new README and restructured website — new developer docs/contributing guide, quick tour, getting started, logging

README refresh: added website link, Papers (Ogden 2023/2025), aligned visuals.
Homepage restructure: clear sections, fixed layout, stable links via {{ site.baseurl }}.
About → Quick Tour: concise overview with images; verification snapshot; pubs links.
Quick Start: streamlined steps; links to Logging and New Model.
New Model guide: folder layout + minimal YAML templates; assumes mesh/HDF5; run commands.
Logging page: flags/behavior/tips; linked from Home and Quick Start.
Dev docs: Build the Docs (Jekyll) + links to CMake basics/structure and contributing.
Docs-only changes; no source code modifications.

Author: dav-og

README.md

@@ -6,17 +6,22 @@
   <a href="#"><img src="https://img.shields.io/badge/status-Prototype-orange.svg" /></a>
 </p>
 
-> ⚠️ HydroChrono is under active development (`v0.3` prototype). This early release focuses on a YAML‑driven CLI and portable HDF5 outputs so you can try the code and share feedback. Expect rapid iteration over the coming year — please open issues/feature requests.
+> ⚠️ HydroChrono is under active development (`v0.3` prototype). This early release focuses on a YAML‑driven CLI and portable HDF5 outputs so you can try the code and share feedback. Expect rapid iteration over the coming year (inc. more advanced PTO, control, mooring & hydrodynamics) — please get in touch if you have any issues or feature requests.
 
 
-HydroChrono (Hydrodynamics for Project Chrono) is a hydrodynamics simulation toolkit built on [Project Chrono](https://projectchrono.org/). It is designed for simulating wave energy converters (WECs) and other complex ocean systems, and is 100% free and open‑source end‑to‑end — no proprietary dependencies required. This repo ships a prototype, YAML‑driven CLI app for running simulations and exporting portable results.
+Website: https://nrel.github.io/HydroChrono/
+
+
+HydroChrono (Hydrodynamics for Project Chrono) is a hydrodynamics simulation toolkit built on [Project Chrono](https://projectchrono.org/). It is designed for simulating wave energy converters (WECs) and other complex ocean systems, and is **100% free and open‑source** end‑to‑end — no proprietary dependencies required. This repo ships a prototype, YAML‑driven CLI app for running simulations and exporting portable results.
+
+📄 See Publications at the end of this README.
 
 ## What it does (under the hood)
 
 - Uses Boundary Element Method (BEM) hydrodynamic coefficients (e.g., from [Capytaine](https://github.com/capytaine/capytaine)) to describe added mass, radiation damping, and wave excitation. HydroChrono reads these coefficients from BEMIO‑format HDF5 (.h5) files, an approach familiar to [WEC‑Sim](https://github.com/WEC-Sim/WEC-Sim) users.
 - Runs time‑domain simulations via the Cummins equation (impulse‑response/convolution form for radiation effects).
 - Builds complex, nonlinear multibody systems using Project Chrono; hydrodynamic loads are currently first‑order, with expanded models planned.
-- Exports portable results to HDF5 for post‑processing and validation.
+- Supports a YAML-driven CLI, with logging, GUI and exports portable results to HDF5 for post‑processing and validation.
 
 ## Download
 
@@ -154,3 +159,8 @@ python .\run_tests.py --sphere-decay --exe ..\..\bin\run_hydrochrono.exe
 ## Developers
 
 - Full build and contribution docs: [Developer documentation](https://nrel.github.io/HydroChrono/developer_docs/build_instructions.html)
+
+## Papers
+
+- Ogden, 2023 — HydroChrono background, theory, and implementation details: [PDF](docs/assets/papers/Ogden2023%20-%20HydroChrono.pdf)
+- Ogden, 2025 — Automated design exploration with meshing, Capytaine, and HydroChrono in the loop: [PDF](docs/assets/papers/Ogden2025%20-%20Automated%20Design%20Exploration%20of%20TALOS%20Using%20TOP-WEC.pdf)

docs/_config.yml

@@ -19,10 +19,10 @@
 # in the templates via {{ site.myvariable }}.
 
 title: HydroChrono
-copyright:             © 2023 National Renewable Energy Laboratory. All rights reserved.
+copyright: 
 email: hydrochrono@outlook.com
 description: >- # this means to ignore newlines until "baseurl:"
-  [HydroChrono](https://github.com/NREL/HydroChrono/) is a powerful, fully open-source simulation tool for offshore renewable energy systems. It leverages [Project Chrono](https://projectchrono.org/) to model complex floating multibody systems and their subsystems.
+  [HydroChrono](https://github.com/NREL/HydroChrono/) (Hydrodynamics for Project Chrono) is a hydrodynamics simulation toolkit built on [Project Chrono](https://projectchrono.org/). It is designed for simulating wave energy converters (WECs) and other complex ocean systems, and is **100% free and open‑source**
 baseurl: "/HydroChrono"
 url: "" # the base hostname & protocol for your site, e.g. http://example.com
 twitter_username: NREL
@@ -35,7 +35,7 @@ plugins:
   - jekyll-remote-theme
   - jekyll-include-cache
 
