occ::io Namespace Reference

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

Namespaces
namespace	basis
namespace	crystalgrower
namespace	kmcpp
namespace	conversion
namespace	impl

Classes
struct	ColumnConfiguration
struct	RowConfiguration
class	Table
struct	AdaptiveBounds
class	AdaptiveGridBounds
struct	AtomData
struct	AdpData
struct	CellData
struct	SymmetryData
class	CifParser
class	CifWriter
	Writer class for crystallographic information files (CIF). More...
class	Cube
class	DftbGenFormat
class	EngradReader
class	GMFWriter
class	JsonCache
	Somewhere to keep expensive intermediate results (monomer energies, wavefunctions, solvation surfaces) as JSON documents, so a repeat calculation can skip them. More...
class	FileJsonCache
	Documents on disk, one file per key. Persists between runs. More...
class	MemoryJsonCache
	Documents held for the lifetime of the object; nothing touches the disk. More...
struct	CrystalBlock
	One structure from a file that may hold several, such as a multi-block CIF. More...
struct	ElectronInput
struct	GeometryInput
struct	OutputInput
struct	DriverInput
struct	COSXSettings
struct	MethodInput
struct	BasisSetInput
struct	SolventInput
struct	RuntimeInput
struct	OptimizationInput
struct	DispersionCorrectionInput
struct	CrystalInput
struct	PairInput
struct	IsosurfaceInput
struct	OccInput
struct	PointChargeFileReader
struct	GridFileHeader
struct	GridSymmetryInfo
class	PeriodicGrid
class	ShelxFile
	Unified reader/writer for SHELX .res/.ins crystallographic files. More...
struct	SiteMultipoles
struct	MoleculeSite
struct	MoleculeType
struct	BuckinghamPair
struct	Potentials
struct	Settings
struct	Basis
	Everything needed to define the energy model, independent of crystal packing. More...
struct	IndependentMolecule
struct	CrystalData
struct	ReferenceEnergies
struct	StructureInput
	Complete input for crystal energy calculations. More...
struct	XyzFileReader
class	FchkReader
class	FchkWriter
struct	GaussianInputFile
class	MoldenReader
	Reader for Molden format wavefunction files. More...
class	OrcaJSONReader
struct	QCSchemaBond
struct	QCSchemaTopology
struct	QCSchemaModel
struct	QCSchemaInput
class	QCSchemaReader
struct	JsonWavefunctionReader
struct	JsonWavefunctionWriter
struct	ElectronShell
struct	ECPShell
struct	ReferenceData
struct	ElementBasis
struct	JsonBasis
struct	JsonBasisReader
class	Element
	Utility class representing and holding data for a chemical element. More...

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

Enumerations
enum class	RIPolicy { Auto , None , JK , COSX }
enum class	GridFormat { GeneralGrid , PeriodicGrid }
enum class	GridDataType { Raw , Indexed }
enum class	JsonFormat {   JSON , UBJSON , CBOR , BSON ,   MSGPACK }
enum	SpinorbitalKind
	Spin treatment for molecular orbitals / SCF. More...

