occ::io Namespace Reference

file input and output module including reading wavefunction files More...

Namespaces
namespace	basis
namespace	conversion
namespace	crystalgrower
namespace	impl
namespace	kmcpp

Classes
struct	AdaptiveBounds
class	AdaptiveGridBounds
struct	AdpData
struct	AtomData
struct	BasisSetInput
struct	CellData
class	CifParser
class	CifWriter
	Writer class for crystallographic information files (CIF) More...
struct	ColumnConfiguration
struct	COSXSettings
struct	CrystalInput
class	Cube
class	DftbGenFormat
struct	DispersionCorrectionInput
struct	DriverInput
struct	ElectronInput
class	EngradReader
class	FchkReader
class	FchkWriter
struct	GaussianInputFile
struct	GeometryInput
class	GMFWriter
struct	GridFileHeader
struct	GridSettings
	Extended settings for Becke grid generation. More...
struct	GridSymmetryInfo
struct	IsosurfaceInput
struct	JsonWavefunctionReader
struct	JsonWavefunctionWriter
struct	MethodInput
class	MoldenReader
struct	OccInput
struct	OptimizationInput
class	OrcaJSONReader
struct	OutputInput
struct	PairInput
class	PeriodicGrid
struct	PointChargeFileReader
struct	QCSchemaBond
struct	QCSchemaInput
struct	QCSchemaModel
class	QCSchemaReader
struct	QCSchemaTopology
struct	RowConfiguration
struct	RuntimeInput
class	ShelxFile
	Unified reader/writer for SHELX .res/.ins crystallographic files. More...
struct	SolventInput
struct	SymmetryData
class	Table
struct	XyzFileReader

Typedefs
using	Position = std::array< double, 3 >
using	PointChargeList = std::vector< occ::core::PointCharge >

Enumerations
enum class	PruningScheme { None , NWChem , NumGrid }
	Enumeration of available angular pruning schemes. More...
enum class	GridQuality { Coarse , Standard , Fine , VeryFine }
	Standard grid quality levels (similar to Q-Chem's SG system) More...
enum class	COSXGridLevel { Grid1 , Grid2 , Grid3 }
	COSX/SGX grid levels matching ORCA's GRIDX scheme. More...
enum class	GridFormat { GeneralGrid , PeriodicGrid }
enum class	GridDataType { Raw , Indexed }
enum class	JsonFormat {   JSON , UBJSON , CBOR , BSON ,   MSGPACK }

Functions
template<typename PropertyFunctor >
auto	make_adaptive_bounds (PropertyFunctor &func, const typename AdaptiveGridBounds< PropertyFunctor >::Parameters &params={})
GridSettings	get_grid_settings (GridQuality quality)
	Get grid settings for a specific quality level.
std::string	grid_quality_to_string (GridQuality quality)
	Convert GridQuality enum to string.
GridQuality	grid_quality_from_string (const std::string &str)
	Convert string to GridQuality enum.
std::string	cosx_grid_level_to_string (COSXGridLevel level)
	Convert COSXGridLevel enum to string.
double	cosx_grid_int_acc (COSXGridLevel level)
	Get IntAcc value for a COSX grid level.
size_t	calculate_radial_points_orca (double int_acc, size_t atomic_number, double b=5.0)
	Calculate number of radial points using ORCA's formula.
void	print_cosx_grid_summary (const GridSettings &settings, COSXGridLevel level, size_t num_points, size_t num_batches, size_t num_atoms)
	Print ORCA-style grid generation summary.
nlohmann::json	isosurface_to_json (const isosurface::Isosurface &surf)
void	write_isosurface_json (const std::string &filename, const isosurface::Isosurface &surf)
std::string	isosurface_to_json_string (const isosurface::Isosurface &surf)
occ::crystal::Crystal	load_crystal (const std::string &filename)
occ::core::Molecule	load_molecule (const std::string &filename)
void	write_obj_file (const std::string &filename, const isosurface::Isosurface &isosurface)
template<typename T >
OccInput	build (const std::string &filename)
template<typename T >
OccInput	build (std::istream &file)
PointChargeFileReader::PointChargeList	point_charges_from_file (const std::string &)
PointChargeFileReader::PointChargeList	point_charges_from_string (const std::string &)
void	write_ply_file (const std::string &filename, const Eigen::Matrix3Xf &vertices, const Eigen::Matrix3Xi &faces)
void	write_ply_mesh (const std::string &filename, const isosurface::Isosurface &isosurface, bool binary=true)
occ::core::Molecule	molecule_from_xyz_file (const std::string &)
occ::core::Molecule	molecule_from_xyz_string (const std::string &)
std::string	to_xyz_string (const occ::core::Molecule &molecule)
std::string	to_xyz_string (const occ::core::Molecule &molecule, const std::string &comment)
JsonFormat	json_format (const std::string &str)
bool	valid_json_format_string (const std::string &str)