-accent_image: /assets/img/sidebar-bg.jpg
+accent_image: /assets/img/sidebar-bg2.png
 
 collections:
   main_pages:

docs/_main_pages/about.md

@@ -1,28 +1,94 @@
 ---
 layout: page
-title: "HydroChrono: Open-Source Renewable Energy Simulation"
+title: "HydroChrono: Quick Tour"
 permalink: /about/
 ---
 
-HydroChrono is an emerging open-source simulator for offshore renewable energy systems, combines a high-speed C++ backend with a user-friendly Python wrapper.
+<p align="center"><img src="{{ site.baseurl }}/assets/img/hydrochrono_banner.png" width="80%" /></p>
 
-## Quick Highlights:
+HydroChrono (Hydrodynamics for Project Chrono) is a hydrodynamics simulation toolkit built on [Project Chrono](https://projectchrono.org/). It is designed for simulating wave energy converters (WECs) and other complex ocean systems, and is **100% free and open‑source** end‑to‑end — no proprietary dependencies required.
 
-- **Efficient & Fast:** C++ backend enhances speed and efficiency and provides support for state of the art parallelization frameworks.
-- **User-Friendly:** Python wrapper for easy and flexible model scripting.
-- **Project Chrono Integration:** A powerful physics engine that provides state-of-the-art modeling capabilities - including FEM, DEM, and integration with cutting-edge control frameworks like ROS and Gym.
-- **Flexible Modeling:** Supports a wide range of multibody floating systems and subsystems.
-- **Scalable Design:** Ready to evolve with the latest advancements in simulation.
-- **Simulink Compatible:** Traditional control development approaches supported via Project Chrono's Simulink coupling, without creating a mandatory paywall.
-- **Open-Source:** Invites community collaboration for ongoing improvements.
+It uses Boundary Element Method (BEM) hydrodynamic coefficients (e.g., from Capytaine) to model added mass, radiation damping, and wave excitation, and runs time‑domain simulations via the Cummins equation on Chrono multibody models. Results are exported to portable HDF5 for analysis and verification.
 
-## Get Involved:
+## Quick start (CLI)
 
-Join us in advancing renewable energy research. For more details, source code access, or to contribute, visit [HydroChrono on GitHub](https://github.com/hydrochrono).
+After downloading a release, open a terminal in the app folder and run:
 
-## Disclaimer:
+```powershell
+run_hydrochrono.exe -h     # help
+run_hydrochrono.exe -i     # info/banner
 
-Please note that HydroChrono is a new and actively developing software. As with any emerging technology, users may encounter bugs or issues. We welcome feedback and contributions to improve HydroChrono and appreciate your understanding and patience as we work towards refining this tool!
+# Run a case by directory (auto-detects setup)
+run_hydrochrono.exe .\cases\my_model\
+
+# Or run directly from a setup file
+run_hydrochrono.exe .\cases\my_model\my_model.setup.yaml
+
+# Some useful options
+run_hydrochrono.exe .\cases\my_model\ --nogui --quiet --log
+```
+
+<p align="center"><img src="{{ site.baseurl }}/assets/img/cli_example.png" width="75%" /></p>
+
+### GUI Example
+
+Use the GUI to visually inspect the assembled multibody system (bodies, joints, actuators) and verify that YAML inputs are wired correctly. Use the `--nogui` option to disable visualization straight from CLI, or change the settings in the `*.simulation.yaml` file.
+
+<p align="center"><img src="{{ site.baseurl }}/assets/img/gui_example.png" width="40%" /></p>
+
+## YAML-based UI
+
+Describe your system in text files that can be versioned and automated:
+
+```
+cases/my_model/
+  my_model.setup.yaml       # references the files below (recommended)
+  my_model.model.yaml       # bodies, joints, actuators
+  my_model.simulation.yaml  # time step, duration, GUI, waves
+  my_model.hydro.yaml       # hydrodynamics
+```
+
+- `my_model.setup.yaml` — orchestrates which inputs to run
+- `my_model.model.yaml` — Chrono multibody system (bodies, joints, constraints, actuators)
+- `my_model.simulation.yaml` — time step, duration, output options, GUI flags
+- `my_model.hydro.yaml` — BEMIO `.h5` path and hydrodynamics mapping/wave inputs
+
+Run with either the folder path (auto‑detects `*.setup.yaml`) or the setup file directly:
+
+```powershell
+run_hydrochrono.exe .\cases\my_model\
+run_hydrochrono.exe .\cases\my_model\my_model.setup.yaml
+```
+
+<p align="center"><img src="{{ site.baseurl }}/assets/img/yaml_example.png" width="25%" /></p>
+
+## HDF5 outputs (portable)
+
+Simulations produce a single `.h5` file with time series and model results. Typical datasets include:
+
+- Body position (XYZ): `/results/model/bodies/<body_name>/position`
+- Body orientation (roll, pitch, yaw): `/results/model/bodies/<body_name>/orientation_xyz`
+- Translational spring–dampers: `/results/model/tsdas/<actuator_name>/...`
+- Rotational spring–dampers: `/results/model/rsdas/<actuator_name>/...`
+
+View and plot with HDFView or common Python tools.
+
+<p align="center"><img src="{{ site.baseurl }}/assets/img/h5_example.png" width="75%" /></p>
+
+## Verification snapshot
+
+Comparison from the OSWEC decay test used in the regression suite.
+
+<p align="center"><img src="{{ site.baseurl }}/assets/img/oswec_decay_test_comparison.png" width="66%" /></p>
+
+## Developers
+
+Full build and contribution docs: [Developer documentation]({{ site.baseurl }}/developer_docs/build_instructions)
+
+## Papers
+
+- Ogden, 2023 — HydroChrono background, theory, and implementation details: [PDF]({{ site.baseurl }}/assets/papers/Ogden2023%20-%20HydroChrono.pdf)
+- Ogden, 2025 — Automated design exploration with meshing, Capytaine, and HydroChrono in the loop: [PDF]({{ site.baseurl }}/assets/papers/Ogden2025%20-%20Automated%20Design%20Exploration%20of%20TALOS%20Using%20TOP-WEC.pdf)
 
