Clean up docs (#546)

.mega-linter.yml

@@ -1,13 +1,13 @@
 APPLY_FIXES: all
 APPLY_FIXES_EVENT: all
+DEFAULT_BRANCH: main
 ENABLE_LINTERS:
   - MARKDOWN_MARKDOWN_LINK_CHECK
   - MARKDOWN_MARKDOWN_TABLE_FORMATTER
   - REPOSITORY_GIT_DIFF
   - YAML_PRETTIER
   - YAML_YAMLLINT
 EXCLUDED_DIRECTORIES: [.github, tests]
-DEFAULT_BRANCH: main
 GITHUB_COMMENT_REPORTER: false
 PRINT_ALPACA: false
 PYTHON_BLACK_CONFIG_FILE: pyproject.toml

.sourcery.yaml

@@ -1,5 +1,5 @@
-rule_settings:
-  python_version: "3.9"
 github:
   ignore_labels:
     - sourcery-ignore
+rule_settings:
+  python_version: "3.9"

CHANGELOG.md

@@ -22,6 +22,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ### Docs
 
+- Switched the docs from Furo to Material for MkDocs.
 - Expanded upon Parsl documentation.
 - Modified tutorials and added example configs for Slurm.
 

CITATION.cff

@@ -1,15 +1,14 @@
-cff-version: 1.2.0
-title: >-
-  quacc – The Quantum Accelerator
-message: >-
-  Please cite this work as follows if you use quacc.
 authors:
-  - given-names: Andrew
-    family-names: Rosen
+  - affiliation: >-
+      Department of Chemical and Biological Engineering Princeton University
     email: [email protected]
+    family-names: Rosen
+    given-names: Andrew
     orcid: "https://orcid.org/0000-0002-0141-7006"
-    affiliation: >-
-      Department of Chemical and Biological Engineering
-      Princeton University
+cff-version: 1.2.0
 doi: 10.5281/zenodo.7720998
+message: >-
+  Please cite this work as follows if you use quacc.
+title: >-
+  quacc – The Quantum Accelerator
 url: https://github.com/Quantum-Accelerators/quacc

docs/about/faq.md

@@ -2,7 +2,7 @@
 
 **Q: Which workflow management system should I use?**
 
-A: Good question! Check out the [Workflow Engines Overview Guide](../user/wflow_engines.md) for a comparison of several common options to see which might be best for you.
+A: Good question! Check out the [Workflow Engines Overview Guide](../user/wflow_overview.md) for a comparison of several common options to see which might be best for you.
 
 **Q: Why is quacc better than `InsertMyFavoriteCode`?**
 

docs/user/database.md

@@ -4,6 +4,8 @@ Oftentimes, it is beneficial to store the results in a database for easy queryin
 
 ![Mongo example](../images/user/schema.gif)
 
+For assistance with setting up a MongoDB instance of your own, refer to the ["Database Setup"](../install/config_db.md) section of the installation instructions.
+
 === "General Purpose"
 
     For a given recipe, you can store the final output summary in your database using the `quacc.util.db.results_to_db` function, as shown in the example below.
@@ -32,7 +34,7 @@ Oftentimes, it is beneficial to store the results in a database for easy queryin
 
     Covalent automatically stores all the inputs and outputs in an SQLite database, which you can find at the `"db_path"` when you run `covalent config`, and the results can be queried using the `ct.get_result(<dispatch ID>)` syntax. However, if you want to store the results in a different database of your choosing, you can use [maggma](https://github.com/materialsproject/maggma) to do so quite easily.
 
-    An example is shown below for storing the results in a MongoDB via the `quacc.util.db.covalent_to_db` function. For assistance with setting up a MongoDB of your own, refer to the ["MongoDB Setup"](../install/config_db.md) section of the installation instructions.
+    An example is shown below for storing the results in a MongoDB via the `quacc.util.db.covalent_to_db` function.
 
