Merge pull request #58 from melekderman/master

Improve deployment and update publications.

Author: melekderman

.github/workflows/jekyll.yml

@@ -1,20 +1,69 @@
-name: Jekyll site CI
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy Jekyll site to Pages
 
 on:
+  # Runs on pushes targeting the default branch
   push:
-    branches: [ master ]
+    branches: ["master"]
   pull_request:
-    branches: [ master ]
+    branches: ["master"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
 
 jobs:
+  # Build job
   build:
-
     runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Ruby
+        # https://github.com/ruby/setup-ruby/releases/tag/v1.207.0
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.2' # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+          cache-version: 1 # Increment this number if you need to re-download cached gems
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v5
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          JEKYLL_ENV: production
+      - name: Upload artifact
+        # Automatically uploads an artifact from the './_site' directory by default
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./_site
 
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
     steps:
-    - uses: actions/checkout@v2
-    - name: Build the site in the jekyll/builder container
-      run: |
-        docker run \
-        -v ${{ github.workspace }}:/srv/jekyll -v ${{ github.workspace }}/_site:/srv/jekyll/_site \
-        jekyll/builder:latest /bin/bash -c "chmod 777 /srv/jekyll && jekyll build --future"
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

Gemfile.lock

@@ -343,4 +343,4 @@ DEPENDENCIES
   webrick (~> 1.8)
 
 BUNDLED WITH
-   2.7.2
+   2.3.25

Makefile

@@ -0,0 +1,13 @@
+.PHONY: install serve build check
+
+install:
+	bundle install
+
+serve:
+	bundle exec jekyll serve --config _config.yml,_config.dev.yml --livereload
+
+build:
+	bundle exec jekyll build --config _config.yml
+
+check:
+	bundle exec jekyll doctor

README.md

@@ -1,5 +1,25 @@
-# CEMeNT Site
+# CEMeNT Website
 
+Jekyll + GitHub Pages.
 
-# For macOS arm
-`bundle add webrick`
+## Local development
+`bundle install`  
+`make serve`  
+Open: `http://localhost:4000`
+
+## Edit these folders
+`_pages/` pages  
+`_members/` team members  
+`_publications/` publications  
+`_posts/` news/posts  
+`assets/` images and styles
+
+## Do not edit
+`_site/` build output  
+`docs/` legacy output (no manual edits)
+
+## Deploy flow
+1. Create a branch.
+2. Make changes.
+3. Open a PR.
+4. Merge into `master` (auto deploy via GitHub Actions).

_members/ethan_lame.md

@@ -1,6 +1,6 @@
 ---
 title: "Ethan Lamé"
-excerpt: "Masters Student, Oregon State University"
+excerpt: "Ph.D. Student, Oregon State University"
 classes: wide
 
 header:
@@ -12,7 +12,8 @@ author: Ethan Lame
 
 ## Education
 
-* M.S. Nuclear Engineering, Oregon State University (In Progress)
+* Ph.D. Nuclear Engineering (In Progress), Oregon State University
+* M.S. Nuclear Engineering, Oregon State University, 2025
 * B.S. Physics, University of Utah, 2022
 
 ## Biography

_members/melek_derman.md

@@ -14,4 +14,19 @@ author: Melek Derman
 * B.S. Physics, Akdeniz University
 
 ## Biography
-Melek is a Ph.D. student and graduate research assistant at Oregon State University, under Dr. Todd Palmer. Melek received her bachelor's degree in the Department of Physics at Akdeniz University and earned her MS degree at Texas A&M University with a study on the MCNP modeling and simulations of Molten Salt Reactors.
+Melek is a Ph.D. student and Graduate Research Assistant in Nuclear Engineering at Oregon State University, working under the supervision of Professor Todd S. Palmer. Her research focuses on Monte Carlo and deterministic particle transport methods, as well as computational techniques for developing scalable algorithms on exascale computing systems.
+
+Melek received her B.S. in Physics with Honors from Akdeniz University (Türkiye) and her M.S. in Nuclear Engineering from Texas A&M University, where her work focused on nuclear safeguards monitoring approaches for molten salt reactors. Her doctoral research involves high-performance computing optimization and multiscale physics simulations, with applications ranging from reactor physics to radiation effects in electronic systems.
+
+## Work at CEMeNT
+
+* Exascale Monte Carlo electron transport method development
+* Development and verification of reactor physics and electron transport benchmarks
+* CAD-based geometry support in MC/DC via GEOUNED integration
+* Nuclear data processing and scientific software development (e.g., PyEEDL, PyEPICS)
+* Deterministic Boltzmann Fokker Plank transport solvers and spectral analysis methods
+* High-performance computing optimization on heterogeneous CPU/GPU systems
+* Scalable radiation transport software development
+
+📄 Full CV: https://melekderman.github.io/files/MelekDerman_CV_Website.pdf
+🌐 Personal Website: https://melekderman.github.io/

