edsam.h File Reference

#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"

Include dependency graph for edsam.h:

Description

Declares functions to calculate both essential dynamics constraints as well as flooding potentials and forces.

Authors

Bert de Groot bgroo.nosp@m.t@gw.nosp@m.dg.de, Oliver Lange olive.nosp@m.r.la.nosp@m.nge@t.nosp@m.um.d.nosp@m.e, Carsten Kutzner ckutz.nosp@m.ne@g.nosp@m.wdg.d.nosp@m.e

Typedefs
typedef struct gmx_edsam *	gmx_edsam_t
	Abstract type for essential dynamics. More...

Functions
void	do_edsam (const t_inputrec *ir, gmx_int64_t step, t_commrec *cr, rvec xs[], rvec v[], matrix box, gmx_edsam_t ed)
	Applies essential dynamics constrains as defined in the .edi input file. More...
gmx_edsam_t	init_edsam (const char *ediFileName, const char *edoFileName, const gmx_mtop_t *mtop, const t_inputrec *ir, t_commrec *cr, struct gmx_constr *constr, const t_state *globalState, ObservablesHistory *oh, const gmx_output_env_t *oenv, gmx_bool bAppend)
	Initializes the essential dynamics and flooding module. More...
void	dd_make_local_ed_indices (gmx_domdec_t *dd, gmx_edsam_t ed)
	Make a selection of the home atoms for the ED groups. More...
void	do_flood (t_commrec *cr, const t_inputrec *ir, rvec x[], rvec force[], gmx_edsam_t ed, matrix box, gmx_int64_t step, gmx_bool bNS)
	Evaluate the flooding potential(s) and forces as requested in the .edi input file. More...
void	done_ed (gmx_edsam_t *ed)
	Clean up. More...

Typedef Documentation

typedef struct gmx_edsam* gmx_edsam_t

Abstract type for essential dynamics.

The main type is defined only in edsam.cpp

Function Documentation

void dd_make_local_ed_indices	(	gmx_domdec_t *	dd,
		gmx_edsam_t	ed
	)

Make a selection of the home atoms for the ED groups.

Should be called at every domain decomposition.

Parameters

dd	Domain decomposition data.
ed	Essential dynamics and flooding data.

void do_edsam	(	const t_inputrec *	ir,
		gmx_int64_t	step,
		t_commrec *	cr,
		rvec	xs[],
		rvec	v[],
		matrix	box,
		gmx_edsam_t	ed
	)

Applies essential dynamics constrains as defined in the .edi input file.

Parameters

ir	MD input parameter record.
step	Number of the time step.
cr	Data needed for MPI communication.
xs	The local positions on this processor.
v	The local velocities.
box	The simulation box.
ed	The essential dynamics data.

void do_flood	(	t_commrec *	cr,
		const t_inputrec *	ir,
		rvec	x[],
		rvec	force[],
		gmx_edsam_t	ed,
		matrix	box,
		gmx_int64_t	step,
		gmx_bool	bNS
	)

Evaluate the flooding potential(s) and forces as requested in the .edi input file.

Parameters

cr	Data needed for MPI communication.
ir	MD input parameter record.
x	Positions on the local processor.
force	Forcefield forces to which the flooding forces are added.
ed	The essential dynamics data.
box	The simulation box.
step	Number of the time step.
bNS	Are we in a neighbor searching step?

void done_ed

(

gmx_edsam_t *

ed

)

Clean up.

Parameters

ed	The essential dynamics data

gmx_edsam_t init_edsam	(	const char *	ediFileName,
		const char *	edoFileName,
		const gmx_mtop_t *	mtop,
		const t_inputrec *	ir,
		t_commrec *	cr,
		struct gmx_constr *	constr,
		const t_state *	globalState,
		ObservablesHistory *	oh,
		const gmx_output_env_t *	oenv,
		gmx_bool	bAppend
	)

Initializes the essential dynamics and flooding module.

Parameters

ediFileName	Essential dynamics input file.
edoFileName	Output file for essential dynamics data.
mtop	Molecular topology.
ir	MD input parameter record.
cr	Data needed for MPI communication.
constr	Data structure keeping the constraint information.
globalState	The global state, only used on the master rank.
oh	The observables history container.
oenv	The output environment information.
bAppend	Append to existing output files?

Returns

A pointer to the ED data structure.