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mkdocs.yml
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mkdocs.yml
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# get docs dir from the environment. Defaults to lang/en/docs.
docs_dir: !!python/object/apply:os.getenv ["DOCS_DIR", "lang/en/docs"]
site_name: Mat3ra Documentation
site_url: https://docs.mat3ra.com
site_description: Documentation for the users of Mat3ra materials modeling platform.
dev_addr: "localhost:8000"
repo_name: 'exabyte-io/documentation'
repo_url: 'https://github.com/exabyte-io/documentation'
edit_uri: 'edit/master/lang/en/docs/'
extra_css:
- https://cdnjs.cloudflare.com/ajax/libs/material-design-iconic-font/2.2.0/css/material-design-iconic-font.min.css
- extra/css/general.css
- extra/css/tables.css
- extra/css/images.css
- extra/css/super-fences.css
- extra/css/properties.css
extra_javascript:
- extra/js/giffer.js
- 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/MathJax.js?config=TeX-MML-AM_CHTML'
- extra/js/ga.js
- 'https://www.googletagmanager.com/gtag/js?id=UA-69270713-5'
- extra/js/url_parameters.js
copyright: <a target="_blank" href="https://mat3ra.com">Exabyte Inc</a>. All rights reserved. | <a target="_blank" href="https://platform.mat3ra.com">Back to platform</a>
extra:
version: "2024.3.14"
preload_javascript:
- /extra/js/preload_hotjar.js
- /extra/js/preload.js
social:
- type: github
link: https://github.com/exabyte-io
- type: linkedin
link: https://www.linkedin.com/company/mat3ra/
# Doesn't work with our version. It works from version 7.1.8
# analytics:
# provider: google
# property: UA-69270713-5
markdown_extensions:
- markdown_include.include:
base_path: data
- admonition
- codehilite:
linenums: true
- def_list
# https://squidfunk.github.io/mkdocs-material/extensions/footnotes
- footnotes:
PLACE_MARKER: "///FOOTNOTES GO HERE///"
- toc:
permalink: true
- markdown.extensions.def_list
# https://facelessuser.github.io/pymdown-extensions/
- pymdownx.arithmatex # Render Latex Formulas
- pymdownx.details # Allow admonition-type collapsible <details>
- pymdownx.superfences # Allow for code blocks "fencing"
# https://python-markdown.github.io/extensions/extra/#markdown-inside-html-blocks
- pymdownx.extrarawhtml # Enables parsing of markdown inside html tags
- pymdownx.betterem # Better bold/italic text
- pymdownx.striphtml # Strip html comments before processing
- attr_list
# https://github.com/facelessuser/pymdown-extensions/blob/master/mkdocs.yml
# https://squidfunk.github.io/mkdocs-material/extensions/codehilite/
theme:
name: material
custom_dir: theme
palette:
primary: indigo
accent: indigo
logo: "images/logo/logo-white.png"
favicon: "images/logo/favicon.ico"
font:
text: Roboto
code: Roboto Mono
feature:
tabs: false
nav:
- Home: index.md
# INTRODUCTION
- Getting Started:
- Content highlights: getting-started/content-highlights.md
- Important Concepts: getting-started/important-concepts.md
- Terminology: getting-started/terminology.md
- Useful Links: getting-started/useful-links.md
- Frequestly Asked Questions: other/faq.md
- Run first simulation:
- Web Interface: getting-started/run-first-simulation/web-interface.md
- Command Line: getting-started/run-first-simulation/cli-job.md
# IMPORTANT TO CONVERT NEW USERS
- Pricing:
- Service Levels: pricing/service-levels.md
- Storage Pricing: pricing/storage-quota.md
- 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
- Privacy: site-policy/privacy-statement.md
# TUTORIALS
- Tutorials:
- Overview: tutorials/overview.md
- Jobs via Command Line:
- Overview: tutorials/jobs-cli/overview.md
- 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
- Templating:
- Overview: tutorials/templating/overview.md
- Flags by Elemental Composition: tutorials/templating/set-flag-by-composition.md
- Magnetic Moment on Atoms by Specie: tutorials/templating/set-magnetic-moment.md
- Machine Learning (ML):
# Differentiate between Legacy and PythonML tutorials in Overview
- Overview: tutorials/ml/overview.md
- ExabyteML (legacy):
- Train ML Model: tutorials/ml/train-ml-model.md
- Predict New Properties: tutorials/ml/predict-ml-properties.md
- Python ML:
- Training a Regression Model: tutorials/python-ml/train-regression-model.md