_pages/publications.md

@@ -24,6 +24,12 @@ Springer, New York (2021) ISBN: [978-3030703875](https://link.springer.com/book/
 
 # Journal Articles
 
+* [J. Farmer](../members/joey_farmer/), A. Murray, [J. Krotz](../members/johannes_krotz/), and [R. G. McClarren](../members/ryan_mcclarren/). Generative Monte Carlo Sampling for Constant-Cost Particle Transport. (Submitted). 2025. [arXiv:2512.13965](https://arxiv.org/abs/2512.13965)
+
+* [B. Whewell](../previous/ben_whewell/), [R. G. McClarren](../members/ryan_mcclarren/). Single Grid Error Estimation for Neutron Transport Solvers. *Journal of Verification, Validation, and Uncertainty Quantification* **10**(2): 021001. (2025). DOI [10.1115/1.4069426](https://doi.org/10.1115/1.4069426)
+
+* [B. Whewell](../previous/ben_whewell/), [R. G. McClarren](../members/ryan_mcclarren/). Collision-Based Hybrid Method for Two-Dimensional Neutron Transport Problems. *Nuclear Science and Engineering* **200**(3), 502–524. (2025). DOI [10.1080/00295639.2025.2489778](https://doi.org/10.1080/00295639.2025.2489778)
+
 * [V. N. Novellino](../members/vincent_novellino), [D.  Y. Anistratov](../members/dmitriy_anistratov) Multi-Level Hybrid Monte Carlo / Deterministic  Methods for Particle Transport Problems. 2025 (submitted)
 
 * [J. P. Morgan](../members/joanna_morgan), [I. Variansyah](../members/ilham_variansyah), [K. B. Clements](../members/kayla_clements/), [T. S. Palmer](../members/todd_palmer) and [K. E. Niemeyer](../members/kyle_niemeyer). Hybrid Delta Tracking Schemes Using a Track-Length Estimator. 2025.(submitted). [arXiv:2510.00152](https://doi.org/10.48550/arXiv.2510.00152)
@@ -32,7 +38,7 @@ Springer, New York (2021) ISBN: [978-3030703875](https://link.springer.com/book/
 
 * [J. P. Morgan](../members/joanna_morgan), [I. Variansyah](../members/ilham_variansyah), [T. S. Palmer](../members/todd_palmer) and  [K. E. Niemeyer](../members/kyle_niemeyer). 2024.. Impacts of dynamic radiation transport to one-cell inversions on modern GPUs with higher-order discretization. *Nuclear Science and Engineering* doi [10.1080/00295639.2025.2510004](https://doi.org/10.1080/00295639.2025.2510004) [arXiv:2503.00264](https://doi.org/10.48550/arXiv.2503.00264).
 
-* [A. Mote](../members/alexander_mote) [T. S. Palmer](../members/todd_palmer) and [L. Chen](../members/lizhong_chen). 2024. Neurons for Neutrons: A Transformer Model for Computation Load Estimation on Domain-Decomposed Neutron Transport Problems. *Nuclear Science and Engineering* **54** (5) pp 381--407. doi [10.1080/23324309.2025.2540757](https://doi.org/10.1080/23324309.2025.2540757), [arXiv:2411.03389](https://arxiv.org/abs/2411.03389)
+* [A. Mote](../members/alexander_mote) [T. S. Palmer](../members/todd_palmer) and [L. Chen](../members/lizhong_chen). 2024. Neurons for Neutrons: A Transformer Model for Computation Load Estimation on Domain-Decomposed Neutron Transport Problems. *Nuclear Science and Engineering* **54** (5) pp 381--407. DOI [10.1080/23324309.2025.2540757](https://doi.org/10.1080/23324309.2025.2540757), [arXiv:2411.03389](https://arxiv.org/abs/2411.03389)
 
