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 struct t_fcdata;
  48
  49 #ifdef __cplusplus
  50 extern "C" {
  51 #endif
  52
  53 struct t_graph;
  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(t_inputrec *ir);
  60
  61 /* Store the random state from sd in state */
  62 void get_stochd_state(gmx_update_t sd, t_state *state);
  63
  64 /* Set the random in sd from state */
  65 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 void set_deform_reference_box(gmx_update_t upd,
  71                               gmx_int64_t step, matrix box);
  72
  73 void update_tcouple(gmx_int64_t       step,
  74                     t_inputrec       *inputrec,
  75                     t_state          *state,
  76                     gmx_ekindata_t   *ekind,
  77                     t_extmass        *MassQ,
  78                     t_mdatoms        *md
  79                     );
  80
  81 void update_pcouple(FILE             *fplog,
  82                     gmx_int64_t       step,
  83                     t_inputrec       *inputrec,
  84                     t_state          *state,
  85                     matrix            pcoupl_mu,
  86                     matrix            M,
  87                     gmx_bool          bInitStep);
  88
  89 void update_coords(FILE              *fplog,
  90                    gmx_int64_t        step,
  91                    t_inputrec        *inputrec, /* input record and box stuff   */
  92                    t_mdatoms         *md,
  93                    t_state           *state,
  94                    gmx_bool           bMolPBC,
  95                    rvec              *f, /* forces on home particles */
  96                    gmx_bool           bDoLR,
  97                    rvec              *f_lr,
  98                    tensor            *vir_lr_constr,
  99                    t_fcdata          *fcd,
 100                    gmx_ekindata_t    *ekind,
 101                    matrix             M,
 102                    gmx_update_t       upd,
 103                    gmx_bool           bInitStep,
 104                    int                bUpdatePart,
 105                    t_commrec         *cr, /* these shouldn't be here -- need to think about it */
 106                    t_nrnb            *nrnb,
 107                    struct gmx_constr *constr,
 108                    t_idef            *idef);
 109
 110 /* Return TRUE if OK, FALSE in case of Shake Error */
 111
 112 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);
 113
 114 void update_constraints(FILE              *fplog,
 115                         gmx_int64_t        step,
 116                         real              *dvdlambda, /* FEP stuff */
 117                         t_inputrec        *inputrec,  /* input record and box stuff     */
 118                         t_mdatoms         *md,
 119                         t_state           *state,
 120                         gmx_bool           bMolPBC,
 121                         struct t_graph    *graph,
 122                         rvec               force[], /* forces on home particles */
 123                         t_idef            *idef,
 124                         tensor             vir_part,
 125                         t_commrec         *cr,
 126                         t_nrnb            *nrnb,
 127                         gmx_wallcycle_t    wcycle,
 128                         gmx_update_t       upd,
 129                         struct gmx_constr *constr,
 130                         gmx_bool           bFirstHalf,
 131                         gmx_bool           bCalcVir);
 132
 133 /* Return TRUE if OK, FALSE in case of Shake Error */
 134
 135 void update_box(FILE             *fplog,
 136                 gmx_int64_t       step,
 137                 t_inputrec       *inputrec, /* input record and box stuff       */
 138                 t_mdatoms        *md,
 139                 t_state          *state,
 140                 rvec              force[], /* forces on home particles */
 141                 matrix            pcoupl_mu,
 142                 t_nrnb           *nrnb,
 143                 gmx_update_t      upd);
 144 /* Return TRUE if OK, FALSE in case of Shake Error */
 145
 146 void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
 147                   gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel);
 148 /*
 149  * Compute the partial kinetic energy for home particles;
 150  * will be accumulated in the calling routine.
 151  * The tensor is
 152  *
 153  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 154  *
 155  *     use v[i] = v[i] - u[i] when calculating temperature
 156  *
 157  * u must be accumulated already.
 158  *
 159  * Now also computes the contribution of the kinetic energy to the
 160  * free energy
 161  *
 162  */
 163
 164
 165 void
 166 init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir);
 167
 168 void
 169 update_ekinstate(ekinstate_t *ekinstate, gmx_ekindata_t *ekind);
 170
 171 void
 172 restore_ekinstate_from_state(t_commrec *cr,
 173                              gmx_ekindata_t *ekind, ekinstate_t *ekinstate);
 174
 175 void berendsen_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt);
 176
 177 void andersen_tcoupl(t_inputrec *ir, gmx_int64_t step,
 178                      const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac);
 179
 180 void nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt,
 181                        double xi[], double vxi[], t_extmass *MassQ);
 182
 183 t_state *init_bufstate(const t_state *template_state);
 184
 185 void destroy_bufstate(t_state *state);
 186
 187 void trotter_update(t_inputrec *ir, gmx_int64_t step, gmx_ekindata_t *ekind,
 188                     gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
 189                     t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
 190
 191 int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
 192
 193 real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
 194 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 195
 196 void NBaroT_trotter(t_grpopts *opts, real dt,
 197                     double xi[], double vxi[], real *veta, t_extmass *MassQ);
 198
 199 void vrescale_tcoupl(t_inputrec *ir, gmx_int64_t step,
 200                      gmx_ekindata_t *ekind, real dt,
 201                      double therm_integral[]);
 202 /* Compute temperature scaling. For V-rescale it is done in update. */
 203
 204 real vrescale_energy(t_grpopts *opts, double therm_integral[]);
 205 /* Returns the V-rescale contribution to the conserved energy */
 206
 207 void rescale_velocities(gmx_ekindata_t *ekind, t_mdatoms *mdatoms,
 208                         int start, int end, rvec v[]);
 209 /* Rescale the velocities with the scaling factor in ekind */
 210
 211 void update_annealing_target_temp(t_grpopts *opts, real t);
 212 /* Set reference temp for simulated annealing at time t*/
 213
 214 real calc_temp(real ekin, real nrdf);
 215 /* Calculate the temperature */
 216
 217 real calc_pres(int ePBC, int nwall, matrix box, tensor ekin, tensor vir,
 218                tensor pres);
 219 /* Calculate the pressure tensor, returns the scalar pressure.
 220  * The unit of pressure is bar.
 221  */
 222
 223 void parrinellorahman_pcoupl(FILE *fplog, gmx_int64_t step,
 224                              t_inputrec *ir, real dt, tensor pres,
 225                              tensor box, tensor box_rel, tensor boxv,
 226                              tensor M, matrix mu,
 227                              gmx_bool bFirstStep);
 228
 229 void berendsen_pcoupl(FILE *fplog, gmx_int64_t step,
 230                       t_inputrec *ir, real dt, tensor pres, matrix box,
 231                       matrix mu);
 232
 233
 234 void berendsen_pscale(t_inputrec *ir, matrix mu,
 235                       matrix box, matrix box_rel,
 236                       int start, int nr_atoms,
 237                       rvec x[], unsigned short cFREEZE[],
 238                       t_nrnb *nrnb);
 239
 240 void correct_ekin(FILE *log, int start, int end, rvec v[],
 241                   rvec vcm, real mass[], real tmass, tensor ekin);
 242 /* Correct ekin for vcm */
 243
 244
 245 #ifdef __cplusplus
 246 }
 247 #endif
 248
 249 #endif  /* _update_h */