A quick post-process for resolve or assistant the VASP calculations
Project description
GVasp Manual
Table of contents
About GVasp
A quick post-process for resolve or assistant the VASP calculations, which can involve in many kinds of tasks as below:
- generate inputs
- visualize output
- 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
-
From sourcecode
You can install the
GVasp
using the following command (under the root directory):python3 setup.py install
or
pip3 install .
-
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 gvasp
If the download speed is too slow, we suggest you change the pip mirror by modifying the
~/.pip/pip.conf
file. -
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 gvasp
If you run the gvasp -v
and print version information, then you install the GVasp
successful ~~
GVasp version 0.0.3 (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
! scheduler: slurm
! 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
andpot
-
scheduler: represents the job control system, now only support slurm (but you can specify a .submit file in your parent-chain path)
-
LogDir: represents the directory of
logs
-
INCAR:
INCAR template
file for allGVasp
submit tasks -
UValue.yaml: define the
UValue
for elements -
pot: directory of the elements'
POTCAR
(please prepare it by yourself)
The structure of pot
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
(or other name, but json
format), the structure
of config.json
like this:
{
"config_dir": "/your_directory_to_three_mentioned_files",
"potdir": "/your_pot_directory",
"logdir": "/your_logs_directory"
}
and run command:
gvasp config -f config.json
Then the environment will be reset, GVasp
will auto search the INCAR
and UValue.yaml
under the config_dir
.
User template
GVasp
support user to define their incar or submit template with the following steps:
-
Named the incar or submit template as the
*.incar
and*.submit
files. -
Put them in your parent directory or parent’s parent directory and so on (defined as the parent-chain).
After these two steps, the GVasp generate the inputs will apply your templates.
Code Structure
-
gvasp: source code directory
-
gvasp/common: main module
-
gvasp/neb: neb-related path module
-
gvasp/lib: store the dynamic library (*.so and *.pyd)
-
extension:
C++
/Cython
extensions (source code) -
docs: documents file (*.rst format)
-
tests: test files
Requirements
- Python >= 3.9
- Cython
- pybind11
- numpy
- matplotlib
Copyright © 2022 Hui Zhou
All rights reserved.
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