CEPTR: PLOG reaction support at constant pressure (#549)

* ceptr: Added functionality for reading and converting PLOG reactions.

* Do formatting with black

* Run isort and flake8

* Latest upstream pull (#2)

* pin intel-oneapi version in CI (#541)

* Bump Submodules/amrex from `8349789` to `00e6f75` (#540)

Bumps [Submodules/amrex](https://github.com/AMReX-Codes/amrex) from `8349789` to `00e6f75`.
- [Release notes](https://github.com/AMReX-Codes/amrex/releases)
- [Commits](AMReX-Codes/amrex@8349789...00e6f75)

---
updated-dependencies:
- dependency-name: Submodules/amrex
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Bruce Perry <Bruce.Perry@nrel.gov>

* Make EOS functions templates to allow for CellData as an argument (#536)

* template for celldata in EOS

* static asserts in templates

* templating for RY2 functions for all EOS

* Fix clang-tidy (#535)

* fix unused variable

* free shared ptr for manfunc parm

---------

Co-authored-by: Marc T. Henry de Frahan <marc.henrydefrahan@nrel.gov>

* Unit conversions (#539)

* Utilities and unit conversions

* Formatting

* 2 structs and renamed functions to avoid macros issue

* Templating and namespaces

* Added Utilities to Docs

* Overload instead of templating

* Fixed nested namespaces for clang-tidy error in PeleLMeX, removed Utilities.H from PelePhysics.H.wq (#545)

* Update CI to ubuntu-24.04 (#546)

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Bruce Perry <Bruce.Perry@nrel.gov>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Marc T. Henry de Frahan <marc.henrydefrahan@nrel.gov>
Co-authored-by: Dave Montgomery <David.Montgomery@nrel.gov>
Co-authored-by: Jon Rood <jon.rood@nrel.gov>

* Adding example mechanism for PLOG evaluation

* Bump Submodules/amrex from `00e6f75` to `f27eb69` (#550)

Bumps [Submodules/amrex](https://github.com/AMReX-Codes/amrex) from `00e6f75` to `f27eb69`.
- [Release notes](https://github.com/AMReX-Codes/amrex/releases)
- [Commits](AMReX-Codes/amrex@00e6f75...f27eb69)

---
updated-dependencies:
- dependency-name: Submodules/amrex
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* speciesNames for Manifold EOS (#542)

* simplify templated functions in EOS.cpp

* rearrange template specializations in EOS.cpp so they are all in header; improve speciesNames function for manifold

* SYCL ifdef for manifold speciesnames

* pass host eosparm to reactors

* ignitionDelay: remove one invalid call for manifold eos

* fix dumb bug

* clang-tidy unused arguments

* ceptr: create pressure-specific folders for plog mechanism, move plog_pressure var into mechanism object

* ceptr: implement command line and list options to specify plog pressure

* ceptr: Add plog mech to list_mech

* ceptr: Copy Make.package to the plog subfolder

* add docs on plog mechanism conversion

* fix typo

fix another typo

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Thomas Howarth <69794367+ThomasHowarth@users.noreply.github.com>
Co-authored-by: Bruce Perry <Bruce.Perry@nrel.gov>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Marc T. Henry de Frahan <marc.henrydefrahan@nrel.gov>
Co-authored-by: Dave Montgomery <David.Montgomery@nrel.gov>
Co-authored-by: Jon Rood <jon.rood@nrel.gov>

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
-
-

Mechanisms/POLIMI2020/1_000atm/Make.package

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