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
  44 #include "typedefs.h"
  45 #include "mshift.h"
  46 #include "tgroup.h"
  47 #include "network.h"
  48 #include "force.h"
  49 #include "pull.h"
  50 #include "gmx_random.h"
  51 #include "maths.h"
  52
  53 #ifdef __cplusplus
  54 extern "C" {
  55 #endif
  56
  57 /* Abstract type for stochastic dynamics */
  58 typedef struct gmx_update *gmx_update_t;
  59
  60 /* Initialize the stochastic dynamics struct */
  61 extern gmx_update_t init_update(FILE *fplog,t_inputrec *ir);
  62
  63 /* Store the random state from sd in state */
  64 extern void get_stochd_state(gmx_update_t sd,t_state *state);
  65
  66 /* Set the random in sd from state */
  67 extern 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 extern void set_deform_reference_box(gmx_update_t upd,
  73                                      gmx_large_int_t step,matrix box);
  74
  75 extern void update_tcouple(FILE         *fplog,
  76                            gmx_large_int_t   step,
  77                            t_inputrec   *inputrec,
  78                            t_state      *state,
  79                            gmx_ekindata_t *ekind,
  80                            gmx_wallcycle_t wcycle,
  81                            gmx_update_t upd,
  82                            t_extmass    *MassQ,
  83                            t_mdatoms    *md
  84 );
  85
  86 extern void update_pcouple(FILE         *fplog,
  87                            gmx_large_int_t   step,
  88                            t_inputrec   *inputrec,
  89                            t_state      *state,
  90                            matrix       pcoupl_mu,
  91                            matrix       M,
  92                            gmx_wallcycle_t wcycle,
  93                            gmx_update_t upd,
  94                            bool         bInitStep);
  95
  96 extern void update_coords(FILE         *fplog,
  97                           gmx_large_int_t   step,
  98                           t_inputrec   *inputrec,  /* input record and box stuff        */
  99                           t_mdatoms    *md,
 100                           t_state      *state,
 101                           rvec         *f,    /* forces on home particles */
 102                           bool         bDoLR,
 103                           rvec         *f_lr,
 104                           t_fcdata     *fcd,
 105                           gmx_ekindata_t *ekind,
 106                           matrix       M,
 107                           gmx_wallcycle_t wcycle,
 108                           gmx_update_t upd,
 109                           bool         bInitStep,
 110                           int          bUpdatePart,
 111                           t_commrec    *cr,  /* these shouldn't be here -- need to think about it */
 112                           t_nrnb       *nrnb,
 113                           gmx_constr_t constr,
 114                           t_idef       *idef);
 115
 116 /* Return TRUE if OK, FALSE in case of Shake Error */
 117
 118 extern void update_constraints(FILE         *fplog,
 119                                gmx_large_int_t   step,
 120                                real         *dvdlambda, /* FEP stuff */
 121                                t_inputrec   *inputrec,  /* input record and box stuff   */
 122                                gmx_ekindata_t *ekind,
 123                                t_mdatoms    *md,
 124                                t_state      *state,
 125                                t_graph      *graph,
 126                                rvec         force[],    /* forces on home particles */
 127                                t_idef       *idef,
 128                                tensor       vir_part,
 129                                tensor       vir,
 130                                t_commrec    *cr,
 131                                t_nrnb       *nrnb,
 132                                gmx_wallcycle_t wcycle,
 133                                gmx_update_t upd,
 134                                gmx_constr_t constr,
 135                                bool         bInitStep,
 136                                bool         bFirstHalf,
 137                                bool         bCalcVir,
 138                                real         vetanew);
 139
 140 /* Return TRUE if OK, FALSE in case of Shake Error */
 141
 142 extern void update_box(FILE         *fplog,
 143                        gmx_large_int_t   step,
 144                        t_inputrec   *inputrec,  /* input record and box stuff   */
 145                        t_mdatoms    *md,
 146                        t_state      *state,
 147                        t_graph      *graph,
 148                        rvec         force[],    /* forces on home particles */
 149                        matrix       *scale_tot,
 150                        matrix       pcoupl_mu,
 151                        t_nrnb       *nrnb,
 152                        gmx_wallcycle_t wcycle,
 153                        gmx_update_t upd,
 154                        bool         bInitStep,
 155                        bool         bFirstHalf);
 156 /* Return TRUE if OK, FALSE in case of Shake Error */
 157
 158 extern void calc_ke_part(t_state *state,t_grpopts *opts,t_mdatoms *md,
 159                          gmx_ekindata_t *ekind,t_nrnb *nrnb,bool bEkinAveVel, bool bSaveOld);
 160 /*
 161  * Compute the partial kinetic energy for home particles;
 162  * will be accumulated in the calling routine.
