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37 #ifndef GMX_MDLIB_UPDATE_H
38 #define GMX_MDLIB_UPDATE_H
40 #include "gromacs/math/paddedvector.h"
41 #include "gromacs/math/vectypes.h"
42 #include "gromacs/timing/wallcycle.h"
43 #include "gromacs/utility/arrayref.h"
44 #include "gromacs/utility/basedefinitions.h"
45 #include "gromacs/utility/real.h"
48 struct gmx_ekindata_t;
49 struct gmx_enerdata_t;
59 /* Abstract type for update */
68 /* Initialize the stochastic dynamics struct */
69 gmx_update_t *init_update(const t_inputrec *ir,
70 gmx::BoxDeformation *deform);
72 /* Update pre-computed constants that depend on the reference
73 * temperature for coupling.
75 * This could change e.g. in simulated annealing. */
76 void update_temperature_constants(gmx_update_t *upd, const t_inputrec *ir);
78 /* Update the size of per-atom arrays (e.g. after DD re-partitioning,
79 which might increase the number of home atoms). */
80 void update_realloc(gmx_update_t *upd, int natoms);
82 /* Store the box at step step
83 * as a reference state for simulations with box deformation.
85 void set_deform_reference_box(gmx_update_t *upd,
86 int64_t step, matrix box);
88 void update_tcouple(int64_t step,
91 gmx_ekindata_t *ekind,
96 /* Update Parrinello-Rahman, to be called before the coordinate update */
97 void update_pcouple_before_coordinates(FILE *fplog,
99 const t_inputrec *inputrec,
101 matrix parrinellorahmanMu,
105 /* Update the box, to be called after the coordinate update.
106 * For Berendsen P-coupling, also calculates the scaling factor
107 * and scales the coordinates.
108 * When the deform option is used, scales coordinates and box here.
110 void update_pcouple_after_coordinates(FILE *fplog,
112 const t_inputrec *inputrec,
114 const matrix pressure,
115 const matrix forceVirial,
116 const matrix constraintVirial,
117 const matrix parrinellorahmanMu,
122 void update_coords(int64_t step,
123 t_inputrec *inputrec, /* input record and box stuff */
126 gmx::PaddedArrayRef<gmx::RVec> f, /* forces on home particles */
128 gmx_ekindata_t *ekind,
132 const t_commrec *cr, /* these shouldn't be here -- need to think about it */
133 gmx::Constraints *constr);
135 /* Return TRUE if OK, FALSE in case of Shake Error */
137 extern gmx_bool update_randomize_velocities(t_inputrec *ir, int64_t step, const t_commrec *cr, t_mdatoms *md, t_state *state, gmx_update_t *upd, gmx::Constraints *constr);
139 void constrain_velocities(int64_t step,
140 real *dvdlambda, /* the contribution to be added to the bonded interactions */
143 gmx_wallcycle_t wcycle,
144 gmx::Constraints *constr,
149 void constrain_coordinates(int64_t step,
150 real *dvdlambda, /* the contribution to be added to the bonded interactions */
153 gmx_wallcycle_t wcycle,
155 gmx::Constraints *constr,
160 void update_sd_second_half(int64_t step,
161 real *dvdlambda, /* the contribution to be added to the bonded interactions */
162 const t_inputrec *inputrec, /* input record and box stuff */
167 gmx_wallcycle_t wcycle,
169 gmx::Constraints *constr,
173 void finish_update(const t_inputrec *inputrec,
178 gmx_wallcycle_t wcycle,
180 gmx::Constraints *constr);
182 /* Return TRUE if OK, FALSE in case of Shake Error */
184 void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
185 gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel);
187 * Compute the partial kinetic energy for home particles;
188 * will be accumulated in the calling routine.
191 * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
193 * use v[i] = v[i] - u[i] when calculating temperature
195 * u must be accumulated already.
197 * Now also computes the contribution of the kinetic energy to the
204 init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir);
207 update_ekinstate(ekinstate_t *ekinstate, gmx_ekindata_t *ekind);
209 /*! \brief Restores data from \p ekinstate to \p ekind, then broadcasts it
210 to the rest of the simulation */
212 restore_ekinstate_from_state(const t_commrec *cr,
213 gmx_ekindata_t *ekind, const ekinstate_t *ekinstate);
215 void berendsen_tcoupl(const t_inputrec *ir, const gmx_ekindata_t *ekind, real dt,
216 std::vector<double> &therm_integral);
218 void andersen_tcoupl(t_inputrec *ir, int64_t step,
219 const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac);
221 void nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt,
222 double xi[], double vxi[], t_extmass *MassQ);
224 void trotter_update(t_inputrec *ir, int64_t step, gmx_ekindata_t *ekind,
225 gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
226 t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
228 int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
230 real NPT_energy(const t_inputrec *ir, const t_state *state, const t_extmass *MassQ);
231 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
233 void NBaroT_trotter(t_grpopts *opts, real dt,
234 double xi[], double vxi[], real *veta, t_extmass *MassQ);
236 void vrescale_tcoupl(t_inputrec *ir, int64_t step,
237 gmx_ekindata_t *ekind, real dt,
238 double therm_integral[]);
239 /* Compute temperature scaling. For V-rescale it is done in update. */
241 void rescale_velocities(gmx_ekindata_t *ekind, t_mdatoms *mdatoms,
242 int start, int end, rvec v[]);
243 /* Rescale the velocities with the scaling factor in ekind */
245 void update_annealing_target_temp(t_inputrec *ir, real t, gmx_update_t *upd);
246 /* Set reference temp for simulated annealing at time t*/
248 real calc_temp(real ekin, real nrdf);
249 /* Calculate the temperature */
251 real calc_pres(int ePBC, int nwall, matrix box, tensor ekin, tensor vir,
253 /* Calculate the pressure tensor, returns the scalar pressure.
254 * The unit of pressure is bar.
257 void parrinellorahman_pcoupl(FILE *fplog, int64_t step,
258 const t_inputrec *ir, real dt, const tensor pres,
259 tensor box, tensor box_rel, tensor boxv,
261 gmx_bool bFirstStep);
263 void berendsen_pcoupl(FILE *fplog, int64_t step,
264 const t_inputrec *ir, real dt,
265 const tensor pres, const matrix box,
266 const matrix force_vir, const matrix constraint_vir,
267 matrix mu, double *baros_integral);
269 void berendsen_pscale(const t_inputrec *ir, const matrix mu,
270 matrix box, matrix box_rel,
271 int start, int nr_atoms,
272 rvec x[], const unsigned short cFREEZE[],
275 void correct_ekin(FILE *log, int start, int end, rvec v[],
276 rvec vcm, real mass[], real tmass, tensor ekin);
277 /* Correct ekin for vcm */