orires.h File Reference

#include <cstdio>
#include "gromacs/topology/ifunc.h"

Include dependency graph for orires.h:

Description

Declares functions for handling orientation restraints.

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	init_orires (FILE *fplog, const gmx_mtop_t *mtop, const t_inputrec *ir, const t_commrec *cr, const gmx_multisim_t *ms, t_state *globalState, t_oriresdata *od)
	Decides whether orientation restraints can work, and initializes all the orientation restraint stuff in *od (and assumes *od is already allocated. If orientation restraint are used, globalState is read and modified on the master rank (which is the only rank, since orientation restraints can not run in parallel).
real	calc_orires_dev (const gmx_multisim_t *ms, int nfa, const t_iatom fa[], const t_iparams ip[], const t_mdatoms *md, gmx::ArrayRef< const gmx::RVec > xWholeMolecules, const rvec x[], const t_pbc *pbc, t_oriresdata *oriresdata, history_t *hist)
	Calculates the time averaged D matrices, the S matrix for each experiment. More...
void	diagonalize_orires_tensors (t_oriresdata *od)
	Diagonalizes the order tensor(s) of the orienation restraints. More...
void	print_orires_log (FILE *log, t_oriresdata *od)
	Prints order parameter, eigenvalues and eigenvectors to the log file.
real	orires (int nfa, const t_iatom forceatoms[], const t_iparams ip[], const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, real lambda, real *dvdlambda, const t_mdatoms *md, t_fcdata *fcd, int *global_atom_index)
	Calculates the orientation restraint forces.
void	update_orires_history (const t_oriresdata &oriresdata, history_t *hist)
	Copies the new time averages that have been calculated in calc_orires_dev.

Function Documentation

real calc_orires_dev	(	const gmx_multisim_t *	ms,
		int	nfa,
		const t_iatom	fa[],
		const t_iparams	ip[],
		const t_mdatoms *	md,
		gmx::ArrayRef< const gmx::RVec >	xWholeMolecules,
		const rvec	x[],
		const t_pbc *	pbc,
		t_oriresdata *	oriresdata,
		history_t *	hist
	)

Calculates the time averaged D matrices, the S matrix for each experiment.

Returns the weighted RMS deviation of the orientation restraints.

void diagonalize_orires_tensors

(

t_oriresdata *

od

)

Diagonalizes the order tensor(s) of the orienation restraints.

For each experiment eig containts first 3 eigenvalues and then the 3 eigenvectors. The eigenvalues are ordered on magnitude.