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Function4 - Calculators

This script provides a menu-driven interface to perform various tasks related to property calculations.

Menu Options

------------>>
401) Calc ionic conductivity
402) Calc properties by nep
403) Developing ... 
000) Return to the main menu
------------>>
Input the function number:

Option 401: Calc ionic conductivity

This script will read the msd.out file and then calculate the diffusivity and ionic conductivity.

Select option 401 from the menu:

401

You will see the following prompt:

 >-------------------------------------------------<
 | This function calls the script in calculators   |
 | Script: calc_ion_conductivity.py                |
 | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
 >-------------------------------------------------<
 Input <element> <charge> (eg. Li 1)
 ------------>>

Enter the <element> and <charge>:

Li 1

If required files (thermo.out and model.xyz) are not found, the script will prompt for manual input of structure volume, number of ions, and temperature.

 Files 'thermo.out' and 'model.xyz' are not found.
 Please provide the following values:
 --------------------------->
 Enter average temperature (in K): 800
 Enter system volume (in Å^3): 16785
 Enter number of ions: 448

You will see the following output:

Diffusivity (D):
D_x: 4.153e-07 cm^2/s
D_y: 4.174e-07 cm^2/s
D_z: 2.610e-07 cm^2/s
D_total: 3.646e-07 cm^2/s
------------------------------
Ionic Conductivity:
Sigma_x: 2.576e-02 mS/cm
Sigma_y: 2.589e-02 mS/cm
Sigma_z: 1.619e-02 mS/cm
Sigma_total: 2.261e-02 mS/cm

The script calc_ion_conductivity.py in the Scripts/calculators will be called to perform the calculations.

Option 402: Calc properties by nep

This script will calculate energies, forces, and stresses by using the calorine package.

Select option 402 from the menu:

402

You will see the following prompt:

 >-------------------------------------------------<
 | This function calls the script in calculators   |
 | Script: calc_properties_with_nep.py             |
 | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
 >-------------------------------------------------<
 Input <input.xyz> <output.xyz> <nep_model> 
 Examp: input.xyz outpt.xyz nep.txt
 ------------>>

Enter the <input.xyz> <output.xyz> and <nep_model>:

input.xyz output.xyz nep.txt

The script calc_properties_with_nep.py in the Scripts/calculators will be called to perform the calculations.

Option 403: Calc descriptors of specific elements

This script will calculate the descriptors of specific elements by using the calorine package.

Select option 403 from the menu:

403

You will see the following prompt:

 >-------------------------------------------------<
 | This function calls the script in calculators   |
 | Script: calc_descriptors.py                     |
 | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
 >-------------------------------------------------<
 Input <input.xyz> <output.npy> <nep_model> <element>
 Examp: train.xyz des_Li.npy nep.txt Li
 ------------>>

Enter the <input.xyz> <output.npy>, <nep_model> and <element>:

train.xyz des_Li.npy nep.txt Li

The script calc_descriptors.py in the Scripts/calculators will be called to perform the calculations, and output des_Li.npy for the analysis.