Create the initial skeleton and try to make the first major content b…

…lock acceptors.

In theory, all we have to do is transfer the wiki pages to markdown files to at least get material. I can clean up later.

.gitignore

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+# Bundler cache
+.bundle
+vendor
+Gemfile.lock
+
+# Jekyll cache
+.jekyll-cache
+_site
+
+# RubyGems
+*.gem
+
+# NPM dependencies
+node_modules
+package-lock.json
+
+# IDE configurations
+.idea
+
+# Misc
+assets/js/dist

.gitmodules

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+[submodule "assets/lib"]
+	path = assets/lib
+	url = https://github.com/cotes2020/chirpy-static-assets.git

.nojekyll

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+

404.html

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+---
+permalink: /404.html
+layout: default
+---
+
+<style type="text/css" media="screen">
+  .container {
+    margin: 10px auto;
+    max-width: 600px;
+    text-align: center;
+  }
+  h1 {
+    margin: 30px 0;
+    font-size: 4em;
+    line-height: 1;
+    letter-spacing: -1px;
+  }
+</style>
+
+<div class="container">
+  <h1>404</h1>
+
+  <p><strong>Page not found :(</strong></p>
+  <p>The requested page could not be found.</p>
+</div>

Gemfile

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+# frozen_string_literal: true
+
+source "https://rubygems.org"
+
+gem "jekyll-theme-chirpy", "~> 6.5", ">= 6.5.3"
+
+group :test do
+  gem "html-proofer", "~> 4.4"
+end
+
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library.
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", ">= 1", "< 3"
+  gem "tzinfo-data"
+end
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
+
+# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem
+# do not have a Java counterpart.
+gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]

_config.yml

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+# The Site Configuration
+
+# Import the theme
+theme: jekyll-theme-chirpy
+
+# The language of the webpage › http://www.lingoes.net/en/translator/langcode.htm
+# If it has the same name as one of the files in folder `_data/locales`, the layout language will also be changed,
+# otherwise, the layout language will use the default value of 'en'.
+lang: en
+
+# Change to your timezone › https://kevinnovak.github.io/Time-Zone-Picker
+timezone:
+
+# jekyll-seo-tag settings › https://github.com/jekyll/jekyll-seo-tag/blob/master/docs/usage.md
+# ↓ --------------------------
+
+title: Alchemistry.org # the main title
+
+tagline: A place to learn, share, and discuss Computational Free Energy Calculations # it will display as the sub-title
+
+description: >- # used by seo meta and the atom feed
+  Modern alchemy, done computationally, can turn protein structural information into the
+  "gold" of binding free energies and other information. In these pages, learn how it
+  works, and how to do it yourself.
+
+# Fill in the protocol & hostname for your site.
+# e.g. 'https://username.github.io', note that it does not end with a '/'.
+url: "https://alchemistry.org"
+
+github:
+  username: github_username # change to your github username
+
+twitter:
+  username: twitter_username # change to your twitter username
+
+social:
+  # Change to your full name.
+  # It will be displayed as the default author of the posts and the copyright owner in the Footer
+  name: The Alchemistry.org Team
+  email: [email protected] # change to your email address
+  links:
+    # The first element serves as the copyright owner's link
+    - https://twitter.com/username # change to your twitter homepage
+    - https://github.com/username # change to your github homepage
+    # Uncomment below to add more social links
+    # - https://www.facebook.com/username
+    # - https://www.linkedin.com/in/username
+
+google_site_verification: # fill in to your verification string
+
+# ↑ --------------------------
+# The end of `jekyll-seo-tag` settings
+
+google_analytics:
+  id: # fill in your Google Analytics ID
+
+goatcounter:
+  id: # fill in your Goatcounter ID
+
+# Prefer color scheme setting.
+#
+# Note: Keep empty will follow the system prefer color by default,
+# and there will be a toggle to switch the theme between dark and light
+# on the bottom left of the sidebar.
+#
+# Available options:
+#
+#     light  - Use the light color scheme
+#     dark   - Use the dark color scheme
+#
+theme_mode: # [light | dark]
+
+# The CDN endpoint for images.
+# Notice that once it is assigned, the CDN url
+# will be added to all image (site avatar & posts' images) paths starting with '/'
+#
+# e.g. 'https://cdn.com'
+img_cdn:
+
+# the avatar on sidebar, support local or CORS resources
+avatar: /assets/images/staurosporine-hydrated-1.png
+
+# The URL of the site-wide social preview image used in SEO `og:image` meta tag.
+# It can be overridden by a customized `page.image` in front matter.
+social_preview_image: # string, local or CORS resources
+
+# boolean type, the global switch for TOC in posts.
+toc: true
+
+comments:
+  active: # The global switch for posts comments, e.g., 'disqus'.  Keep it empty means disable
+  # The active options are as follows:
+  disqus:
+    shortname: # fill with the Disqus shortname. › https://help.disqus.com/en/articles/1717111-what-s-a-shortname
+  # utterances settings › https://utteranc.es/
+  utterances:
+    repo: # <gh-username>/<repo>
+    issue_term: # < url | pathname | title | ...>
+  # Giscus options › https://giscus.app
+  giscus:
+    repo: # <gh-username>/<repo>
+    repo_id:
+    category:
+    category_id:
+    mapping: # optional, default to 'pathname'
+    input_position: # optional, default to 'bottom'
+    lang: # optional, default to the value of `site.lang`
+    reactions_enabled: # optional, default to the value of `1`
+
+# Self-hosted static assets, optional › https://github.com/cotes2020/chirpy-static-assets
+assets:
+  self_host:
+    enabled: # boolean, keep empty means false
+    # specify the Jekyll environment, empty means both
+    # only works if `assets.self_host.enabled` is 'true'
+    env: # [development | production]
+
+pwa:
+  enabled: true # the option for PWA feature (installable)
+  cache:
+    enabled: true # the option for PWA offline cache
+    # Paths defined here will be excluded from the PWA cache.
+    # Usually its value is the `baseurl` of another website that
+    # shares the same domain name as the current website.
+    deny_paths:
+      # - "/example"  # URLs match `<SITE_URL>/example/*` will not be cached by the PWA
+
+paginate: 10
+
+# The base URL of your site
+baseurl: ""
+
+# ------------ The following options are not recommended to be modified ------------------
+
+kramdown:
+  syntax_highlighter: rouge
+  syntax_highlighter_opts: # Rouge Options › https://github.com/jneen/rouge#full-options
+    css_class: highlight
+    # default_lang: console
+    span:
+      line_numbers: false
+    block:
+      line_numbers: true
+      start_line: 1
+
+collections:
+  tabs:
+    output: true
+    sort_by: order
+  lessons:
+    output: true
+    sort_by: order
+  examples:
+    output: true
+    sort_by: order
+
+defaults:
+  - scope:
+      path: "" # An empty string here means all files in the project
+      type: posts
+    values:
+      layout: post
+      comments: true # Enable comments in posts.
+      toc: true # Display TOC column in posts.
+      # DO NOT modify the following parameter unless you are confident enough
+      # to update the code of all other post links in this project.
+      permalink: /posts/:title/
+  - scope:
+      path: _drafts
+    values:
+      comments: false
+  - scope:
+      path: ""
+      type: tabs # see `site.collections`
+    values:
+      layout: page
+      permalink: /:title/
+  - scope:
+      path: assets/js/dist
+    values:
+      swcache: true
+
+sass:
+  style: compressed
+
+compress_html:
+  clippings: all
+  comments: all
+  endings: all
+  profile: false
+  blanklines: false
+  ignore:
+    envs: [development]
+
+exclude:
+  - "*.gem"
+  - "*.gemspec"
+  - docs
+  - tools
+  - README.md
+  - LICENSE
+  - rollup.config.js
+  - package*.json
+
+jekyll-archives:
+  enabled: [categories, tags]
+  layouts:
+    category: category
+    tag: tag
+  permalinks:
+    tag: /tags/:name/
+    category: /categories/:name/

