swapcoords.h File Reference

#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/timing/wallcycle.h"

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Description

The "Computational Electrophysiology" protocol for ion/water position swapping.

Author

Carsten Kutzner ckutz.nosp@m.ne@g.nosp@m.wdg.d.nosp@m.e

Functions
void	init_swapcoords (FILE *fplog, gmx_bool bVerbose, t_inputrec *ir, const char *fn, gmx_mtop_t *mtop, rvec x[], matrix box, swapstate_t *swapstate, t_commrec *cr, const output_env_t oenv, unsigned long Flags)
	Initialize ion / water position swapping ("Computational Electrophysiology"). More...
void	dd_make_local_swap_groups (gmx_domdec_t *dd, t_swapcoords *si_pub)
	Make a selection of the home atoms for the swap groups. These are the ions, the water, and the channels. This routine should be called at every domain decomposition. More...
gmx_bool	do_swapcoords (t_commrec *cr, gmx_int64_t step, double t, t_inputrec *ir, gmx_wallcycle_t wcycle, rvec x[], matrix box, gmx_mtop_t *mtop, gmx_bool bVerbose, gmx_bool bRerun)
	"Computational Electrophysiology" main routine within MD loop. More...

Function Documentation

void dd_make_local_swap_groups	(	gmx_domdec_t *	dd,
		t_swapcoords *	si_pub
	)

Make a selection of the home atoms for the swap groups. These are the ions, the water, and the channels. This routine should be called at every domain decomposition.

Parameters

[in]	dd	Structure containing domain decomposition data.
[in]	si_pub	Pointer to the swap data structure.

gmx_bool do_swapcoords	(	t_commrec *	cr,
		gmx_int64_t	step,
		double	t,
		t_inputrec *	ir,
		gmx_wallcycle_t	wcycle,
		rvec	x[],
		matrix	box,
		gmx_mtop_t *	mtop,
		gmx_bool	bVerbose,
		gmx_bool	bRerun
	)

"Computational Electrophysiology" main routine within MD loop.

Parameters

[in]	cr	Pointer to MPI communication data.
[in]	step	The number of the MD time step.
[in]	t	The time.
[in]	ir	Structure containing MD input parameters, among those also the structure needed for position swapping.
[in]	wcycle	Count wallcycles of swap routines for diagnostic output.
[in]	x	Positions of home particles this node owns.
[in]	box	The simulation box.
[in]	mtop	Molecular topology.
[in]	bVerbose	Should we be quiet or verbose?
[in]	bRerun	Are we doing a rerun?

Returns

Whether at least one pair of molecules was swapped.

void init_swapcoords	(	FILE *	fplog,
		gmx_bool	bVerbose,
		t_inputrec *	ir,
		const char *	fn,
		gmx_mtop_t *	mtop,
		rvec	x[],
		matrix	box,
		swapstate_t *	swapstate,
		t_commrec *	cr,
		const output_env_t	oenv,
		unsigned long	Flags
	)

Initialize ion / water position swapping ("Computational Electrophysiology").

This routine does the memory allocation for various helper arrays, opens the output file, sets up swap data checkpoint writing, etc.

Parameters

[in]	fplog	General output file, normally md.log.
[in]	bVerbose	Should we be quiet or verbose?
[in]	ir	Structure containing MD input parameters, among those also the structure needed for position swapping.
[in]	fn	Output file name for swap data.
[in]	mtop	Molecular topology.
[in]	x	The initial positions of all particles.
[in]	box	The simulation box.
[in]	swapstate	Swap-related data that is read from or written to checkpoint.
[in]	cr	Pointer to MPI communication data.
[in]	oenv	Needed to open the swap output XVGR file.
[in]	Flags	Flags passed over from main, used to determine whether we are doing a rerun, appending, etc.