src/gromacs/legacyheaders/update.h

   1 /*
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  37
  38 #ifndef _update_h
  39 #define _update_h
  40
  41 #include "gromacs/legacyheaders/network.h"
  42 #include "gromacs/legacyheaders/tgroup.h"
  43 #include "gromacs/legacyheaders/typedefs.h"
  44 #include "gromacs/timing/wallcycle.h"
  45
  46 struct gmx_constr;
  47
  48 #ifdef __cplusplus
  49 extern "C" {
  50 #endif
  51
  52 struct t_graph;
  53
  54 /* Abstract type for stochastic dynamics */
  55 typedef struct gmx_update *gmx_update_t;
  56
  57 /* Initialize the stochastic dynamics struct */
  58 gmx_update_t init_update(t_inputrec *ir);
  59
  60 /* Store the random state from sd in state */
  61 void get_stochd_state(gmx_update_t sd, t_state *state);
  62
  63 /* Set the random in sd from state */
  64 void set_stochd_state(gmx_update_t sd, t_state *state);
  65
  66 /* Store the box at step step
  67  * as a reference state for simulations with box deformation.
  68  */
  69 void set_deform_reference_box(gmx_update_t upd,
  70                               gmx_int64_t step, matrix box);
  71
  72 void update_tcouple(gmx_int64_t       step,
  73                     t_inputrec       *inputrec,
  74                     t_state          *state,
  75                     gmx_ekindata_t   *ekind,
  76                     t_extmass        *MassQ,
  77                     t_mdatoms        *md
  78                     );
  79
  80 void update_pcouple(FILE             *fplog,
  81                     gmx_int64_t       step,
  82                     t_inputrec       *inputrec,
  83                     t_state          *state,
  84                     matrix            pcoupl_mu,
  85                     matrix            M,
  86                     gmx_bool          bInitStep);
  87
  88 void update_coords(FILE              *fplog,
  89                    gmx_int64_t        step,
  90                    t_inputrec        *inputrec, /* input record and box stuff   */
  91                    t_mdatoms         *md,
  92                    t_state           *state,
  93                    gmx_bool           bMolPBC,
  94                    rvec              *f, /* forces on home particles */
  95                    gmx_bool           bDoLR,
  96                    rvec              *f_lr,
  97                    tensor            *vir_lr_constr,
  98                    t_fcdata          *fcd,
  99                    gmx_ekindata_t    *ekind,
 100                    matrix             M,
 101                    gmx_update_t       upd,
 102                    gmx_bool           bInitStep,
 103                    int                bUpdatePart,
 104                    t_commrec         *cr, /* these shouldn't be here -- need to think about it */
 105                    t_nrnb            *nrnb,
 106                    struct gmx_constr *constr,
 107                    t_idef            *idef);
 108
 109 /* Return TRUE if OK, FALSE in case of Shake Error */
 110
 111 extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_int64_t step, const t_commrec *cr, t_mdatoms *md, t_state *state, gmx_update_t upd, struct gmx_constr *constr);
 112
 113 void update_constraints(FILE              *fplog,
 114                         gmx_int64_t        step,
 115                         real              *dvdlambda, /* FEP stuff */
 116                         t_inputrec        *inputrec,  /* input record and box stuff     */
 117                         t_mdatoms         *md,
 118                         t_state           *state,
 119                         gmx_bool           bMolPBC,
 120                         struct t_graph    *graph,
 121                         rvec               force[], /* forces on home particles */
 122                         t_idef            *idef,
 123                         tensor             vir_part,
 124                         t_commrec         *cr,
 125                         t_nrnb            *nrnb,
 126                         gmx_wallcycle_t    wcycle,
 127                         gmx_update_t       upd,
 128                         struct gmx_constr *constr,
 129                         gmx_bool           bFirstHalf,
 130                         gmx_bool           bCalcVir);
 131
 132 /* Return TRUE if OK, FALSE in case of Shake Error */
 133
 134 void update_box(FILE             *fplog,
 135                 gmx_int64_t       step,
 136                 t_inputrec       *inputrec, /* input record and box stuff       */
 137                 t_mdatoms        *md,
 138                 t_state          *state,
 139                 rvec              force[], /* forces on home particles */
 140                 matrix            pcoupl_mu,
 141                 t_nrnb           *nrnb,
 142                 gmx_update_t      upd);
 143 /* Return TRUE if OK, FALSE in case of Shake Error */
 144
 145 void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
 146                   gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel);
 147 /*
 148  * Compute the partial kinetic energy for home particles;
 149  * will be accumulated in the calling routine.
 150  * The tensor is
 151  *
 152  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 153  *
 154  *     use v[i] = v[i] - u[i] when calculating temperature
 155  *
 156  * u must be accumulated already.
 157  *
 158  * Now also computes the contribution of the kinetic energy to the
 159  * free energy
 160  *
 161  */
 162
 163
 164 void
 165 init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir);
 166
 167 void
 168 update_ekinstate(ekinstate_t *ekinstate, gmx_ekindata_t *ekind);
 169
 170 void
 171 restore_ekinstate_from_state(t_commrec *cr,
 172                              gmx_ekindata_t *ekind, ekinstate_t *ekinstate);
 173
 174 void berendsen_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt);
 175
 176 void andersen_tcoupl(t_inputrec *ir, gmx_int64_t step,
 177                      const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac);
 178
 179 void nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt,
 180                        double xi[], double vxi[], t_extmass *MassQ);
 181
 182 t_state *init_bufstate(const t_state *template_state);
 183
 184 void destroy_bufstate(t_state *state);
 185
 186 void trotter_update(t_inputrec *ir, gmx_int64_t step, gmx_ekindata_t *ekind,
 187                     gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
 188                     t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
 189
 190 int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
 191
 192 real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
 193 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 194
 195 void NBaroT_trotter(t_grpopts *opts, real dt,
 196                     double xi[], double vxi[], real *veta, t_extmass *MassQ);
 197
 198 void vrescale_tcoupl(t_inputrec *ir, gmx_int64_t step,
 199                      gmx_ekindata_t *ekind, real dt,
 200                      double therm_integral[]);
 201 /* Compute temperature scaling. For V-rescale it is done in update. */
 202
 203 real vrescale_energy(t_grpopts *opts, double therm_integral[]);
 204 /* Returns the V-rescale contribution to the conserved energy */
 205
 206 void rescale_velocities(gmx_ekindata_t *ekind, t_mdatoms *mdatoms,
 207                         int start, int end, rvec v[]);
 208 /* Rescale the velocities with the scaling factor in ekind */
 209
 210 void update_annealing_target_temp(t_grpopts *opts, real t);
 211 /* Set reference temp for simulated annealing at time t*/
 212
 213 real calc_temp(real ekin, real nrdf);
 214 /* Calculate the temperature */
 215
 216 real calc_pres(int ePBC, int nwall, matrix box, tensor ekin, tensor vir,
 217                tensor pres);
 218 /* Calculate the pressure tensor, returns the scalar pressure.
 219  * The unit of pressure is bar.
 220  */
 221
 222 void parrinellorahman_pcoupl(FILE *fplog, gmx_int64_t step,
 223                              t_inputrec *ir, real dt, tensor pres,
 224                              tensor box, tensor box_rel, tensor boxv,
 225                              tensor M, matrix mu,
 226                              gmx_bool bFirstStep);
 227
 228 void berendsen_pcoupl(FILE *fplog, gmx_int64_t step,
 229                       t_inputrec *ir, real dt, tensor pres, matrix box,
 230                       matrix mu);
 231
 232
 233 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 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 */