docs:add IAMReX documentation

.github/workflows/docs.yaml

@@ -0,0 +1,38 @@
+name: Build and Deploy
+on:
+  push:
+    paths: 
+      - 'Docs/IAMReX_documentation/source/**'
+      - '.github/workflows/docs.yaml'
+
+concurrency:
+  group: ${{ github.head_ref }}-docs
+  cancel-in-progress: true
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Dependencies
+        run: |
+          echo "Installing python packages for docs..."
+          python3 -m pip install --upgrade pip
+          python3 -m pip install sphinx sphinx_rtd_theme breathe sphinxcontrib.bibtex docutils
+
+      - name: Install and Build
+        run: |
+          echo "Build the Sphinx documentation for IAMR."
+          make html
+
+      - name: Deploy
+        if: github.event_name == 'push' && github.repository == 'ruohai0925/IAMReX' && github.ref == 'refs/heads/development'
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          ssh-key: ${{ secrets.DEPLOY_KEY }} # repo secrets env
+          branch: gh-pages # The branch the action should deploy to.
+          folder: build/html # The folder the action should deploy.
+          target-folder: docs # The folder the action should deploy to.
+          clean: false # Do not remove existing files from the deploy target.

Docs/IAMReX_documentation/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

Docs/IAMReX_documentation/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

Docs/IAMReX_documentation/source/Acknowledgements.rst

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+.. _Chap:Acknowledgements:
+
+Acknowledgements
+=================
+
+We are grateful to Ann Almgren, Andy Nonaka, Andrew Myers, Axel Huebl, and Weiqun Zhang in the Lawrence Berkeley National Laboratory (LBNL) for their discussions related to `AMReX <https://github.com/AMReX-Codes/amrex>`_ and `IAMR <https://github.com/AMReX-Fluids/IAMR>`_. Y.Z. and Z.Z. also thank Prof. Lian Shen, Prof. Ruifeng Hu, and Prof. Xiaojing Zheng during their Ph.D. studies.