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Function2 - Sample Structures

This script provides a menu-driven interface to perform various tasks related to structure sampling.

Menu Options

------------>>
201) Sample structures from extxyz
202) Sample structures by pynep
203) Find the outliers in training set
204) Perturb structure
205) Select max force deviation structs from active.xyz
206) Developing ...
000) Return to the main menu
------------>>
Input the function number:

Option 201: Sample Structures from extxyz

This option allows you to sample structures from an extxyz file using a specified method.

Select option 201 from the menu:

201

You will see the following prompt:

>-------------------------------------------------<
| This function calls the script in Scripts       |
| Script: sample_structures.py                    |
| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
>-------------------------------------------------<
Input <extxyz_file> <sampling_method> <num_samples>
Sampling_method: 'uniform' or 'random'
Examp: train.xyz uniform 50
------------>>

Enter the extxyz file name, sampling method, and number of samples:

train.xyz uniform 50

The script sample_structures.py in the Scripts/sample_strcutures will be called to perform the sampling.

Option 202: Sample structures by pynep

This function calls the pynep_select_structs.py in the Scripts/sample_structures to sampling the structures by pynep.

Select option 202 from the menu:

202

You will see the following prompt:

>-------------------------------------------------<
| This function calls the script in Scripts       |
| Script: pynep_select_structs.py                 |
| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
>-------------------------------------------------<
Input <sample.xyz> <train.xyz> <nep_model> <min_dist>
Examp: dump.xyz train.xyz ./nep.txt 0.01
------------>>

<samle.xyz>: extxyz file

<train.xyz>: train.xyz

<nep_model>: nep.txt

<min_dist>: min_dist for pynep sampling

Enter the following parameters:

dump.xyz train.xyz nep.txt 0.01

Option 203: Find the outliers in training set

This function calls the get_max_rmse_xyz.py script to find outliers in a training set.

Select option 203 from the menu:

203

You will see the following prompt:

>-------------------------------------------------<
| This function calls the script in GPUMD's tools |
| Script: get_max_rmse_xyz.py                     |
| Developer: Ke XU (kickhsu@gmail.com)            |
>-------------------------------------------------<
Input <extxyz_file> <*_train.out> <num_outliers>
Examp: train.xyz energy_train.out 13 
------------>>

<extxyz_file>: extxyz file

<*_train.out>: energy_train.out/force_train.out/`virial_train.out``

<num_outliers>: number of outliers

Enter the extxyz file name, <*_train.out>, and number of outliers:

train.xyz energy_train.out 13

The script sample_structures.py in the Scripts/sample_strcutures will be called to perform the sampling.

Option 204: Perturb structure

This function calls the perturb_structure.py script to generate the perturbed structures.

Select option 204 from the menu:

204

You will see the following prompt:

>-------------------------------------------------<
| This function calls the script in Scripts       |
| Script: perturb_structure.py                    |
| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
>-------------------------------------------------<
Input <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>
The default paramters for perturb are 20 0.03 0.2 uniform
Examp: POSCAR 20 0.03 0.2 normal
------------>>

<input.vasp>: filename.vasp

<pert_num>: number of perturbed structures

<cell_pert_fraction>: A fraction determines how much (relatively) will cell deform

<atom_pert_distance>: A distance determines how far atoms will move (in angstrom).

<atom_pert_style>: <uniform>, <normal>, <const>

Enter your parameters like:

POSCAR 20 0.03 0.2 uniform

The script perturb_structure.py in the Scripts/sample_strcutures will be called to perform the perturbation.

Option 205: Select max force deviation structs from active.xyz

This option allows you to select max force deviation structures from active.xyz generated by the command active in gpumd.

Select option 205 from the menu:

205

You will see the following prompt:

>-------------------------------------------------<
| This function calls the script in Scripts       |
| Script: select_max_modev.py                    |
| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
>-------------------------------------------------<
Input <structs_num> <threshold> (eg. 200 0.15)
------------>>

Enter the number of structures and the threshold used in your run.in:

200 0.15

The script select_max_modev.py in the Scripts/sample_strcutures will be called to perform the sampling.

Thank you for using GPUMDkit! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).