Update stencils and the energy model

.clang-tidy

@@ -16,6 +16,7 @@ Checks: 'bugprone-*,
          -readability-function-cognitive-complexity'
 WarningsAsErrors: ''
 HeaderFilterRegex: '.*'
+HeaderFileExtensions: ['', "H", 'h', 'hh', 'hpp', 'hxx']
 FormatStyle:     none
 User:            user
 CheckOptions:
@@ -55,6 +56,12 @@ CheckOptions:
     value:           llvm
   - key:             modernize-use-nullptr.NullMacros
     value:           'NULL'
+  - { key: readability-identifier-length.MinimumVariableNameLength, value: 2 }
+  - { key: readability-identifier-length.IgnoredVariableNames, value: "^[ijkp]$" }
+  - { key: readability-identifier-length.MinimumParameterNameLength, value: 2 }
+  - { key: readability-identifier-length.IgnoredParameterNames, value: "^[ijknp]$" }
+  - { key: readability-identifier-length.MinimumExceptionNameLength, value: 2 }
+  - { key: readability-identifier-length.MinimumLoopCounterNameLength, value: 1 }
   - { key: readability-identifier-naming.NamespaceCase,       value: lower_case }
   - { key: readability-identifier-naming.ClassCase,           value: CamelCase  }
   - { key: readability-identifier-naming.PrivateMemberPrefix, value: m_         }

.github/workflows/ci.yml

@@ -39,7 +39,7 @@ jobs:
           echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
           echo "CCACHE_COMPRESSLEVEL=5" >> $GITHUB_ENV
           echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
-          echo "CCACHE_MAXSIZE=1G" >> $GITHUB_ENV
+          echo "CCACHE_MAXSIZE=500M" >> $GITHUB_ENV
       - name: Install Ccache
         run: |
           wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
@@ -143,7 +143,7 @@ jobs:
           echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
           echo "CCACHE_COMPRESSLEVEL=5" >> $GITHUB_ENV
           echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
-          echo "CCACHE_MAXSIZE=1G" >> $GITHUB_ENV
+          echo "CCACHE_MAXSIZE=500M" >> $GITHUB_ENV
           cmake -E make_directory ${{runner.workspace}}/deps
       - name: Dependencies
         run: |
@@ -264,7 +264,7 @@ jobs:
   GPU-AMD:
     name: GPU-HIP
     needs: [Formatting, CPU-GNUmake]
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Clone
         uses: actions/checkout@v4
@@ -276,18 +276,17 @@ jobs:
           echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
           echo "CCACHE_COMPRESSLEVEL=5" >> $GITHUB_ENV
           echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
-          echo "CCACHE_MAXSIZE=1G" >> $GITHUB_ENV
+          echo "CCACHE_MAXSIZE=500M" >> $GITHUB_ENV
       - name: Dependencies
         run: |
           ${{github.workspace}}/Submodules/AMReX/.github/workflows/dependencies/ubuntu_free_disk_space.sh
-          curl -O https://repo.radeon.com/rocm/rocm.gpg.key
-          sudo apt-key add rocm.gpg.key
-          echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/5.6.1/ ubuntu main' \
-              | sudo tee /etc/apt/sources.list.d/rocm.list
-          echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
-              | sudo tee -a /etc/profile.d/rocm.sh
+          sudo mkdir --parents --mode=0755 /etc/apt/keyrings
+          wget https://repo.radeon.com/rocm/rocm.gpg.key -O - | gpg --dearmor | sudo tee /etc/apt/keyrings/rocm.gpg > /dev/null
+          echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/rocm.gpg] https://repo.radeon.com/rocm/apt/6.3.3 noble main" | sudo tee --append /etc/apt/sources.list.d/rocm.list
+          echo -e 'Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600' | sudo tee /etc/apt/preferences.d/rocm-pin-600
+          echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' | sudo tee -a /etc/profile.d/rocm.sh
           sudo apt-get update
-          sudo apt-get install -y rocm-dev rocrand-dev rocprim-dev
+          sudo apt-get install -y --no-install-recommends build-essential rocm-dev rocrand-dev rocprim-dev hiprand-dev
       - name: Install Ccache
         run: |
           wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
@@ -346,7 +345,7 @@ jobs:
           echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
           echo "CCACHE_COMPRESSLEVEL=5" >> $GITHUB_ENV
           echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
-          echo "CCACHE_MAXSIZE=1G" >> $GITHUB_ENV
+          echo "CCACHE_MAXSIZE=500M" >> $GITHUB_ENV
           echo "CCACHE_DEPEND=1" >> $GITHUB_ENV
       - name: Dependencies
         run: |
@@ -458,7 +457,7 @@ jobs:
           echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
           echo "CCACHE_COMPRESSLEVEL=5" >> $GITHUB_ENV
           echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
-          echo "CCACHE_MAXSIZE=1G" >> $GITHUB_ENV
+          echo "CCACHE_MAXSIZE=500M" >> $GITHUB_ENV
       - name: Install Ccache
         run: |
           wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
@@ -520,7 +519,7 @@ jobs:
           echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
           echo "CCACHE_COMPRESSLEVEL=5" >> $GITHUB_ENV
           echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
-          echo "CCACHE_MAXSIZE=1G" >> $GITHUB_ENV
+          echo "CCACHE_MAXSIZE=500M" >> $GITHUB_ENV
       - name: Install Ccache
         run: |
           wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz

Build/GNUmakefile

@@ -9,7 +9,7 @@ DIM	= 3
 
 COMP    = gnu
 
-USE_MPI   = TRUE 
+USE_MPI   = TRUE
 USE_OMP   = FALSE
 USE_CUDA  = FALSE
 USE_EB    = TRUE

Docs/sphinx/LBM.rst

@@ -50,4 +50,9 @@ where :math:`u` is the velocity vector, :math:`\rho` is the density, :math:`w_i`
 
    u(x, t) &= \frac{1}{\rho} \sum_{i} e_i f_i(x, t)
 
-MARBLES implements both the D2Q9 and D3Q27 LBM approaches for two dimensional and three dimensional flow, respectively.
+MARBLES implements both the D3Q27 LBM approach for two dimensional and three dimensional flow, respectively.
+
+For the thermal version of MARBLES, please refer to additional theory related to the additional energy lattice and cross coupling, 
+in the PhD thesis  
+"Sawant, Nilesh. 'Kinetic Modeling of Reactive Flows.'. ETH Zurich, 2023. https://doi.org/10.3929/ETHZ-B-000607045."
+

Docs/sphinx/VandV.rst

@@ -24,3 +24,54 @@ This demonstrates MARBLES ability to simulate flow through complex, porous media
 
 .. image:: /figs/pine_box.gif
    :width: 600pt
+
+
+Viscosity verification
+----------------------
+
+This test case demonstrates MARBLES ability to maintain the correct viscosity over a wide range of temperatures. 
+Viscosity is computed from the simulation by tracking the maximum of velocity over time arising from an initial 
+condition consisting of a sinusoidal velocity perturbation.
+The temperature is not restricted to 1/3, but it can be set to any value less than or equal to 1/3. 
+This feature has been enabled by incorporating product-form of the equilibrium distribition which 
+improves stability due to maximisation of the entropy and the incorporation of an extended lattice 
+Boltzmann approach which adds a non-local correction term to the pressure tensor to correct the insufficient 
+Galilean invariance of the standard lattice at the third order moment.
+
+Input and post processing files: `Tests/test_files/viscosityTest/`
+
+.. image:: /figs/kinematicViscosity.png
+   :width: 400pt   
+
+
+Thermal diffusivity verification
+---------------------------------
+
+This test case demonstrates MARBLES ability to maintain the correct thermal diffusivity over a wide range of temperatures, 
+as well as at different Prandtl numbers, adiabatic exponents and mean molecular masses.
+Themal diffusivity is computed from the simulation by tracking the maximum of temperature over time arising from an initial 
+condition consisting of a sinusoidal temperature perturbation.
+The capability to solve for temperature has been enabled by an additional lattice which conserves the total energy of the fluid.
+The new lattice representing energy has been two way coupled with the existing momentum lattice which had been augmented with 
+product-form equilibrium and extended pressure term to compensate the third order error. The new energy lattice adds an 
+energy equation, while the multi-relaxation on the energy lattice enables a variable Prandtl number and an adjustable adiabatic 
+exponent. The mean molecular mass is allowed to be a variable because the product form of the equilibrium on the 
+first lattice allows the variance of the equilibrium distribution to be RT instead of T.
+
+Input and post processing files: `Tests/test_files/thermalDiffusivityTest/`
+
+.. image:: /figs/thermalDiffusivity.png
+   :width: 400pt     
+
+Sod test tube
+----------------------
+
+This test case demonstrates MARBLES ability to solve compressible flows with realistic parameters of practical interest. 
+The correct position of the wave structures confirm that the speed of sound is correct in the thermal version of the solver. The model 
+is the same as that built for the thermal diffusivity test. The sod shock test marks the completion of the MARBLES solver to the 
+extent of a contunuum limit, single-component, single-phase, transient computational fluid dynamics solver with mass, momentum and energy equations.    
+
+Input and post processing files: `Tests/test_files/sodTest/`
+
+.. image:: /figs/sodShock.png
+   :width: 600pt