constr.h File Reference

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

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Description

Declares interface to constraint 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::ListOfLists< typename >
	A list of lists, optimized for performance. More...
class	gmx::Constraints
	Handles constraints. More...

Enumerations
enum	gmx::ConstraintVariable : int {   Positions, Velocities, Derivative, Deriv_FlexCon,   Force, ForceDispl }
	Describes supported flavours of constrained updates.
enum	gmx::FlexibleConstraintTreatment { gmx::FlexibleConstraintTreatment::Include, gmx::FlexibleConstraintTreatment::Exclude }
	Tells make_at2con how to treat flexible constraints. More...

Functions
void	gmx::too_many_constraint_warnings (ConstraintAlgorithm eConstrAlg, int warncount)
	Generate a fatal error because of too many LINCS/SETTLE warnings.
static bool	gmx::isConstraintFlexible (ArrayRef< const t_iparams > iparams, int iparamsIndex)
	Returns whether constraint with parameter iparamsIndex is a flexible constraint.
FlexibleConstraintTreatment	gmx::flexibleConstraintTreatment (bool haveDynamicsIntegrator)
	Returns the flexible constraint treatment depending on whether the integrator is dynamic.
ListOfLists< int >	gmx::make_at2con (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns a ListOfLists object to go from atoms to constraints. More...
ListOfLists< int >	gmx::make_at2con (int numAtoms, ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns a ListOfLists object to go from atoms to constraints. More...
int	gmx::countFlexibleConstraints (ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > iparams)
	Return the number of flexible constraints in the ilist and iparams.
const int *	gmx::constr_iatomptr (gmx::ArrayRef< const int > iatom_constr, gmx::ArrayRef< const int > iatom_constrnc, int con)
	Returns the constraint iatoms for a constraint number con which comes from a list where F_CONSTR and F_CONSTRNC constraints are concatenated.
void	gmx::do_constrain_first (FILE *log, gmx::Constraints *constr, const t_inputrec *inputrec, int numAtoms, int numHomeAtoms, ArrayRefWithPadding< RVec > x, ArrayRefWithPadding< RVec > v, const matrix box, real lambda)
	Constrain the initial coordinates and velocities.
void	gmx::constrain_velocities (gmx::Constraints *constr, bool do_log, bool do_ene, int64_t step, t_state *state, real *dvdlambda, bool computeVirial, tensor constraintsVirial)
	Constrain velocities only. More...
void	gmx::constrain_coordinates (gmx::Constraints *constr, bool do_log, bool do_ene, int64_t step, t_state *state, ArrayRefWithPadding< RVec > xp, real *dvdlambda, bool computeVirial, tensor constraintsVirial)
	Constraint coordinates. More...
bool	gmx::hasTriangleConstraints (const gmx_mtop_t &mtop, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns True if there is at least one triangular constraint.