postmd.avetime package

class postmd.avetime.AveTime(path=None, timestep: float = 1.0)

Bases: MDFile

process the data generated from “fix ave/time” command in LAMMPS (see https://docs.lammps.org/fix_ave_time.html).

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].

read_file(header: list | None = None, header_line: int = 2, **kwargs) → DataFrame

read file generated from fix ave/time 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.

class postmd.avetime.GreenKubo(path=None, timestep: float = 1.0)

Bases: AveTime

calculate the auto-correlation function (acf) and corresponding integration for Green-Kubo formula. But you need to pay attention to the true equation of Green-Kubo formula, because this script just do the integration of acf, not including other parts, like multiply or divide by some properties.

process the data generated from “fix ave/time” command in LAMMPS (see https://docs.lammps.org/fix_ave_time.html).

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].

cal_acf(data_type='raw', col: int | None = None, nlag: int | None = None, nlag_col: int = 1, unit_trans=1.0) → ndarray

calculate the acf from data file and store in self.nlag and self.acf.

Parameters:

• data_type (str, optional) – the data type of self.data (raw or acf). Defaults to "raw".

• col (int, optional) – the column number(start from 0) of data to process in self.data. Defaults to None.

• nlag (int, optional) – Limit the number of autocovariances returned. Size of returned array is nlag + 1. Defaults to None.

• nlag_col (int, optional) – the column number(start from 0) of nlag in data, usually named “TimeDelta”. Defaults to 1.

• unit_trans (float, optional) – transform the unit of property to SI unit. Defaults to 1.0.

Returns:

None

integrate_acf(nlag=None, acf=None, *, method='simpson')

Integrate the acf data to the Green-Kubo formula and store in self.int_acf.

Parameters:

• nlag (np.ndarray, optional) – the nlag data. Defaults to None.

• acf (np.ndarray, optional) – the acf data. Defaults to None.

• method (str, optional) – the integration method ("simpson" or "trap"). Defaults to "simpson".

write_result(filename='gk.csv')

write the data of nlag, acf and integration of acf to file

Parameters:

filename (str, optional) – the filename for output. Defaults to "gk.csv".

finite_size_correct_friction_coeff()

Submodules

postmd.avetime.avetime module

class postmd.avetime.avetime.AveTime(path=None, timestep: float = 1.0)

Bases: MDFile

process the data generated from “fix ave/time” command in LAMMPS (see https://docs.lammps.org/fix_ave_time.html).

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].

read_file(header: list | None = None, header_line: int = 2, **kwargs) → DataFrame

read file generated from fix ave/time 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.

postmd.avetime.greenkubo module

class postmd.avetime.greenkubo.GreenKubo(path=None, timestep: float = 1.0)

Bases: AveTime

calculate the auto-correlation function (acf) and corresponding integration for Green-Kubo formula. But you need to pay attention to the true equation of Green-Kubo formula, because this script just do the integration of acf, not including other parts, like multiply or divide by some properties.

process the data generated from “fix ave/time” command in LAMMPS (see https://docs.lammps.org/fix_ave_time.html).

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].

cal_acf(data_type='raw', col: int | None = None, nlag: int | None = None, nlag_col: int = 1, unit_trans=1.0) → ndarray

calculate the acf from data file and store in self.nlag and self.acf.

Parameters:

• data_type (str, optional) – the data type of self.data (raw or acf). Defaults to "raw".

• col (int, optional) – the column number(start from 0) of data to process in self.data. Defaults to None.

• nlag (int, optional) – Limit the number of autocovariances returned. Size of returned array is nlag + 1. Defaults to None.

• nlag_col (int, optional) – the column number(start from 0) of nlag in data, usually named “TimeDelta”. Defaults to 1.

• unit_trans (float, optional) – transform the unit of property to SI unit. Defaults to 1.0.

Returns:

None

integrate_acf(nlag=None, acf=None, *, method='simpson')

Integrate the acf data to the Green-Kubo formula and store in self.int_acf.

Parameters:

• nlag (np.ndarray, optional) – the nlag data. Defaults to None.

• acf (np.ndarray, optional) – the acf data. Defaults to None.

• method (str, optional) – the integration method ("simpson" or "trap"). Defaults to "simpson".

write_result(filename='gk.csv')

write the data of nlag, acf and integration of acf to file

Parameters:

filename (str, optional) – the filename for output. Defaults to "gk.csv".

finite_size_correct_friction_coeff()