From 666b5939d15a2580858f7f8903a804182bc4c83b Mon Sep 17 00:00:00 2001
From: baperry2 <Bruce.Perry@nrel.gov>
Date: Mon, 23 Dec 2024 17:55:46 +0000
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---
 Ceptr.html             | 12 +++++++++++-
 _sources/Ceptr.rst.txt | 27 +++++++++++++++++----------
 _static/js/versions.js | 10 +++++++---
 searchindex.js         |  2 +-
 4 files changed, 36 insertions(+), 15 deletions(-)

diff --git a/Ceptr.html b/Ceptr.html
index de657cb1d..5d062344f 100644
--- a/Ceptr.html
+++ b/Ceptr.html
@@ -137,7 +137,8 @@ <h3>Generating Pele-compatible mechanisms for a single chemistry<a class="header
 <div class="highlight-rst notranslate"><div class="highlight"><pre><span></span>$ 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}
 </pre></div>
 </div>
 <p>The <code class="docutils literal notranslate"><span class="pre">--chemistry</span></code> (or <code class="docutils literal notranslate"><span class="pre">-c</span></code>) argument allows users to convey if the <code class="docutils literal notranslate"><span class="pre">${chemistry}</span></code> of interest is either one of two valid options, namely, <code class="docutils literal notranslate"><span class="pre">homogeneous</span></code> or <code class="docutils literal notranslate"><span class="pre">heterogeneous</span></code>. The default value for <code class="docutils literal notranslate"><span class="pre">{chemistry-type}</span></code> is <code class="docutils literal notranslate"><span class="pre">homogeneous</span></code>.
@@ -153,6 +154,15 @@ <h3>Generating Pele-compatible mechanisms for a single chemistry<a class="header
 <p class="admonition-title">Note</p>
 <p>CEPTR interpretations of heterogeneous mechanisms is currently a work in progress.</p>
 </div>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>CEPTR offers only partial support for mechanisms with pressure-dependent Arrhenius (PLOG) reactions.
+These reactions are fixed to a constant pressure, specified with the <code class="docutils literal notranslate"><span class="pre">--plog_pressure</span></code> argument,
+in the CEPTR-generated source code. Mechanisms with PLOG reactions generated in this way are limited
+in validity to that specific pressure and would not be suitable for compressible flows with significant
+pressure variation. For that reason, source code for these mechanisms is saved in pressure-specific directories, for
+example <code class="docutils literal notranslate"><span class="pre">${PELE_PHYSICS_HOME}/Mechanisms/POLIMI2020/1_000atm/</span></code>.</p>
+</div>
 </li>
 <li><p>Using a helper script in the directory containing the <code class="docutils literal notranslate"><span class="pre">mechanism.yaml</span></code> file:</p>
 <div class="highlight-rst notranslate"><div class="highlight"><pre><span></span>$ ./convert.sh
diff --git a/_sources/Ceptr.rst.txt b/_sources/Ceptr.rst.txt
index a91a72128..71a205423 100644
--- a/_sources/Ceptr.rst.txt
+++ b/_sources/Ceptr.rst.txt
@@ -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
-
-
diff --git a/_static/js/versions.js b/_static/js/versions.js
index 818bc9969..4958195e0 100644
--- a/_static/js/versions.js
+++ b/_static/js/versions.js
@@ -1,6 +1,6 @@
 const themeFlyoutDisplay = "hidden";
-const themeVersionSelector = "True";
-const themeLanguageSelector = "True";
+const themeVersionSelector = true;
+const themeLanguageSelector = true;
 
 if (themeFlyoutDisplay === "attached") {
   function renderLanguages(config) {
@@ -8,10 +8,14 @@ if (themeFlyoutDisplay === "attached") {
       return "";
     }
 
+    // Insert the current language to the options on the selector
+    let languages = config.projects.translations.concat(config.projects.current);
+    languages = languages.sort((a, b) => a.language.name.localeCompare(b.language.name));
+
     const languagesHTML = `
       <dl>
         <dt>Languages</dt>
-        ${config.projects.translations
+        ${languages
           .map(
             (translation) => `
         <dd ${translation.slug == config.projects.current.slug ? 'class="rtd-current-item"' : ""}>
diff --git a/searchindex.js b/searchindex.js