Functions
template<typename PropertyFunctor>
auto	make_adaptive_bounds (PropertyFunctor &func, const typename AdaptiveGridBounds< PropertyFunctor >::Parameters &params={})
occ::crystal::Crystal	load_crystal (const std::string &filename)
std::vector< CrystalBlock >	load_crystal_blocks (const std::string &filename)
	Every crystal in the file: one per data block of a CIF, otherwise the single structure load_crystal() reads.
occ::core::Molecule	load_molecule (const std::string &filename)
template<typename T>
OccInput	build (const std::string &filename)
template<typename T>
OccInput	build (std::istream &file)
OccInput	read_occ_input_file (const std::string path)
PointChargeFileReader::PointChargeList	point_charges_from_file (const std::string &)
PointChargeFileReader::PointChargeList	point_charges_from_string (const std::string &)
void	to_json (nlohmann::json &j, const SiteMultipoles &m)
void	from_json (const nlohmann::json &j, SiteMultipoles &m)
void	to_json (nlohmann::json &j, const MoleculeSite &s)
void	from_json (const nlohmann::json &j, MoleculeSite &s)
void	to_json (nlohmann::json &j, const MoleculeType &mt)
void	from_json (const nlohmann::json &j, MoleculeType &mt)
void	to_json (nlohmann::json &j, const IndependentMolecule &im)
void	from_json (const nlohmann::json &j, IndependentMolecule &im)
void	to_json (nlohmann::json &j, const BuckinghamPair &bp)
void	from_json (const nlohmann::json &j, BuckinghamPair &bp)
void	to_json (nlohmann::json &j, const Potentials &p)
void	from_json (const nlohmann::json &j, Potentials &p)
void	to_json (nlohmann::json &j, const Settings &s)
void	from_json (const nlohmann::json &j, Settings &s)
void	to_json (nlohmann::json &j, const ReferenceEnergies &r)
void	from_json (const nlohmann::json &j, ReferenceEnergies &r)
void	to_json (nlohmann::json &j, const Basis &b)
void	from_json (const nlohmann::json &j, Basis &b)
void	to_json (nlohmann::json &j, const CrystalData &c)
void	from_json (const nlohmann::json &j, CrystalData &c)
void	to_json (nlohmann::json &j, const StructureInput &si)
void	from_json (const nlohmann::json &j, StructureInput &si)
StructureInput	read_structure_json (const std::string &path)
void	write_structure_json (const std::string &path, const StructureInput &input)
void	write_force_field_json (const std::string &path, const Basis &basis, const std::string &title="")
	Write only the force-field section (molecule definitions, multipoles, pair potentials, and model settings) to a standalone JSON file.
bool	is_structure_format (const std::string &json_path)
	Detect whether a JSON file uses the structure format.
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)
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)
void	write_obj_file (const std::string &filename, const isosurface::Isosurface &isosurface)
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)
void	write_molden (const occ::qm::Wavefunction &wfn, std::ostream &os)
	Write a wavefunction in Molden format.
void	write_molden (const occ::qm::Wavefunction &wfn, const std::string &filename)
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

ElementMap

using occ::gto::io::ElementMap

PointChargeList

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

Position

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

Enumeration Type Documentation

GridDataType

enum class occ::io::GridDataType

strong

Enumerator
Raw
Indexed

GridFormat

enum class occ::io::GridFormat

strong

Enumerator
GeneralGrid
PeriodicGrid

JsonFormat

enum class occ::io::JsonFormat

strong

Enumerator
JSON
UBJSON
CBOR
BSON
MSGPACK

RIPolicy

enum class occ::io::RIPolicy

strong

Enumerator
Auto
None
JK
COSX

SpinorbitalKind

enum occ::core::SpinorbitalKind

Spin treatment for molecular orbitals / SCF.

Unscoped enum: the enumerators are intentionally usable unqualified within the enclosing namespace. The canonical definition lives here (occ_core) so that low-level consumers (e.g. input/config structs) can reference it without depending on occ_qm; occ::qm re-exports the type and enumerators for backwards compatibility (see occ/qm/spinorbital.h).

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

)

from_json() [1/11]

void occ::io::from_json	(	const nlohmann::json &	j,
		Basis &	b )

from_json() [2/11]

void occ::io::from_json	(	const nlohmann::json &	j,
		BuckinghamPair &	bp )

from_json() [3/11]

void occ::io::from_json	(	const nlohmann::json &	j,
		CrystalData &	c )

from_json() [4/11]

void occ::io::from_json	(	const nlohmann::json &	j,
		IndependentMolecule &	im )

from_json() [5/11]

void occ::io::from_json	(	const nlohmann::json &	j,
		MoleculeSite &	s )

from_json() [6/11]