#Todo: Tutorial demonstrates how to share a trained model with another user
#- Sharing Trained Models: tutorials/python-ml/share-ml-model.md
- Predictions with Regression: tutorials/python-ml/predict-with-regression.md
- Unsupervised Learning with Clustering: tutorials/python-ml/train-clustering-model.md
- Training a Classifier: tutorials/python-ml/train-classification-model.md
- Predicting with a Classifier: tutorials/python-ml/predict-with-classification.md
- DeePMD (molecular dynamics): tutorials/ml/deepmd-mlff-with-espresso-cp-and-lammps.md
- Density Functional Theory:
- Electronic Properties:
- Overview: tutorials/dft/electronic/overview.md
- Effective Screening Medium: tutorials/dft/electronic/esm-qe.md
- Electronic band structure: tutorials/dft/electronic/band-structure.md
- Electronic band structure, HSE (QE): tutorials/dft/electronic/hse-qe-bs.md
- Electronic band structure, HSE (VASP): tutorials/dft/electronic/hse-vasp-bg.md
- Electronic band structure, GW, Full Freq., (QE): tutorials/dft/electronic/gw-qe-bs-fullfreq.md
- Electronic band structure, GW, Plasmon P., (QE): tutorials/dft/electronic/gw-qe-bs-plasmon.md
- Electronic band gap: tutorials/dft/electronic/band-gap.md
- Electronic band gap, HSE (QE): tutorials/dft/electronic/hse-qe-bg.md
- Electronic band gap, GW (VASP): tutorials/dft/electronic/gw-vasp-bg.md
- Electronic density of states: tutorials/dft/electronic/density-of-states.md
- Electronic 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
- Hubbard U (QE): tutorials/dft/electronic/hubbard.md
- Spin-magnetic (QE): tutorials/dft/electronic/spin-magnetic-qe.md
- Optical Properties:
- Dielectric constant (QE, simple.x): tutorials/dft/optical/epsilon-optimal-basis.md
- Vibrational Prop.:
- Overview: tutorials/dft/vibrational/overview.md
- Zero Point Energy: tutorials/dft/vibrational/zero-point-energy.md
- Phonons: tutorials/dft/vibrational/phonon-dispersion-dos.md
- Phonons on Grid: tutorials/dft/vibrational/phonons-grid.md
- Thermodynamic Prop.:
- Surface Energy: tutorials/dft/thermodynamic/surface-energy.md
- Chemical Prop.:
- Reaction Energy Profile (QE): tutorials/dft/chemical/reaction-profile-qe.md
- Reaction Energy Profile (VASP): tutorials/dft/chemical/reaction-profile-vasp.md
- Add-ons:
- k-point convergence: tutorials/dft/addons/kpt-convergence.md
- Structural Relaxation: tutorials/dft/addons/structural-relaxation.md
- General Functionality:
- Jupyter Notebook: tutorials/other/jupyter.md
- Restart from Previous Job: tutorials/other/restart-job.md
- Upload External Job Data: tutorials/other/external-upload.md
- TensorFlow (GPU): tutorials/general-functionality/tensorflow-gpu.md
- Materials:
- Overview: tutorials/materials/overview.md
- VESTA via Remote Desktop: tutorials/materials/vesta-remote-desktop.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, no strain minimization (Python Transformation): tutorials/materials/interface-with-python.md
- Interface, minimal strain (JupyterLite Session): tutorials/materials/jupyterlite-zsl.md
- Import materials from files in various formats: tutorials/materials/import-from-files.md
# COMMON UI COMPONENTS
- Interface Components:
- Overview: ui/overview.md
- Header and Footer: ui/header-footer.md
- Left-hand Sidebar: ui/left-sidebar.md
- Right-hand Sidebar: ui/right-sidebar.md
- Support: ui/support.md
- Specific:
- Homepage Navigation: ui/specific/homepage.md
- Dashboard: ui/specific/dashboard.md
- Tabs Navigation: ui/specific/tabs-navigator.md
# ACCOUNTS
- 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
- User Interface:
- Overview: accounts/ui/overview.md
- Profile Page: accounts/ui/profile-page.md
- Account Badge: accounts/ui/account-badge.md
- Switcher: accounts/ui/switcher.md
- Explorer: accounts/ui/explorer.md
- Bio: accounts/ui/bio.md
- Service Levels: accounts/ui/service-level.md
- Payments and Charges: accounts/ui/charges-payments.md
- Preferences: accounts/ui/preferences-overview.md
- Preferences > Profile: accounts/ui/preferences/profile.md
- Preferences > User Settings: accounts/ui/preferences/settings.md
- Preferences > API Tokens: accounts/ui/preferences/api.md
- Preferences > SSH Keys: accounts/ui/preferences/ssh.md
