From 03fc05a1313d9700d22fdd4f60d892cea19b6785 Mon Sep 17 00:00:00 2001
From: GitHub Action <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 26 Feb 2024 12:46:03 +0000
Subject: [PATCH] Update about.md to fix front-matter YAML [ci skip]
---
.all-contributorsrc | 45 -
.github/FUNDING.yml | 12 -
.github/ISSUE_TEMPLATE/bug_report.md | 38 -
.github/ISSUE_TEMPLATE/feature_request.md | 20 -
.github/stale.yml | 18 -
.github/workflows/deploy-docker-tag.yml | 40 -
.github/workflows/deploy-image.yml | 31 -
.github/workflows/deploy.yml | 42 -
.nojekyll | 0
404.html | 10 +-
Gemfile | 23 -
_bibliography/all_papers.bib | 48 -
_bibliography/one_paper.bib | 28 -
_bibliography/papers.bib | 117 -
_bibliography/papers_orcid.bib | 45 -
_bibliography/template_papers.bib | 82 -
_config.yml | 345 -
_data/coauthors.yml | 34 -
_data/cv.yml | 97 -
_data/repositories.yml | 12 -
_data/venues.yml | 6 -
_includes/cv/list.html | 5 -
_includes/cv/map.html | 8 -
_includes/cv/nested_list.html | 14 -
_includes/cv/time_table.html | 59 -
_includes/figure.html | 36 -
_includes/footer.html | 25 -
_includes/head.html | 36 -
_includes/header.html | 122 -
_includes/metadata.html | 192 -
_includes/news.html | 31 -
_includes/pagination.html | 17 -
_includes/projects.html | 36 -
_includes/projects_horizontal.html | 40 -
_includes/repository/repo.html | 14 -
_includes/repository/repo_user.html | 6 -
_includes/scripts/analytics.html | 18 -
_includes/scripts/bootstrap.html | 3 -
_includes/scripts/jquery.html | 2 -
_includes/scripts/masonry.html | 6 -
_includes/scripts/mathjax.html | 12 -
_includes/scripts/misc.html | 14 -
_includes/scripts/netlify_identity.html | 14 -
_includes/selected_papers.html | 5 -
_includes/social.html | 84 -
_layouts/about.html | 66 -
_layouts/archive-category.html | 27 -
_layouts/archive-tag.html | 27 -
_layouts/archive-year.html | 27 -
_layouts/bib.html | 196 -
_layouts/cv.html | 35 -
_layouts/default.html | 34 -
_layouts/distill.html | 109 -
_layouts/none.html | 1 -
_layouts/page.html | 16 -
_layouts/post.html | 61 -
_pages/about.md | 19 -
_pages/projects.md | 58 -
_pages/publications.md | 18 -
_plugins/external-posts.rb | 36 -
_plugins/hideCustomBibtex.rb | 15 -
...2022-10-02-spack-time-1-getting-started.md | 40 -
.../2022-10-04-spack-time-2-glyphs-of-doom.md | 102 -
_projects/5_project.md | 80 -
_projects/6_project.md | 80 -
_projects/CPMMD_project.md | 18 -
_projects/FAIRMD_project.md | 26 -
_projects/NEMD_project.md | 19 -
_projects/RSE_project.md | 21 -
_sass/_base.scss | 673 -
_sass/_distill.scss | 126 -
_sass/_layout.scss | 50 -
_sass/_themes.scss | 65 -
_sass/_variables.scss | 38 -
assets/css/main.css | 3 +
assets/css/main.css.map | 1 +
assets/css/main.scss | 15 -
assets/img/1-1400.webp | Bin 0 -> 59658 bytes
assets/img/1-480.webp | Bin 0 -> 23150 bytes
assets/img/1-800.webp | Bin 0 -> 59658 bytes
assets/img/10-1400.webp | Bin 0 -> 31262 bytes
assets/img/10-480.webp | Bin 0 -> 12604 bytes
assets/img/10-800.webp | Bin 0 -> 31262 bytes
assets/img/11-1400.webp | Bin 0 -> 52656 bytes
assets/img/11-480.webp | Bin 0 -> 23566 bytes
assets/img/11-800.webp | Bin 0 -> 52656 bytes
assets/img/12-1400.webp | Bin 0 -> 6342 bytes
assets/img/12-480.webp | Bin 0 -> 3236 bytes
assets/img/12-800.webp | Bin 0 -> 6342 bytes
assets/img/2-1400.webp | Bin 0 -> 47992 bytes
assets/img/2-480.webp | Bin 0 -> 25188 bytes
assets/img/2-800.webp | Bin 0 -> 47992 bytes
assets/img/3-1400.webp | Bin 0 -> 29256 bytes
assets/img/3-480.webp | Bin 0 -> 14168 bytes
assets/img/3-800.webp | Bin 0 -> 29256 bytes
assets/img/4-1400.webp | Bin 0 -> 20262 bytes
assets/img/4-480.webp | Bin 0 -> 8804 bytes
assets/img/4-800.webp | Bin 0 -> 20262 bytes
assets/img/5-1400.webp | Bin 0 -> 20368 bytes
assets/img/5-480.webp | Bin 0 -> 9546 bytes
assets/img/5-800.webp | Bin 0 -> 20368 bytes
assets/img/6-1400.webp | Bin 0 -> 40440 bytes
assets/img/6-480.webp | Bin 0 -> 15694 bytes
assets/img/6-800.webp | Bin 0 -> 40440 bytes
assets/img/7-1400.webp | Bin 0 -> 4248 bytes
assets/img/7-480.webp | Bin 0 -> 1998 bytes
assets/img/7-800.webp | Bin 0 -> 4248 bytes
assets/img/8-1400.webp | Bin 0 -> 12272 bytes
assets/img/8-480.webp | Bin 0 -> 5710 bytes
assets/img/8-800.webp | Bin 0 -> 12272 bytes
assets/img/9-1400.webp | Bin 0 -> 25740 bytes
assets/img/9-480.webp | Bin 0 -> 10534 bytes
assets/img/9-800.webp | Bin 0 -> 25740 bytes
assets/img/al-folio-preview-1400.webp | Bin 0 -> 20624 bytes
assets/img/al-folio-preview-480.webp | Bin 0 -> 8004 bytes
assets/img/al-folio-preview-800.webp | Bin 0 -> 20624 bytes
assets/img/code-screenshot-1400.webp | Bin 0 -> 25418 bytes
assets/img/code-screenshot-480.webp | Bin 0 -> 13630 bytes
assets/img/code-screenshot-800.webp | Bin 0 -> 25418 bytes
assets/img/cond-1400.webp | Bin 0 -> 29648 bytes
assets/img/cond-480.webp | Bin 0 -> 10262 bytes
assets/img/cond-800.webp | Bin 0 -> 29648 bytes
assets/img/distill-screenshot-1400.webp | Bin 0 -> 26622 bytes
assets/img/distill-screenshot-480.webp | Bin 0 -> 14676 bytes
assets/img/distill-screenshot-800.webp | Bin 0 -> 26622 bytes
assets/img/math-screenshot-1400.webp | Bin 0 -> 27084 bytes
assets/img/math-screenshot-480.webp | Bin 0 -> 14160 bytes
assets/img/math-screenshot-800.webp | Bin 0 -> 27084 bytes
assets/img/photos-screenshot-1400.webp | Bin 0 -> 26808 bytes
assets/img/photos-screenshot-480.webp | Bin 0 -> 14090 bytes
assets/img/photos-screenshot-800.webp | Bin 0 -> 26808 bytes
assets/img/prof_pic-1400.webp | Bin 0 -> 18168 bytes
assets/img/prof_pic-480.webp | Bin 0 -> 9780 bytes
assets/img/prof_pic-800.webp | Bin 0 -> 18168 bytes
assets/img/projects-screenshot-1400.webp | Bin 0 -> 24838 bytes
assets/img/projects-screenshot-480.webp | Bin 0 -> 14244 bytes
assets/img/projects-screenshot-800.webp | Bin 0 -> 24838 bytes
assets/img/publications-screenshot-1400.webp | Bin 0 -> 21604 bytes
assets/img/publications-screenshot-480.webp | Bin 0 -> 11546 bytes
assets/img/publications-screenshot-800.webp | Bin 0 -> 21604 bytes
assets/js/common.js | 10 +-
assets/js/dark_mode.js | 9 +-
assets/js/distillpub/overrides.js | 25 +-
assets/js/distillpub/template.v2.js | 9314 +----------
assets/js/distillpub/transforms.v2.js | 13248 +---------------
assets/js/masonry.js | 13 +-
assets/js/theme.js | 65 +-
assets/js/zoom.js | 9 +-
bin/cibuild | 1 -
bin/deploy | 118 -
bin/docker_build_image.sh | 5 -
bin/docker_run.sh | 7 -
bin/dockerhub_run.sh | 7 -
blog/2022/index.html | 1 +
.../spack-time-1-getting-started/index.html | 1 +
.../spack-time-2-glyphs-of-doom/index.html | 20 +
blog/index.html | 101 +-
blog/tag/doco/index.html | 1 +
blog/tag/spack/index.html | 1 +
feed.xml | 20 +
index.html | 1 +
projects/5_project/index.html | 15 +
projects/6_project/index.html | 15 +
projects/CPMMD_project/index.html | 1 +
projects/FAIRMD_project/index.html | 1 +
projects/NEMD_project/index.html | 1 +
projects/RSE_project/index.html | 1 +
projects/index.html | 1 +
publications/index.html | 1 +
robots.txt | 5 +-
sitemap.xml | 1 +
171 files changed, 231 insertions(+), 26782 deletions(-)
delete mode 100644 .all-contributorsrc
delete mode 100644 .github/FUNDING.yml
delete mode 100644 .github/ISSUE_TEMPLATE/bug_report.md
delete mode 100644 .github/ISSUE_TEMPLATE/feature_request.md
delete mode 100644 .github/stale.yml
delete mode 100644 .github/workflows/deploy-docker-tag.yml
delete mode 100644 .github/workflows/deploy-image.yml
delete mode 100644 .github/workflows/deploy.yml
create mode 100644 .nojekyll
delete mode 100644 Gemfile
delete mode 100644 _bibliography/all_papers.bib
delete mode 100755 _bibliography/one_paper.bib
delete mode 100644 _bibliography/papers.bib
delete mode 100644 _bibliography/papers_orcid.bib
delete mode 100644 _bibliography/template_papers.bib
delete mode 100644 _config.yml
delete mode 100644 _data/coauthors.yml
delete mode 100644 _data/cv.yml
delete mode 100644 _data/repositories.yml
delete mode 100644 _data/venues.yml
delete mode 100644 _includes/cv/list.html
delete mode 100644 _includes/cv/map.html
delete mode 100644 _includes/cv/nested_list.html
delete mode 100644 _includes/cv/time_table.html
delete mode 100644 _includes/figure.html
delete mode 100644 _includes/footer.html
delete mode 100644 _includes/head.html
delete mode 100644 _includes/header.html
delete mode 100644 _includes/metadata.html
delete mode 100644 _includes/news.html
delete mode 100644 _includes/pagination.html
delete mode 100644 _includes/projects.html
delete mode 100644 _includes/projects_horizontal.html
delete mode 100644 _includes/repository/repo.html
delete mode 100644 _includes/repository/repo_user.html
delete mode 100644 _includes/scripts/analytics.html
delete mode 100644 _includes/scripts/bootstrap.html
delete mode 100644 _includes/scripts/jquery.html
delete mode 100644 _includes/scripts/masonry.html
delete mode 100644 _includes/scripts/mathjax.html
delete mode 100644 _includes/scripts/misc.html
delete mode 100644 _includes/scripts/netlify_identity.html
delete mode 100644 _includes/selected_papers.html
delete mode 100644 _includes/social.html
delete mode 100644 _layouts/about.html
delete mode 100644 _layouts/archive-category.html
delete mode 100644 _layouts/archive-tag.html
delete mode 100644 _layouts/archive-year.html
delete mode 100644 _layouts/bib.html
delete mode 100644 _layouts/cv.html
delete mode 100644 _layouts/default.html
delete mode 100644 _layouts/distill.html
delete mode 100644 _layouts/none.html
delete mode 100644 _layouts/page.html
delete mode 100644 _layouts/post.html
delete mode 100644 _pages/about.md
delete mode 100644 _pages/projects.md
delete mode 100644 _pages/publications.md
delete mode 100644 _plugins/external-posts.rb
delete mode 100644 _plugins/hideCustomBibtex.rb
