interactions energies including CrystalExplorer model energies More...

Namespaces
namespace	polarization_partitioning

namespace	transform

Classes
struct	CEEnergyComponents

class	CEEnergyModel

struct	CEModelInteraction

struct	CEMonomerCalculationParameters

struct	CEParameterizedModel

struct	ElatResults

class	EnergyModelBase

class	ExternalEnergyModel

struct	ExternalEnergyOptions

class	FileSystemPairEnergyStore

struct	LatticeConvergenceSettings

class	LatticeEnergyCalculator

struct	LatticeEnergyResult

class	MemoryPairEnergyStore

struct	PairEnergy

class	PairEnergyStore

class	PairEnergyStoreBase

struct	WolfCouplingResult

struct	WolfCouplingTerm

struct	WolfParameters

class	WolfSum

class	XTBEnergyModel

Functions
double	coulomb_energy (Eigen::Ref< const Vec > charges, Eigen::Ref< const Mat3N > positions)

double	coulomb_pair_energy (Eigen::Ref< const Vec > charges_a, Eigen::Ref< const Mat3N > positions_a, Eigen::Ref< const Vec > charges_b, Eigen::Ref< const Mat3N > positions_b)

Vec3	coulomb_efield (Eigen::Ref< const Vec > charges, Eigen::Ref< const Mat3N > positions, Eigen::Ref< const Vec3 > point)

std::pair< Mat3N, Mat3N >	coulomb_pair_efield (Eigen::Ref< const Vec > charges_a, Eigen::Ref< const Mat3N > positions_a, Eigen::Ref< const Vec > charges_b, Eigen::Ref< const Mat3N > positions_b)

double	coulomb_interaction_energy_asym_charges (const occ::core::Dimer &, Eigen::Ref< const Vec > charges_asym)

std::pair< Mat3N, Mat3N >	coulomb_efield_asym_charges (const occ::core::Dimer &, Eigen::Ref< const Vec > charges_asym)

double	coulomb_self_energy_asym_charges (const occ::core::Molecule &, Eigen::Ref< const Vec > charges)

void	to_json (nlohmann::json &j, const CEEnergyComponents &)

void	from_json (const nlohmann::json &j, CEEnergyComponents &)

void	to_json (nlohmann::json &j, const polarization_partitioning::CouplingTerm &)

void	from_json (const nlohmann::json &j, polarization_partitioning::CouplingTerm &)

void	to_json (nlohmann::json &j, const polarization_partitioning::MoleculeCouplingResults &)

void	from_json (const nlohmann::json &j, polarization_partitioning::MoleculeCouplingResults &)

void	write_elat_json (const std::string &filename, const ElatResults &results)
	Write elat JSON results in compact format.

ElatResults	read_elat_json (const std::string &filename)
	Read elat JSON results and reconstruct data structures.

Wavefunction	load_wavefunction (const std::string &filename)

template<int derivative_order = 0>
Mat	lennard_jones (Eigen::Ref< const Mat3N > positions, Eigen::Ref< const Mat > params)

template<>
Mat	lennard_jones< 0 > (Eigen::Ref< const Mat3N > positions, Eigen::Ref< const Mat > params)

template<>
Mat	lennard_jones< 1 > (Eigen::Ref< const Mat3N > positions, Eigen::Ref< const Mat > params)

double	dreiding_type_hb_correction (double eps, double sigma, const occ::core::Dimer &dimer)

void	compute_ce_model_energies (Wavefunction &wfn, HartreeFock &hf, const CEMonomerCalculationParameters &params={})

template<typename Procedure >
double	compute_polarization_energy (const Wavefunction &wfn_a, const Procedure &proc_a, const Wavefunction &wfn_b, const Procedure &proc_b)

CEParameterizedModel	ce_model_from_string (const std::string &name)
	The CrystalExplorer model called `name` (case-insensitive): ce-b3lyp, ce-hf, ce-1p, ce-2p or ce-5p, with their -xdm and -wb97m-v aliases.

bool	model_name_implies_xtb (const std::string &name)
	Whether `name` selects the in-tree xtb backend, which implements GFN2-xTB only: xtb, gfn2 or gfn2-xtb, case-insensitive.

double	ce_model_polarization_energy (const occ::IVec &atomic_numbers, const occ::Mat3N &efield, bool charged=false)

double	polarization_energy (const occ::Vec &polarizabilities, const occ::Mat3N &efield)

double	wolf_coulomb_energy (double qi, const Vec3 &pi, Eigen::Ref< const Vec > qj, Eigen::Ref< const Mat3N > pj, const WolfParameters &params)

double	wolf_pair_energy (Eigen::Ref< const Vec > charges_a, Eigen::Ref< const Mat3N > positions_a, Eigen::Ref< const Vec > charges_b, Eigen::Ref< const Mat3N > positions_b, const WolfParameters &params)