- Preferences > Change Password: accounts/ui/preferences/password.md
- Accounting Actions:
- Overview: accounts/accounting/overview.md
- Check balance and quota: accounts/accounting/check-balance-quota.md
- Increase balance: accounts/accounting/increase-balance.md
- Increase Quota: accounts/accounting/increase-quota.md
- Change Payment Method: accounts/accounting/payment-methods.md
- Charges > Advanced search: accounts/accounting/charges-advanced-search.md
- Collaboration:
- Organizations:
- Overview: collaboration/organizations/overview.md
- Roles: collaboration/organizations/roles.md
- Teams: collaboration/organizations/teams.md
- User Interface:
- Overview: collaboration/ui/overview.md
- Teams Explorer: collaboration/ui/teams-explorer.md
- Team Page: collaboration/ui/team-page.md
- People Explorer: collaboration/ui/people-explorer.md
- Entity Sharing:
- User Interface: collaboration/sharing/ui.md
- Actions: collaboration/sharing/actions.md
- Account Access Levels: collaboration/sharing/access-levels.md
- Actions:
- Organization > Overview: collaboration/actions/organization/overview.md
- Organization > Create: collaboration/actions/organization/create.md
- Organization > Add / Remove Member: collaboration/actions/organization/add-remove-member.md
- Organization > Make / Revoke Admin: collaboration/actions/organization/make-revoke-admin.md
- Organization > Create / Delete Team: collaboration/actions/organization/create-delete-team.md
- Organization > Create Entities: collaboration/actions/organization/create-entities.md
- Team > Overview: collaboration/actions/team/overview.md
- Team > Edit Permissions: collaboration/actions/team/edit-permissions.md
- Team > Add / Remove Member: collaboration/actions/team/add-remove-member.md
- Team > Add / Remove Entity: collaboration/actions/team/add-remove-entity.md
# CONCEPTS
- Models:
- Overview: models/overview.md
- Accuracy: models/accuracy.md
- Data: models/data.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
- Data: models-directory/dft/data.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
- Data: models-directory/machine-learning/data.md
- Example Workflow: models-directory/machine-learning/example-workflow.md
- Accuracy: models-directory/machine-learning/accuracy.md
- Methods:
- Overview: methods/overview.md
- Data: methods/data.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
- Data: methods-directory/pseudopotential/data.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
- Data: methods-directory/linear-regression/data.md
- Software:
- Overview: software/overview.md
- Components: software/components.md
- Data: software/data.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
- 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
- Data: software-directory/modeling/quantum-espresso/data.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
- Data: software-directory/modeling/vasp/data.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
- Data: software-directory/scripting/shell/data.md
- Python:
- Overview: software-directory/scripting/python/overview.md
- Data: software-directory/scripting/python/data.md
- Jupyter Lab:
- Overview: software-directory/scripting/jupyter-lab/overview.md
- Data: software-directory/scripting/jupyter-lab/data.md
- Machine Learning (ML):
- TensorFlow: software-directory/machine-learning/tensorflow.md
- Exabyte ML:
- Overview: software-directory/machine-learning/exabyte/overview.md
- Data: software-directory/machine-learning/exabyte/data.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
- Data: software-directory/machine-learning/python-ml/data.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
# ENTITIES
- Entities & Common Aspects:
- Overview: entities-general/overview.md
- Lifecycle: entities-general/lifecycle.md
- Ownership: entities-general/ownership.md
- Permissions: entities-general/permissions.md
- Data: entities-general/data.md
- Sets: entities-general/sets.md
- Bank: entities-general/bank.md
- Default: entities-general/default.md
- User Interface:
- Overview: entities-general/ui/overview.md
- Explorer: entities-general/ui/explorer.md
- Designer: entities-general/ui/designer.md
- Viewer: entities-general/ui/viewer.md
