Classes
struct	LayerStack

Functions
double	normHeightPercent (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, int nPrisms, double avgPrismHeight)
std::vector< double >	calcCoverageArea (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &rings, double sheetArea)
std::vector< double >	projAreaSingleRing (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< int > &ring)
	Calculates the projected area on the XY, YZ and XZ planes.
std::vector< double >	rodgerF4 (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &nList, int oxygenType, int hydrogenType)
double	meanFinite (const std::vector< double > &values)
	Mean of the finite per-atom F4 values; quiet_NaN when none are finite.
double	jumpRotorTau90 (const molSys::PointCloud< molSys::Point< double >, double > &frame0, const molSys::PointCloud< molSys::Point< double >, double > &frame1, double dt, int oxygenType, int hydrogenType)
LayerStack	layerCubicity (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, int axis=2, double layerWidth=3.7)
LayerStack	tumLayerStack (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &rings, const std::vector< bool > &basal, const std::vector< bool > &equatorial, int axis=2, double layerWidth=3.7)

Function Documentation

◆ calcCoverageArea()

std::vector< double > topoparam::calcCoverageArea	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< std::vector< int > > &	rings,
		double	sheetArea )

Calculates the coverage area%, an area-based measure of relative proportion of monolayer ices.

◆ jumpRotorTau90()

double topoparam::jumpRotorTau90	(	const molSys::PointCloud< molSys::Point< double >, double > &	frame0,
		const molSys::PointCloud< molSys::Point< double >, double > &	frame1,
		double	dt,
		int	oxygenType,
		int	hydrogenType )

Jump-rotor tau_90 from two frames. Each water is the H-H vector of the two hydrogens that share the oxygen molID. Returns dt when any molecule rotates by at least 90 degrees, quiet_NaN otherwise.

◆ layerCubicity()

LayerStack topoparam::layerCubicity	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		int	axis = 2,
		double	layerWidth = 3.7 )

◆ meanFinite()

double topoparam::meanFinite ( const std::vector< double > & values )

Mean of the finite per-atom F4 values; quiet_NaN when none are finite.

◆ normHeightPercent()

double topoparam::normHeightPercent	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		int	nPrisms,
		double	avgPrismHeight )

Calculates the height%, an average measure of filled volume. The average height of a prism can be taken to be 2.75-2.85 Angstrom. (Koga et. al., 2001)

◆ projAreaSingleRing()

std::vector< double > topoparam::projAreaSingleRing	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< int > &	ring )

Calculates the projected area on the XY, YZ and XZ planes.

◆ rodgerF4()

std::vector< double > topoparam::rodgerF4	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< std::vector< int > > &	nList,
		int	oxygenType,
		int	hydrogenType )

Per-atom Rodger F4 = mean of cos(3 phi) over H-O...O-H dihedrals of this oxygen with its oxygen neighbours. Hydrogens share molID with their oxygen. An oxygen with no hydrogens (mW) is quiet_NaN. nList is by atom ID with the leading self entry, as neighListO.

◆ tumLayerStack()

LayerStack topoparam::tumLayerStack	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< std::vector< int > > &	rings,
		const std::vector< bool > &	basal,
		const std::vector< bool > &	equatorial,
		int	axis = 2,
		double	layerWidth = 3.7 )

Literature I_sd reference: CHILL+ molecules binned by coordinate. TUM/rings stacking: only HC-basal and DDC-equatorial six-rings vote. Prismatic/peripheral rings and non-plane cages (clathrate 5^12) do not write a letter. Ions stay off the ring graph the caller passes. phiC is N_equatorial / (N_basal + N_equatorial) over plane rings.

Classes

Functions