NWChem/contrib/mkdocs/mkdocs.yml

site_name: NWChem
site_description: NWChem Website
repo_url: https://github.com/nwchemgit/nwchem-wiki
site_url: https://nwchemgit.github.io
edit_uri_template: 'edit/master/{path}'
theme:
  name: material
  logo: assets/MS3logo.png
  font: false
  icon:
    edit: material/pencil
    view: material/eye
    repo: fontawesome/brands/github
  palette:
#    primary: light blue
#    accent: indigo
#    font: false
    - scheme: default
      toggle:
        icon: material/brightness-7 
        name: Switch to dark mode

    # Palette toggle for dark mode
    - scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
#    - navigation.expand
    - navigation.top
    - navigation.instant
    - navigation.tracking
#    - navigation.tabs
#    - navigation.tabs.sticky
    - navigation.indexes
    - navigation.footer
    - search.highlight
    - search.share
    - content.action.edit
    - content.action.view
    - content.code.copy
extra_css:
  - stylesheets/extra.css
use_directory_urls: false
markdown_extensions:
    - smarty
    - toc:
        permalink: True
    - tables
    - table_captions:
        caption_top: false
        numbering: true
    - caption
    - footnotes:
        SEPARATOR: _footnote_
#    - markdown_katex:
#         no_inline_svg: True
#         insert_fonts_css: True
#         macro-file: macros.tex
    - pymdownx.arithmatex:
        generic: true
#extra_javascript:
#  - 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-MML-AM_CHTML'
    - mdx_math:
        enable_dollar_delimiter: True
    - pymdownx.tilde
    - attr_list
    - md_in_html
extra_javascript:
  - css/mathjax.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js
#  - https://cdnjs.cloudflare.com/ajax/libs/mathjax/3.2.2/MathJax.js?config=TeX-AMS_HTML
nav:
      - 'NWChem Homepage': index.md
      - 'NWChem Manual': Home.md
      - 'How to get NWChem':
          - Download.md
          - Compiling-NWChem.md
      - 'Introduction ':
          - Getting-Started.md
          - NWChem-Architecture.md
      - Capabilities.md
      - Top-level.md
      - Geometry.md
      - Basis.md
      - ECP.md
      - Relativistic-All-electron-Approximations.md
      - Quantum-Mechanical-Methods:
          - Hartree-Fock-Theory-for-Molecules.md
          - Density-Functional-Theory-for-Molecules.md
          - Excited-State-Calculations.md
          - RT-TDDFT.md
          - 'Plane-Wave Density Functional Theory': Plane-Wave-Density-Functional-Theory.md
          - TCE.md
          - MP2.md
          - CCSD.md
          - Multiconfiguration_SCF.md
          - 'Molecular GW': GW.md
      - Quantum Molecular Dynamics:
          - Plane-Wave-Density-Functional-Theory.md
          - Gaussian-Basis-AIMD.md
      - Hybrid Approaches:
          - Solvation-Models.md
          - VEM-Model.md
          - ONIOM.md
          - QMMM:
              - qmmm_introduction.md
              - QMMM table of contents: QMMM.md
              - QMMM Restart and Topology Files:
                  - Overview: QMMM_Restart_and_Topology_Files.md
                  - QMMM_Preparation_Prerequisites.md
                  - Qmmm_preparation_basic.md
                  - Qmmm_preparation_solvation.md
                  - Qmmm_preparation_constraints.md
              - QMMM Input File:
                  - Overview: QMMM_Input_File.md
                  - QMMM_QM_Parameters.md
                  - QMMM_MM_Parameters.md
                  - QMMM_QMMM_Parameters.md
              - QMMMM Single Point Calculations:
                  - QMMM Ground State Energy and Gradient: qmmm_sp_energy.md
                  - QMMM Excited State Energy: QMMM_Excited_States.md
                  - QMMM Properties: qmmm_sp_property.md
                  - QMMM ESP Charge Analysis: QMMM_ESP.md
              - QMMM Potential Energy Surface Analysis:
                  - QMMM Optimization: Qmmm_optimization.md
                  - QMMM Transition States: QMMM_Transition_States.md
                  - QMMM Hessians and Frequency: Qmmm_freq.md
                  - QMMM Reaction Pathway Calculations with NEB: Qmmm_NEB_Calculations.md
              - QMMM_Dynamics.md
              - QMMM_Free_Energy.md
              - QMMM_Appendix.md
          - Bq.md
          - 1D-RISM.md
      - Potential Energy Surface Analysis:
          - Geometry-Optimization.md
          - Hessians-and-Vibrational-Frequencies.md
          - Constraints.md
          - Nudged-Elastic-Band-and-Zero-Temperature-String-Methods.md
      - Electronic Structure Analysis:
          - Properties.md
          - ESP.md
          - DPLOT.md 
      - Other-Capabilities:
          - Electron-Transfer.md
          - Python.md
          - Quantum.md
          - VSCF.md
          - CCCA_method.md
          - Interface.md
      - Molecular Mechanics:
          - Prepare.md
          - MD.md
          - Analysis.md
          - Format_of_MD_Files.md
      - Python.md
      - NWChem Examples:
          - Sample.md
          - Geometry-examples.md
      - Benchmarks.md
      - Known-Bugs.md
      - 'FAQ': FAQ.md
      - 'NWChem Tutorials': Tutorials.md
      - Forum.md
      - 'Archived Forum': Archived-Forum.md
      - 'EMSL Arrows': EMSL_Arrows.md
      - Supplementary Information:
          - Global Arrays: "https://hpc.pnl.gov/globalarrays/"
          - ARMCI.md
      - Interfaces-with-External-Software.md
      - Software-supporting-NWChem.md
      - Containers: Containers.md
      - Documentation in PDF format: "https://nwchemgit.github.io/nwchemusermanual.pdf"
plugins:
  - search
  - alternate-link
  - bibtex:
      bib_file: "docs/refs.bib"
      csl_file: "docs/journal-of-chemical-theory-and-computation.csl"
  - print-site:
      add_to_navigation: false
      print_page_title: 'Print Site'
      add_print_site_banner: false
      # Table of contents
      add_table_of_contents: true 
      toc_title: 'Table of Contents'
      toc_depth: 6
      # Content-related
      add_full_urls: false
      enumerate_headings: true
      enumerate_figures: true
      add_cover_page: true
      cover_page_template: "docs/assets/other_cover_page.tpl"
      path_to_pdf: ""
      include_css: false
      enabled: true
      exclude:
        - Home*
        - Archived-Forum*
        - EMSL*