- Actions:
- Overview: entities-general/actions/overview.md
- Select: entities-general/actions/select.md
- Search: entities-general/actions/search.md
- Advanced search: entities-general/actions/advanced-search.md
- Open: entities-general/actions/open-edit.md
- Clone: entities-general/actions/clone.md
- Delete: entities-general/actions/delete.md
- Set default: entities-general/actions/set-default.md
- Add metadata: entities-general/actions/metadata.md
- Change name: entities-general/actions/name.md
- Create: entities-general/actions/create.md
- Bank > Copy from: entities-general/actions/copy-bank.md
- Sets > Create / Delete: entities-general/actions/create-sets.md
- Sets > Change Type: entities-general/actions/change-set-type.md
- Sets > Set Index: entities-general/actions/set-entity-index.md
- Sets > Move To: entities-general/actions/move-to-sets.md
# ENTITIES - SPECIFIC
- Materials:
- Overview: materials/overview.md
- Data: materials/data.md
- Bank: materials/bank.md
- Default: materials/default.md
- Classification:
- Crystalline: materials/classification/crystalline.md
- Non-Periodic: materials/classification/non-periodic.md
- User Interface:
- Explorer: materials/ui/explorer.md
- Designer: materials-designer/overview.md
- Viewer: materials/ui/viewer.md
- Actions:
- Overview: materials/actions/overview.md
- Import: materials/actions/import.md
- Upload: materials/actions/upload.md
- Set default: materials/actions/set-default.md
- Advanced search: materials/actions/advanced-search.md
- Bank > Copy from: materials/actions/copy-bank.md
- Materials Designer:
- Overview: materials-designer/overview.md
- Header Menu:
- Overview: materials-designer/header-menu/header-menu-intro.md
- Input/Output: materials-designer/header-menu/input-output.md
- "Input/Output > Import": materials-designer/header-menu/input-output/import.md
- "Input/Output > Import from Standata": materials-designer/header-menu/input-output/standata-import.md
- "Input/Output > Export": materials-designer/header-menu/input-output/export.md
- "Input/Output > Save": materials-designer/header-menu/input-output/save.md
- Edit: materials-designer/header-menu/edit.md
- View: materials-designer/header-menu/view.md
- Advanced: materials-designer/header-menu/advanced.md
- "Advanced > Supercell": materials-designer/header-menu/advanced/supercell.md
- "Advanced > Combinatorial Set": materials-designer/header-menu/advanced/combinatorial-set.md
- "Advanced > Interpolated Set": materials-designer/header-menu/advanced/interpolated-set.md
- "Advanced > Surface / Slab": materials-designer/header-menu/advanced/surface-slab.md
- "Advanced > Boundary Conditions": materials-designer/header-menu/advanced/boundary-conditions.md
- "Advanced > JupyterLite Transformation": materials-designer/header-menu/advanced/jupyterlite-dialog.md
- Help: materials-designer/header-menu/help.md
- Sidebar:
- Items List: materials-designer/sidebar-items.md
- Source Editor:
- Overview: materials-designer/source-editor.md
- Lattice Editor: materials-designer/source-editor/lattice.md
- Basis Editor: materials-designer/source-editor/basis.md
- 3D Viewer/Editor:
- Overview: materials-designer/3d-editor.md
- View Options: materials-designer/3d-editor/view.md
- Parameters Options: materials-designer/3d-editor/parameters.md
- Edit Options: materials-designer/3d-editor/edit.md
- "Edit Actions > Overview": materials-designer/3d-editor/editor-actions/overview.md
- "Edit Actions > Add/Remove Atoms": materials-designer/3d-editor/editor-actions/add-remove-atoms.md
- "Edit Actions > Adjust Cell Parameters": materials-designer/3d-editor/editor-actions/adjust-cell-parameters.md
- "Edit Actions > Move/Rotate Atoms": materials-designer/3d-editor/editor-actions/move-rotate-atoms.md
- Export Options: materials-designer/3d-editor/export.md
- 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
- Data:
- Overview: workflows/data/overview.md
- Workflows: workflows/data/workflows.md
- Subworkflows: workflows/data/subworkflows.md
- Units: workflows/data/units.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
- User Interface:
- Explorer: workflows/ui/explorer.md
- Designer: workflow-designer/overview.md
