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45 #include "../timing/wallcycle.h"
53 /* Abstract type for stochastic dynamics */
54 typedef struct gmx_update *gmx_update_t;
56 /* Initialize the stochastic dynamics struct */
57 gmx_update_t init_update(t_inputrec *ir);
59 /* Store the random state from sd in state */
60 void get_stochd_state(gmx_update_t sd, t_state *state);
62 /* Set the random in sd from state */
63 void set_stochd_state(gmx_update_t sd, t_state *state);
65 /* Store the box at step step
66 * as a reference state for simulations with box deformation.
68 void set_deform_reference_box(gmx_update_t upd,
69 gmx_int64_t step, matrix box);
71 void update_tcouple(gmx_int64_t step,
74 gmx_ekindata_t *ekind,
79 void update_pcouple(FILE *fplog,
87 void update_coords(FILE *fplog,
89 t_inputrec *inputrec, /* input record and box stuff */
93 rvec *f, /* forces on home particles */
96 tensor *vir_lr_constr,
98 gmx_ekindata_t *ekind,
103 t_commrec *cr, /* these shouldn't be here -- need to think about it */
108 /* Return TRUE if OK, FALSE in case of Shake Error */
110 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, gmx_constr_t constr);
112 void update_constraints(FILE *fplog,
114 real *dvdlambda, /* FEP stuff */
115 t_inputrec *inputrec, /* input record and box stuff */
116 gmx_ekindata_t *ekind,
120 struct t_graph *graph,
121 rvec force[], /* forces on home particles */
126 gmx_wallcycle_t wcycle,
133 /* Return TRUE if OK, FALSE in case of Shake Error */
135 void update_box(FILE *fplog,
137 t_inputrec *inputrec, /* input record and box stuff */
140 rvec force[], /* forces on home particles */
145 /* Return TRUE if OK, FALSE in case of Shake Error */
147 void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
148 gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel, gmx_bool bSaveOld);
150 * Compute the partial kinetic energy for home particles;
151 * will be accumulated in the calling routine.
154 * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
156 * use v[i] = v[i] - u[i] when calculating temperature
158 * u must be accumulated already.
160 * Now also computes the contribution of the kinetic energy to the
167 init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir);
170 update_ekinstate(ekinstate_t *ekinstate, gmx_ekindata_t *ekind);
173 restore_ekinstate_from_state(t_commrec *cr,
174 gmx_ekindata_t *ekind, ekinstate_t *ekinstate);
176 void berendsen_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt);
178 void andersen_tcoupl(t_inputrec *ir, gmx_int64_t step,
179 const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac);
181 void nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt,
182 double xi[], double vxi[], t_extmass *MassQ);
184 t_state *init_bufstate(const t_state *template_state);
186 void destroy_bufstate(t_state *state);
188 void trotter_update(t_inputrec *ir, gmx_int64_t step, gmx_ekindata_t *ekind,
189 gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
190 t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
192 int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
194 real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
195 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
197 void NBaroT_trotter(t_grpopts *opts, real dt,
198 double xi[], double vxi[], real *veta, t_extmass *MassQ);
200 void vrescale_tcoupl(t_inputrec *ir, gmx_int64_t step,
201 gmx_ekindata_t *ekind, real dt,
202 double therm_integral[]);
203 /* Compute temperature scaling. For V-rescale it is done in update. */
205 real vrescale_energy(t_grpopts *opts, double therm_integral[]);
206 /* Returns the V-rescale contribution to the conserved energy */
208 void rescale_velocities(gmx_ekindata_t *ekind, t_mdatoms *mdatoms,
209 int start, int end, rvec v[]);
210 /* Rescale the velocities with the scaling factor in ekind */
212 void update_annealing_target_temp(t_grpopts *opts, real t);
213 /* Set reference temp for simulated annealing at time t*/
215 real calc_temp(real ekin, real nrdf);
216 /* Calculate the temperature */
218 real calc_pres(int ePBC, int nwall, matrix box, tensor ekin, tensor vir,
220 /* Calculate the pressure tensor, returns the scalar pressure.
221 * The unit of pressure is bar.
224 void parrinellorahman_pcoupl(FILE *fplog, gmx_int64_t step,
225 t_inputrec *ir, real dt, tensor pres,
226 tensor box, tensor box_rel, tensor boxv,
228 gmx_bool bFirstStep);
230 void berendsen_pcoupl(FILE *fplog, gmx_int64_t step,
231 t_inputrec *ir, real dt, tensor pres, matrix box,
235 void berendsen_pscale(t_inputrec *ir, matrix mu,
236 matrix box, matrix box_rel,
237 int start, int nr_atoms,
238 rvec x[], unsigned short cFREEZE[],
241 void correct_ekin(FILE *log, int start, int end, rvec v[],
242 rvec vcm, real mass[], real tmass, tensor ekin);
243 /* Correct ekin for vcm */
250 #endif /* _update_h */