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diff --git a/.buildinfo b/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 9a3d4214e6a2e49bf4ab0dce6f4aa92a
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,88 @@
+name: Nalu-Wind-CI
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Clone
+      uses: actions/checkout@v4
+    - name: Check formatting
+      uses: DoozyX/[email protected]
+      with:
+        source: 'nalu.C unit_tests.C ./include ./src ./unit_tests'
+        extensions: 'H,h,cpp,C'
+        clangFormatVersion: 18
+  CPU-Trilinos:
+    needs: Formatting
+    runs-on: ubuntu-latest
+    container:
+      image: ecpe4s/exawind-snapshot
+      env:
+          EXAWIND_MANAGER: /exawind-manager
+          E4S_MACHINE: true
+    steps:
+      - name: Cancel previous runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{github.token}}
+      - name: Clone
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+      - name: Tests
+        run: |
+          /bin/bash -c " \
+            source ${EXAWIND_MANAGER}/start.sh && \
+            mkdir -p ${EXAWIND_MANAGER}/environments/exawind && \
+            cd ${EXAWIND_MANAGER}/environments/exawind && \
+            ln -s ${GITHUB_WORKSPACE} nalu-wind && \
+            spack-start && \
+            spack -e e4s-build config add view:true && \
+            spack -e e4s-build add cmake && \
+            spack -e e4s-build install && \
+            quick-create-dev -s nalu-wind@master+tioga+hypre && \
+            spack manager external ${EXAWIND_MANAGER}/environments/e4s-build --exclude nalu-wind && \
+            spack install && \
+            spack cd -b nalu-wind && \
+            spack build-env nalu-wind ctest -j $(nproc) -L unit --output-on-failure \
+          "
+  CPU-Hypre-Only:
+    needs: Formatting
+    runs-on: ubuntu-latest
+    container:
+      image: ecpe4s/exawind-snapshot
+      env:
+          EXAWIND_MANAGER: /exawind-manager
+          E4S_MACHINE: true
+    steps:
+      - name: Cancel previous runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{github.token}}
+      - name: Clone
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+      - name: Tests
+        run: |
+          /bin/bash -c " \
+            source ${EXAWIND_MANAGER}/start.sh && \
+            mkdir -p ${EXAWIND_MANAGER}/environments/exawind && \
+            cd ${EXAWIND_MANAGER}/environments/exawind && \
+            ln -s ${GITHUB_WORKSPACE} nalu-wind && \
+            spack-start && \
+            spack -e e4s-build config add view:true && \
+            spack -e e4s-build add cmake && \
+            spack -e e4s-build install && \
+            quick-create-dev -s nalu-wind@master+tioga+hypre~trilinos-solvers && \
+            spack manager external ${EXAWIND_MANAGER}/environments/e4s-build --exclude nalu-wind && \
+            spack install && \
+            spack cd -b nalu-wind && \
+            spack build-env nalu-wind ctest -j $(nproc) -L unit --output-on-failure \
+          "
diff --git a/.nojekyll b/.nojekyll
diff --git a/_downloads/38e30086138adf766dc3b1dab4054c5d/example.h b/_downloads/38e30086138adf766dc3b1dab4054c5d/example.h
@@ -0,0 +1,105 @@
+/** @file example.h
+ *  @brief Brief description of a documented file.
+ *
+ *  Longer description of a documented file.
+ */
+
+/** Here is a brief description of the example class.
+ *
+ * This is a more in-depth description of the class.
+ * This class is meant as an example.
+ * It is not useful by itself, rather its usefulness is only a
+ * function of how much it helps the reader. It is in a sense
+ * defined by the person who reads it and otherwise does
+ * not exist in any real form.
+ *
+ * @note This is a note.
+ *
+ */
+
+#ifndef EXAMPLECLASS_H
+#define EXAMPLECLASS_H
+
+class ExampleClass
+{
+
+public:
+  /// Create an ExampleClass.
+  ExampleClass();
+
+  /** Create an ExampleClass with lot's of intial values.
+   *
+   * @param a This is a description of parameter a.
+   * @param b This is a description of parameter b.
+   *
+   * The distance between \f$(x_1,y_1)\f$ and \f$(x_2,y_2)\f$ is
+   * \f$\sqrt{(x_2-x_1)^2+(y_2-y_1)^2}\f$.
+   */
+  ExampleClass(int a, float b);
+
+  /** ExampleClass destructor description.
+   */
+  ~ExampleClass();
+
+  /// This method does something.
+  void DoSomething();
+
+  /**
+   * This is a method that does so
+   * much that I must write an epic
+   * novel just to describe how much
+   * it truly does.