Mat3N	wolf_electric_field (Eigen::Ref< const Vec > charges, Eigen::Ref< const Mat3N > source_positions, Eigen::Ref< const Mat3N > target_positions, const WolfParameters &params)

WolfCouplingResult	compute_wolf_coupling_terms (const std::vector< Mat3N > &electric_fields_per_neighbor, Eigen::Ref< const Vec > polarizabilities)

Variables
CEParameterizedModel	CE_HF_321G

CEParameterizedModel	CE_B3LYP_631Gdp

CEParameterizedModel	CE_XDM_FIT

constexpr double	CE1p_XDM_KREP {0.77850434}

CEParameterizedModel	CE1_XDM_B3LYP

CEParameterizedModel	CE1_XDM_WB97MV

CEParameterizedModel	CE2_XDM_B3LYP

CEParameterizedModel	CE2_XDM_WB97MV

CEParameterizedModel	CE5_XDM_WB97MV

CEParameterizedModel	CE1_XDM = CE1_XDM_B3LYP

CEParameterizedModel	CE2_XDM = CE2_XDM_B3LYP

CEParameterizedModel	CE5_XDM = CE5_XDM_WB97MV

const std::array< double, 110 >	Thakkar_atomic_polarizability

const std::array< double, 110 >	Charged_atomic_polarizibility

Detailed Description

interactions energies including CrystalExplorer model energies

Function Documentation

◆ ce_model_from_string()

CEParameterizedModel occ::interaction::ce_model_from_string ( const std::string & name )

inline

The CrystalExplorer model called name (case-insensitive): ce-b3lyp, ce-hf, ce-1p, ce-2p or ce-5p, with their -xdm and -wb97m-v aliases.

An unknown name is an error.

◆ ce_model_polarization_energy()

double occ::interaction::ce_model_polarization_energy	(	const occ::IVec &	atomic_numbers,
		const occ::Mat3N &	efield,
		bool	charged = `false`
	)

◆ compute_ce_model_energies()

void occ::interaction::compute_ce_model_energies	(	Wavefunction &	wfn,
		HartreeFock &	hf,
		const CEMonomerCalculationParameters &	params = `{}`
	)

◆ compute_polarization_energy()

template<typename Procedure >

double occ::interaction::compute_polarization_energy	(	const Wavefunction &	wfn_a,
		const Procedure &	proc_a,
		const Wavefunction &	wfn_b,
		const Procedure &	proc_b
	)

◆ compute_wolf_coupling_terms()

WolfCouplingResult occ::interaction::compute_wolf_coupling_terms	(	const std::vector< Mat3N > &	electric_fields_per_neighbor,
		Eigen::Ref< const Vec >	polarizabilities
	)

◆ coulomb_efield()

Vec3 occ::interaction::coulomb_efield	(	Eigen::Ref< const Vec >	charges,
		Eigen::Ref< const Mat3N >	positions,
		Eigen::Ref< const Vec3 >	point
	)

◆ coulomb_efield_asym_charges()

std::pair< Mat3N, Mat3N > occ::interaction::coulomb_efield_asym_charges	(	const occ::core::Dimer &	,
		Eigen::Ref< const Vec >	charges_asym
	)

◆ coulomb_energy()

double occ::interaction::coulomb_energy	(	Eigen::Ref< const Vec >	charges,
		Eigen::Ref< const Mat3N >	positions
	)

◆ coulomb_interaction_energy_asym_charges()

double occ::interaction::coulomb_interaction_energy_asym_charges	(	const occ::core::Dimer &	,
		Eigen::Ref< const Vec >	charges_asym
	)

◆ coulomb_pair_efield()

std::pair< Mat3N, Mat3N > occ::interaction::coulomb_pair_efield	(	Eigen::Ref< const Vec >	charges_a,
		Eigen::Ref< const Mat3N >	positions_a,
		Eigen::Ref< const Vec >	charges_b,
		Eigen::Ref< const Mat3N >	positions_b
	)

◆ coulomb_pair_energy()

double occ::interaction::coulomb_pair_energy	(	Eigen::Ref< const Vec >	charges_a,
		Eigen::Ref< const Mat3N >	positions_a,
		Eigen::Ref< const Vec >	charges_b,
		Eigen::Ref< const Mat3N >	positions_b
	)

