include/update.h

   1 /*
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  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 #ifdef __cplusplus
  52 extern "C" {
  53 #endif
  54
  55 /* Abstract type for stochastic dynamics */
  56 typedef struct gmx_update *gmx_update_t;
  57
  58 /* Initialize the stochastic dynamics struct */
  59 extern gmx_update_t init_update(FILE *fplog,t_inputrec *ir);
  60
  61 /* Store the random state from sd in state */
  62 extern void get_stochd_state(gmx_update_t sd,t_state *state);
  63
  64 /* Set the random in sd from state */
  65 extern void set_stochd_state(gmx_update_t sd,t_state *state);
  66
  67 /* Store the box at step step
  68  * as a reference state for simulations with box deformation.
  69  */
  70 extern void set_deform_reference_box(gmx_update_t upd,
  71                                      gmx_large_int_t step,matrix box);
  72
  73 extern void update_extended(FILE         *fplog,
  74                    gmx_large_int_t   step,
  75                    t_inputrec   *inputrec,
  76                    t_mdatoms    *md,
  77                    t_state      *state,
  78                    gmx_ekindata_t *ekind,
  79                    matrix       pcoupl_mu,
  80                    matrix       M,
  81                    gmx_wallcycle_t wcycle,
  82                    gmx_update_t upd,
  83                    bool         bInitStep,
  84                    bool         bFirstHalf,
  85                    t_extmass    *MassQ
  86 );
  87 /* Return TRUE if OK, FALSE in case of Shake Error */
  88
  89 extern void update_coords(FILE         *fplog,
  90                           gmx_large_int_t   step,
  91                           t_inputrec   *inputrec,  /* input record and box stuff        */
  92                           t_mdatoms    *md,
  93                           t_state      *state,
  94                           rvec         *f,    /* forces on home particles */
  95                           bool         bDoLR,
  96                           rvec         *f_lr,
  97                           t_fcdata     *fcd,
  98                           gmx_ekindata_t *ekind,
  99                           matrix       M,
 100                           gmx_wallcycle_t wcycle,
 101                           gmx_update_t upd,
 102                           bool         bInitStep,
 103                           int          bUpdatePart,
 104                           t_commrec    *cr,  /* these shouldn't be here -- need to think about it */
 105                           t_nrnb       *nrnb,
 106                           gmx_constr_t constr,
 107                           t_idef       *idef);
 108
 109 /* Return TRUE if OK, FALSE in case of Shake Error */
 110
 111 extern void update_constraints(FILE         *fplog,
 112                                gmx_large_int_t   step,
 113                                real         *dvdlambda, /* FEP stuff */
 114                                t_inputrec   *inputrec,  /* input record and box stuff   */
 115                                gmx_ekindata_t *ekind,
 116                                t_mdatoms    *md,
 117                                t_state      *state,
 118                                t_graph      *graph,
 119                                rvec         force[],    /* forces on home particles */
 120                                t_idef       *idef,
 121                                tensor       vir_part,
 122                                tensor       vir,
 123                                t_commrec    *cr,
 124                                t_nrnb       *nrnb,
 125                                gmx_wallcycle_t wcycle,
 126                                gmx_update_t upd,
 127                                gmx_constr_t constr,
 128                                bool         bInitStep,
 129                                bool         bFirstHalf,
 130                                bool         bCalcVir,
 131                                real         vetanew);
 132
 133 /* Return TRUE if OK, FALSE in case of Shake Error */
 134
 135 extern void update_box(FILE         *fplog,
 136                        gmx_large_int_t   step,
 137                        t_inputrec   *inputrec,  /* input record and box stuff   */
 138                        t_mdatoms    *md,
 139                        t_state      *state,
 140                        t_graph      *graph,
 141                        rvec         force[],    /* forces on home particles */
 142                        matrix       *scale_tot,
 143                        matrix       pcoupl_mu,
 144                        t_nrnb       *nrnb,
 145                        gmx_wallcycle_t wcycle,
 146                        gmx_update_t upd,
 147                        bool         bInitStep,
 148                        bool         bFirstHalf);
 149 /* Return TRUE if OK, FALSE in case of Shake Error */
 150
 151 extern void calc_ke_part(t_state *state,t_grpopts *opts,t_mdatoms *md,
 152                          gmx_ekindata_t *ekind,t_nrnb *nrnb,bool bEkinAveVel, bool bSaveOld);
 153 /*
 154  * Compute the partial kinetic energy for home particles;
 155  * will be accumulated in the calling routine.
