mkdocs-guide.yml

INHERIT: mkdocs-base.yml

# Platform Guide — tutorials, software directory, and CLI reference.
# Deploy to: docs.mat3ra.com/guide/

docs_dir: !!python/object/apply:os.getenv ["DOCS_DIR", "lang/en/docs"]

# Exclude pages that belong to other sites.
exclude_docs: |
  # Concepts/Reference top-level dirs
  benchmarks/
  data/
  data-structured/
  methods/
  methods-directory/
  models/
  models-directory/
  properties-directory/
  security/
  site-policy/
  software/
  software-directory/

  # Resources site top-level dirs
  data-on-disk/
  infrastructure/

  # Developers site top-level dirs
  rest-api/

  other/terms-of-service.md

  # Interface site top-level dirs
  jobs-designer/
  materials-designer/
  ui/
  workflow-designer/

  # CLI site top-level dirs
  /cli/
  /jobs-cli/
  /jupyterlite/
  /remote-connection/

  # Home site sections (linked from homepage)
  getting-started/
  pricing/
  /other/

  # Concepts-only pages in shared dirs
  accounts/overview.md
  accounts/users.md
  accounts/balance.md
  accounts/payments-charges.md
  accounts/quota.md
  accounts/service-levels.md
  accounts/collections.md
  collaboration/organizations/
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  entities-general/data.md
  entities-general/sets.md
  entities-general/bank.md
  entities-general/permissions.md
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  properties/lifecycle/
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  workflows/components/
  workflows/data/
  workflows/templating/
  other/publications.md
  other/documentation.md
  other/citation.md

  # Interface site pages in shared dirs
  accounts/accounting/
  accounts/ui/
  collaboration/actions/
  collaboration/sharing/
  collaboration/ui/
  entities-general/actions/
  entities-general/ui/
  jobs/actions/
  jobs/ui/
  materials/actions/
  materials/ui/
  properties/ui/
  workflows/actions/
  workflows/ui/
  data-in-objectstorage/

  # Dev-only pages in shared dirs
  data-in-objectstorage/overview.md
  data-in-objectstorage/files.md
  data-in-objectstorage/security.md
  data-in-objectstorage/dropbox.md

  # Other sites' homepages
  index.md
  index-concepts.md
  index-dev.md
  index-resources.md
  index-developers.md
  index-standards.md
  index-interface.md
  index-cli.md

  # Data Standards site pages
  software-directory/modeling/vasp/data.md
  software-directory/modeling/quantum-espresso/data.md
  software-directory/scripting/python/data.md
  software-directory/scripting/shell/data.md
  software-directory/scripting/jupyter-lab/data.md
  software-directory/machine-learning/python-ml/data.md
  models/data.md
  methods/data.md
  software/data.md
  models-directory/dft/data.md
  models-directory/machine-learning/data.md
  methods-directory/pseudopotential/data.md
  methods-directory/linear-regression/data.md
  materials/data.md
  jobs/data.md

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site_name: "Tutorials"
site_url: https://docs.mat3ra.com/guide
site_description: "Step-by-step tutorials for DFT, ML, materials construction, and simulation workflows."
dev_addr: "localhost:8001"

theme:
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extra:
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    guide_url: https://docs.mat3ra.com/guide
    interface_url: https://docs.mat3ra.com/interface
    reference_url: https://docs.mat3ra.com/reference
    resources_url: https://docs.mat3ra.com/resources
    developers_url: https://docs.mat3ra.com/developers
    cli_url: https://docs.mat3ra.com/command-line
    data_url: https://docs.mat3ra.com/standards




nav:
    - "← All Docs":                                      /
    - Home:                                              /guide/

# 1. Materials Design
    - 1. Materials Design:
        - 1.1. General:
            - Import from Files:                                                tutorials/materials/import-from-files.md
            - Combinatorial Sets:                                               tutorials/materials/combinatorial-screening.md
            - Interpolated Sets:                                                tutorials/materials/interpolated-sets.md
            - Molecule on a Surface:                                            tutorials/materials/molecule-surface.md
            - Interface, quick setup (3D Editor):                               tutorials/materials/slabs-interface.md
            - Interface, minimal strain (JupyterLite):                          tutorials/materials/jupyterlite-zsl.md
            - VESTA via Remote Desktop:                                         tutorials/materials/vesta-remote-desktop.md
        - 1.2. Reproducing Published Structures:
            - Overview:                                                         tutorials/materials/specific/overview.md
            - Substitutional Defects in Graphene:                               tutorials/materials/specific/defect-point-substitution-graphene.md
            - Substitutional Defects in Graphene (Band Structure):              tutorials/materials/specific/defect-point-substitution-graphene-simulation.md
            - Vacancy-Substitution Pair in GaN:                                 tutorials/materials/specific/defect-point-pair-gallium-nitride.md
            - Vacancy Defect in h-BN:                                           tutorials/materials/specific/defect-point-vacancy-boron-nitride.md
            - Interstitial Defect in SnO:                                       tutorials/materials/specific/defect-point-interstitial-tin-oxide.md
            - Island Surface Defect in TiN:                                     tutorials/materials/specific/defect-surface-island-titanium-nitride.md
            - Step Surface Defect on Pt(111):                                   tutorials/materials/specific/defect-surface-step-platinum.md
            - Twisted Bilayer h-BN Nanoribbons:                                 tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md
            - Twisted Bilayer MoS2:                                             tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md
            - Adatom Surface Defects on Graphene:                               tutorials/materials/specific/defect-surface-adatom-graphene.md
            - H-Passivated Silicon Nanowire:                                    tutorials/materials/specific/passivation-edge-nanowire-silicon.md
            - H-Passivated Silicon (100) Surface:                               tutorials/materials/specific/passivation-surface-silicon.md
            - Gold Nanoclusters:                                                tutorials/materials/specific/nanocluster-gold.md
            - SrTiO3 Slab:                                                      tutorials/materials/specific/slab-strontium-titanate.md
            - Graphene / h-BN Interface:                                        tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md
            - Cu / SiO2 Interface:                                              tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md
            - Graphene / SiO2 Interface:                                        tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md
            - High-k Metal Gate Stack:                                          tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md
            - Ripple Perturbation in Graphene:                                  tutorials/materials/specific/perturbation-ripples-graphene.md
            - Grain Boundary in Cu (FCC):                                       tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md
            - Grain Boundary (2D) in h-BN:                                      tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md
            - Gr/Ni(111) Interface Optimization:                                tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md
            - Pt Adatoms Island on MoS2:                                        tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md

