mkdocs-concepts.yml

INHERIT: mkdocs-base.yml

# Concepts & Reference — encyclopedic documentation of platform abstractions.
# Covers entities, models, methods, software, and properties.
# Deploy to: docs.mat3ra.com/reference/

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

# Exclude pages that belong to other sites (Guide or Dev).
# Cross-site links use absolute URLs instead.
exclude_docs: |
  # Guide-only top-level dirs
  cli/
  data-in-objectstorage/
  getting-started/
  /jobs-cli/
  jobs-designer/
  jupyterlite/
  materials-designer/
  pricing/
  remote-connection/
  tutorials/
  ui/
  workflow-designer/
  migrating-to-new-platform.md

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

  # Developers site top-level dirs
  rest-api/

  # Guide-only pages in shared dirs
  accounts/accounting/
  accounts/ui/
  collaboration/actions/
  collaboration/sharing/actions.md
  collaboration/sharing/ui.md
  collaboration/ui/
  entities-general/actions/
  entities-general/ui/
  jobs/actions/
  jobs/ui/
  materials/actions/
  materials/ui/
  properties/ui/
  workflows/actions/
  workflows/ui/
  other/support.md
  other/community-programs.md
  other/registration.md
  other/faq.md

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

  # Data Standards site pages
  data/
  data-structured/
  properties/data/
  workflows/data/
  entities-general/data.md
  materials/data.md
  jobs/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

validation:
  nav:
    omitted_files: info
    not_found: warn
  links:
    absolute_links: info

site_name: "Concepts & Reference"
site_url: https://docs.mat3ra.com/reference
site_description: "Explanatory reference for Mat3ra platform concepts, data models, and scientific methods."
dev_addr: "localhost:8002"

extra:
    # Cross-site URL variables (resolved by macros plugin at build time)
    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:                                              index-concepts.md

# ENTITIES — Concepts
    - Entities & Common Aspects:
        - Overview:                                     entities-general/overview.md
        - Lifecycle:                                    entities-general/lifecycle.md
        - Ownership:                                    entities-general/ownership.md
        - Permissions:                                  entities-general/permissions.md
        - Sets:                                         entities-general/sets.md
        - Bank:                                         entities-general/bank.md
        - Default:                                      entities-general/default.md

# ACCOUNTS — Concepts
    - Accounts:
        - Overview:                                      accounts/overview.md
        - Users:                                         accounts/users.md
        - Balance:                                       accounts/balance.md
        - Service Levels:                                accounts/service-levels.md
        - Quota:                                         accounts/quota.md
        - Payments and Charges:                          accounts/payments-charges.md
        - Collections:                                   accounts/collections.md

# COLLABORATION — Concepts
    - Collaboration:
        - Organizations:
            - Overview:                                  collaboration/organizations/overview.md
            - Roles:                                     collaboration/organizations/roles.md
            - Teams:                                     collaboration/organizations/teams.md
        - Entity Sharing:
            - Account Access Levels:                     collaboration/sharing/access-levels.md

# MATERIALS — Concepts
    - Materials:
        - Overview:                                     materials/overview.md
        - Bank:                                         materials/bank.md
        - Default:                                      materials/default.md
        - Classification:
            - Crystalline:                              materials/classification/crystalline.md
            - Non-Periodic:                             materials/classification/non-periodic.md

# WORKFLOWS — Concepts
    - Workflows:
        - Overview:                                     workflows/overview.md
        - Bank:                                         workflows/bank.md
        - Default:                                      workflows/default.md
        - Components:
            - Overview:                                 workflows/components/overview.md
            - Subworkflows:                             workflows/components/subworkflows.md
            - Units:                                    workflows/components/units.md
            - Maps:                                     workflows/components/maps.md

        - Templating:
            - Overview:                                 workflows/templating/overview.md
            - Concept:                                  workflows/templating/concept.md
            - Jinja:                                    workflows/templating/jinja.md
            - Swig:                                     workflows/templating/swig.md
            - Exabyte Convention:                       workflows/templating/exabyte-convention.md
            - Examples:                                 workflows/templating/examples.md
            - UI Implementation:                        workflows/templating/ui.md
        - Add-ons:
            - Overview:                                 workflows/addons/overview.md
            - Convergence:                              workflows/addons/convergence-algorithms.md
            - Structural Relaxation:                    workflows/addons/structural-relaxation.md

# JOBS — Concepts
    - Jobs:
        - Overview:                                     jobs/overview.md
        - Projects:                                     jobs/projects.md
        - Status:                                       jobs/status.md

