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/*
* $Id$
*
* This source code is part of
*
* G R O M A C S
*
* GROningen MAchine for Chemical Simulations
*
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team,
* check out http://www.gromacs.org for more information.
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
*
* For more info, check our website at http://www.gromacs.org
*
* And Hey:
* Gromacs Runs On Most of All Computer Systems
*/
#ifndef _update_h
#define _update_h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include "typedefs.h"
#include "mshift.h"
#include "tgroup.h"
#include "network.h"
#include "force.h"
#include "pull.h"
#include "gmx_random.h"
/* Abstract type for stochastic dynamics */
typedef struct gmx_stochd *gmx_stochd_t;
/* Initialize the stochastic dynamics struct */
extern gmx_stochd_t init_stochd(FILE *fplog,t_inputrec *ir);
/* Store the random state from sd in state */
extern void get_stochd_state(gmx_stochd_t sd,t_state *state);
/* Set the random in sd from state */
extern void set_stochd_state(gmx_stochd_t sd,t_state *state);
/* Store the box at step step
* as a reference state for simulations with box deformation.
*/
extern void set_deform_reference_box(int step,matrix box);
extern void update(FILE *fplog,
int step,
real *dvdlambda, /* FEP stuff */
t_inputrec *inputrec, /* input record and box stuff */
t_mdatoms *md,
t_state *state,
t_graph *graph,
rvec force[], /* forces on home particles */
rvec xprime[], /* buffer for x for update */
t_fcdata *fcd,
t_idef *idef,
gmx_ekindata_t *ekind,
tensor vir_part,
matrix *scale_tot,
t_commrec *cr,
t_nrnb *nrnb,
gmx_wallcycle_t wcycle,
gmx_stochd_t sd,
gmx_constr_t constr,
bool bHaveConstr,
bool bNEMD,
bool bInitStep);
/* Return TRUE if OK, FALSE in case of Shake Error */
extern void calc_ke_part(rvec v[],t_grpopts *opts,t_mdatoms *md,
gmx_ekindata_t *ekind,t_nrnb *nrnb,
real lambda);
/*
* Compute the partial kinetic energy for home particles;
* will be accumulated in the calling routine.
* The tensor is
*
* Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
*
* use v[i] = v[i] - u[i] when calculating temperature
*
* u must be accumulated already.
*
* Now also computes the contribution of the kinetic energy to the
* free energy
*
*/
extern void calc_ke_part_visc(matrix box,rvec x[],rvec v[],
t_grpopts *opts,t_mdatoms *md,
gmx_ekindata_t *ekind,t_nrnb *nrnb,
real lambda);
/* The same as calc_ke_part, but for viscosity calculations.
* The cosine velocity profile is excluded from the kinetic energy.
* The new amplitude of the velocity profile is calculated for this
* node and stored in grps->cosacc.mvcos.
*/
extern void
init_ekinstate(ekinstate_t *ekinstate,t_inputrec *ir);
extern void
update_ekinstate(ekinstate_t *ekinstate,gmx_ekindata_t *ekind);
extern void
restore_ekinstate_from_state(t_commrec *cr,
gmx_ekindata_t *ekind,ekinstate_t *ekinstate);
extern real run_aver(real old,real cur,int step,int nmem);
extern void berendsen_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt);
extern void nosehoover_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
real xi[],double ixi[]);
/* Compute temperature scaling. For Nose-Hoover it is done in update. */
extern real nosehoover_energy(t_grpopts *opts,gmx_ekindata_t *ekind,
real *xi,double *ixi);
/* Returns the Nose-Hoover contribution to the conserved energy */
extern void vrescale_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
double therm_integral[],
gmx_rng_t rng);
/* Compute temperature scaling. For V-rescale it is done in update. */
extern real vrescale_energy(t_grpopts *opts,double therm_integral[]);
/* Returns the V-rescale contribution to the conserved energy */
/* Set reference temp for simulated annealing at time t*/
extern void update_annealing_target_temp(t_grpopts *opts,real t);
extern real calc_temp(real ekin,real nrdf);
/* Calculate the temperature */
extern real calc_pres(int ePBC,int nwall,matrix box,
tensor ekin,tensor vir,tensor pres,real Elr);
/* Calculate the pressure tensor, returns the scalar pressure.
* The unit of pressure is bar, If Elr != 0
* a long range correction based on Ewald/PPPM is made (see c-code)
*/
extern void parrinellorahman_pcoupl(FILE *fplog,int step,
t_inputrec *ir,tensor pres,
tensor box,tensor box_rel,tensor boxv,
tensor M,matrix mu,
bool bFirstStep);
extern void berendsen_pcoupl(FILE *fplog,int step,
t_inputrec *ir,tensor pres,matrix box,
matrix mu);
extern void berendsen_pscale(t_inputrec *ir,matrix mu,
matrix box,matrix box_rel,
int start,int nr_atoms,
rvec x[],unsigned short cFREEZE[],
t_nrnb *nrnb);
extern void correct_ekin(FILE *log,int start,int end,rvec v[],
rvec vcm,real mass[],real tmass,tensor ekin);
/* Correct ekin for vcm */
#endif /* _update_h */
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