◆ coulomb_self_energy_asym_charges()

double occ::interaction::coulomb_self_energy_asym_charges	(	const occ::core::Molecule &	,
		Eigen::Ref< const Vec >	charges
	)

◆ dreiding_type_hb_correction()

double occ::interaction::dreiding_type_hb_correction	(	double	eps,
		double	sigma,
		const occ::core::Dimer &	dimer
	)

◆ from_json() [1/3]

void occ::interaction::from_json	(	const nlohmann::json &	j,
		CEEnergyComponents &
	)

◆ from_json() [2/3]

void occ::interaction::from_json	(	const nlohmann::json &	j,
		polarization_partitioning::CouplingTerm &
	)

◆ from_json() [3/3]

void occ::interaction::from_json	(	const nlohmann::json &	j,
		polarization_partitioning::MoleculeCouplingResults &
	)

◆ lennard_jones()

template<int derivative_order = 0>

Mat occ::interaction::lennard_jones	(	Eigen::Ref< const Mat3N >	positions,
		Eigen::Ref< const Mat >	params
	)

◆ lennard_jones< 0 >()

template<>

Mat occ::interaction::lennard_jones< 0 >	(	Eigen::Ref< const Mat3N >	positions,
		Eigen::Ref< const Mat >	params
	)

◆ lennard_jones< 1 >()

template<>

Mat occ::interaction::lennard_jones< 1 >	(	Eigen::Ref< const Mat3N >	positions,
		Eigen::Ref< const Mat >	params
	)

◆ load_wavefunction()

Wavefunction occ::interaction::load_wavefunction ( const std::string & filename )

◆ model_name_implies_xtb()

bool occ::interaction::model_name_implies_xtb ( const std::string & name )

inline

Whether name selects the in-tree xtb backend, which implements GFN2-xTB only: xtb, gfn2 or gfn2-xtb, case-insensitive.

Any other name starting with "gfn" or "xtb" (gfn1, gfnff, ...) is an error.

◆ polarization_energy()

double occ::interaction::polarization_energy	(	const occ::Vec &	polarizabilities,
		const occ::Mat3N &	efield
	)

◆ read_elat_json()

ElatResults occ::interaction::read_elat_json ( const std::string & filename )

Read elat JSON results and reconstruct data structures.

Loads crystal and reconstructs LatticeEnergyResult with energies mapped from the compact JSON format produced by write_elat_json()

Parameters

filename Path to elat JSON results file

Returns: ElatResults containing crystal and lattice energy data

◆ to_json() [1/3]

void occ::interaction::to_json	(	nlohmann::json &	j,
		const CEEnergyComponents &
	)

◆ to_json() [2/3]

void occ::interaction::to_json	(	nlohmann::json &	j,
		const polarization_partitioning::CouplingTerm &
	)

◆ to_json() [3/3]

void occ::interaction::to_json	(	nlohmann::json &	j,
		const polarization_partitioning::MoleculeCouplingResults &
	)

◆ wolf_coulomb_energy()

double occ::interaction::wolf_coulomb_energy	(	double	qi,
		const Vec3 &	pi,
		Eigen::Ref< const Vec >	qj,
		Eigen::Ref< const Mat3N >	pj,
		const WolfParameters &	params
	)

◆ wolf_electric_field()

Mat3N occ::interaction::wolf_electric_field	(	Eigen::Ref< const Vec >	charges,
		Eigen::Ref< const Mat3N >	source_positions,
		Eigen::Ref< const Mat3N >	target_positions,
		const WolfParameters &	params
	)

◆ wolf_pair_energy()

double occ::interaction::wolf_pair_energy	(	Eigen::Ref< const Vec >	charges_a,
		Eigen::Ref< const Mat3N >	positions_a,
		Eigen::Ref< const Vec >	charges_b,
		Eigen::Ref< const Mat3N >	positions_b,
		const WolfParameters &	params
	)

◆ write_elat_json()

void occ::interaction::write_elat_json	(	const std::string &	filename,
		const ElatResults &	results
	)

Write elat JSON results in compact format.