# MODELS
    - Models:
        - Overview:                                     models/overview.md
        - Accuracy:                                     models/accuracy.md
        - Parameters:                                   models/parameters.md
        - Auxiliary Concepts:
            - Nudged Elastic Band:                       models/auxiliary-concepts/nudged-elastic-band.md
            - Effective Screening Medium:                models/auxiliary-concepts/esm.md
            - Reciprocal space:                          models/auxiliary-concepts/reciprocal-space.md
            - Reciprocal space > sampling:               models/auxiliary-concepts/reciprocal-space/sampling.md
            - Reciprocal space > paths:                  models/auxiliary-concepts/reciprocal-space/paths.md
            - Reciprocal space > convergence:            models/auxiliary-concepts/reciprocal-space/convergence.md
            - Reciprocal space > electronic occupations: models/auxiliary-concepts/reciprocal-space/electronic-occupations.md

    - Models Directory:
        - Overview:                                     models-directory/overview.md
        - Density Functional Theory:
            - Overview:                                 models-directory/dft/overview.md
            - Parameters:                               models-directory/dft/parameters.md
            - Accuracy:                                 models-directory/dft/accuracy.md
            - Special Notes:                            models-directory/dft/notes.md
            - References:                               models-directory/dft/references.md
        - Machine Learning:
            - Overview:                                 models-directory/machine-learning/overview.md
            - Parameters:                               models-directory/machine-learning/parameters.md
            - Units:                                    models-directory/machine-learning/units.md
            - Example Workflow:                         models-directory/machine-learning/example-workflow.md
            - Accuracy:                                 models-directory/machine-learning/accuracy.md

# METHODS
    - Methods:
        - Overview:                                     methods/overview.md
        - Parameters:                                   methods/parameters.md
        - Precision:                                    methods/precision.md
        - Auxiliary Concepts:
            - Optimization Algorithms:                  methods/auxiliary-concepts/optimization-algorithms.md

    - Methods Directory:
        - Overview:                                     methods-directory/overview.md
        - Plane-waves and Pseudopotentials:
            - Overview:                                 methods-directory/pseudopotential/overview.md
            - Default:                                  methods-directory/pseudopotential/default.md
            - Parameters:                               methods-directory/pseudopotential/parameters.md
            - Precision:                                methods-directory/pseudopotential/precision.md
            - Important Settings:                       methods-directory/pseudopotential/important-settings.md
            - Actions:                                  methods-directory/pseudopotential/actions.md
        - Linear Regression:
            - Overview:                                 methods-directory/linear-regression/overview.md
            - Parameters:                               methods-directory/linear-regression/parameters.md

# SOFTWARE
    - Software:
        - Overview:                                     software/overview.md
        - Components:                                   software/components.md
        - Classification:
            - Overview:                                 software/classification/overview.md
            - Analysis:                                 software/classification/analysis.md
            - Development:                              software/classification/development.md
            - Machine Learning:                         software/classification/machine-learning.md
            - Modeling:                                 software/classification/modeling.md
            - Scripting:                                software/classification/scripting.md

# PROPERTIES
    - Properties:
        - Overview:                                     properties/overview.md
        - Lifecycle:
            - Overview:                                 properties/lifecycle/overview.md
            - Extractors:                               properties/lifecycle/extractor.md
            - Refinement:                               properties/lifecycle/refinement.md
            - Retrieval:                                properties/lifecycle/retrieval.md

        - Classification:
            - Overview:                                 properties/classification/overview.md
            - General:                                  properties/classification/general.md
            - Machine Learning:                         properties/classification/machine-learning.md
            - Materials:                                properties/classification/materials.md