- Viewer: workflows/ui/viewer.md
- Actions:
- Overview: workflows/actions/overview.md
- Update: workflows/actions/update.md
- Set default: workflows/actions/set-default.md
- Bank > Copy from: workflows/actions/copy-bank.md
- Add-ons:
- Overview: workflows/addons/overview.md
- Convergence: workflows/addons/convergence-algorithms.md
- Structural Relaxation: workflows/addons/structural-relaxation.md
- Workflow Designer:
- Overview: workflow-designer/overview.md
- Header Menu:
- Overview: workflow-designer/header-menu.md
- Sidebar:
- Items List: workflow-designer/sidebar.md
- Subworkflow Editor:
- Overview: workflow-designer/subworkflow-editor/overview.md
- Actions Menu: workflow-designer/subworkflow-editor/actions-menu.md
- Tabs: workflow-designer/subworkflow-editor/tabs-general.md
- Tabs > Overview: workflow-designer/subworkflow-editor/overview-tab.md
- Tabs > Important Settings: workflow-designer/subworkflow-editor/important-settings.md
- Tabs > Detailed View: workflow-designer/subworkflow-editor/detailed-view.md
- Tabs > Compute: workflow-designer/subworkflow-editor/compute.md
- Units Flowchart: workflow-designer/subworkflow-editor/units-flowchart.md
- Unit Editor:
- Overview: workflow-designer/unit-editor.md
- Input Templates: workflow-designer/unit-editor/input-templates.md
- Jobs:
- Overview: jobs/overview.md
- Projects: jobs/projects.md
- Data: jobs/data.md
- Status: jobs/status.md
- User Interface:
- Explorer: jobs/ui/explorer.md
- Designer: jobs-designer/overview.md
- Viewer: jobs/ui/viewer.md
- Results Tab: jobs/ui/results-tab.md
- Files Tab: jobs/ui/files-tab.md
- Projects Explorer: jobs/ui/projects-explorer.md
- Projects Page: jobs/ui/project-page.md
- Actions:
- Overview: jobs/actions/overview.md
- Create: jobs/actions/create.md
- Run: jobs/actions/run.md
- Terminate: jobs/actions/terminate.md
- Purge: jobs/actions/purge.md
- Projects > Create / Delete: jobs/actions/create-delete-project.md
- Jobs Designer:
- Overview: jobs-designer/overview.md
- Header Menu: jobs-designer/header-menu.md
- Materials Tab: jobs-designer/materials-tab.md
- Workflow Tab: jobs-designer/workflow-tab.md
- Compute Tab: jobs-designer/compute-tab.md
- Actions > Header Menu:
- Select Materials: jobs-designer/actions-header-menu/select-materials.md
- Select Workflow: jobs-designer/actions-header-menu/select-workflow.md
- Select Parent: jobs-designer/actions-header-menu/select-parent.md
- Jobs via Command Line:
- Overview: jobs-cli/overview.md
- Accounting: jobs-cli/accounting.md
- Batch Scripts:
- Overview: jobs-cli/batch-scripts/overview.md
- General Structure: jobs-cli/batch-scripts/general-structure.md
- Directives: jobs-cli/batch-scripts/directives.md
- Working Directory: jobs-cli/batch-scripts/directories.md
- Sample Scripts: jobs-cli/batch-scripts/sample-scripts.md
- Actions:
- Overview: jobs-cli/actions/overview.md
- Create: jobs-cli/actions/create.md
- Submit: jobs-cli/actions/submit.md
- Check status: jobs-cli/actions/check-status.md
- Terminate: jobs-cli/actions/terminate.md
- View Jobs List: jobs-cli/actions/view-job-list.md
- External Uploads:
- Overview: external/overview.md
- Status: external/status.md
- User Interface:
- Explorer: external/ui/explorer.md
- Actions:
- Overview: external/actions/overview.md
- Create: external/actions/create.md
- 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
- Data:
- Overview: properties/data/overview.md
- Core: properties/data/core.md
- List of Schemas: properties/data/list.md
- Periodic Table: properties/data/periodic-table.md
- Classification:
- Overview: properties/classification/overview.md
- General: properties/classification/general.md
- Machine Learning: properties/classification/machine-learning.md
- Materials: properties/classification/materials.md
- User Interface:
- Explorer: properties/ui/explorer.md
- Viewer: properties/ui/viewer.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
# TODO: re-enable when implemented
# - Formation Energy: properties-directory/scalar/formation-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
# COMPUTATIONAL ASPECTS
- General Infrastructure:
- Overview: infrastructure/overview.md
- Storage System: infrastructure/storage.md
- Login Node:
