GPUMD IO

calorine.gpumd.read_hac(filename)

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.

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_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_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.