include/update.h

   1 /*
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  35
  36 #ifndef _update_h
  37 #define _update_h
  38
  39 #include "typedefs.h"
  40 #include "mshift.h"
  41 #include "tgroup.h"
  42 #include "network.h"
  43 #include "force.h"
  44 #include "pull.h"
  45 #include "gmx_random.h"
  46 #include "maths.h"
  47
  48 #ifdef __cplusplus
  49 extern "C" {
  50 #endif
  51
  52 /* Abstract type for stochastic dynamics */
  53 typedef struct gmx_update *gmx_update_t;
  54
  55 /* Initialize the stochastic dynamics struct */
  56 gmx_update_t init_update(FILE *fplog,t_inputrec *ir);
  57
  58 /* Store the random state from sd in state */
  59 void get_stochd_state(gmx_update_t sd,t_state *state);
  60
  61 /* Set the random in sd from state */
  62 void set_stochd_state(gmx_update_t sd,t_state *state);
  63
  64 /* Store the box at step step
  65  * as a reference state for simulations with box deformation.
  66  */
  67 void set_deform_reference_box(gmx_update_t upd,
  68                                      gmx_large_int_t step,matrix box);
  69
  70 void update_tcouple(FILE         *fplog,
  71                            gmx_large_int_t   step,
  72                            t_inputrec   *inputrec,
  73                            t_state      *state,
  74                            gmx_ekindata_t *ekind,
  75                            gmx_wallcycle_t wcycle,
  76                            gmx_update_t upd,
  77                            t_extmass    *MassQ,
  78                            t_mdatoms    *md
  79 );
  80
  81 void update_pcouple(FILE         *fplog,
  82                            gmx_large_int_t   step,
  83                            t_inputrec   *inputrec,
  84                            t_state      *state,
  85                            matrix       pcoupl_mu,
  86                            matrix       M,
  87                            gmx_wallcycle_t wcycle,
  88                            gmx_update_t upd,
  89                            gmx_bool         bInitStep);
  90
  91 void update_coords(FILE         *fplog,
  92                           gmx_large_int_t   step,
  93                           t_inputrec   *inputrec,  /* input record and box stuff        */
  94                           t_mdatoms    *md,
  95                           t_state      *state,
  96                           gmx_bool     bMolPBC,
  97                           rvec         *f,    /* forces on home particles */
  98                           gmx_bool         bDoLR,
  99                           rvec         *f_lr,
 100                           t_fcdata     *fcd,
 101                           gmx_ekindata_t *ekind,
 102                           matrix       M,
 103                           gmx_wallcycle_t wcycle,
 104                           gmx_update_t upd,
 105                           gmx_bool         bInitStep,
 106                           int          bUpdatePart,
 107                           t_commrec    *cr,  /* these shouldn't be here -- need to think about it */
 108                           t_nrnb       *nrnb,
 109                           gmx_constr_t constr,
 110                           t_idef       *idef);
 111
 112 /* Return TRUE if OK, FALSE in case of Shake Error */
 113
 114 extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_large_int_t step, t_mdatoms *md, t_state *state, gmx_update_t upd, t_idef *idef, gmx_constr_t constr);
 115
 116 void update_constraints(FILE         *fplog,
 117                                gmx_large_int_t   step,
 118                                real         *dvdlambda, /* FEP stuff */
 119                                t_inputrec   *inputrec,  /* input record and box stuff   */
 120                                gmx_ekindata_t *ekind,
 121                                t_mdatoms    *md,
 122                                t_state      *state,
 123                                gmx_bool     bMolPBC,
 124                                t_graph      *graph,
 125                                rvec         force[],    /* forces on home particles */
 126                                t_idef       *idef,
 127                                tensor       vir_part,
 128                                tensor       vir,
 129                                t_commrec    *cr,
 130                                t_nrnb       *nrnb,
 131                                gmx_wallcycle_t wcycle,
 132                                gmx_update_t upd,
 133                                gmx_constr_t constr,
 134                                gmx_bool         bInitStep,
 135                                gmx_bool         bFirstHalf,
 136                                gmx_bool         bCalcVir,
 137                                real         vetanew);
 138
 139 /* Return TRUE if OK, FALSE in case of Shake Error */
 140
 141 void update_box(FILE         *fplog,
 142                        gmx_large_int_t   step,
 143                        t_inputrec   *inputrec,  /* input record and box stuff   */
 144                        t_mdatoms    *md,
 145                        t_state      *state,
 146                        t_graph      *graph,
 147                        rvec         force[],    /* forces on home particles */
 148                        matrix       *scale_tot,
 149                        matrix       pcoupl_mu,
 150                        t_nrnb       *nrnb,
 151                        gmx_wallcycle_t wcycle,
 152                        gmx_update_t upd,
 153                        gmx_bool         bInitStep,
 154                        gmx_bool         bFirstHalf);
 155 /* Return TRUE if OK, FALSE in case of Shake Error */
 156
 157 void calc_ke_part(t_state *state,t_grpopts *opts,t_mdatoms *md,
 158                          gmx_ekindata_t *ekind,t_nrnb *nrnb,gmx_bool bEkinAveVel, gmx_bool bSaveOld);
 159 /*
 160  * Compute the partial kinetic energy for home particles;
 161  * will be accumulated in the calling routine.