delete mode 100644 _posts/2022-10-02-spack-time-1-getting-started.md
delete mode 100644 _posts/2022-10-04-spack-time-2-glyphs-of-doom.md
delete mode 100644 _projects/5_project.md
delete mode 100644 _projects/6_project.md
delete mode 100644 _projects/CPMMD_project.md
delete mode 100644 _projects/FAIRMD_project.md
delete mode 100644 _projects/NEMD_project.md
delete mode 100644 _projects/RSE_project.md
delete mode 100644 _sass/_base.scss
delete mode 100644 _sass/_distill.scss
delete mode 100644 _sass/_layout.scss
delete mode 100644 _sass/_themes.scss
delete mode 100644 _sass/_variables.scss
create mode 100644 assets/css/main.css
create mode 100644 assets/css/main.css.map
delete mode 100644 assets/css/main.scss
create mode 100644 assets/img/1-1400.webp
create mode 100644 assets/img/1-480.webp
create mode 100644 assets/img/1-800.webp
create mode 100644 assets/img/10-1400.webp
create mode 100644 assets/img/10-480.webp
create mode 100644 assets/img/10-800.webp
create mode 100644 assets/img/11-1400.webp
create mode 100644 assets/img/11-480.webp
create mode 100644 assets/img/11-800.webp
create mode 100644 assets/img/12-1400.webp
create mode 100644 assets/img/12-480.webp
create mode 100644 assets/img/12-800.webp
create mode 100644 assets/img/2-1400.webp
create mode 100644 assets/img/2-480.webp
create mode 100644 assets/img/2-800.webp
create mode 100644 assets/img/3-1400.webp
create mode 100644 assets/img/3-480.webp
create mode 100644 assets/img/3-800.webp
create mode 100644 assets/img/4-1400.webp
create mode 100644 assets/img/4-480.webp
create mode 100644 assets/img/4-800.webp
create mode 100644 assets/img/5-1400.webp
create mode 100644 assets/img/5-480.webp
create mode 100644 assets/img/5-800.webp
create mode 100644 assets/img/6-1400.webp
create mode 100644 assets/img/6-480.webp
create mode 100644 assets/img/6-800.webp
create mode 100644 assets/img/7-1400.webp
create mode 100644 assets/img/7-480.webp
create mode 100644 assets/img/7-800.webp
create mode 100644 assets/img/8-1400.webp
create mode 100644 assets/img/8-480.webp
create mode 100644 assets/img/8-800.webp
create mode 100644 assets/img/9-1400.webp
create mode 100644 assets/img/9-480.webp
create mode 100644 assets/img/9-800.webp
create mode 100644 assets/img/al-folio-preview-1400.webp
create mode 100644 assets/img/al-folio-preview-480.webp
create mode 100644 assets/img/al-folio-preview-800.webp
create mode 100644 assets/img/code-screenshot-1400.webp
create mode 100644 assets/img/code-screenshot-480.webp
create mode 100644 assets/img/code-screenshot-800.webp
create mode 100644 assets/img/cond-1400.webp
create mode 100644 assets/img/cond-480.webp
create mode 100644 assets/img/cond-800.webp
create mode 100644 assets/img/distill-screenshot-1400.webp
create mode 100644 assets/img/distill-screenshot-480.webp
create mode 100644 assets/img/distill-screenshot-800.webp
create mode 100644 assets/img/math-screenshot-1400.webp
create mode 100644 assets/img/math-screenshot-480.webp
create mode 100644 assets/img/math-screenshot-800.webp
create mode 100644 assets/img/photos-screenshot-1400.webp
create mode 100644 assets/img/photos-screenshot-480.webp
create mode 100644 assets/img/photos-screenshot-800.webp
create mode 100644 assets/img/prof_pic-1400.webp
create mode 100644 assets/img/prof_pic-480.webp
create mode 100644 assets/img/prof_pic-800.webp
create mode 100644 assets/img/projects-screenshot-1400.webp
create mode 100644 assets/img/projects-screenshot-480.webp
create mode 100644 assets/img/projects-screenshot-800.webp
create mode 100644 assets/img/publications-screenshot-1400.webp
create mode 100644 assets/img/publications-screenshot-480.webp
create mode 100644 assets/img/publications-screenshot-800.webp
delete mode 100755 bin/cibuild
delete mode 100755 bin/deploy
delete mode 100755 bin/docker_build_image.sh
delete mode 100755 bin/docker_run.sh
delete mode 100755 bin/dockerhub_run.sh
create mode 100644 blog/2022/index.html
create mode 100644 blog/2022/spack-time-1-getting-started/index.html
create mode 100644 blog/2022/spack-time-2-glyphs-of-doom/index.html
create mode 100644 blog/tag/doco/index.html
create mode 100644 blog/tag/spack/index.html
create mode 100644 feed.xml
create mode 100644 index.html
create mode 100644 projects/5_project/index.html
create mode 100644 projects/6_project/index.html
create mode 100644 projects/CPMMD_project/index.html
create mode 100644 projects/FAIRMD_project/index.html
create mode 100644 projects/NEMD_project/index.html
create mode 100644 projects/RSE_project/index.html
create mode 100644 projects/index.html
create mode 100644 publications/index.html
create mode 100644 sitemap.xml
diff --git a/.all-contributorsrc b/.all-contributorsrc
deleted file mode 100644
index bc6a910..0000000
--- a/.all-contributorsrc
+++ /dev/null
@@ -1,45 +0,0 @@
-{
- "files": [
- "README.md"
- ],
- "imageSize": 100,
- "commit": false,
- "contributorsPerLine": 7,
- "projectName": "al-folio",
- "projectOwner": "alshedivat",
- "repoType": "github",
- "repoHost": "https://github.com",
- "badgeTemplate": "[core_contributors]: https://img.shields.io/badge/core_contributors-<%= contributors.length %>-orange.svg 'Number of core contributors'",
- "contributorTemplate": "\">\" width=\"<%= options.imageSize %>px;\" alt=\"\"/> <%= contributor.name %>",
- "skipCi": true,
- "contributors": [
- {
- "login": "alshedivat",
- "name": "Maruan",
- "avatar_url": "https://avatars.githubusercontent.com/u/2126561?v=4",
- "profile": "http://maruan.alshedivat.com",
- "contributions": [
- "design",
- "code"
- ]
- },
- {
- "login": "rohandebsarkar",
- "name": "Rohan Deb Sarkar",
- "avatar_url": "https://avatars.githubusercontent.com/u/50144004?v=4",
- "profile": "http://rohandebsarkar.github.io",
- "contributions": [
- "code"
- ]
- },
- {
- "login": "pourmand1376",
- "name": "Amir Pourmand",
- "avatar_url": "https://avatars.githubusercontent.com/u/32064808?v=4",
- "profile": "https://amirpourmand.ir",
- "contributions": [
- "code"
- ]
- }
- ]
-}
diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml
deleted file mode 100644
index c78502f..0000000
--- a/.github/FUNDING.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-# These are supported funding model platforms
-
-github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2]
-patreon: # Replace with a single Patreon username
-open_collective: # Replace with a single Open Collective username
-ko_fi: alshedivat
-tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
-community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
-liberapay: # Replace with a single Liberapay username
-issuehunt: # Replace with a single IssueHunt username
-otechie: # Replace with a single Otechie username
-custom: # ['https://www.buymeacoffee.com/TkFxuKo']
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
deleted file mode 100644
index 511f585..0000000
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ /dev/null
@@ -1,38 +0,0 @@
----
-name: Bug report
-about: Create a report to help us improve
-title: ''
-labels: bug
-assignees: ''
-
----
-
-**Acknowledge the following**
-- [ ] I carefully read and followed the [Getting Started](https://github.com/alshedivat/al-folio#getting-started) guide.
-- [ ] I read through [FAQ](https://github.com/alshedivat/al-folio#faq) and searched through the [past issues](https://github.com/alshedivat/al-folio/issues), none of which addressed my issue.
-- [ ] The issue I am raising is a potential bug in al-folio and not just a usage question. [For usage questions, please post in the [Discussions](https://github.com/alshedivat/al-folio/discussions) instead of raising an issue.]
-
-**Describe the bug**
-A clear and concise description of what the bug is.
-
-**To Reproduce**
-Steps to reproduce the behavior:
-1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
-4. See error
-
-**Expected behavior**
-A clear and concise description of what you expected to happen.
-
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
-
-**System (please complete the following information):**
- - OS: [e.g. iOS]
- - Browser (and its version) [e.g. chrome, safari]
- - Jekyll version [e.g. 3.8.7]
-- Ruby version [e.g. 2.6.5]
-
-**Additional context**
-Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
deleted file mode 100644
index 11fc491..0000000
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ /dev/null
@@ -1,20 +0,0 @@
----
-name: Feature request
-about: Suggest an idea for this project
-title: ''
-labels: enhancement
-assignees: ''
-
----
-
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
-
-**Describe the solution you'd like**
-A clear and concise description of what you want to happen.
-
-**Describe alternatives you've considered**
-A clear and concise description of any alternative solutions or features you've considered.
-
-**Additional context**
-Add any other context or screenshots about the feature request here.
diff --git a/.github/stale.yml b/.github/stale.yml
deleted file mode 100644
index 8ec2004..0000000
--- a/.github/stale.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-# Number of days of inactivity before an issue becomes stale
-daysUntilStale: 60
-# Number of days of inactivity before a stale issue is closed
-daysUntilClose: 7
-# Issues with these labels will never be considered stale
-exemptLabels:
- - pinned
- - security
- - enhancement
-# Label to use when marking an issue as stale
-staleLabel: wontfix
-# Comment to post when marking an issue as stale. Set to `false` to disable
-markComment: >
- This issue has been automatically marked as stale because it has not had
- recent activity. It will be closed if no further activity occurs. Thank you
- for your contributions.
