ElectronVisualized provides an web-based interactive visualization in the areas of chemistry and quantum mechanics. The app showcases atomic orbitals through electron density — alongside with molecular orbitals — beautifully and elegantly.
| iOS, iPadOS, and visionOS |
|---|
 |
1. Depending on OS environment, install the same OS-level dependencies written down on Dockerfile
If virtualenv is not installed
pip install virtualenv
python -m virtualenv venv
venv/bin/activate
pip install -r requirements.txt
python electron_visualized.py
cd client && npm install
npm run start
Designed and Developed by John Seong.
 |
 |
TIPS & TRICKS
PIP FREEZE LOCALLY: pip3 freeze -l > requirements.txt
DEPLOYING FLASK + REACT APP ON HEROKU: https://www.realpythonproject.com/how-to-setup-automated-deployment-for-multiple-apps-under-a-single-github-repository-in-heroku/
HOW TO INSTALL ASE AND GPAW ON LINUX (SERVER): http://dtu.cnwiki.dk/10302/page/2699/optional-install-ase-and-gpaw-on-your-laptop
ATOMIC ORBITAL (SPHERICAL HARMONICS) MLAB: https://dpotoyan.github.io/Chem324/H-atom-wavef.html
SHIFT+ALT+CLICK BELOW = MULTIPLE CURSORS ON VSCODE
UPDATED (NOV. 29, 2022): MAKE SURE YOU brew install jpeg BEFORE PERFORMING PIP INSTALL FROM REQUIREMENTS.TXT ACTION!
ALSO COMMENT OUT THE GPAW LINE IF YOU HAVE INSTALLED PREVIOUSLY USING BREW...
-----------------------------------------------------------------------------
VVIP: ENVIRONMENTAL VARIABLES REQUIRED
(ON THE SERVER, GO ON THE SETTINGS, OR LOCALLY, CREATE A NEW .ENV FILE IN THE ROOT FOLDER)
<< BELOW IS A VERY IMPORTANT STEP TO SUCCESSFULLY RUN ASE AND GPAW LOCALLY (MACOS) >>
1. export C_INCLUDE_PATH=/my/path/to/libxc/5.2.0/include
2. export LIBRARY_PATH=/my/path/to/libxc/5.2.0/lib
3. export LD_LIBRARY_PATH=/my/path/to/libxc/5.2.0/lib
(IN CASE OF MACOS: /opt/homebrew/Cellar/libxc/6.1.0 IS THE PATH FOR LIBXC)
4. GPAW_SETUP_PATH="server/datasets/gpaw-setups-0.9.20000"
5. SECRET_KEY — FOR FLASK
6. AWS_SECRET_ACCESS_KEY, AWS_DEFAULT_REGION="us-east-2", AWS_ACCESS_KEY_ID
How to connect to DigitalOcean VPS console terminal from your local machine:
1. ssh <username>@<IP_ADDRESS>
2. Enter password
<username> can be root, or your own username
Celery Setup Guide:
https://flask.palletsprojects.com/en/2.3.x/patterns/celery/
Both atomic and molecular orbitals are displayed on a three-dimensional plane where you can freely rotate around.
With our playground feature, you can draw any molecules with dots and lines. Auto-snapping allows users to do this in an easiest way possible.
Our robust search feature provides an extraordinary insight into the properties of molecules. Unapologetically — it is the most efficient way of navigating the PubChem database.
 |
 |
 |
 |