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41 #include "visibility.h"
48 #include "gmx_random.h"
55 /* Abstract type for stochastic dynamics */
56 typedef struct gmx_update
*gmx_update_t
;
58 /* Initialize the stochastic dynamics struct */
59 gmx_update_t
init_update(FILE *fplog
,t_inputrec
*ir
);
61 /* Store the random state from sd in state */
63 void get_stochd_state(gmx_update_t sd
,t_state
*state
);
65 /* Set the random in sd from state */
67 void set_stochd_state(gmx_update_t sd
,t_state
*state
);
69 /* Store the box at step step
70 * as a reference state for simulations with box deformation.
73 void set_deform_reference_box(gmx_update_t upd
,
74 gmx_large_int_t step
,matrix box
);
77 void update_tcouple(FILE *fplog
,
81 gmx_ekindata_t
*ekind
,
82 gmx_wallcycle_t wcycle
,
89 void update_pcouple(FILE *fplog
,
95 gmx_wallcycle_t wcycle
,
100 void update_coords(FILE *fplog
,
101 gmx_large_int_t step
,
102 t_inputrec
*inputrec
, /* input record and box stuff */
106 rvec
*f
, /* forces on home particles */
110 gmx_ekindata_t
*ekind
,
112 gmx_wallcycle_t wcycle
,
116 t_commrec
*cr
, /* these shouldn't be here -- need to think about it */
121 /* Return TRUE if OK, FALSE in case of Shake Error */
124 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
);
127 void update_constraints(FILE *fplog
,
128 gmx_large_int_t step
,
129 real
*dvdlambda
, /* FEP stuff */
130 t_inputrec
*inputrec
, /* input record and box stuff */
131 gmx_ekindata_t
*ekind
,
136 rvec force
[], /* forces on home particles */
142 gmx_wallcycle_t wcycle
,
150 /* Return TRUE if OK, FALSE in case of Shake Error */
153 void update_box(FILE *fplog
,
154 gmx_large_int_t step
,
155 t_inputrec
*inputrec
, /* input record and box stuff */
159 rvec force
[], /* forces on home particles */
163 gmx_wallcycle_t wcycle
,
166 gmx_bool bFirstHalf
);
167 /* Return TRUE if OK, FALSE in case of Shake Error */
169 void calc_ke_part(t_state
*state
,t_grpopts
*opts
,t_mdatoms
*md
,
170 gmx_ekindata_t
*ekind
,t_nrnb
*nrnb
,gmx_bool bEkinAveVel
, gmx_bool bSaveOld
);
172 * Compute the partial kinetic energy for home particles;
173 * will be accumulated in the calling routine.
176 * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
178 * use v[i] = v[i] - u[i] when calculating temperature
180 * u must be accumulated already.
182 * Now also computes the contribution of the kinetic energy to the
189 init_ekinstate(ekinstate_t
*ekinstate
,const t_inputrec
*ir
);
193 update_ekinstate(ekinstate_t
*ekinstate
,gmx_ekindata_t
*ekind
);
196 restore_ekinstate_from_state(t_commrec
*cr
,
197 gmx_ekindata_t
*ekind
,ekinstate_t
*ekinstate
);
199 void berendsen_tcoupl(t_inputrec
*ir
,gmx_ekindata_t
*ekind
,real dt
);
201 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
);
203 void nosehoover_tcoupl(t_grpopts
*opts
,gmx_ekindata_t
*ekind
,real dt
,
204 double xi
[],double vxi
[],t_extmass
*MassQ
);
207 t_state
*init_bufstate(const t_state
*template_state
);
209 void destroy_bufstate(t_state
*state
);
212 void trotter_update(t_inputrec
*ir
, gmx_large_int_t step
, gmx_ekindata_t
*ekind
,
213 gmx_enerdata_t
*enerd
, t_state
*state
, tensor vir
, t_mdatoms
*md
,
214 t_extmass
*MassQ
, int **trotter_seqlist
, int trotter_seqno
);
217 int **init_npt_vars(t_inputrec
*ir
, t_state
*state
, t_extmass
*Mass
, gmx_bool bTrotter
);
219 real
NPT_energy(t_inputrec
*ir
, t_state
*state
, t_extmass
*MassQ
);
220 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
222 void NBaroT_trotter(t_grpopts
*opts
, real dt
,
223 double xi
[],double vxi
[],real
*veta
, t_extmass
*MassQ
);
225 void vrescale_tcoupl(t_inputrec
*ir
,gmx_ekindata_t
*ekind
,real dt
,
226 double therm_integral
[],
228 /* Compute temperature scaling. For V-rescale it is done in update. */
230 real
vrescale_energy(t_grpopts
*opts
,double therm_integral
[]);
231 /* Returns the V-rescale contribution to the conserved energy */
233 void rescale_velocities(gmx_ekindata_t
*ekind
,t_mdatoms
*mdatoms
,
234 int start
,int end
,rvec v
[]);
235 /* Rescale the velocities with the scaling factor in ekind */
238 void update_annealing_target_temp(t_grpopts
*opts
,real t
);
239 /* Set reference temp for simulated annealing at time t*/
241 real
calc_temp(real ekin
,real nrdf
);
242 /* Calculate the temperature */
244 real
calc_pres(int ePBC
,int nwall
,matrix box
,tensor ekin
,tensor vir
,
246 /* Calculate the pressure tensor, returns the scalar pressure.
247 * The unit of pressure is bar.
250 void parrinellorahman_pcoupl(FILE *fplog
,gmx_large_int_t step
,
251 t_inputrec
*ir
,real dt
,tensor pres
,
252 tensor box
,tensor box_rel
,tensor boxv
,
254 gmx_bool bFirstStep
);
256 void berendsen_pcoupl(FILE *fplog
,gmx_large_int_t step
,
257 t_inputrec
*ir
,real dt
,tensor pres
,matrix box
,
261 void berendsen_pscale(t_inputrec
*ir
,matrix mu
,
262 matrix box
,matrix box_rel
,
263 int start
,int nr_atoms
,
264 rvec x
[],unsigned short cFREEZE
[],
267 void correct_ekin(FILE *log
,int start
,int end
,rvec v
[],
268 rvec vcm
,real mass
[],real tmass
,tensor ekin
);
269 /* Correct ekin for vcm */
276 #endif /* _update_h */