Command-line tools
cij
cij [OPTIONS] COMMAND [ARGS]...
Options
- --version
Show the version and exit.
Commands
- extract
Extract data from cij calculation results…
- fill
Fill Cij tensor components table INPUT02…
- geotherm
Extract data from cij calculation results…
- modes
Plot interpolated mode frequency vs volume…
- plot
Plot SAM-Cij calculation results for files…
- run
Perform SAM-Cij calculation details…
- run-static
Fit equation of state based on E, V given…
cij run
Perform SAM-Cij calculation details specified in SETTINGS.
cij run [OPTIONS] SETTINGS
Options
- --version
Show the version and exit.
- --debug <debug>
Verbosity level of debug log emitted to the standard output.
- Options
CRITICAL | ERROR | WARNING | INFO | DEBUG | NOTSET
Arguments
- SETTINGS
Required argument
cij run-static
Fit equation of state based on E, V given in INPUT01, and also elastic moduli and acoustic velocities if static Cij table INPUT02 (elast.dat) is given.
cij run-static [OPTIONS] INPUT01 [INPUT02]
Options
- -I, --interp <interp>
Interpolate result vs. volume or pressure or don’t interpolate (none).
- Default
none- Options
none | pressure | volume
- -n, --ntv <ntv>
Number of volumes (or equivivalently, pressures) on the grid when interpolating results.
- Default
201
- --p-min <p_min>
Lower bound of pressure range when interpolate result vs. P, in GPa unit.
- Default
0
- --delta-p <delta_p>
The interval between two nearest pressures on the grid when interpolate result vs. P, in GPa unit.
- Default
1.0
- --delta-p-sample <delta_p_sample>
The interval between two nearest pressures on the grid when interpolate result vs. P, in GPa unit, same as DELTA_P by default.
- --cellmass <cellmass>
Mass of the unitcell, value in amu unit.
- --v-ratio <v_ratio>
Ratio to expand the volume range when extrapolate equation of states. (from (vmin, vmax) to (vmin / volume_ratio, vmax * volume_ratio)).
- Default
1.2
- -s, --system <system>
Name of the crystal system whose symmetry is applied to fill the missing elastic tensor components. Should be Should be one of: triclinic, monoclinic, hexagonal, trigonal6, trigonal7, orthorhombic, tetragonal6, tetragonal7, cubic.
Arguments
- INPUT01
Required argument
- INPUT02
Optional argument
cij extract
Extract data from cij calculation results to a table at specific P or T (e.g., table with c11s, c12s, K, G vs. P at 300 K).
cij extract [OPTIONS]
Options
- -v, --variables <variables>
Required Variables to output, (e.g., ‘c11s,c12s,bm,G’), values should be seperated with comma.
- -T, --temperature <temperature>
Specify temperature to extract data at, value in unit K, result will be tabulated vs. P.
- -P, --pressure <pressure>
Specify pressure to extract data at, value in unit GPa, result will be tabulated vs. T.
- -h, --hide-header
Hide table header or not.
- Default
False
cij fill
Fill Cij tensor components table INPUT02 (elast.dat) based on the symmetry constraints of the crystal system.
cij fill [OPTIONS] INPUT02
Options
- -s, --system <system>
Name of the crystal system whose symmetry is applied to fill the missing elastic tensor components. Should be Should be one of: triclinic, monoclinic, hexagonal, trigonal6, trigonal7, orthorhombic, tetragonal6, tetragonal7, cubic.
- --ignore-residuals
Keep filling the missing elastic tensor components based on the crystal system even if the disagreements exceeds tolerance.
- --ignore-rank
Keep filling the missing elastic tensor components based on the crystal system even if not all necessary components are given
- --drop-atol <drop_atol>
Drop the elastic tensor components if the magnitude of the elastic tenor components if this components in all volume points are less than this value.
Arguments
- INPUT02
Required argument
cij geotherm
Extract data from cij calculation results to table along a geotherm P, T and D (depth) map given in PATH.
cij geotherm [OPTIONS]
Options
- -i, -g, --geotherm <geotherm>
Required The file name of geotherm P, D, T map.
- --t-col <t_col>
The name of geotherm pressure column.
- Default
P
- --p-col <p_col>
The name of geotherm temperature column
- Default
T
- -v, --variables <variables>
Required Variables to output, (e.g., ‘c11s,c12s,bm,G’), values should be seperated with comma.
- -h, --hide-header
Hide header or not.
- Default
False
cij modes
Plot interpolated mode frequency vs volume for calculation details specified in SETTINGS.
cij modes [OPTIONS] SETTINGS
Options
- -q, --iq <iq>
Plot for i-th q-point
- Default
0
- -n <n>
Plot for n-th derivative
- Default
0
- -o, --output <output>
File name for the output figure.
- Default
modes.png
- --y-max <y_max>
y-max limit
- -p, --interval <interval>
p-tick interval
Arguments
- SETTINGS
Required argument