jcwang587 / xdatbus

A Python package for enhancing VASP AIMD simulations and analysis

Hi there 👋

Visit my personal webpage for more details about my experience.

• 🎓 I am a UMass BTP Fellow and Douglas Fellow, currently a 4th-year Chemical Engineering Ph.D. candidate at UMass Amherst.
• 🔋 I am currently working on electrochemical systems for energy storage and conversion using computational methods.
• ⚛️ I am interested in visualizing structural chemical data. You can view my work on my Sketchfab webpage.

Python Package

• 🚌 xdatbus - A Python package enhancing VASP AIMD simulation

xdatbus's Issues

Functions for Metadynamics analysis

Several scripts are currently available for analyzing metadynamics results:

1. fmtd01_xdc2xtc.py: Converts from the XDATCAR format to the .xtc trajectory, a compressed trajectory format from Gromacs.
2. fmtd02_hillspot2hills.py: Converts from the VASP-supported hillspot/penaltypot format to the PLUMED-supported hills format.
3. fmtd03_report_loader.py: Implements a loader function that reads and extracts CV information from VASP-supported report files. It currently supports multiple dimensions of CVs.

The expected functions for metadynamics:

• Calculate 1D and 2D free energy profiles.
• Track the time evolution of CVs (supports multiple dimensions) using extracted information from hills or report files.
• Calculate the 3D free energy profiles, now taking into account the .cube output. This output should be compatible with various visualization software, such as VESTA.

Cannot import name 'xdc_aggregate' from partially initialized module 'xdatbus' (most likely due to a circular import)

Hi,

Thanks for sharing the tool!

I have accounted the following error on "cannot import the xdatbus". I have pip install xdatbus with 3.12.0 python in the created environment and it is running in Bash.

I am hoping to get insight from this. Thank you in advance!

Here is the details of the error:

(myenv) yuyan@perlmutter:login34:/bin/xdatbus/examples> pip install xdatbus
Requirement already satisfied: xdatbus in /global/homes/y/yuyan/.conda/envs/myenv/lib/python3.12/site-packages (0.0.43)
(myenv) yuyan@perlmutter:login34:/bin/xdatbus/examples> python
Python 3.12.0 | packaged by Anaconda, Inc. | (main, Oct 2 2023, 17:29:18) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

from xdatbus
File "", line 1
from xdatbus
^
SyntaxError: invalid syntax
import xdatbus
Traceback (most recent call last):
File "", line 1, in
File "/global/u2/y/yuyan/bin/xdatbus/examples/xdatbus.py", line 2, in
from xdatbus import xdc_aggregate, xdc_unwrap
ImportError: cannot import name 'xdc_aggregate' from partially initialized module 'xdatbus' (most likely due to a circular import) (/global/u2/y/yuyan/bin/xdatbus/examples/xdatbus.py)