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                           rvec         *f,    /* forces on home particles */
  97                           gmx_bool         bDoLR,
  98                           rvec         *f_lr,
  99                           t_fcdata     *fcd,
 100                           gmx_ekindata_t *ekind,
 101                           matrix       M,
 102                           gmx_wallcycle_t wcycle,
 103                           gmx_update_t upd,
 104                           gmx_bool         bInitStep,
 105                           int          bUpdatePart,
 106                           t_commrec    *cr,  /* these shouldn't be here -- need to think about it */
 107                           t_nrnb       *nrnb,
 108                           gmx_constr_t constr,
 109                           t_idef       *idef);
 110
 111 /* Return TRUE if OK, FALSE in case of Shake Error */
 112
 113 void update_constraints(FILE         *fplog,
 114                                gmx_large_int_t   step,
 115                                real         *dvdlambda, /* FEP stuff */
 116                                t_inputrec   *inputrec,  /* input record and box stuff   */
 117                                gmx_ekindata_t *ekind,
 118                                t_mdatoms    *md,
 119                                t_state      *state,
 120                                t_graph      *graph,
 121                                rvec         force[],    /* forces on home particles */
 122                                t_idef       *idef,
 123                                tensor       vir_part,
 124                                tensor       vir,
 125                                t_commrec    *cr,
 126                                t_nrnb       *nrnb,
 127                                gmx_wallcycle_t wcycle,
 128                                gmx_update_t upd,
 129                                gmx_constr_t constr,
 130                                gmx_bool         bInitStep,
 131                                gmx_bool         bFirstHalf,
 132                                gmx_bool         bCalcVir,
 133                                real         vetanew);
 134
 135 /* Return TRUE if OK, FALSE in case of Shake Error */
 136
 137 void update_box(FILE         *fplog,
 138                        gmx_large_int_t   step,
 139                        t_inputrec   *inputrec,  /* input record and box stuff   */
 140                        t_mdatoms    *md,
 141                        t_state      *state,
 142                        t_graph      *graph,
 143                        rvec         force[],    /* forces on home particles */
 144                        matrix       *scale_tot,
 145                        matrix       pcoupl_mu,
 146                        t_nrnb       *nrnb,
 147                        gmx_wallcycle_t wcycle,
 148                        gmx_update_t upd,
 149                        gmx_bool         bInitStep,
 150                        gmx_bool         bFirstHalf);
 151 /* Return TRUE if OK, FALSE in case of Shake Error */
 152
 153 void calc_ke_part(t_state *state,t_grpopts *opts,t_mdatoms *md,
 154                          gmx_ekindata_t *ekind,t_nrnb *nrnb,gmx_bool bEkinAveVel, gmx_bool bSaveOld);
 155 /*
 156  * Compute the partial kinetic energy for home particles;
 157  * will be accumulated in the calling routine.
 158  * The tensor is
 159  *
 160  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 161  *
 162  *     use v[i] = v[i] - u[i] when calculating temperature
 163  *
 164  * u must be accumulated already.
 165  *
 166  * Now also computes the contribution of the kinetic energy to the
 167  * free energy
 168  *
 169  */
 170
 171 void
 172 init_ekinstate(ekinstate_t *ekinstate,const t_inputrec *ir);
 173
 174 void
 175 update_ekinstate(ekinstate_t *ekinstate,gmx_ekindata_t *ekind);
 176
 177 void
 178 restore_ekinstate_from_state(t_commrec *cr,
 179                              gmx_ekindata_t *ekind,ekinstate_t *ekinstate);
 180
 181 void berendsen_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt);
 182
 183 void nosehoover_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
 184                               double xi[],double vxi[],t_extmass *MassQ);
 185
 186 t_state *init_bufstate(const t_state *template_state);
 187
 188 void destroy_bufstate(t_state *state);
 189
 190 void trotter_update(t_inputrec *ir, gmx_large_int_t step, gmx_ekindata_t *ekind,
 191                            gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
 192                            t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
 193
 194 int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
 195
 196 real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
 197 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 198
 199 void NBaroT_trotter(t_grpopts *opts, real dt,
 200                            double xi[],double vxi[],real *veta, t_extmass *MassQ);
 201
 202 void vrescale_tcoupl(t_inputrec *ir,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 real vrescale_energy(t_grpopts *opts,double therm_integral[]);
 208 /* Returns the V-rescale contribution to the conserved energy */
 209
 210 void rescale_velocities(gmx_ekindata_t *ekind,t_mdatoms *mdatoms,
 211                                int start,int end,rvec v[]);
 212 /* Rescale the velocities with the scaling factor in ekind */
 213
 214 void update_annealing_target_temp(t_grpopts *opts,real t);
 215 /* Set reference temp for simulated annealing at time t*/
 216
 217 real calc_temp(real ekin,real nrdf);
 218 /* Calculate the temperature */
 219
 220 real calc_pres(int ePBC,int nwall,matrix box,
 221                       tensor ekin,tensor vir,tensor pres,real Elr);
 222 /* Calculate the pressure tensor, returns the scalar pressure.
 223  * The unit of pressure is bar, If Elr != 0
 224  * a long range correction based on Ewald/PPPM is made (see c-code)
 225  */
 226
 227 void parrinellorahman_pcoupl(FILE *fplog,gmx_large_int_t step,
 228                                     t_inputrec *ir,real dt,tensor pres,
 229                                     tensor box,tensor box_rel,tensor boxv,
 230                                     tensor M,matrix mu,
 231                                     gmx_bool bFirstStep);
 232
 233 void berendsen_pcoupl(FILE *fplog,gmx_large_int_t step,
 234                              t_inputrec *ir,real dt,tensor pres,matrix box,
 235                              matrix mu);
 236
 237
 238 void berendsen_pscale(t_inputrec *ir,matrix mu,
 239                              matrix box,matrix box_rel,
 240                              int start,int nr_atoms,
 241                              rvec x[],unsigned short cFREEZE[],
 242                              t_nrnb *nrnb);
 243
 244 void correct_ekin(FILE *log,int start,int end,rvec v[],
 245                          rvec vcm,real mass[],real tmass,tensor ekin);
 246 /* Correct ekin for vcm */
 247
 248
 249 #ifdef __cplusplus
 250 }
 251 #endif
 252
 253 #endif  /* _update_h */
 254