-# Comment to post when closing a stale issue. Set to `false` to disable
-closeComment: false
diff --git a/.github/workflows/deploy-docker-tag.yml b/.github/workflows/deploy-docker-tag.yml
deleted file mode 100644
index 3e6b6a3..0000000
--- a/.github/workflows/deploy-docker-tag.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-name: Docker Image CI (Upload Tag)
-
-on:
- push:
- tags:
- - 'v*'
-
-jobs:
-
- build:
-
- runs-on: ubuntu-latest
-
- steps:
- - name: Checkout
- uses: actions/checkout@v2
- - name: Buildx
- uses: docker/setup-buildx-action@v1
-
- -
- name: Docker meta
- id: meta
- uses: docker/metadata-action@v4
- with:
- images: amirpourmand/al-folio
-
- - name: Login
- uses: docker/login-action@v1
- with:
- username: ${{ secrets.DOCKER_USERNAME }}
- password: ${{ secrets.DOCKER_PASSWORD }}
-
- - name: Build and push
- uses: docker/build-push-action@v3
- with:
- context: .
- push: ${{ github.event_name != 'pull_request' }}
- tags: ${{ steps.meta.outputs.tags }}
- labels: ${{ steps.meta.outputs.labels }}
-
diff --git a/.github/workflows/deploy-image.yml b/.github/workflows/deploy-image.yml
deleted file mode 100644
index b747dfc..0000000
--- a/.github/workflows/deploy-image.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-name: Docker Image CI
-
-on:
- push:
- branches: [ master ]
-
-jobs:
-
- build:
-
- runs-on: ubuntu-latest
- if: github.repository_owner == 'alshedivat'
-
- steps:
- - name: Checkout
- uses: actions/checkout@v2
- - name: Buildx
- uses: docker/setup-buildx-action@v1
-
- - name: Login
- uses: docker/login-action@v1
- with:
- username: ${{ secrets.DOCKER_USERNAME }}
- password: ${{ secrets.DOCKER_PASSWORD }}
-
- - name: Build and push
- uses: docker/build-push-action@v2
- with:
- context: .
- push: true
- tags: amirpourmand/al-folio
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
deleted file mode 100644
index f6455fd..0000000
--- a/.github/workflows/deploy.yml
+++ /dev/null
@@ -1,42 +0,0 @@
-name: deploy
-
-on:
- push:
- branches:
- - master
- - main
- pull_request:
- branches:
- - master
- - main
-
-jobs:
- deploy:
- runs-on: ubuntu-latest
- steps:
- - name: Checkout code
- uses: actions/checkout@v3
- - name: Setup Ruby
- uses: ruby/setup-ruby@v1
- with:
- ruby-version: '3.0.2'
- bundler-cache: true
- - name: Install deps
- run: |
- npm install -g mermaid.cli
- - name: Setup deploy options
- id: setup
- run: |
- git config --global user.name "GitHub Action"
- git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
- if [[ ${GITHUB_REF} = refs/pull/*/merge ]]; then # pull request
- echo "::set-output name=SRC_BRANCH::${GITHUB_HEAD_REF}"
- echo "::set-output name=NO_PUSH::--no-push"
- elif [[ ${GITHUB_REF} = refs/heads/* ]]; then # branch, e.g. master, source etc
- echo "::set-output name=SRC_BRANCH::${GITHUB_REF#refs/heads/}"
- fi
- echo "::set-output name=DEPLOY_BRANCH::gh-pages"
- - name: Deploy website
- run: yes | bash bin/deploy --verbose ${{ steps.setup.outputs.NO_PUSH }}
- --src ${{ steps.setup.outputs.SRC_BRANCH }}
- --deploy ${{ steps.setup.outputs.DEPLOY_BRANCH }}
diff --git a/.nojekyll b/.nojekyll
new file mode 100644
index 0000000..e69de29
diff --git a/404.html b/404.html
index 0da4ee0..d2a4616 100644
--- a/404.html
+++ b/404.html
@@ -1,9 +1 @@
----
-layout: page
-permalink: /404.html
-title: "Page not found"
-description: "Looks like there has been a mistake. Nothing exists here."
-redirect: true
----
-
-
You will be redirected to the main page within 3 seconds. If not redirected, please click here.
+ Page not found | Shern Ren Tee
Page not found
Looks like there has been a mistake. Nothing exists here.
You will be redirected to the main page within 3 seconds. If not redirected, please click here.
\ No newline at end of file
diff --git a/Gemfile b/Gemfile
deleted file mode 100644
index 782a0c4..0000000
--- a/Gemfile
+++ /dev/null
@@ -1,23 +0,0 @@
-source 'https://rubygems.org'
-group :jekyll_plugins do
- gem 'jekyll'
- gem 'jekyll-archives'
- gem 'jekyll-diagrams'
- gem 'jekyll-email-protect'
- gem 'jekyll-feed'
- gem 'jekyll-imagemagick'
- gem 'jekyll-minifier'
- gem 'jekyll-paginate-v2'
- gem 'jekyll-scholar'
- gem 'jekyll-sitemap'
- gem 'jekyll-target-blank'
- gem 'jekyll-twitter-plugin'
- gem 'jemoji'
- gem 'mini_racer'
- gem 'unicode_utils'
- gem 'webrick'
-end
-group :other_plugins do
- gem 'httparty'
- gem 'feedjira'
-end
diff --git a/_bibliography/all_papers.bib b/_bibliography/all_papers.bib
deleted file mode 100644
index 532f6ab..0000000
--- a/_bibliography/all_papers.bib
+++ /dev/null
@@ -1,48 +0,0 @@
----
----
-
-@article{Ahrens_Iwers_2022,
- doi = {10.1063/5.0099239},
- url = {https://doi.org/10.1063/2F5.0099239},
- year = 2022,
- month = {jul},
- publisher = {{AIP} Publishing},
- author = {Ludwig Jo Ahrens-Iwers and Mathijs Janssen and Shern Ren Tee and Robert Horst Meißner},
- title = {{ELECTRODE}: An electrochemistry package for atomistic simulations},
- journal = {The Journal of Chemical Physics}
-},
-@article{Tee_2022,
- doi = {10.1063/5.0086986},
- url = {https://doi.org/10.1063/2F5.0086986},
- year = 2022,
- month = {apr},
- publisher = {{AIP} Publishing},
- author = {Shern Ren Tee and Debra J. Searles},
- title = {Fully Periodic, Computationally Efficient Constant Potential Molecular Dynamics Simulations of Ionic Liquid Supercapacitors},
- journal = {The Journal of Chemical Physics}
-},
-@article{Zhou_2021,
- doi = {10.1083/jcb.202005138},
- url = {https://doi.org/10.1083/2Fjcb.202005138},
- year = 2021,
- month = {jan},
- publisher = {Rockefeller University Press},
- volume = {220},
- number = {3},
- author = {Yong Zhou and Nicholas Ariotti and James Rae and Hong Liang and Vikas Tillu and Shern Tee and Michele Bastiani and Adekunle T. Bademosi and Brett M. Collins and Frederic A. Meunier and John F. Hancock and Robert G. Parton},
- title = {Caveolin-1 and cavin1 act synergistically to generate a unique lipid environment in caveolae},
- journal = {Journal of Cell Biology}
-},
-@book{Shern_Ren_Tee_98165405,
-title={Theory and Practice in Constant Potential Molecular Dynamics Simulations},
-author={Shern Ren Tee and Shern Ren Tee},
-doi={10.1063/9780735422377\_004},
-url={http://doi.org/10.1063/9780735422377\_004},
-year={2021}
-},
-@article{Tee_2018,doi = {10.1103/physrevapplied.9.034025},url = {https://doi.org/10.1103/2Fphysrevapplied.9.034025},year = 2018,month = {mar},publisher = {American Physical Society ({APS})},volume = {9},number = {3},author = {Shern Ren Tee and Xinpeng Hu and Iong Ying Loh and Zhisong Wang},title = {Mechanosensing Potentials Gate Fuel Consumption in a Bipedal {DNA} Nanowalker},journal = {Physical Review Applied}},
-@article{Tee_2018,doi = {10.1021/acsomega.7b01692},url = {https://doi.org/10.1021/2Facsomega.7b01692},year = 2018,month = {jan},publisher = {American Chemical Society ({ACS})},volume = {3},number = {1},pages = {292--301},author = {Shern Ren Tee and Zhisong Wang},title = {How Well Can {DNA} Rupture {DNA}? Shearing and Unzipping Forces inside {DNA} Nanostructures},journal = {{ACS} Omega}},
-@article{Chiang_2018,doi = {10.1039/c7nr09724g},url = {https://doi.org/10.1039/2Fc7nr09724g},year = 2018,publisher = {Royal Society of Chemistry ({RSC})},volume = {10},number = {19},pages = {9199--9211},author = {Y. H. Chiang and S. L. Tsai and S. R. Tee and O. L. Nair and I. Y. Loh and M. H. Liu and Z. S. Wang},title = {Inchworm bipedal nanowalker},journal = {Nanoscale}},
-@article{Tee2017,title = {A DNA bipedal nanowalker with a piston-like expulsion stroke},journal = {Nanoscale},year = {2017},volume = {9},number = {33},pages = {12142-12149},author = {Yeo, Q.Y. and Loh, I.Y. and Tee, S.R. and Chiang, Y.H. and Cheng, J. and Liu, M.H. and Wang, Z.S.}},
-@article{Tee2016,title = {Biomimetic Autonomous Enzymatic Nanowalker of High Fuel Efficiency},journal = {ACS Nano},year = {2016},volume = {10},number = {6},pages = {5882-5890},author = {Liu, M. and Cheng, J. and Tee, S.R. and Sreelatha, S. and Loh, I.Y. and Wang, Z.}},
-@article{Tee2014,title = {From bistate molecular switches to self-directed track-walking nanomotors},journal = {ACS Nano},year = {2014},volume = {8},number = {10},pages = {10293-10304},author = {Loh, I.Y. and Cheng, J. and Tee, S.R. and Efremov, A. and Wang, Z.}}
diff --git a/_bibliography/one_paper.bib b/_bibliography/one_paper.bib
deleted file mode 100755
index 24fac48..0000000
--- a/_bibliography/one_paper.bib
+++ /dev/null
@@ -1,28 +0,0 @@
-
-
-
-
-
-
-@article{doi:10.1063/5.0086986,
-author = {Tee,Shern R. and Searles,Debra J. },
-title = {Fully periodic, computationally efficient constant potential molecular dynamics simulations of ionic liquid supercapacitors},
-journal = {The Journal of Chemical Physics},
-volume = {156},
-number = {18},
-pages = {184101},
-year = {2022},
-doi = {10.1063/5.0086986},
-
-URL = {
- https://doi.org/10.1063/5.0086986
-
-},
-eprint = {
- https://doi.org/10.1063/5.0086986
-
-}
-
-}
-
-
diff --git a/_bibliography/papers.bib b/_bibliography/papers.bib
deleted file mode 100644
index f658eec..0000000
--- a/_bibliography/papers.bib
+++ /dev/null
@@ -1,117 +0,0 @@
-@article{ahrens2022electrode,
- title={ELECTRODE: An electrochemistry package for atomistic simulations},
- author={Ahrens-Iwers, Ludwig JV and Janssen, Mathijs and Tee, Shern R and Mei{\ss}ner, Robert H},
- journal={The Journal of Chemical Physics},
- volume={157},
- number={8},
- pages={084801},
- year={2022},
- month ={jul},
- publisher={AIP Publishing LLC},
- doi = {10.1063/5.0099239},
- url = {https://doi.org/10.1063/5.0099239},
- selected = {true}
-}
-
-@article{tee2022fully,
- title={Fully periodic, computationally efficient constant potential molecular dynamics simulations of ionic liquid supercapacitors},
- author={Tee, Shern R and Searles, Debra J},
- journal={The Journal of Chemical Physics},
- volume={156},
- number={18},
- pages={184101},
- year={2022},
- mount = {apr},
- publisher={AIP Publishing LLC},
