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45 #include "gmx_random.h"
52 /* Abstract type for stochastic dynamics */
53 typedef struct gmx_update *gmx_update_t;
55 /* Initialize the stochastic dynamics struct */
56 gmx_update_t init_update(FILE *fplog,t_inputrec *ir);
58 /* Store the random state from sd in state */
59 void get_stochd_state(gmx_update_t sd,t_state *state);
61 /* Set the random in sd from state */
62 void set_stochd_state(gmx_update_t sd,t_state *state);
64 /* Store the box at step step
65 * as a reference state for simulations with box deformation.
67 void set_deform_reference_box(gmx_update_t upd,
68 gmx_large_int_t step,matrix box);
70 void update_tcouple(FILE *fplog,
74 gmx_ekindata_t *ekind,
75 gmx_wallcycle_t wcycle,
81 void update_pcouple(FILE *fplog,
87 gmx_wallcycle_t wcycle,
91 void update_coords(FILE *fplog,
93 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 void update_constraints(FILE *fplog,
114 gmx_large_int_t step,
115 real *dvdlambda, /* FEP stuff */
116 t_inputrec *inputrec, /* input record and box stuff */
117 gmx_ekindata_t *ekind,
121 rvec force[], /* forces on home particles */
127 gmx_wallcycle_t wcycle,
135 /* Return TRUE if OK, FALSE in case of Shake Error */
137 void update_box(FILE *fplog,
138 gmx_large_int_t step,
139 t_inputrec *inputrec, /* input record and box stuff */
143 rvec force[], /* forces on home particles */
147 gmx_wallcycle_t wcycle,
150 gmx_bool bFirstHalf);
151 /* Return TRUE if OK, FALSE in case of Shake Error */
153 void calc_ke_part(t_state *state,t_grpopts *opts,t_mdatoms *md,
154 gmx_ekindata_t *ekind,t_nrnb *nrnb,gmx_bool bEkinAveVel, gmx_bool bSaveOld);
156 * Compute the partial kinetic energy for home particles;
157 * will be accumulated in the calling routine.
160 * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
162 * use v[i] = v[i] - u[i] when calculating temperature
164 * u must be accumulated already.
166 * Now also computes the contribution of the kinetic energy to the
172 init_ekinstate(ekinstate_t *ekinstate,const t_inputrec *ir);
175 update_ekinstate(ekinstate_t *ekinstate,gmx_ekindata_t *ekind);
178 restore_ekinstate_from_state(t_commrec *cr,
179 gmx_ekindata_t *ekind,ekinstate_t *ekinstate);
181 void berendsen_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt);
183 void nosehoover_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
184 double xi[],double vxi[],t_extmass *MassQ);
186 t_state *init_bufstate(const t_state *template_state);
188 void destroy_bufstate(t_state *state);
190 void trotter_update(t_inputrec *ir, gmx_large_int_t step, gmx_ekindata_t *ekind,
191 gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
192 t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
194 int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
196 real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
197 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
199 void NBaroT_trotter(t_grpopts *opts, real dt,
200 double xi[],double vxi[],real *veta, t_extmass *MassQ);
202 void vrescale_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt,
203 double therm_integral[],
205 /* Compute temperature scaling. For V-rescale it is done in update. */
207 real vrescale_energy(t_grpopts *opts,double therm_integral[]);
208 /* Returns the V-rescale contribution to the conserved energy */
210 void rescale_velocities(gmx_ekindata_t *ekind,t_mdatoms *mdatoms,
211 int start,int end,rvec v[]);
212 /* Rescale the velocities with the scaling factor in ekind */
214 void update_annealing_target_temp(t_grpopts *opts,real t);
215 /* Set reference temp for simulated annealing at time t*/
217 real calc_temp(real ekin,real nrdf);
218 /* Calculate the temperature */
220 real calc_pres(int ePBC,int nwall,matrix box,
221 tensor ekin,tensor vir,tensor pres,real Elr);
222 /* Calculate the pressure tensor, returns the scalar pressure.
223 * The unit of pressure is bar, If Elr != 0
224 * a long range correction based on Ewald/PPPM is made (see c-code)
227 void parrinellorahman_pcoupl(FILE *fplog,gmx_large_int_t step,
228 t_inputrec *ir,real dt,tensor pres,
229 tensor box,tensor box_rel,tensor boxv,
231 gmx_bool bFirstStep);
233 void berendsen_pcoupl(FILE *fplog,gmx_large_int_t step,
234 t_inputrec *ir,real dt,tensor pres,matrix box,
238 void berendsen_pscale(t_inputrec *ir,matrix mu,
239 matrix box,matrix box_rel,
240 int start,int nr_atoms,
241 rvec x[],unsigned short cFREEZE[],
244 void correct_ekin(FILE *log,int start,int end,rvec v[],
245 rvec vcm,real mass[],real tmass,tensor ekin);
246 /* Correct ekin for vcm */
253 #endif /* _update_h */