pull_rotation.h File Reference

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

Include dependency graph for pull_rotation.h:

Description

Declares functions to enforce rotational motion upon a group of particles.

Author

Carsten Kutzner ckutz.nosp@m.ne@g.nosp@m.wdg.d.nosp@m.e

Functions
std::unique_ptr < gmx::EnforcedRotation >	init_rot (FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[], const t_commrec *cr, gmx::LocalAtomSetManager *atomSets, const t_state *globalState, gmx_mtop_t *mtop, const gmx_output_env_t *oenv, const gmx::MdrunOptions &mdrunOptions, gmx::StartingBehavior startingBehavior)
	Initializes the enforced rotation groups. More...
void	do_rotation (const t_commrec *cr, gmx_enfrot *er, const matrix box, rvec x[], real t, int64_t step, gmx_bool bNS)
	Calculates the enforced rotation potential(s). More...
real	add_rot_forces (gmx_enfrot *er, rvec f[], const t_commrec *cr, int64_t step, real t)
	Add the enforced rotation forces to the official force array. More...

Function Documentation

real add_rot_forces	(	gmx_enfrot *	er,
		rvec	f[],
		const t_commrec *	cr,
		int64_t	step,
		real	t
	)

Add the enforced rotation forces to the official force array.

Adds the forces from enforced rotation potential to the local forces and sums up the contributions to the rotation potential from all the nodes. Since this needs communication, this routine should be called after the short range forces have been evaluated (in order not to spoil cycle counts). This routine also outputs data to the rotation output files (e.g. the potential, the angle of the group(s), and torques).

Parameters

er	Pointer to the enforced rotation working data.
f	The local forces to which the rotational forces have to be added.
cr	Pointer to MPI communication data.
step	The time step, used for output.
t	Time, used for output.

Returns

The potential energy of the rotation potentials.

void do_rotation	(	const t_commrec *	cr,
		gmx_enfrot *	er,
		const matrix	box,
		rvec	x[],
		real	t,
		int64_t	step,
		gmx_bool	bNS
	)

Calculates the enforced rotation potential(s).

This is the main enforced rotation module which is called during every time step. Here the rotation potential as well as the resulting forces are calculated.

Parameters

cr	Pointer to MPI communication data.
er	Pointer to the enforced rotation working data.
box	Simulation box, needed to make group whole.
x	The positions of all the local particles.
t	Time.
step	The time step.
bNS	After domain decomposition / neighbor searching several local arrays have to be updated (masses, shifts)

std::unique_ptr<gmx::EnforcedRotation> init_rot	(	FILE *	fplog,
		t_inputrec *	ir,
		int	nfile,
		const t_filenm	fnm[],
		const t_commrec *	cr,
		gmx::LocalAtomSetManager *	atomSets,
		const t_state *	globalState,
		gmx_mtop_t *	mtop,
		const gmx_output_env_t *	oenv,
		const gmx::MdrunOptions &	mdrunOptions,
		gmx::StartingBehavior	startingBehavior
	)

Initializes the enforced rotation groups.

This routine does the memory allocation for various helper arrays, opens the output files etc.

Parameters

fplog	General output file, normally md.log.
ir	Struct containing MD input parameters, among those also the enforced rotation parameters.
nfile	Number of entries in the fnm structure.
fnm	The filenames struct containing also the names of the rotation output files.
atomSets	Tracks indices of atoms subject to enforced rotation for each DD rank.
cr	Pointer to MPI communication data.
globalState	The global state, only used on the master rank.
mtop	Molecular topology.
oenv	Needed to open the rotation output xvgr file.
mdrunOptions	Options for mdrun.
startingBehavior	Describes whether this is a restart appending to output files

Returns

An enforced rotation module.