 156  * The tensor is
 157  *
 158  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 159  *
 160  *     use v[i] = v[i] - u[i] when calculating temperature
 161  *
 162  * u must be accumulated already.
 163  *
 164  * Now also computes the contribution of the kinetic energy to the
 165  * free energy
 166  *
 167  */
 168
 169 extern void
 170 init_ekinstate(ekinstate_t *ekinstate,t_inputrec *ir);
 171
 172 extern void
 173 update_ekinstate(ekinstate_t *ekinstate,gmx_ekindata_t *ekind);
 174
 175 extern void
 176 restore_ekinstate_from_state(t_commrec *cr,
 177                              gmx_ekindata_t *ekind,ekinstate_t *ekinstate);
 178
 179 extern void berendsen_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt);
 180
 181 extern void nosehoover_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
 182                               double xi[],double vxi[],t_extmass *MassQ);
 183
 184 extern t_state *init_bufstate(const t_state *template_state);
 185
 186 extern void destroy_bufstate(t_state *state);
 187
 188 extern void trotter_update(t_inputrec *ir,gmx_large_int_t step,
 189                            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_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, bool bTrotter);
 194
 195 extern real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
 196 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 197
 198 extern void NBaroT_trotter(t_grpopts *opts, real dt,
 199                            double xi[],double vxi[],real *veta, t_extmass *MassQ);
 200
 201 extern void vrescale_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
 202                             double therm_integral[],
 203                             gmx_rng_t rng);
 204 /* Compute temperature scaling. For V-rescale it is done in update. */
 205
 206 extern real vrescale_energy(t_grpopts *opts,double therm_integral[]);
 207 /* Returns the V-rescale contribution to the conserved energy */
 208
 209 extern void update_annealing_target_temp(t_grpopts *opts,real t);
 210 /* Set reference temp for simulated annealing at time t*/
 211
 212 extern real calc_temp(real ekin,real nrdf);
 213 /* Calculate the temperature */
 214
 215 extern real calc_pres(int ePBC,int nwall,matrix box,
 216                       tensor ekin,tensor vir,tensor pres,real Elr);
 217 /* Calculate the pressure tensor, returns the scalar pressure.
 218  * The unit of pressure is bar, If Elr != 0
 219  * a long range correction based on Ewald/PPPM is made (see c-code)
 220  */
 221
 222 extern void parrinellorahman_pcoupl(FILE *fplog,gmx_large_int_t step,
 223                                     t_inputrec *ir,real dt,tensor pres,
 224                                     tensor box,tensor box_rel,tensor boxv,
 225                                     tensor M,matrix mu,
 226                                     bool bFirstStep);
 227
 228 extern void berendsen_pcoupl(FILE *fplog,gmx_large_int_t step,
 229                              t_inputrec *ir,real dt,tensor pres,matrix box,
 230                              matrix mu);
 231
 232
 233 extern void berendsen_pscale(t_inputrec *ir,matrix mu,
 234                              matrix box,matrix box_rel,
 235                              int start,int nr_atoms,
 236                              rvec x[],unsigned short cFREEZE[],
 237                              t_nrnb *nrnb);
 238
 239 extern void correct_ekin(FILE *log,int start,int end,rvec v[],
 240                          rvec vcm,real mass[],real tmass,tensor ekin);
 241 /* Correct ekin for vcm */
 242
 243
 244 #ifdef __cplusplus
 245 }
 246 #endif
 247
 248 #endif  /* _update_h */
 249