lincs.h File Reference

#include <cstdio>
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/idef.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

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Description

Declares interface to LINCS code.

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Mark Abraham mark..nosp@m.j.ab.nosp@m.raham.nosp@m.@gma.nosp@m.il.co.nosp@m.m

Classes
class	gmx::ArrayRefWithPadding< typename >
	Interface to a C array of T (or part of a std container of T), that includes padding that is suitable for the kinds of SIMD operations GROMACS uses. More...
class	gmx::ArrayRef< typename >
	STL-like interface to a C array of T (or part of a std container of T). More...
class	gmx::ListOfLists< typename >
	A list of lists, optimized for performance. More...

Functions
real	gmx::lincs_rmsd (const Lincs *lincsd)
	Return the RMSD of the constraint.
Lincs *	gmx::init_lincs (FILE *fplog, const gmx_mtop_t &mtop, int nflexcon_global, ArrayRef< const ListOfLists< int >> atomsToConstraintsPerMolType, bool bPLINCS, int nIter, int nProjOrder, ObservablesReducerBuilder *observablesReducerBuilder)
	Initializes and returns the lincs data struct.
void	gmx::done_lincs (Lincs *li)
	Destructs the lincs object when it is not nullptr.
void	gmx::set_lincs (const InteractionDefinitions &idef, int numAtoms, ArrayRef< const real > invmass, real lambda, bool bDynamics, const t_commrec *cr, Lincs *li)
	Initialize lincs stuff.
bool	gmx::constrain_lincs (bool computeRmsd, const t_inputrec &ir, int64_t step, Lincs *lincsd, ArrayRef< const real > invmass, const t_commrec *cr, const gmx_multisim_t *ms, ArrayRefWithPadding< const RVec > x, ArrayRefWithPadding< RVec > xprime, ArrayRef< RVec > min_proj, const matrix box, t_pbc *pbc, bool hasMassPerturbed, real lambda, real *dvdlambda, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, ConstraintVariable econq, t_nrnb *nrnb, int maxwarn, int *warncount, gmx_wallcycle *wcycle)
	Applies LINCS constraints. More...
int	gmx::count_triangle_constraints (const InteractionLists &ilist, const ListOfLists< int > &at2con)
	Counts the number of constraint triangles, i.e. triplets of atoms connected by three constraints. More...