GPUMD IO

calorine.gpumd.read_hac(filename, exclude_currents=True, exclude_in_out=True)

Parses a file in hac.out format from GPUMD and returns the content as a data frame. More information concerning file format, content and units can be found here.

Parameters:

• filename (str) – Input file name.

• exclude_currents (bool) – Do not include currents in output to save memory.

• exclude_in_out (bool) – Do not include in and out parts of conductivity in output to save memory.

Return type:

DataFrame

calorine.gpumd.read_kappa(filename)

Parses a file in kappa.out format from GPUMD and returns the content as a data frame. More information concerning file format, content and units can be found here.

Parameters:

filename (str) – Input file name.

Return type:

DataFrame

calorine.gpumd.read_mcmd(filename, accumulate=True)

Parses a Monte Carlo output file in mcmd.out format and returns the content in the form of a DataFrame.

Parameters:

• filename (str) – Path to file to be parsed.

• accumulate (bool) – If True the MD steps between subsequent Monte Carlo runs in the same output file will be accumulated.

Return type:

DataFrame

Returns:

DataFrame containing acceptance ratios and concentrations (if available), as well as key Monte Carlo parameters.

calorine.gpumd.read_msd(filename)

Parses a file in msd.out format from GPUMD and returns the content as a data frame. More information concerning file format, content and units can be found here.

Parameters:

filename (str) – Input file name.

Return type:

DataFrame

calorine.gpumd.read_runfile(filename)

Parses a GPUMD input file in run.in format and returns the content in the form a list of keyword-value pairs.

Parameters:

filename (str) – Input file name.

Return type:

List[Tuple[str, list]]

Returns:

List of keyword-value pairs.

calorine.gpumd.read_thermo(filename, natoms=1)

Parses a file in thermo.out format from GPUMD and returns the content as a data frame. More information concerning file format, content and units can be found here.

Parameters:

• filename (str) – Input file name.

• natoms (int) – Number of atoms; used to normalize energies.

Return type:

DataFrame

calorine.gpumd.read_thermodynamic_data(directory_name, normalize=False)

Parses the data in a GPUMD output directory and returns the content in the form of a DataFrame. This function reads the thermo.out, run.in, and model.xyz (optionally) files, and returns the thermodynamic data including the time (in ps), the pressure (in GPa), the side lengths of the simulation cell (in Å), and the volume (in Å:sup:3 or Å:sup:3/atom).

Parameters:

• directory_name (str) – Path to directory to be parsed.

• normalize (bool) – Normalize thermodynamic quantities per atom. This requires the model.xyz file to be present.

Return type:

DataFrame

Returns:

DataFrame containing (augmented) thermodynamic data.

calorine.gpumd.read_xyz(filename)

Reads the structure input file (model.xyz) for GPUMD and returns the structure.

This is a wrapper function around ase.io.read_xyz() since the ASE implementation does not read velocities properly.

Parameters:

filename (str) – Name of file from which to read the structure.

Return type:

Atoms

Returns:

Structure as ASE Atoms object with additional per-atom arrays representing atomic masses, velocities etc.

calorine.gpumd.write_runfile(file, parameters)

Write a file in run.in format to define input parameters for MD simulation.

Parameters:

• file (Path) – Path to file to be written.

• parameters (dict) – Defines all key-value pairs used in run.in file (see GPUMD documentation for a complete list). Values can be either floats, integers, or lists/tuples.

calorine.gpumd.write_xyz(filename, structure, groupings=None)

Writes a structure into GPUMD input format (model.xyz).

Parameters:

• filename (str) – Name of file to which the structure should be written.

• structure (Atoms) – Input structure.

• groupings (Optional[List[List[List[int]]]]) – Groups into which the individual atoms should be divided in the form of a list of list of lists. Specifically, the outer list corresponds to the grouping methods, of which there can be three at the most, which contains a list of groups in the form of lists of site indices. The sum of the lengths of the latter must be the same as the total number of atoms.

Raises:

ValueError – Raised if parameters are incompatible.