- doi = {10.1063/5.0086986},
- url = {https://doi.org/10.1063/5.0086986},
- selected = {true}
-}
-
-@article{liu2016biomimetic,
- title={Biomimetic autonomous enzymatic nanowalker of high fuel efficiency},
- author={Liu, Meihan and Cheng, Juan and Tee, Shern Ren and Sreelatha, Sarangapani and Loh, Iong Ying and Wang, Zhisong},
- journal={ACS nano},
- volume={10},
- number={6},
- pages={5882--5890},
- year={2016},
- publisher={ACS Publications}
-}
-
-@article{tee2018well,
- title={How Well Can DNA Rupture DNA? Shearing and Unzipping Forces inside DNA Nanostructures},
- author={Tee, Shern Ren and Wang, Zhisong},
- journal={ACS Omega},
- volume={3},
- number={1},
- pages={292--301},
- year={2018},
- publisher={ACS Publications}
-}
-
-@article{tee2018mechanosensing,
- title={Mechanosensing Potentials Gate Fuel Consumption in a Bipedal DNA Nanowalker},
- author={Tee, Shern Ren and Hu, Xinpeng and Loh, Iong Ying and Wang, Zhisong},
- journal={Physical Review Applied},
- volume={9},
- number={3},
- pages={034025},
- year={2018},
- publisher={APS}
-}
-
-@article{yeo2017dna,
- title={A DNA bipedal nanowalker with a piston-like expulsion stroke},
- author={Yeo, QY and Loh, IY and Tee, SR and Chiang, YH and Cheng, J and Liu, MH and Wang, ZS},
- journal={Nanoscale},
- volume={9},
- number={33},
- pages={12142--12149},
- year={2017},
- publisher={Royal Society of Chemistry}
-}
-
-@article{loh2014bistate,
- title={From bistate molecular switches to self-directed track-walking nanomotors},
- author={Loh, Iong Ying and Cheng, Juan and Tee, Shern Ren and Efremov, Artem and Wang, Zhisong},
- journal={Acs Nano},
- volume={8},
- number={10},
- pages={10293--10304},
- year={2014},
- publisher={ACS Publications}
-}
-
-@article{chiang2018inchworm,
- title={Inchworm bipedal nanowalker},
- author={Chiang, YH and Tsai, SL and Tee, SR and Nair, OL and Loh, IY and Liu, MH and Wang, ZS},
- journal={Nanoscale},
- volume={10},
- number={19},
- pages={9199--9211},
- year={2018},
- publisher={Royal Society of Chemistry}
-}
-
-@article{zhou2021caveolin,
- title={Caveolin-1 and cavin1 act synergistically to generate a unique lipid environment in caveolae},
- author={Zhou, Yong and Ariotti, Nicholas and Rae, James and Liang, Hong and Tillu, Vikas and Tee, Shern and Bastiani, Michele and Bademosi, Adekunle T and Collins, Brett M and Meunier, Frederic A and others},
- journal={Journal of Cell Biology},
- volume={220},
- number={3},
- year={2021},
- publisher={The Rockefeller University Press},
- doi = {10.1083/jcb.202005138},
- url = {https://doi.org/10.1083/jcb.202005138}
-}
-
-@article{tee2021theory,
- title={Theory and Practice in Constant Potential Molecular Dynamics Simulations},
- author={Tee, Shern Ren},
- year={2021},
- publisher={AIP Publishing LLC, Melville, New York},
- doi={10.1063/9780735422377_004},
- url={http://doi.org/10.1063/9780735422377_004}
-}
-
diff --git a/_bibliography/papers_orcid.bib b/_bibliography/papers_orcid.bib
deleted file mode 100644
index b9fd7a0..0000000
--- a/_bibliography/papers_orcid.bib
+++ /dev/null
@@ -1,45 +0,0 @@
-@article{Ahrens_Iwers_2022,
- doi = {10.1063/5.0099239},
- url = {https://doi.org/10.1063%2F5.0099239},
- year = 2022,
- month = {jul},
- publisher = {{AIP} Publishing},
- author = {Ludwig Jo Ahrens-Iwers and Mathijs Janssen and Shern Ren Tee and Robert Horst Mei{\ss}ner},
- title = {{ELECTRODE}: An electrochemistry package for atomistic simulations},
- journal = {The Journal of Chemical Physics}
-},
-@article{Tee_2022,
- doi = {10.1063/5.0086986},
- url = {https://doi.org/10.1063%2F5.0086986},
- year = 2022,
- month = {apr},
- publisher = {{AIP} Publishing},
- author = {Shern Ren Tee and Debra J. Searles},
- title = {Fully Periodic, Computationally Efficient Constant Potential Molecular Dynamics Simulations of Ionic Liquid Supercapacitors},
- journal = {The Journal of Chemical Physics}
-},
-@article{Zhou_2021,
- doi = {10.1083/jcb.202005138},
- url = {https://doi.org/10.1083%2Fjcb.202005138},
- year = 2021,
- month = {jan},
- publisher = {Rockefeller University Press},
- volume = {220},
- number = {3},
- author = {Yong Zhou and Nicholas Ariotti and James Rae and Hong Liang and Vikas Tillu and Shern Tee and Michele Bastiani and Adekunle T. Bademosi and Brett M. Collins and Frederic A. Meunier and John F. Hancock and Robert G. Parton},
- title = {Caveolin-1 and cavin1 act synergistically to generate a unique lipid environment in caveolae},
- journal = {Journal of Cell Biology}
-},
-@book{Shern_Ren_Tee_98165405,
-title={Theory and Practice in Constant Potential Molecular Dynamics Simulations},
-author={Shern Ren Tee and Shern Ren Tee},
-doi={10.1063/9780735422377\_004},
-url={http://doi.org/10.1063/9780735422377\_004},
-year={2021}
-},
-@article{Tee_2018,doi = {10.1103/physrevapplied.9.034025},url = {https://doi.org/10.1103%2Fphysrevapplied.9.034025},year = 2018,month = {mar},publisher = {American Physical Society ({APS})},volume = {9},number = {3},author = {Shern Ren Tee and Xinpeng Hu and Iong Ying Loh and Zhisong Wang},title = {Mechanosensing Potentials Gate Fuel Consumption in a Bipedal {DNA} Nanowalker},journal = {Physical Review Applied}},
-@article{Tee_2018,doi = {10.1021/acsomega.7b01692},url = {https://doi.org/10.1021%2Facsomega.7b01692},year = 2018,month = {jan},publisher = {American Chemical Society ({ACS})},volume = {3},number = {1},pages = {292--301},author = {Shern Ren Tee and Zhisong Wang},title = {How Well Can {DNA} Rupture {DNA}? Shearing and Unzipping Forces inside {DNA} Nanostructures},journal = {{ACS} Omega}},
-@article{Chiang_2018,doi = {10.1039/c7nr09724g},url = {https://doi.org/10.1039%2Fc7nr09724g},year = 2018,publisher = {Royal Society of Chemistry ({RSC})},volume = {10},number = {19},pages = {9199--9211},author = {Y. H. Chiang and S. L. Tsai and S. R. Tee and O. L. Nair and I. Y. Loh and M. H. Liu and Z. S. Wang},title = {Inchworm bipedal nanowalker},journal = {Nanoscale}},
-@article{Tee2017,title = {A DNA bipedal nanowalker with a piston-like expulsion stroke},journal = {Nanoscale},year = {2017},volume = {9},number = {33},pages = {12142-12149},author = {Yeo, Q.Y. and Loh, I.Y. and Tee, S.R. and Chiang, Y.H. and Cheng, J. and Liu, M.H. and Wang, Z.S.}},
-@article{Tee2016,title = {Biomimetic Autonomous Enzymatic Nanowalker of High Fuel Efficiency},journal = {ACS Nano},year = {2016},volume = {10},number = {6},pages = {5882-5890},author = {Liu, M. and Cheng, J. and Tee, S.R. and Sreelatha, S. and Loh, I.Y. and Wang, Z.}},
-@article{Tee2014,title = {From bistate molecular switches to self-directed track-walking nanomotors},journal = {ACS Nano},year = {2014},volume = {8},number = {10},pages = {10293-10304},author = {Loh, I.Y. and Cheng, J. and Tee, S.R. and Efremov, A. and Wang, Z.}}
\ No newline at end of file
diff --git a/_bibliography/template_papers.bib b/_bibliography/template_papers.bib
deleted file mode 100644
index 1c707bc..0000000
--- a/_bibliography/template_papers.bib
+++ /dev/null
@@ -1,82 +0,0 @@
----
----
-
-@string{aps = {American Physical Society,}}
-
-@book{einstein1956investigations,
- bibtex_show={true},
- title={Investigations on the Theory of the Brownian Movement},
- author={Einstein, Albert},
- year={1956},
- publisher={Courier Corporation,},
- preview={brownian-motion.gif}
-}
-
-@article{einstein1950meaning,
- abbr={AJP},
- bibtex_show={true},
- title={The meaning of relativity},
- author={Einstein, Albert and Taub, AH},
- journal={American Journal of Physics,},
- volume={18},
- number={6},
- pages={403--404},
- year={1950},
- publisher={American Association of Physics Teachers,}
-}
-
-@article{PhysRev.47.777,
- abbr={PhysRev},
- title={Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?},
- author={Einstein, A. and Podolsky, B. and Rosen, N.},
- abstract={In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.},
- journal={Phys. Rev.,},
- volume={47},
- issue={10},
- pages={777--780},
- numpages={0},
- year={1935},
- month={May},
- publisher=aps,
- doi={10.1103/PhysRev.47.777},
- url={http://link.aps.org/doi/10.1103/PhysRev.47.777},
- html={https://journals.aps.org/pr/abstract/10.1103/PhysRev.47.777},
- pdf={example_pdf.pdf},
- selected={true}
-}
-
-@article{einstein1905molekularkinetischen,
- title={{\"U}ber die von der molekularkinetischen Theorie der W{\"a}rme geforderte Bewegung von in ruhenden Fl{\"u}ssigkeiten suspendierten Teilchen},
- author={Einstein, A.},
- journal={Annalen der physik,},
- volume={322},
- number={8},
- pages={549--560},
- year={1905},
- publisher={Wiley Online Library}
-}
-
-@article{einstein1905movement,
- abbr={Ann. Phys.},
- title={Un the movement of small particles suspended in statiunary liquids required by the molecular-kinetic theory 0f heat},
- author={Einstein, A.},
- journal={Ann. Phys.,},
- volume={17},
- pages={549--560},
- year={1905}
-}
-
-@article{einstein1905electrodynamics,
- title={On the electrodynamics of moving bodies},
- author={Einstein, A.},
- year={1905}
-}
-
-@book{przibram1967letters,
- bibtex_show={true},
- title={Letters on wave mechanics},
- author={Einstein, Albert and Schrödinger, Erwin and Planck, Max and Lorentz, Hendrik Antoon and Przibram, Karl},
- year={1967},
- publisher={Vision},
- preview={wave-mechanics.gif}
-}
diff --git a/_config.yml b/_config.yml
deleted file mode 100644
index f3c90a2..0000000
--- a/_config.yml
+++ /dev/null
@@ -1,345 +0,0 @@
-# -----------------------------------------------------------------------------
-# Site settings
-# -----------------------------------------------------------------------------
-
-title: blank # the website title (if blank, full name will be used instead)
-first_name: Shern
-middle_name: Ren
-last_name: Tee
-email: shernren@gmail.com
-description: > # the ">" symbol means to ignore newlines until "footer_text:"
- unconventional molecular dynamics researcher, open source scientific coder, sleep-deprived father
-footer_text: >
- Powered by Jekyll with al-folio theme.