     ```python
     from maggma.stores import MongoStore

mkdocs.yml

@@ -1,48 +1,4 @@
-site_name: quacc
-site_author: Andrew S. Rosen
-site_description: >-
-  Quacc is a flexible and extensible platform
-  for high-throughput computational materials
-  science and quantum chemistry.
-repo_url: https://github.com/Quantum-Accelerators/quacc/
 edit_uri: blob/main/docs/
-theme:
-  name: material
-  palette:
-    scheme: slate
-    primary: orange
-  logo: images/quacc_logo_wide.svg
-  favicon: images/quacc_favicon.png
-  plugins:
-    - search:
-        separator: '[\s\-,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
-    - minify:
-        minify_html: true
-    - social
-    - blog
-    - tags
-    - git-revision-date-localized:
-        enable_creation_date: true
-    - offline
-    - mkdocstrings
-    - mkdocs-click
-    - autorefs
-
-  features:
-    - content.action.edit
-    - content.code.copy
-    - content.code.select
-    - content.code.annotate
-    - content.tabs.link
-    - content.tooltips
-    - navigation.footer
-    - navigation.path
-    - navigation.tracking
-    - navigation.sections
-    - search.highlight
-    - search.suggest
-    - search.share
-    - header.autohide
 extra:
   social:
     - icon: fontawesome/brands/twitter
@@ -66,8 +22,8 @@ markdown_extensions:
   - pymdownx.caret
   - pymdownx.details
   - pymdownx.emoji:
-      emoji_index: !!python/name:materialx.emoji.twemoji
-      emoji_generator: !!python/name:materialx.emoji.to_svg
+      emoji_generator: !!python/name:materialx.emoji.to_svg ""
+      emoji_index: !!python/name:materialx.emoji.twemoji ""
   - pymdownx.highlight:
       anchor_linenums: true
       line_spans: __span
@@ -79,9 +35,9 @@ markdown_extensions:
   - pymdownx.smartsymbols
   - pymdownx.superfences:
       custom_fences:
-        - name: mermaid
-          class: mermaid
-          format: !!python/name:pymdownx.superfences.fence_code_format
+        - class: mermaid
+          format: !!python/name:pymdownx.superfences.fence_code_format ""
+          name: mermaid
   - pymdownx.tabbed:
       alternate_style: true
   - pymdownx.tasklist:
@@ -115,6 +71,49 @@ nav:
       - about/contributors.md
       - about/changelog.md
       - about/license.md
-  # - Code Reference:
-  #     - Calculators:
-  #         - references/calculators.md
+  - Code Reference:
+      - Calculators:
+          - references/calculators.md
+repo_url: https://github.com/Quantum-Accelerators/quacc/
+site_author: Andrew S. Rosen
+site_description: >-
+  Quacc is a flexible and extensible platform for
+  high-throughput computational materials science and quantum chemistry.
+site_name: quacc
+theme:
+  favicon: images/quacc_favicon.png
+
+  features:
+    - content.action.edit
+    - content.code.copy
+    - content.code.select
+    - content.code.annotate
+    - content.tabs.link
+    - content.tooltips
+    - navigation.footer
+    - navigation.path
+    - navigation.tracking
+    - navigation.sections
+    - search.highlight
+    - search.suggest
+    - search.share
+    - header.autohide
+  logo: images/quacc_logo_wide.svg
+  name: material
+  palette:
+    primary: orange
+    scheme: slate
+  plugins:
+    - search:
+        separator: '[\s\-,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
+    - minify:
+        minify_html: true
+    - social
+    - blog
+    - tags
+    - git-revision-date-localized:
+        enable_creation_date: true
+    - offline
+    - mkdocstrings
+    - mkdocs-click
+    - autorefs

quacc/presets/vasp/BulkSet.yaml

@@ -1,20 +1,20 @@
-parent_magmoms: magmoms_base.yaml
-parent_setups: setups_pbe54_MP.yaml
 inputs:
+  algo: fast
   auto_kpts:
     max_mixed_density: [100, 1000]
-  algo: fast
-  ediff: 1.0e-5
+  ediff: 1e-5
   efermi: midgap
   encut: 520
   ismear: 0
   isym: 0
   ivdw: 12
+  lasph: true
   lcharg: false
   lorbit: 11
-  lasph: true
   lwave: false
   nelm: 150
   prec: accurate
   sigma: 0.05
   xc: pbe
+parent_magmoms: magmoms_base.yaml
+parent_setups: setups_pbe54_MP.yaml

