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44 #include "gmx_random.h"
51 /* Abstract type for stochastic dynamics */
52 typedef struct gmx_update *gmx_update_t;
54 /* Initialize the stochastic dynamics struct */
55 gmx_update_t init_update(FILE *fplog, t_inputrec *ir);
57 /* Store the random state from sd in state */
58 void get_stochd_state(gmx_update_t sd, t_state *state);
60 /* Set the random in sd from state */
61 void set_stochd_state(gmx_update_t sd, t_state *state);
63 /* Store the box at step step
64 * as a reference state for simulations with box deformation.
66 void set_deform_reference_box(gmx_update_t upd,
67 gmx_large_int_t step, matrix box);
69 void update_tcouple(FILE *fplog,
73 gmx_ekindata_t *ekind,
74 gmx_wallcycle_t wcycle,
80 void update_pcouple(FILE *fplog,
86 gmx_wallcycle_t wcycle,
90 void update_coords(FILE *fplog,
92 t_inputrec *inputrec, /* input record and box stuff */
96 rvec *f, /* forces on home particles */
100 gmx_ekindata_t *ekind,
102 gmx_wallcycle_t wcycle,
106 t_commrec *cr, /* these shouldn't be here -- need to think about it */
111 /* Return TRUE if OK, FALSE in case of Shake Error */
113 extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_large_int_t step, t_mdatoms *md, t_state *state, gmx_update_t upd, t_idef *idef, gmx_constr_t constr);
115 void update_constraints(FILE *fplog,
116 gmx_large_int_t step,
117 real *dvdlambda, /* FEP stuff */
118 t_inputrec *inputrec, /* input record and box stuff */
119 gmx_ekindata_t *ekind,
124 rvec force[], /* forces on home particles */
130 gmx_wallcycle_t wcycle,
138 /* Return TRUE if OK, FALSE in case of Shake Error */
140 void update_box(FILE *fplog,
141 gmx_large_int_t step,
142 t_inputrec *inputrec, /* input record and box stuff */
146 rvec force[], /* forces on home particles */
150 gmx_wallcycle_t wcycle,
153 gmx_bool bFirstHalf);
154 /* Return TRUE if OK, FALSE in case of Shake Error */
156 void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
157 gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel, gmx_bool bSaveOld);
159 * Compute the partial kinetic energy for home particles;
160 * will be accumulated in the calling routine.
163 * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
165 * use v[i] = v[i] - u[i] when calculating temperature
167 * u must be accumulated already.
169 * Now also computes the contribution of the kinetic energy to the
176 init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir);
179 update_ekinstate(ekinstate_t *ekinstate, gmx_ekindata_t *ekind);
182 restore_ekinstate_from_state(t_commrec *cr,
183 gmx_ekindata_t *ekind, ekinstate_t *ekinstate);
185 void berendsen_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt);
187 void andersen_tcoupl(t_inputrec *ir, t_mdatoms *md, t_state *state, gmx_rng_t rng, real rate, t_idef *idef, int nblocks, int *sblock, gmx_bool *randatom, int *randatom_list, gmx_bool *randomize, real *boltzfac);
189 void nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt,
190 double xi[], double vxi[], t_extmass *MassQ);
192 t_state *init_bufstate(const t_state *template_state);
194 void destroy_bufstate(t_state *state);
196 void trotter_update(t_inputrec *ir, gmx_large_int_t step, gmx_ekindata_t *ekind,
197 gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
198 t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
200 int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
202 real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
203 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
205 void NBaroT_trotter(t_grpopts *opts, real dt,
206 double xi[], double vxi[], real *veta, t_extmass *MassQ);
208 void vrescale_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt,
209 double therm_integral[],
211 /* Compute temperature scaling. For V-rescale it is done in update. */
213 real vrescale_energy(t_grpopts *opts, double therm_integral[]);
214 /* Returns the V-rescale contribution to the conserved energy */
216 void rescale_velocities(gmx_ekindata_t *ekind, t_mdatoms *mdatoms,
217 int start, int end, rvec v[]);
218 /* Rescale the velocities with the scaling factor in ekind */
220 void update_annealing_target_temp(t_grpopts *opts, real t);
221 /* Set reference temp for simulated annealing at time t*/
223 real calc_temp(real ekin, real nrdf);
224 /* Calculate the temperature */
226 real calc_pres(int ePBC, int nwall, matrix box, tensor ekin, tensor vir,
228 /* Calculate the pressure tensor, returns the scalar pressure.
229 * The unit of pressure is bar.
232 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,
236 gmx_bool bFirstStep);
238 void berendsen_pcoupl(FILE *fplog, gmx_large_int_t step,
239 t_inputrec *ir, real dt, tensor pres, matrix box,
243 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[],
249 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 */
258 #endif /* _update_h */