Detailed Description

file input and output module including reading wavefunction files

Typedef Documentation

PointChargeList

using occ::io::PointChargeList = typedef std::vector<occ::core::PointCharge>

Position

typedef std::array< double, 3 > occ::io::Position

Enumeration Type Documentation

COSXGridLevel

enum class occ::io::COSXGridLevel

strong

COSX/SGX grid levels matching ORCA's GRIDX scheme.

ORCA uses 3 grid levels for COSX with specific IntAcc values and 5-region angular pruning. These correspond to GRIDX 1, 2, 3 in ORCA.

Enumerator
Grid1	GRIDX 1: IntAcc=3.816, max 50 Lebedev points.
Grid2	GRIDX 2: IntAcc=4.020, max 110 Lebedev points.
Grid3	GRIDX 3: IntAcc=4.338, max 194 Lebedev points.

GridDataType

enum class occ::io::GridDataType

strong

Enumerator
Raw
Indexed

GridFormat

enum class occ::io::GridFormat

strong

Enumerator
GeneralGrid
PeriodicGrid

GridQuality

enum class occ::io::GridQuality

strong

Standard grid quality levels (similar to Q-Chem's SG system)

Enumerator
Coarse	Like SG-0: ~23 radial, ~170 angular points - fastest, basic accuracy.
Standard	Like SG-1: ~50 radial, ~194 angular points - standard for LDA/GGA.
Fine	Like SG-2: ~75 radial, ~302 angular points - meta-GGAs, B95/B97.
VeryFine	Like SG-3: ~99 radial, ~590 angular points - Minnesota functionals, highest accuracy.

JsonFormat

enum class occ::io::JsonFormat

strong

Enumerator
JSON
UBJSON
CBOR
BSON
MSGPACK

PruningScheme

enum class occ::io::PruningScheme

strong

Enumeration of available angular pruning schemes.

Enumerator
None	No pruning (uniform angular points)
NWChem	NWChem pruning scheme.
NumGrid	NumGrid pruning scheme.

Function Documentation

build() [1/2]

template<typename T >

OccInput occ::io::build

(

const std::string &

filename

)

build() [2/2]

template<typename T >

OccInput occ::io::build

(

std::istream &

file

)

calculate_radial_points_orca()

size_t occ::io::calculate_radial_points_orca	(	double	int_acc,
		size_t	atomic_number,
		double	b = 5.0
	)

Calculate number of radial points using ORCA's formula.

Uses: nr = (15 * IntAcc - 40) + b * ROW where ROW is the periodic table row of the element

Parameters

int_acc	IntAcc parameter
atomic_number	Atomic number of the element
b	Row multiplier (default 5.0)

Returns

size_t Number of radial points

cosx_grid_int_acc()

double occ::io::cosx_grid_int_acc

(

COSXGridLevel

level

)

Get IntAcc value for a COSX grid level.