void occ::io::from_json	(	const nlohmann::json &	j,
		MoleculeType &	mt )

from_json() [7/11]

void occ::io::from_json	(	const nlohmann::json &	j,
		Potentials &	p )

from_json() [8/11]

void occ::io::from_json	(	const nlohmann::json &	j,
		ReferenceEnergies &	r )

from_json() [9/11]

void occ::io::from_json	(	const nlohmann::json &	j,
		Settings &	s )

from_json() [10/11]

void occ::io::from_json	(	const nlohmann::json &	j,
		SiteMultipoles &	m )

from_json() [11/11]

void occ::io::from_json	(	const nlohmann::json &	j,
		StructureInput &	si )

is_structure_format()

bool occ::io::is_structure_format

(

const std::string &

json_path

)

Detect whether a JSON file uses the structure format.

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_crystal_blocks()

std::vector< CrystalBlock > occ::io::load_crystal_blocks

(

const std::string &

filename

)

Every crystal in the file: one per data block of a CIF, otherwise the single structure load_crystal() reads.

A block that is not a crystal (no cell or symmetry, say) is returned with its error rather than skipped, so the result lines up with the file's blocks; so is a single-structure file that cannot be read.

Exceptions

std::runtime_error

if a CIF cannot be read or holds no data block.

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 &

)

read_occ_input_file()

OccInput occ::io::read_occ_input_file

(

const std::string

path

)

read_structure_json()

StructureInput occ::io::read_structure_json

(

const std::string &

path

)

to_json() [1/11]

void occ::io::to_json	(	nlohmann::json &	j,
		const Basis &	b )

to_json() [2/11]

void occ::io::to_json	(	nlohmann::json &	j,
		const BuckinghamPair &	bp )

to_json() [3/11]

void occ::io::to_json	(	nlohmann::json &	j,
		const CrystalData &	c )

to_json() [4/11]

void occ::io::to_json	(	nlohmann::json &	j,
		const IndependentMolecule &	im )

to_json() [5/11]

void occ::io::to_json	(	nlohmann::json &	j,
		const MoleculeSite &	s )

to_json() [6/11]

void occ::io::to_json	(	nlohmann::json &	j,
		const MoleculeType &	mt )

to_json() [7/11]

void occ::io::to_json	(	nlohmann::json &	j,
		const Potentials &	p )

to_json() [8/11]

void occ::io::to_json	(	nlohmann::json &	j,
		const ReferenceEnergies &	r )

to_json() [9/11]

void occ::io::to_json	(	nlohmann::json &	j,
		const Settings &	s )

to_json() [10/11]

void occ::io::to_json	(	nlohmann::json &	j,
		const SiteMultipoles &	m )

to_json() [11/11]

void occ::io::to_json	(	nlohmann::json &	j,
		const StructureInput &	si )

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_force_field_json()

void occ::io::write_force_field_json	(	const std::string &	path,
		const Basis &	basis,
		const std::string &	title = "" )

Write only the force-field section (molecule definitions, multipoles, pair potentials, and model settings) to a standalone JSON file.

Despite the serialized key being "basis" for historical reasons, this is distinct from the GTO basis set used elsewhere in OCC.

write_isosurface_json()

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

write_molden() [1/2]

void occ::io::write_molden	(	const occ::qm::Wavefunction &	wfn,
		const std::string &	filename )

write_molden() [2/2]

void occ::io::write_molden	(	const occ::qm::Wavefunction &	wfn,
		std::ostream &	os )

Write a wavefunction in Molden format.

Coordinates are in bohr. Spherical bases are flagged with [5D] [7F] [9G]; Cartesian functions are written unit-normalized, as the format requires. Unrestricted wavefunctions are written as alpha then beta orbitals in one [MO] section. ECPs cannot be represented in Molden files.

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 )

write_structure_json()

void occ::io::write_structure_json	(	const std::string &	path,
		const StructureInput &	input )