occ::cg Namespace Reference

Namespaces
namespace	components

Classes
struct	CavitySurface
	One cavity's worth of per-element solvation data. More...
struct	ContributionPair
struct	CornerMorphology
	A symmetry-unique corner type of the particle shape. More...
struct	CrystalGrowthResult
struct	DimerResult
struct	DimerSolventTerm
struct	EdgeMorphology
	A symmetry-unique edge type of the particle shape. More...
struct	EnergyTotal
struct	FacetMorphology
	A facet of the (Wulff or user) particle shape. More...
class	InteractionMapper
struct	MoleculeResult
struct	MorphologyResult
	Particle size/shape-dependent (surface + edge + corner) energies. More...
struct	NeighborAtoms
struct	ParticleSample
	Broken-bond excess energy of a finite particle at one size, decomposed by inclusion-exclusion so e_excess == e_surface + e_edge + e_corner exactly. More...
class	SMDCalculator
struct	SMDSettings
class	SolvationContribution
	Solvation attributed to one neighbour contact, as a set of named channels. More...
struct	SolvationData
	Every cavity a solvation model produced for one molecule, plus the scalar bookkeeping cg reports. More...
class	SolventSurfacePartitioner
struct	SurfaceField
	A named per-element quantity defined on one cavity. More...

Typedefs
using	Crystal = occ::crystal::Crystal
using	CrystalDimers = occ::crystal::CrystalDimers
using	DimerMappingTable = occ::crystal::DimerMappingTable
using	DimerIndex = occ::crystal::DimerIndex
using	DimerIndexHash = occ::crystal::DimerIndexHash
using	Molecule = occ::core::Molecule
using	Dimer = occ::core::Dimer
using	PairEnergies = std::vector< occ::interaction::CEEnergyComponents >
using	CGEnergyComponents = ankerl::unordered_dense::map< std::string, double >
using	CGEnergies = std::vector< CGEnergyComponents >
using	DimerResults = std::vector< DimerResult >

Functions
	NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE (SurfaceField, name, values)
	NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE (CavitySurface, name, positions, areas, energies, descriptors)
	NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE (SolvationData, cavities, total_solvation_energy, electronic_contribution)
void	exchange_matching_forward_reverse_pairs (const crystal::CrystalDimers::MoleculeNeighbors &neighbors, std::vector< SolvationContribution > &energy_contribution)
CavitySurface *	coulomb_cavity (SolvationData &)
	Convenience accessors for the two SMD/CPCM-X cavities.
const CavitySurface *	coulomb_cavity (const SolvationData &)
CavitySurface *	cds_cavity (SolvationData &)
const CavitySurface *	cds_cavity (const SolvationData &)
CavitySurface &	add_cavity (SolvationData &, const std::string &name, const Mat3N &positions, const Vec &areas, const Vec &energies)
	Add a named cavity with a single energy channel of the same name.
SolvationData	from_scrf_surfaces (const occ::scrf::SolvationSurfaces &)
	Build from the unified occ::scrf::SolvationSurfaces bundle produced by the HF/DFT and xTB pipelines.
SolvationData	from_xtb_surfaces (const occ::xtb::SolvationSurfaces &surfaces)
void	to_json (nlohmann::json &, const MorphologyResult &)

Typedef Documentation

CGEnergies

using occ::cg::CGEnergies = typedef std::vector<CGEnergyComponents>

CGEnergyComponents

using occ::cg::CGEnergyComponents = typedef ankerl::unordered_dense::map<std::string, double>

Crystal

using occ::cg::Crystal = typedef occ::crystal::Crystal

CrystalDimers

using occ::cg::CrystalDimers = typedef occ::crystal::CrystalDimers

Dimer

using occ::cg::Dimer = typedef occ::core::Dimer

DimerIndex

using occ::cg::DimerIndex = typedef occ::crystal::DimerIndex

DimerIndexHash

using occ::cg::DimerIndexHash = typedef occ::crystal::DimerIndexHash

DimerMappingTable

using occ::cg::DimerMappingTable = typedef occ::crystal::DimerMappingTable

DimerResults

using occ::cg::DimerResults = typedef std::vector<DimerResult>

Molecule

using occ::cg::Molecule = typedef occ::core::Molecule

PairEnergies

using occ::cg::PairEnergies = typedef std::vector<occ::interaction::CEEnergyComponents>

Function Documentation

add_cavity()

CavitySurface & occ::cg::add_cavity	(	SolvationData &	,
		const std::string &	name,
		const Mat3N &	positions,
		const Vec &	areas,
		const Vec &	energies
	)

Add a named cavity with a single energy channel of the same name.

Warning

Returns a reference into cavities, so it is invalidated by the next add_cavity exactly as std::vector::emplace_back would be. Finish with one cavity before adding the next.

cds_cavity() [1/2]

const CavitySurface * occ::cg::cds_cavity

(

const SolvationData &

)

cds_cavity() [2/2]

CavitySurface * occ::cg::cds_cavity

(

SolvationData &

)

coulomb_cavity() [1/2]

const CavitySurface * occ::cg::coulomb_cavity

(

const SolvationData &

)

coulomb_cavity() [2/2]

CavitySurface * occ::cg::coulomb_cavity

(

SolvationData &

)

Convenience accessors for the two SMD/CPCM-X cavities.

exchange_matching_forward_reverse_pairs()

void occ::cg::exchange_matching_forward_reverse_pairs	(	const crystal::CrystalDimers::MoleculeNeighbors &	neighbors,
		std::vector< SolvationContribution > &	energy_contribution
	)

from_scrf_surfaces()

SolvationData occ::cg::from_scrf_surfaces

(

const occ::scrf::SolvationSurfaces &

)

Build from the unified occ::scrf::SolvationSurfaces bundle produced by the HF/DFT and xTB pipelines.

CPCM-X has no CDS branch, so that cavity is simply absent.

from_xtb_surfaces()

SolvationData occ::cg::from_xtb_surfaces ( const occ::xtb::SolvationSurfaces &  surfaces )

inline

NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE() [1/3]

occ::cg::NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE	(	CavitySurface	,
		name	,
		positions	,
		areas	,
		energies	,
		descriptors
	)

NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE() [2/3]

occ::cg::NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE	(	SolvationData	,
		cavities	,
		total_solvation_energy	,
		electronic_contribution
	)

NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE() [3/3]

occ::cg::NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE	(	SurfaceField	,
		name	,
		values
	)

to_json()

void occ::cg::to_json	(	nlohmann::json &	,
		const MorphologyResult &
	)