edsam.h File Reference

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

Functions
void	do_edsam (const t_inputrec *ir, int64_t step, const t_commrec *cr, rvec xs[], rvec v[], const matrix box, gmx_edsam *ed)
	Applies essential dynamics constrains as defined in the .edi input file. More...
std::unique_ptr < gmx::EssentialDynamics >	init_edsam (const gmx::MDLogger &mdlog, const char *ediFileName, const char *edoFileName, const gmx_mtop_t *mtop, const t_inputrec *ir, const t_commrec *cr, gmx::Constraints *constr, const t_state *globalState, ObservablesHistory *oh, const gmx_output_env_t *oenv, gmx::StartingBehavior startingBehavior)
	Initializes the essential dynamics and flooding module. More...
void	dd_make_local_ed_indices (gmx_domdec_t *dd, gmx_edsam *ed)
	Make a selection of the home atoms for the ED groups. More...
void	do_flood (const t_commrec *cr, const t_inputrec *ir, const rvec x[], rvec force[], gmx_edsam *ed, const matrix box, int64_t step, gmx_bool bNS)
	Evaluate the flooding potential(s) and forces as requested in the .edi input file. More...

Function Documentation

void dd_make_local_ed_indices	(	gmx_domdec_t *	dd,
		gmx_edsam *	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,
		int64_t	step,
		const t_commrec *	cr,
		rvec	xs[],
		rvec	v[],
		const matrix	box,
		gmx_edsam *	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	(	const t_commrec *	cr,
		const t_inputrec *	ir,
		const rvec	x[],
		rvec	force[],
		gmx_edsam *	ed,
		const matrix	box,
		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?

std::unique_ptr<gmx::EssentialDynamics> init_edsam	(	const gmx::MDLogger &	mdlog,
		const char *	ediFileName,
		const char *	edoFileName,
		const gmx_mtop_t *	mtop,
		const t_inputrec *	ir,
		const t_commrec *	cr,
		gmx::Constraints *	constr,
		const t_state *	globalState,
		ObservablesHistory *	oh,
		const gmx_output_env_t *	oenv,
		gmx::StartingBehavior	startingBehavior
	)

Initializes the essential dynamics and flooding module.

Parameters

mdlog	Logger.
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.
startingBehavior	Describes whether this is a restart appending to output files

Returns

A pointer to the ED data structure.