- Hosted by GitHub Pages.
- Photos from Unsplash.
-keywords: >
- molecular-dynamics, nonequilibrium, statistical-mechanics, constant-potential,
- electrode, LAMMPS, C++, FAIR, open-source, academia
-
-lang: en # the language of your site (for example: en, fr, cn, ru, etc.)
-icon: ⚛️ # the emoji used as the favicon (alternatively, provide image name in /assets/img/)
-
-url: https://srtee.github.io # the base hostname & protocol for your site
-baseurl: # the subpath of your site, e.g. /blog/
-last_updated: false # set to true if you want to display last updated in the footer
-impressum_path: # set to path to include impressum link in the footer, use the same path as permalink in a page, helps to conform with EU GDPR
-
-# -----------------------------------------------------------------------------
-# Theme
-# -----------------------------------------------------------------------------
-
-# code highlighter theme
-highlight_theme_light: github # https://github.com/jwarby/jekyll-pygments-themes
-highlight_theme_dark: native # https://github.com/jwarby/jekyll-pygments-themes
-
-# repo color theme
-repo_theme_light: default # https://github.com/anuraghazra/github-readme-stats/blob/master/themes/README.md
-repo_theme_dark: dark # https://github.com/anuraghazra/github-readme-stats/blob/master/themes/README.md
-
-# -----------------------------------------------------------------------------
-# RSS Feed
-# -----------------------------------------------------------------------------
-# will use title and url fields
-# Take a look to https://github.com/jekyll/jekyll-feed for more customization
-
-rss_icon: true
-
-# -----------------------------------------------------------------------------
-# Layout
-# -----------------------------------------------------------------------------
-
-navbar_fixed: true
-footer_fixed: true
-
-# Dimensions
-max_width: 800px
-
-# TODO: add layout settings (single page vs. multi-page)
-
-# -----------------------------------------------------------------------------
-# Open Graph & Schema.org
-# -----------------------------------------------------------------------------
-# Display links to the page with a preview object on social media.
-serve_og_meta: false # Include Open Graph meta tags in the HTML head
-serve_schema_org: false # Include Schema.org in the HTML head
-og_image: # The site-wide (default for all links) Open Graph preview image
-
-# -----------------------------------------------------------------------------
-# Social integration
-# -----------------------------------------------------------------------------
-
-github_username: srtee
-gitlab_username: # your GitLab user name
-twitter_username: # your Twitter handle
-linkedin_username: shern-tee-8172241b3
-scholar_userid: JgXtTSUAAAAJ
-semanticscholar_id: # your Semantic Scholar ID
-orcid_id: 0000-0003-2701-005X
-medium_username: # your Medium username
-quora_username: # your Quora username
-publons_id: # your ID on Publons
-research_gate_profile: # your profile on ResearchGate
-blogger_url: # your blogger URL
-work_url: # work page URL
-keybase_username: # your keybase user name
-wikidata_id: # your wikidata id
-dblp_url: # your DBLP profile url
-stackoverflow_id: # your stackoverflow id
-kaggle_id: # your kaggle id
-lastfm_id: # your lastfm id
-spotify_id: # your spotify id
-pinterest_id: # your pinterest id
-unsplash_id: # your unsplash id
-instagram_id: # your instagram id
-facebook_id: # your facebook id
-discord_id: # your discord id (18-digit unique numerical identifier)
-
-contact_note: >
-
-# -----------------------------------------------------------------------------
-# Analytics and search engine verification
-# -----------------------------------------------------------------------------
-
-google_analytics: # your Goole Analytics measurement ID (format: G-XXXXXXXXXX)
-panelbear_analytics: # panelbear analytics site ID (format: XXXXXXXXX)
-
-google_site_verification: # your google-site-verification ID (Google Search Console)
-bing_site_verification: # out your bing-site-verification ID (Bing Webmaster)
-
-# -----------------------------------------------------------------------------
-# Blog
-# -----------------------------------------------------------------------------
-
-blog_name: shernanigans # blog_name will be displayed in your blog page
-blog_nav_title: blog # your blog must have a title for it to be displayed in the nav bar
-blog_description: >
- unconventional molecular dynamics researcher, open source scientific coder, sleep-deprived father
-permalink: /blog/:year/:title/
-
-# Pagination
-pagination:
- enabled: true
-
-# Comments
-disqus_shortname: # al-folio # put your disqus shortname
-# https://help.disqus.com/en/articles/1717111-what-s-a-shortname
-
-# External sources.
-# If you have blog posts published on medium.com or other exteranl sources,
-# you can display them in your blog by adding a link to the RSS feed.
-external_sources:
- # - name: medium.com
- # rss_url: https://medium.com/@al-folio/feed
-
-# -----------------------------------------------------------------------------
-# Collections
-# -----------------------------------------------------------------------------
-
-collections:
- news:
- defaults:
- layout: post
- output: true
- permalink: /news/:path/
- projects:
- output: true
- permalink: /projects/:path/
-
-news_scrollable: true # adds a vertical scroll bar if there are more than 3 news items
-news_limit: 5 # leave blank to include all the news in the `_news` folder
-
-# -----------------------------------------------------------------------------
-# Jekyll settings
-# -----------------------------------------------------------------------------
-
-# Markdown and syntax highlight
-markdown: kramdown
-highlighter: rouge
-kramdown:
- input: GFM
- syntax_highlighter_opts:
- css_class: 'highlight'
- span:
- line_numbers: false
- block:
- line_numbers: false
- start_line: 1
-
-# Includes & excludes
-include: ['_pages']
-exclude:
- - bin
- - Gemfile
- - Gemfile.lock
- - vendor
-keep_files:
- - CNAME
- - .nojekyll
- - .git
-
-# Plug-ins
-plugins:
- - jekyll-archives
- - jekyll-diagrams
- - jekyll-email-protect
- - jekyll-feed
- - jekyll-imagemagick
- - jekyll-minifier
- - jekyll-paginate-v2
- - jekyll/scholar
- - jekyll-sitemap
- - jekyll-target-blank
- - jekyll-twitter-plugin
- - jemoji
-
-# Sitemap settings
-defaults:
- - scope:
- path: "assets/**/*.*"
- values:
- sitemap: false
-
-# -----------------------------------------------------------------------------
-# Jekyll Minifier
-# -----------------------------------------------------------------------------
-
-jekyll-minifier:
- exclude: ['robots.txt']
- uglifier_args:
- harmony: true
-
-# -----------------------------------------------------------------------------
-# Jekyll Archives
-# -----------------------------------------------------------------------------
-
-jekyll-archives:
- enabled: [year, tags] # enables year, tag and category archives (remove if you need to disable one of them).
- layouts:
- year: archive-year
- tag: archive-tag
- # category: archive-category
- permalinks:
- year: '/blog/:year/'
- tag: '/blog/tag/:name/'
- # category: '/blog/category/:name/'
-
-display_tags: ['spack', 'doco'] # this tags will be dispalyed on the front page of your blog
-
-# -----------------------------------------------------------------------------
-# Jekyll Scholar
-# -----------------------------------------------------------------------------
-
-scholar:
-
- last_name: [Tee]
- first_name: [Shern, R.]
-
- style: american-chemical-society
- locale: en
-
- source: /_bibliography/
- bibliography: papers.bib
- bibliography_template: bib
- # Note: if you have latex math in your bibtex, the latex filter
- # preprocessing may conflict with MathJAX if the latter is enabled.
- # See https://github.com/alshedivat/al-folio/issues/357.
- bibtex_filters: [latex, smallcaps, superscript]
-
- replace_strings: true
- join_strings: true
-
- details_dir: bibliography
- details_layout: bibtex.html
- details_link: Details
-
- query: "@*"
-
-# Filter out certain bibtex entry keywords used internally from the bib output
-filtered_bibtex_keywords: [abbr, abstract, arxiv, bibtex_show, html, pdf, selected, supp, blog, code, poster, slides, website, preview]
-
-# Maximum number of authors to be shown for each publication (more authors are visible on click)
-max_author_limit: 5 # leave blank to always show all authors
-more_authors_animation_delay: 10 # more authors are revealed on click using animation; smaller delay means faster animation
-
-
-# -----------------------------------------------------------------------------
-# Responsive WebP Images
-# -----------------------------------------------------------------------------
-
-imagemagick:
- enabled: true # enables responsive images for your site (recomended, see https://github.com/alshedivat/al-folio/issues/537)
- widths:
- - 480
- - 800
- - 1400
- input_directories:
- - assets/img/
- input_formats:
- - ".jpg"
- - ".jpeg"
- - ".png"
- - ".tiff"
- output_formats:
- webp: "-resize 800x"
-
-# -----------------------------------------------------------------------------
-# Jekyll Diagrams
-# -----------------------------------------------------------------------------
-
-jekyll-diagrams:
- # configuration, see https://github.com/zhustec/jekyll-diagrams.
- # feel free to comment out this section if not using jekyll diagrams.
