_toc.yml

# Learn more at https://jupyterbook.org/customize/toc.html
format: jb-book
root: index
options:  # The options key will be applied to all chapters, but not sub-sections
  numbered: True
parts:

- caption: Chapters
  chapters:
  - file: schedule
  - file: 1_stats/intro
    sections: 
    - file: 1_stats/Probabilities_Counting
    - file: 1_stats/Random_Variables
    - file: 1_stats/Diffusion
    - file: 1_stats/Entropy
    
  - file: 2_thermo/intro
    sections:
    - file: 2_thermo/01_Thermo
    - file: 2_thermo/02_FreeEnergies

  - file: 3_ensembles/intro
    sections:
    - file: 3_ensembles/nve
    - file: 3_ensembles/nvt
    - file: 3_ensembles/npt
    - file: 3_ensembles/ensemble_overview

  - file: 4_ising/intro
    sections:
    - file: 4_ising/00_MC
    - file: 4_ising/01_MCMC
    - file: 4_ising/02_phase_tranistions
    - file: 4_ising/03_MeanField
    - file: 4_ising/03_vdw
    - file: 4_ising/04_analytic
    - file: 4_ising/05_EnhanceSampl
   
  - file: 5_fluids/intro
    sections:
    - file: 5_fluids/Intro2Fluids
    - file: 5_fluids/mc_lj
    - file: 5_fluids/Intro2MD.ipynb
    - file: 5_fluids/md_lj
    
  - file: 6_kinetics/intro
    sections:
    - file: 6_kinetics/langevin


- caption: Tutorials 
  chapters:

  - file: labs/py-lab/intro
    sections:
    - file: labs/py-lab/intro2py
    - file: labs/py-lab/intro2numpy
    - file: labs/py-lab/intro2viz
    - file: labs/py-lab/python_OOP_challenge

  - file: labs/np-lab/intro
    sections:
    - file: labs/np-lab/np_prob
    - file: labs/np-lab/sinc_function
    - file: labs/np-lab/linear_functions
    - file: labs/np-lab/1d_gas_sim
    - file: labs/np-lab/2d_gas_sim
    
  - file: labs/rw-lab/intro
    sections:
    - file: labs/rw-lab/rw_lab
    - file: labs/rw-lab/InverseTransform
    - file: labs/rw-lab/change_rv_jax
    - file: labs/rw-lab/polymer-conf
    - file: labs/rw-lab/langevin

  - file: labs/lab4/intro
    sections:
    - file: labs/lab4/nvt_application
    - file: labs/lab4/TwoState
    - file: labs/lab4/mass_action

  - file: labs/lab5/intro
    sections:
    - file: labs/lab5/torch_ising
    - file: labs/lab5/Wolf
    - file: labs/lab5/enhance-sampling

  - file: labs/lab6/intro
    sections:
    - file: labs/lab6/openmm_double_well
    - file: labs/lab6/openmm_lj_chain
    - file: labs/lab6/openmm_ethane
    - file: labs/lab6/openmm_villin