edsam.h File Reference

#include <cstdint>
#include <memory>
#include "gromacs/utility/vectypes.h"

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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

Classes
class	gmx::ArrayRef< typename >
	STL-like interface to a C array of T (or part of a std container of T). More...

Functions
void	do_edsam (const t_inputrec *ir, int64_t step, const gmx::MpiComm &mpiComm, gmx::ArrayRef< gmx::RVec > coords, gmx::ArrayRef< gmx::RVec > velocities, 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 gmx::MpiComm &mpiComm, const gmx_domdec_t *dd, 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 gmx::MpiComm &mpiComm, const t_inputrec &ir, gmx::ArrayRef< const gmx::RVec > coords, gmx::ArrayRef< gmx::RVec > force, gmx_edsam *ed, const matrix box, int64_t step, 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 gmx::MpiComm &	mpiComm,
		gmx::ArrayRef< gmx::RVec >	coords,
		gmx::ArrayRef< gmx::RVec >	velocities,
		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.
mpiComm	Communication object for my group.
coords	The local positions on this processor.
velocities	The local velocities.
box	The simulation box.
ed	The essential dynamics data.

void do_flood	(	const gmx::MpiComm &	mpiComm,
		const t_inputrec &	ir,
		gmx::ArrayRef< const gmx::RVec >	coords,
		gmx::ArrayRef< gmx::RVec >	force,
		gmx_edsam *	ed,
		const matrix	box,
		int64_t	step,
		bool	bNS
	)

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

Parameters

mpiComm	Communication object for my group.
ir	MD input parameter record.
coords	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 gmx::MpiComm &	mpiComm,
		const gmx_domdec_t *	dd,
		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.
mpiComm	Communication object for my group.
dd	Domain decomposition object, pass nullptr when DD is not active.
constr	Data structure keeping the constraint information.
globalState	The global state, only used on the main 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.