-
-
-# -----------------------------------------------------------------------------
-# Optional Features
-# -----------------------------------------------------------------------------
-
-enable_google_analytics: false # enables google analytics
-enable_panelbear_analytics: false # enables panelbear analytics
-enable_google_verification: false # enables google site verification
-enable_bing_verification: false # enables bing site verification
-enable_masonry: true # enables automatic project cards arangement
-enable_math: true # enables math typesetting (uses MathJax)
-enable_tooltips: false # enables automatic tooltip links generated
- # for each section titles on pages and posts
-enable_darkmode: true # enables switching between light/dark modes
-enable_navbar_social: false # enables displaying social links in the
- # navbar on the about page
-enable_project_categories: true # enables categorization of projects into
- # multiple categories
-enable_medium_zoom: true # enables image zoom feature (as on medium.com)
-enable_header_netlify_identity: false # enables Netlify Identity button in header
-
-# -----------------------------------------------------------------------------
-# Library versions
-# -----------------------------------------------------------------------------
-
-academicons:
- version: "1.9.1"
- integrity: "sha256-i1+4qU2G2860dGGIOJscdC30s9beBXjFfzjWLjBRsBg="
-bootstrap:
- version: "4.6.1"
- integrity:
- css: "sha256-DF7Zhf293AJxJNTmh5zhoYYIMs2oXitRfBjY+9L//AY="
- js: "sha256-fgLAgv7fyCGopR/gBNq2iW3ZKIdqIcyshnUULC4vex8="
-fontawesome:
- version: "5.15.4"
- integrity: "sha256-mUZM63G8m73Mcidfrv5E+Y61y7a12O5mW4ezU3bxqW4="
-jquery:
- version: "3.6.0"
- integrity: "sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4="
-mathjax:
- version: "3.2.0"
-masonry:
- version: "4.2.2"
- integrity: "sha256-Nn1q/fx0H7SNLZMQ5Hw5JLaTRZp0yILA/FRexe19VdI="
-mdb:
- version: "4.20.0"
- integrity:
- css: "sha256-jpjYvU3G3N6nrrBwXJoVEYI/0zw8htfFnhT9ljN3JJw="
- js: "sha256-NdbiivsvWt7VYCt6hYNT3h/th9vSTL4EDWeGs5SN3DA="
-medium_zoom:
- version: "1.0.6"
- integrity: "sha256-EdPgYcPk/IIrw7FYeuJQexva49pVRZNmt3LculEr7zM="
diff --git a/_data/coauthors.yml b/_data/coauthors.yml
deleted file mode 100644
index 8ed5212..0000000
--- a/_data/coauthors.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-"Adams":
- - firstname: ["Edwin", "E.", "E. P.", "Edwin Plimpton"]
- url: https://en.wikipedia.org/wiki/Edwin_Plimpton_Adams
-
-"Podolsky":
- - firstname: ["Boris", "B.", "B. Y.", "Boris Yakovlevich"]
- url: https://en.wikipedia.org/wiki/Boris_Podolsky
-
-"Rosen":
- - firstname: ["Nathan", "N."]
- url: https://en.wikipedia.org/wiki/Nathan_Rosen
-
-"Bach":
- - firstname: ["Johann Sebastian", "J. S."]
- url: https://en.wikipedia.org/wiki/Johann_Sebastian_Bach
-
- - firstname: ["Carl Philipp Emanuel", "C. P. E."]
- url: https://en.wikipedia.org/wiki/Carl_Philipp_Emanuel_Bach
-
-"Przibram":
- - firstname: ["Karl"]
- url: https://link.springer.com/article/10.1007/s00016-019-00242-z
-
-"Schrödinger":
- - firstname: ["Erwin"]
- url: https://en.wikipedia.org/wiki/Erwin_Schr%C3%B6dinger
-
-"Lorentz":
- - firstname: ["Hendrik Antoon"]
- url: https://en.wikipedia.org/wiki/Hendrik_Lorentz
-
-"Planck":
- - firstname: ["Max"]
- url: https://en.wikipedia.org/wiki/Max_Planck
diff --git a/_data/cv.yml b/_data/cv.yml
deleted file mode 100644
index 5b11572..0000000
--- a/_data/cv.yml
+++ /dev/null
@@ -1,97 +0,0 @@
-- title: General Information
- type: map
- contents:
- - name: Full Name
- value: Albert Einstein
- - name: Date of Birth
- value: 14th March 1879
- - name: Languages
- value: English, German
-
-- title: Education
- type: time_table
- contents:
- - title: PhD
- institution: University of Zurich, Zurich, Switzerland
- year: 1905
- description:
- - Description 1.
- - Description 2.
- - title: Description 3.
- contents:
- - Sub-description 1.
- - Sub-description 2.
- - title: Federal teaching diploma
- institution: Eidgenössische Technische Hochschule, Zurich, Switzerland
- year: 1900
- description:
- - Description 1.
- - Description 2.
-
-- title: Experience
- type: time_table
- contents:
- - title: Professor of Theoretical Physics
- institution: Institute for Advanced Study, Princeton University
- year: 1933 - 1955
- description:
- - Description 1.
- - Description 2.
- - title: Description 3.
- contents:
- - Sub-description 1.
- - Sub-description 2.
- - title: Visiting Professor
- institution: California Institute of Technology, Pasadena, California, US
- year: 1933
- description:
- - Description 1.
- - Description 2.
-
- - title: Director
- institution: Kaiser Wilhelm Institute for Physics, Berlin, Germany.
- year: 1917-1933
-
- - title: Professor of Theoretical Physics
- institution: Karl-Ferdinand University, Prague, Czechoslovakia
- year: 1911 - 1917
- description:
-
- - title: Associate Professor of Theoretical Physics
- institution: University of Zurich, Zurich, Switzerland
- year: 1909 - 1911
-
-- title: Open Source Projects
- type: time_table
- contents:
- - title: al-folio
- year: 2015-now
- description: A beautiful, simple, clean, and responsive Jekyll theme for academics.
-
-- title: Honors and Awards
- type: time_table
- contents:
- - year: 1921
- items:
- - Nobel Prize in Physics
- - Matteucci Medal
- - year: 2029
- items:
- - Max Planck Medal
-
-- title: Academic Interests
- type: nested_list
- contents:
- - title: Topic 1.
- items:
- - Description 1.
- - Description 2.
- - title: Topic 2.
- items:
- - Description 1.
- - Description 2.
-
-- title: Other Interests
- type: list
- contents:
- - Hobbies: Hobby 1, Hobby 2, etc.
diff --git a/_data/repositories.yml b/_data/repositories.yml
deleted file mode 100644
index 5205c9f..0000000
--- a/_data/repositories.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-github_users:
- - torvalds
- - alshedivat
-
-github_repos:
- - alshedivat/al-folio
- - twbs/bootstrap
- - jekyll/jekyll
- - jquery/jquery
- - FortAwesome/Font-Awesome
- - jpswalsh/academicons
- - mathjax/MathJax
diff --git a/_data/venues.yml b/_data/venues.yml
deleted file mode 100644
index 6c16ad5..0000000
--- a/_data/venues.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-"AJP":
- url: https://aapt.scitation.org/journal/ajp
- color: "#00369f"
-
-"PhysRev":
- url: https://journals.aps.org/
diff --git a/_includes/cv/list.html b/_includes/cv/list.html
deleted file mode 100644
index 7562585..0000000
--- a/_includes/cv/list.html
+++ /dev/null
@@ -1,5 +0,0 @@
-
- {% for content in entry.contents %}
-
{{ content }}
- {% endfor %}
-
\ No newline at end of file
diff --git a/_includes/cv/map.html b/_includes/cv/map.html
deleted file mode 100644
index e0d1983..0000000
--- a/_includes/cv/map.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
- {% for content in entry.contents %}
-
-
{{ content.name }}
-
{{ content.value }}
-
- {% endfor %}
-
\ No newline at end of file
diff --git a/_includes/cv/nested_list.html b/_includes/cv/nested_list.html
deleted file mode 100644
index 4778aca..0000000
--- a/_includes/cv/nested_list.html
+++ /dev/null
@@ -1,14 +0,0 @@
-
- {% for content in entry.contents %}
-
-
{{ content.title }}
- {% if content.items %}
-
- {% for subitem in content.items %}
-
{{ subitem }}
- {% endfor %}
-
- {% endif %}
-
- {% endfor %}
-
\ No newline at end of file
diff --git a/_includes/cv/time_table.html b/_includes/cv/time_table.html
deleted file mode 100644
index 123b9d0..0000000
--- a/_includes/cv/time_table.html
+++ /dev/null
@@ -1,59 +0,0 @@
-
- {% for content in entry.contents %}
-
-
- {% if content.year %}
-
-
- {{ content.year }}
-
-
- {% endif %}
-
- {% if content.title %}
-
{{content.title}}
- {% endif %}
- {% if content.institution %}
-
{{content.institution}}
- {% endif %}
- {% if content.description %}
-
- {% for item in content.description %}
-
- {% if item.contents %}
- {{ item.title }}
-
- {% for subitem in item.contents %}
-
{{ subitem }}
- {% endfor %}
-
- {% else %}
- {{ item }}
- {% endif %}
-
- {% endfor %}
-
- {% endif %}
- {% if content.items %}
-
- {% for item in content.items %}
-
- {% if item.contents %}
- {{ item.title }}
-
- {% for subitem in item.contents %}
-
{{ subitem }}
- {% endfor %}
-
- {% else %}
- {{ item }}
- {% endif %}
-
- {% endfor %}
-
- {% endif %}
-
-
-
- {% endfor %}
-
\ No newline at end of file
diff --git a/_includes/figure.html b/_includes/figure.html
deleted file mode 100644
index e67e804..0000000
--- a/_includes/figure.html
+++ /dev/null
@@ -1,36 +0,0 @@
-{%- assign img_path = include.path | remove: ".jpg" | remove: ".jpeg" | remove: ".png" | remove: ".tiff" -%}
-
-
diff --git a/_includes/footer.html b/_includes/footer.html
deleted file mode 100644
index acc4688..0000000
--- a/_includes/footer.html
+++ /dev/null
@@ -1,25 +0,0 @@
- {% if site.footer_fixed %}
-
- {%- else -%}
-
- {%- endif %}
\ No newline at end of file
diff --git a/_includes/head.html b/_includes/head.html
deleted file mode 100644
index 3e13b7d..0000000
--- a/_includes/head.html
+++ /dev/null
@@ -1,36 +0,0 @@
-
- {% include metadata.html %}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- {% if site.enable_header_netlify_identity %}
-
- {% endif %}
-
-
- {% if site.icon.size < 3 %}
-
- {% elsif site.icon != blank %}
-
- {% endif %}
-
-
-
-
- {% if site.enable_darkmode %}
-
-
-
-
- {% endif %}
diff --git a/_includes/header.html b/_includes/header.html
deleted file mode 100644
index 674ed3b..0000000
--- a/_includes/header.html
+++ /dev/null
@@ -1,122 +0,0 @@
-
-
-
-
-
-
diff --git a/_includes/metadata.html b/_includes/metadata.html
deleted file mode 100644
index f94e6cc..0000000
--- a/_includes/metadata.html
+++ /dev/null
@@ -1,192 +0,0 @@
-{% if site.enable_google_verification or site.enable_bing_verification %}
-
- {% if site.enable_google_verification -%}
-
- {%- endif -%}
- {% if site.enable_bing_verification -%}
-
- {%- endif -%}
-{%- endif %}
-
-
-
-
-
-
- {%- if site.title == "blank" -%}
- {%- capture title -%}{{ site.first_name }} {{ site.middle_name }} {{ site.last_name }}{%- endcapture -%}
- {%- else -%}
- {%- capture title -%}{{ site.title }}{%- endcapture -%}
- {%- endif -%}
- {% if page.url == '/blog/index.html' %}
- {{ site.blog_nav_title }} | {{ title }}
- {%- elsif page.title != "blank" and page.url != "/" -%}
- {{ page.title }} | {{ title }}
- {%- else -%}
- {{ title }}
- {%- endif -%}
-
-
-
-{%- if page.keywords or site.keywords %}
-
-{%- endif %}
-
-{%- if site.serve_og_meta %}
-
-
-
-
-
-
-
- {% if page.og_image or site.og_image -%}
-
- {%- endif %}
-
-
-
-
-
-
- {% if page.og_image or site.og_image -%}
-
- {%- endif %}
- {% if site.twitter_username -%}
-
-
- {%- endif %}
-{%- endif %}
-
-{%- if site.serve_schema_org %}
-
-
- {%- comment -%} Social links generator for "sameAs schema" {%- endcomment %}
- {% assign sameaslinks = "" | split: "," %}
- {%- if site.orcid_id -%}
- {%- capture link -%}https://orcid.org/{{ site.orcid_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.scholar_userid -%}
- {%- capture link -%}https://scholar.google.com/citations?user={{ site.scholar_userid }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.semanticscholar_id -%}