Returns the ORCA IntAcc parameter for the given COSX grid level

Parameters

level

COSX grid level

Returns

double IntAcc value

cosx_grid_level_to_string()

std::string occ::io::cosx_grid_level_to_string

(

COSXGridLevel

level

)

Convert COSXGridLevel enum to string.

Parameters

level

COSX grid level

Returns

std::string String representation (e.g., "GRIDX 1")

get_grid_settings()

GridSettings occ::io::get_grid_settings

(

GridQuality

quality

)

Get grid settings for a specific quality level.

Parameters

quality

Grid quality level

Returns

GridSettings configured for the specified quality

grid_quality_from_string()

GridQuality occ::io::grid_quality_from_string

(

const std::string &

str

)

Convert string to GridQuality enum.

Parameters

str	String representation (case-insensitive)

Returns

GridQuality Grid quality level

Exceptions

std::invalid_argument

if string is not recognized

grid_quality_to_string()

std::string occ::io::grid_quality_to_string

(

GridQuality

quality

)

Convert GridQuality enum to string.

Parameters

quality

Grid quality level

Returns

std::string String representation of the quality level

isosurface_to_json()

nlohmann::json occ::io::isosurface_to_json

(

const isosurface::Isosurface &

surf

)

isosurface_to_json_string()

std::string occ::io::isosurface_to_json_string

(

const isosurface::Isosurface &

surf

)

json_format()

JsonFormat occ::io::json_format ( const std::string &  str )

inline

load_crystal()

occ::crystal::Crystal occ::io::load_crystal

(

const std::string &

filename

)

load_molecule()

occ::core::Molecule occ::io::load_molecule

(

const std::string &

filename

)

make_adaptive_bounds()

template<typename PropertyFunctor >

auto occ::io::make_adaptive_bounds	(	PropertyFunctor &	func,
		const typename AdaptiveGridBounds< PropertyFunctor >::Parameters &	params = {}
	)

molecule_from_xyz_file()

occ::core::Molecule occ::io::molecule_from_xyz_file

(

const std::string &

)

molecule_from_xyz_string()

occ::core::Molecule occ::io::molecule_from_xyz_string

(

const std::string &

)

point_charges_from_file()

PointChargeFileReader::PointChargeList occ::io::point_charges_from_file

(

const std::string &

)

point_charges_from_string()

PointChargeFileReader::PointChargeList occ::io::point_charges_from_string

(

const std::string &

)

print_cosx_grid_summary()

void occ::io::print_cosx_grid_summary	(	const GridSettings &	settings,
		COSXGridLevel	level,
		size_t	num_points,
		size_t	num_batches,
		size_t	num_atoms
	)

Print ORCA-style grid generation summary.

Prints a summary similar to ORCA's "COSX GRID GENERATION" output:

• IntAcc, angular grid level, pruning method
• Total grid points, batches, average points per batch/atom

Parameters

settings	Grid settings used
level	COSX grid level (Grid1, Grid2, Grid3)
num_points	Total number of grid points
num_batches	Number of batches
num_atoms	Number of atoms

to_xyz_string() [1/2]

std::string occ::io::to_xyz_string

(

const occ::core::Molecule &

molecule

)

to_xyz_string() [2/2]

std::string occ::io::to_xyz_string	(	const occ::core::Molecule &	molecule,
		const std::string &	comment
	)

valid_json_format_string()

bool occ::io::valid_json_format_string ( const std::string &  str )

inline

write_isosurface_json()

void occ::io::write_isosurface_json	(	const std::string &	filename,
		const isosurface::Isosurface &	surf
	)

write_obj_file()

void occ::io::write_obj_file	(	const std::string &	filename,
		const isosurface::Isosurface &	isosurface
	)

write_ply_file()

void occ::io::write_ply_file	(	const std::string &	filename,
		const Eigen::Matrix3Xf &	vertices,
		const Eigen::Matrix3Xi &	faces
	)

write_ply_mesh()

void occ::io::write_ply_mesh	(	const std::string &	filename,
		const isosurface::Isosurface &	isosurface,
		bool	binary = true
	)