwall,matrix box,
 218                       tensor ekin,tensor vir,tensor pres,real Elr);
 219 /* Calculate the pressure tensor, returns the scalar pressure.
 220  * The unit of pressure is bar, If Elr != 0
 221  * a long range correction based on Ewald/PPPM is made (see c-code)
 222  */
 223
 224 extern void parrinellorahman_pcoupl(FILE *fplog,gmx_large_int_t step,
 225                                     t_inputrec *ir,real dt,tensor pres,
 226                                     tensor box,tensor box_rel,tensor boxv,
 227                                     tensor M,matrix mu,
 228                                     bool bFirstStep);
 229
 230 extern void berendsen_pcoupl(FILE *fplog,gmx_large_int_t step,
 231                              t_inputrec *ir,real dt,tensor pres,matrix box,
 232                              matrix mu);
 233
 234
 235 extern void berendsen_pscale(t_inputrec *ir,matrix mu,
 236                              matrix box,matrix box_rel,
 237                              int start,int nr_atoms,
 238                              rvec x[],unsigned short cFREEZE[],
 239                              t_nrnb *nrnb);
 240
 241 extern void correct_ekin(FILE *log,int start,int end,rvec v[],
 242                          rvec vcm,real mass[],real tmass,tensor ekin);
 243 /* Correct ekin for vcm */
 244
 245 #endif  /* _update_h */
 246