- {%- capture link -%}https://www.semanticscholar.org/author/{{ site.semanticscholar_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.publons_id -%}
- {%- capture link -%}https://publons.com/a/{{ site.publons_id }}/{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.research_gate_profile -%}
- {%- capture link -%}https://www.researchgate.net/profile/{{site.research_gate_profile}}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.github_username -%}
- {%- capture link -%}https://github.com/{{ site.github_username }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.linkedin_username -%}
- {%- capture link -%}https://www.linkedin.com/in/{{ site.linkedin_username }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.twitter_username -%}
- {%- capture link -%}https://twitter.com/{{ site.twitter_username }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.medium_username -%}
- {%- capture link -%}https://medium.com/@{{ site.medium_username }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.quora_username -%}
- {%- capture link -%}https://www.quora.com/profile/{{ site.quora_username }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.blogger_url -%}
- {%- capture link -%}{{ site.blogger_url }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.work_url -%}
- {%- capture link -%}{{ site.work_url }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.wikidata_id -%}
- {%- capture link -%}https://www.wikidata.org/wiki/{{ site.wikidata_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.strava_userid -%}
- {%- capture link -%}https://www.strava.com/athletes/{{ site.strava_userid }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.keybase_username -%}
- {%- capture link -%}https://keybase.io/{{ site.keybase_username }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.gitlab_username -%}
- {%- capture link -%}https://gitlab.com/{{ site.gitlab_username }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.dblp_url -%}
- {%- capture link -%}{{ site.dblp_url }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.stackoverflow_id -%}
- {%- capture link -%}https://stackoverflow.com/users/{{ site.stackoverflow_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.kaggle_id -%}
- {%- capture link -%}https://www.kaggle.com/{{ site.kaggle_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.lastfm_id -%}
- {%- capture link -%}https://www.last.fm/user/{{ site.lastfm_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.spotify_id -%}
- {%- capture link -%}https://open.spotify.com/user/{{ site.spotify_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.pinterest_id -%}
- {%- capture link -%}https://www.pinterest.com/{{ site.pinterest_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.unsplash_id -%}
- {%- capture link -%}https://unsplash.com/@{{ site.unsplash_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.instagram_id -%}
- {%- capture link -%}https://instagram.com/{{ site.instagram_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.facebook_id -%}
- {%- capture link -%}https://facebook.com/{{ site.facebook_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if site.discord_id -%}
- {%- capture link -%}https://discord.com/users/{{ site.discord_id }}{%- endcapture -%}
- {%- assign sameaslinks = sameaslinks | push: link -%}
- {%- endif -%}
- {%- if sameaslinks != blank -%}
- {%- assign sameaslinks = sameaslinks | split: "" -%}
- {%- endif -%}
-
-
-{%- endif %}
diff --git a/_includes/news.html b/_includes/news.html
deleted file mode 100644
index 307e532..0000000
--- a/_includes/news.html
+++ /dev/null
@@ -1,31 +0,0 @@
-
-
diff --git a/_pages/about.md b/_pages/about.md
deleted file mode 100644
index 3a92963..0000000
--- a/_pages/about.md
+++ /dev/null
@@ -1,19 +0,0 @@
----
-layout: about
-title: about
-permalink: /
-subtitle: Lecturer at Griffith University
-profile:
- align: right
- image: prof_pic.jpg
- image_circular: false # crops the image to make it circular
-news: true # includes a list of news items
-selected_papers: true # includes a list of papers marked as "selected={true}"
-social: true # includes social icons at the bottom of the page
----
-
-I am a physicist and coder who specializes in all molecular dynamics simulations weird and unusual. I currently focus on developing new theoretical methods in [constant potential molecular dynamics](/projects/constant-potential-molecular-dynamics/) and [nonequilibrium molecular dynamics](/projects/nonequilibrium-molecular-dynamics/), together with implementations in [LAMMPS](https://www.lammps.org) using C++.
-
-I am also a passionate [Research Software Engineer](https://researchsoftware.org). Current academic pathways provide little recognition or progression for the work RSEs, like myself, put into developing open source software and making it accessible to the wider research community. I hope to somehow help to change that! I've joined the [RSE Association of Australia and New Zealand](https://rse-aunz.github.io) and I'm keeping an eye out for opportunities to contribute.
-
-When I'm not at work I am kept busy by two young children, an air fryer, and a growing assortment of obsolete devices which I will someday transform back into something useful. I regularly answer questions about molecular dynamics at the [MatSci forums](https://matsci.org/c/lammps/40) and [Matter Modeling on StackExchange](https://mattermodeling.stackexchange.com). I am a Christian scientist (not a Christian Scientist!) and I regularly worship at [City Chapel, Kenmore](https://www.citychapel.com.au/).
diff --git a/_pages/projects.md b/_pages/projects.md
deleted file mode 100644
index 04cf6a4..0000000
--- a/_pages/projects.md
+++ /dev/null
@@ -1,58 +0,0 @@
----
-layout: page
-title: projects
-permalink: /projects/
-description: A growing collection of your cool projects.
-nav: true
-nav_order: 1
-display_categories: [work, community]
-horizontal: true
----
-
-
-
-{%- if site.enable_project_categories and page.display_categories %}
-
- {%- for category in page.display_categories %}
-
diff --git a/_plugins/external-posts.rb b/_plugins/external-posts.rb
deleted file mode 100644
index e4fd5eb..0000000
--- a/_plugins/external-posts.rb
+++ /dev/null
@@ -1,36 +0,0 @@
-require 'feedjira'
-require 'httparty'
-require 'jekyll'
-
-module ExternalPosts
- class ExternalPostsGenerator < Jekyll::Generator
- safe true
- priority :high
-
- def generate(site)
- if site.config['external_sources'] != nil
- site.config['external_sources'].each do |src|
- p "Fetching external posts from #{src['name']}:"
- xml = HTTParty.get(src['rss_url']).body
- feed = Feedjira.parse(xml)
- feed.entries.each do |e|
- p "...fetching #{e.url}"
- slug = e.title.downcase.strip.gsub(' ', '-').gsub(/[^\w-]/, '')
- path = site.in_source_dir("_posts/#{slug}.md")
- doc = Jekyll::Document.new(
- path, { :site => site, :collection => site.collections['posts'] }
- )
- doc.data['external_source'] = src['name'];
- doc.data['feed_content'] = e.content;
- doc.data['title'] = "#{e.title}";
- doc.data['description'] = e.summary;
- doc.data['date'] = e.published;
- doc.data['redirect'] = e.url;
- site.collections['posts'].docs << doc
- end
- end
- end
- end
- end
-
-end
diff --git a/_plugins/hideCustomBibtex.rb b/_plugins/hideCustomBibtex.rb
deleted file mode 100644
index 4a852fd..0000000
--- a/_plugins/hideCustomBibtex.rb
+++ /dev/null
@@ -1,15 +0,0 @@
- module Jekyll
- module HideCustomBibtex
- def hideCustomBibtex(input)
- keywords = @context.registers[:site].config['filtered_bibtex_keywords']
-
- keywords.each do |keyword|
- input = input.gsub(/^.*#{keyword}.*$\n/, '')
- end
-
- return input
- end
- end
-end
-
-Liquid::Template.register_filter(Jekyll::HideCustomBibtex)
diff --git a/_posts/2022-10-02-spack-time-1-getting-started.md b/_posts/2022-10-02-spack-time-1-getting-started.md
deleted file mode 100644
index c2372c4..0000000
--- a/_posts/2022-10-02-spack-time-1-getting-started.md
+++ /dev/null
@@ -1,40 +0,0 @@
----
-layout: post
-title: "Spack Time 1: Getting started"
-date: 2022-10-02 01:32:00 +1000
-tags: spack doco
----
-
-## Introduction
-
-I[^1] have some time after sending a big paper off to my supervisor to read, and I've decided to overhaul my build environments. My work desktop has accumulated enough entropy that I can't even power-cycle the *monitors* without having to hard-reset! So it's time to back everything up and put on a fresh Linux install -- which means I might as well do everything right.
-
-*Right*, in this case, means documenting my build environment. To get all evangelistic, documentation is foundational to making science more [FAIR](https://www.go-fair.org/fair-principles/). Documentation is how a complete stranger in the scientific ecosystem can be confident that code I develop and deploy is safe to run on their computer, let alone that it will produce the right results. But guess who's the biggest stranger in my life? It's *me*! I can count on "me" of six months or six years from now to remember practically nothing first-hand, so being all documentative and FAIRy is good for myself as much as for the wider world.
-
-So here I am, documenting how I intend to set everything up correctly, and my first step is Spack.
-
-## Spack (and Singularity)
-
-> Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy.
->
-> from: [Spack](https://spack.io/)
-
-What? "Makes installing scientific software easy?" Sign me right up!
-
-I'll start by trialling Spack on my home computer, which I'm not turning upside down and rattling at the same time as my work desktop, to see how it goes, and then see how the process goes on my work desktop.
-
-My specific use case is that I (with collaborators at the Hamburg University of Technology) develop the [ELECTRODE package](https://aip.scitation.org/doi/10.1063/5.0099239), as well as working on non-equilibrium methods in molecular dynamics with [CTCMS](https://ctcms-uq.github.io/) at the University of Queensland, in the [LAMMPS](https://www.lammps.org/) code. Besides developing generic code (and writing papers about it) I try to co-develop code with the INTEL package, which relies on Intel directives to go zoom zoom on Intel processors, and I am also co-developing code with the KOKKOS package to (soon) go zoom zoom on AMD GPUs on the brand new [Setonix](https://pawsey.org.au/systems/setonix/) supercomputer.
-
-This means I need to test code against at least three compiler toolchains: Intel, AMD, and good old GCC (because I'm not a monster). In addition, I also want to link against a variety of FFT and linear algebra codes (such as MKL, openBLAS, or openBLIS). This kind of wacky combinatorial development is, supposedly, what Spack is good for. We're about to find out!
-
-(I read lots of chatter about containerizing everything, and I know Singularity / Apptainer is a big deal for eventually deploying to HPC. But, from everything I've read, it sounds like Spack is great on boxes which I *own*, and eventually containers would be important for deploying either to HPC or cloud computes.)