- Overview: infrastructure/login/overview.md
- Directory Structure: infrastructure/login/directories.md
- Clusters:
- Overview: infrastructure/clusters/overview.md
- Directory Structure: infrastructure/clusters/directories.md
- Hardware Specifications: infrastructure/clusters/hardware.md
- AWS Clusters: infrastructure/clusters/aws.md
- Azure Clusters: infrastructure/clusters/azure.md
- Resource Management:
- Overview: infrastructure/resource/overview.md
- Category: infrastructure/resource/category.md
- Queues: infrastructure/resource/queues.md
- Compute:
- Overview: infrastructure/compute/overview.md
- Parameters: infrastructure/compute/parameters.md
- Data: infrastructure/compute/data.md
- Data Practices:
- Overview: data/overview.md
- Classification: data/classification.md
- Lifecycle: data/lifecycle.md
- Data Structures:
- Overview: data-structured/overview.md
- Convention: data-structured/convention.md
- Data on Disk:
- Overview: data-on-disk/overview.md
- Directory Structure: data-on-disk/directories.md
- Quotas: data-on-disk/quotas.md
- Security: data-on-disk/security.md
- Data in Object Storage:
- Overview: data-in-objectstorage/overview.md
- Files: data-in-objectstorage/files.md
- Security: data-in-objectstorage/security.md
- Dropbox: data-in-objectstorage/dropbox.md
- User Interface:
- Dropbox Page: data-in-objectstorage/ui/dropbox-page.md
- Files Tab: jobs/ui/files-tab.md
- Files Explorer: data-in-objectstorage/ui/explorer.md
- Actions > Files:
- Overview: data-in-objectstorage/actions/overview.md
- Download: data-in-objectstorage/actions/download.md
- Copy Path: data-in-objectstorage/actions/copy-path.md
- Upload: data-in-objectstorage/actions/upload.md
- Create Folder: data-in-objectstorage/actions/create-folder.md
- Remote Connection:
- Overview: remote-connection/overview.md
- SSH Terminal (SSH): remote-connection/ssh.md
- Web Terminal (WT): remote-connection/web-terminal.md
- Remote Desktop (RD): remote-connection/remote-desktop.md
- Actions > (WT) & (RD):
- Overview: remote-connection/actions/overview.md
- Open Web Terminal: remote-connection/actions/open-terminal.md
- Open Remote Desktop: remote-connection/actions/open-desktop.md
- Open Sidebar: remote-connection/actions/sidebar.md
- Upload: remote-connection/actions/upload.md
- Download: remote-connection/actions/download.md
- Transfer Files via SCP: remote-connection/actions/transfer-files-scp.md
- Copy / Paste Text: remote-connection/actions/copy-paste.md
- Access data in Web Platfrom: remote-connection/actions/access-data.md
- Actions > Remote Desktop:
- Overview: remote-connection/actions-rd/overview.md
- Browse Directories: remote-connection/actions-rd/browse.md
- Open Applications: remote-connection/actions-rd/open-app.md
- Command Line Interface:
- Overview: cli/overview.md
- Environment: cli/environment.md
- Environment Modules: cli/modules.md
- Accounting: cli/accounting.md
- Actions:
- Overview: cli/actions/overview.md
- Load / Unload Modules: cli/actions/modules-actions.md
- Customize Environment: cli/actions/customize.md
- Add new software: cli/actions/add-software.md
- Create Python Environment: cli/actions/create-python-env.md
- Create Anaconda Environment: cli/actions/create-anaconda-env.md
- List Clusters and Nodes: cli/actions/list-clusters.md
- Check Balance and Quota: cli/actions/balance-quota.md
- REST-API:
- Overview: rest-api/overview.md
- Authentication: rest-api/authentication.md
- Query structure: rest-api/query-structure.md
- Endpoints: rest-api/endpoints.md
- Exabyte API client: rest-api/api-client.md
- Exabyte API examples: rest-api/api-examples.md
# TODO: refactor/re-implement and re-enable
# - Tutorials:
# - Upload a Pseudopotential: tutorials/dft/upload-pseudopotential.md
# - Custom-input workflow: tutorials/other/custom-input-workflow.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:
- FAQ: other/faq.md
- Publications: other/publications.md
- Help & Support: other/support.md
- Community Programs: other/community-programs.md
- Terms of Service: other/terms-of-service.md # duplicate through link
- Restricted Content: other/restricted.md
- Account Registration: other/registration.md
- 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