shuod / scripts_for_academic_projects

Scripts made for academic projects during my doctorate study in condensed matter physics, MS in biophysics

scripts_for_projects

Codes(shell, python, matlab, labview, etc ) made for my projects.

license

The codes in this folder adopt MIT license. For details, check website: https://opensource.org/licenses/MIT

The documents in this folder adopt Creative Common 4.0 with : BY-NC-ND

BY-NC-ND – [Attribution-NonCommercial-NoDerivatives]

For details, check website: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode

1_benchmarking_DFT_functionals

Varies scripts on benchmark DFT/TD-DFT functionals and machine learning algorithm:

scripts:

• (python) data extraction from Gaussian09 result files (HOMO/Bandgap)

• (python) linear regression on data points

• (python) random forest on data points

2_bio-inspired_melanin_design_for_photovoltaic

Varies scripts on calculating electronic properties of virtual molecules.

scripts:

• (python) data extraction from Gaussian09 result files (HOMO/Bandgap)
• (python) plot heatmap
• (python) plot Scharber model

3_top1000_molecule_screening_for_tandem_solar_cells

Varies scripts on calculating spectra on top1000 molecules in the Harvard Clean Energy Project.

Scripts:

• (python) data scraping from website (with login/ cookies)
• (python) data extraction, conversion and initial optimizations
• (Bash shell) files name extraction and submission to high performance computing
• (Bash shell) PostgreSQL Database manipulation (Jobs: Gaussian calculating, Octopus GS calculating, Octopus TD calculating, spectra calculating, finished, result harvested )
• (python) plot spectrum figures

4 spectra_database

• A database contains our results from the "project 3: top1000_molecule_screening_for_tandem_solar_cells";
• implemented using Linux+Nginx+MySQL+PHP;
• results show our recommendations on which material to choose in order to build a better tandem solar cell;
• It is online at http://3.84.114.73

5 Helix melanin

• (python) scripts on electrostatic interaction visualization