_examples/ExamplesA.md

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+---
+layout: example
+order: 1
+title: Example Free Energy Calculations
+summary: A look into practical examples without software-specific details. We outline the steps needed for realistic free energy problem, detailing problems you can expect to encounter, and how to analyze the data to get a robust free energy difference.
+---
+
+I am the first Example
+
+# Behold my example form!

_includes/post-like-gen.html

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+<div id="post-list" class="flex-grow-1 px-xl-1">
+  {% for iterator in site.[include.content_type] %}
+    <article class="card-wrapper card">
+      <a href="{{ iterator.url | relative_url }}" class="post-preview row g-0 flex-md-row-reverse">
+        {% assign card_body_col = '12' %}
+
+        {% if iterator.image %}
+          {% assign src = iterator.image.path | default: iterator.image %}
+          {% unless src contains '//' %}
+            {% assign src = iterator.img_path | append: '/' | append: src | replace: '//', '/' %}
+          {% endunless %}
+
+          {% assign alt = iterator.image.alt | xml_escape | default: 'Preview Image' %}
+
+          {% assign lqip = null %}
+
+          {% if iterator.image.lqip %}
+            {% capture lqip %}lqip="{{ iterator.image.lqip }}"{% endcapture %}
+          {% endif %}
+
+          <div class="col-md-5">
+            <img src="{{ src }}" alt="{{ alt }}" {{ lqip }}>
+          </div>
+
+          {% assign card_body_col = '7' %}
+        {% endif %}
+
+        <div class="col-md-{{ card_body_col }}">
+          <div class="card-body d-flex flex-column">
+            <h1 class="card-title my-2 mt-md-0">{{ iterator.title }}</h1>
+
+            <div class="card-text content mt-0 mb-3">
+              <p>
+                <!-- Check for content -->
+                {% assign summary = iterator.summary | strip_newlines %}
+                {% if summary != "" %}
+                  {% include no-linenos.html content=summary %}
+                  {{ summary | markdownify | strip_html | escape }}
+                {% else % }
+                  {% include no-linenos.html content=iterator.content %}
+                  {{ iterator.content | markdownify | strip_html | truncate: 200 | escape }}
+                {% endif %}
+              </p>
+            </div>
+            <!-- .post-meta -->
+          </div>
+          <!-- .card-body -->
+        </div>
+      </a>
+    </article>
+  {% endfor %}
+</div>
+<!-- #iterator-list -->
+