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Rapid

This repo contains code, data and jupyter notebook related to RAPID.

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Repository contents

The following sections indicate the folders which contain code and related data

Jupyter notebooks

  1. RAPID.ipynb - Notebook containing all visualizations
  2. Visualization and Statistical Analysis.ipynb - Initial analysis notebook
  3. Perovskite learning curve.ipynb - ML code and visualizations notebook

Raw data

All raw data files are located in the data folder

  1. cifs - Contains the Crystallographic Information Files
  2. images - Contains side vial images of each experiment performed
  3. xrd/xy - Contains xy files for XRD data
  4. 0042.perovskitedata_RAPID.csv - Escalate generated data file including 8 experimental features (with "rxn" as header prefix) and 67 chemical features (with "feat" as header prefix). The detailed explanations of these features are listed in "Explanation of Features-Descriptors" section in "Perovskite Dataset Description.pdf". This CSV file is used in visualization and machine learning.
  5. 0042.perovskitedata_RAPID_full.csv - This escalate generated data file contains the same experiments as "0042.perovskitedata_RAPID.csv" but has all 787 features, including additional "raw" features describing experiment details (see "Explanation of Features-Descriptors" section in "Perovskite Dataset Description" for the explanations of "raw" prefix). The csv file is not used for visualization or machine learning.
  6. image_list.json - Keeps track of all image files in the image folder
  7. ml_data.pkl - Python pickle file containing ML results
  8. inventory.csv - Chemical inventory data
  9. organic_inchikey.csv - Inchi keys and chemical names
  10. s_spaces.json - Co-ordinates of state space for each amine

Scripts

The following python scripts are used in the RAPID.ipynb notebook to generate visualizations

  1. plots.py - Generates the reaction outcomes 3D plot widget
  2. xrd_plot.py - Generates the xrd plot widget
  3. ml_section.py - Generates machine learning outcomes widget
  4. cif_plots.py - Generates the cif plot widget. Note that jsmol is used to create the widget