swapcoords.h File Reference

#include <cstdio>
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"

Include dependency graph for swapcoords.h:

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, t_inputrec *ir, const char *fn, gmx_mtop_t *mtop, const t_state *globalState, ObservablesHistory *oh, t_commrec *cr, const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions)
	Initialize ion / water position swapping ("Computational Electrophysiology"). More...
void	finish_swapcoords (t_swapcoords *sc)
	Finalizes ion / water position swapping. 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 *wcycle, rvec x[], matrix box, 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 *	wcycle,
		rvec	x[],
		matrix	box,
		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]	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 finish_swapcoords

(

t_swapcoords *

sc

)

Finalizes ion / water position swapping.

Parameters

[in]

sc

Pointer to swap data.

void init_swapcoords	(	FILE *	fplog,
		t_inputrec *	ir,
		const char *	fn,
		gmx_mtop_t *	mtop,
		const t_state *	globalState,
		ObservablesHistory *	oh,
		t_commrec *	cr,
		const gmx_output_env_t *	oenv,
		const MdrunOptions &	mdrunOptions
	)

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]	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]	globalState	The global state, only used on the master rank.
[in]	oh	Contains struct with swap 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]	mdrunOptions	Options for mdrun.