# 2. Simulations
    - 2. Simulations:
        - 2.1. Density Functional Theory:
            - Electronic Properties:
                - Band Structure:                          tutorials/dft/electronic/band-structure.md
                - Band Structure, HSE (QE):                tutorials/dft/electronic/hse-qe-bs.md
                - Band Structure, HSE (VASP):              tutorials/dft/electronic/hse-vasp-bg.md
                - Band Structure, GW Full Freq. (QE):      tutorials/dft/electronic/gw-qe-bs-fullfreq.md
                - Band Structure, GW Plasmon P. (QE):      tutorials/dft/electronic/gw-qe-bs-plasmon.md
                - Band Gap:                                tutorials/dft/electronic/band-gap.md
                - Band Gap, HSE (QE):                      tutorials/dft/electronic/hse-qe-bg.md
                - Band Gap, GW (VASP):                     tutorials/dft/electronic/gw-vasp-bg.md
                - Density of States:                       tutorials/dft/electronic/density-of-states.md
                - Density Mesh:                            tutorials/dft/electronic/electronic-density-mesh.md
                - Fermi Surface:                           tutorials/dft/electronic/fermi-surface.md
                - Valence Band Offset:                     tutorials/dft/electronic/valence-band-offset.md
                - Effective Screening Medium:              tutorials/dft/electronic/esm-qe.md
                - Hubbard U (QE):                          tutorials/dft/electronic/hubbard.md
                - Magnetic Properties (QE):                tutorials/dft/electronic/spin-magnetic-qe.md
                - Spin-Orbit Coupling (QE):                tutorials/dft/electronic/spin-orbit-coupling-qe.md
            - Optical Properties:
                - Dielectric Constant (QE):                tutorials/dft/optical/epsilon-optimal-basis.md
            - Vibrational Properties:
                - Zero Point Energy:                       tutorials/dft/vibrational/zero-point-energy.md
                - Phonons:                                 tutorials/dft/vibrational/phonon-dispersion-dos.md
                - Phonons on a Grid:                       tutorials/dft/vibrational/phonons-grid.md
            - Thermodynamic Properties:
                - Surface Energy:                          tutorials/dft/thermodynamic/surface-energy.md
            - Chemical Properties:
                - Reaction Energy Profile (QE):            tutorials/dft/chemical/reaction-profile-qe.md
                - Reaction Energy Profile (VASP):          tutorials/dft/chemical/reaction-profile-vasp.md
            - Workflow Add-ons:
                - k-point Convergence:                     tutorials/dft/addons/kpt-convergence.md
                - Structural Relaxation:                   tutorials/dft/addons/structural-relaxation.md
        - 2.2. Machine Learning:
            - Train a NN Potential (QE, DeePMD, LAMMPS):   tutorials/ml/deepmd-mlff-with-espresso-cp-and-lammps.md
            - Python MLFF (MatterSim/GPU):                 tutorials/ml/run-mlff-python-workflows-mattersim.md

# 3. Other
    - 3. Other:
        - 3.1. Command-Line Jobs:
            - Create + Run a CLI Job:                      tutorials/jobs-cli/job-cli-example.md
            - Import a CLI Job to Web Interface:           tutorials/jobs-cli/cli-job-import.md
            - QE GPU Job:                                  tutorials/jobs-cli/qe-gpu.md
        - 3.2. Templating:
            - Flags by Elemental Composition:              tutorials/templating/set-flag-by-composition.md
            - Magnetic Moment on Atoms by Specie:          tutorials/templating/set-magnetic-moment.md
        - 3.3. Tools and Environments:
            - Accessing the Platform:                      tutorials/platform-access.md
            - Jupyter Notebook:                            tutorials/other/jupyter.md
            - Restart from Previous Job:                   tutorials/other/restart-job.md
            - TensorFlow (GPU):                            tutorials/general-functionality/tensorflow-gpu.md
            - Add New Software:                            /command-line/cli/actions/add-software/