anonymous_namespace{bonded.cpp} Namespace Reference

Typedefs
using	BondedFunction = real(*)(int nbonds, const t_iatom iatoms[], const t_iparams iparams[], const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const t_graph *g, real lambda, real *dvdlambda, const t_mdatoms *md, t_fcdata *fcd, int *ddgatindex)
	Type of CPU function to compute a bonded interaction.

Functions
int	pbc_rvec_sub (const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
	Compute dx = xi - xj, modulo PBC if non-NULL. More...
template<BondedKernelFlavor flavor>
void	spreadBondForces (const real bondForce, const rvec dx, const int ai, const int aj, rvec4 *f, int shiftIndex, const t_graph *g, rvec *fshift)
	Spreads and accumulates the bonded forces to the two atoms and adds the virial contribution when needed. More...
template<BondedKernelFlavor flavor>
real	morse_bonds (int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const t_graph *g, real lambda, real *dvdlambda, const t_mdatoms *md, t_fcdata *fcd, int *global_atom_index)
	Morse potential bond. More...
int	cmap_setup_grid_index (int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
	Mysterious undocumented function.

Variables
const int	cmap_coeff_matrix []
	Mysterious CMAP coefficient matrix. More...

Function Documentation

template<BondedKernelFlavor flavor>

real anonymous_namespace{bonded.cpp}::morse_bonds	(	int	nbonds,
		const t_iatom	forceatoms[],
		const t_iparams	forceparams[],
		const rvec	x[],
		rvec4	f[],
		rvec	fshift[],
		const t_pbc *	pbc,
		const t_graph *	g,
		real	lambda,
		real *	dvdlambda,
		const t_mdatoms *	md,
		t_fcdata *	fcd,
		int *	global_atom_index
	)

Morse potential bond.

By Frank Everdij. Three parameters needed:

b0 = equilibrium distance in nm be = beta in nm^-1 (actually, it's nu_e*Sqrt(2*pi*pi*mu/D_e)) cb = well depth in kJ/mol

Note: the potential is referenced to be +cb at infinite separation and zero at the equilibrium distance!

int anonymous_namespace{bonded.cpp}::pbc_rvec_sub	(	const t_pbc *	pbc,
		const rvec	xi,
		const rvec	xj,
		rvec	dx
	)

Compute dx = xi - xj, modulo PBC if non-NULL.

Todo:

This kind of code appears in many places. Consolidate it

template<BondedKernelFlavor flavor>

void anonymous_namespace{bonded.cpp}::spreadBondForces ( const real  bondForce, const rvec  dx, const int  ai, const int  aj, rvec4 *  f, int  shiftIndex, const t_graph *  g, rvec *  fshift  )

inline

Spreads and accumulates the bonded forces to the two atoms and adds the virial contribution when needed.

When g==nullptr, shiftIndex is used as the periodic shift. When g!=nullptr, the graph is used to compute the periodic shift.

Variable Documentation

const int anonymous_namespace{bonded.cpp}::cmap_coeff_matrix[]

Initial value:

= {
    1,  0,  -3, 2,  0,  0, 0,  0,  -3, 0,  9,  -6, 2, 0,  -6, 4,  0,  0,  0, 0,  0, 0, 0,  0,
    3,  0,  -9, 6,  -2, 0, 6,  -4, 0,  0,  0,  0,  0, 0,  0,  0,  0,  0,  9, -6, 0, 0, -6, 4,
    0,  0,  3,  -2, 0,  0, 0,  0,  0,  0,  -9, 6,  0, 0,  6,  -4, 0,  0,  0, 0,  1, 0, -3, 2,
    -2, 0,  6,  -4, 1,  0, -3, 2,  0,  0,  0,  0,  0, 0,  0,  0,  -1, 0,  3, -2, 1, 0, -3, 2,
    0,  0,  0,  0,  0,  0, 0,  0,  0,  0,  -3, 2,  0, 0,  3,  -2, 0,  0,  0, 0,  0, 0, 3,  -2,
    0,  0,  -6, 4,  0,  0, 3,  -2, 0,  1,  -2, 1,  0, 0,  0,  0,  0,  -3, 6, -3, 0, 2, -4, 2,
    0,  0,  0,  0,  0,  0, 0,  0,  0,  3,  -6, 3,  0, -2, 4,  -2, 0,  0,  0, 0,  0, 0, 0,  0,
    0,  0,  -3, 3,  0,  0, 2,  -2, 0,  0,  -1, 1,  0, 0,  0,  0,  0,  0,  3, -3, 0, 0, -2, 2,
    0,  0,  0,  0,  0,  1, -2, 1,  0,  -2, 4,  -2, 0, 1,  -2, 1,  0,  0,  0, 0,  0, 0, 0,  0,
    0,  -1, 2,  -1, 0,  1, -2, 1,  0,  0,  0,  0,  0, 0,  0,  0,  0,  0,  1, -1, 0, 0, -1, 1,
    0,  0,  0,  0,  0,  0, -1, 1,  0,  0,  2,  -2, 0, 0,  -1, 1
}

Mysterious CMAP coefficient matrix.