bonded.h File Reference

#include <string>
#include "gromacs/libgromacs_export.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/basedefinitions.h"

Include dependency graph for bonded.h:

Description

This file contains declarations necessary for low-level functions for computing energies and forces for bonded interactions.

Author

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

Classes
struct	gmx::EnumerationArray< EnumType, DataType, ArraySize >
	Wrapper for a C-style array with size and indexing defined by an enum. Useful for declaring arrays of enum names for debug or other printing. An ArrayRef<DataType> may be constructed from an object of this type. More...
class	gmx::ArrayRef< typename >
	STL-like interface to a C array of T (or part of a std container of T). More...

Enumerations
enum	BondedKernelFlavor {   BondedKernelFlavor::ForcesSimdWhenAvailable, BondedKernelFlavor::ForcesNoSimd, BondedKernelFlavor::ForcesAndVirialAndEnergy, BondedKernelFlavor::ForcesAndEnergy,   BondedKernelFlavor::Count }
	For selecting which flavor of bonded kernel is used for simple bonded types. More...

Functions
real	bond_angle (const rvec xi, const rvec xj, const rvec xk, const struct t_pbc *pbc, rvec r_ij, rvec r_kj, real *costh, int *t1, int *t2)
	Calculate bond-angle. No PBC is taken into account (use mol-shift)
real	dih_angle (const rvec xi, const rvec xj, const rvec xk, const rvec xl, const struct t_pbc *pbc, rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, int *t1, int *t2, int *t3)
	Calculate dihedral-angle. No PBC is taken into account (use mol-shift)
void	do_dih_fup (int i, int j, int k, int l, real ddphi, rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, rvec4 f[], rvec fshift[], const struct t_pbc *pbc, const rvec *x, int t1, int t2, int t3)
	Do an update of the forces for dihedral potentials.
void	make_dp_periodic (real *dp)
	Make a dihedral fall in the range (-pi,pi)
real	cmap_dihs (int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const gmx_cmap_t *cmap_grid, const rvec x[], rvec4 f[], rvec fshift[], const struct t_pbc *pbc, real gmx_unused lambda, real gmx_unused *dvdlambda, gmx::ArrayRef< const real >, t_fcdata gmx_unused *fcd, t_disresdata gmx_unused *disresdata, t_oriresdata gmx_unused *oriresdata, int gmx_unused *global_atom_index)
	Compute CMAP dihedral energies and forces.
static constexpr bool	computeEnergy (const BondedKernelFlavor flavor)
	Returns whether the energy should be computed.
static constexpr bool	computeVirial (const BondedKernelFlavor flavor)
	Returns whether the virial should be computed.
static constexpr bool	computeEnergyOrVirial (const BondedKernelFlavor flavor)
	Returns whether the energy and/or virial should be computed.
real	calculateSimpleBond (int ftype, int numForceatoms, const t_iatom forceatoms[], const t_iparams forceparams[], const rvec x[], rvec4 f[], rvec fshift[], const struct t_pbc *pbc, real lambda, real *dvdlambda, gmx::ArrayRef< const real > charge, t_fcdata *fcd, t_disresdata *disresdata, t_oriresdata *oriresdata, int gmx_unused *global_atom_index, BondedKernelFlavor bondedKernelFlavor)
	Calculates bonded interactions for simple bonded types. More...
int	nrnbIndex (int ftype)
	Getter for finding the flop count for an ftype interaction.

Variables
LIBGROMACS_EXPORT const gmx::EnumerationArray < BondedKernelFlavor, std::string, BondedKernelFlavor::Count >	c_bondedKernelFlavorStrings
	Helper strings for human-readable messages.

Enumeration Type Documentation

enum BondedKernelFlavor

strong

For selecting which flavor of bonded kernel is used for simple bonded types.

Enumerator
ForcesSimdWhenAvailable	Compute only forces, use SIMD when available; should not be used with perturbed parameters.
ForcesNoSimd	Compute only forces, do not use SIMD.
ForcesAndVirialAndEnergy	Compute forces, virial and energy (no SIMD)
ForcesAndEnergy	Compute forces and energy (no SIMD)
Count	The number of flavors.

Function Documentation

real calculateSimpleBond	(	int	ftype,
		int	numForceatoms,
		const t_iatom	forceatoms[],
		const t_iparams	forceparams[],
		const rvec	x[],
		rvec4	f[],
		rvec	fshift[],
		const struct t_pbc *	pbc,
		real	lambda,
		real *	dvdlambda,
		gmx::ArrayRef< const real >	charge,
		t_fcdata *	fcd,
		t_disresdata *	disresdata,
		t_oriresdata *	oriresdata,
		int gmx_unused *	global_atom_index,
		BondedKernelFlavor	bondedKernelFlavor
	)

Calculates bonded interactions for simple bonded types.

Exits with an error when the bonded type is not simple All pointers should be non-null, except for pbc and g which can be nullptr.

Returns

the energy or 0 when bondedKernelFlavor did not request the energy.