Merge branch 'development' into mani-variance

.github/workflows/dependencies/dependencies_cuda.sh

@@ -19,6 +19,7 @@ sudo apt-get install -y \
     libcusparse-dev-${CUDA_VERSION}         \
     libcublas-dev-${CUDA_VERSION}           \
     libcurand-dev-${CUDA_VERSION}           \
+    libcusparse-dev-${CUDA_VERSION}         \
     libnvjitlink-${CUDA_VERSION}
 
 export PATH=/usr/local/nvidia/bin:/usr/local/cuda-12.6/bin:${PATH}

.github/workflows/dependencies/dependencies_hip.sh

@@ -8,7 +8,7 @@ echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/rocm.gpg] https://repo.radeon.
 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 hiprand-dev
+sudo apt-get install -y rocm-dev rocrand-dev rocprim-dev hiprand-dev rocsparse-dev
 
 source /etc/profile.d/rocm.sh
 which hipcc

.github/workflows/docs.yml

@@ -46,9 +46,9 @@ jobs:
           exit $(tail -n 1 build-output-warnings.txt | awk '{print $2}')
       - name: Deploy
         if: github.event_name == 'push' && github.ref == 'refs/heads/development'
-        uses: JamesIves/github-pages-deploy-action@releases/v3
+        uses: JamesIves/github-pages-deploy-action@releases/v4
         with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          BRANCH: gh-pages
-          FOLDER: ${{runner.workspace}}/build-docs/sphinx/html
-          SINGLE_COMMIT: true
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages
+          folder: ${{runner.workspace}}/build-docs/sphinx/html
+          single-commit: true

Docs/sphinx/Ceptr.rst

@@ -19,7 +19,7 @@ To install CEPTR dependencies::
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
   $ poetry update
 
-.. note:: Note that the install requires a specific Python version, which is specified in the ``Support/ceptr/pyproject.toml``. If a compatible version exists in your system then poetry will try to find and use it. Otherwise, think about using a `conda <https://conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_ environment to manage packages and their dependencies without tampering with your system. 
+.. note:: Note that the install requires a specific Python version, which is specified in the ``Support/ceptr/pyproject.toml``. If a compatible version exists in your system then poetry will try to find and use it. Otherwise, think about using a `conda <https://conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_ environment to manage packages and their dependencies without tampering with your system.
 
 Usage
 -----
@@ -48,7 +48,8 @@ There are three ways to use CEPTR to generate C++ mechanism files for a given ch
      $ poetry run convert -f ${PELEPHYSICS_HOME}/Mechanisms/${chemistry}/mechanism.yaml \
        --chemistry {chemistry-type} \
        --gas_name {gas-name} \
-       --interface_name {interface-name}
+       --interface_name {interface-name} \
+       --plog_pressure {value in Pa}
 
    The ``--chemistry`` (or ``-c``) argument allows users to convey if the ``${chemistry}`` of interest is either one of two valid options, namely, ``homogeneous`` or ``heterogeneous``. The default value for ``{chemistry-type}`` is ``homogeneous``.
    The ``--gas_name`` argument allows users to specify the names of the homogeneous phase to use, as several different ones can be defined in the corresponding ``mechanism.yaml`` file (under the ``phases:`` item). The default value for ``{gas-name}`` is ``gas``.
@@ -63,17 +64,25 @@ There are three ways to use CEPTR to generate C++ mechanism files for a given ch
 
    .. note:: CEPTR interpretations of heterogeneous mechanisms is currently a work in progress.
 
+   .. note:: CEPTR offers only partial support for mechanisms with pressure-dependent Arrhenius (PLOG) reactions.
+             These reactions are fixed to a constant pressure, specified with the ``--plog_pressure`` argument,
+             in the CEPTR-generated source code. Mechanisms with PLOG reactions generated in this way are limited
+             in validity to that specific pressure and would not be suitable for compressible flows with significant
+             pressure variation. For that reason, source code for these mechanisms is saved in pressure-specific directories, for
+             example ``${PELE_PHYSICS_HOME}/Mechanisms/POLIMI2020/1_000atm/``.
+
+
 2. Using a helper script in the directory containing the ``mechanism.yaml`` file::
 
      $ ./convert.sh
 
-   .. note:: It is possible that using this option will require for you to have a valid Cantera installed somewhere. Again, we strongly suggest using a `conda <https://conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_ environment to install all required package. A simple ceptr environment can be generated using the following yaml script:: 
+   .. note:: It is possible that using this option will require for you to have a valid Cantera installed somewhere. Again, we strongly suggest using a `conda <https://conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_ environment to install all required package. A simple ceptr environment can be generated using the following yaml script::
 
      $ name: ceptr
-     $ channels:  
-     $ - conda-forge 
-     $ dependencies: 
-     $ - python=3.10  
+     $ channels:
+     $ - conda-forge
+     $ dependencies:
+     $ - python=3.10
      $ - cantera
 
 3. Using a helper script in the ``Mechanisms`` directory::
@@ -110,7 +119,7 @@ For a detailed description of these options and a further information on the way
 
 To generate a QSS C++ mechanism from the ``.yaml`` file thus created, tailored to your needs, please refer to Tutorials :ref:`Generating NC12H26 QSS mechanism with analytical jacobian <sec_tutqss1>` and :ref:`Generating NC12H26 QSS mechanism without analytical jacobian <sec_tutqss2>`.
 
-Batched generation of Pele-compatible mechanisms 
+Batched generation of Pele-compatible mechanisms
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. note::
@@ -138,5 +147,3 @@ To generate all mechanisms::
   $ poetry run convert -l ${PELE_PHYSICS_HOME}/Mechanisms/list_mech
   $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
   $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
-
-

Docs/sphinx/GettingStarted.rst

@@ -4,7 +4,7 @@
 `PelePhysics` Quickstart
 ************************
 
-Greetings impatient user. As a word of caution, this documentation is in progress. Some parts of the code remain undocumented,
+Greetings users. As a word of caution, this documentation is in progress. Some parts of the code remain undocumented,
 and some parts of the documentation are out of data. If you are confused by something you read here, or otherwise
 need help with `PelePhysics`, the best course of action is to open a Discussion on the `GitHub page <https://github.com/AMReX-Combustion/PelePhysics/discussions>`_,
 so the development team and other users can help.

Mechanisms/POLIMI2020/1_000atm/Make.package

@@ -0,0 +1 @@
+CEXE_sources+=mechanism.cpp