 <p align="center">
   <img src="{{ site.baseurl }}/assets/img/wave_animation2.gif" alt="Wave Energy" width="80%" />

docs/_main_pages/developer_docs.md

@@ -3,11 +3,13 @@ layout: page
 title: Developer Documentation
 ---
 
-Welcome to the Developer Documentation section of HydroChrono. Here, you'll find comprehensive guides and resources to help you understand and contribute to the development of HydroChrono.
+Welcome to the Developer Documentation section of HydroChrono. Use these guides to build, understand, and contribute to the project.
 
-- [Prerequisites]({{ site.baseurl }}/developer_docs/prerequisites)
-- [Build Instructions]({{ site.baseurl }}/developer_docs/build_instructions)
-- [Contribution Guidelines]({{ site.baseurl }}/developer_docs/contribution_guidelines)
+- [Build & Setup]({{ site.baseurl }}/developer_docs/build_instructions) - install dependencies, configure, build, and run tests
+- [Contribution Guidelines]({{ site.baseurl }}/developer_docs/contribution_guidelines) - coding conventions, best practices, MUST/SHOULD summary, PR checklist
+- [CMake Build Basics]({{ site.baseurl }}/developer_docs/cmake_build_basics) - generators, single vs multi-config, build types
+- [CMake Build Structure]({{ site.baseurl }}/developer_docs/cmake_build_structure) - how `CMakeLists.txt` is organized, targets, install/packaging
+- [Build the Docs]({{ site.baseurl }}/developer_docs/build_docs) - run Jekyll site locally and build `_site/`
 
 <p align="center">
   <img src="{{ site.baseurl }}/assets/img/wave_animation2.gif" alt="Wave Energy" width="80%" />

docs/_main_pages/developer_docs/build_docs.md

@@ -0,0 +1,68 @@
+---
+layout: page
+title: Build the Docs
+---
+
+This page explains how to build and preview the documentation site locally.
+
+## Prerequisites
+
+- Ruby 3.1.x (Windows: install Ruby+Devkit)
+- Bundler (`gem install bundler`)
+
+## Quick start (Windows, PowerShell)
+
+1. Open PowerShell and navigate to the docs directory:
+
+   ```powershell
+   cd <path>\HydroChrono\docs
+   ```
+
+2. Install dependencies:
+
+   ```powershell
+   gem install bundler
+   bundle config set --local path vendor/bundle
+   bundle install
+   ```
+
+3. Serve the site locally:
+
+   ```powershell
+   bundle exec jekyll serve --livereload
+   ```
+
+   The site uses `baseurl: /HydroChrono`. Open:
+
+   - `http://localhost:4000/HydroChrono/`
+
+   For root paths locally, you can override the baseurl:
+
+   ```powershell
+   bundle exec jekyll serve --livereload --baseurl ""
+   ```
+
+## Build only
+
+```powershell
+bundle exec jekyll build
+```
+
+The generated site will be in `_site/`.
+
+## Containerized option
+
+```powershell
+docker run --rm -p 4000:4000 -v ${PWD}:/srv/jekyll -w /srv/jekyll jekyll/jekyll:3.9 jekyll serve --livereload
+```
+
+Then open `http://localhost:4000/HydroChrono/`.
+
+## Troubleshooting
+
+- Use Ruby 3.1.x for best compatibility with Jekyll 3.9.x.
+- On Windows, ensure you installed the MSYS2 toolchain during Ruby+Devkit setup (`ridk install`).
+- If port 4000 is in use, add `--port 4001`.
+- First run fetches the remote theme; ensure internet connectivity.
+
+