utilities package

utilities.utils module

Created on Wed Dec 3 14:25:06 2014

@author: Matti Ropo @author: Henrik Levämäki

utilities.utils.distort(dist_mat, mat)[source]

Apply distortion matrix to lattice vectors or sites.

Coordinates are assumed to be Cartesian.

utilities.utils.extrapolate_0k(a=None, Ta=None, bmod=None, TB=None, lat=None, TD=None, alpha=None, Talpha=None, B1=None, T0=None, ca=None, ZP=True)[source]

Extrapolates experimental data to zero Kelvin.

A function to extrapolate experimental room temperature lattice constants and bulk moduli to zero Kelvin. Zero point effects are also taken into account.

Input parameter Description
a Experimental lattice constant measured at temperature Ta (in Angstroms)
Ta The temperature at which a was measured (in Kelvin)
bmod Experimental bulk modulus measured at temperature TB (in GPa)
TB The temperature at which bmod was measured (in Kelvin)
lat Lattice structure
TD Experimental Debye temperature of the substance
alpha VOLUMETRIC!!! thermal expansion coefficient at temperature T (in 10⁻6 1/K)
Talpha The temperature at which alpha was measured (in Kelvin)
B1 Pressure derivative of the bulk modulus
T0 The temperature to which we want to extrapolate (Optional argument, if not given assume 0K)
ca c/a lattice parameter for hcp structures
ZP Whether or not zero-point (ZP) corrections are performed. If one only wants to calculate the fractional volume change due to dropping temperature, ZP=False.
Parameters:
  • a – (Default value = None)
  • Ta – (Default value = None)
  • bmod – (Default value = None)
  • TB – (Default value = None)
  • lat – (Default value = None)
  • TD – (Default value = None)
  • alpha – (Default value = None)
  • Talpha – (Default value = None)
  • B1 – (Default value = None)
  • T0 – (Default value = None)
  • ca – (Default value = None)
  • ZP – (Default value = True)
Returns:

ZPAE corrected 0K lattice constant (in Angstrom), ZPPE corrected 0K bulk modulus (in GPa)
Return type:

float,float
utilities.utils.latparam_to_wsrad(a=None, lat=None, ca=None, c=None)[source]
Parameters:
  • a – (Default value = None)
  • lat – (Default value = None)
  • ca – (Default value = None)
  • c – (Default value = None)
Returns:
Return type:
utilities.utils.rotation_matrix(axis, theta)[source]

Return the rotation matrix associated with counterclockwise rotation about the given axis by theta radians.

Parameters:
  • axis –
  • theta –
utilities.utils.run_bash(cmd)[source]
Parameters:cmd (str) – Command to run
Returns:
Return type:
utilities.utils.run_emto(name, folder='./')[source]

Submits a batch script to the queue.

Finds all the files in a folder that start with the name

Parameters:
  • name –
  • folder – (Default value = “./”)
Returns:
Return type:
utilities.utils.submit_to_batch(folder, jobname, system='slurm')[source]
Parameters:
  • folder –
  • jobname –
  • system – (Default value = ‘slurm’)
Returns:
Return type:
utilities.utils.write_batch(folder, jobname)[source]
Parameters:
  • folder (str) – Folder to write batch file
  • jobname (str) – Name of the job
Returns:
Return type:
utilities.utils.write_job(folder, jobname, atom, conc, sws)[source]
Parameters:
  • folder –
  • jobname –
  • atom –
  • conc –
  • sws –
Returns:
Return type:
utilities.utils.wsrad_to_latparam(sws, lat, ca=None, c=None)[source]
Parameters:
  • sws –
  • lat –
  • ca – (Default value = None)
  • c – (Default value = None)
Returns:
Return type: