swapcoords.h File Reference

#include <cstdio>
#include <memory>
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.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
std::unique_ptr< IMDModule >	gmx::createSwapCoordinatesModule ()
	Creates a module for Computational Electrophysiology swapping.
t_swap *	init_swapcoords (FILE *fplog, const t_inputrec *ir, const char *fn, const gmx_mtop_t &mtop, const t_state *globalState, ObservablesHistory *oh, t_commrec *cr, gmx::LocalAtomSetManager *atomSets, const gmx_output_env_t *oenv, const gmx::MdrunOptions &mdrunOptions, gmx::StartingBehavior startingBehavior)
	Initialize ion / water position swapping ("Computational Electrophysiology"). More...
void	finish_swapcoords (t_swap *s)
	Finalizes ion / water position swapping, if it was active. More...
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)
	"Computational Electrophysiology" main routine within MD loop. More...

Function Documentation

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
	)

"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
[in,out]	s	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_swap *

s

)

Finalizes ion / water position swapping, if it was active.

Parameters

[in]

s

Pointer to swap data.

t_swap* init_swapcoords	(	FILE *	fplog,
		const t_inputrec *	ir,
		const char *	fn,
		const gmx_mtop_t &	mtop,
		const t_state *	globalState,
		ObservablesHistory *	oh,
		t_commrec *	cr,
		gmx::LocalAtomSetManager *	atomSets,
		const gmx_output_env_t *	oenv,
		const gmx::MdrunOptions &	mdrunOptions,
		gmx::StartingBehavior	startingBehavior
	)

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. and returns it.

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 main rank.
[in]	oh	Contains struct with swap data that is read from or written to checkpoint.
[in]	cr	Pointer to MPI communication data.
[in]	atomSets	Manager tending to swap atom indices.
[in]	oenv	Needed to open the swap output XVGR file.
[in]	mdrunOptions	Options for mdrun.
[in]	startingBehavior	Describes whether this is a restart appending to output files