3.6.6. horton.io.iodata
– Input/output dispatcher for different file formats¶
The IOData.from_file
and IOData.to_file
methods read/write data
from/to a file. The format is deduced from the prefix or extension of the
filename.
-
class
horton.io.iodata.
IOData
(**kwargs)¶ Bases:
object
A container class for data loaded from (or to be written to) a file.
In principle, the constructor accepts any keyword argument, which is stored as an attribute. All attributes are optional. Attributes can be set are removed after the IOData instance is constructed. The following attributes are supported by at least one of the io formats:
Type checked array attributes (if present):
- cube_data
- A (L, M, N) array of data on a uniform grid (defined by ugrid).
- coordinates
- A (N, 3) float array with Cartesian coordinates of the atoms.
- numbers
- A (N,) int vector with the atomic numbers.
- polar
- A (3, 3) matrix containing the dipole polarizability tensor.
- pseudo_numbers
- A (N,) float array with pseudo-potential core charges.
Unspecified type (duck typing):
- cell
- A Cell object that describes the (generally triclinic) periodic boundary conditions.
- core_energy
- The Hartree-Fock energy due to the core orbitals
- energy
- The total energy (electronic+nn)
- er
- The electron repulsion four-index operator
- exp_alpha
- The alpha orbitals (coefficients, occupations and energies).
- exp_beta
- The beta orbitals (coefficients, occupations and energies).
- esp_charges
- Charges fitted to the electrostatic potential
- dm_full (optionally with a suffix like _mp2, _mp3, _cc, _ci, _scf).
- The spin-summed first-order density matrix.
- dm_spin (optionally with a suffix like _mp2, _mp3, _cc, _ci, _scf).
- The spin-difference first-order density matrix.
- grid
- An integration grid (usually a UniformGrid instance).
- kin
- The kinetic energy operator.
- lf
- A LinalgFactory instance.
- links
- A mapping between the atoms in the primitive unit and the crystallographic unit.
- ms2
- The spin multiplicity.
- mulliken_charges
- Mulliken AIM charges.
- na
- The nuclear attraction operator.
- nelec
- The number of electrons.
- npa_charges
- Natural charges.
- obasis
- An instance of the GOBasis class.
- olp
- The overlap operator.
- one_mo
- One-electron integrals in the (Hartree-Fock) molecular-orbital basis
- permutation
- The permutation applied to the basis functions.
- signs
- The sign changes applied to the basis functions.
- symmetry
- An instance of the Symmetry class, describing the geometric symmetry.
- title
- A suitable name for the data.
- two_mo
- Two-electron integrals in the (Hartree-Fock) molecular-orbital basis
-
__init__
(**kwargs)¶
-
copy
()¶ Return a shallow copy
-
classmethod
from_file
(*filenames, **kwargs)¶ Load data from a file.
Arguments:
- filename1, filename2, …
- The files to load data from. When multiple files are given, data from the first file is overwritten by data from the second, etc. When one file contains sign and permutation changes for the orbital basis, these changes will be applied to data from all other files.
Optional arguments:
- lf
- A LinalgFactory instance. DenseLinalgFactory is used as default.
This routine uses the extension or prefix of the filename to determine the file format. It returns a dictionary with data loaded from the file.
For each file format, a specialized function is called that returns a dictionary with data from the file.
-
get_dm_full
()¶ Return a spin-summed density matrix using availlable attributes
-
get_dm_spin
()¶ Return a spin-difference density matrix using availlable attributes
-
to_file
(filename)¶ Write data to a file
Arguments:
- filename
- The file to write the data to
This routine uses the extension or prefix of the filename to determine the file format. For each file format, a specialized function is called that does the real work.
-
coordinates
¶ A type-checked attribute
-
cube_data
¶ A type-checked attribute
-
natom
¶ The number of atoms
-
numbers
¶ A type-checked attribute
-
polar
¶ A type-checked attribute
-
pseudo_numbers
¶ A type-checked attribute