_toc.yml

format: jb-book
root: notebook/README.md

parts:
  # - caption: Introduction to MD
  #   chapters:
  #   - file: notebook/0_1_dft_intro.ipynb

  # - caption: MD from scratch
  #   chapters:
  #     - file: notebook/1_1_md_from_scratch/1_overview.md
  #     - file: notebook/1_1_md_from_scratch/1_scratch_LJ.ipynb

  # - caption: Enhanced Sampling
  #   chapters:
  #   - file: notebook/1_2_md_enhanced_sampling/1_free_energy_overview.ipynb
  #   - file: notebook/1_2_md_enhanced_sampling/2_enhanced_sampling.ipynb
  #   - file: notebook/1_2_md_enhanced_sampling/3_mlcvs_overview.ipynb
  #     sections:
  #     - file: notebook/1_2_md_enhanced_sampling/mlcvs/1_2d_model_discriminant.ipynb
  #     - file: notebook/1_2_md_enhanced_sampling/mlcvs/2_Deep_LDA_Alanine_dipeptide.ipynb




  - caption: Data Analysis with Python
    chapters:
      - file: notebook/1_data_analysis/README.md



  - caption: Code snippets
    chapters:
      - file: notebook/2_code_tips/README.md
      - file: notebook/2_code_tips/1_jupyter_notebook.ipynb
      - file: notebook/2_code_tips/2_Matplotlib.ipynb
      - file: notebook/2_code_tips/3_Ovito.ipynb
      - file: notebook/2_code_tips/4_Pandas.ipynb
      - file: notebook/2_code_tips/5_Regular_Expressions.ipynb
      - file: notebook/2_code_tips/0_colab_github.ipynb
      - file: https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab07_MDsims.ipynb


  - caption: Python
    chapters:
      - file: notebook/3_learnPy/0_intro.ipynb
      - file: notebook/3_learnPy/1_unittest.ipynb
      - file: notebook/3_learnPy/2_multiprocessing.ipynb




  - caption: C++
    chapters:
      - file: notebook/4_learnCpp/0_setup_devCpp.ipynb
      - file: notebook/4_learnCpp/1_pointers.ipynb
      - file: notebook/4_learnCpp/2_oop1_intro.ipynb
      - file: notebook/4_learnCpp/3_oop2_constructor.ipynb
      - file: notebook/4_learnCpp/4_oop3_inheritance.ipynb
      - file: notebook/4_learnCpp/5_oop4_polymorphism.ipynb
      - file: notebook/4_learnCpp/6_oop5_h_cpp_file.ipynb

  - caption: Webapp
    chapters:
      - file: notebook/5_webapp/0_overview.ipynb
      - file: notebook/5_webapp/1_chatGPT.ipynb