    - Properties Directory:
        - Overview:                                     properties-directory/overview.md
        - Scalar:
            - Total Energy:                             properties-directory/scalar/total-energy.md
            - Fermi Energy:                             properties-directory/scalar/fermi-energy.md
            - Surface Energy:                           properties-directory/scalar/surface-energy.md
            - Zero Point Energy:                        properties-directory/scalar/zero-point-energy.md
            - Pressure:                                 properties-directory/scalar/pressure.md
            - Total Force:                              properties-directory/scalar/total-force.md
            - Reaction Energy Barrier:                  properties-directory/scalar/reaction-energy-barrier.md
            - Valence Band Offset:                      properties-directory/scalar/valence-band-offset.md
        - Non-scalar:
            - Stress Tensor:                            properties-directory/non-scalar/stress-tensor.md
            - Band Structure:                           properties-directory/non-scalar/bandstructure.md
            - Electronic Density of States:             properties-directory/non-scalar/electronic-dos.md
            - Band Gaps:                                properties-directory/non-scalar/band-gaps.md
            - Phonon Dispersions:                       properties-directory/non-scalar/phonon-dispersions.md
            - Phonon Density of States:                 properties-directory/non-scalar/phonon-dos.md
            - Reaction Energy Profile:                  properties-directory/non-scalar/reaction-energy-profile.md
            - File Content:                             properties-directory/non-scalar/file-content.md
            - Workflow:                                 properties-directory/non-scalar/workflow.md
        - Elemental:
            - Atomic Radius:                            properties-directory/elemental/atomic-radius.md
            - Electronegativity:                        properties-directory/elemental/electronegativity.md
            - Ionization Potential:                     properties-directory/elemental/ionization-potential.md
        - Structural:
            - Basis:                                    properties-directory/structural/basis.md
            - Atomic Forces:                            properties-directory/structural/atomic-forces.md
            - Lattice:                                  properties-directory/structural/lattice.md
            - Symmetry:                                 properties-directory/structural/symmetry.md
            - Final Structure:                          properties-directory/structural/final-structure.md
            - Magnetic Moment:                          properties-directory/structural/magnetic-moment.md
            - Inchi:                                    properties-directory/structural/inchi.md
            - Inchi Key:                                properties-directory/structural/inchi-key.md


# SOFTWARE DIRECTORY
    - Software Directory:
        - Overview:                                     software-directory/overview.md
        - Modeling:
            - Quantum ESPRESSO:
                - Overview:                             software-directory/modeling/quantum-espresso/overview.md
                - Components:                           software-directory/modeling/quantum-espresso/components.md
                - Compute Parameters:                   software-directory/modeling/quantum-espresso/compute-parameters.md
            - VASP:
                - Overview:                             software-directory/modeling/vasp/overview.md
                - Components:                           software-directory/modeling/vasp/components.md
                - Compute Parameters:                   software-directory/modeling/vasp/compute-parameters.md
            - TurboMole:                                software-directory/modeling/turbomole.md
            - LAMMPS:                                   software-directory/modeling/lammps.md
            - NWChem:                                   software-directory/modeling/nwchem.md
            - CP2K:                                     software-directory/modeling/cp2k.md
            - Gromacs:                                  software-directory/modeling/gromacs.md
            - WIEN2k:                                   software-directory/modeling/wien2k.md
        - Scripting:
            - Shell:
                - Overview:                             software-directory/scripting/shell/overview.md
            - Python:
                - Overview:                             software-directory/scripting/python/overview.md
            - Jupyter Lab:
                - Overview:                             software-directory/scripting/jupyter-lab/overview.md
        - Machine Learning (ML):
            - TensorFlow:                               software-directory/machine-learning/tensorflow.md
            - Python ML:
                - Overview:                             software-directory/machine-learning/python-ml/overview.md
                - Components:                           software-directory/machine-learning/python-ml/components.md
                - Workflow Structure:                   software-directory/machine-learning/python-ml/workflow-structure.md
        - Analysis & Visualization:
            - VESTA:                                    software-directory/analysis/vesta.md
            - XCRYSDEN:                                 software-directory/analysis/xcrysden.md
            - P4VASP:                                   software-directory/analysis/p4vasp.md
            - VMD:                                      software-directory/analysis/vmd.md
        - Development Tools:
            - Compilers:                                software-directory/development/compilers.md
            - Libraries:                                software-directory/development/libraries.md
            - Text Editors:                             software-directory/development/text-editors.md

# SECURITY
    - Security:
        - Current State of Cloud Security:               security/current-state.md
        - Overview:                                      security/overview.md
        - Security Policies:                             security/security-policies.md
        - Threats Analysis:                              security/threats-analysis.md

# BENCHMARKS
    - Benchmarks:
        - Overview:                      benchmarks/overview.md
        - High Throughput Screening:     benchmarks/high-throughput-screening.md
        - Distributed Memory Runs:       benchmarks/distributed-memory.md
        - Vendor Comparison:             benchmarks/vendor-comparison.md
        - High-Performance Linpack:      benchmarks/hpl-benchmark.md
        - 2018-11 HPL VASP GROMACS:      benchmarks/2018-11-12-comparison.md

# LEGAL
    - Site Policy:
        - Privacy:                                      site-policy/privacy-statement.md
        - Sharing:                                      site-policy/sharing-policy.md
        - Terms of Service:                             site-policy/terms-of-service.md

# OTHER
    - Other:
        - Publications:                                 other/publications.md
        - Terms of Service:                             other/terms-of-service.md
        - Restricted Content:                           other/restricted.md