-
-## Installing Spack and LAMMPS
-
-So I installed Spack from GitHub using the [tutorial instructions](https://spack-tutorial.readthedocs.io/en/latest/tutorial_basics.html). Then, naively and straightforwardly, I typed in:
-
-`spack install lammps`
-
-and ... it looks like it will take a while. This seems like a complete post now, so I'll be back when it's done!
-
-[^1]: You might not know who I am yet, and that's okay! I really should write something about me before diving right into this blog, but Documenting Everything takes priority right now.
diff --git a/_posts/2022-10-04-spack-time-2-glyphs-of-doom.md b/_posts/2022-10-04-spack-time-2-glyphs-of-doom.md
deleted file mode 100644
index baeab78..0000000
--- a/_posts/2022-10-04-spack-time-2-glyphs-of-doom.md
+++ /dev/null
@@ -1,102 +0,0 @@
----
-layout: post
-title: "Spack Time 2: Pigz flying off glyphs of doom"
-date: 2022-10-04 10:32:00 +1000
-tags: spack doco
----
-
-## GCC, aka Getting Code Compiled
-
-Last I wrote, I'd typed in:
-
-`spack install lammps`
-
-An hour of computer time later, everything had Just Worked! Amazing!
-
-Excitedly, I fired up my new install with a `spack load lammps` and confirmed that I had ... the 2021 stable version of LAMMPS. That was exciting in itself, because this confirmed that I could smoothly switch between my custom-compiled LAMMPS versions (based off the Sept 2022 patch) and what Spack had built. Time to build the latest version:
-
-`spack install lammps@20220623`
-
-and again, everything Just Worked!
-
-## Time to get my OneAPI on
-
-Following [Spack's instructions](https://spack.readthedocs.io/en/latest/build_systems/inteloneapipackage.html), I installed the latest versions of Intel's OneAPI and linked it up with Spack. That didn't cause any trouble, which is notable because using Intel compilers on clusters has caused me grief in the past.
-
-So now it was time to get Spack going on my next big job:
-
-`spack install lammps@20220915 %oneapi ^intel-oneapi-mkl ^intel-oneapi-mpi`
-
-Let's unspack[^1] the "sigils" Spack uses:
-
-1. `@` denotes a version string -- LAMMPS uses patch dates, I'm not sure what Spack does with other packages.
-2. `%` denotes the compiler used.
-3. `^` denotes a specific dependency, because Spack can track abstract dependencies -- for example, Spack knows that LAMMPS can use any MPI, so `^intel-oneapi-mpi` will tell Spack to use Intel MPI in that slot.
-
-And of course, everything compiled perfectly, and Shern coded happily ever after ... *not*.
-
-## The glyphs of doom!
-
-The first package which refused to compile was ... `font-util`! This was an unpleasant surprise. If you're familiar with LAMMPS you will be wondering, *why*? LAMMPS is after all a command-line-only molecular dynamics simulator, so what on earth is it doing looking for fonts? I haven't looked at the dependency graphs but my guess is that some of the output modes probably feature fonts and therefore ask for `font-util` -- or perhaps some other package in line has some odd dependency there.
-
-In any case, I was staring this right in the face:
-
-```
- 12934 /home/shernren/anaconda3/bin/fc-cache /home/shernren/spack/opt/spack/linux-ubuntu22.04-zen/oneapi-2022.1.0/font-util-1.3.2-yvqiyb6jnjnpo5ocw5nh4bfcplh2yqhq/share/fonts/X11/cyrillic
- 12935 /home/shernren/spack/opt/spack/linux-ubuntu22.04-zen/oneapi-2022.1.0/font-util-1.3.2-yvqiyb6jnjnpo5ocw5nh4bfcplh2yqhq/share/fonts/X11/cyrillic: failed to write cache
- >> 12936 make[2]: *** [Makefile:755: install-data-hook] Error 1
- 12937 make[2]: Leaving directory '/tmp/shernren/spack-stage/spack-stage-font-util-1.3.2-yvqiyb6jnjnpo5ocw5nh4bfcplh2yqhq/spack-src/font-cronyx-cyrillic/font-cronyx-cyrillic-1.0.3'
- >> 12938 make[1]: *** [Makefile:681: install-data-am] Error 2
- 12939 make[1]: Leaving directory '/tmp/shernren/spack-stage/spack-stage-font-util-1.3.2-yvqiyb6jnjnpo5ocw5nh4bfcplh2yqhq/spack-src/font-cronyx-cyrillic/font-cronyx-cyrillic-1.0.3'
- >> 12940 make: *** [Makefile:632: install-am] Error 2
-```
-
-Urgh! Argh! What on Earth! I duly googled "failed to write cache" and dived into a morass of old, odd bug reports. Eventually, it turned out that (1) this was [an old bug in fontconfig](https://gitlab.freedesktop.org/fontconfig/fontconfig/-/issues/107); (2) it was being triggered by *fontconfig from my Anaconda*.
-
-Of course Spack can't solve my snake issues. But what I like about Spack is that, to me at least, it seems more transparent about the whole process. Instead of downloading wheels which magically go round and round and end up making my bus go forward, Spack is just (!) downloading source, compiling, and installing, and it happens to keep track of all its work with the hashes to show for it. I tacked on a few extra options: `-v --keep-prefix` to, respectively, give verbose output and keep all its temporary files around after a failed install. The install files eventually let me confirm that, yes, my Anaconda `fc-cache` was bugged while `/usr/bin/fc-cache` was updated to the latest version. After a quick and very dirty:
-
-```
-mv ~/anaconda/bin/fc-cache ~/anaconda/bin/fc-cache-old
-ln -s /usr/bin/fc-cache ~/anaconda/bin/fc-cache
-```
-
-I was on my way!
-
-## Pigz go fly
-
-Almost immediately another package decided to lie down and not compile, and it was [`pigz`](https://zlib.net/pigz/). Another unpleasant surprise with an even more cryptic error message:
-
-```
-==> [2022-10-04-21:59:46.995345] 'make' '-j8'
-gcc -O3 -Wall -Wextra -Wno-unknown-pragmas -Wcast-qual -c -o pigz.o pigz.c
-make: gcc: Permission denied
-make: *** [: pigz.o] Error 127
-==> Error: ProcessError: Command exited with status 2:
- 'make' '-j8'
-
-2 errors found in build log:
- >> 6 make: gcc: Permission denied
- >> 7 make: *** [: pigz.o] Error 127
-```
-
-Well, not very cryptic, in that I wasn't able to use GCC while wanting to build everything with Intel's ICPX! That again is a good sign that Spack really was going to compile everything with ICPX or die trying.
-
-But why was `pigz` asking for GCC? Again, Spack helpfully saved the source tar for me to peruse, and what should I find at the top of the Makefile but `CC=gcc`! Well, I don't know how to get Spack to override the source it downloads[^2], but I knew I was never going to ask "but what if I compiled a parallel GZ compressor with Intel instead of GCC?", so off we go changing the dependencies again:
-
-`spack install lammps@20220915 %oneapi ^intel-oneapi-mkl ^intel-oneapi-mpi ^pigz%gcc`
-
-And ... it all worked! This last command has been running the whole time I've been typing this entry, and it's built (glances at other terminal) an entire new Python, LLVM for AMD GPU (which, whoops, it's just tripped over), and (hilariously) *a new fontconfig*, which would have been nice to have while font-util was tripping over itself!
-
-And instead of deciding to stop here (I can see it's already decided that it can't build Intel MPI without that mysterious AMD GPU LLVM, and therefore that it can't build LAMMPS -- sensible), it's gone on now to build *Rust*!
-
-## If only this were a conclusion
-
-It seems that the journey goes on and on. But what I can tell is that Spack really, really does prioritize documenting a reproducible build. Of course it takes a lot of disk space to rebuild everything just to make sure it's the same compiler throughout -- but in the intended HPC use case, that totally makes sense.
-
-Even though I'm laughing (and crying) and some of the more ridiculous errors here, I don't think they're Spack's fault. If I were building LAMMPS from ground up, especially with a list of different compilers and some of the more esoteric sub-packages, I'd be running headfirst into these speed bumps too. Spack is simply doing what I want it to do -- and doing an admirable job keeping track of it all, and giving me the information I need to --
-
-dear heavens above, why is it building me *a brand new NumPy*???
-
-[^1]: I love my puns and I will not lie.
-
-[^2]: Spack does have a "develop mode" where it will build from my specified source directory instead of downloading from a Git repository. But I want to reserve that for developing LAMMPS, not pigz, and so I'll wait until I have all my reference binaries compiled before tinkering with that.
diff --git a/_projects/5_project.md b/_projects/5_project.md
deleted file mode 100644
index efd9b6c..0000000
--- a/_projects/5_project.md
+++ /dev/null
@@ -1,80 +0,0 @@
----
-layout: page
-title: project 5
-description: a project with a background image
-img: assets/img/1.jpg
-importance: 3
-category: fun
----
-
-Every project has a beautiful feature showcase page.
-It's easy to include images in a flexible 3-column grid format.
-Make your photos 1/3, 2/3, or full width.
-
-To give your project a background in the portfolio page, just add the img tag to the front matter like so:
-
- ---
- layout: page
- title: project
- description: a project with a background image
- img: /assets/img/12.jpg
- ---
-
-
- Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles.
-
- This image can also have a caption. It's like magic.
-
-
-You can also put regular text between your rows of images.
-Say you wanted to write a little bit about your project before you posted the rest of the images.
-You describe how you toiled, sweated, *bled* for your project, and then... you reveal its glory in the next row of images.
-
-
-
- You can also have artistically styled 2/3 + 1/3 images, like these.
-
-
-
-The code is simple.
-Just wrap your images with `
` and place them inside `
` (read more about the Bootstrap Grid system).
-To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes.
-Here's the code for the last row of images above:
-
-{% raw %}
-```html
-
-```
-{% endraw %}
diff --git a/_projects/6_project.md b/_projects/6_project.md
deleted file mode 100644
index 9a95d6e..0000000
--- a/_projects/6_project.md
+++ /dev/null
@@ -1,80 +0,0 @@
----
-layout: page
-title: project 6
-description: a project with no image
-img:
-importance: 4
-category: fun
----
-
-Every project has a beautiful feature showcase page.
-It's easy to include images in a flexible 3-column grid format.
-Make your photos 1/3, 2/3, or full width.
-
-To give your project a background in the portfolio page, just add the img tag to the front matter like so:
-
- ---
- layout: page
- title: project
- description: a project with a background image
- img: /assets/img/12.jpg
- ---
-
-
- Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles.
-
- This image can also have a caption. It's like magic.
-
-
-You can also put regular text between your rows of images.
-Say you wanted to write a little bit about your project before you posted the rest of the images.
-You describe how you toiled, sweated, *bled* for your project, and then... you reveal its glory in the next row of images.
-
-
-
- You can also have artistically styled 2/3 + 1/3 images, like these.
-
-
-
-The code is simple.
-Just wrap your images with `
` and place them inside `
` (read more about the Bootstrap Grid system).
-To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes.
-Here's the code for the last row of images above:
-
-{% raw %}
-```html
-