 * [J. P. Morgan](../members/joanna_morgan), [I. Variansyah](../members/ilham_variansyah), [B. Cuneo](../members/braxton_cuneo), [T. S. Palmer](../members/todd_palmer) and  [K. E. Niemeyer](../members/kyle_niemeyer). 2024. Accepted *IEEE Computing in Science and Engineering*. Performance Portable Monte Carlo Neutron Transport in MCDC via Numba. Preprint DOI [10.48550/arXiv.2409.04668](    
 https://doi.org/10.48550/arXiv.2409.04668). DOI [10.1109/MCSE.2025.3550863](https://doi.org/10.1109/MCSE.2025.3550863).
@@ -65,6 +71,8 @@ https://doi.org/10.48550/arXiv.2409.04668). DOI [10.1109/MCSE.2025.3550863](http
 
 # Conference Publications
 
+* [B. Whewell](../previous/ben_whewell/), [R. G. McClarren](../members/ryan_mcclarren/). (2025) "Single Grid Error Estimation in Two-Dimensional Neutron Transport Problems." *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (ANS M&C 2025).* Denver, CO, USA.
+
 * [K. B. Clements](../members/kayla_clements/), [T. S. Palmer](../members/todd_palmer), A. J. Olson, G. Geraci, [I. Variansyah](../members/ilham_variansyah). (2025) Monte Carlo Uncertainty Quantification and Sensitivity Analysis for the C5G7 Benchmark. To appear in *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (ANS M&C 2025).* Denver, CO, USA.
 
 * [A. Mote](../members/alex_mote), [T. S. Palmer](../members/todd_palmer), [L. Chen](../members/lizhong_chen). (2025) Improvements in MC/DC Domain Decomposition Functionality. (2025). To appear in *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (ANS M&C 2025).* Denver, CO, USA. 
@@ -73,7 +81,7 @@ https://doi.org/10.48550/arXiv.2409.04668). DOI [10.1109/MCSE.2025.3550863](http
 
 * [S. Pasmann](../previous/sam_pasmann/), [I. Variansyah](../members/ilham_variansyah), [C. T. Kelley](../members/ct_kelley/) and [R. G. McClarren](../members/ryan_mcclarren/). (2025) A Batch Power Iteration Approach for the Iterative Quasi-Monte Carlo Method Using a Randomized-Halton Sequence. To appear in *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (ANS M&C 2025).* Denver, CO, USA.
 
-* [C. Shaw](../members/caleb_shaw), [D.  Y. Anistratov](../members/dmitriy_anistratov). (2025) Hybrid Weight Window Techniques for Time-Dependent Monte Carlo Neutronics. (2025). *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (ANS M&C 2025).* Denver, CO, USA. April 2025, pp. 1861-1870 doi [10.13182/xyz-47085](https://doi.org/10.13182/xyz-47085), [arXiv:2501.06144](https://doi.org/10.48550/arXiv.2501.06144)
+* [C. Shaw](../members/caleb_shaw), [D.  Y. Anistratov](../members/dmitriy_anistratov). (2025) Hybrid Weight Window Techniques for Time-Dependent Monte Carlo Neutronics. (2025). *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (ANS M&C 2025).* Denver, CO, USA. April 2025, pp. 1861-1870 DOI [10.13182/xyz-47085](https://doi.org/10.13182/xyz-47085), [arXiv:2501.06144](https://doi.org/10.48550/arXiv.2501.06144)
 
 * [I. Variansyah](../members/ilham_variansyah), [R. G. McClarren](../members/ryan_mcclarren/), [T. S. Palmer](../members/todd_palmer). (2025) Implicit Collision Multiplicity Adjustment for Efficient Monte Carlo Transport Simulation of Reactivity Excursion. To appear in *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (ANS M&C 2025).* Denver, CO, USA.
 