+   */
+  void DoNothing();
+
+  /** Brief description of a useful method.
+   * @param level An integer setting how useful to be.
+   * @return Description of the output.
+   *
+   * This method does unbelievably useful things.
+   * And returns exceptionally useful results.
+   * Use it everyday with good health.
+   * \f[
+   *    |I_2|=\left| \int_{0}^T \psi(t)
+   *        \left\{
+   *           u(a,t)-
+   *           \int_{\gamma(t)}^a
+   *           \frac{d\theta}{k(\theta,t)}
+   *           \int_{a}^\theta c(\xi)u_t(\xi,t)\,d\xi
+   *        \right\} dt
+   *     \right|
+   * \f]
+   */
+  void* VeryUsefulMethod(bool level);
+
+  /** Brief description of a useful method.
+   * @param level An integer setting how useful to be.
+   * @return Description of the output.
+   *
+   * - Item 1
+   *
+   *   More text for this item.
+   *
+   * - Item 2
+   *   + nested list item.
+   *   + another nested item.
+   * - Item 3
+   *
+   * # Markdown Example
+   * [Here is a link.](http://www.google.com/)
+   */
+  void* AnotherMethod(bool level);
+
+protected:
+  /** The protected methods can be documented and extracted too.
+   *
+   */
+  void SomeProtectedMethod();
+
+private:
+  const char* fQuestion; ///< The question
+  int fAnswer;           ///< The answer
+
+}; // End of class ExampleClass
+
+#endif // EXAMPLE_H
diff --git a/_downloads/9479a46ef6805a408bce963d5fe58798/nalu.i b/_downloads/9479a46ef6805a408bce963d5fe58798/nalu.i
@@ -0,0 +1,102 @@
+# -*- mode: yaml -*-
+#
+# Example Nalu input file for a heat conduction problem
+#
+
+Simulations:
+  - name: sim1
+    time_integrator: ti_1
+    optimizer: opt1
+
+linear_solvers:
+  - name: solve_scalar
+    type: tpetra
+    method: gmres 
+    preconditioner: sgs 
+    tolerance: 1e-3
+    max_iterations: 75 
+    kspace: 75 
+    output_level: 0
+
+realms:
+
+  - name: realm_1
+    mesh: periodic3d.g
+    use_edges: no 
+    automatic_decomposition_type: rcb
+
+    equation_systems:
+      name: theEqSys
+      max_iterations: 2 
+
+      solver_system_specification:
+        temperature: solve_scalar
+
+      systems:
+        - HeatConduction:
+            name: myHC
+            max_iterations: 1
+            convergence_tolerance: 1e-5
+
+    initial_conditions:
+
+      - constant: ic_1
+        target_name: block_1
+        value:
+         temperature: 10.0
+
+    material_properties:
+      target_name: block_1
+      specifications:
+        - name: density
+          type: constant
+          value: 1.0
+        - name: thermal_conductivity
+          type: constant
+          value: 1.0
+        - name: specific_heat
+          type: constant
+          value: 1.0
+
+    boundary_conditions:
+
+    - wall_boundary_condition: bc_left
+      target_name: surface_1
+      wall_user_data:
+        temperature: 20.0
+
+
+    - wall_boundary_condition: bc_right
+      target_name: surface_2
+      wall_user_data:
+        temperature: 40.0
+
+    solution_options:
+      name: myOptions
+
+      use_consolidated_solver_algorithm: yes
+
+      options:
+      - element_source_terms:
+          temperature: FEM_DIFF
+
+    output:
+      output_data_base_name: femHC.e
+      output_frequency: 10
+      output_node_set: no 
+      output_variables:
+       - dual_nodal_volume
+       - temperature
+
+Time_Integrators:
+  - StandardTimeIntegrator:
+      name: ti_1
+      start_time: 0
+      termination_step_count: 25 
+      time_step: 10.0 
+      time_stepping_type: fixed
+      time_step_count: 0
+      second_order_accuracy: no
+
+      realms:
+        - realm_1
diff --git a/_images/T_123.png b/_images/T_123.png
diff --git a/_images/T_linear_gradBC.png b/_images/T_linear_gradBC.png
