ramannoodle.io

Functions for interacting with files used and produced by DFT codes.

Subpackages

• ramannoodle.io.vasp
  • Submodules
  • ramannoodle.io.vasp.outcar module
    • read_phonons()
    • read_polarizability_dataset()
    • read_positions()
    • read_positions_and_polarizability()
    • read_ref_structure()
    • read_structure_and_polarizability()
    • read_trajectory()
  • ramannoodle.io.vasp.poscar module
    • read_positions()
    • read_ref_structure()
    • read_structure()
    • write_structure()
  • ramannoodle.io.vasp.vasprun module
    • read_phonons()
    • read_polarizability_dataset()
    • read_positions()
    • read_positions_and_polarizability()
    • read_ref_structure()
    • read_structure_and_polarizability()
    • read_trajectory()
  • ramannoodle.io.vasp.xdatcar module
    • read_positions_ts()
    • read_trajectory()
    • write_trajectory()

Submodules

ramannoodle.io.generic module

Generic IO functions.

Generic IO functions are somewhat inflexible but are necessary for certain functionality. Users are strongly encouraged to use IO functions contained in the code-specific subpackages. For example, IO for VASP POSCAR and OUTCAR files can be accomplished using ramannoodle.io.vasp.poscar and ramannoodle.io.vasp.outcar respectively.

ramannoodle.io.generic.read_phonons(filepath, file_format)

Read phonons from a file.

Parameters:

• filepath (str | Path)

• file_format (str) – Supports "outcar", "vasprun.xml" (see Supported file formats).

Raises:

• FileNotFoundError – File not found.

• InvalidFileException – Invalid file.

Return type:

Phonons

ramannoodle.io.generic.read_polarizability_dataset(filepaths, file_format)

Read polarizability dataset from files.

Parameters:

• filepaths (str | Path | list[str] | list[Path])

• file_format (str) – Supports "outcar", "vasprun.xml" (see Supported file formats)

Raises:

• FileNotFoundError – File not found.

• InvalidFileException – Invalid file.

• IncompatibleFileException – File is incompatible with the dataset.

Return type:

PolarizabilityDataset

ramannoodle.io.generic.read_positions(filepath, file_format)

Read fractional positions from a file.

Parameters:

• filepath (str | Path)

• file_format (str) – Supports "outcar", "poscar", "xdatcar", "vasprun.xml" (see Supported file formats).

Return type:

ndarray[Any, dtype[float64]]

Returns:

(fractional) Array with shape (N,3) where N is the number of atoms.

Raises:

• FileNotFoundError – File not found.

• InvalidFileException – Invalid file.

ramannoodle.io.generic.read_positions_and_polarizability(filepath, file_format)

Read fractional positions and polarizability from a file.

Parameters:

• filepath (str | Path)

• file_format (str) – Supports "outcar", "vasprun.xml" (see Supported file formats).

Return type:

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

Returns:

0. positions – (fractional) Array with shape (N,3) where N is the number of atoms.

1. polarizability – Array with shape (3,3).

Raises:

• FileNotFoundError – File not found.

• InvalidFileException – Invalid file.

ramannoodle.io.generic.read_ref_structure(filepath, file_format)

Read reference structure from a file.

Parameters:

• filepath (str | Path)

• file_format (str) – Supports "outcar", "poscar", "xdatcar", "vasprun.xml" (see Supported file formats).

Raises:

• FileNotFoundError – File not found.

• InvalidFileException – Invalid file.

• SymmetryException – Structural symmetry determination failed.

Return type:

ReferenceStructure

ramannoodle.io.generic.read_structure_and_polarizability(filepath, file_format)

Read lattice, atomic numbers, fractional positions, polarizability from a file.

Parameters:

• filepath (str | Path)

• file_format (str) – Supports "outcar", "vasprun.xml" (see Supported file formats)

Return type:

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

Returns:

0. lattice – (Å) Array with shape (3,3).