quacc/presets/vasp/MPScanSet.yaml

@@ -2,29 +2,29 @@
 # using the r2SCAN functional.
 # Caution: The pseudopotentials should be used with the .54 PAW PBE set
 # Source: https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/vasp/MPSCANRelaxSet.yaml
-parent_magmoms: magmoms_MP.yaml
-parent_setups: setups_pbe54_MP.yaml
 inputs:
   algo: all
-  ediff: 1.0e-05
+  ediff: 1e-5
   ediffg: -0.02
   enaug: 1360
   encut: 680
   ibrion: 2
   isif: 3
   ismear: 2
   kspacing: 0.22
-  lorbit: 11
+  laechg: True
   lasph: True
-  lreal: auto
-  lmixtau: True
   lcharg: True
-  laechg: True
   lelf: True
-  lwave: False
+  lmixtau: True
+  lorbit: 11
+  lreal: auto
   lvtot: True
+  lwave: False
   nelm: 200
   nsw: 99
   prec: accurate
   sigma: 0.2
   xc: r2scan
+parent_magmoms: magmoms_MP.yaml
+parent_setups: setups_pbe54_MP.yaml

quacc/presets/vasp/QMOFSet.yaml

@@ -1,20 +1,20 @@
-parent_magmoms: magmoms_qmof.yaml
-parent_setups: setups_qmof.yaml
 inputs:
+  algo: all
   auto_kpts:
     grid_density: 1000
-  algo: all
-  ediff: 1.0e-6
+  ediff: 1e-6
   encut: 520
   ismear: 0
   isym: 0
   ivdw: 12
-  lorbit: 11
   lasph: false
+  lorbit: 11
   lreal: false
   nelm: 150
   nelmin: 3
   prec: accurate
   sigma: 0.01
-  symprec: 1.0e-8
+  symprec: 1e-8
   xc: pbe
+parent_magmoms: magmoms_qmof.yaml
+parent_setups: setups_qmof.yaml

quacc/presets/vasp/SlabSet.yaml

@@ -1,8 +1,8 @@
-parent: BulkSet.yaml
 inputs:
   auto_dipole: true
   auto_kpts:
     length_density: [50, 50, 1]
   encut: 450
   ivdw: 0
   xc: rpbe
+parent: BulkSet.yaml

quacc/presets/vasp/magmoms_base.yaml

@@ -3,35 +3,35 @@
 # 2+ or 3+.
 inputs:
   elemental_magmoms:
-    Ti: 2
-    V: 3
-    Cr: 4
-    Mn: 5
-    Fe: 5
+    Am: 7
+    Bk: 6
+    Ce: 2
+    Cf: 5
+    Cm: 7
     Co: 4
-    Ni: 3
+    Cr: 4
     Cu: 2
-    Ce: 2
-    Pr: 3
+    Dy: 5
+    Er: 3
+    Es: 4
+    Eu: 7
+    Fe: 5
+    Fm: 3
+    Gd: 7
+    Ho: 4
+    Md: 2
+    Mn: 5
     Nd: 4
+    Ni: 3
+    Np: 5
+    Pa: 3
     Pm: 5
+    Pr: 3
+    Pu: 6
     Sm: 6
-    Eu: 7
-    Gd: 7
     Tb: 6
-    Dy: 5
-    Ho: 4
-    Er: 3
-    Tm: 2
     Th: 2
-    Pa: 3
+    Ti: 2
+    Tm: 2
     U: 4
-    Np: 5
-    Pu: 6
-    Am: 7
-    Cm: 7
-    Bk: 6
-    Cf: 5
-    Es: 4
-    Fm: 3
-    Md: 2
+    V: 3