lammps¶
Calculations¶
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thermo.lammps.calc.get_GKTC(directory='.', T=300, vol=1, dt=None, rate=None, tau=None, heatflux_file='heat_out.heatflux', mat_file='heat_flux.mat')[source]¶ Gets the thermal conductivity vs. time profile using the Green-Kubo formalism. thermal conductivity vector and time vector. Assumptions with no info given by user: dt = 1 fs, vol = 1, T=300, rate=dt, tau=total time
- Args:
- directory (string):
- This is the directory in which the simulation results are located. If not provided, the current directory is used.
- T (float):
- This is the temperature at which the equlibrium simulation was run at. If not provided, T=300 is used. Units are in [K]
- vol (float):
- This is the volume of the simulation system. If not provided, vol=1 is used. Units are [angstroms^3].
- dt (float):
- This is the timestep of the green-kubo part of the simulation. If not provided, dt=1 fs is used. units are in [fs]
- rate (int):
- This is the rate at which the heat flux is sampled. This is in number of timesteps. If not provided, we assume we sample once per timestep so, rate=dt
- tau (int):
- max lag time to integrate over. This is in units of [ns]
- heatflux_file (str): Filename of heatflux output. If not provided
- ‘heat_out.heatflux’ is used.
- mat_file (str): MATLAB file to load, if exists. If not provided,
- ‘heat_flux.mat’ will be used. Also used as filename for saved MATLAB file.
- Returns:
- dict: kx, ky, kz, t, directory, dt, tot_time, tau, T, vol, srate, jxjx, jyjy, jzjz
Output keys:
- kx (ndarray): x-direction thermal conductivity [W/m/K]
- ky (ndarray): y-direction thermal conductivity [W/m/K]
- kz (ndarray): z-direction thermal conductivity [W/m/K]
- t (ndarray): time [ns]
- directory (str): directory of results
- dt (float): timestep [fs]
- tot_time (float): total simulated time [ns]
- tau (int): Lag time [ns]
- T (float): [K]
- vol (float): Volume of simulation cell [angstroms^3]
- srate (float): See above
- jxjx (ndarray): x-direction heat flux autocorrelation
- jyjy (ndarray): y-direction heat flux autocorrelation
- jzjz (ndarray): z-direction heat flux autocorrelation
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thermo.lammps.calc.get_heat_flux(directory='.', heatflux_file='heat_out.heatflux', mat_file='heat_flux.mat')[source]¶ Gets the heat flux from a LAMMPS EMD simulation. Creates a compressed .mat file if only in text form. Loads .mat form if exists.
- Args:
- directory (str): This is the directory in which the simulation results
- are located. If not provided, the current directory is used.
- heatflux_file (str): Filename of heatflux output. If not provided
- ‘heat_out.heatflux’ is used.
- mat_file (str): MATLAB file to load, if exists. If not provided,
- ‘heat_flux.mat’ will be used. Also used as filename for saved MATLAB file.
- Returns:
- dict:Jx (list), Jy (list), Jz (list), rate (float)
Data Loaders¶
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thermo.lammps.data.extract_dt(log_file)[source]¶ Finds all time steps given in the lammps output log
- Args:
- log_file (str):
- LAMMPS log file to examine
- Returns:
- list(float): The timesteps found in log_file in [ps]
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thermo.lammps.data.get_dimensions(filename, directory=None)[source]¶ Gets the dimensions of a 3D simulation from a LAMMPS trajectory.
- Args:
- filename (str):
- LAMMPS trajectory file to extract dimensions from
- directory (str):
- The directory the trajectory file is found in
- Returns:
- dict: Dictionary with keys given in the table below
Output dictionary¶ key x y z A V xy xz yz units distance distance distance distance2 distance3 distance distance distance