gvasp 0.0.1

A quick post-process for resolve or assistant the VASP calculations

GVasp Manual

Table of contents

• About GVasp
• Install
  • Create Environment
  • Install GVasp
• Setting Environment
  • Default Environment
  • Modify Environment
• Code Structure
• Requirements

About GVasp

A quick post-process for resolve or assistant the VASP calculations, which can involve in four kinds of tasks as below:

• generate inputs
• visualize trajectory
• plot interface
• charge related work

More detailed information can see here.

Install

Create Environment

Before install the GVasp, we strongly recommend you to install conda before.

After install conda, create a new environment, e.g. GVasp, and install a python (version=3.9), using following command:

conda create -n GVasp python=3.9

Install GVasp

1. From sourcecode

   You can install the GVasp using the following command (under the root directory):

   python3 setup.py install
   

   or

   pip3 install .
   

2. Use PyPi

   We have made the wheel (production process can see [here]) and upload to the pypi, you can also install from it:

   pip3 install QVasp
   

   If the download speed is too slow, we suggest you change the pip mirror by modifying the ~/.pip/pip.conf file.

3. Use conda

   We now also made a conda package (production process can see [here]) and uploaded to the Anaconda, so you can also install GVasp from it:

   conda install -c hui_zhou -c conda-forge qvasp
   

If you run the gvasp -v and print version information, then you install the GVasp successful ~~

GVasp version 0.0.1 (Linux-5.10.16.3-microsoft-standard-WSL2-x86_64-with-glibc2.35)

Setting Environment

Default Environment

Default environment can display by following command:

gvasp -l/--list

Initial environment is like this:

------------------------------------Configure Information---------------------------------
! ConfigDir:      /mnt/c/Users/hui_zhou/Desktop/packages/gvasp/gvasp
! INCAR-template: /mnt/c/Users/hui_zhou/Desktop/packages/gvasp/gvasp/INCAR
! UValue:         /mnt/c/Users/hui_zhou/Desktop/packages/gvasp/gvasp/UValue.yaml
! PotDir:         /mnt/c/Users/hui_zhou/Desktop/packages/gvasp/gvasp/pot
! LogDir:         /mnt/c/Users/hui_zhou/Desktop/packages/gvasp/gvasp/logs
------------------------------------------------------------------------------------------

• ConfigDir: represents the directory of INCAR (template), UValue.yaml and pot

• LogDir: represents the directory of logs

• INCAR: INCAR template file of all GVasp submit tasks

• UValue.yaml: define the UValue for elements

• pot: directory of the elements' POTCAR

The structure of pot is like this:

pot
├── PAW_LDA
├── PAW_PBE
├── PAW_PW91
├── USPP_LDA
├── USPP_PW91
└── vdw_kernel.bindat

Modify Environment

If you don’t like the default environment, you can modify the environment by writing a config.json, the format of config.json is like this:

{
  "config_dir": "/your_directory_to_three_mentioned_files",
  "logdir": "/your_logs_directory",
}

and run command:

gvasp config -f config.json

Then the environment will be reset, GVasp will auto search the INCAR, UValue.yaml, pot under the config_dir.

Code Structure

• gvasp source code directory of GVasp gvasp

• gvasp/common (main module of GVasp) gvasp

• gvasp/lib (store the *.pyd files)

• extension (C++/Cython extensions for GVasp)

• docs (document description)

• tests (test files of GVasp)

Requirements

• Python >= 3.9
• Cython
• matplotlib
• numpy == 1.23.1 (other version may conflict with pymatgen, not test)
• pymatgen == 2022.7.25
• pymatgen-diffusion == 2020.10.8