1. atomic_numbers – List of length N where N is the number of atoms.

2. positions – (fractional) Array with shape (N,3) where N is the number of atoms.

3. polarizability – Array with shape (3,3).

Raises:

• FileNotFoundError – File not found.

• InvalidFileException – Invalid file.

ramannoodle.io.generic.read_trajectory(filepath, file_format)

Read molecular dynamics trajectory from a file.

Parameters:

• filepath (str | Path)

• file_format (str) – Supports "outcar", "vasprun.xml", (see Supported file formats). Use vasp.xdatcar.read_trajectory() to read a trajectory from an XDATCAR.

Raises:

• FileNotFoundError – File not found.

• InvalidFileException – Invalid file.

Return type:

Trajectory

ramannoodle.io.generic.write_structure(lattice, atomic_numbers, positions, filepath, file_format, overwrite=False)

Write structure to file.

Parameters:

• lattice (ndarray[Any, dtype[float64]]) – (Å) Array with shape (3,3).

• atomic_numbers (list[int]) – List of length N where N is the number of atoms.

• positions (ndarray[Any, dtype[float64]]) – (fractional) Array with shape (N,3).

• filepath (str | Path)

• file_format (str) – Supports "poscar" (see Supported file formats).

• overwrite (bool) – Overwrite the file if it exists.

• label – POSCAR label (first line).

Raises:

FileExistsError – File exists and overwrite == False.

Return type:

None

ramannoodle.io.generic.write_trajectory(lattice, atomic_numbers, positions_ts, filepath, file_format, overwrite=False)

Write trajectory to file.

Parameters:

• lattice (ndarray[Any, dtype[float64]]) – (Å) Array with shape (3,3).

• atomic_numbers (list[int]) – List of length N where N is the number of atoms.

• positions_ts (ndarray[Any, dtype[float64]]) – (fractional) Array with shape (S,N,3) where S is the number of configurations.

• filepath (str | Path)

• file_format (str) – Supports "xdatcar" (see Supported file formats).

• overwrite (bool) – Overwrite the file if it exists.

Raises:

FileExistsError – File exists and overwrite == False.

Return type:

None

ramannoodle.io.pymatgen module

Functions for interacting with pymatgen.

ramannoodle.io.pymatgen.construct_polarizability_dataset(pymatgen_structures, polarizabilities)

Create a PolarizabilityDataset from of pymatgen Structures and polarizabilities.

Parameters:

• pymatgen_structures (list[Structure]) – List of length M.

• polarizabilities (ndarray[Any, dtype[float64]]) – Array with shape (M,3,3).

Return type:

PolarizabilityDataset

ramannoodle.io.pymatgen.construct_ref_structure(pymatgen_structure)

Create a ReferenceStructure from a pymatgen Structure.

Parameters:

pymatgen_structure (Structure)

Return type:

ReferenceStructure

ramannoodle.io.pymatgen.construct_trajectory(pymatgen_trajectory, timestep)

Create a Trajectory from a pymatgen Trajectory.

Parameters:

• pymatgen_trajectory (Trajectory)

• timestep (float) – (fs)

Return type:

Trajectory

ramannoodle.io.pymatgen.get_positions(pymatgen_structure)

Read fractional positions from a pymatgen Structure.

Parameters:

pymatgen_structure (Structure)

Return type:

ndarray[Any, dtype[float64]]

Returns:

(fractional) Array with shape (N,3) where N is the number of atoms.

ramannoodle.io.pymatgen.get_structure(pymatgen_structure)

Get lattice, positions, and atomic numbers from a pymatgen Structure.

Parameters:

pymatgen_structure (Structure)

Return type:

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

Returns:

0. lattice – (Å) Array with shape (3,3).

1. atomic numbers – List of length N where N is the number of atoms.

2. positions – (fractional) Array with shape (N,3) where N is the number of atoms.