* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
-void EnergyOutput::printAnnealingTemperatures(FILE* log, const SimulationGroups* groups, t_grpopts* opts)
+void EnergyOutput::printAnnealingTemperatures(FILE* log, const SimulationGroups* groups, const t_grpopts* opts)
{
if (log)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \param[in] opts Atom temperature coupling groups options
* (annealing is done by groups).
*/
- static void printAnnealingTemperatures(FILE* log, const SimulationGroups* groups, t_grpopts* opts);
+ static void printAnnealingTemperatures(FILE* log, const SimulationGroups* groups, const t_grpopts* opts);
/*! \brief Prints average values to log file.
*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017, The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int64_t step,
int64_t step_rel,
double t,
- t_inputrec* ir,
+ const t_inputrec* ir,
t_state* state,
t_state* state_global,
ObservablesHistory* observablesHistory,
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int64_t step,
int64_t step_rel,
double t,
- t_inputrec* ir,
+ const t_inputrec* ir,
t_state* state,
t_state* state_global,
ObservablesHistory* observablesHistory,
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Compute the norm and max of the force array in parallel
static void get_f_norm_max(const t_commrec* cr,
- t_grpopts* opts,
+ const t_grpopts* opts,
t_mdatoms* mdatoms,
gmx::ArrayRef<const gmx::RVec> f,
real* fnorm,
}
//! Compute the norm of the force
-static void get_state_f_norm_max(const t_commrec* cr, t_grpopts* opts, t_mdatoms* mdatoms, em_state_t* ems)
+static void get_state_f_norm_max(const t_commrec* cr, const t_grpopts* opts, t_mdatoms* mdatoms, em_state_t* ems)
{
get_f_norm_max(cr, opts, mdatoms, ems->f.view().force(), &ems->fnorm, &ems->fmax, &ems->a_fmax);
}
const gmx::MDLogger& mdlog,
const char* title,
const t_commrec* cr,
- t_inputrec* ir,
+ const t_inputrec* ir,
gmx::ImdSession* imdSession,
pull_t* pull_work,
t_state* state_global,
gmx_bool bF,
const char* confout,
const gmx_mtop_t* top_global,
- t_inputrec* ir,
+ const t_inputrec* ir,
int64_t step,
em_state_t* state,
t_state* state_global,
//
// \returns true when the step succeeded, false when a constraint error occurred
static bool do_em_step(const t_commrec* cr,
- t_inputrec* ir,
+ const t_inputrec* ir,
t_mdatoms* md,
em_state_t* ems1,
real a,
int step,
const t_commrec* cr,
const gmx_mtop_t* top_global,
- t_inputrec* ir,
+ const t_inputrec* ir,
gmx::ImdSession* imdSession,
pull_t* pull_work,
em_state_t* ems,
//! Holds the domain topology.
gmx_localtop_t* top;
//! User input options.
- t_inputrec* inputrec;
+ const t_inputrec* inputrec;
//! The Interactive Molecular Dynamics session.
gmx::ImdSession* imdSession;
//! The pull work object.
//! Parallel utility summing energies and forces
static double reorder_partsum(const t_commrec* cr,
- t_grpopts* opts,
+ const t_grpopts* opts,
const gmx_mtop_t* top_global,
const em_state_t* s_min,
const em_state_t* s_b)
//! Print some stuff, like beta, whatever that means.
