postmd.avechunk package

class postmd.avechunk.Bin1d(path=None, timestep: float = 1.0, dim: str | None = None, delta: float | None = None)[source]

Bases: MDFile

post-process the file generated from fix ave/chunk bin1d command.

Parameters:

  • path (str, optional) – path to the file. Defaults to None.

  • timestep (float, optional) – temperature you set in LAMMPS input file. Defaults to 1.0 [fs].

  • dim (str) – the dimension of chunk: 'x', 'y' or 'z'.

  • delta (float) – the chunk size, in Angstrom.

read_file(header: list | None = None, header_line: int = 3, **kwargs) → DataFrame[source]

read file generated from fix ave/chunk bin1d command.

Parameters:

  • header (list, optional) – a list of data headers. Defaults to None, means extracting headers from header_line.

  • header_line (int, optional) – when header=None, the content in line=<header_line> will be used as the headers. Defaults to 2.

  • **kwargs – received parameters of pd.read_csv().

Returns:

DataFrame object read from the file.

Return type:

pd.DataFrame

Notes

There are some default setting in read files: - comment="#" in the files generated by fix ave/time``command in LAMMPS. - ``sep="\s+" set the separator to \s+, matching one or more whitespace characters.

apply_function(func)[source]

Submodules

postmd.avechunk.bin1d module

class postmd.avechunk.bin1d.Bin1d(path=None, timestep: float = 1.0, dim: str | None = None, delta: float | None = None)[source]

Bases: MDFile

post-process the file generated from fix ave/chunk bin1d command.

Parameters:

  • path (str, optional) – path to the file. Defaults to None.

  • timestep (float, optional) – temperature you set in LAMMPS input file. Defaults to 1.0 [fs].

  • dim (str) – the dimension of chunk: 'x', 'y' or 'z'.

  • delta (float) – the chunk size, in Angstrom.

read_file(header: list | None = None, header_line: int = 3, **kwargs) → DataFrame[source]

read file generated from fix ave/chunk bin1d command.

Parameters:

  • header (list, optional) – a list of data headers. Defaults to None, means extracting headers from header_line.

  • header_line (int, optional) – when header=None, the content in line=<header_line> will be used as the headers. Defaults to 2.

  • **kwargs – received parameters of pd.read_csv().

Returns:

DataFrame object read from the file.

Return type:

pd.DataFrame

Notes

There are some default setting in read files: - comment="#" in the files generated by fix ave/time``command in LAMMPS. - ``sep="\s+" set the separator to \s+, matching one or more whitespace characters.

apply_function(func)[source]