Property Calculations

This module provides some additional methods to calculate some physical properties. As GPUMD efficiently calculates most properties during run time, there are not many methods needed here at this time, but the section may expand in the future based on user feedback.

List of all methods

gpyumd.calc.calc_gkma_kappa(data: dict, dt: float, sample_interval: int, temperature: float = 300, vol: float = 1, max_tau: Optional[float] = None, directions: str = 'xyz', outputfile: str = 'heatmode.npy', save: bool = False, directory: Optional[str] = None) → Union[None, Dict[str, ndarray]][source]

Calculate the Green-Kubo thermal conductivity from modal heat current data from ‘load_heatmode’

Parameters

  • data – Dictionary with heat currents loaded by ‘load_heatmode’

  • dt – Time step during data collection in fs

  • sample_interval – Number of time steps per sample of modal heat flux

  • temperature – Temperature of system during data collection

  • vol – Volume of system in angstroms^3

  • max_tau – Correlation time to calculate up to. Units of ns

  • directions – Directions to gather data from. Any order of ‘xyz’ is accepted. Excluding directions also allowed (i.e. ‘xz’ is accepted)

  • outputfile – File name to save read data to. Output file is a binary dictionary. Loading from a binary file is much faster than re-reading data files and saving is recommended

  • save – Toggle saving data to binary dictionary. Loading from save file is much faster and recommended

  • directory – Name of directory storing the input file to read

gpyumd.calc.calc_reduced_freq_info(freq: dict, ndiv: int = 1) → dict[source]

Recalculates modal analysis frequency binning information based on how many times larger bins are wanted.

Parameters

  • freq – Dictionary with frequency binning information from the get_frequency_info function output

  • ndiv – Divisor used to shrink number of bins output. If originally have 10 bins, but want 5, ndiv=2. nbins/ndiv need not be an integer

Returns

Dictionary with the system eigen freqeuency information along

with binning information

gpyumd.calc.calc_spectral_kappa(shc: dict, driving_force: float, temperature: float, volume: float) → None[source]

Spectral thermal conductivity calculation from the spectral heat current from an SHC run. Updates the shc dict from data.load_shc()

Parameters

  • shc – The data from a single SHC run as output by load_shc

  • driving_force – HNEMD force in (1/A)

  • temperature – HNEMD run temperature (K)

  • volume – Volume (A^3) during HNEMD run

Returns

New dict entries of spectral thermal conductivity. Units are [kwi,

kwo -> W(m^-1)(K^-1)(THz^-1)].