@@ -89,6 +97,8 @@ https://doi.org/10.48550/arXiv.2409.04668). DOI [10.1109/MCSE.2025.3550863](http
 
 * [V. N. Novellino](../previous_members/vincent_novellino) and  [D. Anistratov](../members/dmitriy_anistratov), Analysis of Hybrid MC/Deterministic Methods for Transport Problems  Based on Low-Order Equations Discretized by Finite Volume Scheme. *Transaction of American Nuclear Society*, v. 130, 408-411, 2024 [arXiv:2403.05673](https://doi.org/10.48550/arXiv.2403.05673)
 
+* [B. Whewell](../previous/ben_whewell/), [R. G. McClarren](../members/ryan_mcclarren/). (2023) "Solution Verification with the Method of Nearby Problems for Neutron Transport Applications." *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (ANS M&C 2023).* Niagara Falls, Ontario, Canada.
+
 * [I. Variansyah](../members/ilham_variansyah/), [J. P. Morgan](../members/joanna_morgan/), [J. Northrop](../members/jordan_northrop) [K. E. Niemeyer](../members/kyle_niemeyer/), and [R. G. McClarren](../members/ryan_mcclarren/). “Development of MC/DC: a performant, scalable, and portable Python-based Monte Carlo neutron transport code.” In *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering*. Niagara Falls, Ontario, Canada (2023). Preprint DOI [10.48550/arXiv.2305.13555](https://doi.org/10.48550/arXiv.2305.13555).
 
 * [I. Variansyah](../members/ilham_variansyah/) and [R. G. McClarren](../members/ryan_mcclarren/). “High-fidelity treatment for object movement in time-dependent Monte Carlo transport simulations.” In *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering*. Niagara Falls, Ontario, Canada (2023). Preprint [DOI 10.48550/arXiv.2305.07641](https://doi.org/10.48550/arXiv.2305.07641).
@@ -189,6 +199,8 @@ for Thermal Radiation and Neutron Transport, M.S. project report, School of MIME
 
 # Presentations
 
+* [B. Whewell](../previous/ben_whewell/) and [R. G. McClarren](../members/ryan_mcclarren/). "Single Grid Error Estimation in Two-Dimensional Neutron Transport Problems." *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (ANS M&C 2025).* Denver, CO, USA.
+
 * [J. P. Morgan](../members/joanna_morgan/) and [K. E. Niemeyer](../members/kyle_niemeyer/). Monte Carlo/Dynamic Code: Performant and Portable High-Performance Computing at Scale via Python and Numba. *Proceedings of the 23rd Python in Science Conference* July 12 2024. Tachoma, WA, USA. DOI [10.25080/cdrf9272](https://doi.org/10.25080/cdrf9272)
 
 * [C. T. Kelley](../members/ct_kelley/). Newton's Method in Three Precisions. *18th Copper Mountain Conference On Iterative Methods*. Copper Mtn., CO, USA. (April 2024).
@@ -242,6 +254,8 @@ AZURV1 Benchmark”, American Nuclear Society Annual Meeting, Anaheim, CA, June
 
 # Poster Presentations
 
+* [B. Whewell](../previous/ben_whewell/), [R. G. McClarren](../members/ryan_mcclarren/). (2023) "Solution Verification with the Method of Nearby Problems for Neutron Transport Applications." *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (ANS M&C 2023).* Niagara Falls, Ontario, Canada.
+
 * [J. P. Morgan](../members/joanna_morgan/), T. J. Trahan, T. P. Burke, C. J. Josey, and [K. E. Niemeyer](../members/kyle_niemeyer/). “Hybrid-Delta Tracking on a Structured Mesh in MCATK.” International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering. Niagara Falls, Ontario, Canada (August 2023). DOI [10.5281/zenodo.10511913](https://doi.org/10.5281/zenodo.10511913)
 
 * [J. P. Morgan](../members/joanna_morgan/), [I. Variansyah](../members/ilham_variansyah/), [T. S. Palmer](../members/todd_palmer/), and [K. E. Niemeyer](../members/kyle_niemeyer/). “Exploring One-Cell Inversion Method for Transient Transport on GPU.” High Energy Density Summer School, San Diego, California. (July 2023) DOI [10.5281/zenodo.10515702](https://doi.org/10.5281/zenodo.10515702).