 163  * The tensor is
 164  *
 165  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 166  *
 167  *     use v[i] = v[i] - u[i] when calculating temperature
 168  *
 169  * u must be accumulated already.
 170  *
 171  * Now also computes the contribution of the kinetic energy to the
 172  * free energy
 173  *
 174  */
 175
 176 extern void
 177 init_ekinstate(ekinstate_t *ekinstate,const t_inputrec *ir);
 178
 179 extern void
 180 update_ekinstate(ekinstate_t *ekinstate,gmx_ekindata_t *ekind);
 181
 182 extern void
 183 restore_ekinstate_from_state(t_commrec *cr,
 184                              gmx_ekindata_t *ekind,ekinstate_t *ekinstate);
 185
 186 extern void berendsen_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt);
 187
 188 extern void nosehoover_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
 189                               double xi[],double vxi[],t_extmass *MassQ);
 190
 191 extern t_state *init_bufstate(const t_state *template_state);
 192
 193 extern void destroy_bufstate(t_state *state);
 194
 195 extern void trotter_update(t_inputrec *ir, gmx_large_int_t step, gmx_ekindata_t *ekind,
 196                            gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
 197                            t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
 198
 199 extern int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, bool bTrotter);
 200
 201 extern real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
 202 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 203
 204 extern void NBaroT_trotter(t_grpopts *opts, real dt,
 205                            double xi[],double vxi[],real *veta, t_extmass *MassQ);
 206
 207 extern void vrescale_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt,
 208                             double therm_integral[],
 209                             gmx_rng_t rng);
 210 /* Compute temperature scaling. For V-rescale it is done in update. */
 211
 212 extern real vrescale_energy(t_grpopts *opts,double therm_integral[]);
 213 /* Returns the V-rescale contribution to the conserved energy */
 214
 215 extern void rescale_velocities(gmx_ekindata_t *ekind,t_mdatoms *mdatoms,
 216                                int start,int end,rvec v[]);
 217 /* Rescale the velocities with the scaling factor in ekind */
 218
 219 extern void update_annealing_target_temp(t_grpopts *opts,real t);
 220 /* Set reference temp for simulated annealing at time t*/
 221
 222 extern real calc_temp(real ekin,real nrdf);
 223 /* Calculate the temperature */
 224
 225 extern real calc_pres(int ePBC,int nwall,matrix box,
 226                       tensor ekin,tensor vir,tensor pres,real Elr);
 227 /* Calculate the pressure tensor, returns the scalar pressure.
 228  * The unit of pressure is bar, If Elr != 0
 229  * a long range correction based on Ewald/PPPM is made (see c-code)
 230  */
 231
 232 extern void parrinellorahman_pcoupl(FILE *fplog,gmx_large_int_t step,
 233                                     t_inputrec *ir,real dt,tensor pres,
 234                                     tensor box,tensor box_rel,tensor boxv,
 235                                     tensor M,matrix mu,
 236                                     bool bFirstStep);
 237
 238 extern void berendsen_pcoupl(FILE *fplog,gmx_large_int_t step,
 239                              t_inputrec *ir,real dt,tensor pres,matrix box,
 240                              matrix mu);
 241
 242
 243 extern void berendsen_pscale(t_inputrec *ir,matrix mu,
 244                              matrix box,matrix box_rel,
 245                              int start,int nr_atoms,
 246                              rvec x[],unsigned short cFREEZE[],
 247                              t_nrnb *nrnb);
 248
 249 extern void correct_ekin(FILE *log,int start,int end,rvec v[],
 250                          rvec vcm,real mass[],real tmass,tensor ekin);
 251 /* Correct ekin for vcm */
 252
 253
 254 #ifdef __cplusplus
 255 }
 256 #endif
 257
 258 #endif  /* _update_h */
 259