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, real lambda, real *dvdlambda, gmx::ArrayRef< const real > charge, t_fcdata *fcd, t_disresdata *disresdata, t_oriresdata *oriresdata, int *ddgatindex)
	Type of CPU function to compute a bonded interaction.
using	CmapForceStructure = std::array< real, 4 >

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, 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, real lambda, real *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)
	Morse potential bond. More...
int	cmap_setup_grid_index (int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
	Mysterious undocumented function.
gmx::RVec	processCmapForceComponent (const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim)
CmapForceStructure	applyCmapForceComponent (const gmx::RVec forceComponent)
void	accumulateCmapForces (const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2)

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,
		real	lambda,
		real *	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
	)

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, rvec *  fshift  )

inline

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

shiftIndex is used as 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.