 162  * The tensor is
 163  *
 164  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 165  *
 166  *     use v[i] = v[i] - u[i] when calculating temperature
 167  *
 168  * u must be accumulated already.
 169  *
 170  * Now also computes the contribution of the kinetic energy to the
 171  * free energy
 172  *
 173  */
 174
 175
 176 void
 177 init_ekinstate(ekinstate_t *ekinstate,const t_inputrec *ir);
 178
 179 void
 180 update_ekinstate(ekinstate_t *ekinstate,gmx_ekindata_t *ekind);
 181
 182 void
 183 restore_ekinstate_from_state(t_commrec *cr,
 184                              gmx_ekindata_t *ekind,ekinstate_t *ekinstate);
 185
 186 void berendsen_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt);
 187
 188 void andersen_tcoupl(t_inputrec *ir,t_mdatoms *md,t_state *state, gmx_rng_t rng, real rate, t_idef *idef, int nblocks, int *sblock,gmx_bool *randatom, int *randatom_list, gmx_bool *randomize, real *boltzfac);
 189
 190 void nosehoover_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
 191                               double xi[],double vxi[],t_extmass *MassQ);
 192
 193 t_state *init_bufstate(const t_state *template_state);
 194
 195 void destroy_bufstate(t_state *state);
 196
 197 void trotter_update(t_inputrec *ir, gmx_large_int_t step, gmx_ekindata_t *ekind,
 198                            gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
 199                            t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
 200
 201 int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
 202
 203 real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
 204 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 205
 206 void NBaroT_trotter(t_grpopts *opts, real dt,
 207                            double xi[],double vxi[],real *veta, t_extmass *MassQ);
 208
 209 void vrescale_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt,
 210                             double therm_integral[],
 211                             gmx_rng_t rng);
 212 /* Compute temperature scaling. For V-rescale it is done in update. */
 213
 214 real vrescale_energy(t_grpopts *opts,double therm_integral[]);
 215 /* Returns the V-rescale contribution to the conserved energy */
 216
 217 void rescale_velocities(gmx_ekindata_t *ekind,t_mdatoms *mdatoms,
 218                                int start,int end,rvec v[]);
 219 /* Rescale the velocities with the scaling factor in ekind */
 220
 221 void update_annealing_target_temp(t_grpopts *opts,real t);
 222 /* Set reference temp for simulated annealing at time t*/
 223
 224 real calc_temp(real ekin,real nrdf);
 225 /* Calculate the temperature */
 226
 227 real calc_pres(int ePBC,int nwall,matrix box,tensor ekin,tensor vir,
 228                tensor pres);
 229 /* Calculate the pressure tensor, returns the scalar pressure.
 230  * The unit of pressure is bar.
 231  */
 232
 233 void parrinellorahman_pcoupl(FILE *fplog,gmx_large_int_t step,
 234                                     t_inputrec *ir,real dt,tensor pres,
 235                                     tensor box,tensor box_rel,tensor boxv,
 236                                     tensor M,matrix mu,
 237                                     gmx_bool bFirstStep);
 238
 239 void berendsen_pcoupl(FILE *fplog,gmx_large_int_t step,
 240                              t_inputrec *ir,real dt,tensor pres,matrix box,
 241                              matrix mu);
 242
 243
 244 void berendsen_pscale(t_inputrec *ir,matrix mu,
 245                              matrix box,matrix box_rel,
 246                              int start,int nr_atoms,
 247                              rvec x[],unsigned short cFREEZE[],
 248                              t_nrnb *nrnb);
 249
 250 void correct_ekin(FILE *log,int start,int end,rvec v[],
 251                          rvec vcm,real mass[],real tmass,tensor ekin);
 252 /* Correct ekin for vcm */
 253
 254
 255 #ifdef __cplusplus
 256 }
 257 #endif
 258
 259 #endif  /* _update_h */
 260