diff --git a/_images/T_parabolic_gradBC.png b/_images/T_parabolic_gradBC.png
diff --git a/_images/U_x_CTV_subsequent_L2.pdf b/_images/U_x_CTV_subsequent_L2.pdf
diff --git a/_images/U_x_precursor.pdf b/_images/U_x_precursor.pdf
diff --git a/_images/Ux_123.png b/_images/Ux_123.png
diff --git a/_images/Ux_23.png b/_images/Ux_23.png
diff --git a/_images/Uz_L2_dp.pdf b/_images/Uz_L2_dp.pdf
diff --git a/_images/abl_sub_check_one_two.png b/_images/abl_sub_check_one_two.png
diff --git a/_images/abl_sub_cycle_T.pdf b/_images/abl_sub_cycle_T.pdf
diff --git a/_images/actuatorDisk.png b/_images/actuatorDisk.png
diff --git a/_images/contactSearchAndEval.pdf b/_images/contactSearchAndEval.pdf
diff --git a/_images/convTaylorVortexFO.pdf b/_images/convTaylorVortexFO.pdf
diff --git a/_images/convTaylorVortexSO.pdf b/_images/convTaylorVortexSO.pdf
diff --git a/_images/convTaylorVortexSO_ElemLagElemPf.pdf b/_images/convTaylorVortexSO_ElemLagElemPf.pdf
diff --git a/_images/cvfem_conv.png b/_images/cvfem_conv.png
diff --git a/_images/cvfem_nodes.png b/_images/cvfem_nodes.png
diff --git a/_images/cvfem_onecv.png b/_images/cvfem_onecv.png
diff --git a/_images/cylinder_overset.png b/_images/cylinder_overset.png
diff --git a/_images/dgHex8Tet4Duct.png b/_images/dgHex8Tet4Duct.png
diff --git a/_images/dgNonconformalCVFEM_3dTempMMS_OoC.pdf b/_images/dgNonconformalCVFEM_3dTempMMS_OoC.pdf
diff --git a/_images/dgNonconformalCVFEM_3dTempMMS_OoCPNG.pdf b/_images/dgNonconformalCVFEM_3dTempMMS_OoCPNG.pdf
diff --git a/_images/dgNonconformalCVFEM_3dTempMMS_tempField.pdf b/_images/dgNonconformalCVFEM_3dTempMMS_tempField.pdf
diff --git a/_images/ew_aoa.pdf b/_images/ew_aoa.pdf
diff --git a/_images/ew_dragcoeff.pdf b/_images/ew_dragcoeff.pdf
diff --git a/_images/ew_dragforceperunitlength.pdf b/_images/ew_dragforceperunitlength.pdf
diff --git a/_images/ew_liftcoeff.pdf b/_images/ew_liftcoeff.pdf
diff --git a/_images/ew_liftforceperunitlength.pdf b/_images/ew_liftforceperunitlength.pdf
diff --git a/_images/fw_bladeresults.png b/_images/fw_bladeresults.png
diff --git a/_images/fw_bladeschematic.png b/_images/fw_bladeschematic.png
diff --git a/_images/grid07_conformal10_surf_tip.png b/_images/grid07_conformal10_surf_tip.png
diff --git a/_images/grid07_conformal10_surf_tip_close.png b/_images/grid07_conformal10_surf_tip_close.png
diff --git a/_images/hadapt.pdf b/_images/hadapt.pdf
diff --git a/_images/hadapt2.pdf b/_images/hadapt2.pdf
diff --git a/_images/hadapt3.pdf b/_images/hadapt3.pdf
diff --git a/_images/hex8_tet4_one_two_ten_R0_R1.png b/_images/hex8_tet4_one_two_ten_R0_R1.png
diff --git a/_images/ho_heatCondMMM_dtdx.pdf b/_images/ho_heatCondMMM_dtdx.pdf
diff --git a/_images/ho_stvUandDpDx.pdf b/_images/ho_stvUandDpDx.pdf
diff --git a/_images/hybrid_T_L2.pdf b/_images/hybrid_T_L2.pdf
diff --git a/_images/hybrid_T_Loo.pdf b/_images/hybrid_T_Loo.pdf
diff --git a/_images/hybrid_laplace.png b/_images/hybrid_laplace.png
diff --git a/_images/openJetFlowStill.pdf b/_images/openJetFlowStill.pdf
diff --git a/_images/openJetInlet.pdf b/_images/openJetInlet.pdf
diff --git a/_images/ordinate.pdf b/_images/ordinate.pdf
diff --git a/_images/oversetBlockOneTwo.png b/_images/oversetBlockOneTwo.png
diff --git a/_images/oversetBlockOneTwoCut.png b/_images/oversetBlockOneTwoCut.png
diff --git a/_images/oversetHC.png b/_images/oversetHC.png
diff --git a/_images/oversetNodes.png b/_images/oversetNodes.png
diff --git a/_images/oversetSphere.png b/_images/oversetSphere.png
diff --git a/_images/pecletFactor.pdf b/_images/pecletFactor.pdf
diff --git a/_images/ramp.png b/_images/ramp.png
diff --git a/_images/rotbox_overset.png b/_images/rotbox_overset.png
diff --git a/_images/tioga_cyl_velocity.png b/_images/tioga_cyl_velocity.png
