ramannoodle

Facilitates calculation of Raman spectra from first principles calculations.

Subpackages

• ramannoodle.dataset
  • Subpackages
    • ramannoodle.dataset.torch
      • PolarizabilityDataset
      • Submodules
      • ramannoodle.dataset.torch.utils module
• ramannoodle.dynamics
  • Phonons
    • Phonons.get_raman_spectrum()
    • Phonons.displacements
    • Phonons.ref_positions
    • Phonons.wavenumbers
  • Trajectory
    • Trajectory.get_raman_spectrum()
    • Trajectory.positions_ts
    • Trajectory.timestep
• ramannoodle.io
  • Subpackages
    • ramannoodle.io.vasp
      • Submodules
      • ramannoodle.io.vasp.outcar module
      • ramannoodle.io.vasp.poscar module
      • ramannoodle.io.vasp.vasprun module
      • ramannoodle.io.vasp.xdatcar module
  • Submodules
  • ramannoodle.io.generic module
    • read_phonons()
    • read_polarizability_dataset()
    • read_positions()
    • read_positions_and_polarizability()
    • read_ref_structure()
    • read_structure_and_polarizability()
    • read_trajectory()
    • write_structure()
    • write_trajectory()
  • ramannoodle.io.pymatgen module
    • construct_polarizability_dataset()
    • construct_ref_structure()
    • construct_trajectory()
    • get_positions()
    • get_structure()
• ramannoodle.pmodel
  • ARTModel
    • ARTModel.add_art()
    • ARTModel.add_art_from_files()
    • ARTModel.add_art_from_pymatgen()
    • ARTModel.get_dof_indexes()
    • ARTModel.get_masked_model()
    • ARTModel.get_specification_tuples()
  • InterpolationModel
    • InterpolationModel.add_dof()
    • InterpolationModel.add_dof_from_files()
    • InterpolationModel.add_dof_from_pymatgen()
    • InterpolationModel.calc_polarizabilities()
    • InterpolationModel.get_masked_model()
    • InterpolationModel.unmask()
    • InterpolationModel.cart_basis_vectors
    • InterpolationModel.interpolations
    • InterpolationModel.is_dummy_model
    • InterpolationModel.mask
    • InterpolationModel.ref_polarizability
    • InterpolationModel.ref_structure
  • Subpackages
    • ramannoodle.pmodel.torch
      • PotGNN
      • train_single_epoch()
• ramannoodle.spectrum
  • MDRamanSpectrum
    • MDRamanSpectrum.measure()
    • MDRamanSpectrum.polarizability_ts
    • MDRamanSpectrum.timestep
  • PhononRamanSpectrum
    • PhononRamanSpectrum.measure()
    • PhononRamanSpectrum.phonon_wavenumbers
    • PhononRamanSpectrum.raman_tensors
  • Submodules
  • ramannoodle.spectrum.utils module
    • calc_signal_spectrum()
    • convolve_spectrum()
• ramannoodle.structure
  • ReferenceStructure
    • ReferenceStructure.get_atom_indexes()
    • ReferenceStructure.get_cart_direction()
    • ReferenceStructure.get_cart_displacement()
    • ReferenceStructure.get_equivalent_atom_dict()
    • ReferenceStructure.get_equivalent_displacements()
    • ReferenceStructure.get_frac_direction()
    • ReferenceStructure.get_frac_displacement()
    • ReferenceStructure.atomic_numbers
    • ReferenceStructure.lattice
    • ReferenceStructure.num_atoms
    • ReferenceStructure.num_nonequivalent_atoms
    • ReferenceStructure.positions
  • get_ast_displaced_positions()
  • get_displaced_positions()
  • write_ast_displaced_structures()
  • write_displaced_structures()
  • Submodules
  • ramannoodle.structure.utils module
    • apply_pbc()
    • apply_pbc_displacement()
    • calc_displacement()
    • displace_positions()
    • transform_positions()

Submodules

ramannoodle.abstract module

Abstract classes.

class ramannoodle.abstract.Dynamics

Bases: ABC

Abstract class for atomic dynamics.

abstract get_raman_spectrum(polarizability_model)

Calculate a raman spectrum using a polarizability model.

Parameters:

polarizability_model (PolarizabilityModel) – Must be compatible with the dynamics.

Return type:

RamanSpectrum

class ramannoodle.abstract.PolarizabilityModel

Bases: ABC

Abstract polarizability model.

abstract calc_polarizabilities(positions_batch)

Return estimated polarizabilities for a batch of fractional positions.

Parameters:

positions_batch (ndarray[Any, dtype[float64]]) – (fractional) Array with shape (S,N,3) where S is the number of samples and N is the number of atoms.

Return type:

ndarray[Any, dtype[float64]]

Returns:

Array with shape (S,3,3).

class ramannoodle.abstract.RamanSpectrum

Bases: ABC

Abstract class for Raman spectra.

abstract measure(orientation='polycrystalline', laser_correction=False, laser_wavelength=522, bose_einstein_correction=False, temperature=300)

Calculate and return a raw Raman spectrum.

Parameters:

• orientation (str | ndarray[Any, dtype[float64]]) – Supports "polycrystalline". Future versions will support arbitrary orientations.

• laser_correction (bool) – If True, applies laser-wavelength-dependent intensity correction.

• laser_wavelength (float) – (nm) Ignored if laser_correction == False.

• bose_einstein_correction (bool) – If True, applies temperature-dependent Bose Einstein correction.

• temperature (float) –

  11. Ignored if bose_einstein_correction == False.

Return type:

tuple[ndarray[Any, dtype[float64]], ndarray[Any, dtype[float64]]]

Returns:

0. wavenumbers – (cm^-1) Array with shape (M,).

1. intensities – (arbitrary units) Array with shape (M,).

ramannoodle.constants module

Useful globals.

ramannoodle.exceptions module

Exceptions, warnings, and related functions.

exception ramannoodle.exceptions.DOFWarning

Bases: UserWarning

A degree of freedom may not have been specified as intended.

exception ramannoodle.exceptions.IncompatibleStructureException

Bases: Exception

File contains structure that is incompatible with the current operation.

exception ramannoodle.exceptions.InvalidDOFException

Bases: Exception

A supplied degree of freedom is invalid.

exception ramannoodle.exceptions.InvalidFileException

Bases: Exception

File cannot not be read, likely due to due to invalid or unexpected format.

exception ramannoodle.exceptions.NoMatchingLineFoundException

Bases: Exception

No matching line can be found in file.

exception ramannoodle.exceptions.SymmetryException

Bases: Exception

Symmetry operation failed.

exception ramannoodle.exceptions.UserError

Bases: Exception

The user has done something they shouldn’t.

This exception is used sparingly, as (ideally) the structure of the API should dictate what the user should and shouldn’t do.

ramannoodle.exceptions.get_pymatgen_missing_error()

Get error indicating that pymatgen is not installed.

Return type:

UserError

ramannoodle.exceptions.get_torch_missing_error()

Get error indicating that torch is not installed.

Return type:

UserError