Building input

The executation the cij program requires a configuration file and two input data files. They are described below.

Program configuration file (settings.yaml)

The configuration file in JSON and YAML format controls the behavior of the program: where to look for the input data, which parameters to calculate, the pressure and temperature range to work on.

This files contains three sections, qha, elast and output. The qha and elast will be control the behavior of QHA calculation module and thermalelasticity calculation module; the output module controls output files and formats.

For example in YAML format these sections are written nested:

qha:
  input: # the qha::input
  settings:
    # the qha::settings section
elast:
  input: # The elast::input
  settings:
    # The the elast::settings section
output:
    # the output section

In the following table, we summarize the functionalities for these sections in the configurational file.

The structure of the configuration file

key	type	description
additionalProperties
output	object	The list of output variables
elast	object	Configuration for thermalelasticity calculation
elast::settings	object
elast::input	string	Static elasticity input file name
qha	object	Configuration passed to QHA
qha::settings	object
qha::input	string	The file name of the QHA input data file

The following two tables decribes the accepted parameters for qha::settings and elast::settings.

QHA calculation settings (qha::settings)

key	type	description
additionalProperties
order	number	The order of equation of state to fit energy vs. volume.
volume_ratio	number	Ratio to expand the volume range when extrapolate equation of states. (from (vmin, vmax) to (vmin / volume_ratio, vmax * volume_ratio))
DELTA_P_SAMPLE	number	Pressure-sampling interval, used for output, the default value is 1 GPa
DELTA_P	number	The interval between two nearest pressures on the grid
P_MIN	number	Desired minimum pressure to calculate, in GPa.
NTV	integer	Number of volumes (or equivivalently, pressures) on the grid.
T_MIN	number	The minimum temperature, in Kelvin.
DT	number	The interval between two nearest temperatures on the grid, in Kelvin.
NT	integer	Number of temperatures on the grid

Themoelasticity calculation setttings (elast::settings)

key	type	description
symmetry	object
symmetry::residual_atol	number	Disagreement allowed between the input elastic tenor components and constraints enforced by the symmetry of the system.
symmetry::drop_atol	number	Drop the elastic tensor components if the magnitude of the elastic tensor components if this component in all volume points are less than this value.
symmetry::ignore_rank	boolean	Keep filling the missing elastic tensor components based on the crystal system even if not all necessary components are given.
symmetry::ignore_residuals	boolean	Keep filling the missing elastic tensor components based on the crystal system even if the disagreements exceeds tolerance.
symmetry::system	string	Name of the crystal system whose symmetry is applied to fill the missing elastic tensor components. Should be one of: triclinic, monoclinic, hexagonal, trigonal6, trigonal7, orthorhombic, tetragonal6, tetragonal7, cubic.
mode_gamma	object
mode_gamma::order	integer	The order of phonon frequencies spline interpolation.
mode_gamma::interpolator	string	The method to interpolate phonon frequencies vs. volume. Should be one of: spline, lsq_poly, lagrange, krogh, pchip, hermite, akima.

Default values are:

qha:
  input: input01
  settings:
    T_MIN: 0
    DT: 100
    DT_SAMPLE: 100
    NT: 16
    P_MIN: 0
    DELTA_P: 1
    DELTA_P_SAMPLE: 1
    order: 3
    static_only: False
    volume_ratio: 1.2
elast:
  input: elast.dat
  settings:
    mode_gamma:
      interpolator: lsq_poly
      order: 3
    symmetry:
      system: triclinic
      ignore_residuals: False
      ignore_rank: False
      drop_atol: 1.0e-8
      residual_atol: 0.1
output:
  pressure_base:
    - cij
    - bm_VRH
    - G_VRH
    - v
    - vs
    - vp
  volume_base:
    - p

The QHA input data file (input01)

The first input data is similar to the QHA’s input data.

The static elastic moduli data file (elast.dat)

The static elasticity input data file tabulates the static elastic coefficients (\(c_{ij}^\text{st}\), \(i,j = 1 \text{ to } 6\)) and axial length along three axes in Cartesian coordinates (\(a_{ii}, i=1,2,3\)) at a series of volume points.

To compute Voigt-Reuss-Hill (VRH) averaged elastic moduli and acoustic velocities, unless all non-zero terms are listed one needs to either specify the crystal system in settings.yaml or manually preprocess the elast.dat with the cij fill utility to generate a new elast.dat which contains all non-zero terms. The column names in this table also determine the output thermoelastic coefficient terms.