include/update.h

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  38
  39 #ifndef _update_h
  40 #define _update_h
  41 #include "visibility.h"
  42 #include "typedefs.h"
  43 #include "mshift.h"
  44 #include "tgroup.h"
  45 #include "network.h"
  46 #include "force.h"
  47 #include "pull.h"
  48 #include "gmx_random.h"
  49 #include "maths.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 gmx_update_t init_update(FILE *fplog,t_inputrec *ir);
  60
  61 /* Store the random state from sd in state */
  62 GMX_LIBMD_EXPORT
  63 void get_stochd_state(gmx_update_t sd,t_state *state);
  64
  65 /* Set the random in sd from state */
  66 GMX_LIBMD_EXPORT
  67 void set_stochd_state(gmx_update_t sd,t_state *state);
  68
  69 /* Store the box at step step
  70  * as a reference state for simulations with box deformation.
  71  */
  72 GMX_LIBMD_EXPORT
  73 void set_deform_reference_box(gmx_update_t upd,
  74                                      gmx_large_int_t step,matrix box);
  75
  76 GMX_LIBMD_EXPORT
  77 void update_tcouple(FILE         *fplog,
  78                            gmx_large_int_t   step,
  79                            t_inputrec   *inputrec,
  80                            t_state      *state,
  81                            gmx_ekindata_t *ekind,
  82                            gmx_wallcycle_t wcycle,
  83                            gmx_update_t upd,
  84                            t_extmass    *MassQ,
  85                            t_mdatoms    *md
  86 );
  87
  88 GMX_LIBMD_EXPORT
  89 void update_pcouple(FILE         *fplog,
  90                            gmx_large_int_t   step,
  91                            t_inputrec   *inputrec,
  92                            t_state      *state,
  93                            matrix       pcoupl_mu,
  94                            matrix       M,
  95                            gmx_wallcycle_t wcycle,
  96                            gmx_update_t upd,
  97                            gmx_bool         bInitStep);
  98
  99 GMX_LIBMD_EXPORT
 100 void update_coords(FILE         *fplog,
 101                           gmx_large_int_t   step,
 102                           t_inputrec   *inputrec,  /* input record and box stuff        */
 103                           t_mdatoms    *md,
 104                           t_state      *state,
 105                           gmx_bool     bMolPBC,
 106                           rvec         *f,    /* forces on home particles */
 107                           gmx_bool         bDoLR,
 108                           rvec         *f_lr,
 109                           t_fcdata     *fcd,
 110                           gmx_ekindata_t *ekind,
 111                           matrix       M,
 112                           gmx_wallcycle_t wcycle,
 113                           gmx_update_t upd,
 114                           gmx_bool         bInitStep,
 115                           int          bUpdatePart,
 116                           t_commrec    *cr,  /* these shouldn't be here -- need to think about it */
 117                           t_nrnb       *nrnb,
 118                           gmx_constr_t constr,
 119                           t_idef       *idef);
 120
 121 /* Return TRUE if OK, FALSE in case of Shake Error */
 122
 123 GMX_LIBMD_EXPORT
 124 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);
 125
 126 GMX_LIBMD_EXPORT
 127 void update_constraints(FILE         *fplog,
 128                                gmx_large_int_t   step,
 129                                real         *dvdlambda, /* FEP stuff */
 130                                t_inputrec   *inputrec,  /* input record and box stuff   */
 131                                gmx_ekindata_t *ekind,
 132                                t_mdatoms    *md,
 133                                t_state      *state,
 134                                gmx_bool     bMolPBC,
 135                                t_graph      *graph,
 136                                rvec         force[],    /* forces on home particles */
 137                                t_idef       *idef,
 138                                tensor       vir_part,
 139                                tensor       vir,
 140                                t_commrec    *cr,
 141                                t_nrnb       *nrnb,
 142                                gmx_wallcycle_t wcycle,
 143                                gmx_update_t upd,
 144                                gmx_constr_t constr,
 145                                gmx_bool         bInitStep,
 146                                gmx_bool         bFirstHalf,
 147                                gmx_bool         bCalcVir,
 148                                real         vetanew);
 149
 150 /* Return TRUE if OK, FALSE in case of Shake Error */
 151
 152 GMX_LIBMD_EXPORT
 153 void update_box(FILE         *fplog,
 154                        gmx_large_int_t   step,
 155                        t_inputrec   *inputrec,  /* input record and box stuff   */
 156                        t_mdatoms    *md,
 157                        t_state      *state,
 158                        t_graph      *graph,
 159                        rvec         force[],    /* forces on home particles */
 160                        matrix       *scale_tot,
 161                        matrix       pcoupl_mu,
 162                        t_nrnb       *nrnb,
 163                        gmx_wallcycle_t wcycle,
 164                        gmx_update_t upd,
 165                        gmx_bool         bInitStep,
 166                        gmx_bool         bFirstHalf);
 167 /* Return TRUE if OK, FALSE in case of Shake Error */
 168
 169 void calc_ke_part(t_state *state,t_grpopts *opts,t_mdatoms *md,
 170                          gmx_ekindata_t *ekind,t_nrnb *nrnb,gmx_bool bEkinAveVel, gmx_bool bSaveOld);
 171 /*
 172  * Compute the partial kinetic energy for home particles;
 173  * will be accumulated in the calling routine.
 174  * The tensor is
 175  *
 176  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 177  *
 178  *     use v[i] = v[i] - u[i] when calculating temperature
 179  *
 180  * u must be accumulated already.
 181  *
 182  * Now also computes the contribution of the kinetic energy to the
 183  * free energy
 184  *
 185  */
 186
 187
 188 void
 189 init_ekinstate(ekinstate_t *ekinstate,const t_inputrec *ir);
 190
 191 GMX_LIBMD_EXPORT
 192 void
 193 update_ekinstate(ekinstate_t *ekinstate,gmx_ekindata_t *ekind);
 194
 195 void
 196 restore_ekinstate_from_state(t_commrec *cr,
 197                              gmx_ekindata_t *ekind,ekinstate_t *ekinstate);
 198
 199 void berendsen_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt);
 200
 201 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);
 202
 203 void nosehoover_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
 204                               double xi[],double vxi[],t_extmass *MassQ);
 205
 206 GMX_LIBMD_EXPORT
 207 t_state *init_bufstate(const t_state *template_state);
 208
 209 void destroy_bufstate(t_state *state);
 210
 211 GMX_LIBMD_EXPORT
 212 void trotter_update(t_inputrec *ir, gmx_large_int_t step, gmx_ekindata_t *ekind,
 213                            gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
 214                            t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
 215
 216 GMX_LIBMD_EXPORT
 217 int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
 218
 219 real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
 220 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 221
 222 void NBaroT_trotter(t_grpopts *opts, real dt,
 223                            double xi[],double vxi[],real *veta, t_extmass *MassQ);
 224
 225 void vrescale_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt,
 226                             double therm_integral[],
 227                             gmx_rng_t rng);
 228 /* Compute temperature scaling. For V-rescale it is done in update. */
 229
 230 real vrescale_energy(t_grpopts *opts,double therm_integral[]);
 231 /* Returns the V-rescale contribution to the conserved energy */
 232
 233 void rescale_velocities(gmx_ekindata_t *ekind,t_mdatoms *mdatoms,
 234                                int start,int end,rvec v[]);
 235 /* Rescale the velocities with the scaling factor in ekind */
 236
 237 GMX_LIBMD_EXPORT
 238 void update_annealing_target_temp(t_grpopts *opts,real t);
 239 /* Set reference temp for simulated annealing at time t*/
 240
 241 real calc_temp(real ekin,real nrdf);
 242 /* Calculate the temperature */
 243
 244 real calc_pres(int ePBC,int nwall,matrix box,tensor ekin,tensor vir,
 245                tensor pres);
 246 /* Calculate the pressure tensor, returns the scalar pressure.
 247  * The unit of pressure is bar.
 248  */
 249
 250 void parrinellorahman_pcoupl(FILE *fplog,gmx_large_int_t step,
 251                                     t_inputrec *ir,real dt,tensor pres,
 252                                     tensor box,tensor box_rel,tensor boxv,
 253                                     tensor M,matrix mu,
 254                                     gmx_bool bFirstStep);
 255
 256 void berendsen_pcoupl(FILE *fplog,gmx_large_int_t step,
 257                              t_inputrec *ir,real dt,tensor pres,matrix box,
 258                              matrix mu);
 259
 260
 261 void berendsen_pscale(t_inputrec *ir,matrix mu,
 262                              matrix box,matrix box_rel,
 263                              int start,int nr_atoms,
 264                              rvec x[],unsigned short cFREEZE[],
 265                              t_nrnb *nrnb);
 266
 267 void correct_ekin(FILE *log,int start,int end,rvec v[],
 268                          rvec vcm,real mass[],real tmass,tensor ekin);
 269 /* Correct ekin for vcm */
 270
 271
 272 #ifdef __cplusplus
 273 }
 274 #endif
 275
 276 #endif  /* _update_h */
 277