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(FILE         *fplog,
  74                    gmx_large_int_t   step,
  75                    real         *dvdlambda, /* FEP stuff */
  76                    t_inputrec   *inputrec,  /* input record and box stuff */
  77                    t_mdatoms    *md,
  78                    t_state      *state,
  79                    t_graph      *graph,
  80                    rvec         *f,         /* forces on home particles */
  81                    bool         bDoLR,
  82                    rvec         *f_lr,      /* LR forces, only with dDoLR */
  83                    t_fcdata     *fcd,
  84                    t_idef       *idef,
  85                    gmx_ekindata_t *ekind,
  86                    matrix       *scale_tot,
  87                    t_commrec    *cr,
  88                    t_nrnb       *nrnb,
  89                    gmx_wallcycle_t wcycle,
  90                    gmx_update_t upd,
  91                    gmx_constr_t constr,
  92                    bool         bCalcVir,
  93                    tensor       vir_part,
  94                    bool         bNEMD,
  95                    bool         bInitStep);
  96 /* Return TRUE if OK, FALSE in case of Shake Error */
  97
  98 extern void calc_ke_part(t_state *state,t_grpopts *opts,t_mdatoms *md,
  99                          gmx_ekindata_t *ekind,t_nrnb *nrnb);
 100 /*
 101  * Compute the partial kinetic energy for home particles;
 102  * will be accumulated in the calling routine.
 103  * The tensor is
 104  *
 105  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 106  *
 107  *     use v[i] = v[i] - u[i] when calculating temperature
 108  *
 109  * u must be accumulated already.
 110  *
 111  * Now also computes the contribution of the kinetic energy to the
 112  * free energy
 113  *
 114  */
 115
 116 extern void
 117 init_ekinstate(ekinstate_t *ekinstate,t_inputrec *ir);
 118
 119 extern void
 120 update_ekinstate(ekinstate_t *ekinstate,gmx_ekindata_t *ekind);
 121
 122 extern void
 123 restore_ekinstate_from_state(t_commrec *cr,
 124                              gmx_ekindata_t *ekind,ekinstate_t *ekinstate);
 125
 126 extern void berendsen_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt);
 127
 128 extern void nosehoover_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
 129                               real xi[],double ixi[]);
 130 /* Compute temperature scaling. For Nose-Hoover it is done in update. */
 131
 132 extern real nosehoover_energy(t_grpopts *opts,gmx_ekindata_t *ekind,
 133                               real *xi,double *ixi);
 134 /* Returns the Nose-Hoover contribution to the conserved energy */
 135
 136 extern void vrescale_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
 137                             double therm_integral[],
 138                             gmx_rng_t rng);
 139 /* Compute temperature scaling. For V-rescale it is done in update. */
 140
 141 extern real vrescale_energy(t_grpopts *opts,double therm_integral[]);
 142 /* Returns the V-rescale contribution to the conserved energy */
 143
 144 /* Set reference temp for simulated annealing at time t*/
 145 extern void update_annealing_target_temp(t_grpopts *opts,real t);
 146
 147 extern real calc_temp(real ekin,real nrdf);
 148 /* Calculate the temperature */
 149
 150 extern real calc_pres(int ePBC,int nwall,matrix box,
 151                       tensor ekin,tensor vir,tensor pres,real Elr);
 152 /* Calculate the pressure tensor, returns the scalar pressure.
 153  * The unit of pressure is bar, If Elr != 0
 154  * a long range correction based on Ewald/PPPM is made (see c-code)
 155  */
 156
 157 extern void parrinellorahman_pcoupl(FILE *fplog,gmx_large_int_t step,
 158                                     t_inputrec *ir,real dt,tensor pres,
 159                                     tensor box,tensor box_rel,tensor boxv,
 160                                     tensor M,matrix mu,
 161                                     bool bFirstStep);
 162
 163 extern void berendsen_pcoupl(FILE *fplog,gmx_large_int_t step,
 164                              t_inputrec *ir,real dt,tensor pres,matrix box,
 165                              matrix mu);
 166
 167
 168 extern void berendsen_pscale(t_inputrec *ir,matrix mu,
 169                              matrix box,matrix box_rel,
 170                              int start,int nr_atoms,
 171                              rvec x[],unsigned short cFREEZE[],
 172                              t_nrnb *nrnb);
 173
 174 extern void correct_ekin(FILE *log,int start,int end,rvec v[],
 175                          rvec vcm,real mass[],real tmass,tensor ekin);
 176 /* Correct ekin for vcm */
 177
 178 #ifdef __cplusplus
 179 }
 180 #endif
 181
 182 #endif  /* _update_h */
 183