libint2::molden::PBCExport Class Reference

Extension of the Molden exporter to support JMOL extensions for crystal orbitals (see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java#l25) More...

#include <molden.h>

Inheritance diagram for libint2::molden::PBCExport:

Collaboration diagram for libint2::molden::PBCExport:

Public Member Functions
template<typename Coeffs , typename Occs , typename Energies = Eigen::VectorXd>
	PBCExport (const std::vector< Atom > &atoms, const std::array< Eigen::Vector3d, 3 > &cell_axes, const std::vector< Shell > &basis, const Coeffs &coefficients, const Occs &occupancies, int space_group, const Energies &energies=Energies(), const std::vector< std::string > &symmetry_labels=std::vector< std::string >(), const std::vector< bool > &spincases=std::vector< bool >(), const double bohr_to_angstrom=constants::codata_2018::bohr_to_angstrom)
void	write_space_group (std::ostream &os) const
	writes the "[SpaceGroup]" section to ostream os
void	write_operators (std::ostream &os) const
	writes the "[Operators]" section to ostream os
void	write_cell_axes (std::ostream &os) const
	writes the "[Cell]" section to ostream os
void	write (const std::string &filename) const
Public Member Functions inherited from libint2::molden::Export
template<typename ShellSequence , typename Coeffs , typename Occs , typename Energies = Eigen::VectorXd>
	Export (const std::vector< Atom > &atoms, const ShellSequence &basis, const Coeffs &coefficients, const Occs &occupancies, const Energies &energies=Energies(), const std::vector< std::string > &symmetry_labels=std::vector< std::string >(), const std::vector< bool > &spincases=std::vector< bool >(), const double bohr_to_angstrom=constants::codata_2018::bohr_to_angstrom, double coefficient_epsilon=5e-11)
void	write_prologue (std::ostream &os) const
	writes "[Molden Format]" to ostream os
void	write_atoms (std::ostream &os) const
	writes the "[Atoms]" section to ostream os
void	write_basis (std::ostream &os) const
	writes the "[GTO]" section, as well as optional Cartesian/solid harmonics keywords, to ostream os
void	write_lcao (std::ostream &os) const
	writes the "[MO]" section to ostream os
void	write (std::ostream &os) const
	writes "prologue", atoms, basis, and LCAOs to ostream os
void	write (const std::string &filename) const
	same as write(ostream), but creates new file named filename
double	bohr_to_angstrom () const

Detailed Description

Extension of the Molden exporter to support JMOL extensions for crystal orbitals (see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java#l25)

Constructor & Destructor Documentation

PBCExport()

template<typename Coeffs , typename Occs , typename Energies = Eigen::VectorXd>

libint2::molden::PBCExport::PBCExport ( const std::vector< Atom > & atoms, const std::array< Eigen::Vector3d, 3 > & cell_axes, const std::vector< Shell > & basis, const Coeffs & coefficients, const Occs & occupancies, int space_group, const Energies & energies = Energies(), const std::vector< std::string > & symmetry_labels = std::vector<std::string>(), const std::vector< bool > & spincases = std::vector<bool>(), const double bohr_to_angstrom = constants::codata_2018::bohr_to_angstrom )

inline

Template Parameters

Coeffs	the type of LCAO coefficient matrix
Energies	the type of LCAO energy vector
Occs	the type of LCAO occupancy vector

Parameters

atoms	the set of atoms (coordinates in atomic units)
cell_axes	the primitive vectors of the unit cell (in atomic units)
basis	the set of shells; must meet Molden requirements (see below)
coefficients	the matrix of LCAO coefficients (columns are LCAOs, rows are AOs; AOs are ordered according to the order of shells in basis and by the ordering conventions of this Libint configuration)
occupancies	the vector of occupancies (size = # LCAOs)
space_group	(base-0) index of the space group in the International Tables of Crystallography (https://it.iucr.org/Ac/)
energies	the vector of energies (size = # of LCAOs); the default is to assign zero to each LCAO
symmetry_labels	the vector of symmetry labels (size = # LCAOs); the default is to assign empty label to each LCAO
spincases	the vector of spin cases (size = # LCAOs; true = spin-up or m_s=1/2, false = spin-down or m_s=-1/2); the default is to assign spin-up to each LCAO
bohr_to_angstrom	the conversion factor from bohr to angstrom; the default is CODATA 2018 value

Exceptions

std::logic_error

if the basis does not conforms Molden requirements

Note

Molden can only handle basis sets that:

• p (l=1) shells are Cartesian, not solid harmonics
• d, f, and g (l=2..4) shells are all Cartesian or all solid harmonics
• there are no shells with l>5

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The documentation for this class was generated from the following file:

• molden.h