index 636b5c9d7..1f2748c70 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"A brief introduction to CVODE": [[7, null]], "Activating the different CVODE solver options via the input files": [[2, "activating-the-different-cvode-solver-options-via-the-input-files"]], "Analytical Jacobian": [[8, "analytical-jacobian"]], "Analytically reduced chemistry via quasi-steady state (QSS) assumption in PelePhysics": [[8, null]], "Batched generation of Pele-compatible mechanisms": [[0, "batched-generation-of-pele-compatible-mechanisms"]], "Building and Running Test Cases": [[5, "building-and-running-test-cases"]], "C++ Code": [[3, "c-code"]], "CEPTR: Chemistry Evaluation for Pele Through Recasting": [[0, null]], "CVODE implementation in PelePhysics": [[2, null]], "CVODE implementation in PelePhysics on GPU": [[2, "cvode-implementation-in-pelephysics-on-gpu"]], "Chemical potential": [[4, "chemical-potential"]], "Chemistry": [[1, null]], "Chemistry contents:": [[1, null]], "Constant": [[13, "constant"]], "Current Limitations": [[2, "current-limitations"], [2, "id13"]], "Dependencies": [[5, "dependencies"]], "Developer Guidelines": [[3, null]], "Developing": [[15, "developing"]], "Diagnostics": [[15, "diagnostics"]], "Disclaimer": [[11, "disclaimer"]], "Documentation contents:": [[16, null]], "Equation of State": [[4, null]], "Error control, step-sizing, order determination": [[7, "error-control-step-sizing-order-determination"]], "Evolution of major species in a CV reactor, computed with the LiDryer mechanism. Black: CANTERA, red: PelePhysics.": [[2, "id16"]], "Evolution of temperature, pressure and enthalpy in a CV reactor, computed with the LiDryer mechanism. Black: CANTERA, red: PelePhysics.": [[2, "id15"]], "Filter": [[15, "filter"]], "From non-QSS species to QSS species concentration": [[8, "from-non-qss-species-to-qss-species-concentration"]], "Fuego": [[4, "fuego"]], "GammaLaw": [[4, "gammalaw"]], "Generating Inflow Files": [[11, "generating-inflow-files"]], "Generating Pele-compatible mechanisms for a single chemistry": [[0, "generating-pele-compatible-mechanisms-for-a-single-chemistry"]], "Generating YAML chemistry files: converting from CHEMKIN files": [[0, "generating-yaml-chemistry-files-converting-from-chemkin-files"]], "Generating a PMF file": [[15, "generating-a-pmf-file"]], "Generating a reduced, QSS chemistry file": [[0, "generating-a-reduced-qss-chemistry-file"]], "Generating a turbulence file": [[15, "generating-a-turbulence-file"]], "Generating an HIT File": [[11, "generating-an-hit-file"]], "Grouping cells together": [[2, "grouping-cells-together"]], "How does CVODE compare with DVODE ?": [[2, "how-does-cvode-compare-with-dvode"]], "How to naviguate this documentation": [[6, "how-to-naviguate-this-documentation"]], "Indices and tables": [[16, "indices-and-tables"]], "Input file options": [[15, "input-file-options"]], "Internal energy and Enthalpy": [[4, "internal-energy-and-enthalpy"]], "Introduction": [[6, null]], "Linear Algebra": [[7, "linear-algebra"]], "Linearizing the set of equations": [[8, "linearizing-the-set-of-equations"]], "MechanismPAH": [[11, "mechanismpah"]], "Mixing rules": [[4, "mixing-rules"]], "Numerical methods overview": [[7, "numerical-methods-overview"]], "Objectives and State-Of-The-Art": [[6, "objectives-and-state-of-the-art"]], "Obtaining PelePhysics": [[5, "obtaining-pelephysics"]], "Other primitive variable derivatives": [[4, "other-primitive-variable-derivatives"]], "Parameters for initializing simulation": [[2, "id14"]], "Parameters used to initialize T in the ReactEval_C test case": [[2, "id18"]], "PelePhysics": [[16, null]], "PelePhysics Quickstart": [[5, null]], "Plt File Management": [[15, "plt-file-management"]], "Premixed Flame Initialization": [[15, "premixed-flame-initialization"]], "Python": [[3, "python"]], "Relative errors on the temperature, pressure, enthalpy and major species in a CV reactor, computed with the LiDryer mechanism.": [[2, "id17"]], "Requirements and input files": [[2, "requirements-and-input-files"]], "Results": [[2, "results"], [2, "id7"]], "Simple": [[13, "simple"]], "Single Droplet Tests": [[10, "single-droplet-tests"]], "Soave-Redlich-Kwong (SRK)": [[4, "soave-redlich-kwong-srk"]], "Software requirements": [[0, "software-requirements"]], "Soot": [[9, null]], "Soot Equations": [[9, "soot-equations"]], "Soot Flags and Inputs": [[9, "soot-flags-and-inputs"]], "Species enthalpy": [[4, "species-enthalpy"]], "Specific heat": [[4, "specific-heat"]], "Speed of Sound": [[4, "speed-of-sound"]], "Spray": [[10, null]], "Spray