Writes crystal, dimers, and energy data to JSON file

Parameters

filename	Output filename
results	ElatResults to write

Variable Documentation

◆ CE1_XDM

CEParameterizedModel occ::interaction::CE1_XDM = CE1_XDM_B3LYP

inline

◆ CE1_XDM_B3LYP

CEParameterizedModel occ::interaction::CE1_XDM_B3LYP

inline

Initial value:

{
    1.0,     1.0,        CE1p_XDM_KREP, CE1p_XDM_KREP, 1.0, "CE-1p-B3LYP",
    "b3lyp", "def2-svp", true,          0.65,          1.70}

◆ CE1_XDM_WB97MV

CEParameterizedModel occ::interaction::CE1_XDM_WB97MV

inline

Initial value:

{
    1.0,       1.0,        CE1p_XDM_KREP, CE1p_XDM_KREP, 1.0, "CE-1p-wB97M-V",
    "wb97m-v", "def2-svp", true,          0.65,          1.70}

◆ CE1p_XDM_KREP

constexpr double occ::interaction::CE1p_XDM_KREP {0.77850434}

inlineconstexpr

◆ CE2_XDM

CEParameterizedModel occ::interaction::CE2_XDM = CE2_XDM_B3LYP

inline

◆ CE2_XDM_B3LYP

CEParameterizedModel occ::interaction::CE2_XDM_B3LYP

inline

Initial value:

{
    1.0,     0.485,      0.485, 0.803, 1.0, "CE-2p-B3LYP",
    "b3lyp", "def2-svp", true,  0.65,  1.70}

◆ CE2_XDM_WB97MV

CEParameterizedModel occ::interaction::CE2_XDM_WB97MV

inline

Initial value:

{
    1.0,       0.485,      0.485, 0.803, 1.0, "CE-2p-wB97M-V",
    "wb97m-v", "def2-svp", true,  0.65,  1.70}

◆ CE5_XDM

CEParameterizedModel occ::interaction::CE5_XDM = CE5_XDM_WB97MV

inline

◆ CE5_XDM_WB97MV

CEParameterizedModel occ::interaction::CE5_XDM_WB97MV

inline

Initial value:

{
    1.0051,    0.6705,     0.6,  0.7929, 1.0509, "CE5p-XDM-wB97M-V",
    "wb97m-v", "def2-svp", true, 0.65,   1.70}

◆ CE_B3LYP_631Gdp

CEParameterizedModel occ::interaction::CE_B3LYP_631Gdp

inline

Initial value:

{1.0573,  0.6177,    0.6177,
                                            0.7399,  0.8708,    "CE-B3LYP",
                                            "b3lyp", "6-31g**", false}

◆ CE_HF_321G

CEParameterizedModel occ::interaction::CE_HF_321G

inline

Initial value:

{1.019, 0.811, 0.811, 0.651, 0.901,

"CE-HF", "hf", "3-21g", false}

◆ CE_XDM_FIT

CEParameterizedModel occ::interaction::CE_XDM_FIT

inline

Initial value:

{
    1.0,       1.0,        1.0,  1.0,  1.0, "CE-XDM-FIT",
    "wb97m-v", "def2-svp", true, 0.65, 1.70}

◆ Charged_atomic_polarizibility

const std::array<double, 110> occ::interaction::Charged_atomic_polarizibility

extern

◆ Thakkar_atomic_polarizability

const std::array<double, 110> occ::interaction::Thakkar_atomic_polarizability

extern

Namespaces

Classes

Functions

Variables

Detailed Description

Function Documentation

◆ ce_model_from_string()

◆ ce_model_polarization_energy()

◆ compute_ce_model_energies()

◆ compute_polarization_energy()

◆ compute_wolf_coupling_terms()

◆ coulomb_efield()

◆ coulomb_efield_asym_charges()

◆ coulomb_energy()

◆ coulomb_interaction_energy_asym_charges()

◆ coulomb_pair_efield()

◆ coulomb_pair_energy()

◆ coulomb_self_energy_asym_charges()

◆ dreiding_type_hb_correction()

◆ from_json() [1/3]

◆ from_json() [2/3]

◆ from_json() [3/3]

◆ lennard_jones()

◆ lennard_jones< 0 >()

◆ lennard_jones< 1 >()

◆ load_wavefunction()

◆ model_name_implies_xtb()

◆ polarization_energy()

◆ read_elat_json()

◆ to_json() [1/3]

◆ to_json() [2/3]

◆ to_json() [3/3]

◆ wolf_coulomb_energy()

◆ wolf_electric_field()

◆ wolf_pair_energy()

◆ write_elat_json()

Variable Documentation

◆ CE1_XDM

◆ CE1_XDM_B3LYP

◆ CE1_XDM_WB97MV

◆ CE1p_XDM_KREP

◆ CE2_XDM

◆ CE2_XDM_B3LYP

◆ CE2_XDM_WB97MV

◆ CE5_XDM

◆ CE5_XDM_WB97MV

◆ CE_B3LYP_631Gdp

◆ CE_HF_321G

◆ CE_XDM_FIT

◆ Charged_atomic_polarizibility

◆ Thakkar_atomic_polarizability