diff --git a/_images/tioga_cyl_vorticity.png b/_images/tioga_cyl_vorticity.png
diff --git a/_images/tquadEdgeCvfemTdiff.pdf b/_images/tquadEdgeCvfemTdiff.pdf
diff --git a/_images/tquadLaplaceMMS.pdf b/_images/tquadLaplaceMMS.pdf
diff --git a/_images/tquadLaplaceMMSCVFEM.pdf b/_images/tquadLaplaceMMSCVFEM.pdf
diff --git a/_images/twoBlockDiag.pdf b/_images/twoBlockDiag.pdf
diff --git a/_images/we_cvfem_p1.png b/_images/we_cvfem_p1.png
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
@@ -0,0 +1,12 @@
+Nalu-Wind Documentation
+=======================
+.. toctree::
+   :maxdepth: 2
+
+   Nalu-Wind Homepage <https://github.com/Exawind/nalu-wind>
+   Nalu-Wind Nightly Test Results <http://my.cdash.org/index.php?project=Exawind>
+   User Manual <source/user/index.rst>
+   Developer Manual <source/developer/index.rst>
+   Theory Manual <source/theory/index.rst>
+   Verification Manual <source/verification/index.rst>
+   zrefs.rst
diff --git a/_sources/source/developer/build_doc.rst.txt b/_sources/source/developer/build_doc.rst.txt
@@ -0,0 +1,47 @@
+Building the Documentation
+==========================
+
+This document describes how to build Nalu-Wind's documentation.
+The documentation is based on the use of Doxygen, Sphinx,
+and Doxylink. Therefore we will need to install these tools
+as well as some extensions of Sphinx that are utilized.
+
+Install the Tools
+-----------------
+
+Install CMake, Doxygen, Sphinx, Doxylink, and the
+extensions used. Doxygen uses the ``dot`` application
+installed with GraphViz. Sphinx uses a combination
+of extensions installed with ``pip install`` as well as some
+that come with Nalu-Wind located in the ``_extensions``
+directory. Using Homebrew on Mac OS X, 
+this would look something like:
+
+::
+
+  brew install cmake
+  brew install python
+  brew install doxygen
+  brew install graphviz
+  pip2 install sphinx
+  pip2 install sphinxcontrib-bibtex
+  pip2 install breathe
+  pip2 install sphinx_rtd_theme
+
+On Linux, CMake, Python, Doxygen, and GraphViz could be installed
+using your package manager, e.g. ``sudo apt-get install cmake``.
+
+Build the Docs
+--------------
+
+In the `Nalu-Wind repository <https://github.com/Exawind/nalu-wind>`__ checkout, execute:
+
+::
+
+  sphinx-build -M html ./docs/sphinx ./build_docs/manual -W --keep-going -n
+  doxygen ./docs/doxygen/Doxyfile
+
+If all of the main tools are found successfully, the command will
+complete successfully and the entry point to the documentation should
+be in ``build_docs/manual/html/index.html`` for the manual and
+``build_docs/doxygen/html/index.html`` for the source code.
diff --git a/_sources/source/developer/contrib.rst.txt b/_sources/source/developer/contrib.rst.txt
@@ -0,0 +1,11 @@
+Contributing to Nalu-Wind
+=========================
+
+1. There is no rush to push. We only support production tested capability. Better yet, peform code verification and unit testing.
+
+2. Always run the full regression test suite. No exceptions.
+
+3. Peer review when fully appropriate (ask for a pull request).
+
+4. If adding a new feature, include a regression test for this feature. Refer to the section of this documentation on adding a test :ref:`here <add-test>`.
+
diff --git a/_sources/source/developer/index.rst.txt b/_sources/source/developer/index.rst.txt
@@ -0,0 +1,13 @@
+Developer Manual
+================
+.. toctree::
+   :maxdepth: 2
+
+   Testing Nalu-Wind <testing.rst>
+   How to Document Source Code <write_developer_doc.rst>
+   How to Write User Documentation <write_user_doc.rst>
+   Building the Documentation <build_doc.rst>
+   Developer Workflow Best Practices <workflow.rst>
+   Code Style Guide <style.rst>
+   Contributing <contrib.rst>
+   Project Development Infrastructure <infra.rst>