Equations": [[10, "spray-equations"]], "Spray Flags and Inputs": [[10, "spray-flags-and-inputs"]], "Spray Injection": [[10, "spray-injection"]], "Spray Validation": [[10, "spray-validation"]], "Summary of ReactEvalCvode runs with various algorithms (n-dodecane/air)": [[2, "id20"]], "Summary of ReactEvalCvode_GPU runs with various algorithms (methane/air)": [[2, "id22"]], "Summary of ReactEval_C runs with various algorithms (methane/air)": [[2, "id19"]], "Summary of a CVODE vs a DVODE chemistry integration on the same test case": [[2, "id21"]], "Support": [[11, null]], "Sutherland": [[13, "sutherland"]], "The GNUmakefile": [[2, "the-gnumakefile"], [2, "id2"], [2, "id5"], [2, "id8"], [2, "id11"]], "The QSS assumption": [[8, "the-qss-assumption"]], "The ReactEval_C test case with CVODE in details": [[2, "the-reacteval-c-test-case-with-cvode-in-details"]], "The ReactEval_C_GPU test case in details": [[2, "the-reacteval-c-gpu-test-case-in-details"]], "The Results": [[2, "the-results"]], "The advantage of the QSS assumption": [[8, 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\ No newline at end of file
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Black: CANTERA, red: PelePhysics.": [[2, "id16"]], "Evolution of temperature, pressure and enthalpy in a CV reactor, computed with the LiDryer mechanism. Black: CANTERA, red: PelePhysics.": [[2, "id15"]], "Filter": [[15, "filter"]], "From non-QSS species to QSS species concentration": [[8, "from-non-qss-species-to-qss-species-concentration"]], "Fuego": [[4, "fuego"]], "GammaLaw": [[4, "gammalaw"]], "Generating Inflow Files": [[11, "generating-inflow-files"]], "Generating Pele-compatible mechanisms for a single chemistry": [[0, "generating-pele-compatible-mechanisms-for-a-single-chemistry"]], "Generating YAML chemistry files: converting from CHEMKIN files": [[0, "generating-yaml-chemistry-files-converting-from-chemkin-files"]], "Generating a PMF file": [[15, "generating-a-pmf-file"]], "Generating a reduced, QSS chemistry file": [[0, "generating-a-reduced-qss-chemistry-file"]], "Generating a turbulence file": [[15, "generating-a-turbulence-file"]], "Generating an HIT File": [[11, "generating-an-hit-file"]], "Grouping cells together": [[2, "grouping-cells-together"]], "How does CVODE compare with DVODE ?": [[2, "how-does-cvode-compare-with-dvode"]], "How to naviguate this documentation": [[6, "how-to-naviguate-this-documentation"]], "Indices and tables": [[16, "indices-and-tables"]], "Input file options": [[15, "input-file-options"]], "Internal energy and Enthalpy": [[4, "internal-energy-and-enthalpy"]], "Introduction": [[6, null]], "Linear Algebra": [[7, "linear-algebra"]], "Linearizing the set of equations": [[8, "linearizing-the-set-of-equations"]], "MechanismPAH": [[11, "mechanismpah"]], "Mixing rules": [[4, "mixing-rules"]], "Numerical methods overview": [[7, "numerical-methods-overview"]], "Objectives and State-Of-The-Art": [[6, "objectives-and-state-of-the-art"]], "Obtaining PelePhysics": [[5, "obtaining-pelephysics"]], "Other primitive variable derivatives": [[4, "other-primitive-variable-derivatives"]], "Parameters for initializing simulation": [[2, "id14"]], "Parameters used to initialize T in the ReactEval_C test case": [[2, "id18"]], "PelePhysics": [[16, null]], "PelePhysics Quickstart": [[5, null]], "Plt File Management": [[15, "plt-file-management"]], "Premixed Flame Initialization": [[15, "premixed-flame-initialization"]], "Python": [[3, "python"]], "Relative errors on the temperature, pressure, enthalpy and major species in a CV reactor, computed with the LiDryer mechanism.": [[2, "id17"]], "Requirements and input files": [[2, "requirements-and-input-files"]], "Results": [[2, "results"], [2, "id7"]], "Simple": [[13, "simple"]], "Single Droplet Tests": [[10, "single-droplet-tests"]], "Soave-Redlich-Kwong (SRK)": [[4, "soave-redlich-kwong-srk"]], "Software requirements": [[0, "software-requirements"]], "Soot": [[9, null]], "Soot Equations": [[9, "soot-equations"]], "Soot Flags and Inputs": [[9, "soot-flags-and-inputs"]], "Species enthalpy": [[4, "species-enthalpy"]], "Specific heat": [[4, "specific-heat"]], "Speed of Sound": [[4, "speed-of-sound"]], "Spray": [[10, null]], "Spray Equations": [[10, "spray-equations"]], "Spray Flags and Inputs": [[10, 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