static real pr_beta(const t_commrec* cr,
- t_grpopts* opts,
+ const t_grpopts* opts,
t_mdatoms* mdatoms,
const gmx_mtop_t* top_global,
const em_state_t* s_min,
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \endcode
*/
-static void detect_flux_per_channel(t_swapgrp* g,
- int iAtom,
- int comp,
- rvec atomPosition,
- unsigned char* comp_now,
- unsigned char* comp_from,
- unsigned char* channel_label,
- t_swapcoords* sc,
- t_swap* s,
- real cyl0_r2,
- real cyl1_r2,
- int64_t step,
- gmx_bool bRerun,
- FILE* fpout)
+static void detect_flux_per_channel(t_swapgrp* g,
+ int iAtom,
+ int comp,
+ rvec atomPosition,
+ unsigned char* comp_now,
+ unsigned char* comp_from,
+ unsigned char* channel_label,
+ const t_swapcoords* sc,
+ t_swap* s,
+ real cyl0_r2,
+ real cyl1_r2,
+ int64_t step,
+ gmx_bool bRerun,
+ FILE* fpout)
{
int sd, chan_nr;
gmx_bool in_cyl0, in_cyl1;
/*! \brief Determines which ions or solvent molecules are in compartment A and B */
-static void sortMoleculesIntoCompartments(t_swapgrp* g,
- t_commrec* cr,
- t_swapcoords* sc,
- t_swap* s,
- const matrix box,
- int64_t step,
- FILE* fpout,
- gmx_bool bRerun,
- gmx_bool bIsSolvent)
+static void sortMoleculesIntoCompartments(t_swapgrp* g,
+ t_commrec* cr,
+ const t_swapcoords* sc,
+ t_swap* s,
+ const matrix box,
+ int64_t step,
+ FILE* fpout,
+ gmx_bool bRerun,
+ gmx_bool bIsSolvent)
{
int nMolNotInComp[eCompNR]; /* consistency check */
real cyl0_r2 = sc->cyl0r * sc->cyl0r;
* From the requested and average molecule counts we determine whether a swap is needed
* at this time step.
*/
-static gmx_bool need_swap(t_swapcoords* sc, t_swap* s)
+static gmx_bool need_swap(const t_swapcoords* sc, t_swap* s)
{
int ic, ig;
t_swapgrp* g;
}
-gmx_bool do_swapcoords(t_commrec* cr,
- int64_t step,
- double t,
- t_inputrec* ir,
- t_swap* s,
- gmx_wallcycle* wcycle,
- rvec x[],
- matrix box,
- gmx_bool bVerbose,
- gmx_bool bRerun)
+gmx_bool do_swapcoords(t_commrec* cr,
+ int64_t step,
+ double t,
+ const t_inputrec* ir,
+ t_swap* s,
+ gmx_wallcycle* wcycle,
+ rvec x[],
+ matrix box,
+ gmx_bool bVerbose,
+ gmx_bool bRerun)
{
- t_swapcoords* sc;
- int j, ic, ig, nswaps;
- int thisC, otherC; /* Index into this compartment and the other one */
- gmx_bool bSwap = FALSE;
- t_swapgrp * g, *gsol;
- int isol, iion;
- rvec com_solvent, com_particle; /* solvent and swap molecule's center of mass */
+ const t_swapcoords* sc = ir->swap;
+ int j, ic, ig, nswaps;
+ int thisC, otherC; /* Index into this compartment and the other one */
+ gmx_bool bSwap = FALSE;
+ t_swapgrp * g, *gsol;
+ int isol, iion;
+ rvec com_solvent, com_particle; /* solvent and swap molecule's center of mass */
wallcycle_start(wcycle, ewcSWAP);
- sc = ir->swap;
-
set_pbc(s->pbc, ir->pbcType, box);
/* Assemble the positions of the split groups, i.e. the channels.
*
* Copyright (c) 2013, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \returns Whether at least one pair of molecules was swapped.
*/
-gmx_bool do_swapcoords(t_commrec* cr,
- int64_t step,
- double t,
- t_inputrec* ir,
- t_swap* s,
- gmx_wallcycle* wcycle,
- rvec x[],
- matrix box,
- gmx_bool bVerbose,
- gmx_bool bRerun);
+gmx_bool do_swapcoords(t_commrec* cr,
+ int64_t step,
+ double t,
+ const t_inputrec* ir,
+ t_swap* s,
+ gmx_wallcycle* wcycle,
+ rvec x[],
+ matrix box,
+ gmx_bool bVerbose,
+ gmx_bool bRerun);
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff