Create FUNDING.yml

Links to NumFOCUS donate page

.github/FUNDING.yml

@@ -0,0 +1,2 @@
+github: [numfocus]
+custom: ['https://numfocus.org/donate-to-cantera']

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,42 @@
+---
+name: Bug report
+about: Report reproducible software issues so we can improve
+title: ''
+labels: ''
+assignees: ''
+---
+
+Please fill in the following information to report a problem with Cantera.
+If you have a question about using Cantera, please post it on our
+[Google Users' Group](https://groups.google.com/forum/#!forum/cantera-users).
+
+**System information**
+
+- Cantera version: [e.g. 2.4]
+- OS: [e.g. Windows 10]
+- Python/MATLAB version:
+
+**Expected behavior**
+
+A clear and concise description of what you expected to happen.
+
+**Actual behavior**
+
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+
+Steps to reproduce the behavior:
+
+1. Open '...'
+2. Run '....'
+3. See error '....'
+
+**Attachments**
+
+If applicable, attach scripts and/or input files to help explain your problem.
+Please do *not* attach screenshots of code or terminal output.
+
+**Additional context**
+
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,25 @@
+---
+name: Feature request
+about: Suggest a new feature to enhance Cantera's capabilities
+title: ''
+labels: ''
+assignees: ''
+---
+
+**Is your feature request related to a problem? Please describe**
+
+A clear and concise description of the problem you're trying to solve.
+
+**Describe the desired solution**
+
+A clear and concise description of a new feature and its application. For
+example, "It would be great if Cantera could..."
+
+**Describe alternatives you have considered**
+
+A clear and concise description of any alternative solutions or features you
+have considered.
+
+**Additional context**
+
+Add any other context about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,17 @@
+Thanks for contributing code! Please include a description of your change and
+check your PR against the list below (for further questions, refer to the
+[contributing guide](https://github.com/Cantera/cantera/blob/master/CONTRIBUTING.md)).
+
+- [ ] There is a clear use-case for this code change
+- [ ] The commit message has a short title & references relevant issues
+- [ ] Build passes (`scons build` & `scons test`) and unit tests address code coverage
+
+**Please fill in the issue number this pull request is fixing**
+
+Fixes #
+
+**Changes proposed in this pull request**
+
+-
+-
+-

.github/SUPPORT.md

@@ -0,0 +1,38 @@
+# How to get support
+
+> This project has a [Code of Conduct](https://github.com/Cantera/cantera/blob/master/CODE_OF_CONDUCT.md).
+> By interacting with this repository, organisation, or community you agree to
+> abide by its terms.
+
+For **help**, **support** and **questions** please create a post on the
+**[Cantera Users' Group](https://groups.google.com/group/cantera-users)**.
+Any discussion of Cantera functionality such as how to use certain function
+calls, syntax problems, input files, etc. should be directed to the Users' Group.
+
+Further, the **[Cantera Gitter Chat](https://gitter.im/Cantera/Lobby)** is an
+infrequently monitored chat room that can be used to discuss tangentially-related
+topics such as how to model the underlying physics of a problem, share cool
+applications that you have developed, etc.
+
+Please **_do not_** raise an issue on GitHub unless it is a bug report or a
+feature request. Issues that do not fall into these categories will be closed.
+If you're not sure, please make a post on the
+[Users' Group](https://groups.google.com/group/cantera-users) and someone will
+be able to help you out.
+
+## Documentation
+
+The [documentation](https://cantera.org/documentation)
+offers a number of starting points:
+
+- [Python tutorial](https://cantera.org/tutorials/python-tutorial.html)
+- [Application Examples in Python (Jupyter)](https://github.com/Cantera/cantera-jupyter#cantera-jupyter)
+- [A guide to Cantera's input file format](https://cantera.org/tutorials/input-files.html)
+- [Information about the Cantera community](https://cantera.org/community.html)
+
+Documentation for the [development version of
+Cantera](https://cantera.org/documentation/dev-docs.html) is also available.
+
+## Contributions
+
+See [`CONTRIBUTING.md`](https://github.com/Cantera/cantera/blob/master/CONTRIBUTING.md) on how to contribute.

.gitignore

@@ -1,4 +1,6 @@
+doc/ctdeploy_key
 *~
+*#
 *.o
 *.so
 *.os
@@ -40,9 +42,11 @@ config.log
 *.gch
 coverage/
 coverage.info
-doc/sphinx/cython/examples
-doc/sphinx/cython/examples.rst
-doc/sphinx/matlab/examples/
-doc/sphinx/matlab/examples.rst
-doc/sphinx/matlab/tutorials/
-doc/sphinx/matlab/code-docs/
+doc/sphinx/matlab/data.rst
+doc/sphinx/matlab/importing.rst
+doc/sphinx/matlab/kinetics.rst
+doc/sphinx/matlab/one-dim.rst
+doc/sphinx/matlab/thermodynamics.rst
+doc/sphinx/matlab/transport.rst
+doc/sphinx/matlab/utilities.rst
+doc/sphinx/matlab/zero-dim.rst

.gitmodules

@@ -9,4 +9,7 @@
 	url = https://github.com/Cantera/sundials-mirror
 [submodule "ext/eigen"]
 	path = ext/eigen
-	url = https://github.com/Cantera/eigen-mirror.git
+	url = https://github.com/eigenteam/eigen-git-mirror
+[submodule "ext/yaml-cpp"]
+	path = ext/yaml-cpp
+	url = https://github.com/jbeder/yaml-cpp.git

.travis.yml

@@ -1,37 +1,90 @@
 language: cpp
 sudo: false
+dist: xenial
 os:
   - linux
   - osx
 addons:
   apt:
     packages:
-      - python-dev
-      - python-numpy
-      - python-pip
+      - python3-pip
       - python3-dev
       - python3-numpy
       - python3-setuptools
+      - scons
       - gfortran
       - libsundials-serial-dev
       - liblapack-dev
       - libblas-dev
       - libboost-dev
+      - doxygen
+      - graphviz
+  ssh_known_hosts:
+    - cantera.org
+
+env:
+  global:
+    secure: "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"
+
+
 before_script: |
-  pip install --user --install-option="--no-cython-compile" cython
-  pip install --user 3to2
+  echo TRAVIS_OS_NAME: $TRAVIS_OS_NAME
   if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-      brew update
-      brew install scons
-      brew install boost
-      brew install python3
-      pip3 install numpy
+      export CONDA_ARCH="${TRAVIS_OS_NAME}_${BUILD_ARCH}"
+      curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o miniconda.sh;
+      bash miniconda.sh -b -p $HOME/miniconda
+      source $HOME/miniconda/etc/profile.d/conda.sh && conda activate
+      conda config --set always_yes yes --set changeps1 no
+      conda install -q numpy cython scons boost ruamel_yaml
+      conda install -q -c conda-forge openmp
+  else
+      pip3 install --user --upgrade pip
+      pip3 install --user --upgrade setuptools wheel
+      pip3 install --user cython
+      pip3 install --user ruamel.yaml==0.15.94  # Need a version compatible with Python 3.4
+
+      # Install packages for the documentation
+      pip3 install --user sphinx sphinxcontrib-matlabdomain sphinxcontrib-doxylink
+      pip3 install --user https://github.com/hagenw/sphinxcontrib-katex/archive/master.tar.gz
   fi
   rm -f cantera.conf
-script:
-  - scons build -j2 VERBOSE=y python_package=full python3_package=y blas_lapack_libs=lapack,blas optimize=n coverage=y
-  - scons test
+script: |
+  set -e
+  if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+      scons build -j2 python_cmd=/usr/bin/python3 VERBOSE=y python_package=full blas_lapack_libs=lapack,blas optimize=n coverage=y
+      scons test
+      scons samples
+      scons build sphinx_docs=y doxygen_docs=y sphinx_cmd="/usr/bin/python3 `which sphinx-build`"
+      if [[ "${TRAVIS_PULL_REQUEST}" == "false" ]] && [[ "${TRAVIS_BRANCH}" == "master" ]] && [[ "${TRAVIS_REPO_SLUG}" == "Cantera/cantera" ]]; then
+        cd build
+        find docs -type f | grep -v /xml/ | grep -v .map$ | grep -v .md5$ | tar cjvf docs/dev-docs.tar.bz2 --files-from - >/dev/null
+        cd -
+        openssl aes-256-cbc -k "${ctdeploy_pass}" -in ./doc/ctdeploy_key.enc -out ./doc/ctdeploy_key -d
+        chmod 0600 ./doc/ctdeploy_key
+        RSYNC_OPTIONS=(
+          -avzP
+          --checksum
+          --rsh='ssh -i ./doc/ctdeploy_key'
+          --exclude='*.map'
+          --exclude='*.md5'
+          --exclude='/doxygen/xml'
+          --delete
+          --delete-excluded
+        )
+        RSYNC_USER="ctdeploy"
+        RSYNC_SERVER="cantera.org"
+        RSYNC_DEST="cantera/documentation/dev"
+        DOCS_OUTPUT_DIR="./build/docs/"
+        rsync "${RSYNC_OPTIONS[@]}" "${DOCS_OUTPUT_DIR}" ${RSYNC_USER}@${RSYNC_SERVER}:${RSYNC_DEST}
+      else
+        echo "Skipping documentation upload from source other than Cantera/cantera:master"
+      fi
+  else
+      scons build -j2 python_cmd=python3 VERBOSE=y python_package=full blas_lapack_libs=lapack,blas optimize=n coverage=y extra_inc_dirs=$CONDA_PREFIX/include extra_lib_dirs=$CONDA_PREFIX/lib
+      scons test
+      scons samples
+  fi
 after_success: |
-  if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+  if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
       bash <(curl -s https://codecov.io/bash)
   fi

AUTHORS

@@ -4,16 +4,42 @@ partial, alphabetical list of developers and contributors to Cantera over the
 years. If you've been left off, please report the omission on the Github issue
 tracker.
 
+Emil Atz
 Philip Berndt
+Wolfgang Bessler, Offenburg University of Applied Science
+Tilman Bremer
 Victor Brunini, Sandia National Laboratory
-Steven Decaluwe, Colorado School of Mines
+Bang-Shiuh Chen, Purdue University
+Ryan Crisanti
+Nicholas Curtis
+Steven DeCaluwe, Colorado School of Mines
+Vishesh Devgan
 Thomas Fiala, Technische Universität München
 David Fronczek
+@g3bk47
+Matteo Giani
 Dave Goodwin, California Institute of Technology
 John Hewson, Sandia National Laboratory
+Trevor Hickey
+Yuanjie Jiang
+Jon Kristofer
+Kyle Linevitch, Jr.
+Christopher Leuth
 Nicholas Malaya, University of Texas at Austin
+Thanasis Mattas, Aristotle University of Thessaloniki
+Evan McCorkle
+Ivan Mitrichev, Mendeleev University of Chemical Technology of Russia
 Harry Moffat, Sandia National Laboratory
+Christopher Neal
+Kyle Niemeyer, Oregon State University
+Paul Northrop
 Andreas Rücker
+Jeff Santner
+Satyam Saxena
+Ingmar Schoegl, Louisiana State University
 Santosh Shanbhogue, Massachusetts Institute of Technology
+David Sondak
 Raymond Speth, Massachusetts Institute of Technology
+Sergey Torokhov
 Bryan Weber, University of Connecticut
+Armin Wehrfritz

CONTRIBUTING.md

@@ -20,9 +20,9 @@
     followed by a blank line and a more detailed summary, if any)
   * Make related changes in a single commit, and unrelated changes in separate
     commits
-  * Make sure that your commits do not include any undesired files, e.g. files
+  * Make sure that your commits do not include any undesired files, e.g., files
     produced as part of the build process or other temporary files.
-  * Use Git's history-rewriting features (i.e. `git rebase -i`; see
+  * Use Git's history-rewriting features (i.e., `git rebase -i`; see
     https://help.github.com/articles/about-git-rebase/) to organize your commits
     and squash "fixup" commits and reversions.
   * Do not merge your branch with `master`. If needed, you should rebase your branch
@@ -33,7 +33,8 @@
   integration tests run using Travis and AppVeyor and resolve any issues that
   arise.
 * Additional discussion of good Git & Github workflow is provided at
-  http://matplotlib.org/devel/gitwash/development_workflow.html and https://docs.scipy.org/doc/numpy-dev/dev/index.html
+  http://matplotlib.org/devel/gitwash/development_workflow.html and
+  https://docs.scipy.org/doc/numpy-1.15.0/dev/gitwash/development_workflow.html
 * Cantera is licensed under a [BSD
   license](https://github.com/Cantera/cantera/blob/master/License.txt) which
   allows others to freely modify the code, and if your Pull Request is accepted,
@@ -52,8 +53,9 @@
 * Write comments to explain non-obvious operations
 
 ## C++
+
 * All classes, member variables, and methods should have Doxygen-style comments
-  (e.g. comment lines starting with `//!` or comment blocks starting with `/*!`)
+  (e.g., comment lines starting with `//!` or comment blocks starting with `/*!`)
 * Avoid defining non-trivial functions in header files
 * Header files should include an 'include guard'
 * Protected and private member variable names are generally prefixed with
@@ -70,7 +72,10 @@
   `std::shared_ptr` when dynamic allocation is required.
 * Portions of Boost which are "header only" may be used. If possible, include
   Boost header files only within .cpp files rather than other header files to
-  avoid unnecessary increases in compilation time.
+  avoid unnecessary increases in compilation time. Boost should not be added
+  to the public interface unless its existence and use is optional. This keeps
+  the number of dependencies low for users of Cantera. In these cases,
+  `CANTERA_API_NO_BOOST` should be used to conditionally remove Boost dependencies.
 * While Cantera does not specifically follow these rules, the following style
   guides are useful references for possible style choices and the rationales behind them.
   * The Google C++ Style Guide: https://google.github.io/styleguide/cppguide.html
@@ -82,7 +87,7 @@
 ## Python
 
 * Style generally follows PEP8 (https://www.python.org/dev/peps/pep-0008/)
-* Code in .py files needs to be written to work with both Python 2
-  and Python 3. Code in Cython files (.pyx or .pxd) should automatically work with both.
-* Code in the Python examples should be written for Python 3. Python 2 versions
-  are automatically generated as part of the build process
+* Code in `.py` and `.pyx` files needs to be written to work with Python 3
+* The minimum Python version that Cantera supports is Python 3.4, so code should only use features added in Python 3.4 or earlier
+* Code in `ctml_writer.py` and `ck2cti.py` needs to be written to work with both Python 2 and Python 3
+* Code in the Python examples should be written for Python 3

INSTALL

@@ -18,5 +18,4 @@ shown by running `scons` with no other arguments.
 Detailed Instructions
 ---------------------
 
-See the file `doc/sphinx/compiling.rst` or the HTML instructions
-available at http://cantera.github.com/docs/sphinx/html/compiling.html.
+See the instructions available at [online](https://cantera.org/install/index.html)

ISSUE_TEMPLATE.md

@@ -1,14 +0,0 @@
-### Cantera version
-
-### Operating System
-
-### Python/MATLAB version
-
-### Expected Behavior
-
-### Actual Behavior
-
-### Steps to reproduce
-1.
-2.
-3.

License.txt

@@ -6,7 +6,7 @@ Copyright (c) 2009 Sandia Corporation. Under the terms of
 Contract AC04-94AL85000 with Sandia Corporation, the U.S. Government
 retains certain rights in this software.
 
-Copyright (c) 2011-2017, Cantera Developers.
+Copyright (c) 2011-2018, Cantera Developers.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

PULL_REQUEST_TEMPLATE.md

@@ -1,6 +0,0 @@
-Fixes # .
-
-Changes proposed in this pull request:
--
--
--

README.rst

@@ -1,19 +1,16 @@
+.. Cantera
 
-*******
-Cantera
-*******
+|cantera|
 
-Version 2.3.0 (stable)
+|doi| |codecov| |travisci| |appveyor| |release|
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.170284.svg
-   :target: https://doi.org/10.5281/zenodo.170284
 
 What is Cantera?
 ================
 
 Cantera is an open-source collection of object-oriented software tools for
-problems involving chemical kinetics, thermodynamics, and transport
-processes. Among other things, it can be used to:
+problems involving chemical kinetics, thermodynamics, and transport processes.
+Among other things, it can be used to:
 
 * Evaluate thermodynamic and transport properties of mixtures
 * Compute chemical equilibrium
@@ -28,73 +25,72 @@ Cantera can be used from Python and Matlab, or in applications written in C++
 and Fortran 90. A number of `examples of Cantera's capabilities
 <https://github.com/Cantera/cantera-jupyter>`_ are available in the form of
 Jupyter notebooks. These examples can be tried interactively, in the cloud by
-using the following Binder link:
+using the following MyBinder link:
 
-.. image:: http://mybinder.org/badge.svg
-    :target: http://mybinder.org:/repo/cantera/cantera-jupyter
+.. image:: https://mybinder.org/badge.svg
+    :target: https://mybinder.org/repo/cantera/cantera-jupyter
 
 Installation
 ============
 
 `Installation instructions for the current release of Cantera
-<http://cantera.github.io/docs/sphinx/html/install.html>`_ are available from
-the main `Cantera documentation site
-<http://cantera.github.io/docs/sphinx/html/index.html>`_. Installers are
-provided for Windows (MSI packages), Mac OS X (through Homebrew), and
-Ubuntu. Anaconda packages containing the Cantera Python module are also
-available for Windows, OS X, and Linux.
+<https://cantera.org/install/index.html>`_ are available from the main `Cantera
+documentation site <https://cantera.org>`_. Installers are provided for Windows
+(MSI packages), macOS (through Homebrew), and Ubuntu. Anaconda packages
+containing the Cantera Python module are also available for Windows, macOS, and
+Linux.
 
 .. image:: https://anaconda.org/cantera/cantera/badges/installer/conda.svg
     :target: https://anaconda.org/Cantera/cantera
 
 For other platforms, or for users wishing to install a development version of
-Cantera, `compilation instructions
-<http://cantera.github.io/docs/sphinx/html/compiling.html>`_ are also available.
+Cantera, `compilation instructions <https://cantera.org/install/index.html>`_
+are also available.
 
 Documentation
 =============
 
-The `documentation <http://cantera.github.io/docs/sphinx/html/index.html>`_
+The `documentation <https://cantera.org/documentation>`_
 offers a number of starting points:
 
 - `Python tutorial
-  <http://cantera.github.io/docs/sphinx/html/cython/tutorial.html>`_
+  <https://cantera.org/tutorials/python-tutorial.html>`_
 - `Application Examples in Python
   <https://github.com/Cantera/cantera-jupyter#cantera-jupyter>`_
 - `A guide to Cantera's input file format
-  <http://cantera.github.io/docs/sphinx/html/cti/index.html>`_
-- `A list of frequently asked questions
-  <http://cantera.github.io/docs/sphinx/html/faq.html>`_
+  <https://cantera.org/tutorials/input-files.html>`_
+- `Information about the Cantera community
+  <https://cantera.org/community.html>`_
 
 `Documentation for the development version of Cantera
-<http://cantera.github.com/dev-docs/sphinx/html/index.html>`_ is also available.
+<https://cantera.org/documentation/dev-docs.html>`_ is also available.
 
 Code of Conduct
 ===============
 
 .. image:: https://img.shields.io/badge/code%20of%20conduct-contributor%20covenant-green.svg?style=flat-square
     :alt: conduct
-    :target: http://contributor-covenant.org/version/1/4/
+    :target: https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
 
 In order to have a more open and welcoming community, Cantera adheres to a
 `code of conduct <CODE_OF_CONDUCT.md>`_ adapted from the `Contributor Covenent
-code of conduct <http://contributor-covenant.org/>`_.
+code of conduct <https://contributor-covenant.org/>`_.
 
 Please adhere to this code of conduct in any interactions you have in the
 Cantera community. It is strictly enforced on all official Cantera
-repositories, websites, users' group, and other resources.
-If you encounter someone violating these terms, please
-`contact the code of conduct team <mailto:conduct@cantera.org>`_
-(`@speth <https://github.com/speth>`_,
-`@bryanwweber <https://github.com/bryanwweber>`_, and
-`@kyleniemeyer <https://github.com/kyleniemeyer>`_)
-and we will address it as soon as possible.
+repositories, websites, users' group, and other resources. If you encounter
+someone violating these terms, please `contact the code of conduct team
+<mailto:conduct@cantera.org>`_ (`@speth <https://github.com/speth>`_,
+`@bryanwweber <https://github.com/bryanwweber>`_, and `@kyleniemeyer
+<https://github.com/kyleniemeyer>`_) and we will address it as soon as
+possible.
 
 Development Site
 ================
 
-The `latest Cantera source code <https://github.com/Cantera/cantera>`_, the
-`issue tracker <https://github.com/Cantera/cantera/issues>`_ for bugs and
+The current development version is 2.5.0a3. The current stable version is
+2.4.0. The `latest Cantera source code <https://github.com/Cantera/cantera>`_,
+the `issue tracker <https://github.com/Cantera/cantera/issues>`_ for bugs and
 enhancement requests, `downloads of Cantera releases and binary installers
 <https://github.com/Cantera/cantera/releases>`_ , and the `Cantera wiki
 <https://github.com/Cantera/cantera/wiki>`_ can all be found on Github.
@@ -102,18 +98,77 @@ enhancement requests, `downloads of Cantera releases and binary installers
 Users' Group
 ============
 
-The `Cantera Users' Group <http://groups.google.com/group/cantera-users>`_ is a
+The `Cantera Users' Group <https://groups.google.com/group/cantera-users>`_ is a
 message board / mailing list for discussions amongst Cantera users.
 
+Cantera Gitter Chat
+===================
+
+.. image:: https://badges.gitter.im/org.png
+   :target: https://gitter.im/Cantera/Lobby
+
+
+The `Cantera Gitter Chat <https://gitter.im/Cantera/Lobby>`_ is a public chat
+client that is linked to users' Github account. The developers do not closely
+monitor the discussion, so *any* discussion at all of Cantera functionality
+such as how to use certain function calls, syntax problems, input files, etc.
+should be directed the User's Group. All conversations in the Gitter room will
+be covered under the Cantera Code of Conduct, so please be nice.
+
+The chat room is a place to strengthen and develop the Cantera community,
+discuss tangentially-related topics such as how to model the underlying physics
+of a problem , share cool applications you’ve developed, etc.
+
+Summary:
+
+“How do I perform this Cantera function call?” --> User's Group
+
+"What do I do with the variables that a Cantera function call returns?” -->
+Chat
+
+
 Continuous Integration Status
 =============================
 
-Travis builds (Linux & OS X):
+==============  ============  ===================
+Platform        Site          Status
+==============  ============  ===================
+Linux & OS X    Travis CI     |travisci|
+Windows x64     Appveyor      |appveyor|
+==============  ============  ===================
 
-.. image:: https://travis-ci.org/Cantera/cantera.svg?branch=master
+
+NumFOCUS
+========
+
+Cantera is a fiscally-sponsored project of `NumFOCUS <https://numfocus.org>`__,
+a non-profit dedicated to supporting the open source scientific computing
+community. Please consider `making a donation
+<https://numfocus.salsalabs.org/donate-to-cantera/index.html>`__ to support the
+development of Cantera through NumFOCUS.
+
+.. image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A
+    :target: https://numfocus.salsalabs.org/donate-to-cantera/index.html
+    :alt: Powered by NumFOCUS
+
+.. |cantera| image:: https://cantera.org/assets/img/cantera-logo.png
+    :target: https://cantera.org
+    :alt: cantera logo
+    :width: 675px
+    :align: middle
+
+.. |travisci| image:: https://travis-ci.org/Cantera/cantera.svg?branch=master
     :target: https://travis-ci.org/Cantera/cantera
 
-Appveyor builds (Windows):
-
-.. image:: https://ci.appveyor.com/api/projects/status/auhd35qn9cdmkpoj?svg=true
+.. |appveyor| image:: https://ci.appveyor.com/api/projects/status/auhd35qn9cdmkpoj?svg=true
     :target: https://ci.appveyor.com/project/Cantera/cantera
+
+.. |doi| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.170284.svg
+   :target: https://doi.org/10.5281/zenodo.1174508
+
+.. |codecov| image:: https://img.shields.io/codecov/c/github/Cantera/cantera/master.svg
+   :target: https://codecov.io/gh/Cantera/cantera?branch=master
+
+.. |release| image:: https://img.shields.io/github/release/cantera/cantera.svg
+   :target: https://github.com/Cantera/cantera/releases
+   :alt: GitHub release

appveyor.yml

@@ -1,20 +1,22 @@
 version: 1.0.{build}
 install:
 - ps: |
-    C:\Python27-x64\python.exe -m pip install --upgrade pip
-    C:\Python27-x64\Scripts\pip.exe install --egg scons
-    C:\Python27-x64\Scripts\pip.exe install numpy
-    C:\Python27-x64\Scripts\pip.exe install cython
-    C:\Python27-x64\Scripts\pip.exe install 3to2
-    C:\Python27-x64\Scripts\pip.exe install pypiwin32
-    C:\Python35-x64\Scripts\pip.exe install numpy
+    C:\Python37-x64\python.exe -m pip install --no-cache-dir --upgrade pip
+    C:\Python37-x64\python.exe -m pip install --upgrade setuptools
+    C:\Python37-x64\python.exe -m pip install --upgrade --no-warn-script-location wheel
+    C:\Python37-x64\Scripts\pip.exe install scons==3.0.1
+    C:\Python37-x64\Scripts\pip.exe install --no-cache-dir --no-warn-script-location numpy
+    C:\Python37-x64\Scripts\pip.exe install --no-warn-script-location cython
+    C:\Python37-x64\Scripts\pip.exe install pypiwin32
+    C:\Python37-x64\Scripts\pip.exe install ruamel.yaml
 
 build_script:
-- cmd: C:\Python27-x64\scons build -j2 boost_inc_dir=C:\Libraries\boost_1_62_0 debug=n VERBOSE=y python3_cmd=C:\Python35-x64\python.exe
+- cmd: C:\Python37-x64\Scripts\scons build -j2 boost_inc_dir=C:\Libraries\boost_1_62_0 debug=n VERBOSE=y python_package=full
+- cmd: C:\Python37-x64\Scripts\scons samples
 
 test_script:
 - ps: |
-    C:\Python27-x64\scons test
+    C:\Python37-x64\Scripts\scons test
     $sconsstatus = $lastexitcode
     $wc = New-Object 'System.Net.WebClient'
     $wc.UploadFile("https://ci.appveyor.com/api/testresults/junit/$($env:APPVEYOR_JOB_ID)", (Resolve-Path .\test\work\gtest-general.xml))

data/inputs/air.inp

@@ -4,6 +4,41 @@ END
 SPECIES
 O       O2     N   NO      NO2     N2O     N2      AR
 END
+THERMO ALL
+   300.000  1000.000  5000.000
+O                 L 1/90O   1   00   00   00G   200.000  3500.000  1000.000    1
+ 2.56942078E+00-8.59741137E-05 4.19484589E-08-1.00177799E-11 1.22833691E-15    2
+ 2.92175791E+04 4.78433864E+00 3.16826710E+00-3.27931884E-03 6.64306396E-06    3
+-6.12806624E-09 2.11265971E-12 2.91222592E+04 2.05193346E+00                   4
+O2                TPIS89O   2   00   00   00G   200.000  3500.000  1000.000    1
+ 3.28253784E+00 1.48308754E-03-7.57966669E-07 2.09470555E-10-2.16717794E-14    2
+-1.08845772E+03 5.45323129E+00 3.78245636E+00-2.99673416E-03 9.84730201E-06    3
+-9.68129509E-09 3.24372837E-12-1.06394356E+03 3.65767573E+00                   4
+N                 L 6/88N   1    0    0    0G   200.000  6000.000  1000.000    1
+ 0.24159429E+01 0.17489065E-03-0.11902369E-06 0.30226245E-10-0.20360982E-14    2
+ 0.56133773E+05 0.46496096E+01 0.25000000E+01 0.00000000E+00 0.00000000E+00    3
+ 0.00000000E+00 0.00000000E+00 0.56104637E+05 0.41939087E+01                   4
+NO                RUS 78N   1O   1    0    0G   200.000  6000.000  1000.000    1
+ 0.32606056E+01 0.11911043E-02-0.42917048E-06 0.69457669E-10-0.40336099E-14    2
+ 0.99209746E+04 0.63693027E+01 0.42184763E+01-0.46389760E-02 0.11041022E-04    3
+-0.93361354E-08 0.28035770E-11 0.98446230E+04 0.22808464E+01                   4
+NO2               L 7/88N   1O   2    0    0G   200.000  6000.000  1000.000    1
+ 0.48847542E+01 0.21723956E-02-0.82806906E-06 0.15747510E-09-0.10510895E-13    2
+ 0.23164983E+04-0.11741695E+00 0.39440312E+01-0.15854290E-02 0.16657812E-04    3
+-0.20475426E-07 0.78350564E-11 0.28966179E+04 0.63119917E+01                   4
+N2O               L 7/88N   2O   1    0    0G   200.000  6000.000  1000.000    1
+ 0.48230729E+01 0.26270251E-02-0.95850874E-06 0.16000712E-09-0.97752303E-14    2
+ 0.80734048E+04-0.22017207E+01 0.22571502E+01 0.11304728E-01-0.13671319E-04    3
+ 0.96819806E-08-0.29307182E-11 0.87417744E+04 0.10757992E+02                   4
+N2                121286N   2               G   300.000  5000.000  1000.000    1
+ 0.02926640E+02 0.14879768E-02-0.05684760E-05 0.10097038E-09-0.06753351E-13    2
+-0.09227977E+04 0.05980528E+02 0.03298677E+02 0.14082404E-02-0.03963222E-04    3
+ 0.05641515E-07-0.02444854E-10-0.10208999E+04 0.03950372E+02                   4
+AR                120186AR  1               G   300.000  5000.000  1000.000    1
+ 0.02500000E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00    2
+-0.07453750E+04 0.04366000E+02 0.02500000E+02 0.00000000E+00 0.00000000E+00    3
+ 0.00000000E+00 0.00000000E+00-0.07453750E+04 0.04366000E+02                   4
+END
 REACTIONS
 2O+M<=>O2+M                              1.200E+17   -1.000        .00
  AR/.83/ 

data/inputs/airNASA9.xml

@@ -1,317 +0,0 @@
-<?xml version="1.0"?>
-<ctml>
-  <validate reactions="yes" species="yes"/>
-
-  <!-- phase airNASA9     -->
-  <phase dim="3" id="airNASA9">
-    <elementArray datasrc="elements.xml">O  N  E </elementArray>
-    <speciesArray datasrc="#species_data">
-      N2  O2  NO  N  O  N2+  O2+  NO+  N+  O+ 
-      e- </speciesArray>
-    <reactionArray datasrc="#reaction_data"/>
-    <state>
-      <temperature units="K">300.0</temperature>
-      <pressure units="Pa">101325.0</pressure>
-    </state>
-    <thermo model="IdealGas"/>
-    <kinetics model="GasKinetics"/>
-    <transport model="None"/>
-  </phase>
-
-  <!-- species definitions     -->
-  <speciesData id="species_data">
-
-    <!-- species N2    -->
-    <species name="N2">
-      <atomArray>N:2 </atomArray>
-      <note>Ref-Elm. Gurvich,1978 pt1 p280 pt2 p207.                      </note>
-      <thermo>
-        <NASA9 Tmax="1000.0" Tmin="200.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             2.210371497E+04,  -3.818461820E+02,   6.082738360E+00,  -8.530914410E-03, 
-             1.384646189E-05,  -9.625793620E-09,   2.519705809E-12,   7.108460860E+02,
-             -1.076003744E+01</floatArray>
-        </NASA9>
-        <NASA9 Tmax="6000.0" Tmin="1000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             5.877124060E+05,  -2.239249073E+03,   6.066949220E+00,  -6.139685500E-04, 
-             1.491806679E-07,  -1.923105485E-11,   1.061954386E-15,   1.283210415E+04,
-             -1.586640027E+01</floatArray>
-        </NASA9>
-        <NASA9 Tmax="20000.0" Tmin="6000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             8.310139160E+08,  -6.420733540E+05,   2.020264635E+02,  -3.065092046E-02, 
-             2.486903333E-06,  -9.705954110E-11,   1.437538881E-15,   4.938707040E+06,
-             -1.672099740E+03</floatArray>
-        </NASA9>
-      </thermo>
-    </species>
-
-    <!-- species O2    -->
-    <species name="O2">
-      <atomArray>O:2 </atomArray>
-      <note>Ref-Elm. Gurvich,1989 pt1 p94 pt2 p9.                         </note>
-      <thermo>
-        <NASA9 Tmax="1000.0" Tmin="200.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -3.425563420E+04,   4.847000970E+02,   1.119010961E+00,   4.293889240E-03, 
-             -6.836300520E-07,  -2.023372700E-09,   1.039040018E-12,  -3.391454870E+03,
-             1.849699470E+01</floatArray>
-        </NASA9>
-        <NASA9 Tmax="6000.0" Tmin="1000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -1.037939022E+06,   2.344830282E+03,   1.819732036E+00,   1.267847582E-03, 
-             -2.188067988E-07,   2.053719572E-11,  -8.193467050E-16,  -1.689010929E+04,
-             1.738716506E+01</floatArray>
-        </NASA9>
-        <NASA9 Tmax="20000.0" Tmin="6000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             4.975294300E+08,  -2.866106874E+05,   6.690352250E+01,  -6.169959020E-03, 
-             3.016396027E-07,  -7.421416600E-12,   7.278175770E-17,   2.293554027E+06,
-             -5.530621610E+02</floatArray>
-        </NASA9>
-      </thermo>
-    </species>
-
-    <!-- species NO    -->
-    <species name="NO">
-      <atomArray>O:1 N:1 </atomArray>
-      <note>Gurvich,1978,1989 pt1 p326 pt2 p203.                          </note>
-      <thermo>
-        <NASA9 Tmax="1000.0" Tmin="200.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -1.143916503E+04,   1.536467592E+02,   3.431468730E+00,  -2.668592368E-03, 
-             8.481399120E-06,  -7.685111050E-09,   2.386797655E-12,   9.098214410E+03,
-             6.728725490E+00</floatArray>
-        </NASA9>
-        <NASA9 Tmax="6000.0" Tmin="1000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             2.239018716E+05,  -1.289651623E+03,   5.433936030E+00,  -3.656034900E-04, 
-             9.880966450E-08,  -1.416076856E-11,   9.380184620E-16,   1.750317656E+04,
-             -8.501669090E+00</floatArray>
-        </NASA9>
-        <NASA9 Tmax="20000.0" Tmin="6000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -9.575303540E+08,   5.912434480E+05,  -1.384566826E+02,   1.694339403E-02, 
-             -1.007351096E-06,   2.912584076E-11,  -3.295109350E-16,  -4.677501240E+06,
-             1.242081216E+03</floatArray>
-        </NASA9>
-      </thermo>
-    </species>
-
-    <!-- species N    -->
-    <species name="N">
-      <atomArray>N:1 </atomArray>
-      <note>Hf:Cox,1989. Moore,1975. Gordon,1999.                         </note>
-      <thermo>
-        <NASA9 Tmax="1000.0" Tmin="200.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             0.000000000E+00,   0.000000000E+00,   2.500000000E+00,   0.000000000E+00, 
-             0.000000000E+00,   0.000000000E+00,   0.000000000E+00,   5.610463780E+04,
-             4.193905036E+00</floatArray>
-        </NASA9>
-        <NASA9 Tmax="6000.0" Tmin="1000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             8.876501380E+04,  -1.071231500E+02,   2.362188287E+00,   2.916720081E-04, 
-             -1.729515100E-07,   4.012657880E-11,  -2.677227571E-15,   5.697351330E+04,
-             4.865231506E+00</floatArray>
-        </NASA9>
-        <NASA9 Tmax="20000.0" Tmin="6000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             5.475181050E+08,  -3.107574980E+05,   6.916782740E+01,  -6.847988130E-03, 
-             3.827572400E-07,  -1.098367709E-11,   1.277986024E-16,   2.550585618E+06,
-             -5.848769753E+02</floatArray>
-        </NASA9>
-      </thermo>
-    </species>
-
-    <!-- species O    -->
-    <species name="O">
-      <atomArray>O:1 </atomArray>
-      <note>D0(O2):Brix,1954. Moore,1976. Gordon,1999.                    </note>
-      <thermo>
-        <NASA9 Tmax="1000.0" Tmin="200.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -7.953611300E+03,   1.607177787E+02,   1.966226438E+00,   1.013670310E-03, 
-             -1.110415423E-06,   6.517507500E-10,  -1.584779251E-13,   2.840362437E+04,
-             8.404241820E+00</floatArray>
-        </NASA9>
-        <NASA9 Tmax="6000.0" Tmin="1000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             2.619020262E+05,  -7.298722030E+02,   3.317177270E+00,  -4.281334360E-04, 
-             1.036104594E-07,  -9.438304330E-12,   2.725038297E-16,   3.392428060E+04,
-             -6.679585350E-01</floatArray>
-        </NASA9>
-        <NASA9 Tmax="20000.0" Tmin="6000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             1.779004264E+08,  -1.082328257E+05,   2.810778365E+01,  -2.975232262E-03, 
-             1.854997534E-07,  -5.796231540E-12,   7.191720164E-17,   8.890942630E+05,
-             -2.181728151E+02</floatArray>
-        </NASA9>
-      </thermo>
-    </species>
-
-    <!-- species N2+    -->
-    <species name="N2+">
-      <atomArray>E:-1 N:2 </atomArray>
-      <note>Gurvich,1989 pt1 p323 pt2 p200.                               </note>
-      <charge>1</charge>
-      <thermo>
-        <NASA9 Tmax="1000.0" Tmin="298.14999999999998" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -3.474047470E+04,   2.696222703E+02,   3.164916370E+00,  -2.132239781E-03, 
-             6.730476400E-06,  -5.637304970E-09,   1.621756000E-12,   1.790004424E+05,
-             6.832974166E+00</floatArray>
-        </NASA9>
-        <NASA9 Tmax="6000.0" Tmin="1000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -2.845599002E+06,   7.058893030E+03,  -2.884886385E+00,   3.068677059E-03, 
-             -4.361652310E-07,   2.102514545E-11,   5.411996470E-16,   1.340388483E+05,
-             5.090897022E+01</floatArray>
-        </NASA9>
-        <NASA9 Tmax="20000.0" Tmin="6000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -3.712829770E+08,   3.139287234E+05,  -9.603518050E+01,   1.571193286E-02, 
-             -1.175065525E-06,   4.144441230E-11,  -5.621893090E-16,  -2.217361867E+06,
-             8.436270947E+02</floatArray>
-        </NASA9>
-      </thermo>
-    </species>
-
-    <!-- species O2+    -->
-    <species name="O2+">
-      <atomArray>E:-1 O:2 </atomArray>
-      <note>Gurvich,1989 pt1 p98 pt2 p11.                                 </note>
-      <charge>1</charge>
-      <thermo>
-        <NASA9 Tmax="1000.0" Tmin="298.14999999999998" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -8.607205450E+04,   1.051875934E+03,  -5.432380470E-01,   6.571166540E-03, 
-             -3.274263750E-06,   5.940645340E-11,   3.238784790E-13,   1.345544668E+05,
-             2.902709750E+01</floatArray>
-        </NASA9>
-        <NASA9 Tmax="6000.0" Tmin="1000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             7.384654880E+04,  -8.459559540E+02,   4.985164160E+00,  -1.611010890E-04, 
-             6.427083990E-08,  -1.504939874E-11,   1.578465409E-15,   1.446321044E+05,
-             -5.811230650E+00</floatArray>
-        </NASA9>
-        <NASA9 Tmax="20000.0" Tmin="6000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -1.562125524E+09,   1.161406778E+06,  -3.302504720E+02,   4.710937520E-02, 
-             -3.354461380E-06,   1.167968599E-10,  -1.589754791E-15,  -8.857866270E+06,
-             2.852035602E+03</floatArray>
-        </NASA9>
-      </thermo>
-    </species>
-
-    <!-- species NO+    -->
-    <species name="NO+">
-      <atomArray>E:-1 O:1 N:1 </atomArray>
-      <note>Cp,S,IP(NO): Gurvich,1989 pt1 p330 pt2 p205.                  </note>
-      <charge>1</charge>
-      <thermo>
-        <NASA9 Tmax="1000.0" Tmin="298.14999999999998" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             1.398106635E+03,  -1.590446941E+02,   5.122895400E+00,  -6.394388620E-03, 
-             1.123918342E-05,  -7.988581260E-09,   2.107383677E-12,   1.187495132E+05,
-             -4.398433810E+00</floatArray>
-        </NASA9>
-        <NASA9 Tmax="6000.0" Tmin="1000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             6.069876900E+05,  -2.278395427E+03,   6.080324670E+00,  -6.066847580E-04, 
-             1.432002611E-07,  -1.747990522E-11,   8.935014060E-16,   1.322709615E+05,
-             -1.519880037E+01</floatArray>
-        </NASA9>
-        <NASA9 Tmax="20000.0" Tmin="6000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             2.676400347E+09,  -1.832948690E+06,   5.099249390E+02,  -7.113819280E-02, 
-             5.317659880E-06,  -1.963208212E-10,   2.805268230E-15,   1.443308939E+07,
-             -4.324044462E+03</floatArray>
-        </NASA9>
-      </thermo>
-    </species>
-
-    <!-- species N+    -->
-    <species name="N+">
-      <atomArray>E:-1 N:1 </atomArray>
-      <note>Moore,1975. Gordon,1999.                                      </note>
-      <charge>1</charge>
-      <thermo>
-        <NASA9 Tmax="1000.0" Tmin="298.14999999999998" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             5.237079210E+03,   2.299958315E+00,   2.487488821E+00,   2.737490756E-05, 
-             -3.134447576E-08,   1.850111332E-11,  -4.447350984E-15,   2.256284738E+05,
-             5.076830786E+00</floatArray>
-        </NASA9>
-        <NASA9 Tmax="6000.0" Tmin="1000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             2.904970374E+05,  -8.557908610E+02,   3.477389290E+00,  -5.288267190E-04, 
-             1.352350307E-07,  -1.389834122E-11,   5.046166279E-16,   2.310809984E+05,
-             -1.994146545E+00</floatArray>
-        </NASA9>
-        <NASA9 Tmax="20000.0" Tmin="6000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             1.646092148E+07,  -1.113165218E+04,   4.976986640E+00,  -2.005393583E-04, 
-             1.022481356E-08,  -2.691430863E-13,   3.539931593E-18,   3.136284696E+05,
-             -1.706646380E+01</floatArray>
-        </NASA9>
-      </thermo>
-    </species>
-
-    <!-- species O+    -->
-    <species name="O+">
-      <atomArray>E:-1 O:1 </atomArray>
-      <note>Martin,W.C.,1993. Gordon,1999.                                </note>
-      <charge>1</charge>
-      <thermo>
-        <NASA9 Tmax="1000.0" Tmin="298.14999999999998" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             0.000000000E+00,   0.000000000E+00,   2.500000000E+00,   0.000000000E+00, 
-             0.000000000E+00,   0.000000000E+00,   0.000000000E+00,   1.879352842E+05,
-             4.393376760E+00</floatArray>
-        </NASA9>
-        <NASA9 Tmax="6000.0" Tmin="1000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -2.166513208E+05,   6.665456150E+02,   1.702064364E+00,   4.714992810E-04, 
-             -1.427131823E-07,   2.016595903E-11,  -9.107157762E-16,   1.837191966E+05,
-             1.005690382E+01</floatArray>
-        </NASA9>
-        <NASA9 Tmax="20000.0" Tmin="6000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             -2.143835383E+08,   1.469518523E+05,  -3.680864540E+01,   5.036164540E-03, 
-             -3.087873854E-07,   9.186834870E-12,  -1.074163268E-16,  -9.614208960E+05,
-             3.426193080E+02</floatArray>
-        </NASA9>
-      </thermo>
-    </species>
-
-    <!-- species e-    -->
-    <species name="e-">
-      <atomArray>E:1 </atomArray>
-      <note>Ref-Species. Chase,1998 3/82.                                 </note>
-      <charge>-1</charge>
-      <thermo>
-        <NASA9 Tmax="1000.0" Tmin="298.14999999999998" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             0.000000000E+00,   0.000000000E+00,   2.500000000E+00,   0.000000000E+00, 
-             0.000000000E+00,   0.000000000E+00,   0.000000000E+00,  -7.453750000E+02,
-             -1.172081224E+01</floatArray>
-        </NASA9>
-        <NASA9 Tmax="6000.0" Tmin="1000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             0.000000000E+00,   0.000000000E+00,   2.500000000E+00,   0.000000000E+00, 
-             0.000000000E+00,   0.000000000E+00,   0.000000000E+00,  -7.453750000E+02,
-             -1.172081224E+01</floatArray>
-        </NASA9>
-        <NASA9 Tmax="20000.0" Tmin="6000.0" P0="100000.0">
-           <floatArray name="coeffs" size="9">
-             0.000000000E+00,   0.000000000E+00,   2.500000000E+00,   0.000000000E+00, 
-             0.000000000E+00,   0.000000000E+00,   0.000000000E+00,  -7.453750000E+02,
-             -1.172081224E+01</floatArray>
-        </NASA9>
-      </thermo>
-    </species>
-  </speciesData>
-  <reactionData id="reaction_data"/>
-</ctml>

data/inputs/diamond.cti

@@ -1,96 +1,107 @@
-# simplified version of Harris and Goodwin diamond (100) growth
-# mechanism, J. Phys. Chem., 1993.
+
+# Trough mechanism from 'S. J. Harris and D. G. Goodwin, 'Growth on
+# the reconstructed diamond (100) surface, 'J. Phys. Chem. vol. 97,
+# 23-28 (1993). reactions a - t are taken directly from Table II,
+# with thermochemistry from Table IV. Reaction u is added here.
 
 
 units(length = 'cm', quantity = 'mol', act_energy = 'kcal/mol')
 
+#------------- the gas -------------------------------------
+
 ideal_gas(name = 'gas',
           elements = 'H C',
           species = 'gri30: H H2 CH3 CH4',
-          initial_state = state(temperature = 1200.0,
-                                pressure = 1.0e3,
-                                mole_fractions = 'H:0.002, H2:1, CH4:0.01, CH3:0.0002'))
+          initial_state = state(
+              temperature = 1200.0,
+              pressure = 20.0 * OneAtm / 760.0,
+              mole_fractions = 'H:0.002, H2:0.988, CH3:0.0002, CH4:0.01',
+          )
+)
+
+#------------- bulk diamond -------------------------------------
 
 stoichiometric_solid(name = 'diamond',
-           elements = 'C',
-           density = (3.52, 'g/cm3'),
-           species = 'C(d)')
+                     elements = 'C',
+                     density = (3.52, 'g/cm3'),
+                     species = 'C(d)')
+
+species(name = 'C(d)',
+        atoms = 'C:1')  # no thermo needed (reaction is irreversible)
+
+#------------- the diamond surface -------------------------------------
 
 ideal_interface(name = 'diamond_100',
                 elements = 'H C',
                 species = 'c6HH c6H* c6*H c6** c6HM c6HM* c6*M c6B ',
                 reactions = 'all',
                 phases = 'gas diamond',
-                site_density = (3.0e-9, 'mol/cm2'),
+                site_density = (3.0E-9, 'mol/cm2'),
                 initial_state = state(temperature = 1200.0,
                                       coverages = 'c6H*:0.1, c6HH:0.9'))
 
-species(name = 'C(d)',
-        atoms = 'C:1',
-        thermo = const_cp() )
-
 # an empty surface site
 species(name = 'c6H*',
         atoms = 'H:1',
-        thermo = const_cp(h0 = (51.7, 'kcal/mol'), s0 = (19.5, 'cal/mol/K') ) )
+        thermo = const_cp(h0 = (51.7, 'kcal/mol'),
+                          s0 = (19.5, 'cal/mol/K')))
 
 species(name = 'c6*H',
         atoms = 'H:1',
-        thermo = const_cp(h0 = (46.1, 'kcal/mol'), s0 = (19.9, 'cal/mol/K') ) )
+        thermo = const_cp(h0 = (46.1, 'kcal/mol'),
+                          s0 = (19.9, 'cal/mol/K')))
 
 # a hydrogen-terminated site
 species(name = 'c6HH',
         atoms = 'H:2',
-        thermo = const_cp(t0 = 1200.0, h0 = (11.4, 'kcal/mol'),
-                          s0 = (21.0, 'cal/mol/K'))
-       )
+        thermo = const_cp(h0 = (11.4, 'kcal/mol'),
+                          s0 = (21.0, 'cal/mol/K')))
 
 species(name = 'c6HM',
         atoms = 'C:1 H:4',
         thermo = const_cp(h0 = (26.9, 'kcal/mol'),
-                          s0 = (40.3, 'cal/mol/K') )
-       )
+                          s0 = (40.3, 'cal/mol/K')))
 
 species(name = 'c6HM*',
         atoms = 'C:1 H:3',
         thermo = const_cp(h0 = (65.8, 'kcal/mol'),
-                          s0 = (40.1, 'cal/mol/K') )
-       )
+                          s0 = (40.1, 'cal/mol/K')))
 
 species(name = 'c6*M',
         atoms = 'C:1 H:3',
         thermo = const_cp(h0 = (53.3, 'kcal/mol'),
-                          s0 = (38.9, 'cal/mol/K') )
-       )
+                          s0 = (38.9, 'cal/mol/K')))
 
 species(name = 'c6**',
         atoms = 'C:0',
         thermo = const_cp(h0 = (90.0, 'kcal/mol'),
-                          s0 = (18.4, 'cal/mol/K') )
-       )
+                          s0 = (18.4, 'cal/mol/K')))
 
 species(name = 'c6B',
         atoms = 'H:2 C:1',
         thermo = const_cp(h0 = (40.9, 'kcal/mol'),
-                          s0 = (26.9, 'cal/mol/K') ) )
+                          s0 = (26.9, 'cal/mol/K')))
 
-surface_reaction('c6HH + H <=> c6H* + H2',        [1.3e14,   0.0,  7.3]) # a
-surface_reaction('c6H* + H <=> c6HH',             [1.0e13,   0.0,  0.0]) # b
-surface_reaction('c6H* + CH3 <=> c6HM',           [5.0e12,   0.0,  0.0]) # c
-surface_reaction('c6HM + H <=> c6*M + H2',        [1.3e14,   0.0,  7.3]) # d
-surface_reaction('c6*M + H <=> c6HM',             [1.0e13,   0.0,  0.0]) # e
-surface_reaction('c6HM + H <=> c6HM* + H2',       [2.8e7,    2.0,  7.7]) # f
-surface_reaction('c6HM* + H <=> c6HM',            [1.0e13,   0.0,  0.0]) # g
-surface_reaction('c6HM* <=> c6*M',               [1.0e8,    0.0,  0.0]) # h
-surface_reaction('c6HM* + H <=> c6H* + CH3',      [3.0e13,   0.0,  0.0]) # i
-surface_reaction('c6HM* + H <=> c6B + H2',        [1.3e14,   0.0,  7.3]) # k
-surface_reaction('c6*M + H <=> c6B + H2',         [2.8e7,    2.0,  7.7]) # l
-surface_reaction('c6HH + H <=> c6*H + H2',        [1.3e14,   0.0,  7.3]) # m
-surface_reaction('c6*H + H <=> c6HH',             [1.0e13,   0.0,  0.0]) # n
-surface_reaction('c6H* + H <=> c6** + H2',        [1.3e14,   0.0,  7.3]) # o
-surface_reaction('c6** + H <=> c6H*',              [1.0e13,   0.0,  0.0]) # p
-surface_reaction('c6*H + H <=> c6** + H2',        [4.5e6,    2.0,  5.0]) # q
-surface_reaction('c6** + H <=> c6*H',             [1.0e13,   0.0,  0.0]) # r
-surface_reaction('c6** + CH3 <=> c6*M',           [5.0e12,   0.0,  0.0]) # s
-surface_reaction('c6H* <=> c6*H',                 [1.0e8,    0.0,  0.0]) # t
-surface_reaction('c6B  => c6HH + C(d)',           [1.0e9,    0.0,  0.0])
+surface_reaction('c6HH + H   <=> c6H* + H2',   [1.3E14, 0.0, 7.3])  # a
+surface_reaction('c6H* + H   <=> c6HH',        [1.0E13, 0.0, 0.0])  # b
+surface_reaction('c6H* + CH3 <=> c6HM',        [5.0E12, 0.0, 0.0])  # c
+surface_reaction('c6HM + H   <=> c6*M + H2',   [1.3E14, 0.0, 7.3])  # d
+surface_reaction('c6*M + H   <=> c6HM',        [1.0E13, 0.0, 0.0])  # e
+surface_reaction('c6HM + H   <=> c6HM* + H2',  [2.8E7,  2.0, 7.7])  # f
+surface_reaction('c6HM* + H  <=> c6HM',        [1.0E13, 0.0, 0.0])  # g
+surface_reaction('c6HM*      <=> c6*M',        [1.0E8,  0.0, 0.0])  # h
+surface_reaction('c6HM* + H  <=> c6H* + CH3',  [3.0E13, 0.0, 0.0])  # i
+surface_reaction('c6HM* + H  <=> c6B + H2',    [1.3E14, 0.0, 7.3])  # k
+surface_reaction('c6*M + H   <=> c6B + H2',    [2.8E7,  2.0, 7.7])  # l
+surface_reaction('c6HH + H   <=> c6*H + H2',   [1.3E14, 0.0, 7.3])  # m
+surface_reaction('c6*H + H   <=> c6HH',        [1.0E13, 0.0, 0.0])  # m
+surface_reaction('c6H* + H   <=> c6** + H2',   [1.3E14, 0.0, 7.3])  # o
+surface_reaction('c6** + H   <=> c6H*',        [1.0E13, 0.0, 0.0])  # p
+surface_reaction('c6*H + H   <=> c6** + H2',   [4.5E6,  2.0, 5.0])  # q
+surface_reaction('c6** + H   <=> c6*H',        [1.0E13, 0.0, 0.0])  # r
+surface_reaction('c6** + CH3 <=> c6*M',        [5.0E12, 0.0, 0.0])  # s
+surface_reaction('c6H*       <=> c6*H',        [1.0E8,  0.0, 0.0])  # t
+
+# reaction to add new carbon atom to bulk and regenerate a new site
+#
+surface_reaction('c6B         => c6HH + C(d)', [1.0E9,  0.0, 0.0])  # u

data/inputs/gri30.cti

@@ -117,7 +117,7 @@ species(name = "O2",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.46,
+                     diam =     3.458,
                      well_depth =   107.40,
                      polar =     1.60,
                      rot_relax =     3.80),
@@ -153,9 +153,9 @@ species(name = "H2O",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     2.60,
+                     diam =     2.605,
                      well_depth =   572.40,
-                     dipole =     1.84,
+                     dipole =     1.844,
                      rot_relax =     4.00),
     note = "L 8/89"
        )
@@ -172,7 +172,7 @@ species(name = "HO2",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.46,
+                     diam =     3.458,
                      well_depth =   107.40,
                      rot_relax =     1.00),
     note = "L 5/89"
@@ -190,7 +190,7 @@ species(name = "H2O2",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.46,
+                     diam =     3.458,
                      well_depth =   107.40,
                      rot_relax =     3.80),
     note = "L 7/88"
@@ -208,7 +208,7 @@ species(name = "C",
              ),
     transport = gas_transport(
                      geom = "atom",
-                     diam =     3.30,
+                     diam =     3.298,
                      well_depth =    71.40),
     note = "L11/88"
        )
@@ -293,7 +293,7 @@ species(name = "CH4",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.75,
+                     diam =     3.746,
                      well_depth =   141.40,
                      polar =     2.60,
                      rot_relax =    13.00),
@@ -331,7 +331,7 @@ species(name = "CO2",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.76,
+                     diam =     3.763,
                      well_depth =   244.00,
                      polar =     2.65,
                      rot_relax =     2.10),
@@ -423,7 +423,7 @@ species(name = "CH3OH",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.63,
+                     diam =     3.626,
                      well_depth =   481.80,
                      rot_relax =     1.00),
     note = "L 8/88"
@@ -495,7 +495,7 @@ species(name = "C2H4",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.97,
+                     diam =     3.971,
                      well_depth =   280.80,
                      rot_relax =     1.50),
     note = "L 1/91"
@@ -513,7 +513,7 @@ species(name = "C2H5",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     4.30,
+                     diam =     4.302,
                      well_depth =   252.30,
                      rot_relax =     1.50),
     note = "L12/92"
@@ -531,7 +531,7 @@ species(name = "C2H6",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     4.30,
+                     diam =     4.302,
                      well_depth =   252.30,
                      rot_relax =     1.50),
     note = "L 8/88"
@@ -603,7 +603,7 @@ species(name = "N",
              ),
     transport = gas_transport(
                      geom = "atom",
-                     diam =     3.30,
+                     diam =     3.298,
                      well_depth =    71.40),
     note = "L 6/88"
        )
@@ -676,7 +676,7 @@ species(name = "NNH",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.80,
+                     diam =     3.798,
                      well_depth =    71.40,
                      rot_relax =     1.00),
     note = "T07/93"
@@ -694,7 +694,7 @@ species(name = "NO",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.62,
+                     diam =     3.621,
                      well_depth =    97.53,
                      polar =     1.76,
                      rot_relax =     4.00),
@@ -731,7 +731,7 @@ species(name = "N2O",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.83,
+                     diam =     3.828,
                      well_depth =   232.40,
                      rot_relax =     1.00),
     note = "L 7/88"
@@ -749,7 +749,7 @@ species(name = "HNO",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.49,
+                     diam =     3.492,
                      well_depth =   116.70,
                      rot_relax =     1.00),
     note = "And93"
@@ -767,7 +767,7 @@ species(name = "CN",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.86,
+                     diam =     3.856,
                      well_depth =    75.00,
                      rot_relax =     1.00),
     note = "HBH92"
@@ -839,7 +839,7 @@ species(name = "HCNO",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.83,
+                     diam =     3.828,
                      well_depth =   232.40,
                      rot_relax =     1.00),
     note = "BDEA94"
@@ -857,7 +857,7 @@ species(name = "HOCN",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.83,
+                     diam =     3.828,
                      well_depth =   232.40,
                      rot_relax =     1.00),
     note = "BDEA94"
@@ -875,7 +875,7 @@ species(name = "HNCO",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.83,
+                     diam =     3.828,
                      well_depth =   232.40,
                      rot_relax =     1.00),
     note = "BDEA94"
@@ -893,7 +893,7 @@ species(name = "NCO",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.83,
+                     diam =     3.828,
                      well_depth =   232.40,
                      rot_relax =     1.00),
     note = "EA 93"
@@ -911,7 +911,7 @@ species(name = "N2",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.62,
+                     diam =     3.621,
                      well_depth =    97.53,
                      polar =     1.76,
                      rot_relax =     4.00),
@@ -947,7 +947,7 @@ species(name = "C3H7",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     4.98,
+                     diam =     4.982,
                      well_depth =   266.80,
                      rot_relax =     1.00),
     note = "L 9/84"
@@ -965,7 +965,7 @@ species(name = "C3H8",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     4.98,
+                     diam =     4.982,
                      well_depth =   266.80,
                      rot_relax =     1.00),
     note = "L 4/85"
@@ -2014,10 +2014,10 @@ reaction( "C2H3 + O2 <=> O + CH2CHO",   [3.03000E+11, 0.29, 11])
 reaction( "C2H3 + O2 <=> HO2 + C2H2",   [1.33700E+06, 1.61, -384])
 
 #  Reaction 296
-reaction( "O + CH3CHO <=> OH + CH2CHO",   [5.84000E+12, 0, 1808])
+reaction( "O + CH3CHO <=> OH + CH2CHO",   [2.920000E+12, 0, 1808])
 
 #  Reaction 297
-reaction( "O + CH3CHO => OH + CH3 + CO",   [5.84000E+12, 0, 1808])
+reaction( "O + CH3CHO => OH + CH3 + CO",   [2.920000E+12, 0, 1808])
 
 #  Reaction 298
 reaction( "O2 + CH3CHO => HO2 + CH3 + CO",   [3.01000E+13, 0, 39150])

data/inputs/gri30.inp

@@ -1,4 +1,4 @@
-! GRI-Mech Version 3.0 3/12/99  CHEMKIN-II format
+! GRI-Mech Version 3.0 7/30/99  CHEMKIN-II format
 ! See README30 file at anonymous FTP site unix.sri.com, directory gri;
 ! WorldWideWeb home page http://www.me.berkeley.edu/gri_mech/ or
 ! through http://www.gri.org , under 'Basic  Research', 
@@ -15,221 +15,9 @@ NH2     NH3     NNH     NO      NO2     N2O     HNO     CN
 HCN     H2CN    HCNN    HCNO    HOCN    HNCO    NCO     N2      
 AR      C3H7    C3H8    CH2CHO  CH3CHO
 END
-THERMO ALL
-   300.000  1000.000  5000.000
-O                 L 1/90O   1   00   00   00G   200.000  3500.000  1000.000    1
- 2.56942078E+00-8.59741137E-05 4.19484589E-08-1.00177799E-11 1.22833691E-15    2
- 2.92175791E+04 4.78433864E+00 3.16826710E+00-3.27931884E-03 6.64306396E-06    3
--6.12806624E-09 2.11265971E-12 2.91222592E+04 2.05193346E+00                   4
-O2                TPIS89O   2   00   00   00G   200.000  3500.000  1000.000    1
- 3.28253784E+00 1.48308754E-03-7.57966669E-07 2.09470555E-10-2.16717794E-14    2
--1.08845772E+03 5.45323129E+00 3.78245636E+00-2.99673416E-03 9.84730201E-06    3
--9.68129509E-09 3.24372837E-12-1.06394356E+03 3.65767573E+00                   4
-H                 L 7/88H   1   00   00   00G   200.000  3500.000  1000.000    1
- 2.50000001E+00-2.30842973E-11 1.61561948E-14-4.73515235E-18 4.98197357E-22    2
- 2.54736599E+04-4.46682914E-01 2.50000000E+00 7.05332819E-13-1.99591964E-15    3
- 2.30081632E-18-9.27732332E-22 2.54736599E+04-4.46682853E-01                   4
-H2                TPIS78H   2   00   00   00G   200.000  3500.000  1000.000    1
- 3.33727920E+00-4.94024731E-05 4.99456778E-07-1.79566394E-10 2.00255376E-14    2
--9.50158922E+02-3.20502331E+00 2.34433112E+00 7.98052075E-03-1.94781510E-05    3
- 2.01572094E-08-7.37611761E-12-9.17935173E+02 6.83010238E-01                   4
-OH                RUS 78O   1H   1   00   00G   200.000  3500.000  1000.000    1
- 3.09288767E+00 5.48429716E-04 1.26505228E-07-8.79461556E-11 1.17412376E-14    2
- 3.85865700E+03 4.47669610E+00 3.99201543E+00-2.40131752E-03 4.61793841E-06    3
--3.88113333E-09 1.36411470E-12 3.61508056E+03-1.03925458E-01                   4
-H2O               L 8/89H   2O   1   00   00G   200.000  3500.000  1000.000    1
- 3.03399249E+00 2.17691804E-03-1.64072518E-07-9.70419870E-11 1.68200992E-14    2
--3.00042971E+04 4.96677010E+00 4.19864056E+00-2.03643410E-03 6.52040211E-06    3
--5.48797062E-09 1.77197817E-12-3.02937267E+04-8.49032208E-01                   4
-HO2               L 5/89H   1O   2   00   00G   200.000  3500.000  1000.000    1
- 4.01721090E+00 2.23982013E-03-6.33658150E-07 1.14246370E-10-1.07908535E-14    2
- 1.11856713E+02 3.78510215E+00 4.30179801E+00-4.74912051E-03 2.11582891E-05    3
--2.42763894E-08 9.29225124E-12 2.94808040E+02 3.71666245E+00                   4
-H2O2              L 7/88H   2O   2   00   00G   200.000  3500.000  1000.000    1
- 4.16500285E+00 4.90831694E-03-1.90139225E-06 3.71185986E-10-2.87908305E-14    2
--1.78617877E+04 2.91615662E+00 4.27611269E+00-5.42822417E-04 1.67335701E-05    3
--2.15770813E-08 8.62454363E-12-1.77025821E+04 3.43505074E+00                   4
-C                 L11/88C   1   00   00   00G   200.000  3500.000  1000.000    1
- 2.49266888E+00 4.79889284E-05-7.24335020E-08 3.74291029E-11-4.87277893E-15    2
- 8.54512953E+04 4.80150373E+00 2.55423955E+00-3.21537724E-04 7.33792245E-07    3
--7.32234889E-10 2.66521446E-13 8.54438832E+04 4.53130848E+00                   4
-CH                TPIS79C   1H   1   00   00G   200.000  3500.000  1000.000    1
- 2.87846473E+00 9.70913681E-04 1.44445655E-07-1.30687849E-10 1.76079383E-14    2
- 7.10124364E+04 5.48497999E+00 3.48981665E+00 3.23835541E-04-1.68899065E-06    3
- 3.16217327E-09-1.40609067E-12 7.07972934E+04 2.08401108E+00                   4
-CH2               L S/93C   1H   2   00   00G   200.000  3500.000  1000.000    1
- 2.87410113E+00 3.65639292E-03-1.40894597E-06 2.60179549E-10-1.87727567E-14    2
- 4.62636040E+04 6.17119324E+00 3.76267867E+00 9.68872143E-04 2.79489841E-06    3
--3.85091153E-09 1.68741719E-12 4.60040401E+04 1.56253185E+00                   4
-CH2(S)            L S/93C   1H   2   00   00G   200.000  3500.000  1000.000    1
- 2.29203842E+00 4.65588637E-03-2.01191947E-06 4.17906000E-10-3.39716365E-14    2
- 5.09259997E+04 8.62650169E+00 4.19860411E+00-2.36661419E-03 8.23296220E-06    3
--6.68815981E-09 1.94314737E-12 5.04968163E+04-7.69118967E-01                   4
-CH3               L11/89C   1H   3   00   00G   200.000  3500.000  1000.000    1
- 2.28571772E+00 7.23990037E-03-2.98714348E-06 5.95684644E-10-4.67154394E-14    2
- 1.67755843E+04 8.48007179E+00 3.67359040E+00 2.01095175E-03 5.73021856E-06    3
--6.87117425E-09 2.54385734E-12 1.64449988E+04 1.60456433E+00                   4
-CH4               L 8/88C   1H   4   00   00G   200.000  3500.000  1000.000    1
- 7.48514950E-02 1.33909467E-02-5.73285809E-06 1.22292535E-09-1.01815230E-13    2
--9.46834459E+03 1.84373180E+01 5.14987613E+00-1.36709788E-02 4.91800599E-05    3
--4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00                   4
-CO                TPIS79C   1O   1   00   00G   200.000  3500.000  1000.000    1
- 2.71518561E+00 2.06252743E-03-9.98825771E-07 2.30053008E-10-2.03647716E-14    2
--1.41518724E+04 7.81868772E+00 3.57953347E+00-6.10353680E-04 1.01681433E-06    3
- 9.07005884E-10-9.04424499E-13-1.43440860E+04 3.50840928E+00                   4
-CO2               L 7/88C   1O   2   00   00G   200.000  3500.000  1000.000    1
- 3.85746029E+00 4.41437026E-03-2.21481404E-06 5.23490188E-10-4.72084164E-14    2
--4.87591660E+04 2.27163806E+00 2.35677352E+00 8.98459677E-03-7.12356269E-06    3
- 2.45919022E-09-1.43699548E-13-4.83719697E+04 9.90105222E+00                   4
-HCO               L12/89H   1C   1O   1   00G   200.000  3500.000  1000.000    1
- 2.77217438E+00 4.95695526E-03-2.48445613E-06 5.89161778E-10-5.33508711E-14    2
- 4.01191815E+03 9.79834492E+00 4.22118584E+00-3.24392532E-03 1.37799446E-05    3
--1.33144093E-08 4.33768865E-12 3.83956496E+03 3.39437243E+00                   4
-CH2O              L 8/88H   2C   1O   1   00G   200.000  3500.000  1000.000    1
- 1.76069008E+00 9.20000082E-03-4.42258813E-06 1.00641212E-09-8.83855640E-14    2
--1.39958323E+04 1.36563230E+01 4.79372315E+00-9.90833369E-03 3.73220008E-05    3
--3.79285261E-08 1.31772652E-11-1.43089567E+04 6.02812900E-01                   4
-CH2OH             GUNL93C   1H   3O   1   00G   200.000  3500.000  1000.000    1
- 3.69266569E+00 8.64576797E-03-3.75101120E-06 7.87234636E-10-6.48554201E-14    2
--3.24250627E+03 5.81043215E+00 3.86388918E+00 5.59672304E-03 5.93271791E-06    3
--1.04532012E-08 4.36967278E-12-3.19391367E+03 5.47302243E+00                   4
-CH3O              121686C   1H   3O   1     G  0300.00   3000.00   1000.000    1
- 0.03770799E+02 0.07871497E-01-0.02656384E-04 0.03944431E-08-0.02112616E-12    2
- 0.12783252E+03 0.02929575E+02 0.02106204E+02 0.07216595E-01 0.05338472E-04    3
--0.07377636E-07 0.02075610E-10 0.09786011E+04 0.13152177E+02                   4
-CH3OH             L 8/88C   1H   4O   1   00G   200.000  3500.000  1000.000    1
- 1.78970791E+00 1.40938292E-02-6.36500835E-06 1.38171085E-09-1.17060220E-13    2
--2.53748747E+04 1.45023623E+01 5.71539582E+00-1.52309129E-02 6.52441155E-05    3
--7.10806889E-08 2.61352698E-11-2.56427656E+04-1.50409823E+00                   4
-C2H               L 1/91C   2H   1   00   00G   200.000  3500.000  1000.000    1
- 3.16780652E+00 4.75221902E-03-1.83787077E-06 3.04190252E-10-1.77232770E-14    2
- 6.71210650E+04 6.63589475E+00 2.88965733E+00 1.34099611E-02-2.84769501E-05    3
- 2.94791045E-08-1.09331511E-11 6.68393932E+04 6.22296438E+00                   4
-C2H2              L 1/91C   2H   2   00   00G   200.000  3500.000  1000.000    1
- 4.14756964E+00 5.96166664E-03-2.37294852E-06 4.67412171E-10-3.61235213E-14    2
- 2.59359992E+04-1.23028121E+00 8.08681094E-01 2.33615629E-02-3.55171815E-05    3
- 2.80152437E-08-8.50072974E-12 2.64289807E+04 1.39397051E+01                   4
-C2H3              L 2/92C   2H   3   00   00G   200.000  3500.000  1000.000    1
- 3.01672400E+00 1.03302292E-02-4.68082349E-06 1.01763288E-09-8.62607041E-14    2
- 3.46128739E+04 7.78732378E+00 3.21246645E+00 1.51479162E-03 2.59209412E-05    3
--3.57657847E-08 1.47150873E-11 3.48598468E+04 8.51054025E+00                   4
-C2H4              L 1/91C   2H   4   00   00G   200.000  3500.000  1000.000    1
- 2.03611116E+00 1.46454151E-02-6.71077915E-06 1.47222923E-09-1.25706061E-13    2
- 4.93988614E+03 1.03053693E+01 3.95920148E+00-7.57052247E-03 5.70990292E-05    3
--6.91588753E-08 2.69884373E-11 5.08977593E+03 4.09733096E+00                   4
-C2H5              L12/92C   2H   5   00   00G   200.000  3500.000  1000.000    1
- 1.95465642E+00 1.73972722E-02-7.98206668E-06 1.75217689E-09-1.49641576E-13    2
- 1.28575200E+04 1.34624343E+01 4.30646568E+00-4.18658892E-03 4.97142807E-05    3
--5.99126606E-08 2.30509004E-11 1.28416265E+04 4.70720924E+00                   4
-C2H6              L 8/88C   2H   6   00   00G   200.000  3500.000  1000.000    1
- 1.07188150E+00 2.16852677E-02-1.00256067E-05 2.21412001E-09-1.90002890E-13    2
--1.14263932E+04 1.51156107E+01 4.29142492E+00-5.50154270E-03 5.99438288E-05    3
--7.08466285E-08 2.68685771E-11-1.15222055E+04 2.66682316E+00                   4
-CH2CO             L 5/90C   2H   2O   1   00G   200.000  3500.000  1000.000    1
- 4.51129732E+00 9.00359745E-03-4.16939635E-06 9.23345882E-10-7.94838201E-14    2
--7.55105311E+03 6.32247205E-01 2.13583630E+00 1.81188721E-02-1.73947474E-05    3
- 9.34397568E-09-2.01457615E-12-7.04291804E+03 1.22156480E+01                   4
-HCCO              SRIC91H   1C   2O   1     G  0300.00   4000.00   1000.000    1
- 0.56282058E+01 0.40853401E-02-0.15934547E-05 0.28626052E-09-0.19407832E-13    2
- 0.19327215E+05-0.39302595E+01 0.22517214E+01 0.17655021E-01-0.23729101E-04    3
- 0.17275759E-07-0.50664811E-11 0.20059449E+05 0.12490417E+02                   4
-HCCOH              SRI91C   2O   1H   20   0G   300.000  5000.000  1000.000    1
- 0.59238291E+01 0.67923600E-02-0.25658564E-05 0.44987841E-09-0.29940101E-13    2
- 0.72646260E+04-0.76017742E+01 0.12423733E+01 0.31072201E-01-0.50866864E-04    3
- 0.43137131E-07-0.14014594E-10 0.80316143E+04 0.13874319E+02                   4
-H2CN               41687H   2C   1N   1     G  0300.00   4000.000  1000.000    1
- 0.52097030E+01 0.29692911E-02-0.28555891E-06-0.16355500E-09 0.30432589E-13    2
- 0.27677109E+05-0.44444780E+01 0.28516610E+01 0.56952331E-02 0.10711400E-05    3
--0.16226120E-08-0.23511081E-12 0.28637820E+05 0.89927511E+01                   4
-HCN               GRI/98H   1C   1N   1    0G   200.000  6000.000  1000.000    1
- 0.38022392E+01 0.31464228E-02-0.10632185E-05 0.16619757E-09-0.97997570E-14    2
- 0.14407292E+05 0.15754601E+01 0.22589886E+01 0.10051170E-01-0.13351763E-04    3
- 0.10092349E-07-0.30089028E-11 0.14712633E+05 0.89164419E+01                   4
-HNO               And93 H   1N   1O   1    0G   200.000  6000.000  1000.000    1
- 0.29792509E+01 0.34944059E-02-0.78549778E-06 0.57479594E-10-0.19335916E-15    2
- 0.11750582E+05 0.86063728E+01 0.45334916E+01-0.56696171E-02 0.18473207E-04    3
--0.17137094E-07 0.55454573E-11 0.11548297E+05 0.17498417E+01                   4
-N                 L 6/88N   1    0    0    0G   200.000  6000.000  1000.000    1
- 0.24159429E+01 0.17489065E-03-0.11902369E-06 0.30226245E-10-0.20360982E-14    2
- 0.56133773E+05 0.46496096E+01 0.25000000E+01 0.00000000E+00 0.00000000E+00    3
- 0.00000000E+00 0.00000000E+00 0.56104637E+05 0.41939087E+01                   4
-NNH               T07/93N   2H   1   00   00G   200.000  6000.000  1000.000    1
- 0.37667544E+01 0.28915082E-02-0.10416620E-05 0.16842594E-09-0.10091896E-13    2
- 0.28650697E+05 0.44705067E+01 0.43446927E+01-0.48497072E-02 0.20059459E-04    3
--0.21726464E-07 0.79469539E-11 0.28791973E+05 0.29779410E+01                   4
-N2O               L 7/88N   2O   1    0    0G   200.000  6000.000  1000.000    1
- 0.48230729E+01 0.26270251E-02-0.95850874E-06 0.16000712E-09-0.97752303E-14    2
- 0.80734048E+04-0.22017207E+01 0.22571502E+01 0.11304728E-01-0.13671319E-04    3
- 0.96819806E-08-0.29307182E-11 0.87417744E+04 0.10757992E+02                   4
-NH                And94 N   1H   1    0    0G   200.000  6000.000  1000.000    1
- 0.27836928E+01 0.13298430E-02-0.42478047E-06 0.78348501E-10-0.55044470E-14    2
- 0.42120848E+05 0.57407799E+01 0.34929085E+01 0.31179198E-03-0.14890484E-05    3
- 0.24816442E-08-0.10356967E-11 0.41880629E+05 0.18483278E+01                   4
-NH2               And89 N   1H   2    0    0G   200.000  6000.000  1000.000    1
- 0.28347421E+01 0.32073082E-02-0.93390804E-06 0.13702953E-09-0.79206144E-14    2
- 0.22171957E+05 0.65204163E+01 0.42040029E+01-0.21061385E-02 0.71068348E-05    3
--0.56115197E-08 0.16440717E-11 0.21885910E+05-0.14184248E+00                   4
-NH3               J 6/77N   1H   3    0    0G   200.000  6000.000  1000.000    1
- 0.26344521E+01 0.56662560E-02-0.17278676E-05 0.23867161E-09-0.12578786E-13    2
--0.65446958E+04 0.65662928E+01 0.42860274E+01-0.46605230E-02 0.21718513E-04    3
--0.22808887E-07 0.82638046E-11-0.67417285E+04-0.62537277E+00                   4
-NO                RUS 78N   1O   1    0    0G   200.000  6000.000  1000.000    1
- 0.32606056E+01 0.11911043E-02-0.42917048E-06 0.69457669E-10-0.40336099E-14    2
- 0.99209746E+04 0.63693027E+01 0.42184763E+01-0.46389760E-02 0.11041022E-04    3
--0.93361354E-08 0.28035770E-11 0.98446230E+04 0.22808464E+01                   4
-NO2               L 7/88N   1O   2    0    0G   200.000  6000.000  1000.000    1
- 0.48847542E+01 0.21723956E-02-0.82806906E-06 0.15747510E-09-0.10510895E-13    2
- 0.23164983E+04-0.11741695E+00 0.39440312E+01-0.15854290E-02 0.16657812E-04    3
--0.20475426E-07 0.78350564E-11 0.28966179E+04 0.63119917E+01                   4
-HCNO              BDEA94H   1N   1C   1O   1G   300.000  5000.000  1382.000    1
- 6.59860456E+00 3.02778626E-03-1.07704346E-06 1.71666528E-10-1.01439391E-14    2
- 1.79661339E+04-1.03306599E+01 2.64727989E+00 1.27505342E-02-1.04794236E-05    3
- 4.41432836E-09-7.57521466E-13 1.92990252E+04 1.07332972E+01                   4
-HOCN              BDEA94H   1N   1C   1O   1G   300.000  5000.000  1368.000    1
- 5.89784885E+00 3.16789393E-03-1.11801064E-06 1.77243144E-10-1.04339177E-14    2
--3.70653331E+03-6.18167825E+00 3.78604952E+00 6.88667922E-03-3.21487864E-06    3
- 5.17195767E-10 1.19360788E-14-2.82698400E+03 5.63292162E+00                   4
-HNCO              BDEA94H   1N   1C   1O   1G   300.000  5000.000  1478.000    1
- 6.22395134E+00 3.17864004E-03-1.09378755E-06 1.70735163E-10-9.95021955E-15    2
--1.66599344E+04-8.38224741E+00 3.63096317E+00 7.30282357E-03-2.28050003E-06    3
--6.61271298E-10 3.62235752E-13-1.55873636E+04 6.19457727E+00                   4
-NCO               EA 93 N   1C   1O   1    0G   200.000  6000.000  1000.000    1
- 0.51521845E+01 0.23051761E-02-0.88033153E-06 0.14789098E-09-0.90977996E-14    2
- 0.14004123E+05-0.25442660E+01 0.28269308E+01 0.88051688E-02-0.83866134E-05    3
- 0.48016964E-08-0.13313595E-11 0.14682477E+05 0.95504646E+01                   4
-CN                HBH92 C   1N   1    0    0G   200.000  6000.000  1000.000    1
- 0.37459805E+01 0.43450775E-04 0.29705984E-06-0.68651806E-10 0.44134173E-14    2
- 0.51536188E+05 0.27867601E+01 0.36129351E+01-0.95551327E-03 0.21442977E-05    3
--0.31516323E-09-0.46430356E-12 0.51708340E+05 0.39804995E+01                   4
-HCNN              SRI/94C   1N   2H   10   0G   300.000  5000.000  1000.000    1
- 0.58946362E+01 0.39895959E-02-0.15982380E-05 0.29249395E-09-0.20094686E-13    2
- 0.53452941E+05-0.51030502E+01 0.25243194E+01 0.15960619E-01-0.18816354E-04    3
- 0.12125540E-07-0.32357378E-11 0.54261984E+05 0.11675870E+02                   4
-N2                121286N   2               G   300.000  5000.000  1000.000    1
- 0.02926640E+02 0.14879768E-02-0.05684760E-05 0.10097038E-09-0.06753351E-13    2
--0.09227977E+04 0.05980528E+02 0.03298677E+02 0.14082404E-02-0.03963222E-04    3
- 0.05641515E-07-0.02444854E-10-0.10208999E+04 0.03950372E+02                   4
-AR                120186AR  1               G   300.000  5000.000  1000.000    1
- 0.02500000E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00    2
--0.07453750E+04 0.04366000E+02 0.02500000E+02 0.00000000E+00 0.00000000E+00    3
- 0.00000000E+00 0.00000000E+00-0.07453750E+04 0.04366000E+02                   4
-C3H8              L 4/85C   3H   8    0    0G   300.000  5000.000  1000.00     1
- 0.75341368E+01 0.18872239E-01-0.62718491E-05 0.91475649E-09-0.47838069E-13    2
--0.16467516E+05-0.17892349E+02 0.93355381E+00 0.26424579E-01 0.61059727E-05    3
--0.21977499E-07 0.95149253E-11-0.13958520E+05 0.19201691E+02                   4
-C3H7              L 9/84C   3H   7    0    0G   300.000  5000.000  1000.00     1
- 0.77026987E+01 0.16044203E-01-0.52833220E-05 0.76298590E-09-0.39392284E-13    2
- 0.82984336E+04-0.15480180E+02 0.10515518E+01 0.25991980E-01 0.23800540E-05    3
--0.19609569E-07 0.93732470E-11 0.10631863E+05 0.21122559E+02                   4
-CH3CHO            L 8/88C   2H   4O   1    0G   200.000  6000.000  1000.00     1
- 0.54041108E+01 0.11723059E-01-0.42263137E-05 0.68372451E-09-0.40984863E-13    2
--0.22593122E+05-0.34807917E+01 0.47294595E+01-0.31932858E-02 0.47534921E-04    3
--0.57458611E-07 0.21931112E-10-0.21572878E+05 0.41030159E+01                   4
-CH2CHO            SAND86O   1H   3C   2     G   300.00   5000.00   1000.00     1
- 0.05975670E+02 0.08130591E-01-0.02743624E-04 0.04070304E-08-0.02176017E-12    2
- 0.04903218E+04-0.05045251E+02 0.03409062E+02 0.10738574E-01 0.01891492E-04    3
--0.07158583E-07 0.02867385E-10 0.15214766E+04 0.09558290E+02                   4
-END
+!THERMO
+! Insert GRI-Mech thermodynamics here or use in default file
+!END
 REACTIONS
 2O+M<=>O2+M                              1.200E+17   -1.000        .00
 H2/ 2.40/ H2O/15.40/ CH4/ 2.00/ CO/ 1.75/ CO2/ 3.60/ C2H6/ 3.00/ AR/  .83/ 
@@ -616,8 +404,8 @@ CH2+CH2=>2H+C2H2                         2.000E+14     .000   10989.00
 CH2(S)+H2O=>H2+CH2O                      6.820E+10     .250    -935.00
 C2H3+O2<=>O+CH2CHO                       3.030E+11     .290      11.00
 C2H3+O2<=>HO2+C2H2                       1.337E+06    1.610    -384.00
-O+CH3CHO<=>OH+CH2CHO                     5.840E+12     .000    1808.00
-O+CH3CHO=>OH+CH3+CO                      5.840E+12     .000    1808.00
+O+CH3CHO<=>OH+CH2CHO                     2.920E+12     .000    1808.00
+O+CH3CHO=>OH+CH3+CO                      2.920E+12     .000    1808.00
 O2+CH3CHO=>HO2+CH3+CO                    3.010E+13     .000   39150.00
 H+CH3CHO<=>CH2CHO+H2                     2.050E+09    1.160    2405.00
 H+CH3CHO=>CH3+H2+CO                      2.050E+09    1.160    2405.00

data/inputs/gri30_highT.cti

@@ -117,7 +117,7 @@ species(name = "O2",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.46,
+                     diam =     3.458,
                      well_depth =   107.40,
                      polar =     1.60,
                      rot_relax =     3.80),
@@ -153,9 +153,9 @@ species(name = "H2O",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     2.60,
+                     diam =     2.605,
                      well_depth =   572.40,
-                     dipole =     1.84,
+                     dipole =     1.844,
                      rot_relax =     4.00),
     note = "L 8/89"
        )
@@ -172,7 +172,7 @@ species(name = "HO2",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.46,
+                     diam =     3.458,
                      well_depth =   107.40,
                      rot_relax =     1.00),
     note = "L 5/89"
@@ -190,7 +190,7 @@ species(name = "H2O2",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.46,
+                     diam =     3.458,
                      well_depth =   107.40,
                      rot_relax =     3.80),
     note = "L 7/88"
@@ -208,7 +208,7 @@ species(name = "C",
              ),
     transport = gas_transport(
                      geom = "atom",
-                     diam =     3.30,
+                     diam =     3.298,
                      well_depth =    71.40),
     note = "L11/88"
        )
@@ -293,7 +293,7 @@ species(name = "CH4",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.75,
+                     diam =     3.746,
                      well_depth =   141.40,
                      polar =     2.60,
                      rot_relax =    13.00),
@@ -331,7 +331,7 @@ species(name = "CO2",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.76,
+                     diam =     3.763,
                      well_depth =   244.00,
                      polar =     2.65,
                      rot_relax =     2.10),
@@ -423,7 +423,7 @@ species(name = "CH3OH",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.63,
+                     diam =     3.626,
                      well_depth =   481.80,
                      rot_relax =     1.00),
     note = "L 8/88"
@@ -495,7 +495,7 @@ species(name = "C2H4",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.97,
+                     diam =     3.971,
                      well_depth =   280.80,
                      rot_relax =     1.50),
     note = "L 1/91"
@@ -513,7 +513,7 @@ species(name = "C2H5",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     4.30,
+                     diam =     4.302,
                      well_depth =   252.30,
                      rot_relax =     1.50),
     note = "L12/92"
@@ -531,7 +531,7 @@ species(name = "C2H6",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     4.30,
+                     diam =     4.302,
                      well_depth =   252.30,
                      rot_relax =     1.50),
     note = "L 8/88"
@@ -603,7 +603,7 @@ species(name = "N",
              ),
     transport = gas_transport(
                      geom = "atom",
-                     diam =     3.30,
+                     diam =     3.298,
                      well_depth =    71.40),
     note = "L 6/88"
        )
@@ -676,7 +676,7 @@ species(name = "NNH",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.80,
+                     diam =     3.798,
                      well_depth =    71.40,
                      rot_relax =     1.00),
     note = "T07/93"
@@ -694,7 +694,7 @@ species(name = "NO",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.62,
+                     diam =     3.621,
                      well_depth =    97.53,
                      polar =     1.76,
                      rot_relax =     4.00),
@@ -731,7 +731,7 @@ species(name = "N2O",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.83,
+                     diam =     3.828,
                      well_depth =   232.40,
                      rot_relax =     1.00),
     note = "L 7/88"
@@ -749,7 +749,7 @@ species(name = "HNO",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.49,
+                     diam =     3.492,
                      well_depth =   116.70,
                      rot_relax =     1.00),
     note = "And93"
@@ -767,7 +767,7 @@ species(name = "CN",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.86,
+                     diam =     3.856,
                      well_depth =    75.00,
                      rot_relax =     1.00),
     note = "HBH92"
@@ -839,7 +839,7 @@ species(name = "HCNO",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.83,
+                     diam =     3.828,
                      well_depth =   232.40,
                      rot_relax =     1.00),
     note = "BDEA94"
@@ -857,7 +857,7 @@ species(name = "HOCN",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.83,
+                     diam =     3.828,
                      well_depth =   232.40,
                      rot_relax =     1.00),
     note = "BDEA94"
@@ -875,7 +875,7 @@ species(name = "HNCO",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     3.83,
+                     diam =     3.828,
                      well_depth =   232.40,
                      rot_relax =     1.00),
     note = "BDEA94"
@@ -893,7 +893,7 @@ species(name = "NCO",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.83,
+                     diam =     3.828,
                      well_depth =   232.40,
                      rot_relax =     1.00),
     note = "EA 93"
@@ -911,7 +911,7 @@ species(name = "N2",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.62,
+                     diam =     3.621,
                      well_depth =    97.53,
                      polar =     1.76,
                      rot_relax =     4.00),
@@ -947,7 +947,7 @@ species(name = "C3H7",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     4.98,
+                     diam =     4.982,
                      well_depth =   266.80,
                      rot_relax =     1.00),
     note = "L 9/84"
@@ -965,7 +965,7 @@ species(name = "C3H8",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     4.98,
+                     diam =     4.982,
                      well_depth =   266.80,
                      rot_relax =     1.00),
     note = "L 4/85"
@@ -2014,10 +2014,10 @@ reaction( "C2H3 + O2 <=> O + CH2CHO",   [3.03000E+11, 0.29, 11])
 reaction( "C2H3 + O2 <=> HO2 + C2H2",   [1.33700E+06, 1.61, -384])
 
 #  Reaction 296
-reaction( "O + CH3CHO <=> OH + CH2CHO",   [5.84000E+12, 0, 1808])
+reaction( "O + CH3CHO <=> OH + CH2CHO",   [2.920000E+12, 0, 1808])
 
 #  Reaction 297
-reaction( "O + CH3CHO => OH + CH3 + CO",   [5.84000E+12, 0, 1808])
+reaction( "O + CH3CHO => OH + CH3 + CO",   [2.920000E+12, 0, 1808])
 
 #  Reaction 298
 reaction( "O2 + CH3CHO => HO2 + CH3 + CO",   [3.01000E+13, 0, 39150])

data/inputs/gri30_ion.cti

@@ -0,0 +1,231 @@
+units(length='cm', time='s', quantity='mol', act_energy='cal/mol')
+
+ideal_gas(name='gas',
+          elements=' O  H  C  N  Ar  E',
+          species=['H2  O2  H2O  CH4  CO  CO2  N2',
+                   '''gri30: H  O  OH  HO2  H2O2  C  CH
+                   CH2  CH2(S)  CH3  HCO  CH2O  CH2OH  CH3O
+                   CH3OH  C2H  C2H2  C2H3  C2H4  C2H5  C2H6  HCCO  CH2CO  HCCOH
+                   N  NH  NH2  NH3  NNH  NO  NO2  N2O  HNO  CN
+                   HCN  H2CN  HCNN  HCNO  HOCN  HNCO  NCO  AR  C3H7
+                   C3H8  CH2CHO  CH3CHO''',
+                   'HCO+    H3O+    E'],
+          reactions=['gri30: all', 'all'],
+          transport='Ion',
+          options=['skip_undeclared_species', 'skip_undeclared_third_bodies'],
+          initial_state=state(temperature=300.0, pressure=OneAtm))
+
+#-------------------------------------------------------------------------------
+# Species data
+#-------------------------------------------------------------------------------
+# The values of polarizability of H2, O2, H2O, CH4, CO, CO2, and N2 are from
+# the supplementary material of Han, Jie, et al. "Numerical modelling of ion
+# transport in flames." Combustion Theory and Modelling 19.6 (2015): 744-772.
+# DOI: 10.1080/13647830.2015.1090018
+
+species(name = "H2",
+    atoms = " H:2 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  2.344331120E+00,   7.980520750E-03, 
+               -1.947815100E-05,   2.015720940E-08,  -7.376117610E-12,
+               -9.179351730E+02,   6.830102380E-01] ),
+       NASA( [ 1000.00,  3500.00], [  3.337279200E+00,  -4.940247310E-05, 
+                4.994567780E-07,  -1.795663940E-10,   2.002553760E-14,
+               -9.501589220E+02,  -3.205023310E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "linear",
+                     diam =     2.92,
+                     well_depth =    38.00,
+                     polar =     0.455,
+                     rot_relax =   280.00),
+    note = '''The value of polarizability is from the supplementary
+              material of Han, Jie, et al. "Numerical modelling of ion
+              transport in flames." Combustion Theory and Modelling
+              19.6 (2015): 744-772. DOI: 10.1080/13647830.2015.1090018'''
+       )
+
+species(name = "O2",
+    atoms = " O:2 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  3.782456360E+00,  -2.996734160E-03, 
+                9.847302010E-06,  -9.681295090E-09,   3.243728370E-12,
+               -1.063943560E+03,   3.657675730E+00] ),
+       NASA( [ 1000.00,  3500.00], [  3.282537840E+00,   1.483087540E-03, 
+               -7.579666690E-07,   2.094705550E-10,  -2.167177940E-14,
+               -1.088457720E+03,   5.453231290E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "linear",
+                     diam =     3.458,
+                     well_depth =   107.40,
+                     polar =     1.131,
+                     rot_relax =     3.80),
+    note = "TPIS89"
+       )
+
+species(name = "H2O",
+    atoms = " H:2  O:1 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  4.198640560E+00,  -2.036434100E-03, 
+                6.520402110E-06,  -5.487970620E-09,   1.771978170E-12,
+               -3.029372670E+04,  -8.490322080E-01] ),
+       NASA( [ 1000.00,  3500.00], [  3.033992490E+00,   2.176918040E-03, 
+               -1.640725180E-07,  -9.704198700E-11,   1.682009920E-14,
+               -3.000429710E+04,   4.966770100E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "nonlinear",
+                     diam =     2.605,
+                     well_depth =   572.40,
+                     dipole =     1.844,
+                     polar = 1.053,
+                     rot_relax =     4.00),
+    note = "L 8/89"
+       )
+
+species(name = "CH4",
+    atoms = " C:1  H:4 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  5.149876130E+00,  -1.367097880E-02, 
+                4.918005990E-05,  -4.847430260E-08,   1.666939560E-11,
+               -1.024664760E+04,  -4.641303760E+00] ),
+       NASA( [ 1000.00,  3500.00], [  7.485149500E-02,   1.339094670E-02, 
+               -5.732858090E-06,   1.222925350E-09,  -1.018152300E-13,
+               -9.468344590E+03,   1.843731800E+01] )
+             ),
+    transport = gas_transport(
+                     geom = "nonlinear",
+                     diam =     3.746,
+                     well_depth =   141.40,
+                     polar =     2.60,
+                     rot_relax =    13.00),
+    note = "L 8/88"
+       )
+
+species(name = "CO",
+    atoms = " C:1  O:1 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  3.579533470E+00,  -6.103536800E-04, 
+                1.016814330E-06,   9.070058840E-10,  -9.044244990E-13,
+               -1.434408600E+04,   3.508409280E+00] ),
+       NASA( [ 1000.00,  3500.00], [  2.715185610E+00,   2.062527430E-03, 
+               -9.988257710E-07,   2.300530080E-10,  -2.036477160E-14,
+               -1.415187240E+04,   7.818687720E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "linear",
+                     diam =     3.65,
+                     well_depth =    98.10,
+                     polar =     1.95,
+                     rot_relax =     1.80),
+    note = "TPIS79"
+       )
+
+species(name = "CO2",
+    atoms = " C:1  O:2 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  2.356773520E+00,   8.984596770E-03, 
+               -7.123562690E-06,   2.459190220E-09,  -1.436995480E-13,
+               -4.837196970E+04,   9.901052220E+00] ),
+       NASA( [ 1000.00,  3500.00], [  3.857460290E+00,   4.414370260E-03, 
+               -2.214814040E-06,   5.234901880E-10,  -4.720841640E-14,
+               -4.875916600E+04,   2.271638060E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "linear",
+                     diam =     3.763,
+                     well_depth =   244.00,
+                     polar =     2.65,
+                     rot_relax =     2.10),
+    note = "L 7/88"
+       )
+
+species(name = "N2",
+    atoms = " N:2 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  3.298677000E+00,   1.408240400E-03, 
+               -3.963222000E-06,   5.641515000E-09,  -2.444854000E-12,
+               -1.020899900E+03,   3.950372000E+00] ),
+       NASA( [ 1000.00,  5000.00], [  2.926640000E+00,   1.487976800E-03, 
+               -5.684760000E-07,   1.009703800E-10,  -6.753351000E-15,
+               -9.227977000E+02,   5.980528000E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "linear",
+                     diam =     3.621,
+                     well_depth =    97.53,
+                     polar =     1.76,
+                     rot_relax =     4.00),
+    note = "121286"
+       )
+
+species(name = 'HCO+',
+    atoms = ' H:1  C:1  O:1  E:-1 ',
+    thermo = (
+       NASA( [  300.00,  1000.00], [  2.473973600E+00,   8.671559000E-03, 
+               -1.003150000E-05,   6.717052700E-09,  -1.787267400E-12,
+                9.914660800E+04,   8.175711870E+00] ),
+       NASA( [ 1000.00,  5000.00], [  3.741188000E+00,   3.344151700E-03, 
+               -1.239712100E-06,   2.118938800E-10,  -1.370415000E-14,
+                9.888407800E+04,   2.078613570E+00] )
+             ),
+        transport=gas_transport(geom='linear',
+                                diam=3.59,
+                                well_depth=498.0,
+                                polar=1.356),
+    note = '''The polarizability is from Han, Jie, et al.
+              "Numerical modelling of ion transport in flames."
+              ,and the rest of the parameters are from its neutral 
+              counterpart HCO''')
+
+species(name = 'H3O+',
+    atoms = ' H:3  O:1  E:-1 ',
+    thermo = (
+       NASA( [  298.15,  1000.00], [  3.792952700E+00,  -9.108540000E-04, 
+                1.163635490E-05,  -1.213648870E-08,   4.261596630E-12,
+                7.075124010E+04,   1.471568560E+00] ),
+       NASA( [ 1000.00,  6000.00], [  2.496477160E+00,   5.728449200E-03, 
+               -1.839532810E-06,   2.735774390E-10,  -1.540939850E-14,
+                7.097291130E+04,   7.458507790E+00] )
+             ),
+        transport=gas_transport(geom='nonlinear',
+                                diam=3.15,
+                                well_depth=106.2,
+                                dipole=1.417,
+                                polar=0.897),
+     note = '''The transport parameters are from Han, Jie, et al.
+               "Numerical modelling of ion transport in flames."''')
+
+species(name = 'E',
+    atoms = ' E:1 ',
+    thermo = (
+       NASA( [  200.00,  1000.00], [  2.500000000E+00,   0.000000000E+00, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+               -7.453750000E+02,  -1.172469020E+01] ),
+       NASA( [ 1000.00,  6000.00], [  2.500000000E+00,   0.000000000E+00, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+               -7.453750000E+02,  -1.172469020E+01] )
+             ),
+        transport=gas_transport(geom='atom',
+                                diam=2.05,
+                                well_depth=145.0,
+                                polar=0.667),
+     note = 'The transport parameters are not used in IonGasTransport')
+
+#-------------------------------------------------------------------------------
+# Reaction data
+#-------------------------------------------------------------------------------
+
+reaction('CH + O => HCO+ + E', [2.51E+11, 0.0, 1700])
+
+reaction('HCO+ + H2O => H3O+ + CO', [1.51E+15, 0.0, 0.0])
+
+reaction('H3O+ + E => H2O + H', [2.29E+18, -0.5, 0.0])
+
+reaction('H3O+ + E => OH + H + H', [7.95E+21, -1.4, 0.0])
+
+reaction('H3O+ + E => H2 + OH', [1.25E+19, -0.5, 0.0])
+
+reaction('H3O+ + E =>  O + H2 + H', [6.0E+17, -0.3, 0.0])
+

data/inputs/lithium_ion_battery.cti

@@ -0,0 +1,295 @@
+#==============================================================================
+# Cantera input file for an LCO/graphite lithium-ion battery
+#
+# This file includes a full set of thermodynamic and kinetic parameters of a
+# lithium-ion battery, in particular:
+# - Active materials: LiCoO2 (LCO) and LiC6 (graphite)
+# - Organic electrolyte: EC/PC with 1M LiPF6
+# - Interfaces: LCO/electrolyte and LiC6/electrolyte
+# - Charge-transfer reactions at the two interfaces
+#
+# A MATLAB example using this file for simulating a discharge curve is
+# samples/matlab/lithium_ion_battery.m
+#
+# Reference:
+# M. Mayur, S. C. DeCaluwe, B. L. Kee, W. G. Bessler, “Modeling and simulation 
+# of the thermodynamics of lithium-ion battery intercalation materials in the 
+# open-source software Cantera,” Electrochim. Acta 323, 134797 (2019), 
+# https://doi.org/10.1016/j.electacta.2019.134797
+
+#==============================================================================
+
+#==============================================================================
+#   Bulk phases
+#==============================================================================
+#------------------------------------------------------------------------------
+# Graphite (anode)
+# Thermodynamic data based on half-cell measurements by K. Kumaresan et al.,
+# J. Electrochem. Soc. 155, A164-A171 (2008)
+#------------------------------------------------------------------------------
+BinarySolutionTabulatedThermo(
+    name                   = "anode",
+    elements               = "Li C",
+    species                = "Li[anode] V[anode]",
+    standard_concentration = "unity",
+    tabulated_species      = "Li[anode]",
+    tabulated_thermo       = table(
+        moleFraction = ([5.75000E-03, 1.77591E-02, 2.97682E-02, 4.17773E-02, 5.37864E-02, 6.57954E-02, 7.78045E-02, 8.98136E-02, 1.01823E-01, 1.13832E-01,
+                         1.25841E-01, 1.37850E-01, 1.49859E-01, 1.61868E-01, 1.73877E-01, 1.85886E-01, 1.97896E-01, 2.09904E-01, 2.21914E-01, 2.33923E-01,
+                         2.45932E-01, 2.57941E-01, 2.69950E-01, 2.81959E-01, 2.93968E-01, 3.05977E-01, 3.17986E-01, 3.29995E-01, 3.42004E-01, 3.54014E-01,
+                         3.66023E-01, 3.78032E-01, 3.90041E-01, 4.02050E-01, 4.14059E-01, 4.26068E-01, 4.38077E-01, 4.50086E-01, 4.62095E-01, 4.74104E-01,
+                         4.86114E-01, 4.98123E-01, 5.10132E-01, 5.22141E-01, 5.34150E-01, 5.46159E-01, 5.58168E-01, 5.70177E-01, 5.82186E-01, 5.94195E-01,
+                         6.06205E-01, 6.18214E-01, 6.30223E-01, 6.42232E-01, 6.54241E-01, 6.66250E-01, 6.78259E-01, 6.90268E-01, 7.02277E-01, 7.14286E-01,
+                         7.26295E-01, 7.38305E-01, 7.50314E-01, 7.62323E-01, 7.74332E-01, 7.86341E-01, 7.98350E-01],
+                                                                 "1"),
+        enthalpy     = ([-6.40692E+04, -3.78794E+04, -1.99748E+04, -1.10478E+04, -7.04973E+03, -7.13749E+03, -8.79728E+03, -9.93655E+03, -1.03060E+04, -1.00679E+04,
+                         -9.69664E+03, -9.31556E+03, -8.90503E+03, -8.57057E+03, -8.38117E+03, -8.31928E+03, -8.31453E+03, -8.32977E+03, -8.33292E+03, -8.32931E+03,
+                         -8.31339E+03, -8.21331E+03, -8.08920E+03, -8.00131E+03, -7.92294E+03, -7.81543E+03, -7.77498E+03, -7.79440E+03, -7.78804E+03, -7.73218E+03,
+                         -7.69063E+03, -7.69630E+03, -7.63241E+03, -7.41910E+03, -7.06828E+03, -6.64544E+03, -6.17193E+03, -5.67055E+03, -5.14299E+03, -4.55704E+03,
+                         -3.94568E+03, -3.35408E+03, -2.87825E+03, -2.57690E+03, -2.43468E+03, -2.33952E+03, -2.23218E+03, -2.11482E+03, -2.03976E+03, -2.01990E+03,
+                         -2.01329E+03, -1.97991E+03, -1.92686E+03, -1.86602E+03, -1.81419E+03, -1.77693E+03, -1.74908E+03, -1.71494E+03, -1.67287E+03, -1.63685E+03,
+                         -1.59649E+03, -1.52295E+03, -1.39033E+03, -1.11524E+03, -5.34643E+02, 3.73854E+02, 1.60442E+03],
+                                                                 "J/mol"),
+        entropy      = ([3.05724E+01, 4.04307E+01, 4.75718E+01, 5.25690E+01, 5.10953E+01, 4.43414E+01, 3.71575E+01, 3.23216E+01, 2.91586E+01, 2.70081E+01,
+                         2.53501E+01, 2.40845E+01, 2.30042E+01, 2.19373E+01, 2.07212E+01, 1.93057E+01, 1.77319E+01, 1.61153E+01, 1.46399E+01, 1.34767E+01,
+                         1.27000E+01, 1.23377E+01, 1.22815E+01, 1.23700E+01, 1.24863E+01, 1.26368E+01, 1.26925E+01, 1.26250E+01, 1.24861E+01, 1.23294E+01,
+                         1.21865E+01, 1.20723E+01, 1.21228E+01, 1.24383E+01, 1.30288E+01, 1.37342E+01, 1.44460E+01, 1.50813E+01, 1.56180E+01, 1.62213E+01,
+                         1.70474E+01, 1.80584E+01, 1.88377E+01, 1.92094E+01, 1.92957E+01, 1.93172E+01, 1.93033E+01, 1.92971E+01, 1.92977E+01, 1.92978E+01,
+                         1.92980E+01, 1.92978E+01, 1.92945E+01, 1.92899E+01, 1.92877E+01, 1.92882E+01, 1.92882E+01, 1.92882E+01, 1.92882E+01, 1.92882E+01,
+                         1.92885E+01, 1.92876E+01, 1.92837E+01, 1.92769E+01, 1.92850E+01, 1.93100E+01, 1.93514E+01],
+                                                                 "J/mol/K")))
+
+#------------------------------------------------------------------------------
+# Lithium cobalt oxide (cathode)
+# Thermodynamic data based on half-cell measurements by K. Kumaresan et al.,
+# J. Electrochem. Soc. 155, A164-A171 (2008)
+#------------------------------------------------------------------------------
+BinarySolutionTabulatedThermo(
+    name                   = "cathode",
+    elements               = "Li Co O",
+    species                = "Li[cathode] V[cathode]",
+    standard_concentration = "unity",
+    tabulated_species      = "Li[cathode]",
+    tabulated_thermo       = table(
+        moleFraction = ([4.59630E-01, 4.67368E-01, 4.75105E-01, 4.82843E-01, 4.90581E-01, 4.98318E-01, 5.06056E-01, 5.13794E-01, 5.21531E-01, 5.29269E-01,
+                         5.37007E-01, 5.44744E-01, 5.52482E-01, 5.60219E-01, 5.67957E-01, 5.75695E-01, 5.83432E-01, 5.91170E-01, 5.98908E-01, 6.06645E-01,
+                         6.14383E-01, 6.22121E-01, 6.29858E-01, 6.37596E-01, 6.45334E-01, 6.53071E-01, 6.60809E-01, 6.68547E-01, 6.76284E-01, 6.84022E-01,
+                         6.91759E-01, 6.99497E-01, 7.07235E-01, 7.14972E-01, 7.22710E-01, 7.30448E-01, 7.38185E-01, 7.45923E-01, 7.53661E-01, 7.61398E-01,
+                         7.69136E-01, 7.76873E-01, 7.84611E-01, 7.92349E-01, 8.00087E-01, 8.07824E-01, 8.15562E-01, 8.23299E-01, 8.31037E-01, 8.38775E-01,
+                         8.46512E-01, 8.54250E-01, 8.61988E-01, 8.69725E-01, 8.77463E-01, 8.85201E-01, 8.92938E-01, 9.00676E-01, 9.08413E-01, 9.16151E-01,
+                         9.23889E-01, 9.31627E-01, 9.39364E-01, 9.47102E-01, 9.54839E-01, 9.62577E-01, 9.70315E-01, 9.78052E-01, 9.85790E-01],
+                                                                 "1"),
+         enthalpy    = ([-4.16188E+05, -4.14839E+05, -4.12629E+05, -4.09620E+05, -4.05334E+05, -3.99420E+05, -3.92499E+05, -3.85940E+05, -3.81474E+05, -3.80290E+05,
+                          -3.81445E+05, -3.83295E+05, -3.85062E+05, -3.86633E+05, -3.87928E+05, -3.88837E+05, -3.89240E+05, -3.89238E+05, -3.89157E+05, -3.89174E+05,
+                          -3.89168E+05, -3.88988E+05, -3.88675E+05, -3.88478E+05, -3.88443E+05, -3.88346E+05, -3.88083E+05, -3.87768E+05, -3.87531E+05, -3.87356E+05,
+                          -3.87205E+05, -3.87052E+05, -3.86960E+05, -3.86957E+05, -3.86918E+05, -3.86814E+05, -3.86785E+05, -3.86957E+05, -3.87146E+05, -3.87188E+05,
+                          -3.87239E+05, -3.87507E+05, -3.87902E+05, -3.88142E+05, -3.88316E+05, -3.88464E+05, -3.88563E+05, -3.88687E+05, -3.89000E+05, -3.89414E+05,
+                          -3.89735E+05, -3.90005E+05, -3.90317E+05, -3.90632E+05, -3.90865E+05, -3.91100E+05, -3.91453E+05, -3.91742E+05, -3.91833E+05, -3.91858E+05,
+                          -3.91910E+05, -3.91798E+05, -3.91470E+05, -3.91005E+05, -3.90261E+05, -3.89181E+05, -3.85506E+05, -3.73450E+05, -3.53926E+05],
+                                                                 "J/mol"),
+         entropy     = ([-2.52348E+01, -2.54629E+01, -2.26068E+01, -1.68899E+01, -6.74549E+00, 9.76522E+00, 3.08711E+01, 4.98756E+01, 5.85766E+01, 5.46784E+01,
+                          4.40727E+01, 3.30834E+01, 2.37109E+01, 1.61658E+01, 1.02408E+01, 5.75684E+00, 2.19969E+00, -6.93265E-01, -3.40166E+00, -6.03548E+00,
+                         -8.45666E+00, -1.03459E+01, -1.18860E+01, -1.35610E+01, -1.53331E+01, -1.68255E+01, -1.81219E+01, -1.95052E+01, -2.07093E+01, -2.16274E+01,
+                         -2.25743E+01, -2.38272E+01, -2.52029E+01, -2.65835E+01, -2.77164E+01, -2.86064E+01, -2.96044E+01, -3.09551E+01, -3.21990E+01, -3.31284E+01,
+                         -3.40633E+01, -3.53177E+01, -3.66599E+01, -3.76439E+01, -3.85616E+01, -3.96433E+01, -4.06506E+01, -4.15566E+01, -4.27485E+01, -4.41419E+01,
+                         -4.52082E+01, -4.61154E+01, -4.71614E+01, -4.82305E+01, -4.89739E+01, -4.96529E+01, -5.06905E+01, -5.18080E+01, -5.26580E+01, -5.32766E+01,
+                         -5.39817E+01, -5.45468E+01, -5.48125E+01, -5.51520E+01, -5.54526E+01, -5.52961E+01, -5.50219E+01, -5.46653E+01, -5.42305E+01],
+                                                                 "J/mol/K")))
+
+#------------------------------------------------------------------------------
+# Carbonate based electrolyte
+# Solvent: Ethylene carbonate:Propylene carbonate (1:1 v/v)
+# Salt: 1M LiPF6
+#------------------------------------------------------------------------------
+IdealSolidSolution(
+    name                   = "electrolyte",
+    elements               = "Li P F C H O E",
+    species                = "C3H4O3[elyt] C4H6O3[elyt] Li+[elyt] PF6-[elyt]",
+    initial_state          = state(mole_fractions = 'C3H4O3[elyt]:0.47901 C4H6O3[elyt]:0.37563 Li+[elyt]:0.07268 PF6-[elyt]:0.07268'),
+    standard_concentration = "unity")
+
+#------------------------------------------------------------------------------
+# Electron conductor
+#------------------------------------------------------------------------------
+metal(
+    name          = "electron",
+    elements      = "E",
+    species       = "electron",
+    density       = (1.0, 'kg/m3'), # dummy entry
+    initial_state = state( mole_fractions = "electron:1.0"))
+
+
+#==============================================================================
+#   Species
+#==============================================================================
+#------------------------------------------------------------------------------
+# Lithium intercalated in graphite, MW: 79.0070 g/mol.
+# Note this species includes the carbon host matrix.
+# Molar enthalpy and entropy are set to 0 because the values given in the
+# BinarySolidSolutionTabulatedThermo class are used.
+# Density of graphite: 2270 kg/m3 (W. M. Haynes et al, CRC Handbook of Chemistry
+# and Physics, 94th edition, CRC press, Boca Raton, London, New York, 2013)
+# (used to calculate species molar volume as molecular weight (MW)/density).
+#------------------------------------------------------------------------------
+species(
+    name          = "Li[anode]",
+    atoms         = "Li:1 C:6",
+    thermo        = const_cp(h0 = (0.0, 'kJ/mol'), s0 = (0.0, 'J/mol/K')),
+    standardState = constantIncompressible(molarVolume = (79.0070/2.270, 'cm3/mol')))
+
+#------------------------------------------------------------------------------
+# Vacancy in graphite, MW: 72.0660 g/mol.
+# Note this species includes the carbon host matrix.
+# Molar enthalpy and entropy are set to 0 because this is the reference species
+# for this phase.
+# Density of graphite: 2270 kg/m3 (W. M. Haynes et al, CRC Handbook of Chemistry
+# and Physics, 94th edition, CRC press, Boca Raton, London, New York, 2013)
+# (used to calculate species molar volume as molecular weight (MW)/density).
+#------------------------------------------------------------------------------
+species(
+    name          = "V[anode]",
+    atoms         = "C:6",
+    thermo        = const_cp(h0 = (0.0, 'kJ/mol'), s0 = (0.0, 'J/mol/K')),
+    standardState = constantIncompressible(molarVolume = (72.0660/2.270, 'cm3/mol')))
+
+#------------------------------------------------------------------------------
+# Lithium cobalt oxide, MW: 97.8730 g/mol.
+# Note this species includes the cobalt oxide host matrix.
+# Molar enthalpy and entropy are set to 0 because the values given in the
+# BinarySolidSolutionTabulatedThermo class are used.
+# Density of LCO: 4790 kg/m3 (E.J. Cheng et al., J. Asian Ceramic Soc. 5, 113,
+# 2017) (used to calculate species molar volume as molecular weight/density).
+#------------------------------------------------------------------------------
+species(
+    name          = "Li[cathode]",
+    atoms         = "Li:1 Co:1 O:2",
+    thermo        = const_cp(h0 = (0.0, 'kJ/mol'), s0 = (0.0, 'J/mol/K')),
+    standardState = constantIncompressible(molarVolume = (97.8730/4.790, 'cm3/mol')))
+
+#------------------------------------------------------------------------------
+# Vacancy in the cobalt oxide, MW: 90.9320 g/mol.
+# Note this species includes the cobalt oxide host matrix.
+# Molar enthalpy and entropy are set to 0 because this is the reference species
+# for this phase.
+# Density of LCO: 4790 kg/m3 (E.J. Cheng et al., J. Asian Ceramic Soc. 5, 113,
+# 2017) (used to calculate species molar volume as molecular weight/density).
+#------------------------------------------------------------------------------
+species(
+    name          = "V[cathode]",
+    atoms         = "Co:1 O:2",
+    thermo        = const_cp(h0 = (0.0, 'kJ/mol'), s0 = (0.0, 'J/mol/K')),
+    standardState = constantIncompressible(molarVolume = (90.9320/4.790, 'cm3/mol')))
+
+#------------------------------------------------------------------------------
+# Ethylene carbonate, MW: 88.0630 g/mol
+# Density of electrolyte: 1260 kg/m3 (used to calculate species molar volume
+# as molecular weight (MW)/density)
+# Molar enthalpy and entropy set to zero (dummy entries as this species does
+# not participate in chemical reactions)
+#------------------------------------------------------------------------------
+species(
+    name          = "C3H4O3[elyt]",
+    atoms         = "C:3 H:4 O:3",
+    thermo        = const_cp(h0 =(0.0, 'J/mol'), s0 = (0.0, 'J/mol/K')),
+    standardState = constantIncompressible(molarVolume = (88.0630/1.260, 'cm3/mol')))
+
+#------------------------------------------------------------------------------
+# Propylene carbonate, MW: 102.0898 g/mol
+# Density of electrolyte: 1260.0 kg/m3 (used to calculate species molar volume
+# as molecular weight (MW)/density)
+# Molar enthalpy and entropy set to zero (dummy entries as this species does
+# not participate in chemical reactions)
+#------------------------------------------------------------------------------
+species(
+    name          = "C4H6O3[elyt]",
+    atoms         = "C:4 H:6 O:3",
+    thermo        = const_cp(h0 =(0.0, 'J/mol'), s0 = (0.0, 'J/mol/K')),
+    standardState = constantIncompressible(molarVolume = (102.0898/1.260, 'cm3/mol')))
+
+#------------------------------------------------------------------------------
+# Lithium ion, MW: 6.940455 g/mol
+# Density of electrolyte: 1260.0 kg/m3 (used to calculate species molar volume
+# as molecular weight (MW)/density)
+# Molar enthalpy and entropy taken from Li+(aq) from P. Atkins "Physical
+# Chemistry", Wiley-VCH (2006)
+#------------------------------------------------------------------------------
+species(
+    name          = "Li+[elyt]",
+    atoms         = "Li:1 E:-1",
+    thermo        = const_cp(h0 = (-278.49, 'kJ/mol'), s0 = (13.4, 'J/mol/K')),
+    standardState = constantIncompressible(molarVolume = (6.940455/1.260, 'cm3/mol')))
+
+#------------------------------------------------------------------------------
+# Hexafluorophosphate ion, MW: 144.964745 g/mol
+# Density of electrolyte: 1260.0 kg/m3 (used to calculate species molar volume
+# as molecular weight (MW)/density)
+# Molar enthalpy and entropy set to zero (dummy entries as this species does
+# not participate in chemical reactions)
+#------------------------------------------------------------------------------
+species(
+    name          = "PF6-[elyt]",
+    atoms         = "P:1 F:6 E:1",
+    thermo        = const_cp(h0 = (0.0, 'J/mol'), s0 = (0.0, 'J/mol/K')),
+    standardState = constantIncompressible(molarVolume = (144.964745/1.260, 'cm3/mol')))
+
+#------------------------------------------------------------------------------
+# Electron, MW: 0.000545 g/mol
+# Molar enthalpy and entropy set to zero (dummy entries because chemical
+# potential is set to zero for a "metal" phase)
+#------------------------------------------------------------------------------
+species(
+    name   = "electron",
+    atoms  = "E:1",
+    thermo = const_cp(h0 = (0.0, 'kJ/mol'), s0 = (0.0, 'J/mol/K')))
+
+#------------------------------------------------------------------------------
+# Dummy species (needed for defining the interfaces)
+#------------------------------------------------------------------------------
+species(
+    name   = "(dummy)",
+    atoms  = "",
+    thermo = const_cp(h0 = (0.0, 'kJ/mol'), s0 = (0.0, 'J/mol/K')))
+
+
+#==============================================================================
+# Interfaces for electrochemical reactions
+#==============================================================================
+#------------------------------------------------------------------------------
+# Graphite/electrolyte interface
+# Species and site density are dummy entries (as we do not consider surface-
+# adsorbed species)
+#------------------------------------------------------------------------------
+ideal_interface(
+    name         = "edge_anode_electrolyte",
+    phases       = "anode electron electrolyte",
+    reactions    = "anode_*",
+    species      = "(dummy)",
+    site_density = (1.0e-2, 'mol/cm2'))
+
+#------------------------------------------------------------------------------
+# LCO/electrolyte interface
+# Species and site density are dummy entries (as we do not consider surface-
+# adsorbed species)
+#------------------------------------------------------------------------------
+ideal_interface(
+    name         = "edge_cathode_electrolyte",
+    phases       = "cathode electron electrolyte",
+    reactions    = "cathode_*",
+    species      = "(dummy)",
+    site_density = (1.0e-2, 'mol/cm2'))
+
+
+#==============================================================================
+# Electrochemical reactions
+#
+# We use Butler-Volmer kinetics by setting rate_coeff_type = "exchangecurrentdensity".
+# The preexponential factors and activation energies are converted from
+# Guo et al., J. Electrochem. Soc. 158, A122 (2011)
+#==============================================================================
+
+# Graphite/electrolyte interface
+edge_reaction("Li+[elyt] + V[anode] + electron <=> Li[anode]", [2.028e4, 0.0, (20, 'kJ/mol')], rate_coeff_type = "exchangecurrentdensity", beta = 0.5,id="anode_reaction")
+
+# LCO/electrolyte interface
+edge_reaction("Li+[elyt] + V[cathode] + electron <=> Li[cathode]", [5.629e11, 0.0, (58, 'kJ/mol')], rate_coeff_type = "exchangecurrentdensity", beta = 0.5,id="cathode_reaction")
+

data/inputs/sofc.cti

@@ -108,10 +108,10 @@ species( name = "electron",   atoms = "E:1",
 # consider the oxygen sublattice. The only species we define are a
 # lattice oxygen, and an oxygen vacancy. Again, the density is a
 # required input, but is not used here, so may be set arbitrarily.
-incompressible_solid(name = "oxide_bulk",
+lattice(name = "oxide_bulk",
       elements = "O E",
       species = "Ox VO**",
-      density = (0.7, 'g/cm3'),
+      site_density = (0.0176, 'mol/cm3'),
       initial_state = state( temperature = tt,
                              pressure = OneAtm,
                              mole_fractions = "Ox:0.95 VO**:0.05")

data/thermo/gri30_thermo.dat

@@ -0,0 +1,222 @@
+THERMO
+   300.000  1000.000  5000.000
+! GRI-Mech Version 3.0 Thermodynamics released 7/30/99
+! NASA Polynomial format for CHEMKIN-II
+! see README file for disclaimer
+O                 L 1/90O   1               G   200.000  3500.000  1000.000    1
+ 2.56942078E+00-8.59741137E-05 4.19484589E-08-1.00177799E-11 1.22833691E-15    2
+ 2.92175791E+04 4.78433864E+00 3.16826710E+00-3.27931884E-03 6.64306396E-06    3
+-6.12806624E-09 2.11265971E-12 2.91222592E+04 2.05193346E+00                   4
+O2                TPIS89O   2               G   200.000  3500.000  1000.000    1
+ 3.28253784E+00 1.48308754E-03-7.57966669E-07 2.09470555E-10-2.16717794E-14    2
+-1.08845772E+03 5.45323129E+00 3.78245636E+00-2.99673416E-03 9.84730201E-06    3
+-9.68129509E-09 3.24372837E-12-1.06394356E+03 3.65767573E+00                   4
+H                 L 7/88H   1               G   200.000  3500.000  1000.000    1
+ 2.50000001E+00-2.30842973E-11 1.61561948E-14-4.73515235E-18 4.98197357E-22    2
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+ 2.30081632E-18-9.27732332E-22 2.54736599E+04-4.46682853E-01                   4
+H2                TPIS78H   2               G   200.000  3500.000  1000.000    1
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+-9.50158922E+02-3.20502331E+00 2.34433112E+00 7.98052075E-03-1.94781510E-05    3
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+OH                RUS 78O   1H   1          G   200.000  3500.000  1000.000    1
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+-3.88113333E-09 1.36411470E-12 3.61508056E+03-1.03925458E-01                   4
+H2O               L 8/89H   2O   1          G   200.000  3500.000  1000.000    1
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+-5.48797062E-09 1.77197817E-12-3.02937267E+04-8.49032208E-01                   4
+HO2               L 5/89H   1O   2          G   200.000  3500.000  1000.000    1
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+-2.42763894E-08 9.29225124E-12 2.94808040E+02 3.71666245E+00                   4
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+-2.15770813E-08 8.62454363E-12-1.77025821E+04 3.43505074E+00                   4
+C                 L11/88C   1               G   200.000  3500.000  1000.000    1
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+-7.32234889E-10 2.66521446E-13 8.54438832E+04 4.53130848E+00                   4
+CH                TPIS79C   1H   1          G   200.000  3500.000  1000.000    1
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+CH2               L S/93C   1H   2          G   200.000  3500.000  1000.000    1
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+-3.85091153E-09 1.68741719E-12 4.60040401E+04 1.56253185E+00                   4
+CH2(S)            L S/93C   1H   2          G   200.000  3500.000  1000.000    1
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+-6.68815981E-09 1.94314737E-12 5.04968163E+04-7.69118967E-01                   4
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+-6.87117425E-09 2.54385734E-12 1.64449988E+04 1.60456433E+00                   4
+CH4               L 8/88C   1H   4          G   200.000  3500.000  1000.000    1
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+-4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00                   4
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+-1.33144093E-08 4.33768865E-12 3.83956496E+03 3.39437243E+00                   4
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+-3.79285261E-08 1.31772652E-11-1.43089567E+04 6.02812900E-01                   4
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+-0.07377636E-07 0.02075610E-10 0.09786011E+04 0.13152177E+02                   4
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+-0.21977499E-07 0.95149253E-11-0.13958520E+05 0.19201691E+02                   4
+C3H7              L 9/84C   3H   7          G   300.000  5000.000  1000.000    1
+ 0.77026987E+01 0.16044203E-01-0.52833220E-05 0.76298590E-09-0.39392284E-13    2
+ 0.82984336E+04-0.15480180E+02 0.10515518E+01 0.25991980E-01 0.23800540E-05    3
+-0.19609569E-07 0.93732470E-11 0.10631863E+05 0.21122559E+02                   4
+CH3CHO            L 8/88C   2H   4O   1     G   200.000  6000.000  1000.000    1
+ 0.54041108E+01 0.11723059E-01-0.42263137E-05 0.68372451E-09-0.40984863E-13    2
+-0.22593122E+05-0.34807917E+01 0.47294595E+01-0.31932858E-02 0.47534921E-04    3
+-0.57458611E-07 0.21931112E-10-0.21572878E+05 0.41030159E+01                   4
+CH2CHO            SAND86O   1H   3C   2     G   300.000  5000.000  1000.000    1
+ 0.05975670E+02 0.08130591E-01-0.02743624E-04 0.04070304E-08-0.02176017E-12    2
+ 0.04903218E+04-0.05045251E+02 0.03409062E+02 0.10738574E-01 0.01891492E-04    3
+-0.07158583E-07 0.02867385E-10 0.15214766E+04 0.09558290E+02                   4
+END
+
+
+
+

data/thermo/nasathermo.dat

@@ -1849,7 +1849,7 @@ LiO               J 3/64LI 1.O  1.   0.   0.G   300.000  5000.000     22.94040 1
 LiO-              J12/67LI 1.O  1.E  1.   0.G   300.000  5000.000     22.94095 1
  4.18102170E+00 4.17850000E-04-1.50248450E-07 2.83977320E-11-1.97891810E-15    2
 -9.38497020E+03-1.42392337E-01 2.85158660E+00 5.01698800E-03-5.95474750E-06    3
- 03994510E-09-4.78729690E-13-9.07780760E+03 6.45947067E+00-8.05144594E+03    4
+ 3.03994510E-09-4.78729690E-13-9.07780760E+03 6.45947067E+00-8.05144594E+03    4
 LiOH              J 6/71LI 1.O  1.H  1.   0.G   300.000  5000.000     23.94834 1
  5.50969570E+00 1.36854640E-03-3.94414690E-07 5.23321950E-11-2.59586760E-15    2
 -2.98992310E+04-6.50701600E+00 3.34623000E+00 1.17872530E-02-1.82526570E-05    3

doc/SConscript

@@ -1,5 +1,5 @@
+from __future__ import print_function
 from buildutils import *
-import ast
 
 Import('env', 'build', 'install')
 
@@ -8,37 +8,6 @@ localenv = env.Clone()
 from collections import namedtuple
 Page = namedtuple('Page', ['name', 'title', 'objects'])
 
-def extract_python_docstring(pyfile, summary_only=True):
-    """ Returns the docstring from a Python script """
-    with open(pyfile) as f:
-        mod = ast.parse(f.read())
-    doc = ''
-    for node in mod.body:
-        if isinstance(node, ast.Expr) and isinstance(node.value, ast.Str):
-            doc = node.value.s
-
-    doc = doc.strip()
-
-    if summary_only:
-        doc = doc.split('\n\n')[0]
-
-    return doc
-
-def extract_matlab_summary(mfile):
-    """ Returns a one-line summary comment from a .m file """
-    doc = ''
-    with open(mfile) as f:
-        for line in f:
-            line = line.strip()
-            if line.startswith('%'):
-                doc = line.strip('%').strip()
-            if doc:
-                break
-    name = os.path.basename(mfile)[:-2].replace('_', ' ')
-    if doc.lower().replace('_', ' ').startswith(name):
-        doc = doc[len(name):].strip()
-    return doc
-
 
 # Set up functions to pseudo-autodoc the MATLAB toolbox
 def extract_matlab_docstring(mfile, level):
@@ -60,7 +29,7 @@ def extract_matlab_docstring(mfile, level):
     elif level == 1:
         docstring = "    .. mat:function:: "
     else:
-        print "Unknown level for MATLAB documentation."
+        print("Unknown level for MATLAB documentation.")
         sys.exit(1)
 
     # The leader is the number of spaces at the beginning of a regular line
@@ -99,9 +68,10 @@ def extract_matlab_docstring(mfile, level):
 
     return docstring + '\n'
 
+
 def get_function_name(str):
     """
-        Return the function or classdef signature, assuming that
+        Return the Matlab function or classdef signature, assuming that
         the string starts with either 'function ' or 'classdef '.
     """
     if str.startswith('function '):
@@ -109,7 +79,7 @@ def get_function_name(str):
     elif str.startswith('classdef '):
         sig = str[len('classdef '):]
     else:
-        print "Unknown function declaration in MATLAB document", str
+        print("Unknown function declaration in MATLAB document", str)
 
     # Split the function signature on the equals sign, if it exists.
     # We don't care about what comes before the equals sign, since
@@ -130,8 +100,8 @@ if localenv['doxygen_docs']:
                       mglob(env, '#src/cantera/*', 'h', 'cpp'))
 
     env.Alias('doxygen', docs)
-    install('$inst_docdir/doxygen/html',
-            mglob(localenv, '#/build/docs/doxygen/html', 'html', 'svg', 'css', 'png'))
+    install(localenv.RecursiveInstall, '$inst_docdir/doxygen/html',
+            '#/build/docs/doxygen/html', exclude=['\\.map', '\\.md5'])
 
 if localenv['sphinx_docs']:
     localenv['SPHINXBUILD'] = Dir('#build/docs/sphinx')
@@ -142,78 +112,44 @@ if localenv['sphinx_docs']:
         '${sphinx_cmd} -b html -d ${SPHINXBUILD}/doctrees ${SPHINXSRC} ${SPHINXBUILD}/html'))
     env.Alias('sphinx', sphinxdocs)
 
-    # Python examples: Create individual documentation pages with the source
-    # for each example
-    example_root = Dir('#interfaces/cython/cantera/examples').abspath
-    indexenv = env.Clone()
-    for subdir in subdirs(example_root):
-        summaries = []
-        for f in mglob(env, pjoin(example_root, subdir), 'py'):
-            docname = 'examples/{0}_{1}'.format(subdir, f.name[:-3])
-            summaries.append(':doc:`{0} <{1}>`:'.format(f.name, docname))
-            summaries.append(extract_python_docstring(f.abspath))
-            summaries.append('')
-
-            tmpenv = env.Clone()
-            tmpenv['script_name'] = f.name
-            tmpenv['script_path'] = '../../../../interfaces/cython/cantera/examples/%s/%s' % (subdir, f.name)
-            b = tmpenv.SubstFile('#doc/sphinx/cython/{0}.rst'.format(docname),
-                                 '#doc/sphinx/cython/example-script.rst.in')
-            build(b)
-            localenv.Depends(sphinxdocs, b)
-        indexenv['python_{0}_examples'.format(subdir)] = '\n'.join(summaries)
-    b = indexenv.SubstFile('#doc/sphinx/cython/examples.rst',
-                           '#doc/sphinx/cython/examples.rst.in')
-    build(b)
-    localenv.Depends(sphinxdocs, b)
-
     # Create a list of MATLAB classes to document. This uses the NamedTuple
     # structure defined at the top of the file. The @Data and @Utilities
     # classes are fake classes for the purposes of documentation only. Each
     # Page represents one html page of the documentation.
     pages = [
-        Page('importing', 'Importing Phase Objects',
-             ['@Solution', '@Mixture',]
-        ),
+        Page('importing', 'Objects Representing Phases',
+             ['@Solution', '@Mixture', '@Interface', '@Pure Fluid Phases']),
         Page('thermodynamics', 'Thermodynamic Properties',
-             ['@ThermoPhase']
-        ),
+             ['@ThermoPhase']),
         Page('kinetics', 'Chemical Kinetics', ['@Kinetics']),
         Page('transport', 'Transport Properties', ['@Transport']),
         Page('zero-dim', 'Zero-Dimensional Reactor Networks',
-             ['@Func', '@Reactor', '@ReactorNet', '@FlowDevice', '@Wall']
-        ),
-        Page('one-dim', 'One-Dimensional Reacting Flows',
-             ['1D/@Domain1D', '1D/@Stack']
-         ),
-        Page('data', 'Built-In Thermochemical Data',
-             ['@Data']
-        ),
-        Page('utilities', 'Utility Functions',
-             ['@Utilities', '@XML_Node']
-        ),
-        Page('interface', 'Interfaces', ['@Interface']),
+             ['@Func', '@Reactor', '@ReactorNet', '@FlowDevice', '@Wall']),
+        Page('one-dim', 'One-Dimensional Reacting Flows', ['1D/@Domain1D', '1D/@Stack']),
+        Page('data', 'Physical Constants', ['@Data']),
+        Page('utilities', 'Utility Functions', ['@Utilities', '@XML_Node']),
     ]
 
     # Create a dictionary of extra files associated with each class. These
     # files are listed relative to the top directory interfaces/matlab/cantera
     extra = {
-        '@Solution': ['IdealGasMix.m', 'importPhase.m',],
+        '@Solution': ['IdealGasMix.m', 'GRI30.m', 'Air.m'],
+        '@Pure Fluid Phases': ['CarbonDioxide.m', 'HFC134a.m', 'Hydrogen.m',
+                               'Methane.m', 'Nitrogen.m', 'Oxygen.m', 'Water.m'],
         '@Func': ['gaussian.m', 'polynom.m'],
         '@Reactor': ['ConstPressureReactor.m',
-                  'FlowReactor.m', 'IdealGasConstPressureReactor.m',
-                  'IdealGasReactor.m', 'Reservoir.m'],
+                     'FlowReactor.m', 'IdealGasConstPressureReactor.m',
+                     'IdealGasReactor.m', 'Reservoir.m'],
         '@FlowDevice': ['MassFlowController.m', 'Valve.m'],
         '1D/@Domain1D': ['1D/AxiStagnFlow.m', '1D/AxisymmetricFlow.m',
-                      '1D/Inlet.m', '1D/Outlet.m', '1D/OutletRes.m',
-                      '1D/Surface.m', '1D/SymmPlane.m'],
-        '1D/@Stack': ['1D/FreeFlame.m', '1D/npflame_init.m'],
+                         '1D/Inlet.m', '1D/Outlet.m', '1D/OutletRes.m',
+                         '1D/Surface.m', '1D/SymmPlane.m'],
+        '1D/@Stack': ['1D/FreeFlame.m', '1D/CounterFlowDiffusionFlame.m'],
         '@Interface': ['importEdge.m', 'importInterface.m'],
-        '@Data': ['Air.m', 'constants.m', 'gasconstant.m', 'GRI30.m',
-             'Hydrogen.m', 'Methane.m', 'Nitrogen.m', 'oneatm.m',
-             'Oxygen.m', 'Water.m'],
+        '@Data': ['gasconstant.m', 'oneatm.m'],
         '@Utilities': ['adddir.m', 'ck2cti.m', 'cleanup.m', 'geterr.m',
-                       'getDataDirectories.m', 'canteraVersion.m']
+                       'getDataDirectories.m', 'canteraVersion.m',
+                       'canteraGitCommit.m']
     }
 
     # These files do not need to be documented in the MATLAB classes because they
@@ -228,7 +164,7 @@ if localenv['sphinx_docs']:
 
         # Set the title header
         title = page.title
-        tempenv['title'] =  '='*len(title) + '\n' + title + '\n' + '='*len(title)
+        tempenv['title'] = '='*len(title) + '\n' + title + '\n' + '='*len(title)
         doc = ''
 
         # The base directory of the MATLAB toolbox relative to the sphinx build directory
@@ -263,35 +199,11 @@ if localenv['sphinx_docs']:
         # every time the source is changed, we don't want to have to commit the
         # change in the rst file as well as the source - too much code churn. So
         # we use a template and a SubstFile directive.
-        c = tempenv.SubstFile('#doc/sphinx/matlab/code-docs/%s.rst' % page.name,
-                          '#doc/sphinx/matlab/matlab-template.rst.in')
+        c = tempenv.SubstFile('#doc/sphinx/matlab/%s.rst' % page.name,
+                              '#doc/sphinx/matlab/matlab-template.rst.in')
         build(c)
         localenv.Depends(sphinxdocs, c)
 
-    # Matlab examples: create individual documentation pages with the source
-    # for each example
-    examples = []
-    tutorials = []
-    for f in mglob(env, '#samples/matlab', 'm'):
-        tmpenv = env.Clone()
-        tmpenv['script_name'] = f.name
-        tmpenv['script_path'] = '../../../../samples/matlab/%s' % f.name
-        b = tmpenv.SubstFile('#doc/sphinx/matlab/examples/%s.rst' % f.name[:-2],
-                             '#doc/sphinx/matlab/example-script.rst.in')
-        build(b)
-        localenv.Depends(sphinxdocs, b)
-        summary = [':doc:`{0} <examples/{1}>`:'.format(f.name, f.name[:-2]),
-                   extract_matlab_summary(f.abspath),
-                   '']
-        if f.name.startswith('tut'):
-            tutorials.extend(summary)
-        else:
-            examples.extend(summary)
-
-    localenv['matlab_tutorials'] = '\n'.join(tutorials)
-    localenv['matlab_examples'] = '\n'.join(examples)
-    b = localenv.SubstFile('#doc/sphinx/matlab/examples.rst',
-                           '#doc/sphinx/matlab/examples.rst.in')
-    build(b)
-    localenv.Depends(sphinxdocs, b)
     localenv.AlwaysBuild(sphinxdocs)
+    install(localenv.RecursiveInstall, '$inst_docdir/sphinx/html',
+            '#/build/docs/sphinx/html')

doc/doxygen/Doxyfile

@@ -15,7 +15,7 @@
 #---------------------------------------------------------------------------
 
 USE_MATHJAX           = YES
-MATHJAX_RELPATH       = https://cdn.mathjax.org/mathjax/latest
+MATHJAX_RELPATH       = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5
 
 # This tag specifies the encoding used for all characters in the config file
 # that follow. The default is UTF-8 which is also the encoding used for all
@@ -34,13 +34,7 @@ PROJECT_NAME           = Cantera
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 2.3.0
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
-
+PROJECT_NUMBER         = 2.5.0a3
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.
@@ -56,7 +50,7 @@ OUTPUT_DIRECTORY       = build/docs/doxygen
 # source files, where putting all generated files in the same directory would
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = NO
+CREATE_SUBDIRS         = YES
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all
 # documentation generated by doxygen is written. Doxygen will use this
@@ -624,7 +618,7 @@ EXCLUDE_SYMLINKS       = NO
 # against the file with absolute path, so to exclude all test directories
 # for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       = */build/*
+EXCLUDE_PATTERNS       =
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -640,8 +634,7 @@ EXCLUDE_SYMBOLS        = std::*
 
 EXAMPLE_PATH           = samples \
                          data/inputs \
-                         doc/doxygen \
-                         doc/sphinx/cxx-guide
+                         doc/doxygen
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
@@ -1170,7 +1163,7 @@ MAN_LINKS              = NO
 # generate an XML file that captures the structure of
 # the code including all documentation.
 
-GENERATE_XML           = NO
+GENERATE_XML           = YES
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be

doc/doxygen/thermoprops.dox

@@ -89,13 +89,9 @@
  *   class listed above. These classes assume that there exists a standard state
  *   for each species in the phase, where the Thermodynamic functions are specified
  *   as a function of temperature and pressure.  Standard state objects for each
- *   species are all derived from the PDSS virtual base class. Calculators for these
- *   standard state, which coordinate the calculation for all of the species
- *   in a phase, are all derived from the virtual base class VPSSMgr.
- *   In turn, these standard states may employ reference state calculation to
- *   aid in their calculations. And the VPSSMgr calculators may also employ
- *   SimpleThermo calculators to help in calculating the properties for all of the
- *   species in a phase. However, there are some PDSS objects which do not employ
+ *   species are all derived from the PDSS virtual base class. In turn, these
+ *   standard states may employ reference state calculation to aid in their
+ *   calculations. However, there are some PDSS objects which do not employ
  *   reference state calculations. An example of this is real equation of state for
  *   liquid water used within the calculation of brine thermodynamics.
  *   In general, the independent variables that completely describe the state of the
@@ -497,15 +493,6 @@
  *  pick a manager, i.e., a derivative of the SpeciesThermo
  *  object, to use.
  *
- *  If a temperature and pressure dependent standard state is needed
- *  then a call to VPSSMgrFactory::newVPSSMgr()
- *  is made in order
- *  pick a manager, i.e., a derivative of the VPSSMgr
- *  object, to use. Along with the VPSSMgr designation comes a
- *  determination of whether there is an accompanying  SpeciesThermo
- *  and what type of SpeciesThermo object to use in the
- *  VPSSMgr calculations.
- *
  *  Once these determinations are made, the %ThermoPhase object is
  *  ready to start reading in the species information, which includes
  *  all of the available standard state information about the
@@ -524,16 +511,9 @@
  *  call to read the XML data from the input file and install the
  *  correct  SpeciesThermoInterpType object into the SpeciesThermo object.
  *
- *  Within installSpecies(), for standard states, the routine,
- *  SpeciesThermoFactory::installVPThermoForSpecies() is
- *  called. However, this is just a shell routine for calling
- *  the VPSSMgr's derived VPSSMgr::createInstallPDSS() routine.
- *  Within the  VPSSMgr::createInstallPDSS() routine of the derived VPSSMgr's
- *  object, the XML data from the input file is read and the
- *  calculations for the species standard state is installed.
- *  Additionally, the  derived PDSS object is created and installed
- *  into the VPStandardStateTP list containing all of the PDSS objects
- *  for that phase.
+ *  Within installSpecies(), for standard states, derived PDSS object is created
+ *  and installed into the VPStandardStateTP list containing all of the PDSS
+ *  objects for that phase.
  *
  *  Now that all of the species standard states are read in and
  *  installed into the ThermoPhase object, control once again
@@ -574,9 +554,6 @@
  *  In general, factory routines throw specific errors when encountering
  *  unknown thermodynamics models in XML files. All of the error classes
  *  derive from the class, CanteraError.
- *  The newVPSSMgr() routines throws the UnknownVPSSMgr class error when
- *  they encounter an unknown string in the XML input file specifying the
- *  VPSSMgr class to use.
  *
  *  Many of the important member functions in factory routines are
  *  virtual classes. This means that a user may write their own

doc/sphinx/_templates/layout.html

@@ -1,10 +1,162 @@
-{% extends "!layout.html" %}
-
-
-{% block relbar1 %}
-<div style="background-color: white; text-align: left; padding: 10px 10px 15px 15px">
-<a href="{{ pathto('index') }}">
-<img src="{{pathto("_static/cantera-logo.png", 1) }}" border="0" alt="Cantera"/></a>
-</div>
-{{ super() }}
+{%- set render_sidebar = (not embedded) and (not theme_nosidebar|tobool) and (sidebars != []) %}
+{% block doctype %}
+<!DOCTYPE html>
 {% endblock %}
+<html prefix="
+og: http://ogp.me/ns# article: http://ogp.me/ns/article#
+"
+lang="en">
+
+{%- macro script() %}
+    <script type="text/javascript" id="documentation_options" data-url_root="{{ pathto('', 1) }}" src="{{ pathto('_static/documentation_options.js', 1) }}"></script>
+    {%- for scriptfile in script_files %}
+    {%- if scriptfile.startswith("https://cdn.jsdelivr.net") %}
+        <script defer type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
+    {%- else %}
+        <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
+    {%- endif %}
+    {%- endfor %}
+{%- endmacro %}
+
+
+{%- macro css() %}
+  <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.1.2/css/bootstrap.min.css" media="none" onload="this.media='all'" integrity="sha384-Smlep5jCw/wG7hdkwQ/Z5nLIefveQRIY9nfy6xoR1uRYBtpZgI6339F5dgvm/e9B" crossorigin="anonymous" />
+  <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" />
+  <link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css" />
+  {%- for css in css_files %}
+    {%- if css|attr("rel") %}
+  <link rel="{{ css.rel }}" href="{{ pathto(css.filename, 1) }}" media="none" onload="this.media='all'" type="text/css"{% if css.title is not none %} title="{{ css.title }}"{% endif %} />
+    {%- else %}
+  <link rel="stylesheet" href="{{ pathto(css, 1) }}" media="none" onload="this.media='all'" type="text/css" />
+    {%- endif %}
+  {%- endfor %}
+{%- endmacro %}
+
+{%- macro sidebar() %}
+  {%- if render_sidebar %}
+  <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+    <div class="sphinxsidebarwrapper">
+    {%- for sidebartemplate in sidebars %}
+    {%- include sidebartemplate %}
+    {%- endfor %}
+    </div>
+  </div>
+  {%- endif %}
+{%- endmacro %}
+
+  <head>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <title>{{ title|e }} | Cantera </title>
+
+    {%- block csss %}
+    {{- css() }}
+    {%- endblock %}
+    {%- if not embedded %}
+    {%- block scripts %}
+    {{- script() }}
+    {%- endblock %}
+    {%- if use_opensearch %}
+    <link rel="search" type="application/opensearchdescription+xml"
+          title="{% trans docstitle=docstitle|e %}Search within {{ docstitle }}{% endtrans %}"
+          href="{{ pathto('_static/opensearch.xml', 1) }}"/>
+    {%- endif %}
+    <link rel="shortcut icon" href="/assets/img/favicon.ico" sizes="16x16"/>
+    {%- endif %}
+    {% if theme_canonical_url %}
+      <link rel="canonical" href="{{ theme_canonical_url }}{{ pagename }}.html"/>
+    {% endif %}
+    {%- if hasdoc('search') %}
+    <link rel="search" title="{{ _('Search') }}" href="{{ pathto('search') }}" />
+    {%- endif %}
+    {%- if hasdoc('copyright') %}
+    <link rel="copyright" title="{{ _('Copyright') }}" href="{{ pathto('copyright') }}" />
+    {%- endif %}
+    {%- block extrahead %} {% endblock %}
+  </head>
+  <body>
+  <a href="#content" class="sr-only sr-only-focusable">Skip to main content</a>
+
+  <!-- Menubar -->
+
+  <nav class="navbar navbar-expand-md navbar-light bg-light static-top mb-4">
+      <div class="container"><!-- This keeps the margins nice -->
+          <a class="navbar-brand" href="/index.html">
+          <img src="/assets/img/cantera-logo.png" alt="Cantera" id="logo" class="d-inline-block align-top">
+          </a>
+          <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#bs-navbar" aria-controls="bs-navbar" aria-expanded="false" aria-label="Toggle navigation">
+              <span class="navbar-toggler-icon"></span>
+          </button>
+
+          <div class="collapse navbar-collapse" id="bs-navbar">
+            <ul class="navbar-nav ml-auto">
+              <li class="nav-item">
+                <a href="/install/index.html" class="nav-link">Install</a>
+              </li>
+              <li class="nav-item">
+                <a href="/tutorials/index.html" class="nav-link">Tutorials</a>
+              </li>
+              <li class="nav-item">
+                <a href="/examples/index.html" class="nav-link">Examples</a>
+              </li>
+              <li class="nav-item">
+                <a href="/community.html" class="nav-link">Community</a>
+              </li>
+              <li class="nav-item">
+                <a href="/science/index.html" class="nav-link">Science</a>
+              </li>
+              <li class="nav-item">
+                <a href="/documentation/index.html" class="nav-link">Documentation</a>
+              </li>
+              <li class="nav-item">
+                <a href="/blog/index.html" class="nav-link">Blog</a>
+              </li>
+            </ul>
+          </div><!-- /.navbar-collapse -->
+      </div><!-- /.container -->
+  </nav>
+  <!-- End of Menubar -->
+
+  <div class="container" id="content">
+      <div class="body-content">
+          <!--Body content-->
+          {% block content %}
+          <div class="document">
+            {% block document %}
+            <div class="documentwrapper">
+              {%- if render_sidebar %}
+                <div class="bodywrapper">
+              {%- endif %}
+                <div class="body" role="main">
+                  {% block body %} {% endblock %}
+                </div>
+              {%- if render_sidebar %}
+                </div>
+              {%- endif %}
+            </div>
+            {% endblock %} <!-- end of block document -->
+            {%- block sidebar2 %}{{ sidebar() }}{% endblock %}
+                <div class="clearer"></div>
+          </div>
+          {% endblock %} <!--End of block content-->
+
+          <div class="footer">
+            {% if show_copyright %}&copy;{{ copyright }}.{% endif %}
+            {% if theme_show_powered_by|lower == 'true' %}
+            {% if show_copyright %}|{% endif %}
+            Powered by <a href="http://sphinx-doc.org/">Sphinx {{ sphinx_version }}</a>
+            &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster {{ alabaster_version }}</a>
+            {% endif %}
+            {%- if show_source and has_source and sourcename %}
+            {% if show_copyright or theme_show_powered_by %}|{% endif %}
+            <a href="{{ pathto('_sources/' + sourcename, true)|e }}"
+                rel="nofollow">{{ _('Page source') }}</a>
+            {%- endif %}
+          </div>
+      </div>
+  </div>
+
+  <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.3/umd/popper.min.js" integrity="sha256-98vAGjEDGN79TjHkYWVD4s87rvWkdWLHPs5MC3FvFX4=" crossorigin="anonymous"></script>
+  <script async="async" src="https://maxcdn.bootstrapcdn.com/bootstrap/4.1.2/js/bootstrap.min.js" integrity="sha384-o+RDsa0aLu++PJvFqy8fFScvbHFLtbvScb8AjopnFD+iEQ7wo/CG0xlczd+2O/em" crossorigin="anonymous"></script>
+</body>
+</html>

doc/sphinx/_templates/numfocus.html

@@ -0,0 +1,5 @@
+<div id="numfocus">
+<h3>Donate to Cantera</h3>
+<a href="https://numfocus.salsalabs.org/donate-to-cantera/index.html">
+<img src="{{pathto("_static/powered_by_NumFOCUS.png", 1) }}" border="0" alt="NumFOCUS"/></a>
+</div>

doc/sphinx/compiling/config-options.rst

@@ -1,523 +0,0 @@
-
-.. _scons-config:
-
-*********************
-Configuration Options
-*********************
-
-This document lists the options available for compiling Cantera with SCons. The
-default values are operating-system dependent. To see the defaults for your
-current operating system, run the command::
-
-    scons help
-
-from the command prompt.
-
-The following options can be passed to SCons to customize the Cantera
-build process. They should be given in the form::
-
-        scons build option1=value1 option2=value2
-
-Variables set in this way will be stored in the ``cantera.conf`` file and reused
-automatically on subsequent invocations of SCons. Alternatively, the
-configuration options can be entered directly into ``cantera.conf`` before
-running ``scons build``. The format of this file is::
-
-    option1 = 'value1'
-    option2 = 'value2'
-
-Options List
-^^^^^^^^^^^^
-
-.. _msvc-version:
-
-* ``msvc_version``: [ ``string`` ]
-    Version of Visual Studio to use. The default is the newest
-    installed version. Specify ``12.0`` for Visual Studio 2013 or ``14.0``
-    for Visual Studio 2015. Windows MSVC only.
-
-    - default: ``''``
-
-.. _target-arch:
-
-* ``target_arch``: [ ``string`` ]
-    Target architecture. The default is the same architecture as the
-    installed version of Python. Windows only.
-
-    - default: ``''``
-
-.. _toolchain:
-
-* ``toolchain``: [ ``msvc`` | ``mingw`` | ``intel`` ]
-    The preferred compiler toolchain. Windows only.
-
-    - default: ``'msvc'``
-
-.. _CXX:
-
-* ``CXX``: [ ``string`` ]
-    The C++ compiler to use.
-
-    - default: ``''``
-
-.. _CC:
-
-* ``CC``: [ ``string`` ]
-    The C compiler to use. This is only used to compile CVODE.
-
-    - default: ``''``
-
-.. _prefix:
-
-* ``prefix``: [ ``/path/to/prefix`` ]
-    Set this to the directory where Cantera should be installed.
-
-    - default: ``''``
-
-.. _python-package:
-
-* ``python_package``: [ ``new`` | ``full`` | ``minimal`` | ``none`` | ``default`` ]
-    If you plan to work in Python 2, then you need the ``full`` Cantera Python
-    package. If, on the other hand, you will only use Cantera from some
-    other language (e.g. MATLAB or Fortran 90/95) and only need Python
-    to process CTI files, then you only need a ``minimal`` subset of the
-    package and Cython and NumPy are not necessary. The ``none`` option
-    doesn't install any components of the Python interface. The default
-    behavior is to build the full Python 2 module if the required
-    prerequisites (NumPy and Cython) are installed.
-
-    - default: ``'default'``
-
-.. _python-cmd:
-
-* ``python_cmd``: [ ``/path/to/python_cmd`` ]
-    Cantera needs to know where to find the Python interpreter. If the
-    ``python_cmd`` option is not set, then the configuration
-    process will use the same Python interpreter being used by SCons.
-
-    - default: ``''``
-
-.. _python-array-home:
-
-* ``python_array_home``: [ ``/path/to/python_array_home`` ]
-    If NumPy was installed using the ``--home`` option, set this to the home
-    directory for NumPy for Python 2.
-
-    - default: ``''``
-
-.. _python-prefix:
-
-* ``python_prefix``: [ ``/path/to/python_prefix`` ]
-    Use this option if you want to install the Cantera Python 2 package to
-    an alternate location. On Unix-like systems, the default is the same
-    as the ``prefix`` option. If the ``python_prefix`` option is set to
-    the empty string or the ``prefix`` option is not set, then the package
-    will be installed to the system default ``site-packages`` directory.
-    To install to the current user's ``site-packages`` directory, use
-    ``python_prefix=USER``.
-
-    - default: ``''``
-
-.. _python3-package:
-
-* ``python3_package``: [ ``y`` | ``n`` | ``default`` ]
-    Controls whether or not the Python 3 module will be built. By
-    default, the module will be built if the Python 3 interpreter
-    and the required dependencies (NumPy for Python 3 and Cython
-    for the version of Python for which SCons is installed) can be
-    found.
-
-    - default: ``'default'``
-
-.. _python3-cmd:
-
-* ``python3_cmd``: [ ``/path/to/python3_cmd`` ]
-    The path to the Python 3 interpreter. The default is
-    ``python3``; if this executable cannot be found, this
-    value must be specified to build the Python 3 module.
-
-    - default: ``'python3'``
-
-.. _python3-array-home:
-
-* ``python3_array_home``: [ ``/path/to/python3_array_home`` ]
-    If NumPy was installed using the ``--home`` option, set this to the home
-    directory for NumPy for Python 3.
-
-    - default: ``''``
-
-.. _python3-prefix:
-
-* ``python3_prefix``: [ ``/path/to/python3_prefix`` ]
-    Use this option if you want to install the Cantera Python 3 package to
-    an alternate location. On Unix-like systems, the default is the same
-    as the ``prefix`` option. If the ``python_prefix`` option is set to
-    the empty string or the ``prefix`` option is not set, then the package
-    will be installed to the system default ``site-packages`` directory.
-    To install to the current user's ``site-packages`` directory, use
-    ``python_prefix=USER``.
-
-    - default: ``''``
-
-.. _matlab-toolbox:
-
-* ``matlab_toolbox``: [ ``y`` | ``n`` | ``default`` ]
-    This variable controls whether the MATLAB toolbox will be built. If
-    set to ``y``, you will also need to set the value of the ``matlab_path``
-    variable. If ``matlab_toolbox`` is set to ``default``, the MATLAB toolbox
-    will be built if ``matlab_path`` is set.
-
-    - default: ``'default'``
-
-.. _matlab-path:
-
-* ``matlab_path``: [ ``/path/to/matlab_path`` ]
-    Path to the MATLAB install directory. This should be the directory
-    containing the ``extern``, ``bin``, etc. subdirectories. Typical values
-    are: ``C:/Program Files/MATLAB/R2011a`` on Windows,
-    ``/Applications/MATLAB_R2011a.app`` on OS X, or ``/opt/MATLAB/R2011a``
-    on Linux.
-
-    - default: ``''``
-
-.. _f90-interface:
-
-* ``f90_interface``: [ ``y`` | ``n`` | ``default`` ]
-    This variable controls whether the Fortran 90/95 interface will be
-    built. If set to ``default``, the builder will look for a compatible
-    Fortran compiler in the ``PATH`` environment variable, and compile
-    the Fortran 90 interface if one is found.
-
-    - default: ``'default'``
-
-.. _FORTRAN:
-
-* ``FORTRAN``: [ ``/path/to/FORTRAN`` ]
-    The Fortran (90) compiler. If unspecified, the builder will look for
-    a compatible compiler (gfortran, ifort, g95) in the ``PATH`` environment
-    variable. Used only for compiling the Fortran 90 interface.
-
-    - default: ``''``
-
-.. _FORTRANFLAGS:
-
-* ``FORTRANFLAGS``: [ ``string`` ]
-    Compilation options for the Fortran (90) compiler.
-
-    - default: ``'-O3'``
-
-.. _coverage:
-
-* ``coverage``: [ ``yes`` | ``no`` ]
-    Enable collection of code coverage information with gcov. Available
-    only when compiling with gcc.
-
-    - default: ``'no'``
-
-.. _doxygen-docs:
-
-* ``doxygen_docs``: [ ``yes`` | ``no`` ]
-    Build HTML documentation for the C++ interface using Doxygen.
-
-    - default: ``'no'``
-
-.. _sphinx-docs:
-
-* ``sphinx_docs``: [ ``yes`` | ``no`` ]
-    Build HTML documentation for Cantera using Sphinx.
-
-    - default: ``'no'``
-
-.. _sphinx-cmd:
-
-* ``sphinx_cmd``: [ ``/path/to/sphinx_cmd`` ]
-    Command to use for building the Sphinx documentation.
-
-    - default: ``'sphinx-build'``
-
-.. _system-eigen:
-
-* ``system_eigen``: [ ``default`` | ``y`` | ``n`` ]
-    Select whether to use Eigen from a system installation (``y``), from a
-    Git submodule (``n``), or to decide automatically (``default``). If
-    Eigen is not installed directly into a system include directory,
-    e.g. it is installed in ``/opt/include/eigen3/Eigen``, then you will
-    need to add ``/opt/include/eigen3`` to the ``extra_inc_dirs`` option.
-
-    - default: ``'default'``
-
-.. _system-fmt:
-
-* ``system_fmt``: [ ``default`` | ``y`` | ``n`` ]
-    Select whether to use the fmt library from a system installation
-    (``y``), from a Git submodule (``n``), or to decide automatically
-    (``default``).
-
-    - default: ``'default'``
-
-.. _system-sundials:
-
-* ``system_sundials``: [ ``default`` | ``y`` | ``n`` ]
-    Select whether to use SUNDIALS from a system installation (``y``),
-    from a Git submodule (``n``), or to decide automatically (``default``).
-    Specifying ``sundials_include`` or ``sundials_libdir`` changes the
-    default to ``y``.
-
-    - default: ``'default'``
-
-.. _sundials-include:
-
-* ``sundials_include``: [ ``/path/to/sundials_include`` ]
-    The directory where the SUNDIALS header files are installed. This
-    should be the directory that contains the ``cvodes``, ``nvector``, etc.
-    subdirectories. Not needed if the headers are installed in a
-    standard location, e.g., ``/usr/include``.
-
-    - default: ``''``
-
-.. _sundials-libdir:
-
-* ``sundials_libdir``: [ ``/path/to/sundials_libdir`` ]
-    The directory where the SUNDIALS static libraries are installed. Not
-    needed if the libraries are installed in a standard location, e.g.,
-    ``/usr/lib``.
-
-    - default: ``''``
-
-.. _blas-lapack-libs:
-
-* ``blas_lapack_libs``: [ ``string`` ]
-    Cantera can use BLAS and LAPACK libraries available on your system
-    if you have optimized versions available (e.g., Intel MKL).
-    Otherwise, Cantera will use Eigen for linear algebra support. To use
-    BLAS and LAPACK, set ``blas_lapack_libs`` to the the list of libraries
-    that should be passed to the linker, separated by commas, e.g.,
-    ``"lapack,blas"`` or ``"lapack,f77blas,cblas,atlas"``.
-
-    - default: ``''``
-
-.. _blas-lapack-dir:
-
-* ``blas_lapack_dir``: [ ``/path/to/blas_lapack_dir`` ]
-    Directory containing the libraries specified by ``blas_lapack_libs``. Not
-    needed if the libraries are installed in a standard location, e.g.
-    ``/usr/lib``.
-
-    - default: ``''``
-
-.. _lapack-names:
-
-* ``lapack_names``: [ ``lower`` | ``upper`` ]
-    Set depending on whether the procedure names in the specified
-    libraries are lowercase or uppercase. If you don't know, run ``nm`` on
-    the library file (e.g., ``nm libblas.a``).
-
-    - default: ``'lower'``
-
-.. _lapack-ftn-trailing-underscore:
-
-* ``lapack_ftn_trailing_underscore``: [ ``yes`` | ``no`` ]
-    Controls whether the LAPACK functions have a trailing underscore
-    in the Fortran libraries.
-
-    - default: ``'yes'``
-
-.. _lapack-ftn-string-len-at-end:
-
-* ``lapack_ftn_string_len_at_end``: [ ``yes`` | ``no`` ]
-    Controls whether the LAPACK functions have the string length
-    argument at the end of the argument list (``yes``) or after
-    each argument (``no``) in the Fortran libraries.
-    - default: 'yes'
-
-.. _system-googletest:
-
-* ``system_googletest``: [ ``default`` | ``y`` | ``n`` ]
-    Select whether to use gtest from system installation (``y``), from a
-    Git submodule (``n``), or to decide automatically (``default``).
-    - default: 'default'
-
-.. _env-vars:
-
-* ``env_vars``: [ ``string`` ]
-    Environment variables to propagate through to SCons. Either the
-    string ``all`` or a comma separated list of variable names, e.g.
-    ``LD_LIBRARY_PATH,HOME``.
-
-    - default: ``'LD_LIBRARY_PATH,PYTHONPATH'``
-
-.. _use-pch:
-
-* ``use_pch``: [ ``yes`` | ``no`` ]
-    Use a precompiled-header to speed up compilation
-
-    - default: ``'yes'``
-
-.. _cxx-flags:
-
-* ``cxx_flags``: [ ``string`` ]
-    Compiler flags passed to the C++ compiler only. Separate multiple
-    options with spaces, e.g., ``cxx_flags='-g -Wextra -O3 --std=c++11'``
-
-    - default: ``''``
-
-.. _cc-flags:
-
-* ``cc_flags``: [ ``string`` ]
-    Compiler flags passed to both the C and C++ compilers, regardless of
-    optimization level
-
-    - default: ``''``
-
-.. _thread-flags:
-
-* ``thread_flags``: [ ``string`` ]
-    Compiler and linker flags for POSIX multithreading support.
-
-    - default: ``''``
-
-.. _optimize:
-
-* ``optimize``: [ ``yes`` | ``no`` ]
-    Enable extra compiler optimizations specified by the
-    ``optimize_flags`` variable, instead of the flags specified by the
-    ``no_optimize_flags`` variable.
-
-    - default: ``'yes'``
-
-.. _optimize-flags:
-
-* ``optimize_flags``: [ ``string`` ]
-    Additional compiler flags passed to the C/C++ compiler when
-    ``optimize=yes``.
-
-    - default: ``''``
-
-.. _no-optimize-flags:
-
-* ``no_optimize_flags``: [ ``string`` ]
-    Additional compiler flags passed to the C/C++ compiler when
-    ``optimize=no``.
-
-    - default: ``''``
-
-.. _debug:
-
-* ``debug``: [ ``yes`` | ``no`` ]
-    Enable compiler debugging symbols.
-
-    - default: ``'yes'``
-
-.. _debug-flags:
-
-* ``debug_flags``: [ ``string`` ]
-    Additional compiler flags passed to the C/C++ compiler when
-    ``debug=yes``.
-
-    - default: ``''``
-
-.. _no-debug-flags:
-
-* ``no_debug_flags``: [ ``string`` ]
-    Additional compiler flags passed to the C/C++ compiler when
-    ``debug=no``.
-
-    - default: ``''``
-
-.. _debug-linker-flags:
-
-* ``debug_linker_flags``: [ ``string`` ]
-    Additional options passed to the linker when ``debug=yes``.
-
-    - default: ``''``
-
-.. _no-debug-linker-flags:
-
-* ``no_debug_linker_flags``: [ ``string`` ]
-    Additional options passed to the linker when ``debug=no``.
-
-    - default: ``''``
-
-.. _warning-flags:
-
-* ``warning_flags``: [ ``string`` ]
-    Additional compiler flags passed to the C/C++ compiler to enable
-    extra warnings. Used only when compiling source code that is part of
-    Cantera (e.g. excluding code in the 'ext' directory).
-
-    - default: ``''``
-
-.. _extra-inc-dirs:
-
-* ``extra_inc_dirs``: [ ``string`` ]
-    Additional directories to search for header files (colon-separated
-    list).
-
-    - default: ``''``
-
-.. _extra-lib-dirs:
-
-* ``extra_lib_dirs``: [ ``string`` ]
-    Additional directories to search for libraries (colon-separated
-    list).
-
-    - default: ``''``
-
-.. _boost-inc-dir:
-
-* ``boost_inc_dir``: [ ``/path/to/boost_inc_dir`` ]
-    Location of the Boost header files. Not needed if the headers are
-    installed in a standard location, e.g. ``/usr/include``.
-
-    - default: ``''``
-
-.. _stage-dir:
-
-* ``stage_dir``: [ ``/path/to/stage_dir`` ]
-    Directory relative to the Cantera source directory to be used as a
-    staging area for building e.g., a Debian package. If specified,
-    ``scons install`` will install files to ``stage_dir/prefix/...``.
-
-    - default: ``''``
-
-.. _VERBOSE:
-
-* ``VERBOSE``: [ ``yes`` | ``no`` ]
-    Create verbose output about what SCons is doing.
-
-    - default: ``'no'``
-
-.. _renamed-shared-libraries:
-
-* ``renamed_shared_libraries``: [ ``yes`` | ``no`` ]
-    If this option is turned on, the shared libraries that are created
-    will be renamed to have a ``_shared`` extension added to their base
-    name. If not, the base names will be the same as the static
-    libraries. In some cases this simplifies subsequent linking
-    environments with static libraries and avoids a bug with using
-    valgrind with the ``-static`` linking flag.
-
-    - default: ``'yes'``
-
-.. _versioned-shared-library:
-
-* ``versioned_shared_library``: [ ``yes`` | ``no`` ]
-    If enabled, create a versioned shared library, with symlinks to the
-    more generic library name, e.g. ``libcantera_shared.so.2.3.0`` as the
-    actual library and ``libcantera_shared.so`` and ``libcantera_shared.so.2``
-    as symlinks.
-
-    - default: ``'no'``
-
-.. _layout:
-
-* ``layout``: [ ``standard`` | ``compact`` | ``debian`` ]
-    The layout of the directory structure. 'standard' installs files to
-    several subdirectories under 'prefix', e.g. $prefix/bin,
-    $prefix/include/cantera, $prefix/lib. This layout is best used in
-    conjunction with 'prefix'='/usr/local'. 'compact' puts all installed
-    files in the subdirectory defined by 'prefix'. This layout is best
-    with a prefix like '/opt/cantera'. 'debian' installs to the
-    stage directory in a layout used for generating Debian packages.
-
-    - default: ``'standard'``

doc/sphinx/compiling/configure-build.rst

@@ -1,252 +0,0 @@
-
-.. _sec-determine-config:
-
-Determine configuration options
-===============================
-
-* Run ``scons help`` to see a list all configuration options for Cantera, or
-  see :ref:`scons-config`.
-
-* Configuration options are specified as additional arguments to the ``scons``
-  command, e.g.::
-
-    scons command option=value
-
-  where ``scons`` is the program that manages the build steps, and ``command``
-  is most commonly one of
-
-    * ``build``
-    * ``test``
-    * ``clean``
-
-  Other commands are possible, and are explained in :ref:`sec-build-commands`.
-
-* SCons saves configuration options specified on the command line in the file
-  ``cantera.conf`` in the root directory of the source tree, so generally it is
-  not necessary to respecify configuration options when rebuilding Cantera. To
-  unset a previously set configuration option, either remove the corresponding
-  line from ``cantera.conf`` or use the syntax::
-
-    scons command option_name=
-
-* Sometimes, changes in your environment can cause SCons's configuration tests
-  (e.g., checking for libraries or compiler capabilities) to unexpectedly fail.
-  To force SCons to re-run these tests rather than trusting the cached results,
-  run scons with the option ``--config=force``.
-
-* The following lists of options are not complete, they show only some commonly
-  used options. The entire list of options can be found in :ref:`scons-config`.
-
-Common Options
-^^^^^^^^^^^^^^^
-
-* :ref:`blas_lapack_libs <blas-lapack-libs>`
-
-  * On OS X, the Accelerate framework is automatically used to provide
-    optimized versions of BLAS and LAPACK, so the ``blas_lapack_libs``
-    option should generally be left unspecified.
-
-* :ref:`blas_lapack_dir <blas-lapack-dir>`
-* :ref:`boost_inc_dir <boost-inc-dir>`
-* :ref:`debug <debug>`
-* :ref:`optimize <optimize>`
-* :ref:`prefix <prefix>`
-* :ref:`sundials_include <sundials-include>`
-* :ref:`sundials_libdir <sundials-libdir>`
-
-Python 2 Module Options
-^^^^^^^^^^^^^^^^^^^^^^^
-
-By default, SCons will attempt to build the Cython-based Python module for
-Python 2, if both Numpy and Cython are installed. The following options control
-how the Python 2 module is built:
-
-* :ref:`python_cmd <python-cmd>`
-* :ref:`python_package <python-package>`
-* :ref:`python_prefix <python-prefix>`
-
-Python 3 Module Options
-^^^^^^^^^^^^^^^^^^^^^^^
-
-If SCons detects a Python 3 interpreter installed in a default location
-(i.e., ``python3`` is on the ``PATH`` environment variable) or
-``python3_package`` is ``y``, SCons will try to build the Python module
-for Python 3. The following SCons options control how the Python 3 module is
-built:
-
-* :ref:`python3_cmd <python3-cmd>`
-* :ref:`python3_package <python3-package>`
-* :ref:`python3_prefix <python3-prefix>`
-
-Note that even when building the Python 3 Cantera module, you should still use
-Python 2 with SCons, as SCons does not currently support Python 3.
-
-Windows Only Options
-^^^^^^^^^^^^^^^^^^^^
-
-.. note::
-
-    The ``cantera.conf`` file uses the backslash character ``\`` as an escape
-    character. When modifying this file, backslashes in paths need to be escaped
-    like this: ``boost_inc_dir = 'C:\\Program Files (x86)\\boost\\include'``
-    This does not apply to paths specified on the command line. Alternatively,
-    you can use forward slashes (``/``) in paths.
-
-* In Windows there aren't any proper default locations for many of the packages
-  that Cantera depends on, so you will need to specify these paths explicitly.
-
-* Remember to put double quotes around any paths with spaces in them, e.g.
-  ``"C:\Program Files"``.
-
-* By default, SCons attempts to use the same architecture as the copy of Python
-  that is running SCons, and the most recent installed version of the Visual
-  Studio compiler. If you aren't building the Python module, you can override
-  this with the configuration options ``target_arch`` and ``msvc_version``.
-
-* To compile with MinGW, specify the :ref:`toolchain <toolchain>` option::
-
-    toolchain=mingw
-
-* :ref:`msvc_version <msvc-version>`
-* :ref:`target_arch <target-arch>`
-* :ref:`toolchain <toolchain>`
-
-MATLAB Toolbox Options
-^^^^^^^^^^^^^^^^^^^^^^
-
-Building the MATLAB toolbox requires an installed copy of MATLAB, and the path
-to the directory where MATLAB is installed must be specified using the following
-option:
-
-* :ref:`matlab_path <matlab-path>`
-
-Fortran Module Options
-^^^^^^^^^^^^^^^^^^^^^^
-
-Building the Fortran module requires a compatible Fortran comiler. SCons will
-attempt to find a compatible compiler by default in the ``PATH`` environment
-variable. The following options control how the Fortran module is built:
-
-* :ref:`f90_interface <f90-interface>`
-* :ref:`FORTRAN <FORTRAN>`
-
-Documentation Options
-^^^^^^^^^^^^^^^^^^^^^
-
-The following options control if the documentation is built:
-
-* :ref:`doxygen_docs <doxygen-docs>`
-* :ref:`sphinx_docs <sphinx-docs>`
-
-Less Common Options
-^^^^^^^^^^^^^^^^^^^
-
-* :ref:`CC <CC>`
-* :ref:`CXX <CXX>`
-* :ref:`env_vars <env-vars>`
-* :ref:`layout <layout>`
-* :ref:`VERBOSE <VERBOSE>`
-
-.. _sec-build-commands:
-
-Build Commands
-==============
-
-The following options are possible as commands to SCons, i.e., the first
-argument after ``scons``::
-
-    scons command
-
-* ``scons help``
-    Print a description of user-specifiable options.
-
-* ``scons build``
-    Compile Cantera and the language interfaces using
-    default options.
-
-* ``scons clean``
-    Delete files created while building Cantera.
-
-* ``[sudo] scons install``
-    Install Cantera.
-
-* ``[sudo] scons uninstall``
-    Uninstall Cantera.
-
-* ``scons test``
-    Run all tests which did not previously pass or for which the
-    results may have changed.
-
-* ``scons test-reset``
-    Reset the passing status of all tests.
-
-* ``scons test-clean``
-    Delete files created while running the tests.
-
-* ``scons test-help``
-    List available tests.
-
-* ``scons test-NAME``
-    Run the test named "NAME".
-
-* ``scons <command> dump``
-    Dump the state of the SCons environment to the
-    screen instead of doing ``<command>``, e.g.
-    ``scons build dump``. For debugging purposes.
-
-* ``scons samples``
-    Compile the C++ and Fortran samples.
-
-* ``scons msi``
-    Build a Windows installer (.msi) for Cantera.
-
-* ``scons sphinx``
-    Build the Sphinx documentation
-
-* ``scons doxygen``
-    Build the Doxygen documentation
-
-Compile Cantera & Test
-======================
-
-* Run SCons with the list of desired configuration options::
-
-    scons build ...
-
-* If Cantera compiles successfully, you should see a message that looks like::
-
-    *******************************************************
-    Compilation completed successfully.
-
-    - To run the test suite, type 'scons test'.
-    - To install, type '[sudo] scons install'.
-    *******************************************************
-
-* If you do not see this message, check the output for errors to see what went
-  wrong.
-
-* Cantera has a series of tests that can be run with the command::
-
-    scons test
-
-* When the tests finish, you should see a summary indicating the number of
-  tests that passed and failed.
-
-* If you have tests that fail, try looking at the following to determine the
-  source of the error:
-
-    * Messages printed to the console while running ``scons test``
-    * Output files generated by the tests
-
-Building Documentation
-^^^^^^^^^^^^^^^^^^^^^^
-
-* To build the Cantera HTML documentation, run the commands::
-
-    scons doxygen
-    scons sphinx
-
-  or append the options ``sphinx_docs=y`` and ``doxygen_docs=y`` to the build
-  command, e.g.::
-
-    scons build doxygen_docs=y sphinx_docs=y

doc/sphinx/compiling/dependencies.rst

@@ -1,164 +0,0 @@
-
-.. _sec-dependencies:
-
-Software used by Cantera
-========================
-
-This section lists the versions of third-party software that are required to
-build and use Cantera.
-
-Compilers
----------
-
-You must have one of the following C++ compilers installed on your system. A
-Fortran compiler is required only if you plan to build the Fortran module.
-
-* GNU compilers (C/C++/Fortran)
-
-  * Known to work with version 4.8; Expected to work with version >= 4.6
-
-* Clang/LLVM (C/C++)
-
-  * Known to work with versions 3.5 and 3.8. Expected to work with version
-    >= 3.1.
-  * Works with the version included with Xcode 8.2.1.
-
-* Intel compilers (C/C++/Fortran)
-
-  * Known to work with version 14.0.
-
-* Microsoft compilers (C/C++)
-
-  * Known to work with versions 12.0 (Visual Studio 2013) and 14.0 (Visual
-    Studio 2015).
-
-* MinGW (C/C++/Fortran)
-
-  * http://mingw-w64.sourceforge.net/ (64-bit and 32-bit)
-  * http://tdm-gcc.tdragon.net/ (64-bit and 32-bit)
-  * Known to work with Mingw-w64 3.0, which provides GCC 4.8. Expected to work
-    with any version that provides a supported version of GCC and includes C++11
-    thread support.
-
-Other Required Software
------------------------
-
-* SCons:
-
-  * http://scons.org/tag/releases.html
-  * Linux & OS X: Known to work with SCons 2.4.1; Expected to work with versions >= 1.0.0
-  * Version 2.3.6 or newer is required to use Visual Studio 2015.
-
-* Python:
-
-  * http://python.org/download/
-  * Known to work with 2.7 and 3.5. Expected to work with versions >= 3.3.
-  * The Cython module supports Python 2.7 and 3.x. However, SCons requires
-    Python 2, so compilation of the Python 3 module requires two Python
-    installations.
-
-* Boost
-
-  * http://www.boost.org/users/download/
-  * Known to work with version 1.54; Expected to work with versions >= 1.48
-  * Only the "header-only" portions of Boost are required. Cantera does not
-    currently depend on any of the compiled Boost libraries.
-
-* SUNDIALS
-
-  * If SUNDIALS is not installed, it will be automatically downloaded and the
-    necessary portions will be compiled and installed with Cantera.
-  * https://computation.llnl.gov/casc/sundials/download/download.html
-  * Known to work with versions 2.4, 2.5, 2.6, and 2.7.
-  * To use SUNDIALS with Cantera on a Linux/Unix system, it must be compiled
-    with the ``-fPIC`` flag. You can specify this flag when configuring
-    SUNDIALS (2.4 or 2.5)::
-
-          configure --with-cflags=-fPIC
-
-    or SUNDIALS 2.6 or 2.7::
-
-          cmake -DCMAKE_C_FLAGS=-fPIC <other command-line options>
-
-  .. note:: If you are compiling SUNDIALS 2.5.0 on Windows using CMake, you need
-            to edit the ``CMakeLists.txt`` file first and change the lines::
-
-              SET(PACKAGE_STRING "SUNDIALS 2.4.0")
-              SET(PACKAGE_VERSION "2.4.0")
-
-            to read::
-
-              SET(PACKAGE_STRING "SUNDIALS 2.5.0")
-              SET(PACKAGE_VERSION "2.5.0")
-
-            instead, so that Cantera can correctly identify the version of
-            SUNDIALS.
-
-* Eigen
-
-  * If Eigen is not installed, it will be automatically downloaded and installed
-    with Cantera.
-  * http://eigen.tuxfamily.org/
-  * Known to work with version 3.2.8.
-
-* fmt
-
-  * If fmt (previously known as cppformat) is not installed, it will be
-    automatically downloaded and the necessary portions will be compiled and
-    installed with Cantera.
-  * http://fmtlib.net/latest/index.html
-  * Version 3.0.1 or newer is required.
-
-* Google Test
-
-  * If Google Test is not installed, it will be automatically downloaded and the
-    necessary portions will be compiled as part of the Cantera build process.
-  * https://github.com/google/googletest
-  * Known to work with version 1.7.0.
-
-Optional Programs
------------------
-
-* `Numpy <http://www.numpy.org/>`_
-
-  * Required to build the Cantera Python module, and to run significant portions
-    of the test suite.
-  * Known to work with versions 1.7-1.11; Expected to work with version >= 1.4
-
-* `Cython <http://cython.org/>`_
-
-  * Required version >=0.23 installed for Python 2.7 to build the Python module
-    for both Python 2.7 and Python 3.x.
-
-* `3to2 <http://pypi.python.org/pypi/3to2>`_
-
-  * Used to convert Python examples to Python 2 syntax.
-  * Known to work with version 1.0
-
-* Matlab
-
-  * Required to build the Cantera Matlab toolbox.
-  * Known to work with 2009a and 2014b. Expected to work with versions >= 2009a.
-
-* `Windows Installer XML (WiX) toolset <http://wixtoolset.org/>`_
-
-  * Required to build MSI installers on Windows.
-  * Known to work with versions 3.5 and 3.8.
-
-* `Pip <https://pip.pypa.io/en/stable/installing>`_ (Python)
-
-  * Provides the ``pip`` command which can be used to install most of
-    the other Python modules.
-
-* Packages required for building Sphinx documentation
-
-  * `Sphinx <http://sphinx.pocoo.org/>`_ (install with ``pip install --upgrade sphinx``)
-  * `Pygments <http://pygments.org/>`_ (install with ``pip install --upgrade pygments``)
-  * `pyparsing <http://sourceforge.net/projects/pyparsing/>`_ (install with ``pip install --upgrade pyparsing``)
-  * `doxylink <http://pypi.python.org/pypi/sphinxcontrib-doxylink/>`_ (install with ``pip install --upgrade sphinxcontrib-doxylink``)
-  * `matlabdomain <https://pypi.python.org/pypi/sphinxcontrib-matlabdomain>`_ (install with ``pip install sphinxcontrib-matlabdomain``)
-
-* `Doxygen <http://www.stack.nl/~dimitri/doxygen/>`_
-
-  * Required for building the C++ API Documentation
-  * Version 1.8 or newer is recommended.

doc/sphinx/compiling/index.rst

@@ -1,19 +0,0 @@
-
-.. _sec-compiling:
-
-*************************
-Cantera Compilation Guide
-*************************
-
-This guide contains instructions for compiling Cantera on supported operating
-systems and provides some detail of the possible configuration options.
-
-.. toctree::
-   :maxdepth: 2
-
-   installation-reqs
-   source-code
-   configure-build
-   dependencies
-   special-cases
-   config-options

doc/sphinx/compiling/installation-reqs.rst

@@ -1,404 +0,0 @@
-
-.. contents::
-   :local:
-
-.. _sec-installation-reqs:
-
-Installation Prerequisites
-==========================
-
-.. _sec-linux:
-
-Linux
------
-
-General Notes
-^^^^^^^^^^^^^
-
-* To download the source code, installing ``git`` is highly recommended.
-
-* SCons is only available for Python 2, so building the Python 3 module requires
-  two installations of Python (one of Python 2 and one of Python 3), even if you
-  do not intend to build the Python 2 module.
-
-* The following instructions use the system-installed versions of Python, but
-  alternate installations such as the Anaconda distribution of Python can be
-  used as well.
-
-* Cython is only required to be installed for the version of Python that also
-  has SCons installed; following the instructions below will install Cython for
-  the version of Python 2 installed in the system directories. The minimum
-  compatible Cython version is 0.23. If your distribution does not contain a
-  suitable version, you may be able to install a more recent version using
-  ``pip``.
-
-* Users of other distributions should install the equivalent packages, which
-  may have slightly different names.
-
-* In addition to the below operating systems, Cantera should work on any
-  Unix-like system where the necessary prerequisites are available, but some
-  additional configuration may be required.
-
-.. _sec-ubuntu-debian-reqs:
-
-Ubuntu & Debian
-^^^^^^^^^^^^^^^
-
-* Ubuntu 12.04 LTS (Precise Pangolin) or newer is required; 16.04 LTS (Xenial Xerus)
-  or newer is recommended
-
-* Debian 7.0 (Wheezy) or newer; 8.0 (Jessie) or newer is recommended
-
-* The following packages must be installed to build any of the Cantera modules using
-  your choice of package manager::
-
-      g++ python scons libboost-dev
-
-* In addition to the general packages, building the Python 2 module also requires::
-
-      cython python-dev python-numpy python-numpy-dev python-setuptools
-
-* In addition to the general packages, building the Python 3 module also requires::
-
-      cython python3 python3-dev python3-setuptools python3-numpy
-
-* In addition to the general packages, building the Fortran module also requires::
-
-      gfortran
-
-* In addition to the general packages, building the MATLAB toolbox also requires:
-
-  * MATLAB version later than 2009a
-
-    * Typically installed to::
-
-        /opt/MATLAB/R20YYn
-
-      where ``YY`` is a two digit year and ``n`` is either ``a`` or ``b``
-
-.. _sec-fedora-reqs:
-
-Fedora & RHEL
-^^^^^^^^^^^^^
-
-* The following packages must be installed to build any of the Cantera modules using
-  your choice of package manager::
-
-      gcc-c++ python scons boost-devel
-
-* In addition to the general packages, building the Python 2 module also requires::
-
-      python-setuptools python-devel Cython numpy
-
-* In addition to the general packages, building the Python 3 module also requires::
-
-      python3 python3-setuptools python3-devel Cython python3-numpy
-
-* In addition to the general packages, building the Fortran module also requires::
-
-      gcc-gfortran
-
-* In addition to the general packages, building the MATLAB toolbox also requires:
-
-  * MATLAB version later than 2009a
-
-    * Typically installed to::
-
-        /opt/MATLAB/R20YYn
-
-      where ``YY`` is a two digit year and ``n`` is either ``a`` or ``b``
-
-.. _sec-opensuse-reqs:
-
-OpenSUSE & SUSE Linux Enterprise
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-* OpenSUSE 13.2 or newer; Leap 42.2 or newer recommended
-
-* The following packages must be installed to build any of the Cantera modules using
-  your choice of package manager::
-
-      gcc-c++ python scons boost-devel
-
-* In addition to the general packages, building the Python 2 module also requires::
-
-      python-Cython python-devel python-numpy python-numpy-devel python-setuptools
-
-* In addition to the general packages, building the Python 3 module also requires::
-
-      python-Cython python3 python3-devel python3-setuptools python3-numpy python3-numpy-devel
-
-* In addition to the general packages, building the Fortran module also requires::
-
-      gcc-fortran
-
-* In addition to the general packages, building the MATLAB toolbox also requires:
-
-  * MATLAB version later than 2009a
-
-    * Typically installed to::
-
-        /opt/MATLAB/R20YYn
-
-      where ``YY`` is a two digit year and ``n`` is either ``a`` or ``b``
-
-.. _sec-windows:
-
-Windows
--------
-
-General Notes
-^^^^^^^^^^^^^
-
-* SCons is only available for Python 2, so building the Python 3 module requires
-  two installations of Python (one of Python 2 and one of Python 3), even if you
-  do not intend to build the Python 2 module.
-
-* The build process will produce a Python module compatible with the version of
-  Python used for the compilation. To generate different modules for other
-  versions of Python, you will need to install those versions of Python and
-  recompile.
-
-* The following instructions use the versions of Python downloaded from
-  https://www.python.org/downloads, but alternate installations such as the
-  Anaconda distribution of Python can be used as well.
-
-* If you want to build the Matlab toolbox and you have a 64-bit copy of Windows,
-  by default you will be using a 64-bit copy of Matlab, and therefore you need
-  to compile Cantera in 64-bit mode. For simplicity, it is highly recommended
-  that you use a 64-bit version of Python to handle this automatically. Note
-  that the default download from the Python website
-  (https://www.python.org) is for a 32-bit installer, and you will
-  need to select the 64-bit installer specifically.
-
-* It is generally helpful to have SCons and Python in your ``PATH`` environment
-  variable. This can be done by checking the appropriate box during the
-  installation of Python or can be accomplished by adding the top-level Python
-  directory and the ``Scripts`` subdirectory (e.g.,
-  ``C:\Python27;C:\Python27\Scripts``) to your ``PATH``. The dialog to change
-  the ``PATH`` is accessible from::
-
-      Control Panel > System and Security > System > Advanced System Settings > Environment Variables
-
-  Make sure that the installation of Python that has SCons comes first on your
-  ``PATH``.
-
-* In order to use SCons to install Cantera to a system folder (e.g. ``C:\Program
-  Files\Cantera``) you must run the ``scons install`` command in a command
-  prompt that has been launched by selecting the *Run as Administrator* option.
-
-.. _sec-windows-reqs:
-
-Windows Requirements
-^^^^^^^^^^^^^^^^^^^^^^^
-
-* Windows 7 or later; either 32-bit or 64-bit
-
-* To build any of the Cantera modules, you will need to install
-
-  * Python 2.7
-
-    * https://www.python.org/downloads/
-
-    * Be sure to choose the appropriate architecture for your system - either
-      32-bit or 64-bit
-
-    * When installing, make sure to choose the option to add to your ``PATH``
-
-  * SCons
-
-    * https://pypi.python.org/pypi/SCons
-
-    * Be sure to choose the appropriate architecture for your system - either
-      32-bit or 64-bit
-
-  * One of the following supported compilers
-
-    * Microsoft compilers
-
-      * https://www.visualstudio.com/downloads/
-
-      * Known to work with Visual Studio 2013 (MSVC 12.0) and Visual Studio 2015
-        (MSVC 14.0)
-
-    * MinGW compilers
-
-      * http://mingw-w64.org/
-
-      * http://tdm-gcc.tdragon.net/
-
-      * Known to work with Mingw-w64 3.0, which provides GCC 4.8. Expected to
-        work with any version that provides a supported version of GCC and
-        includes C++11 thread support.
-
-      * The version of MinGW from http://www.mingw.org/ cannot be used to build
-        Cantera. Users must use MinGW-w64 or TDM-GCC.
-
-  * The Boost headers
-
-    * http://www.boost.org/doc/libs/1_63_0/more/getting_started/windows.html#get-boost
-
-    * It is not necessary to compile the Boost libraries since Cantera only uses
-      the headers from Boost
-
-* In addition to the general software, building the Python 2 module also requires
-
-  * Pip
-
-    * Pip should be distributed with Python version 2.7.9 and higher.
-      If you are using an older version of Python, see
-      `these instructions to install pip <http://stackoverflow.com/a/12476379>`_
-
-    * Most packages will be downloaded as Wheel (``*.whl``) files. To install
-      these files, type::
-
-          pip install C:\Path\to\downloaded\file\package-file-name.whl
-
-  * Cython
-
-    * http://www.lfd.uci.edu/~gohlke/pythonlibs/#cython
-
-    * Download the ``*.whl`` file for your Python architecture (32-bit or 64-bit)
-      and Python 2.7 (indicated by ``cp27`` in the file name).
-
-    * Cython must be installed in the version of Python that has SCons installed
-
-  * NumPy
-
-    * http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy
-
-    * Download the ``*.whl`` file for your Python architecture (32-bit or 64-bit)
-      and Python 2.7 (indicated by ``cp27`` in the file name).
-
-* In addition to the general software, building the Python 3 module also requires
-
-  * Python 3
-
-    * https://www.python.org/downloads/
-
-    * Cantera supports Python 3.3 and higher
-
-    * Be sure to choose the appropriate architecture for your system - either
-      32-bit or 64-bit
-
-    * Be careful that the installation of Python 3 does not come before Python 2
-      on your ``PATH`` environment variable
-
-  * Pip
-
-    * Pip should be distributed with Python version 3.4 and higher.
-      If you are using an older version of Python, see
-      `these instructions to install pip <http://stackoverflow.com/a/12476379>`_
-
-    * Most packages will be downloaded as Wheel (``*.whl``) files. To install
-      these files, type::
-
-          pip3 install C:\Path\to\downloaded\file\package-file-name.whl
-
-  * Cython
-
-    * http://www.lfd.uci.edu/~gohlke/pythonlibs/#cython
-
-    * Download the ``*.whl`` file for your Python architecture (32-bit or 64-bit)
-      and Python 2.7 (indicated by ``cp27`` in the file name).
-
-    * Cython must be installed in the version of Python that has SCons installed
-
-  * NumPy
-
-    * http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy
-
-    * Download the ``*.whl`` file for your Python architecture (32-bit or 64-bit)
-      and Python 3.x (indicated by ``cp3x`` in the file name, where x matches
-      your version of Python).
-
-* In addition to the general software, building the MATLAB toolbox also requires:
-
-  * MATLAB version later than 2009a
-
-    * Typically installed to::
-
-        C:\Program Files\MATLAB\R20YYn
-
-      where ``YY`` is a two digit year and ``n`` is either ``a`` or ``b``/Applications/MATLAB_R2011a.app
-
-.. _sec-macos:
-
-OS X & macOS
-------------
-
-General Notes
-^^^^^^^^^^^^^
-
-* It is not recommended to use the system-installed version of Python to build
-  Cantera. Instead, the following instructions use Homebrew to install a
-  separate copy of Python, independent from the system Python.
-
-* To download the source code, installing ``git`` via HomeBrew is highly recommended.
-
-* SCons is only available for Python 2, so building the Python 3 module requires
-  two installations of Python (one of Python 2 and one of Python 3), even if you
-  do not intend to build the Python 2 module.
-
-* Cython is only required to be installed for the version of Python that also
-  has SCons installed; following the instructions below will install Cython for
-  the version of Python 2 installed in the system directories. The minimum
-  compatible Cython version is 0.23.
-
-.. _sec-mac-os-reqs:
-
-OS X & macOS Requirements
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-* OS X 10.9 (Mavericks) or newer required; 10.10 (Yosemite) or newer is recommended
-
-* To build any of the Cantera modules, you will need to install
-
-  * Xcode
-
-    * Download and install from the App Store
-
-    * From a Terminal, run::
-
-        sudo xcode-select --install
-
-      and agree to the Xcode license agreement
-
-  * Homebrew
-
-    * http://brew.sh
-
-    * From a Terminal, run::
-
-        /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
-
-  * Once Homebrew is installed, the rest of the dependencies can be installed with::
-
-      brew install python scons boost
-
-* In addition to the general software, building the Python 2 module also requires::
-
-    pip install cython numpy
-
-* In addition to the general software, building the Python 3 module also requires::
-
-    brew install python3
-    pip install cython
-    pip3 install numpy
-
-  Note that Cython should be installed into the version of Python that has SCons
-  installed.
-
-* In addition to the general software, building the Fortran module also requires::
-
-    brew install gcc
-
-* In addition to the general software, building the MATLAB toolbox also requires:
-
-  * MATLAB version later than 2009a
-
-    * Typically installed to::
-
-        /Applications/MATLAB_R20YYn.app
-
-      where ``YY`` is a two digit year and ``n`` is either ``a`` or ``b``

doc/sphinx/compiling/source-code.rst

@@ -1,65 +0,0 @@
-
-.. _sec-source-code:
-
-Downloading the Cantera source code
-===================================
-
-Stable Release
---------------
-
-* **Option 1**: Check out the code using Git::
-
-    git clone --recursive https://github.com/Cantera/cantera.git
-    cd cantera
-
-  Then, check out the tag of the most recent stable version::
-
-    git checkout tags/v2.3.0
-
-  A list of all the tags can be shown by::
-
-    git tag --list
-
-* **Option 2**: Download the most recent source tarball from `Github
-  <https://github.com/Cantera/cantera/releases>`_ and extract the
-  contents.
-
-Beta Release
-------------
-
-* Check out the code using Git::
-
-    git clone --recursive https://github.com/Cantera/cantera.git
-    cd cantera
-
-  Then pick either **Option 1** or **Option 2** below.
-
-* **Option 1**: Check out the tag with the most recent beta release::
-
-    git checkout tags/v2.3.0b1
-
-  Note that the most recent beta version might be older than the most recent
-  stable release. A list of all the tags, including stable and beta versions can
-  be shown by::
-
-    git tag --list
-
-* **Option 2**: Check out the branch with all the bug fixes leading to the
-  next minor release of the stable version::
-
-    git checkout 2.3
-
-  This branch has all the work on the 2.3.x version of the software.
-
-Development Version
--------------------
-
-Check out the code using Git::
-
-  git clone --recursive https://github.com/Cantera/cantera.git
-  cd cantera
-
-Note that by default, the ``master`` branch is checked out, containing all of
-the feature updates and bug fixes to the code since the previous stable release.
-The master branch is usually an "alpha" release, corresponding to the ``a`` in
-the version number, and does not usually get a tag.

doc/sphinx/compiling/special-cases.rst

@@ -1,52 +0,0 @@
-
-.. _sec-special-compiling-cases:
-
-***********************
-Special Compiling Cases
-***********************
-
-This guide explains some of the less common ways to build Cantera
-
-.. contents::
-   :local:
-
-.. _sec-intel-compilers:
-
-Intel Compilers
-===============
-
-* Before compiling Cantera, you may need to set up the appropriate environment
-  variables for the Intel compiler suite, e.g.::
-
-    source /opt/intel/bin/compilervars.sh intel64
-
-* For the Intel compiler to work with SCons, these environment variables need
-  to be passed through SCons by using the command line option::
-
-    env_vars=all
-
-* If you want to use the Intel MKL versions of BLAS and LAPACK, you will need
-  to provide additional options. The following are typically correct on
-  64-bit Linux systems::
-
-    blas_lapack_libs=mkl_rt blas_lapack_dir=$(MKLROOT)/lib/intel64
-
-  Your final SCons call might then look something like::
-
-    scons build env_vars=all CC=icc CXX=icpc FORTRAN=ifort blas_lapack_libs=mkl_rt blas_lapack_dir=$(MKLROOT)/lib/intel64
-
-* When installing Cantera after building with the Intel compiler, the normal
-  method of using ``sudo`` to install Cantera to the system default directories
-  will not work because ``sudo`` does not pass the environment variables needed
-  by the Intel compiler. Instead, you will need to do something like::
-
-    scons build ...
-    sudo -s
-    source /path/to/compilervars.sh intel64
-    scons install
-    exit
-
-  Another option is to set the :ref:`prefix <prefix>` option to a directory
-  for which you have write permissions, and specify the ``USER`` value to the
-  :ref:`python_prefix <python-prefix>` or :ref:`python3_prefix <python3-prefix>`
-  option.

doc/sphinx/conf.py

@@ -16,10 +16,7 @@ import sys, os, re
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-if sys.version_info[0] == 3:
-    sys.path.insert(0, os.path.abspath('../../build/python3'))
-else:
-    sys.path.insert(0, os.path.abspath('../../build/python2'))
+sys.path.insert(0, os.path.abspath('../../build/python'))
 
 sys.path.append(os.path.abspath('.'))
 sys.path.append(os.path.abspath('./exts'))
@@ -41,22 +38,19 @@ extensions = [
               'sphinx.ext.autodoc',
               'sphinx.ext.todo',
               'sphinx.ext.autosummary',
-              'mathjax',
               'sphinxcontrib.doxylink',
+              'sphinxcontrib.katex',  # Use KaTeX because it's faster and the main site uses it
               ]
 
-# @todo: Sphinx version 1.1 adds support for MathJax, so we can remove the
-#        custom extension for that once that version becomes more standard
+katex_version = '0.10.0-beta'
 
 autodoc_default_flags = ['members','show-inheritance','undoc-members']
 
 autoclass_content = 'both'
 
-mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
-
 doxylink = {
-        'ct' : (os.path.abspath('../../build/docs/Cantera.tag'),
-                '../../doxygen/html/')
+        'ct': (os.path.abspath('../../build/docs/Cantera.tag'),
+               '../../doxygen/html/')
 }
 
 # Ensure that the primary domain is the Python domain, since we've added the
@@ -77,7 +71,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = 'Cantera'
-copyright = '2001-2017, Cantera Developers'
+copyright = '2001-2018, Cantera Developers'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -102,9 +96,6 @@ release = re.search('CANTERA_VERSION "(.*?)"', configh).group(1)
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = []
-if sys.version_info[0] == 3:
-    exclude_patterns.append('python/*')
-
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 default_role = 'py:obj'
@@ -132,11 +123,43 @@ pygments_style = 'sphinx'
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 html_theme = 'cttheme'
+html_sidebars = {
+    '**': ['localtoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html', 'numfocus.html'],
+}
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+
+# Copy the Bootstrap 4 font families.
+font_families = [
+    # Default on Apple
+    '-apple-system',
+    # Default for older versions of Chrome on Mac
+    'BlinkMacSystemFont',
+    # Windows
+    '"Segoe UI"',
+    # Android
+    'Roboto',
+    # Standard fallbacks
+    '"Helvetica Neue"', 'Arial', 'sans-serif',
+    # Emoji fonts
+    '"Apple Color Emoji"', '"Segoe UI Emoji"', '"Segoe UI Symbol"']
+
+code_font_families = [
+    'SFMono-Regular',
+    'Menlo',
+    'Monaco',
+    'Consolas',
+    '"Liberation Mono"',
+    '"Courier New"', 'monospace'
+]
+html_theme_options = {
+    'font_family': ','.join(font_families),
+    'head_font_family': ','.join(font_families),
+    'caption_font_family': ','.join(font_families),
+    'code_font_family': ','.join(code_font_families),
+}
 
 # Add any paths that contain custom themes here, relative to this directory.
 html_theme_path = ['.']
@@ -155,7 +178,7 @@ html_short_title = "Cantera"
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-html_favicon = "_static/favicon.ico"
+# html_favicon = "_static/favicon.ico"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

doc/sphinx/cti/classes.rst

@@ -80,9 +80,6 @@ Thermodynamic Properties
 .. autoclass:: Shomate
    :no-undoc-members:
 
-.. autoclass:: Adsorbate
-   :no-undoc-members:
-
 .. autoclass:: const_cp
    :no-undoc-members:
 
@@ -122,6 +119,9 @@ Reactions
 .. autoclass:: edge_reaction
    :no-undoc-members:
 
+.. autoclass:: stick
+   :no-undoc-members:
+
 Falloff Parameterizations
 -------------------------
 

doc/sphinx/cti/example-combustion.rst

@@ -1,4 +0,0 @@
-============================
-Example: Hydrogen Combustion
-============================
-

doc/sphinx/cti/index.rst

@@ -1,19 +0,0 @@
-
-.. _sec-defining-phases:
-
-***************
-Defining Phases
-***************
-
-*A guide to Cantera's input file format*
-
-.. toctree::
-   :maxdepth: 2
-
-   intro
-   input-files
-   phases
-   species
-   reactions
-   classes
-   example-combustion

doc/sphinx/cti/input-files.rst

@@ -1,716 +0,0 @@
-.. py:currentmodule:: cantera.ctml_writer
-
-.. _sec-input-files:
-
-************************
-Working with Input Files
-************************
-
-Before we can describe how to define phases, interfaces, and their components
-(elements, species, and reactions), we need to go over a few points about the
-mechanics of writing and processing input files.
-
-Input File Syntax
-=================
-
-An input file consists of *entries* and *directives*, both of which have a
-syntax much like functions. An entry defines an object---for example, a
-reaction, or a species, or a phase. A directive sets options that affect how the
-entry parameters are interpreted, such as the default unit system, or how
-certain errors should be handled.
-
-Cantera's input files follow the syntax rules for Python, so if you're familiar
-with Python syntax you already understand many of the details and can probably
-skip ahead to :ref:`sec-dimensions`.
-
-Entries have fields that can be assigned values. A species entry is shown below
-that has fields *name* and *atoms* (plus several others)::
-
-    species(name='C60', atoms='C:60')
-
-Most entries have some fields that are required; these must be assigned values,
-or else processing of the file will abort and an error message will be
-printed. Other fields may be optional, and take default values if not assigned.
-
-An entry may be either a *top-level entry* or an *embedded entry*. Top-level
-entries specify a phase, an interface, an element, a species, or a reaction, and
-begin in the first (leftmost) column. Embedded entries specify a model, or a
-group of parameters for a top-level entry, and are usually embedded in a field
-of another entry.
-
-The fields of an entry are specified in the form ``<field_name> = <value>``, and may
-be listed on one line, or extend across several. For example, two entries for
-graphite are shown below. The first is compact::
-
-    stoichiometric_solid(name='graphite', species='C(gr)', elements='C', density=(2.2, 'g/cm3'))
-
-and the second is formatted to be easier to read::
-
-    stoichiometric_solid(
-        name     = 'graphite',
-        elements = 'C',
-        species  = 'C(gr)',
-        density  = (2.2, 'g/cm3')
-    )
-
-Both are completely equivalent.
-
-The species ``C(gr)`` that appears in the definition of the graphite phase is
-also defined by a top-level entry. If the heat capacity of graphite is
-approximated as constant, then the following definition could be used::
-
-    species(name='C(gr)',
-            atoms='C:1',
-            thermo=const_cp(t0=298.15,
-                            h0=0.0,
-                            s0=(5.6, 'J/mol/K'), # NIST
-                            cp0=(8.43, 'J/mol/K'))) # Taylor and Groot (1980)
-
-Note that the thermo field is assigned an embedded entry of type
-:class:`const_cp`. Entries are stored as they are encountered when the file is
-read, and only processed once the end of the file has been reached. Therefore,
-the order in which they appear is unimportant.
-
-Comments
---------
-
-The character ``#`` is the comment character. Everything to the right of this
-character on a line is ignored::
-
-    # set the default units
-    units(length = 'cm',    # use centimeters for length
-          quantity = 'mol') # use moles for quantity
-
-Strings
--------
-
-Strings may be enclosed in single quotes or double quotes, but they must
-match. To create a string containing single quotes, enclose it in double quotes,
-and vice versa. If you want to create a string to extend over multiple lines,
-enclose it in triple quotes::
-
-    string1 = 'A string.'
-    string2 = "Also a 'string'"
-    string3 = """This is
-    a
-    string too."""
-
-The multi-line form is useful when specifying a phase containing a large number
-of species::
-
-    species = """ H2 H O O2 OH H2O HO2 H2O2 C CH
-                  CH2 CH2(S) CH3 CH4 CO CO2 HCO CH2O CH2OH CH3O
-                  CH3OH C2H C2H2 C2H3 C2H4 C2H5 C2H6 HCCO CH2CO HCCOH
-                  N NH NH2 NH3 NNH NO NO2 N2O HNO CN
-                  HCN H2CN HCNN HCNO HOCN HNCO NCO N2 AR C3H7
-                  C3H8 CH2CHO CH3CHO """
-
-Sequences
----------
-
-A sequence of multiple items is specified by separating the items by commas and
-enclosing them in square brackets or parentheses. The individual items can have
-any type---strings, integers, floating-point numbers (or even entries or other
-lists). Square brackets are often preferred, since parentheses are also used for
-other purposes in the input file, but either can be used::
-
-    s0 = (3.5, 'J/mol/K') # these are
-    s0 = [3.5, 'J/mol/K'] # equivalent
-
-Variables
----------
-
-Another way to specify the species C(gr) is shown here::
-
-    graphite_thermo = const_cp(t0=298.15,
-                               h0=0.0,
-                               s0=(5.6, 'J/mol/K'), # NIST
-                               cp0=(8.43, 'J/mol/K')) # Taylor and Groot (1980)
-
-    species(name='C(gr)', atoms='C:1', thermo=graphite_thermo)
-
-In this form, the ``const_cp`` entry is stored in a variable, instead of being
-directly embedded within the species entry.  The *thermo* field is assigned this
-variable.
-
-Variables can also be used for any other parameter type. For example, if you are
-defining several phases in the file, and you want to set them all to the same
-initial pressure, you could define a pressure variable::
-
-    P_initial = (2.0, 'atm')
-
-and then set the pressure field in each embedded state entry to this variable.
-
-Omitting Field Names
---------------------
-
-Field names may be omitted if the values are entered in the order specified in
-the entry declaration. (Entry declarations are the text printed on a colored
-background in the following chapters.) It is also possible to omit only some of
-the field names, as long as these fields are listed first, in order, before any
-named fields.
-
-For example, The first four entries below are equivalent, while the last two are
-incorrect and would generate an error when processed::
-
-    element(symbol="Ar", atomic_mass=39.948) # OK
-    element(atomic_mass=39.948, symbol='Ar') # OK
-    element('Ar', atomic_mass=39.948)        # OK
-    element("Ar", 39.948)                    # OK
-
-    element(39.948, "Ar")                    # error
-    element(symbol="Ar", 39.948)             # error
-
-Validation
-----------
-
-Normally, Cantera will make some checks for errors in the definitions of species
-and reactions, such as checking for duplicate reactions. To slightly speed up
-processing (if a mechanism has previously been validated), or in case of
-spurious validation errors, validation can be disabled using the
-:func:`validate` function. For example, to disable validation of reactions, add
-the following to the CTI file::
-
-    validate(reactions='no')
-
-.. _sec-dimensions:
-
-Dimensional Values
-==================
-
-Many fields have numerical values that represent dimensional quantities---a
-pressure, or a density, for example. If these are entered without specifying the
-units, the default units (set by the :class:`units` directive described in
-:ref:`sec-default-units`) will be used. However, it is also possible to specify
-the units for each individual dimensional quantity (unless stated
-otherwise). All that is required is to group the value in parentheses or square
-brackets with a string specifying the units::
-
-    pressure = 1.0e5 # default is Pascals
-    pressure = (1.0, 'bar') # this is equivalent
-    density = (4.0, 'g/cm3')
-    density = 4000.0 # kg/m3
-
-Compound unit strings may be used, as long as a few rules are followed:
-
-1. Units in the denominator follow ``/``.
-2. Units in the numerator follow ``-``, except for the first one.
-3. Numerical exponents follow the unit string without a ``^`` character, and must
-   be in the range 2--6. Negative values are not allowed.
-
-Examples of compound units::
-
-    A = (1.0e20, 'cm6/mol2/s') # OK
-    h = (6.626e-34, 'J-s')     # OK
-    density = (3.0, 'g/cm3')   # OK
-    A = (1.0e20, 'cm^6/mol/s') # error (^)
-    A = (1.0e20, 'cm6/mol2-s') # error ('s' should be in denominator)
-    density = (3.0, 'g-cm-3')  # error (negative exponent)
-
-.. _sec-default-units:
-
-Setting the Default Units
--------------------------
-
-The default unit system may be set with the :func:`units` directive. Note
-that unit conversions are not done until the entire file has been read. Only one
-units directive should be present in a file, and the defaults it specifies apply
-to the entire file.  If the file does not contain a units directive, the default
-units are meters, kilograms, kilomoles, and seconds.
-
-Shown below are two equivalent ways of specifying the site density for an
-interface. In the first version, the site density is specified without a units
-string, and so its units are constructed from the default units for quantity and
-length, which are set with a units directive::
-
-    units(length = 'cm', quantity = 'molec')
-    interface(name = 'Si-100',
-              site_density = 1.0e15, # molecules/cm2 (default units)
-              # ...
-              )
-
-The second version uses a different default unit system, but overrides the
-default units by specifying an explicit units string for the site density::
-
-    units(length = 'cm', quantity = 'mol')
-    interface(name = 'Si-100',
-              site_density = (1.0e15, 'molec/cm2') # override default units
-              # ...
-              )
-
-The second version is equivalent to the first, but would be very different if
-the units of the site density were not specified!
-
-The *length*, *quantity* and *time* units are used to construct the units for
-reaction pre-exponential factors. The *energy* units are used for molar
-thermodynamic properties, in combination with the units for *quantity*.
-
-Since activation energies are often specified in units other than those used for
-thermodynamic properties, a separate field is devoted to the default units for
-activation energies::
-
-    units(length = 'cm', quantity = 'mol', act_energy = 'kcal/mol')
-    kf = Arrhenius(A = 1.0e14, b = 0.0, E = 54.0) # E is 54 kcal/mol
-
-See :func:`units` for the declaration of the units directive.
-
-Recognized Units
-----------------
-
-Cantera recognizes the following units in various contexts:
-
-===========  ==============
-field        allowed values
-===========  ==============
-length       ``'cm', 'm', 'mm'``
-quantity     ``'mol', 'kmol', 'molec'``
-time         ``'s', 'min', 'hr', 'ms'``
-energy       ``'J', 'kJ', 'cal', 'kcal'``
-act_energy   ``'kJ/mol', 'J/mol', 'J/kmol', 'kcal/mol', 'cal/mol', 'eV', 'K'``
-pressure     ``'Pa', 'atm', 'bar'``
-===========  ==============
-
-Processing Input Files
-======================
-
-A Two-step Process
-------------------
-
-From the point of view of the user, it appears that a Cantera application that
-imports a phase definition reads the input file, and uses the information there
-to construct the object representing the phase or interface in the
-application. While this is the net effect, it is actually a two-step
-process. When a constructor like ``Solution`` is called to import a phase definition
-from a file, a preprocessor runs automatically to read the input file and create
-a string that contains the same information but in an XML-based format called
-CTML. After the preprocessor finishes, Cantera imports the phase definition from
-this CTML data.
-
-Two File Formats
-----------------
-
-Why two file formats? There are several reasons. XML is a widely-used standard
-for data files, and it is designed to be relatively easy to parse. This makes it
-possible for other applications to use Cantera CTML data files, without
-requiring the substantial chemical knowledge that would be required to use .cti
-files. For example, "web services" (small applications that run remotely over a
-network) are often designed to accept XML input data over the network, perform a
-calculation, and send the output in XML back across the network. Supporting an
-XML-based data file format facilitates using Cantera in web services or other
-network computing applications.
-
-The difference between the high-level description in a .cti input file and the
-lower-level description in the CTML file may be illustrated by how reactions are
-handled. In the input file, the reaction stoichiometry and its reversibility or
-irreversibility are determined from the reaction equation. For example::
-
-    O + HCCO <=> H + 2 CO
-
-specifies a reversible reaction between an oxygen atom and the ketenyl radical
-HCCO to produce one hydrogen atom and two carbon monoxide molecules. If ``<=>``
-were replaced with ``=>``, then it would specify that the reaction should be
-treated as irreversible.
-
-Of course, this convention is not spelled out in the input file---the parser
-simply has to know it, and has to also know that a "reactant" appears on the
-left side of the equation, a "product" on the right, that the optional number in
-front of a species name is its stoichiometric coefficient (but if missing the
-value is one), etc. The preprocessor does know all this, but we cannot expect
-the same level of knowledge of chemical conventions by a generic XML parser.
-
-Therefore, in the CTML file, reactions are explicitly specified to be reversible
-or irreversible, and the reactants and products are explicitly listed with their
-stoichiometric coefficients. The XML file is, in a sense, a "dumbed-down"
-version of the input file, spelling out explicitly things that are only implied
-in the input file syntax, so that "dumb" (i.e., easy to write) parsers can be
-used to read the data with minimal risk of misinterpretation.
-
-The reaction definition::
-
-    reaction( "O + HCCO <=> H + 2 CO", [1.00000E+14, 0, 0])
-
-in the input file is translated by the preprocessor to the following CTML text:
-
-.. code-block:: xml
-
-    <reaction id="0028" reversible="yes">
-      <equation>O + HCCO [=] H + 2 CO</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s"> 1.000000E+14</A>
-          <b>0</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>HCCO:1 O:1</reactants>
-      <products>H:1 CO:2</products>
-    </reaction>
-
-The CTML version is much more verbose, and would be much more tedious to write
-by hand, but is much easier to parse, particularly since it is not necessary to
-write a custom parser---virtually any standard XML parser, of which there are
-many, can be used to read the CTML data.
-
-So in general files that are easy for knowledgeable users (you) to write are more
-difficult for machines to parse, because they make use of high-level
-application-specific knowledge and conventions to simplify the
-notation. Conversely, files that are designed to be easily parsed are tedious to
-write because so much has to be spelled out explicitly. A natural solution is to
-use two formats, one designed for writing by humans, the other for reading by
-machines, and provide a preprocessor to convert the human-friendly format to the
-machine-friendly one.
-
-Preprocessor Internals: the ``ctml_writer`` Module
---------------------------------------------------
-
-If you are interested in seeing the internals of how the preprocessing works,
-take a look at file ``ctml_writer.py`` in the Cantera Python package. Or simply
-start Python, and type::
-
-    >>> import cantera.ctml_writer
-    >>> help(cantera.ctml_writer)
-
-The ``ctml_writer.py`` module can also be run as a script to convert input .cti
-files to CTML. For example, if you have an input file ``phasedefs.cti``, then
-simply type at the command line::
-
-    python -m cantera.ctml_writer phasedefs.cti
-
-to create CTML file ``phasedefs.xml``. On systems which support running Python
-scripts directly, a script to run ``ctml_writer`` directly is also installed. If
-the Cantera ``bin`` directory is on your ``PATH``, you can also do the
-conversion by running::
-
-    ctml_writer phasedefs.cti
-
-This can be used to generate XML input files for use on systems where the
-Cantera Python package is not installed. Of course, most of the time creation of
-the CTML file will happen behind the scenes, and you will not need to be
-concerned with CTML files at all.
-
-Error Handling
-==============
-
-During processing of an input file, errors may be encountered. These could be
-syntax errors, or could be ones that are flagged as errors by Cantera due to
-some apparent inconsistency in the data---an unphysical value, a species that
-contains an undeclared element, a reaction that contains an undeclared species,
-missing species or element definitions, multiple definitions of elements,
-species, or reactions, and so on.
-
-Syntax Errors
--------------
-
-Syntax errors are caught by the Python preprocessor, not by Cantera, and must be
-corrected before proceeding further.  Python prints a "traceback" that allows
-you to find the line that contains the error. For example, consider the
-following input file, which is intended to create a gas with the species and
-reactions of GRI-Mech 3.0, but has a misspelled the field name ``reactions``::
-
-    ideal_gas(name = 'gas',
-              elements = 'H O',
-              species = 'gri30: all',
-              reactionss = 'gri30: all')
-
-When this definition is imported into an application, an error message like the
-following would be printed to the screen, and execution of the program or script
-would terminate. ::
-
-    Traceback (most recent call last):
-      File "<stdin>", line 1, in <module>
-      File "/some/path/Cantera/importFromFile.py", line 18, in importPhase
-        return importPhases(file, [name], loglevel, debug)[0]
-      File "/some/path/Cantera/importFromFile.py", line 25, in importPhases
-        s.append(solution.Solution(src=file,id=nm,loglevel=loglevel,debug=debug))
-      File "/some/path/solution.py", line 39, in __init__
-        preprocess = 1, debug = debug)
-      File "/some/path/Cantera/XML.py", line 35, in __init__
-        self._xml_id = _cantera.xml_get_XML_File(src, debug)
-    cantera.error:
-
-    ************************************************
-                    Cantera Error!
-    ************************************************
-
-    Procedure: ct2ctml
-    Error:   Error converting input file "./gas.cti" to CTML.
-    Python command was: '/usr/bin/python'
-    The exit code was: 4
-    -------------- start of converter log --------------
-    TypeError on line 4 of './gas.cti':
-    __init__() got an unexpected keyword argument 'reactionss'
-
-    | Line |
-    |    1 | ideal_gas(name = 'gas',
-    |    2 |           elements = 'H O',
-    |    3 |           species = 'gri30: all',
-    >    4 >           reactionss = 'gri30: all')
-    |    5 |
-    --------------- end of converter log ---------------
-
-The top part of the error message shows the chain of functions that were called
-before the error was encountered. For the most part, these are internal Cantera
-functions not of direct concern here. The relevant part of this error message is
-the part starting with the "Cantera Error" heading, and specifically the
-contents of the *converter log* section. This message says that that on line 4
-of ``gas.cti``, the the keyword argument ``reactionss`` was not
-recognized. Seeing this message, it is clear that the problem is that
-*reactions* is misspelled.
-
-Cantera Errors
---------------
-
-Now let's consider the other class of errors---ones that Cantera, not Python,
-detects. Continuing the example above, suppose that the misspelling is
-corrected, and the input file processed again. Again an error message results,
-but this time it is from Cantera::
-
-    cantera.error:
-    Procedure: installSpecies
-    Error: species C contains undeclared element C
-
-The problem is that the phase definition specifies that all species are to be
-imported from dataset gri30, but only the elements H and O are declared. The
-gri30 datset contains species composed of the elements H, O, C, N, and Ar. If
-the definition is modified to declare these additional elements::
-
-    ideal_gas(name = 'gas',
-              elements = 'H O C N Ar',
-              species = 'gri30: all',
-              reactions = 'gri30: all')
-
-it may be imported successfully.
-
-Errors of this type do not have to be fatal, as long as you tell Cantera how you
-want to handle them. You can, for example, instruct Cantera to quietly skip
-importing any species that contain undeclared elements, instead of flagging them
-as errors. You can also specify that reactions containing undeclared species
-(also usually an error) should be skipped. This allows you to very easily
-extract a portion of a large reaction mechanism, as described in :ref:`sec-phase-options`.
-
-.. _sec-ck-format-conversion:
-
-Converting CK-format files
-==========================
-
-Many existing reaction mechanism files are in "CK format," by which we mean
-the input file format developed for use with the Chemkin-II software package
-as specified in the report describing the Chemkin software [SAND89]_.
-
-Cantera comes with a converter utility program ``ck2cti`` (or ``ck2cti.py``)
-that converts CK format into Cantera format. This program should be run from
-the command line first to convert any CK files you plan to use into Cantera
-format (CTI format).
-
-Usage::
-
-    ck2cti [--input=<filename>]
-           [--thermo=<filename>]
-           [--transport=<filename>]
-           [--surface=<filename>]
-           [--id=<phase-id>]
-           [--output=<filename>]
-           [--permissive]
-           [-d | --debug]
-
-Each of the terms in square brackets is an option that can be passed on the
-command line to ``ck2cti``. ``--input`` is the chemistry input file, containing
-a list of all the element names that are used, a list of all the species names,
-and a list of all the reactions to be considered between the species. This file
-can also optionally contain thermodynamic information for the species. If the
-``--input`` file does not contain the thermodynamic data, a separate file
-containing this information must be specified to the `--thermo`` option. Finally,
-the ``--input`` file can also optionally contain transport information for the
-species. If it does not, and the user wishes to use a part of Cantera that relies
-on some transport properties, the ``--transport`` option must be used to specify
-the file containing all the transport data for the species.
-
-For the case of a surface mechanism, the gas phase input file should be
-specified as ``--input`` and the surface phase input file should be specified as
-``--surface``.
-
-Example::
-
-    ck2cti --input=chem.inp --thermo=therm.dat --transport=tran.dat
-
-If the output file name is not given, an output file with the same name as the
-input file, with the extension changed to '.cti'.
-
-If the ck2cti script is not on your path but the Cantera Python module is,
-ck2cti can also be used by running::
-
-    python -m cantera.ck2cti --input=chem.inp --thermo=therm.dat --transport=tran.dat
-
-An input file containing only species definitions (which can be referenced from
-phase definitions in other input files) can be created by specifying only a
-thermo file.
-
-Many existing CK format files cause errors in ``ck2cti`` when they are
-processed. Some of these errors may be avoided by specifying the
-``--permissive`` option. This option allows certain recoverable parsing errors
-(e.g. duplicate transport or thermodynamic data) to be ignored. Other errors
-may be caused by incorrect formatting of lines in one or more of the input files.
-
-Debugging common errors in CK files
------------------------------------
-
-When ``ck2cti`` encounters an error, it attempts to print the surrounding
-information to help you to locate the error. Many of the most common errors
-are due to an inconsistency of the input files from their standard, as defined
-in the report for Chemkin referenced above. These errors include:
-
-  * Each section of the input files must be started with a keyword representing that
-    section and ending with the keyword ``END``. Keywords that may begin a section
-    include:
-
-    - ``ELEMENTS`` or ``ELEM``
-    - ``SPECIES`` or ``SPEC``
-    - ``THERMO`` or ``THERMO ALL``
-    - ``REACTIONS`` or ``REAC``
-    - ``TRANSPORT``
-
-  * The thermodynamic data is read in a fixed format. This means that each
-    column of the input has a particular meaning. *Many common errors are
-    generated because information is missing or in the wrong column. Check
-    thoroughly for extraneous or missing spaces.* The format for each
-    thermodynamic entry should be as follows::
-
-        N2                      N 2                 G200.000   6000.000  1000.00       1
-         2.95258000E+00 1.39690000E-03-4.92632000E-07 7.86010000E-11-4.60755000E-15    2
-        -9.23949000E+02 5.87189000E+00 3.53101000E+00-1.23661000E-04-5.02999000E-07    3
-         2.43531000E-09-1.40881000E-12-1.04698000E+03 2.96747000E+00                   4
-
-    The following table is adapted from the Chemkin manual [SAND89]_ to describe the
-    column positioning of each required part of the entry. Empty columns should be
-    filled with spaces.
-
-    +---------+-------------------------------------+--------+
-    |Line No. | Contents                            | Column |
-    +=========+=====================================+========+
-    | 1       | Species Name                        | 1--18  |
-    +---------+-------------------------------------+--------+
-    | 1       | Date (Optional)                     | 19--24 |
-    +---------+-------------------------------------+--------+
-    | 1       | Atomic Symbols and formula          | 25--44 |
-    +---------+-------------------------------------+--------+
-    | 1       | Phase of species (S, L, G)          | 45     |
-    +---------+-------------------------------------+--------+
-    | 1       | Low temperature                     | 46--55 |
-    +---------+-------------------------------------+--------+
-    | 1       | High temperature                    | 56--65 |
-    +---------+-------------------------------------+--------+
-    | 1       | Common temperature                  | 66--73 |
-    +---------+-------------------------------------+--------+
-    | 1       | Additional Atomic Symbols           | 74--78 |
-    +---------+-------------------------------------+--------+
-    | 1       | The integer ``1``                   | 80     |
-    +---------+-------------------------------------+--------+
-    | 2       | Coefficients :math:`a_1`            | 1--75  |
-    |         | to :math:`a_5` for the upper        |        |
-    |         | temperature interval                |        |
-    +---------+-------------------------------------+--------+
-    | 2       | The integer ``2``                   | 80     |
-    +---------+-------------------------------------+--------+
-    | 3       | Coefficients :math:`a_6,\ a_7`      | 1--75  |
-    |         | for the upper temperature interval, |        |
-    |         | and :math:`a_1,\ a_2,\ a_3` for     |        |
-    |         | the lower temperature interval      |        |
-    +---------+-------------------------------------+--------+
-    | 3       | The integer ``3``                   | 80     |
-    +---------+-------------------------------------+--------+
-    | 4       | Coefficients :math:`a_4` through    | 1--60  |
-    |         | :math:`a_7` for the lower           |        |
-    |         | temperature interval                |        |
-    +---------+-------------------------------------+--------+
-    | 4       | The integer ``4``                   | 80     |
-    +---------+-------------------------------------+--------+
-
-    The first 18 columns are reserved for the species name. The name assigned
-    to the species in the thermodynamic data must be the same as the species
-    name defined in the ``SPECIES`` section. If the species name is shorter
-    than 18 characters, the rest of the characters should be filled by spaces.
-    The next six columns (columns 19--24) are typically used to write a date;
-    they are not used further. The next 20 columns (25--44) are used to
-    specify the elemental composition of the species. In column 45, the phase
-    of the species (``S``, ``L``, or ``G`` for solid, liquid, or gas
-    respectively) should be specified. The next 28 columns are reserved for
-    the temperatures that delimit the ranges of the polynomials specified on
-    the next several lines. The first two temperatures have a width of 10
-    columns each (46--55 and 56--65), and represent the lowest temperature and
-    highest temperature for which the polynomials are valid. The last
-    temperature has a width of 8 columns (66--73) and is the "common"
-    temperature, where the switch from low to high occurs. The next 5 columns
-    (74--78) are reserved for atomic symbols and are usually left blank for
-    the default behavior. Column 79 is blank and finally, the row is ended in
-    column 80 with the integer ``1``.
-
-    The next three lines of the thermodynamic entry have a similar format.
-    They contain the coefficients of the polynomial described in
-    :ref:`sec-thermo-models` for the NASA 7-coefficient polynomial formulation.
-    The second row of the thermo entry (the first after the information row)
-    contains the first five coefficients that apply the the temperature range
-    between the midpoint and the upper limit. 15 columns are alloted for each
-    coefficient (for a total of 75 columns), with no spaces between them.
-    Although the entry above shows spaces between positive coefficients, it is
-    to be noted that this is done only for formatting consistency with other
-    lines that contain negative numbers. After the coefficients, four spaces
-    in columns 76--79 are followed by the integer ``2`` in column 80. On the
-    next line, the last two coefficients for the upper temperature range and
-    the first three coefficients for the lower temperature range are
-    specified. Once again, this takes up the first 75 columns, columns 76--79
-    are blank, and the integer ``3`` is in column 80. Finally, on the last
-    line of a particular entry, the last four coefficients of the lower
-    temperature range are specified in columns 1--60, 19 blank spaces are
-    present, and the integer ``4`` is in column 80. The 19 blank spaces in the
-    last line are part of the standard. However, since the original Chemkin
-    interpreter ignored those spaces, researchers began using that space to
-    store additional information that was not necessary for the input file.
-    Although these numbers create an error in ``ck2cti`` if present, they are
-    harmless and can be ignored by using the ``--permissive`` option.
-
-  * It may be the case that scientific formatted numbers are missing the ``E``.
-    In this case, numbers often show up as ``1.1+01``, when they should be
-    ``1.1E+01``. You can fix this with a simple Regular Expression find and
-    replace::
-
-        Find: (\d+\.\d+)([+-]\d+)
-        Replace: \1E\2
-
-  * The transport data file also has a specified format, as described in
-    [SAND98]_, although the format is not as strict as for the thermodynamic
-    entries. In particular, the first 15 columns of a line are reserved for
-    the species name. *One common source of errors is a species that is present
-    in the transport data file, but not in the thermodynamic data or in
-    the species list; or a species that is present in the species list but
-    not the transport data file.* The rest of the columns on a given line have
-    no particular format, but must be present in the following order:
-
-    +------------------+------------------------------------------------------+
-    | Parameter Number | Parameter Name                                       |
-    +==================+======================================================+
-    | 1                | An integer with value 0, 1, or 2 indicating          |
-    |                  | monatomic, linear, or non-linear molecular geometry. |
-    +------------------+------------------------------------------------------+
-    | 2                | The Lennard-Jones potential well depth               |
-    |                  | :math:`\varepsilon/k_B` in Kelvin                    |
-    +------------------+------------------------------------------------------+
-    | 3                | The Lennard-Jones collision diameter :math:`\sigma`  |
-    |                  | in Angstrom                                          |
-    +------------------+------------------------------------------------------+
-    | 4                | The dipole moment :math:`\mu` in Debye               |
-    +------------------+------------------------------------------------------+
-    | 5                | The polarizability :math:`\alpha` in Angstrom        |
-    +------------------+------------------------------------------------------+
-    | 6                | The rotational relaxation collision number           |
-    |                  | :math:`Z_{rot}` at 298 K                             |
-    +------------------+------------------------------------------------------+
-
-    Another common error is if all 6 of these numbers are not present for every
-    species.
-
-.. [SAND89] See R. J. Kee, F. M. Rupley, and J. A. Miller, Sandia National
-   Laboratories Report SAND89-8009 (1989).
-   http://www.osti.gov/scitech/biblio/5681118
-
-.. [SAND98] See R. J. Kee, G. Dixon-Lewis, J. Warnatz, M. E. Coltrin, J. A. Miller,
-   H. K. Moffat, Sandia National Laboratories Report SAND86-8246B (1998).

doc/sphinx/cti/intro.rst

@@ -1,40 +0,0 @@
-************
-Introduction
-************
-
-Virtually every Cantera simulation involves one or more phases of
-matter. Depending on the calculation being performed, it may be necessary to
-evaluate thermodynamic properties, transport properties, and/or homogeneous
-reaction rates for the phase(s) present. In problems with multiple phases, the
-properties of the interfaces between phases, and the heterogeneous reaction
-rates at these interfaces, may also be required.
-
-Before the properties can be evaluated, each phase must be defined, meaning that
-the models to use to compute its properties and reaction rates must be
-specified, along with any parameters the models require. For example, a solid
-phase might be defined as being incompressible, with a specified density and
-composition. A gaseous phase for a combustion simulation might be defined as an
-ideal gas consisting of a mixture of many species that react with one another
-via a specified set of reactions.
-
-For phases containing multiple species and reactions, a large amount of data is
-required to define the phase, since the contribution of each species to the
-thermodynamic and transport properties must be specified, and rate information
-must be given for each reaction. While this could be done directly in an
-application program, a better approach is put the phase and interface
-definitions in a text file that can be read by the application, so that a given
-phase model can be re-used for other simulations.
-
-This guide describes how to write such files to define phases and interfaces for
-use in Cantera simulations. Section :ref:`sec-input-files` contains a summary of
-some basic rules for writing input files, a discussion of how they are
-processed, and of how errors are handled. In Section :ref:`sec-phases`, we will
-go over how to define phases and interfaces, including how to import species and
-reactions from external files. Then in :ref:`sec-species` and
-:ref:`sec-reactions`, we'll look in depth at how to specify the component parts
-of phase and interface models---the elements, species, and reactions.
-
-.. In Section ##REF##, we'll put it all together, and present some complete,
-   realistic example problems, showing the input file containing the definitions
-   of all phases and interfaces, the application code to use the input file to
-   solve a problem, and the resulting output.

doc/sphinx/cti/phases.rst

@@ -1,500 +0,0 @@
-.. py:currentmodule:: cantera.ctml_writer
-
-.. _sec-phases:
-
-***************************
-Phases and their Interfaces
-***************************
-
-Now that we have covered how to write syntactically-correct input files, we can
-turn our attention to the content of the file. We'll start by describing the
-entries for phases of various types, and the look at how to define interfaces
-between phases.
-
-Phases
-======
-
-For each phase that appears in a problem, a corresponding entry should be
-present in the input file(s). For example, suppose we want to conduct a
-simulation with detailed chemistry of an idealized solid-oxide fuel cell shown
-below.  The problem involves three solid phases (A nickel anode, a
-platinum cathode, and an oxygen-conducting yttrium-stabilized zirconia
-electrolyte), and two different gas phases (a fuel mixture on the anode side,
-and air on the cathode side). The problem also involves a number of interfaces
-at which heterogeneous chemistry may occur---two gas-metal interfaces, two
-gas-electrolyte interfaces, and two metal-electrolyte interfaces.
-
-.. figure:: /_static/images/sofc-phases.png
-    :align: center
-
-    **Phases entering into a hypothetical microkinetic simulation of an
-    idealized solid-oxide fuel cell.**
-
-How to carry out this fuel cell simulation is beyond the scope of this document;
-we introduce it here only to give an example of the types of phases and
-interfaces that might need to be defined in order to carry out a simulation. (Of
-course, many simulations with Cantera only require defining a single phase.)
-
-There are several different types of entries, corresponding to different types
-of phases. Phases are created using one of the directives corresponding to an
-implemented phase type:
-
-* :class:`ideal_gas`
-* :class:`stoichiometric_solid`
-* :class:`stoichiometric_liquid`
-* :class:`metal`
-* :class:`semiconductor`
-* :class:`incompressible_solid`
-* :class:`lattice`
-* :class:`lattice_solid`
-* :class:`liquid_vapor`
-* :class:`redlich_kwong`
-* :class:`ideal_interface`
-* :class:`edge`
-
-These phase typese share many common features, however, and so we will begin by
-discussing those aspects common to all entries for phases. The :class:`phase`
-class contains the features common to all phase types.
-
-Phase Attributes
-----------------
-
-Phase Name
-^^^^^^^^^^
-
-The ``name`` field is a string that identifies the phase. It must not contain
-any whitespace characters or reserved XML characters, and must be unique within
-the file among all phase definitions of any type.
-
-Phases are referenced by name when importing them into an application program,
-or when defining an interface between phases.
-
-Declaring the Elements
-^^^^^^^^^^^^^^^^^^^^^^
-
-The elements that may be present in the phase are declared in the elements
-field. This must be a string of element symbols separated by spaces. Each symbol
-must either match one listed in the database file ``elements.xml``, or else
-match the symbol of an element entry defined elsewhere in the input file (See
-:ref:`sec-elements`).
-
-The ``elements.xml`` database contains most elements of the periodic table, with
-their natural-abundance atomic masses. It also contains a few isotopes (D, Tr),
-and an "element" for an electron (E). This pseudo-element can be used to specify
-the composition of charged species. Note that two-character symbols should have
-an uppercase first letter, and a lowercase second letter (e.g. ``Cu``, not ``CU``).
-
-It should be noted that the order of the element symbols in the string
-determines the order in which they are stored internally by Cantera. For
-example, if a phase definition specifies the elements as::
-
-    ideal_gas(name = "gasmix",
-              elements = "H C O N Ar",
-              # ...
-              )
-
-then when this definition is imported by an application, element-specific
-properties will be ordered in the same way::
-
-    >>> import cantera as ct
-    >>> gas = ct.Solution('example.cti', 'gasmix')
-    >>> for n in range(gas.nElements()):
-    ...     print n, gas.elementSymbol(n)
-    0 H
-    1 C
-    2 O
-    3 N
-    4 Ar
-
-For some calculations, such as multi-phase chemical equilibrium, it is important
-to synchronize the elements among multiple phases, so that each phase contains
-the same elements with the same ordering. In such cases, simply use the same
-string in the elements field for all phases.
-
-.. _sec-defining-species:
-
-Defining the Species
-^^^^^^^^^^^^^^^^^^^^
-
-The species in the phase are declared in the species field. They are not defined
-there, only declared. Species definitions may be imported from other files, or
-species may be defined locally using species entries elsewhere in the file.
-
-If a single string of species symbols is given, then it is assumed that these
-are locally defined. For each one, a corresponding species entry must be present
-somewhere in the file, either preceding or following the phase entry.  Note that
-the string may extend over multiple lines by delimiting it with triple quotes::
-
-    species = 'AR SI Si2 SiH SiH2 SiH3 SiH4'
-
-    # include all species defined in this file
-    species = 'all'
-
-    # a multi-line species declaration
-    species = """ H2 H O O2 OH H2O HO2 H2O2 C CH
-                  CH2 CH2(S) CH3 CH4 CO CO2 HCO CH2O CH2OH CH3O
-                  CH3OH C2H C2H2 C2H3 C2H4 C2H5 C2H6 HCCO CH2CO HCCOH
-                  N NH NH2 NH3 NNH NO NO2 N2O HNO CN
-                  HCN H2CN HCNN HCNO HOCN HNCO NCO N2 AR C3H7
-                  C3H8 CH2CHO CH3CHO """
-
-If the species are imported from another file, instead of being defined locally,
-then the string should begin with the file name (without extension), followed by
-a colon::
-
-    # import selected species from silicon.xml
-    species = "silicon: SI SI2 SIH SIH2 SIH3 SIH4 SI2H6"
-
-    # import all species from silicon.xml
-    species = "silicon: all"
-
-In this case, the species definitions will be taken from file ``silicon.xml``,
-which must exist either in the local directory or somewhere on the Cantera
-search path.
-
-It is also possible to import species from several sources, or mix local
-definitions with imported ones, by specifying a sequence of strings::
-
-    species = ["CL2 CL F F2 HF HCL", # defined in this file
-               "air: O2 N2 NO", # imported from 'air.xml'
-               "ions: CL- F-"] # imported from 'ions.xml'
-
-Note that the strings must be separated by commas, and enclosed in square
-brackets or parentheses.
-
-.. _sec-declaring-reactions:
-
-Declaring the Reactions
-^^^^^^^^^^^^^^^^^^^^^^^
-
-The reactions among the species are declared in the ``reactions`` field. Just as
-with species, reactions may be defined locally in the file, or may be imported
-from one or more other files. All reactions must only involve species that have
-been declared for the phase.
-
-Unlike species, reactions do not have a name, but do have an optional ``ID``
-field. If the ``ID`` field is not assigned a value, then when the reaction entry
-is read it will be assigned a four-digit string encoding the reaction number,
-beginning with ``'0001'`` for the first reaction in the file, and incrementing
-by one for each new reaction.
-
-If all reactions defined locally in the input file are to be included in the
-phase definition, then assign the ``reactions`` field the string ``'all'``::
-
-    reactions = 'all'
-
-If, on the other hand, only some of the reactions defined in the file are to be
-included, then a range can be specified using the reaction ``ID`` fields::
-
-    reactions = 'nox-12 to nox-24'
-
-In determining which reactions to include, a lexical comparison of id strings is
-performed. This means, for example, that ``'nox-8'`` is greater than
-``'nox-24'``. (If it is rewritten ``'nox-08'``, however, then it would be lexically
-less than ``'nox-24'``.)
-
-Just as described above for species, reactions can be imported from another
-file, and reactions may be imported from several sources. Examples::
-
-    # import all reactions defined in this file
-    reactions = "all"
-
-    # import all reactions defined in rxns.xml
-    reactions = "rxns: all"
-
-    # import reactions 1-14 in rxns.xml
-    reactions = "rxns: 0001 to 0014"
-
-    # import reactions from several sources
-    reactions = ["all",              # all local reactions
-                 "gas: all",         # all reactions in gas.xml
-                 "nox: n005 to n008"] # reactions 5 to 8 in nox.xml
-
-The Kinetics Model
-^^^^^^^^^^^^^^^^^^
-
-A *kinetics model* is a set of equations to use to compute reaction rates. In
-most cases, each type of phase has an associated kinetics model that is used by
-default, and so the ``kinetics`` field does not need to be assigned a value. For
-example, the :class:`ideal_gas` entry has an associated kinetics model called
-``GasKinetics`` that implements mass-action kinetics, computes reverse rates
-from thermochemistry for reversible reactions, and provides various
-pressure-independent and pressure-dependent reaction types. Other models could
-be implemented, and this field would then be used to select the desired
-model. For now, the ``kinetics`` field can be safely ignored.
-
-The Transport Model
-^^^^^^^^^^^^^^^^^^^
-
-A *transport model* is a set of equations used to compute transport
-properties. For :class:`ideal_gas` phases, multiple transport models are
-available; the one desired can be selected by assigning a string to this
-field. See :ref:`sec-gas-transport-models` for more details.
-
-The Initial State
-^^^^^^^^^^^^^^^^^
-
-The phase may be assigned an initial state to which it will be set when the
-definition is imported into an application and an object created. This is done
-by assigning field ``initial_state`` an embedded entry of type :class:`state`,
-described in :ref:`sec-state-entry`.
-
-Most of the attributes defined here are "immutable," meaning that once the
-definition has been imported into an application, they cannot be changed by the
-application. For example, it is not possible to change the elements or the
-species. The temperature, pressure, and composition, however, are "mutable"---
-they can be changed. This is why the field defining the state is called the
-``initial_state``; the object in the application will be initially set to this
-state, but it may be changed at any time.
-
-.. _sec-phase-options:
-
-Special Processing Options
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The options field is used to indicate how certain conditions should be handled
-when importing the phase definition.  The options field may be assigned a string
-or a sequence of strings from the table below.
-
-==================================  ========================================================
-Option String                       Meaning
-==================================  ========================================================
-``'skip_undeclared_elements'``      When importing species, skip any containing undeclared
-                                    elements, rather than flagging them as an error.
-``'skip_undeclared_species'``       When importing reactions, skip any containing undeclared
-                                    species, rather than flagging them as an error.
-``'skip_undeclared_third_bodies'``  When importing reactions with third body efficiencies,
-                                    ignore any efficiencies for undeclared species, rather
-                                    than flagging them as an error.
-``'allow_discontinuous_thermo'``    Disable the automatic adjustment of NASA polynomials to
-                                    eliminate discontinuities in enthalpy and entropy at the
-                                    midpoint temperature.
-==================================  ========================================================
-
-Using the ``options`` field, it is possible to extract a sub-mechanism from a large
-reaction mechanism, as follows::
-
-    ideal_gas(name = 'hydrogen_mech',
-              elements = 'H O',
-              species = 'gri30:all',
-              reactions = 'gri30:all',
-              options = ('skip_undeclared_elements',
-                         'skip_undeclared_species',
-                         'skip_undeclared_third_bodies'))
-
-If we import this into Matlab, for example, we get a gas mixture containing the
-8 species (out of 53 total) that contain only H and O:
-
-.. code-block:: matlabsession
-
-    >> gas = Solution('gas.cti', 'hydrogen_mech')
-
-      hydrogen_mech:
-
-           temperature           0.001  K
-              pressure      0.00412448  Pa
-               density           0.001  kg/m^3
-      mean mol. weight         2.01588  amu
-
-                              1 kg            1 kmol
-                           -----------      ------------
-              enthalpy     -3.786e+006      -7.632e+006     J
-       internal energy     -3.786e+006      -7.632e+006     J
-               entropy         6210.88       1.252e+004     J/K
-        Gibbs function     -3.786e+006      -7.632e+006     J
-     heat capacity c_p         9669.19       1.949e+004     J/K
-     heat capacity c_v          5544.7       1.118e+004     J/K
-
-                               X                 Y          Chem. Pot. / RT
-                         -------------     ------------     ------------
-                    H2              1                1          -917934
-         [   +7 minor]              0                0
-
-    >> eqs = reactionEqn(gas)
-
-    eqs =
-
-        '2 O + M <=> O2 + M'
-        'O + H + M <=> OH + M'
-        'O + H2 <=> H + OH'
-        'O + HO2 <=> OH + O2'
-        'O + H2O2 <=> OH + HO2'
-        'H + O2 + M <=> HO2 + M'
-        'H + 2 O2 <=> HO2 + O2'
-        'H + O2 + H2O <=> HO2 + H2O'
-        'H + O2 <=> O + OH'
-        '2 H + M <=> H2 + M'
-        '2 H + H2 <=> 2 H2'
-        '2 H + H2O <=> H2 + H2O'
-        'H + OH + M <=> H2O + M'
-        'H + HO2 <=> O + H2O'
-        'H + HO2 <=> O2 + H2'
-        'H + HO2 <=> 2 OH'
-        'H + H2O2 <=> HO2 + H2'
-        'H + H2O2 <=> OH + H2O'
-        'OH + H2 <=> H + H2O'
-        '2 OH (+ M) <=> H2O2 (+ M)'
-        '2 OH <=> O + H2O'
-        'OH + HO2 <=> O2 + H2O'
-        'OH + H2O2 <=> HO2 + H2O'
-        'OH + H2O2 <=> HO2 + H2O'
-        '2 HO2 <=> O2 + H2O2'
-        '2 HO2 <=> O2 + H2O2'
-        'OH + HO2 <=> O2 + H2O'
-
-Ideal Gas Mixtures
-------------------
-
-Now we turn to the specific entry types for phases, beginning with
-:class:`ideal_gas`.
-
-Many combustion and CVD simulations make use of reacting ideal gas
-mixtures. These can be defined using the :class:`ideal_gas` entry. The Cantera
-ideal gas model allows any number of species, and any number of reactions among
-them. It supports all of the options in the widely-used model described by Kee
-et al. [#Kee1989]_, plus some additional options for species thermodynamic
-properties and reaction rate expressions.
-
-An example of an ``ideal_gas`` entry is shown below::
-
-    ideal_gas(name='air8',
-              elements='N O Ar',
-              species='gri30: N2 O2 N O NO NO2 N2O AR',
-              reactions='all',
-              transport='Mix',
-              initial_state=state(temperature=500.0,
-                                  pressure=(1.0, 'atm'),
-                                  mole_fractions='N2:0.78, O2:0.21, AR:0.01'))
-
-This entry defines an ideal gas mixture that contains 8 species, the definitions
-of which are imported from dataset gri30 (file ``gri30.xml``). All reactions
-defined in the file are to be included, transport properties are to be computed
-using mixture rules, and the state of the gas is to be set initially to 500 K, 1
-atm, and a composition that corresponds to air.
-
-.. _sec-gas-transport-models:
-
-Transport Models
-^^^^^^^^^^^^^^^^
-
-Two transport models are available for use with ideal gas mixtures. The first is
-a multicomponent transport model that is based on the model described by
-Dixon-Lewis [#dl68]_ (see also Kee et al. [#Kee2003]_). The second is a model that uses
-mixture rules. To select the multicomponent model, set the transport field to
-the string ``'Multi'``, and to select the mixture-averaged model, set it to the
-string ``'Mix'``::
-
-    ideal_gas(name="gas1",
-              # ...
-              transport="Multi", # use multicomponent formulation
-              # ...
-              )
-
-    ideal_gas(name="gas2",
-              # ...
-              transport="Mix", # use mixture-averaged formulation
-              # ...
-              )
-
-Stoichiometric Solid
---------------------
-
-A :class:`stoichiometric_solid` is one that is modeled as having a precise,
-fixed composition, given by the composition of the one species present. A
-stoichiometric solid can be used to define a condensed phase that can
-participate in heterogeneous reactions. (Of course, there cannot be homogeneous
-reactions, since the composition is fixed.) ::
-
-    stoichiometric_solid(name='graphite',
-                         elements='C',
-                         species='C(gr)',
-                         density=(2.2, 'g/cm3'),
-                         initial_state=state(temperature=300.0,
-                                             pressure=(1.0, 'atm')))
-
-In the example above, the definition of the species ``'C(gr)'`` must appear
-elsewhere in the input file.
-
-Stoichiometric Liquid
----------------------
-
-A stoichiometric liquid differs from a stoichiometric solid in only one respect:
-the transport manager computes the viscosity as well as the thermal
-conductivity.
-
-.. _sec-interfaces:
-
-Interfaces
-==========
-
-Now that we have seen how to define bulk, three-dimensional phases, we can
-describe the procedure to define an interface between phases.
-
-Cantera presently implements a simple model for an interface that treats it as a
-two-dimensional ideal solution of interfacial species. There is a fixed site
-density :math:`n^0`, and each site may be occupied by one of several adsorbates,
-or may be empty. The chemical potential of each species is computed using the
-expression for an ideal solution:
-
-.. math::
-
-    \mu_k = \mu^0_k + \hat{R}T \log \theta_k,
-
-where :math:`\theta_k` is the coverage of species :math:`k` on the surface. The
-coverage is related to the surface concentration :math:`C_k` by
-
-.. math::
-
-    \theta_k = \frac{C_k n_k}{n^0} ,
-
-where :math:`n_k` is the number of sites covered or blocked by species
-:math:`k`.
-
-The entry type for this interface model is
-:class:`ideal_interface`. (Additional interface models may be added to allow
-non-ideal, coverage-dependent properties.)
-
-Defining an interface is much like defining a phase. There are two new fields:
-``phases`` and ``site_density``. The ``phases`` field specifies the bulk phases that
-participate in the heterogeneous reactions. Although in most cases this string
-will list one or two phases, no limit is placed on the number. This is
-particularly useful in some electrochemical problems, where reactions take place
-near the triple-phase boundary where a gas, an electrolyte, and a metal all meet.
-
-The ``site_density`` field is the number of adsorption sites per unit area.
-
-Another new aspect is in the embedded :class:`state` entry in the
-``initial_state`` field. When specifying the initial state of an interface, the
-:class:`state` entry has a field *coverages*, which can be assigned a string
-specifying the initial surface species coverages::
-
-    ideal_interface(name='silicon_surface',
-                    elements='Si H',
-                    species='s* s-SiH3 s-H',
-                    reactions='all',
-                    phases='gas bulk-Si',
-                    site_density=(1.0e15, 'molec/cm2'),
-                    initial_state=state(temperature=1200.0,
-                                        coverages='s-H:1'))
-
-.. _sec-state-entry:
-
-The :class:`state` entry
-========================
-
-The initial state of either a phase or an interface may be set using an embedded
-:class:`state` entry. Note that only one of (``pressure``, ``density``) may be
-specified, and only one of (``mole_fractions``, ``mass_fractions``, ``coverages``).
-
-.. rubric:: References
-
-.. [#Kee1989] R. J. Kee, F. M. Rupley, and J. A. Miller. Chemkin-II: A Fortran
-   chemical kinetics package for the analysis of gasphase chemical
-   kinetics. Technical Report SAND89-8009, Sandia National Laboratories, 1989.
-
-.. [#dl68] G. Dixon-Lewis. Flame structure and flame reaction kinetics,
-   II: Transport phenomena in multicomponent systems. *Proc. Roy. Soc. A*,
-   307:111--135, 1968.
-
-.. [#Kee2003] R. J. Kee, M. E. Coltrin, and P. Glarborg. *Chemically Reacting
-   Flow: Theory and Practice*. John Wiley and Sons, 2003.

doc/sphinx/cti/reactions.rst

@@ -1,557 +0,0 @@
-.. py:currentmodule:: cantera.ctml_writer
-
-.. _sec-reactions:
-
-*********
-Reactions
-*********
-
-Cantera supports a number of different types of reactions, including several
-types of homogeneous reactions, surface reactions, and electrochemical
-reactions. For each, there is a corresponding entry type. The simplest entry
-type is :class:`reaction`, which can be used for any homogeneous reaction that
-has a rate expression that obeys the law of mass action, with a rate coefficient
-that depends only on temperature.
-
-Common Attributes
-=================
-
-All of the entry types that define reactions share some common features. These
-are described first, followed by descriptions of the individual reaction types
-in the following sections.
-
-The Reaction Equation
----------------------
-
-The reaction equation determines the reactant and product stoichiometry. A
-relatively simple parsing strategy is currently used, which assumes that all
-coefficient and species symbols on either side of the equation are delimited by
-spaces::
-
-    2 CH2 <=> CH + CH3      # OK
-    2 CH2<=>CH + CH3        # OK
-    2CH2 <=> CH + CH3       # error
-    CH2 + CH2 <=> CH + CH3  # OK
-    2 CH2 <=> CH+CH3        # error
-
-The incorrect versions here would generate "undeclared species" errors and would
-halt processing of the input file. In the first case, the error would be that
-the species ``2CH2`` is undeclared, and in the second case it would be species
-``CH+CH3``.
-
-Whether the reaction is reversible or not is determined by the form of the
-equality sign in the reaction equation. If either ``<=>`` or ``=`` is found,
-then the reaction is regarded as reversible, and the reverse rate will be
-computed from detailed balance. If, on the other hand, ``=>`` is found, the
-reaction will be treated as irreversible.
-
-The rate coefficient is specified with an embedded entry corresponding to the
-rate coefficient type. At present, the only implemented type is the modified
-Arrhenius function
-
-.. math::
-
-    k_f(T) = A T^b \exp(-E/\hat{R}T)
-
-which is defined with an :class:`Arrhenius` entry::
-
-    rate_coeff = Arrhenius(A=1.0e13, b=0, E=(7.3, 'kcal/mol'))
-    rate_coeff = Arrhenius(1.0e13, 0, (7.3, 'kcal/mol'))
-
-As a shorthand, if the ``rate_coeff`` field is assigned a sequence of three numbers, these are assumed to be :math:`(A, b, E)` in the modified Arrhenius function::
-
-    rate_coeff = [1.0e13, 0, (7.3, 'kcal/mol')] # equivalent to above
-
-The units of the pre-exponential factor *A* can be specified explicitly if
-desired. If not specified, they will be constructed using the *quantity*, *length*,
-and *time* units specified in the units directive. Since the units of *A* depend on
-the reaction order, the units of each reactant concentration (different for bulk
-species in solution, surface species, and pure condensed-phase species), and the
-units of the rate of progress (different for homogeneous and heterogeneous
-reactions), it is usually best not to specify units for *A*, in which case they
-will be computed taking all of these factors into account.
-
-Note: if :math:`b \ne 0`, then the term :math:`T^b` should have units of
-:math:`K^b`, which would change the units of *A*. This is not done, however, so
-the units associated with A are really the units for :math:`k_f` . One way to
-formally express this is to replace :math:`T^b` by the non-dimensional quantity
-:math:`[T/(1 K)]^b`.
-
-The ID String
--------------
-
-An optional identifying string can be entered in the ``ID`` field, which can
-then be used in the ``reactions`` field of a :class:`phase` or interface entry
-to identify this reaction. If omitted, the reactions are assigned ID strings as
-they are read in, beginning with ``'0001'``, ``'0002'``, etc.
-
-Note that the ID string is only used when selectively importing reactions. If
-all reactions in the local file or in an external one are imported into a phase
-or interface, then the reaction ``ID`` field is not used.
-
-.. _sec-reaction-options:
-
-Options
--------
-
-Certain conditions are normally flagged as errors by Cantera. In some cases,
-they may not be errors, and the options field can be used to specify how they
-should be handled.
-
-``skip``
-    The ``'skip'`` option can be used to temporarily remove this reaction from
-    the phase or interface that imports it, just as if the reaction entry were
-    commented out. The advantage of using skip instead of commenting it out is
-    that a warning message is printed each time a phase or interface definition
-    tries to import it. This serves as a reminder that this reaction is not
-    included, which can easily be forgotten when a reaction is "temporarily"
-    commented out of an input file.
-
-``duplicate``
-    Normally, when a reaction is imported into a phase, it is checked to see
-    that it is not a duplicate of another reaction already present in the phase,
-    and an error results if a duplicate is found. But in some cases, it may be
-    appropriate to include duplicate reactions, for example if a reaction can
-    proceed through two distinctly different pathways, each with its own rate
-    expression.  Another case where duplicate reactions can be used is if it is
-    desired to implement a reaction rate coefficient of the form:
-
-    .. math::
-
-        k_f(T) = \sum_{n=1}^{N} A_n T^{b_n} exp(-E_n/\hat{R}T)
-
-    While Cantera does not provide such a form for reaction rates, it can be
-    implemented by defining *N* duplicate reactions, and assigning one rate
-    coefficient in the sum to each reaction.  If the ``'duplicate'`` option is
-    specified, then the reaction not only *may* have a duplicate, it *must*. Any
-    reaction that specifies that it is a duplicate, but cannot be paired with
-    another reaction in the phase that qualifies as its duplicate generates an
-    error.
-
-``negative_A``
-    If some of the terms in the above sum have negative :math:`A_n`, this scheme
-    fails, since Cantera normally does not allow negative pre-exponential
-    factors. But if there are duplicate reactions such that the total rate is
-    positive, then negative *A* parameters are acceptable, as long as the
-    ``'negative_A'`` option is specified.
-
-``negative_orders``
-    Reaction orders are normally required to be non-negative, since negative
-    orders are non-physical and undefined at zero concentration. Cantera allows
-    negative orders for a global reaction only if the ``negative_orders``
-    override option is specified for the reaction.
-
-
-Reactions with Pressure-Independent Rate
-========================================
-
-The :class:`reaction` entry is used to represent homogeneous reactions with
-pressure-independent rate coefficients and mass action kinetics.  Examples of
-reaction entries that implement some reactions in the GRI-Mech 3.0 natural gas
-combustion mechanism [#Smith1997]_ are shown below::
-
-    units(length = 'cm', quantity = 'mol', act_energy = 'cal/mol')
-    ...
-    reaction( "O + H2 <=> H + OH", [3.87000E+04, 2.7, 6260])
-    reaction( "O + HO2 <=> OH + O2", [2.00000E+13, 0.0, 0])
-    reaction( "O + H2O2 <=> OH + HO2", [9.63000E+06, 2.0, 4000])
-    reaction( "O + HCCO <=> H + 2 CO", [1.00000E+14, 0.0, 0])
-    reaction( "H + O2 + AR <=> HO2 + AR", kf=Arrhenius(A=7.00000E+17, b=-0.8, E=0))
-    reaction( equation = "HO2 + C3H7 <=> O2 + C3H8", kf=Arrhenius(2.55000E+10, 0.255, -943))
-    reaction( equation = "HO2 + C3H7 => OH + C2H5 + CH2O", kf=[2.41000E+13, 0.0, 0])
-
-Three-Body Reactions
-====================
-
-A three-body reaction is a gas-phase reaction of the form:
-
-.. math::
-
-    {\rm A + B + M} \rightleftharpoons {\rm AB + M}
-
-Here *M* is an unspecified collision partner that carries away excess energy to
-stabilize the *AB* molecule (forward direction) or supplies energy to break the *AB*
-bond (reverse direction).
-
-Different species may be more or less effective in acting as the collision partner. A species that is much lighter than
-*A* and *B* may not be able to transfer much of its kinetic energy, and so would be inefficient as a collision partner. On
-the other hand, a species with a transition from its ground state that is nearly resonant with one in the *AB** activated
-complex may be much more effective at exchanging energy than would otherwise be expected.
-
-These effects can be accounted for by defining a collision efficiency
-:math:`\epsilon` for each species, defined such that the forward reaction rate is
-
-.. math::
-
-    k_f(T)[A][B][M]
-
-where
-
-.. math::
-
-    [M] = \sum_k \epsilon_k C_k
-
-where :math:`C_k` is the concentration of species *k*. Since any constant
-collision efficiency can be absorbed into the rate coefficient :math:`k_f(T)`, the
-default collision efficiency is 1.0.
-
-A three-body reaction may be defined using the :class:`three_body_reaction` entry. The equation string for a three-body
-reaction must contain an ``'M'`` or ``'m'`` on both the reactant and product sides of the equation. The collision
-efficiencies are specified as a string, with the species name followed by a colon and the efficiency.
-
-Some examples from GRI-Mech 3.0 are shown below::
-
-    three_body_reaction( "2 O + M <=> O2 + M", [1.20000E+17, -1, 0],
-                         " AR:0.83 C2H6:3 CH4:2 CO:1.75 CO2:3.6 H2:2.4 H2O:15.4 ")
-
-    three_body_reaction( "O + H + M <=> OH + M", [5.00000E+17, -1, 0],
-                         efficiencies = " AR:0.7 C2H6:3 CH4:2 CO:1.5 CO2:2 H2:2 H2O:6 ")
-
-    three_body_reaction(
-        equation = "H + OH + M <=> H2O + M",
-        rate_coeff = [2.20000E+22, -2, 0],
-        efficiencies = " AR:0.38 C2H6:3 CH4:2 H2:0.73 H2O:3.65 "
-    )
-
-As always, the field names are optional *if* the field values are entered in the
-declaration order.
-
-Falloff Reactions
-=================
-
-A *falloff reaction* is one that has a rate that is first-order in [M] at low
-pressure, like a three-body reaction, but becomes zero-order in [M] as [M]
-increases. Dissociation / association reactions of polyatomic molecules often
-exhibit this behavior.
-
-The simplest expression for the rate coefficient for a falloff reaction is the
-Lindemann form [#Lindemann1922]_:
-
-.. math::
-
-    k_f(T, [{\rm M}]) = \frac{k_0[{\rm M}]}{1 + \frac{k_0{\rm [M]}}{k_\infty}}
-
-In the low-pressure limit, this approaches :math:`k0{\rm [M]}`, and in the
-high-pressure limit it approaches :math:`k_\infty`.
-
-Defining the non-dimensional reduced pressure:
-
-.. math::
-
-    P_r = \frac{k_0 {\rm [M]}}{k_\infty}
-
-The rate constant may be written as
-
-.. math::
-
-    k_f(T, P_r) = k_\infty \left(\frac{P_r}{1 + P_r}\right)
-
-More accurate models for unimolecular processes lead to other, more complex,
-forms for the dependence on reduced pressure. These can be accounted for by
-multiplying the Lindemann expression by a function :math:`F(T, P_r)`:
-
-.. math::
-
-    k_f(T, P_r) = k_\infty \left(\frac{P_r}{1 + P_r}\right) F(T, P_r)
-
-This expression is used to compute the rate coefficient for falloff
-reactions. The function :math:`F(T, P_r)` is the *falloff function*, and is
-specified by assigning an embedded entry to the ``falloff`` field.
-
-The Troe Falloff Function
--------------------------
-
-A widely-used falloff function is the one proposed by Gilbert et
-al. [#Gilbert1983]_:
-
-.. math::
-
-    \log_{10} F(T, P_r) = \frac{\log_{10} F_{cent}(T)}{1 + f_1^2}
-
-    F_{cent}(T) = (1-A) \exp(-T/T_3) + A \exp (-T/T_1) + \exp(-T_2/T)
-
-    f_1 = (\log_{10} P_r + C) / (N - 0.14 (\log_{10} P_r + C))
-
-    C = -0.4 - 0.67\; \log_{10} F_{cent}
-
-    N = 0.75 - 1.27\; \log_{10} F_{cent}
-
-The :class:`Troe` directive requires specifying the first three parameters
-:math:`(A, T_3, T_1)`. The fourth parameter, :math:`T_2`, is optional, defaulting to 0.0.
-
-.. _sec-sri-falloff:
-
-The SRI Falloff Function
-------------------------
-
-This falloff function is based on the one originally due to Stewart et
-al. [#Stewart1989]_, which required three parameters :math:`(a, b, c)`. Kee et
-al. [#Kee1989]_ generalized this function slightly by adding two more parameters
-:math:`(d, e)`. (The original form corresponds to :math:`d = 1, e = 0`.) Cantera
-supports the extended 5-parameter form, given by:
-
-.. math::
-
-    F(T, P_r) = d \bigl[a \exp(-b/T) + \exp(-T/c)\bigr]^{1/(1+\log_{10}^2 P_r )} T^e
-
-In keeping with the nomenclature of Kee et al. [#Kee1989]_, we will refer to this as
-the "SRI" falloff function. It is implemented by the :class:`SRI` directive.
-
-.. :: NOTE: "definingphases.pdf" contains documentation for the Wang-Frenklach falloff
-      function, which has a C++ implementation, but doesn't appear to be implemented
-      in the CTI or CTML parsers.
-
-Chemically-Activated Reactions
-==============================
-
-For these reactions, the rate falls off as the pressure increases, due to
-collisional stabilization of a reaction intermediate. Example:
-
-.. math::
-     \mathrm{Si + SiH_4 (+M) \leftrightarrow Si_2H_2 + H_2 (+M)}
-
-which competes with:
-
-.. math::
-    \mathrm{Si + SiH_4 (+M) \leftrightarrow Si_2H_4 (+M)}
-
-Like falloff reactions, chemically-activated reactions are described by
-blending between a "low pressure" and a "high pressure" rate expression. The
-difference is that the forward rate constant is written as being proportional
-to the *low pressure* rate constant:
-
-.. math::
-
-    k_f(T, P_r) = k_0 \left(\frac{1}{1 + P_r}\right) F(T, P_r)
-
-and the optional blending function *F* may described by any of the
-parameterizations allowed for falloff reactions. Chemically-activated
-reactions can be defined using the :class:`chemically_activated_reaction`
-directive.
-
-An example of a reaction specified with this parameterization::
-
-    chemically_activated_reaction('CH3 + OH (+ M) <=> CH2O + H2 (+ M)',
-                                  kLow=[2.823201e+02, 1.46878, (-3270.56495, 'cal/mol')],
-                                  kHigh=[5.880000e-14, 6.721, (-3022.227, 'cal/mol')],
-                                  falloff=Troe(A=1.671, T3=434.782, T1=2934.21, T2=3919.0))
-
-In this example, the units of :math:`k_0` (`kLow`) are m^3/kmol/s and the
-units of :math:`k_\infty` (`kHigh`) are 1/s.
-
-Pressure-Dependent Arrhenius Rate Expressions (P-Log)
-=====================================================
-
-The :class:`pdep_arrhenius` class represents pressure-dependent reaction rates
-by logarithmically interpolating between Arrhenius rate expressions at various
-pressures. Given two rate expressions at two specific pressures:
-
-.. math::
-
-    P_1: k_1(T) = A_1 T^{b_1} e^{E_1 / RT}
-
-    P_2: k_2(T) = A_2 T^{b_2} e^{E_2 / RT}
-
-The rate at an intermediate pressure :math:`P_1 < P < P_2` is computed as
-
-.. math::
-
-    \log k(T,P) = \log k_1(T) + \bigl(\log k_2(T) - \log k_1(T)\bigr)
-        \frac{\log P - \log P_1}{\log P_2 - \log P_1}
-
-Multiple rate expressions may be given at the same pressure, in which case the
-rate used in the interpolation formula is the sum of all the rates given at that
-pressure. For pressures outside the given range, the rate expression at the nearest
-pressure is used.
-
-An example of a reaction specified in this format::
-
-    pdep_arrhenius('R1 + R2 <=> P1 + P2',
-                   [(0.001315789, 'atm'), 2.440000e+10, 1.04, 3980.0],
-                   [(0.039473684, 'atm'), 3.890000e+10, 0.989, 4114.0],
-                   [(1.0, 'atm'), 3.460000e+12, 0.442, 5463.0],
-                   [(10.0, 'atm'), 1.720000e+14, -0.01, 7134.0],
-                   [(100.0, 'atm'), -7.410000e+30, -5.54, 12108.0],
-                   [(100.0, 'atm'), 1.900000e+15, -0.29, 8306.0])
-
-The first argument is the reaction equation. Each subsequent argument is a
-sequence of four elements specifying a pressure and the Arrhenius parameters at
-that pressure.
-
-Chebyshev Reaction Rate Expressions
-===================================
-
-Class :class:`chebyshev_reaction` represents a phenomenological rate coefficient
-:math:`k(T,P)` in terms of a bivariate Chebyshev polynomial. The rate constant
-can be written as:
-
-.. math:: \log k(T,P) = \sum_{t=1}^{N_T} \sum_{p=1}^{N_P} \alpha_{tp}
-                            \phi_t(\tilde{T}) \phi_p(\tilde{P})
-
-where :math:`\alpha_{tp}` are the constants defining the rate, :math:`\phi_n(x)`
-is the Chebyshev polynomial of the first kind of degree :math:`n` evaluated at
-:math:`x`, and
-
-.. math::
-
-    \tilde{T} \equiv \frac{2T^{-1} - T_\mathrm{min}^{-1} - T_\mathrm{max}^{-1}}
-                          {T_\mathrm{max}^{-1} - T_\mathrm{min}^{-1}}
-
-    \tilde{P} \equiv \frac{2 \log P - \log P_\mathrm{min} - \log P_\mathrm{max}}
-                          {\log P_\mathrm{max} - \log P_\mathrm{min}}
-
-are reduced temperature and reduced pressures which map the ranges
-:math:`(T_\mathrm{min}, T_\mathrm{max})` and :math:`(P_\mathrm{min},
-P_\mathrm{max})` to :math:`(-1, 1)`.
-
-A Chebyshev rate expression is specified in terms of the coefficient matrix
-:math:`\alpha` and the temperature and pressure ranges. An example of a
-Chebyshev rate expression where :math:`N_T = 6` and :math:`N_P = 4` is::
-
-    chebyshev_reaction('R1 + R2 <=> P1 + P2',
-                       Tmin=290.0, Tmax=3000.0,
-                       Pmin=(0.001, 'atm'), Pmax=(100.0, 'atm'),
-                       coeffs=[[-1.44280e+01,  2.59970e-01, -2.24320e-02, -2.78700e-03],
-                               [ 2.20630e+01,  4.88090e-01, -3.96430e-02, -5.48110e-03],
-                               [-2.32940e-01,  4.01900e-01, -2.60730e-02, -5.04860e-03],
-                               [-2.93660e-01,  2.85680e-01, -9.33730e-03, -4.01020e-03],
-                               [-2.26210e-01,  1.69190e-01,  4.85810e-03, -2.38030e-03],
-                               [-1.43220e-01,  7.71110e-02,  1.27080e-02, -6.41540e-04]])
-
-Note that the Chebyshev polynomials are not defined outside the interval
-:math:`(-1,1)`, and therefore extrapolation of rates outside the range of
-temperatures and pressure for which they are defined is strongly discouraged.
-
-Surface Reactions
-=================
-
-Heterogeneous reactions on surfaces are represented by an extended Arrhenius-
-like rate expression, which combines the modified Arrhenius rate expression with
-further corrections dependent on the fractional surface coverages
-:math:`\theta_k` of one or more surface species. The forward rate constant for a
-reaction of this type is:
-
-.. math::
-
-    k_f = A T^b \exp \left( - \frac{E_a}{RT} \right)
-            \prod_k 10^{a_k \theta_k} \theta_k^{m_k}
-            \exp \left( \frac{- E_k \theta_k}{RT} \right)
-
-where :math:`A`, :math:`b`, and :math:`E_a` are the modified Arrhenius
-parameters and :math:`a_k`, :math:`m_k`, and :math:`E_k` are the coverage
-dependencies from species *k*. A reaction of this form with a single coverage
-dependency (on the species ``H(S)``) can be written using class
-:class:`surface_reaction` with the ``coverage`` keyword argument supplied to the
-class :class:`Arrhenius`::
-
-    surface_reaction("2 H(S) => H2 + 2 PT(S)",
-                     Arrhenius(A, b, E_a,
-                               coverage=['H(S)', a_1, m_1, E_1]))
-
-For a reaction with multiple coverage dependencies, the following syntax is
-used::
-
-    surface_reaction("2 H(S) => H2 + 2 PT(S)",
-                     Arrhenius(A, b, E_a,
-                               coverage=[['H(S)', a_1, m_1, E_1],
-                                         ['PT(S)', a_2, m_2, E_2]]))
-
-Sticking Coefficients
----------------------
-
-Collisions between gas-phase molecules and surfaces which result in the gas-
-phase molecule sticking to the surface can be described as a reaction which is
-parameterized by a sticking coefficient:
-
-.. math::
-
-    \gamma = a T^b e^{-c/RT}
-
-where :math:`a`, :math:`b`, and :math:`c` are constants specific to the
-reaction. The values of these constants must be specified so that the sticking
-coefficient :math:`\gamma` is between 0 and 1 for all temperatures.
-
-The sticking coefficient is related to the forward rate constant by the
-formula:
-
-.. math::
-
-    k_f = \frac{\gamma}{\Gamma_\mathrm{tot}^m} \sqrt{\frac{RT}{2 \pi W}}
-
-where :math:`\Gamma_\mathrm{tot}` is the total molar site density, :math:`m` is
-the sum of all the surface reactant stoichiometric coefficients, and :math:`W`
-is the molecular weight of the gas phase species.
-
-A reaction of this form can be written as::
-
-    surface_reaction("H2O + PT(S) => H2O(S)", stick(a, b, c))
-
-
-Additional Options
-==================
-
-Reaction Orders
----------------
-
-Explicit reaction orders different from the stoichiometric coefficients are
-sometimes used for non-elementary reactions. For example, consider the global
-reaction:
-
-.. math::
-    \mathrm{C_8H_{18} + 12.5 O_2 \rightarrow 8 CO_2 + 9 H_2O}
-
-the forward rate constant might be given as [#Westbrook1981]_:
-
-.. math::
-    k_f = 4.6 \times 10^{11} [\mathrm{C_8H_{18}}]^{0.25} [\mathrm{O_2}]^{1.5}
-          \exp\left(\frac{30.0\,\mathrm{kcal/mol}}{RT}\right)
-
-This reaction could be defined as::
-
-    reaction("C8H18 + 12.5 O2 => 8 CO2 + 9 H2O", [4.6e11, 0.0, 30.0],
-             order="C8H18:0.25 O2:1.5")
-
-Special care is required in this case since the units of the pre-exponential
-factor depend on the sum of the reaction orders, which may not be an integer.
-
-Note that you can change reaction orders only for irreversible reactions.
-
-Normally, reaction orders are required to be positive. However, in some cases
-negative reaction orders are found to be better fits for experimental data. In
-these cases, the default behavior may be overridden by adding
-``negative_orders`` to the reaction options, e.g.::
-
-    reaction("C8H18 + 12.5 O2 => 8 CO2 + 9 H2O", [4.6e11, 0.0, 30.0],
-             order="C8H18:-0.25 O2:1.75", options=['negative_orders'])
-
-Some global reactions could have reactions orders for non-reactant species. One
-should add ``nonreactant_orders`` to the reaction options to use this feature::
-
-    reaction("C8H18 + 12.5 O2 => 8 CO2 + 9 H2O", [4.6e11, 0.0, 30.0],
-             order="C8H18:-0.25 CO:0.15",
-             options=['negative_orders', 'nonreactant_orders'])
-
-
-.. rubric:: References
-
-.. [#Gilbert1983] R. G. Gilbert, K. Luther, and
-   J. Troe. *Ber. Bunsenges. Phys. Chem.*, 87:169, 1983.
-
-.. [#Lindemann1922] F. Lindemann. *Trans. Faraday Soc.*, 17:598, 1922.
-
-.. [#Smith1997] Gregory P. Smith, David M. Golden, Michael Frenklach, Nigel
-   W. Moriarty, Boris Eiteneer, Mikhail Goldenberg, C. Thomas Bowman, Ronald
-   K. Hanson, Soonho Song, William C. Gardiner, Jr., Vitali V. Lissianski, , and
-   Zhiwei Qin. GRI-Mech version 3.0, 1997. see
-   http://www.me.berkeley.edu/gri_mech.
-
-.. [#Stewart1989] P. H. Stewart, C. W. Larson, and D. Golden.
-   *Combustion and Flame*, 75:25, 1989.
-
-.. [#Kee1989] R. J. Kee, F. M. Rupley, and J. A. Miller. Chemkin-II: A Fortran
-   chemical kinetics package for the analysis of gas-phase chemical
-   kinetics. Technical Report SAND89-8009, Sandia National Laboratories, 1989.
-
-.. [#Westbrook1981] C. K. Westbrook and F. L. Dryer. Simplified reaction
-   mechanisms for the oxidation of hydrocarbon fuels in flames. *Combustion
-   Science and Technology* **27**, pp. 31--43. 1981.

doc/sphinx/cti/species.rst

@@ -1,340 +0,0 @@
-.. py:currentmodule:: cantera.ctml_writer
-
-.. _sec-species:
-
-********************
-Elements and Species
-********************
-
-.. _sec-elements:
-
-Elements
-========
-
-The :class:`element` entry defines an element or an isotope of an element. Note that
-these entries are not often needed, since the the database file ``elements.xml``
-is searched for element definitions when importing phase and interface
-definitions.  An explicit element entry is needed only if an isotope not in
-``elements.xml`` is required::
-
-    element(symbol='C-13',
-            atomic_mass=13.003354826)
-    element("O-18", 17.9991603)
-
-Species
-=======
-
-For each species, a :class:`species` entry is required. Species are defined at
-the top-level of the input file---their definitions are not embedded in a phase
-or interface entry.
-
-Species Name
-------------
-
-The name field may contain embedded parentheses, ``+`` or ``-`` signs to
-indicate the charge, or just about anything else that is printable and not a
-reserved character in XML.  Some example name specifications::
-
-    name = 'CH4'
-    name = 'methane'
-    name = 'argon_2+'
-    name = 'CH2(singlet)'
-
-Elemental Composition
----------------------
-
-The elemental composition is specified in the atoms entry, as follows::
-
-    atoms = "C:1 O:2"             # CO2
-    atoms = "C:1, O:2"            # CO2 with optional comma
-    atoms = "Y:1 Ba:2 Cu:3 O:6.5" # stoichiometric YBCO
-    atoms = ""                    # a surface species representing an empty site
-    atoms = "Ar:1 E:-2"           # Ar++
-
-For gaseous species, the elemental composition is well-defined, since the
-species represent distinct molecules. For species in solid or liquid solutions,
-or on surfaces, there may be several possible ways of defining the species. For
-example, an aqueous species might be defined with or without including the water
-molecules in the solvation cage surrounding it.
-
-For surface species, it is possible to omit the ``atoms`` field entirely, in
-which case it is composed of nothing, and represents an empty surface site. This
-can also be done to represent vacancies in solids. A charged vacancy can be
-defined to be composed solely of electrons::
-
-    species(name = 'ysz-oxygen-vacancy',
-            atoms = 'O:0, E:2',
-            # ...,
-            )
-
-Note that an atom number of zero may be given if desired, but is completely
-equivalent to omitting that element.
-
-The number of atoms of an element must be non-negative, except for the special
-"element" ``E`` that represents an electron.
-
-Thermodynamic Properties
-------------------------
-
-The :class:`phase` and :class:`ideal_interface` entries discussed in the last
-chapter implement specific models for the thermodynamic properties appropriate
-for the type of phase or interface they represent. Although each one may use
-different expressions to compute the properties, they all require thermodynamic
-property information for the individual species. For the phase types implemented
-at present, the properties needed are:
-
-1. the molar heat capacity at constant pressure :math:`\hat{c}^0_p(T)` for a
-   range of temperatures and a reference pressure :math:`P_0`;
-2. the molar enthalpy :math:`\hat{h}(T_0, P_0)` at :math:`P_0` and a reference
-   temperature :math:`T_0`;
-3. the absolute molar entropy :math:`\hat{s}(T_0, P_0)` at :math:`(T_0, P_0)`.
-
-See: :ref:`sec-thermo-models`
-
-.. _sec-species-transport-models:
-
-Species Transport Coefficients
-------------------------------
-
-Transport property models in general require coefficients that express the
-effect of each species on the transport properties of the phase. The
-``transport`` field may be assigned an embedded entry that provides
-species-specific coefficients.
-
-Currently, the only entry type is :class:`gas_transport`, which supplies
-parameters needed by the ideal-gas transport property models. The field values
-and their units of the :class:`gas_transport` entry are compatible with the
-transport database parameters described by Kee et al. [#Kee1986]_. Entries in
-transport databases in the format described in their report can be used directly
-in the fields of the :class:`gas_transport` entry, without requiring any unit
-conversion. The numeric field values should all be entered as pure numbers, with
-no attached units string.
-
-.. _sec-thermo-models:
-
-Thermodynamic Property Models
-=============================
-
-The entry types described in this section can be used to provide data for the
-``thermo`` field of a :class:`species`. Each implements a different
-*parameterization* (functional form) for the heat capacity. Note that there is
-no requirement that all species in a phase use the same parameterization; each
-species can use the one most appropriate to represent how the heat capacity
-depends on temperature.
-
-Currently, several types are implemented which provide species properties
-appropriate for models of ideal gas mixtures, ideal solutions, and pure
-compounds.
-
-The NASA 7-Coefficient Polynomial Parameterization
---------------------------------------------------
-
-The NASA 7-coefficient polynomial parameterization is used to compute the
-species reference-state thermodynamic properties :math:`\hat{c}^0_p(T)`,
-:math:`\hat{h}^0(T)` and :math:`\hat{s}^0(T)`.
-
-The NASA parameterization represents :math:`\hat{c}^0_p(T)` with a fourth-order
-polynomial:
-
-.. math::
-
-    \frac{c_p^0(T)}{R} = a_0 + a_1 T + a_2 T^2 + a_3 T^3 + a_4 T^4
-
-    \frac{h^0(T)}{RT} = a_0 + \frac{a1}{2}T + \frac{a_2}{3} T^2 +
-                        \frac{a_3}{4} T^3 + \frac{a_4}{5} T^4 + \frac{a_5}{T}
-
-    \frac{s^0(T)}{R} = a_0 \ln T + a_1 T + \frac{a_2}{2} T^2 + \frac{a_3}{3} T^3 +
-                       \frac{a_4}{4} T^4 + a_6
-
-Note that this is the "old" NASA polynomial form, used in the original NASA
-equilibrium program and in Chemkin, which uses 7 coefficients in each of two
-temperature regions. It is not compatible with the form used in the most recent
-version of the NASA equilibrium program, which uses 9 coefficients for each
-temperature region.
-
-A NASA parameterization is defined by an embedded :class:`NASA` entry. Very
-often, two NASA parameterizations are used for two contiguous temperature
-ranges. This can be specified by assigning the ``thermo`` field of the
-``species`` entry a sequence of two :class:`NASA` entries::
-
-    # use one NASA parameterization for T < 1000 K, and another for T > 1000 K.
-    species(name = "O2",
-            atoms = " O:2 ",
-            thermo = (
-                NASA( [ 200.00, 1000.00], [ 3.782456360E+00, -2.996734160E-03,
-                        9.847302010E-06, -9.681295090E-09, 3.243728370E-12,
-                        -1.063943560E+03, 3.657675730E+00] ),
-                NASA( [ 1000.00, 3500.00], [ 3.282537840E+00, 1.483087540E-03,
-                        -7.579666690E-07, 2.094705550E-10, -2.167177940E-14,
-                        -1.088457720E+03, 5.453231290E+00] ) ) )
-
-The NASA 9-Coefficient Polynomial Parameterization
---------------------------------------------------
-
-The NASA 9-coefficient polynomial parameterization [#McBride2002]_ ("NASA9" for
-short) is an extension of the NASA 7-coefficient polynomial parameterization
-which includes two additional terms in each temperature region, as well as
-supporting an arbitrary number of temperature regions.
-
-The NASA9 parameterization represents the species thermodynamic properties with
-the following equations:
-
-.. math::
-
-    \frac{C_p^0(T)}{R} = a_0 T^{-2} + a_1 T^{-1} + a_2 + a_3 T
-                     + a_4 T^2 + a_5 T^3 + a_6 T^4
-
-    \frac{H^0(T)}{RT} = - a_0 T^{-2} + a_1 \frac{\ln T}{T} + a_2
-        + \frac{a_3}{2} T + \frac{a_4}{3} T^2  + \frac{a_5}{4} T^3 +
-        \frac{a_6}{5} T^4 + \frac{a_7}{T}
-
-    \frac{s^0(T)}{R} = - \frac{a_0}{2} T^{-2} - a_1 T^{-1} + a_2 \ln T
-       + a_3 T + \frac{a_4}{2} T^2 + \frac{a_5}{3} T^3  + \frac{a_6}{4} T^4 + a_8
-
-The following is an example of a species defined using the NASA9
-parameterization in three different temperature regions::
-
-    species(name=u'CO2',
-            atoms='C:1 O:2',
-            thermo=(NASA9([200.00, 1000.00],
-                          [ 4.943650540E+04, -6.264116010E+02,  5.301725240E+00,
-                            2.503813816E-03, -2.127308728E-07, -7.689988780E-10,
-                            2.849677801E-13, -4.528198460E+04, -7.048279440E+00]),
-                    NASA9([1000.00, 6000.00],
-                          [ 1.176962419E+05, -1.788791477E+03,  8.291523190E+00,
-                           -9.223156780E-05,  4.863676880E-09, -1.891053312E-12,
-                            6.330036590E-16, -3.908350590E+04, -2.652669281E+01]),
-                    NASA9([6000.00, 20000.00],
-                          [-1.544423287E+09,  1.016847056E+06, -2.561405230E+02,
-                            3.369401080E-02, -2.181184337E-06,  6.991420840E-11,
-                           -8.842351500E-16, -8.043214510E+06,  2.254177493E+03])),
-            note='Gurvich,1991 pt1 p27 pt2 p24. [g 9/99]')
-
-Thermodynamic data for a range of species can be obtained from the `NASA
-ThermoBuild <http://cearun.grc.nasa.gov/cea/index_ds.html>`_ tool. Using the web
-interface, an input file can be obtained for a set of species. This input file
-should then be modified so that the first line reads "`thermo nasa9`", as in the
-following example::
-
-    thermo nasa9
-       200.000  1000.000  6000.000 20000.000   9/09/04
-    CO                Gurvich,1979 pt1 p25 pt2 p29.
-     3 tpis79 C   1.00O   1.00    0.00    0.00    0.00 0   28.0101000    -110535.196
-        200.000   1000.0007 -2.0 -1.0  0.0  1.0  2.0  3.0  4.0  0.0         8671.104
-     1.489045326D+04-2.922285939D+02 5.724527170D+00-8.176235030D-03 1.456903469D-05
-    -1.087746302D-08 3.027941827D-12                -1.303131878D+04-7.859241350D+00
-       1000.000   6000.0007 -2.0 -1.0  0.0  1.0  2.0  3.0  4.0  0.0         8671.104
-     4.619197250D+05-1.944704863D+03 5.916714180D+00-5.664282830D-04 1.398814540D-07
-    -1.787680361D-11 9.620935570D-16                -2.466261084D+03-1.387413108D+01
-       6000.000  20000.0007 -2.0 -1.0  0.0  1.0  2.0  3.0  4.0  0.0         8671.104
-     8.868662960D+08-7.500377840D+05 2.495474979D+02-3.956351100D-02 3.297772080D-06
-    -1.318409933D-10 1.998937948D-15                 5.701421130D+06-2.060704786D+03
-    CO2               Gurvich,1991 pt1 p27 pt2 p24.
-     3 g 9/99 C   1.00O   2.00    0.00    0.00    0.00 0   44.0095000    -393510.000
-        200.000   1000.0007 -2.0 -1.0  0.0  1.0  2.0  3.0  4.0  0.0         9365.469
-     4.943650540D+04-6.264116010D+02 5.301725240D+00 2.503813816D-03-2.127308728D-07
-    -7.689988780D-10 2.849677801D-13                -4.528198460D+04-7.048279440D+00
-       1000.000   6000.0007 -2.0 -1.0  0.0  1.0  2.0  3.0  4.0  0.0         9365.469
-     1.176962419D+05-1.788791477D+03 8.291523190D+00-9.223156780D-05 4.863676880D-09
-    -1.891053312D-12 6.330036590D-16                -3.908350590D+04-2.652669281D+01
-       6000.000  20000.0007 -2.0 -1.0  0.0  1.0  2.0  3.0  4.0  0.0         9365.469
-    -1.544423287D+09 1.016847056D+06-2.561405230D+02 3.369401080D-02-2.181184337D-06
-     6.991420840D-11-8.842351500D-16                -8.043214510D+06 2.254177493D+03
-    END PRODUCTS
-    END REACTANTS
-
-This file (saved for example as `nasathermo.dat`) can then be converted to the
-CTI format using the `ck2cti` script::
-
-    ck2cti --thermo=nasathermo.dat
-
-To generate a full phase definition, create an input file defining the phase as
-well, saved for example as `nasa.inp`::
-
-    elements
-    C O
-    end
-
-    species
-    CO CO2
-    end
-
-The two input files can then be converted together by calling::
-
-    ck2cti --input=nasa.inp --thermo=nasathermo.dat
-
-
-The Shomate Parameterization
-----------------------------
-
-The Shomate parameterization is:
-
-.. math::
-
-    \hat{c}_p^0(T) = A + Bt + Ct^2 + Dt^3 + \frac{E}{t^2}
-
-    \hat{h}^0(T) = At + \frac{Bt^2}{2} + \frac{Ct^3}{3} + \frac{Dt^4}{4} -
-                   \frac{E}{t} + F
-
-    \hat{s}^0(T) = A \ln t + B t + \frac{Ct^2}{2} + \frac{Dt^3}{3} -
-                   \frac{E}{2t^2} + G
-
-where :math:`t = T / 1000 K`. It requires 7 coefficients A, B, C, D, E, F, and
-G. This parameterization is used to represent reference-state properties in the
-`NIST Chemistry WebBook <http://webbook.nist.gov/chemistry>`_. The values of the
-coefficients A through G should be entered precisely as shown there, with no
-units attached. Unit conversions to SI will be handled internally.
-
-Example usage of the :class:`Shomate` directive::
-
-    # use a single Shomate parameterization.
-    species(name = "O2",
-            atoms = " O:2 ",
-            thermo = Shomate( [298.0, 6000.0],
-                              [29.659, 6.137261, -1.186521, 0.09578, -0.219663,
-                               -9.861391, 237.948] ) )
-
-Constant Heat Capacity
-----------------------
-
-In some cases, species properties may only be required at a single temperature
-or over a narrow temperature range. In such cases, the heat capacity can be
-approximated as constant, and simpler expressions can be used for the thermodynamic
-properties. The :class:`const_cp` parameterization computes the properties as
-follows:
-
-.. math::
-
-    \hat{c}_p^0(T) = \hat{c}_p^0(T_0)
-
-    \hat{h}^0(T) = \hat{h}^0(T_0) + \hat{c}_p^0\cdot(T-T_0)
-
-    \hat{s}^0(T) = \hat{s}^0(T_0) + \hat{c}_p^0 \ln (T/T_0)
-
-The parameterization uses four constants: :math:`T_0, \hat{c}_p^0(T_0),
-\hat{h}^0(T_0), \hat{s}^0(T)`. The default value of :math:`T_0` is 298.15 K; the
-default value for the other parameters is 0.0.
-
-Example::
-
-    thermo = const_cp(h0=(-393.51, 'kJ/mol'),
-                      s0=(213.785, 'J/mol/K'),
-                      cp0=(37.12, 'J/mol/K'))
-
-Assuming that the :func:`units` function has been used to set the default energy
-units to Joules and the default quantity unit to kmol, this may be equivalently
-written as::
-
-    thermo = const_cp(h0=-3.9351e8, s0=2.13785e5, cp0=3.712e4)
-
-.. See ##REF## for more examples of use of this parameterization.
-
-.. rubric:: References
-
-.. [#Kee1986] R. J. Kee, G. Dixon-Lewis, J. Warnatz, M. E. Coltrin, and J. A. Miller.
-   A FORTRAN Computer Code Package for the Evaluation of Gas-Phase, Multicomponent
-   Transport Properties. Technical Report SAND86-8246, Sandia National Laboratories, 1986.
-
-.. [#Mcbride2002] B. J. McBride, M. J. Zehe, S. Gordon. "NASA Glenn Coefficients
-   for Calculating Thermodynamic Properties of Individual Species,"
-   NASA/TP-2002-211556, Sept. 2002.

doc/sphinx/cttheme/static/cantera.css

@@ -1,4 +1,4 @@
-@import url('./sphinxdoc.css');
+@import url('./alabaster.css');
 
 dl.method, dl.attribute, dl.staticmethod, dl.classmethod {
      border-top: 1px solid #aaa;
@@ -9,3 +9,11 @@ dl.class, dl.function {
     border-top: 2px solid #888;
     padding-top: 4px;
 }
+
+.nav-link {
+    text-decoration: none !important;
+    font-family: -apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Helvetica Neue",Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol" !important;
+    font-size: 1rem !important;
+}
+
+#logo { width: 250px; }

doc/sphinx/cttheme/theme.conf

@@ -1,3 +1,3 @@
 [theme]
-inherit = sphinxdoc
+inherit = alabaster
 stylesheet = cantera.css

doc/sphinx/cxx-guide/compiling.rst

@@ -1,147 +0,0 @@
-
-******************************
-Compiling Cantera C++ Programs
-******************************
-
-In general, it should be possible to use Cantera with any build system by
-specifying the appropriate header and library paths, and specifying the required
-libraries when linking. It is also necessary to specify the paths for libraries
-used by Cantera, e.g. Sundials, BLAS, and LAPACK.
-
-pkg-config
-==========
-
-On systems where the ``pkg-config`` program is installed, it can be used to
-determine the correct compiler and linker flags for use with Cantera. For
-example:
-
-.. code-block:: bash
-
-   g++ myProgram.cpp -o myProgram $(pkg-config --cflags --libs cantera)
-
-It can also be used to populate variables in a Makefile:
-
-.. code-block:: make
-
-    CFLAGS += $(shell pkg-config --cflags cantera)
-    LIBS += $(shell pkg-config --libs cantera)
-
-Or in an SConstruct file::
-
-    env.ParseConfig("pkg-config --cflags --libs cantera")
-
-Note that ``pkg-config`` will work only if it can find the ``cantera.pc``
-file. If Cantera's libraries are not installed in a standard location such as
-``/usr/lib`` or ``/usr/local/lib``, you may need to set the ``PKG_CONFIG_PATH``
-environment variable appropriately before using ``pkg-config``.
-
-SCons
-=====
-
-SCons is a multi-platform, Python-based build system. It is the build system
-used to compile Cantera. The description of how to build a project is contained
-in a file named ``SConstruct``. The ``SConstruct`` file is actually a Python
-script, which makes it very straightforward to add functionality to a
-SCons-based build system.
-
-A typical ``SConstruct`` file for compiling a program that uses Cantera might
-look like this::
-
-    env = Environment()
-
-    env.Append(CCFLAGS='-g',
-               CPPPATH=['/usr/local/cantera/include',
-                        '/usr/local/sundials/include'],
-               LIBS=['cantera', 'sundials_cvodes', 'sundials_ida',
-                     'sundials_nvecserial', 'lapack', 'blas'],
-               LIBPATH=['/usr/local/cantera/lib',
-                        '/usr/local/sundials/lib'],
-               LINKFLAGS=['-g', '-pthread'])
-
-    sample = env.Program('sample', 'sample.cpp')
-    Default(sample)
-
-This script establishes what SCons refers to as a "construction environment"
-named ``env``, and sets the header (``CPPPATH``) and library (``LIBPATH``) paths
-to include the directories containing the Cantera headers and libraries, as well
-as libraries that Cantera depends on, such as Sundials, BLAS, and LAPACK. Then,
-a program named ``sample`` is compiled using the single source file
-``sample.cpp``.
-
-Several other example ``SConstruct`` files are included with the C++ examples
-contained in the ``samples`` subdirectory of the Cantera installation directory.
-
-For more information on SCons, see the `SCons Wiki <http://scons.org/wiki/>`_
-and the `SCons homepage <http://www.scons.org>`_.
-
-CMake
-=====
-
-CMake is a multi-platform build system which uses a high-level project
-description to generate platform-specific build scripts (i.e. on Linux, CMake
-will generate Makefiles). The configuration file for a CMake project is called
-``CMakeLists.txt``. A typical ``CMakeLists.txt`` file for compiling a program
-that uses Cantera might look like this:
-
-.. code-block:: cmake
-
-    cmake_minimum_required(VERSION 3.1)
-    project (sample)
-
-    set(CMAKE_VERBOSE_MAKEFILE ON)
-    set(CMAKE_CXX_STANDARD 11)
-
-    find_package(Threads REQUIRED)
-
-    include_directories("/opt/cantera/include" "/opt/sundials-2.7.0/include")
-    link_directories("/opt/cantera/lib" "/opt/sundials-2.7.0/lib")
-
-    add_executable(sample sample.cpp)
-    target_link_libraries(sample cantera sundials_cvodes sundials_ida sundials_nvecserial fmt Threads::Threads)
-
-Several example ``CMakeLists.txt`` files are included with the C++ examples
-contained in the ``samples`` subdirectory of the Cantera installation directory,
-which have the paths and lists of libraries correctly configured for system on
-which they are installed.
-
-Make
-====
-
-Cantera is distributed with an "include Makefile" that can be used with
-Make-based build systems. This file ``Cantera.mak`` is located in the
-``samples`` subdirectory of the Cantera installation directory. To use it, add a
-line referencing this file to the top of your Makefile::
-
-    include path/to/Cantera.mak
-
-The path specified should be the relative path from the ``Makefile`` to
-``Cantera.mak``. This file defines several variables which can be used in your
-Makefile. The following is an example ``Makefile`` that uses the definitions
-contained in ``Cantera.mak``:
-
-.. code-block:: makefile
-
-    include ../../Cantera.mak
-
-    CC=gcc
-    CXX=g++
-    RM=rm -f
-    CCFLAGS=-g
-    CPPFLAGS=$(CANTERA_INCLUDES)
-    LDFLAGS=
-    LDLIBS=$(CANTERA_LIBS)
-
-    SRCS=sample.cpp
-    OBJS=$(subst .cpp,.o,$(SRCS))
-
-    all: sample
-
-    kinetics1: $(OBJS)
-	    $(CXX) $(LDFLAGS) -o sample $(OBJS) $(LDLIBS)
-
-    clean:
-	    $(RM) $(OBJS)
-
-    dist-clean: clean
-	    $(RM) *~
-

doc/sphinx/cxx-guide/demo1a.cpp

@@ -1,34 +0,0 @@
-#include "cantera/thermo.h"
-#include <iostream>
-
-using namespace Cantera;
-
-// The actual code is put into a function that
-// can be called from the main program.
-void simple_demo()
-{
-    // Create a new phase
-    std::unique_ptr<ThermoPhase> gas(newPhase("h2o2.cti","ohmech"));
-
-    // Set its state by specifying T (500 K) P (2 atm) and the mole
-    // fractions. Note that the mole fractions do not need to sum to
-    // 1.0 - they will be normalized internally. Also, the values for
-    // any unspecified species will be set to zero.
-    gas->setState_TPX(500.0, 2.0*OneAtm, "H2O:1.0, H2:8.0, AR:1.0");
-
-    // Print a summary report of the state of the gas
-    std::cout << gas->report() << std::endl;
-}
-
-// the main program just calls function simple_demo within
-// a 'try' block, and catches CanteraError exceptions that
-// might be thrown
-int main()
-{
-    try {
-        simple_demo();
-    } catch (CanteraError& err) {
-        std::cout << err.what() << std::endl;
-    }
-}
-

doc/sphinx/cxx-guide/demo1b.cpp

@@ -1,66 +0,0 @@
-#include "cantera/thermo.h"
-#include "cantera/kinetics.h"
-#include "cantera/transport.h"
-
-using namespace Cantera;
-
-// The actual code is put into a function that can be called from the main
-// program.
-void simple_demo2()
-{
-    // Create a new phase
-    std::unique_ptr<ThermoPhase> gas(newPhase("gri30.cti", "gri30_mix"));
-
-    // List of phases participating in reactions (just one for homogeneous
-    // kinetics)
-    std::vector<ThermoPhase*> phases{gas.get()};
-
-    // Create the Kinetics object. Based on the phase definition used, this will
-    // be a GasKinetics object.
-    std::unique_ptr<Kinetics> kin(newKineticsMgr(gas->xml(), phases));
-
-    // Set an "interesting" mixture state where we will observe non-zero reacton
-    // rates.
-    gas->setState_TPX(500.0, 2.0*OneAtm, "CH4:1.0, O2:1.0, N2:3.76");
-    gas->equilibrate("HP");
-    gas->setState_TP(gas->temperature() - 100, gas->pressure());
-
-    // Get the net reaction rates
-    vector_fp wdot(kin->nReactions());
-    kin->getNetRatesOfProgress(wdot.data());
-
-    writelog("Net reaction rates for reactions involving CO2\n");
-    size_t kCO2 = gas->speciesIndex("CO2");
-    for (size_t i = 0; i < kin->nReactions(); i++) {
-        if (kin->reactantStoichCoeff(kCO2, i)
-            || kin->productStoichCoeff(kCO2, i)) {
-            writelog("{:3d}  {:30s}  {: .8e}\n",
-                i, kin->reactionString(i), wdot[i]);
-        }
-    }
-    writelog("\n");
-
-    // Create a Transport object. Based on the transport model specified in the
-    // "gri30_mix" phase, this will be a MixGasTransport object.
-    std::unique_ptr<Transport> trans(newDefaultTransportMgr(gas.get()));
-    writelog("T        viscosity     thermal conductivity\n");
-    writelog("------   -----------   --------------------\n");
-    for (size_t n = 0; n < 5; n++) {
-        double T = 300 + 100 * n;
-        gas->setState_TP(T, gas->pressure());
-        writelog("{:.1f}    {:.4e}    {:.4e}\n",
-            T, trans->viscosity(), trans->thermalConductivity());
-    }
-}
-
-// the main program just calls function simple_demo2 within a 'try' block, and
-// catches exceptions that might be thrown
-int main()
-{
-    try {
-        simple_demo2();
-    } catch (std::exception& err) {
-        std::cout << err.what() << std::endl;
-    }
-}
-

doc/sphinx/cxx-guide/demoequil.cpp

@@ -1,20 +0,0 @@
-#include "cantera/thermo.h"
-
-using namespace Cantera;
-
-void equil_demo()
-{
-    std::unique_ptr<ThermoPhase> gas(newPhase("h2o2.cti","ohmech"));
-    gas->setState_TPX(1500.0, 2.0*OneAtm, "O2:1.0, H2:3.0, AR:1.0");
-    gas->equilibrate("TP");
-    std::cout << gas->report() << std::endl;
-}
-
-int main()
-{
-    try {
-        equil_demo();
-    } catch (CanteraError& err) {
-        std::cout << err.what() << std::endl;
-    }
-}

doc/sphinx/cxx-guide/equil-example.rst

@@ -1,57 +0,0 @@
-
-************************************
-Chemical Equilibrium Example Program
-************************************
-
-In the program below, the `equilibrate` method is called to set the gas to a
-state of chemical equilibrium, holding the temperature and pressure fixed.
-
-.. literalinclude:: demoequil.cpp
-   :language: c++
-
-The program output is::
-
-           temperature            1500  K
-              pressure          202650  Pa
-               density        0.316828  kg/m^3
-      mean mol. weight         19.4985  amu
-
-                              1 kg            1 kmol
-                           -----------      ------------
-              enthalpy    -4.17903e+06       -8.149e+07     J
-       internal energy    -4.81866e+06       -9.396e+07     J
-               entropy         11283.3          2.2e+05     J/K
-        Gibbs function     -2.1104e+07       -4.115e+08     J
-     heat capacity c_p         1893.06        3.691e+04     J/K
-     heat capacity c_v         1466.65         2.86e+04     J/K
-
-                               X                 Y          Chem. Pot. / RT
-                         -------------     ------------     ------------
-                    H2       0.249996        0.0258462         -19.2954
-                     H    6.22521e-06        3.218e-07         -9.64768
-                     O    7.66933e-12      6.29302e-12         -26.3767
-                    O2     7.1586e-12      1.17479e-11         -52.7533
-                    OH    3.55353e-07      3.09952e-07         -36.0243
-                   H2O       0.499998         0.461963          -45.672
-                   HO2    7.30338e-15       1.2363e-14          -62.401
-                  H2O2    3.95781e-13      6.90429e-13         -72.0487
-                    AR       0.249999          0.51219         -21.3391
-
-
-How can we tell that this is really a state of chemical equilibrium? Well, by
-applying the equation of reaction equilibrium to formation reactions from the
-elements, it is straightforward to show that:
-
-.. math:: \mu_k = \sum_m \lambda_m a_{km}.
-
-where :math:`\mu_k` is the chemical potential of species *k*, :math:`a_{km}` is
-the number of atoms of element *m* in species *k*, and :math:`\lambda_m` is the
-chemical potential of the elemental species per atom (the so-called "element
-potential"). In other words, the chemical potential of each species in an
-equilibrium state is a linear sum of contributions from each atom. We see that
-this is true in the output above---the chemical potential of H2 is exactly
-twice that of H, the chemical potential for OH is the sum of the values for H
-and O, the value for H2O2 is twice as large as the value for OH, and so on.
-
-We'll see later how the :ct:`equilibrate <Cantera::ThermoPhase::equilibrate>`
-function really works.

doc/sphinx/cxx-guide/factories.rst

@@ -1,47 +0,0 @@
-Creating ThermoPhase, Kinetics, and Transport objects
-=====================================================
-
-The following program demonstrates the general method for creating the following
-object types:
-
-- `ThermoPhase` - represents the thermodynamic properties of mixtures containing
-  one or more species)
-- `Kinetics` - represents a kinetic mechanism involving one or more phases)
-- `Transport` - computes transport properties for a `ThermoPhase`
-
-This program uses "factory" functions to create derived objects objects of the
-appropriate type which are specified in the input file `gri30.cti`.
-
-.. literalinclude:: demo1b.cpp
-   :language: c++
-
-This program produces the output below::
-
-    Net reaction rates for reactions involving CO2
-     11  CO + O (+M) <=> CO2 (+M)         3.54150724e-08
-     13  HCO + O <=> CO2 + H              1.95680014e-11
-     29  CH2CO + O <=> CH2 + CO2          3.45366988e-17
-     30  CO + O2 <=> CO2 + O              2.70102522e-13
-     41  CO2 + 2 H <=> CO2 + H2           3.45305359e-08
-     98  CO + OH <=> CO2 + H              6.46935907e-03
-    119  CO + HO2 <=> CO2 + OH            1.86807529e-10
-    131  CH + CO2 <=> CO + HCO            9.41365695e-14
-    151  CH2(S) + CO2 <=> CH2 + CO2       3.11161382e-12
-    152  CH2(S) + CO2 <=> CH2O + CO       2.85339329e-11
-    225  NCO + O2 <=> CO2 + NO            3.74127282e-19
-    228  NCO + NO <=> CO2 + N2            6.25672779e-14
-    261  HNCO + O <=> CO2 + NH            6.84524890e-13
-    267  HNCO + OH <=> CO2 + NH2          7.78871264e-10
-    279  CO2 + NH <=> CO + HNO           -3.30333658e-09
-    281  NCO + NO2 <=> CO2 + N2O          2.14286686e-20
-    282  CO2 + N <=> CO + NO              6.42658283e-10
-    289  CH2 + O2 => CO2 + 2 H            1.51032319e-18
-    304  CH2CHO + O => CH2 + CO2 + H      1.00331734e-19
-
-    T        viscosity     thermal conductivity
-    ------   -----------   --------------------
-    300.0    1.6658e-05    4.2089e-02
-    400.0    2.0861e-05    5.2537e-02
-    500.0    2.4681e-05    6.2451e-02
-    600.0    2.8218e-05    7.2157e-02
-    700.0    3.1534e-05    8.1754e-02

doc/sphinx/cxx-guide/headers.rst

@@ -1,41 +0,0 @@
-
-****************
-C++ Header Files
-****************
-
-Cantera provides some header files designed for use in C++ application
-programs. These are designed to include those portions of Cantera needed for
-particular types of calculations.
-
-These headers are designed for use in C++ application programs, and are not
-included by the Cantera core. The headers and their functions are:
-
-``IdealGasMix.h``
-    Provides class :ct:`IdealGasMix`.
-
-``Interface.h``
-    Provides class :ct:`Interface`.
-
-``integrators.h``
-    ODE Integrators.
-
-``kinetics.h``
-    Base kinetics classes and functions for creating :ct:`Kinetics` objects from
-    input files.
-
-``onedim.h``
-    One-dimensional reacting flows.
-
-``reactionpaths.h``
-    Reaction path diagrams.
-
-``thermo.h``
-    Base thermodynamic classes and functions for creating :ct:`ThermoPhase`
-    objects from input files.
-
-``transport.h``
-    Base transport property classes and functions for creating :ct:`Transport`
-    objects from input files.
-
-``zerodim.h``
-    Zero-dimensional reactor networks.

doc/sphinx/cxx-guide/index.rst

@@ -1,14 +0,0 @@
-
-**************************
-C++ Interface User's Guide
-**************************
-
-.. toctree::
-   :maxdepth: 2
-
-   compiling
-   headers
-   thermo
-   simple-example
-   equil-example
-   factories

doc/sphinx/cxx-guide/simple-example.rst

@@ -1,75 +0,0 @@
-
-*************************
-A Very Simple C++ Program
-*************************
-
-A short C++ program that uses Cantera is shown below. This program reads in a
-specification of a gas mixture from an input file, and then builds a new object
-representing the mixture. It then sets the thermodynamic state and composition
-of the gas mixture, and prints out a summary of its properties.
-
-.. literalinclude:: demo1a.cpp
-   :language: c++
-
-Before you can run this program, it first needs to be compiled. On a Linux
-system using the GCC compiler, a typical command line for compiling this program
-might look like this::
-
-    g++ -o combustor -pthread -O3 -std=c++0x -I/opt/cantera-2.3.0/include -L/opt/cantera-2.3.0/lib -lcantera -lsundials_cvodes -lsundials_ida -lsundials_nvecserial combustor.cpp
-
-The locations of the Cantera header files (specified by the `-I` option) and the
-libraries (specified by the `-L` option) will vary depending on where you
-installed Cantera, and the list of libraries (such as `sundials_cvodes`) will
-vary depending on what options you used when compiling Cantera. For more
-advanced and flexible methods of compiling programs which use the Cantera C++
-library, see :doc:`compiling`.
-
-This program produces the output below::
-
-          temperature             500  K
-             pressure          202650  Pa
-              density        0.361163  kg/m^3
-     mean mol. weight         7.40903  amu
-
-                             1 kg            1 kmol
-                          -----------      ------------
-             enthalpy    -2.47725e+06       -1.835e+07     J
-      internal energy    -3.03836e+06       -2.251e+07     J
-              entropy         20700.1        1.534e+05     J/K
-       Gibbs function    -1.28273e+07       -9.504e+07     J
-    heat capacity c_p         3919.29        2.904e+04     J/K
-    heat capacity c_v         2797.09        2.072e+04     J/K
-
-                              X                 Y          Chem. Pot. / RT
-                        -------------     ------------     ------------
-                   H2            0.8         0.217667         -15.6441
-                    H              0                0
-                    O              0                0
-                   O2              0                0
-                   OH              0                0
-                  H2O            0.1         0.243153         -82.9531
-                  HO2              0                0
-                 H2O2              0                0
-                   AR            0.1          0.53918         -20.5027
-
-As C++ programs go, this one is *very* short. It is the Cantera equivalent of
-the "Hello, World" program most programming textbooks begin with. But it
-illustrates some important points in writing Cantera C++ programs.
-
-Catching :ct:`CanteraError` exceptions
-======================================
-
-The entire body of the program is put inside a function that is invoked within
-a ``try`` block in the main program. In this way, exceptions thrown in the
-function or in any procedure it calls may be caught. In this program, a
-``catch`` block is defined for exceptions of type :ct:`CanteraError`. Cantera
-throws exceptions of this type, so it is always a good idea to catch them.
-
-The ``report`` function
-=======================
-
-The :ct:`report` function generates a nicely-formatted report of the properties of
-a phase, including its composition in both mole (X) and mass (Y) units. For
-each species present, the non-dimensional chemical potential is also printed.
-This is handy particularly when doing equilibrium calculations. This function
-is very useful to see at a glance the state of some phase.

doc/sphinx/cxx-guide/thermo.rst

@@ -1,126 +0,0 @@
-**********************************
-Computing Thermodynamic Properties
-**********************************
-
-Class ThermoPhase
-=================
-
-Cantera can be used to compute thermodynamic properties of pure substances,
-solutions, and mixtures of various types, including ones containing multiple
-phases. The first step is to create an object that represents each phase. A
-simple, complete program that creates an object representing a gas mixture and
-prints its temperature is shown below:
-
-.. code-block:: c++
-
-    #include "cantera/thermo.h"
-    #include <iostream>
-
-    int main(int argc, char** argv)
-    {
-        std::unique_ptr<Cantera::ThermoPhase> gas(
-            Cantera::newPhase("h2o2.cti", "ohmech"));
-        std::cout << gas->temperature() << std::endl;
-        return 0;
-    }
-
-Class :ct:`ThermoPhase` is the base class for Cantera classes that represent
-phases of matter. It defines the public interface for all classes that represent
-phases. For example, it specifies that they all have a method :ct:`temperature
-<Phase::temperature>` that returns the current temperature, a method
-:ct:`setTemperature(double T) <Phase::setTemperature>` that sets the
-temperature, a method :ct:`getChemPotentials(double* mu)
-<ThermoPhase::getChemPotentials>` that writes the species chemical potentials
-into array ``mu``, and so on.
-
-Class ThermoPhase can be used to represent the intensive state of any
-single-phase solution of multiple species. The phase may be a bulk,
-three-dimensional phase (a gas, a liquid, or a solid), or it may be a
-two-dimensional surface phase, or even a one-dimensional "edge" phase. The
-specific attributes of each type of phase are specified by deriving a class from
-:ct:`ThermoPhase` and providing implementations for its virtual methods.
-
-Cantera has a wide variety of models for bulk phase currently. Special attention
-(in terms of the speed of execution) has been paid to an ideal gas phase
-implementation, where the species thermodynamic polynomial representations
-adhere to either the NASA polynomial form or to the Shomate polynomial
-form. This is widely used in combustion applications, the original application
-that Cantera was designed for. Recently, a lot of effort has been placed into
-constructing non-ideal liquid phase thermodynamics models that are used in
-electrochemistry and battery applications. These models include a Pitzer
-implementation for brines solutions and a Margules excess Gibbs free energy
-implementation for molten salts.
-
-The Intensive Thermodynamic State
----------------------------------
-
-Class :ct:`ThermoPhase` and classes derived from it work only with the intensive
-thermodynamic state. That is, all extensive properties (enthalpy, entropy,
-internal energy, volume, etc.) are computed for a unit quantity (on a mass or
-mole basis). For example, there is a method :ct:`enthalpy_mole()` that returns
-the molar enthalpy (J/kmol), and a method :ct:`enthalpy_mass()` that returns the
-specific enthalpy (J/kg), but no method *enthalpy()* that would return the total
-enthalpy (J). This is because class ThermoPhase does not store the total amount
-(mass or mole) of the phase.
-
-The intensive state of a single-component phase in equilibrium is fully
-specified by the values of any :math:`r+1` independent thermodynamic properties,
-where :math:`r` is the number of reversible work modes. If the only reversible
-work mode is compression (a "simple compressible substance"), then two
-properties suffice to specify the intensive state. Class ThermoPhase stores
-internally the values of the *temperature*, the *mass density*, and the *mass
-fractions* of all species. These values are sufficient to fix the intensive
-thermodynamic state of the phase, and to compute any other intensive properties.
-This choice is arbitrary, and for most purposes you can't tell which properties
-are stored and which are computed.
-
-Derived Classes
----------------
-
-Many of the methods of ThermoPhase are declared virtual, and are meant to be
-overloaded in classes derived from ThermoPhase. For example, class
-:ct:`IdealGasPhase` derives from :ct:`ThermoPhase`, and represents ideal gas
-mixtures.
-
-Although class ThermoPhase defines the interface for all classes representing
-phases, it only provides implementations for a few of the methods. This is
-because ThermoPhase does not actually know the equation of state of any
-phase---this information is provided by classes that derive from ThermoPhase.
-The methods implemented by ThermoPhase are ones that apply to all phases,
-independent of the equation of state. For example, it implements methods
-``temperature()`` and ``setTemperature()``, since the temperature value is
-stored internally.
-
-* `Classes which inherit from ThermoPhase <../../../doxygen/html/group__thermoprops.html>`_
-* `Classes which handle standard states for species <../../../doxygen/html/group__spthermo.html>`_
-
-
-Example Program
-===============
-
-In the program below, a gas mixture object is created, and a few thermodynamic
-properties are computed and printed out:
-
-.. literalinclude:: thermodemo.cpp
-   :language: c++
-
-Note that the methods that compute the properties take no input parameters. The
-properties are computed for the state that has been previously set and stored
-internally within the object.
-
-Naming Conventions
-------------------
-
-- methods that return *molar* properties have names that end in ``_mole``.
-- methods that return properties *per unit mass* have names that end in
-  ``_mass``.
-- methods that write an array of values into a supplied output array have names
-  that begin with ``get``. For example, the method
-  :ct:`ThermoPhase::getChemPotentials(double* mu)` writes the species chemical
-  potentials into the output array ``mu``.
-
-The thermodynamic property methods are declared in class :ct:`ThermoPhase`,
-which is the base class from which all classes that represent any type of phase
-of matter derive.
-
-See :ct:`ThermoPhase` for the full list of available thermodynamic properties.

doc/sphinx/cxx-guide/thermodemo.cpp

@@ -1,42 +0,0 @@
-#include "cantera/thermo.h"
-
-using namespace Cantera;
-
-void thermo_demo(const std::string& file, const std::string& phase)
-{
-    shared_ptr<ThermoPhase> gas(newPhase(file, phase));
-    gas->setState_TPX(1500.0, 2.0*OneAtm, "O2:1.0, H2:3.0, AR:1.0");
-
-    // temperature, pressure, and density
-    std::cout << gas->temperature() << std::endl;
-    std::cout << gas->pressure() << std::endl;
-    std::cout << gas->density() << std::endl;
-
-    // molar thermodynamic properties
-    std::cout << gas->enthalpy_mole() << std::endl;
-    std::cout << gas->entropy_mole() << std::endl;
-
-    // specific (per unit mass) thermodynamic properties
-    std::cout << gas->enthalpy_mass() << std::endl;
-    std::cout << gas->entropy_mass() << std::endl;
-
-    // chemical potentials of the species
-    int numSpecies = gas->nSpecies();
-    vector_fp mu(numSpecies);
-    gas->getChemPotentials(&mu[0]);
-    int n;
-    for (n = 0; n < numSpecies; n++) {
-        std::cout << gas->speciesName(n) << " " << mu[n] << std::endl;
-    }
-}
-
-int main(int argc, char** argv)
-{
-    try {
-        thermo_demo("h2o2.cti","ohmech");
-    } catch (CanteraError& err) {
-        std::cout << err.what() << std::endl;
-        return 1;
-    }
-    return 0;
-}

doc/sphinx/cython/example-script.rst.in

@@ -1,8 +0,0 @@
-:orphan:
-
-.. _py-example-@script_name@:
-
-@script_name@
-=======================================================================
-
-.. literalinclude:: @script_path@

doc/sphinx/cython/examples.rst.in

@@ -1,48 +0,0 @@
-.. _sec-cython-examples:
-
-.. py:currentmodule:: cantera
-
-Index of Examples
-=================
-
-This is an index of the examples included with the Cantera Python module. They
-can be found in the `examples` subdirectory of the Cantera Python module's
-installation directory. To determine the location of this directory, run the following in your Python interpreter::
-
-    import cantera.examples
-    print(cantera.examples.__path__)
-
-Thermodynamics
---------------
-
-@python_thermo_examples@
-
-Kinetics
---------
-
-@python_kinetics_examples@
-
-Transport
----------
-
-@python_transport_examples@
-
-Reactor Networks
-----------------
-
-@python_reactors_examples@
-
-One-dimensional Flames
-----------------------
-
-@python_onedim_examples@
-
-Multiphase Mixtures
--------------------
-
-@python_multiphase_examples@
-
-Surface Chemistry
------------------
-
-@python_surface_chemistry_examples@

doc/sphinx/cython/index.rst

@@ -8,8 +8,6 @@ Contents:
 .. toctree::
    :maxdepth: 2
 
-   migrating
-   tutorial
    importing
    thermo
    kinetics
@@ -17,6 +15,3 @@ Contents:
    zerodim
    onedim
    constants
-   examples
-
-   Application Examples as Jupyter Notebooks <https://github.com/Cantera/cantera-jupyter#cantera-jupyter>

doc/sphinx/cython/migrating.rst

@@ -1,282 +0,0 @@
-.. _sec-python-migration:
-
-Migrating from the Old Python Module
-************************************
-
-With the introduction of the new Cython-based Python module in Cantera 2.1,
-there are a number of changes to the interface which require modifications to
-scripts in order for them to work with the new module. Broadly speaking, the
-changes to the interface are intended to make the Cantera Python module easier
-to use, and provide a more "Pythonic" interface by making use of common Python
-language idioms, language features, and style guidelines.
-
-This document describes the changes to the Python module which are likely to
-require modifications to existing code.
-
-Importing the Python Module
----------------------------
-
-The name of the Python module is now ``cantera`` with a lowercase "c". This
-change is made partly for compliance with `PEP8
-<http://www.python.org/dev/peps/pep-0008/#package-and-module-names>`_.
-
-Furthermore, the various submodules, e.g. ``Cantera.Reactor`` have been
-eliminated. All classes and functions are available directly in the
-``cantera`` module.
-
-To avoid the namespace clutter introduced by using ``import *``, the following
-syntax is preferred::
-
-    >>> import cantera as ct
-
-Naming Conventions
-------------------
-
-Generally, the names used in the Cantera Python module have been changed to
-follow the recommendations of PEP8. This means that the names of methods and
-properties are generally written as ``lowercase_with_underscores`` instead of
-``capitalizingEachWord``. Also, some abbreviated names have been expanded. For
-example, the following function calls::
-
-    >>> gas.speciesName(0)
-    >>> gas.nAtoms('H2', 'H')
-    >>> gas.reactionEqn(3)
-
-should be replaced with::
-
-    >>> gas.species_name(0)
-    >>> gas.n_atoms('H2', 'H')
-    >>> gas.reaction_equation(3)
-
-Importing Phases
-----------------
-
-The functions ``importPhase`` and ``IdealGasMix`` have been removed.
-`Solution` objects, which represent the phase (regardless of the underlying
-thermodynamic model) as well as providing access to kinetics and transport
-properties, are created directly using the `Solution` class. For example::
-
-    >>> gas = Solution('h2o2.xml')
-
-Creates an object which represents an ``IdealGasPhase`` mixture with a
-``GasKinetics`` reaction mechansm and a ``MixTransport`` transport model,
-based on the parameters specified in the input file.
-
-For importing multiple phases from a single file, the ``importPhases`` function
-has been retained with the new name ``import_phases``::
-
-    >>> gas, anode_bulk, oxide = ct.import_phases('sofc.cti',
-                                                  ['gas', 'metal', 'oxide_bulk'])
-
-Interfaces and edges are created using the `Interface` class, which represents
-both 1D and 2D interfaces, rather than using the ``importEdge`` and
-``importInterface`` functions::
-
-    >>> anode_surf = ct.Interface('sofc.cti', 'metal_surface', [gas])
-    >>> oxide_surf = ct.Interface('sofc.cti', 'oxide_surface', [gas, oxide])
-    >>> tpb = ct.Interface('sofc.cti', 'tpb', [anode_bulk, anode_surf, oxide_surf])
-
-
-Accessing Properties
---------------------
-
-Most methods for accessing and setting the properties of objects have been
-replaced with Python "properties" which do not need to be "called" in order to
-accessed or changed. For example, the following::
-
-    >>> u = gas.intEnergy_mass()
-    >>> Wmx = gas.meanMolecularWeight()
-    >>> kf = gas.fwdRateConstants()
-    >>> gas.setName('foo')
-
-should be replaced with::
-
-    >>> u = gas.int_energy_mass
-    >>> Wmx = gas.mean_molecular_weight
-    >>> kf = gas.forward_rate_constants
-    >>> gas.name = 'foo'
-
-Some common properties have been renamed according to the variable that is
-typically used to represent them::
-
-    >>> gas.temperature()
-    >>> gas.pressure()
-    >>> gas.massFractions()
-
-should be replaced with::
-
-    >>> gas.T
-    >>> gas.P
-    >>> gas.Y
-
-For pure fluid phases, the property ``X`` refers to the vapor mass fraction or
-"quality" of the phase. The following::
-
-    >>> w = Cantera.liquidvapor.Water()
-    >>> w.set(T=400, Vapor=0.5)
-
-should be replaced with::
-
-    >>> w = ct.Water()
-    >>> w.TX = 400, 0.5
-
-Setting Thermodynamic State
----------------------------
-
-The ``set`` method has been removed in favor of property pairs or triplets. The
-following::
-
-    >>> gas.setMoleFractions('CH4:1.0, O2:0.1')
-    >>> gas.set(X='CH4:1.0, O2:0.1')
-    >>> gas.set(U=-1.1e6, V=5.5)
-    >>> gas.set(T=300, P=101325, Y='H2:1.0')
-
-should be replaced with::
-
-    >>> gas.X = 'CH4:1.0, O2:0.1'
-    >>> gas.X = 'CH4:1.0, O2:0.1'
-    >>> gas.UV = -1.1e6, 5.5
-    >>> gas.TPY = 300, 101325, 'H2:1.0'
-
-The ``saveState`` and ``restoreState`` methods have been removed. Their
-functionality can be replicated as follows::
-
-    >>> state = gas.TDY
-    >>> # (operations that modify gas)
-    >>> gas.TDY = state
-
-Printing Phase Summaries
-------------------------
-
-`Solution` objects no longer print out a verbose summary as their string
-representation. Instead, the summary report can be generated using the
-`report()` method, which returns a string, or by calling the `Solution` object
-to print the report to the screen. The following are equivalent::
-
-    >>> print(gas.report())
-    >>> gas()
-
-Getting Properties for a Subset of Species
-------------------------------------------
-
-Some methods previously accepted an optional list of species as a filter, e.g.::
-
-    >>> gas.massFractions(['OH','H'])
-
-This is not compatible with the Python "property" syntax, so the following
-alternative is used instead::
-
-    >>> gas['OH','H2'].Y
-    array([ 0.,  1.])
-
-This works for any property which returns a value for each species, and works
-with species names, indices, and index ranges::
-
-    >>> gas[1,2,6].partial_molar_cp
-    array([ 20786.15525072,  21900.30946418,  34929.99146762])
-
-    >>> gas[3:6].species_names
-    ['O2', 'OH', 'H2O']
-
-Furthermore, the "sliced" object itself can be saved and used without needing
-to specify the species list again::
-
-    >>> reactants = gas['H2','O2']
-    >>> reactants.X
-    array([ 1.,  0.])
-
-Transport Models
-----------------
-
-The old method for setting the transport model, `switchTransportModel` has been
-replaced with the `transport_model` property. To use the multicomponent
-transport model::
-
-    >>> gas.transport_model = 'Multi'
-
-Note that unlike the previous implementation, only one transport model can be
-associated with a `Solution` object at a time, so there is a larger cost with
-switching models. If you need to alternate between transport models, it is
-generally better to use two different `Solution` objects.
-
-Reactor Networks
-----------------
-
-As with the `Solution` class, properties are now used to get and set most
-parameters of reactors, flow devices, walls, etc. The following old code::
-
-    >>> Y = reactor.massFractions()
-    >>> X = reactor.contents().moleFractions()
-    >>> wall.setArea(2.0)
-
-    >>> net.setTolerances(1e-8, 1e-14)
-
-should be replaced with::
-
-    >>> Y = reactor.Y
-    >>> X = reactor.thermo.X
-    >>> wall.area = 2.0
-
-    >>> net.rtol = 1e-8
-    >>> net.atol = 1e-14
-
-Time-varying parameters have not been replaced with properties, since they
-need to be evaluated at a particular time.
-
-Elimination of the ``Func`` Module
-----------------------------------
-
-The ``Func`` module is no longer necessary, as the Cython module allows any
-callable Python object (lambda, function, or class) to be used in places where
-a function of a single variable are needed. For example, to set the velocity
-of a wall as a function of time, the following are equivalent::
-
-    >>> wall.set_velocity(lambda t: np.cos(3*t))
-
-    >>> def myfunc(z):
-    ...     return np.cos(3*z)
-    >>> wall.set_velocity(myfunc)
-
-One-Dimensional Reacting Flows
-------------------------------
-
-As elsewhere, the ``set`` method has been eliminated. The following old usage::
-
-    >>> f.fuel_inlet.set(massflux=mdot_f,
-    >>>                  mole_fractions=comp_f,
-    >>>                  temperature=tin_f)
-
-    >>> f.set(energy = 'off')
-
-should be replaced with::
-
-    >>> f.fuel_inlet.mdot = mdot_f
-    >>> f.fuel_inlet.X = comp_f
-    >>> f.fuel_inlet.T = tin_f
-
-    >>> f.energy_enabled = False
-
-However, the methods for setting tolerances and refinement criteria have been
-retained in slightly modified forms. The following::
-
-    >>> f.set(tol=tol_ss, tol_time=tol_ts)
-    >>> f.setRefineCriteria(ratio=4, slope=0.2, curve=0.3, prune=0.04)
-
-should be replaced with::
-
-    >>> f.flame.set_steady_tolerances(default=tol_ss)
-    >>> f.flame.set_transient_tolerances(default=tol_ts)
-    >>> f.set_refine_criteria(ratio=4, slope=0.2, curve=0.3, prune=0.04)
-
-To change the transport model and enable calculation of the Soret diffusion
-term, the following::
-
-    >>> gas.addTransportModel('Multi')
-    >>> gas.switchTransportModel('Multi')
-    >>> f.flame.setTransportModel(gas)
-    >>> f.flame.enableSoret()
-
-should be replaced with::
-
-    >>> f.transport_model = 'Multi'
-    >>> f.soret_enabled = True

doc/sphinx/cython/onedim.rst

@@ -31,18 +31,41 @@ ImpingingJet
 ^^^^^^^^^^^^
 .. autoclass:: ImpingingJet(gas, grid=None, width=None)
 
+IonFreeFlame
+^^^^^^^^^^^^
+.. autoclass:: IonFreeFlame(gas, grid=None, width=None)
+
+   .. autoattribute:: E
+   .. autoattribute:: electric_field_enabled
+   .. automethod:: solve
+
+IonBurnerFlame
+^^^^^^^^^^^^^^
+.. autoclass:: IonBurnerFlame(gas, grid=None, width=None)
+
+   .. autoattribute:: E
+   .. autoattribute:: electric_field_enabled
+   .. automethod:: solve
+
 Flow Domains
 ------------
 
+IdealGasFlow
+^^^^^^^^^^^^
+.. autoclass:: IdealGasFlow(thermo)
+    :inherited-members:
+
+IonFlow
+^^^^^^^
+.. autoclass:: IonFlow(thermo)
+
 FreeFlow
 ^^^^^^^^
 .. autoclass:: FreeFlow(thermo)
-    :inherited-members:
 
 AxisymmetricStagnationFlow
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 .. autoclass:: AxisymmetricStagnationFlow(thermo)
-    :inherited-members:
 
 Boundaries
 ----------

doc/sphinx/cython/tutorial.rst

@@ -1,442 +0,0 @@
-.. py:currentmodule:: cantera
-
-Tutorial
-========
-
-Getting Started
----------------
-
-Start by opening an interactive Python session, e.g. by running `IPython
-<http://ipython.org/>`_. Import the Cantera Python module and NumPy by running::
-
-    >>> import cantera as ct
-    >>> import numpy as np
-
-When using Cantera, the first thing you usually need is an object representing
-some phase of matter. Here, we'll create a gas mixture::
-
-    >>> gas1 = ct.Solution('gri30.xml')
-
-To view the state of the mixture, *call* the `gas1` object as if it were a
-function::
-
-    >>> gas1()
-
-You should see something like this::
-
-     gri30:
-
-          temperature             300  K
-             pressure          101325  Pa
-              density       0.0818891  kg/m^3
-     mean mol. weight         2.01588  amu
-
-                             1 kg            1 kmol
-                          -----------      ------------
-             enthalpy         26470.1        5.336e+04     J
-      internal energy    -1.21087e+06       -2.441e+06     J
-              entropy         64913.9        1.309e+05     J/K
-       Gibbs function    -1.94477e+07        -3.92e+07     J
-    heat capacity c_p         14311.8        2.885e+04     J/K
-    heat capacity c_v         10187.3        2.054e+04     J/K
-
-                              X                 Y          Chem. Pot. / RT
-                        -------------     ------------     ------------
-                   H2              1                1         -15.7173
-        [  +52 minor]              0                0
-
-What you have just done is to create an object, `gas1` that implements GRI-
-Mech 3.0, the 53-species, 325-reaction natural gas combustion mechanism
-developed by Gregory P. Smith, David M. Golden, Michael Frenklach, Nigel W.
-Moriarty, Boris Eiteneer, Mikhail Goldenberg, C. Thomas Bowman, Ronald K.
-Hanson, Soonho Song, William C. Gardiner, Jr., Vitali V. Lissianski, and
-Zhiwei Qin. See http://www.me.berkeley.edu/gri_mech/ for more information.
-
-The `gas1` object has properties you would expect for a gas mixture - it has a
-temperature, a pressure, species mole and mass fractions, etc. As we'll soon
-see, it has many more properties.
-
-The summary of the state of `gas1` printed above shows that new objects
-created from the `gri30.xml` input file start out with a temperature of 300 K,
-a pressure of 1 atm, and have a composition that consists of only one species,
-in this case hydrogen. There is nothing special about H2 - it just happens to
-be the first species listed in the input file defining GRI-Mech 3.0. In
-general, whichever species is listed first will initially have a mole fraction
-of 1.0, and all of the others will be zero.
-
-Setting the State
-~~~~~~~~~~~~~~~~~
-
-The state of the object can easily be changed. For example::
-
-    >>> gas1.TP = 1200, 101325
-
-sets the temperature to 1200 K and the pressure to 101325 Pa (Cantera always
-uses SI units). After this statement, calling ``gas1()`` results in::
-
-     gri30:
-
-          temperature            1200  K
-             pressure          101325  Pa
-              density       0.0204723  kg/m^3
-     mean mol. weight         2.01588  amu
-
-                             1 kg            1 kmol
-                          -----------      ------------
-             enthalpy     1.32956e+07         2.68e+07     J
-      internal energy     8.34619e+06        1.682e+07     J
-              entropy         85227.6        1.718e+05     J/K
-       Gibbs function    -8.89775e+07       -1.794e+08     J
-    heat capacity c_p         15377.9          3.1e+04     J/K
-    heat capacity c_v         11253.4        2.269e+04     J/K
-
-                              X                 Y          Chem. Pot. / RT
-                        -------------     ------------     ------------
-                   H2              1                1         -17.9775
-        [  +52 minor]              0                0
-
-Notice that the temperature has been changed as requested, but the pressure
-has changed too. The density and composition have not.
-
-Thermodynamics generally requires that *two* properties in addition to
-composition information be specified to fix the intensive state of a substance
-(or mixture). The state of the mixture can be set using several combinations
-of two properties. The following are all equivalent::
-
-    >>> gas1.TP = 1200, 101325           # temperature, pressure
-    >>> gas1.TD = 1200, 0.0204723        # temperature, density
-    >>> gas1.HP = 1.32956e7, 101325      # specific enthalpy, pressure
-    >>> gas1.UV = 8.34619e6, 1/0.0204723 # specific internal energy, specific volume
-    >>> gas1.SP = 85227.6, 101325        # specific entropy, pressure
-    >>> gas1.SV = 85227.6, 1/0.0204723   # specific entropy, specific volume
-
-In each case, the values of the extensive properties must be entered *per unit
-mass*.
-
-Properties may be read independently or together::
-
-    >>> gas1.T
-    1200.0
-    >>> gas1.h
-    13295567.68
-    >>> gas1.UV
-    (8346188.494954427, 48.8465747765848)
-
-The composition can be set in terms of either mole fractions (``X``) or mass
-fractions (``Y``)::
-
-    >>> gas1.X = 'CH4:1, O2:2, N2:7.52'
-
-Mass and mole fractions can also be set using `dict` objects, for cases where
-the composition is stored in a variable or being computed::
-
-    >>> phi = 0.8
-    >>> gas1.X = {'CH4':1, 'O2':2/phi, 'N2':2*3.76/phi}
-
-When the composition alone is changed, the temperature and density are held
-constant. This means that the pressure and other intensive properties will
-change. The composition can also be set in conjunction with the intensive
-properties of the mixture::
-
-    >>> gas1.TPX = 1200, 101325, 'CH4:1, O2:2, N2:7.52'
-    >>> gas1()
-
-results in::
-
-     gri30:
-
-          temperature            1200  K
-             pressure          101325  Pa
-              density        0.280629  kg/m^3
-     mean mol. weight         27.6332  amu
-
-                             1 kg            1 kmol
-                          -----------      ------------
-             enthalpy          861943        2.382e+07     J
-      internal energy          500879        1.384e+07     J
-              entropy          8914.3        2.463e+05     J/K
-       Gibbs function    -9.83522e+06       -2.718e+08     J
-    heat capacity c_p         1397.26        3.861e+04     J/K
-    heat capacity c_v         1096.38         3.03e+04     J/K
-
-                              X                 Y          Chem. Pot. / RT
-                        -------------     ------------     ------------
-                   O2       0.190114         0.220149         -28.7472
-                  CH4       0.095057        0.0551863          -35.961
-                   N2       0.714829         0.724665         -25.6789
-        [  +50 minor]              0                0
-
-The composition above was specified using a string. The format is a comma-
-separated list of ``<species name>:<relative mole numbers>`` pairs. The mole
-numbers will be normalized to produce the mole fractions, and therefore they
-are "relative" mole numbers. Mass fractions can be set in this way too by
-changing ``X`` to ``Y`` in the above statements.
-
-The composition can also be set using an array, which must have the same size
-as the number of species. For example, to set all 53 mole fractions to the
-same value, do this::
-
-    >>> gas1.X = np.ones(53) # NumPy array of 53 ones
-
-Or, to set all the mass fractions to equal values::
-
-    >>> gas1.Y = np.ones(53)
-
-When setting the state, you can control what properties are held constant by
-passing the special value `None` to the property setter. For example, to
-change the specific volume to 2.1 m^3/kg while holding entropy constant::
-
-    >>> gas1.SV = None, 2.1
-
-Or to set the mass fractions while holding temperature and pressure constant::
-
-    >>> gas1.TPX = None, None, 'CH4:1.0, O2:0.5'
-
-Working with a Subset of Species
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Many properties of a `Solution` provide values for each species present in the
-phase. If you want to get values only for a subset of these species, you can use
-Python's "slicing" syntax to select data for just the species of interest. To
-get the mole fractions of just the major species in `gas1`, in the order
-specified, you can write:
-
-    >>> Xmajor = gas1['CH4','O2','CO2','H2O','N2'].X
-
-If you want to use the same set of species repeatedly, you can keep a reference
-to the sliced phase object:
-
-    >>> major = gas1['CH4','O2','CO2','H2O','N2']
-    >>> cp_major = major.partial_molar_cp
-    >>> wdot_major = major.net_production_rates
-
-The slice object and the original object share the same internal state, so
-modifications to one will affect the other.
-
-Working With Mechanism Files
-----------------------------
-
-In previous example, we created an object that models an ideal gas mixture
-with the species and reactions of GRI-Mech 3.0, using the ``gri30.xml`` input
-file included with Cantera. This is a "pre-processed" XML input file written
-in a format that is easy for Cantera to parse. Cantera also supports an input
-file format that is easier to write, called *CTI*. Several reaction mechanism
-files in this format are included with Cantera, including ones that model
-high- temperature air, a hydrogen/oxygen reaction mechanism, and a few surface
-reaction mechanisms. These files are usually located in the ``data``
-subdirectory of the Cantera installation directory, e.g. ``C:\\Program
-Files\\Cantera\\data`` on Windows or ``/usr/local/cantera/data/`` on
-Unix/Linux/Mac OS X machines, depending on how you installed Cantera and the
-options you specified.
-
-If for some reason Cantera has difficulty finding where these files are on your
-system, set environment variable ``CANTERA_DATA`` to the directory or
-directories (separated using ``;`` on Windows or ``:`` on other operating
-systems) where they are located. Alternatively, you can call function
-`add_directory` to add a directory to the Cantera search path::
-
-    >>> ct.add_directory('/usr/local/cantera/my_data_files')
-
-Cantera input files are plain text files, and can be created with any text
-editor. See the document :ref:`sec-defining-phases` for more information.
-
-A Cantera input file may contain more than one phase specification, or may
-contain specifications of interfaces (surfaces). Here we import definitions of
-two bulk phases and the interface between them from file ``diamond.cti``::
-
-    >>> gas2 = ct.Solution('diamond.cti', 'gas')
-    >>> diamond = ct.Solution('diamond.cti', 'diamond')
-    >>> diamond_surf = ct.Interface('diamond.cti' , 'diamond_100',
-                                    [gas2, diamond])
-
-Note that the bulk (i.e., 3D or homogeneous) phases that participate in the
-surface reactions must also be passed as arguments to `Interface`.
-
-Converting CK-format files
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-See :ref:`sec-ck-format-conversion` in the :ref:`sec-input-files` documentation.
-
-
-Getting Help
-------------
-
-In addition to the Sphinx-generated :ref:`sec-cython-documentation`,
-documentation of the Python classes and their methods can be accessed from
-within the Python interpreter as well.
-
-Suppose you have created a Cantera object and want to know what methods are
-available for it, and get help on using the methods::
-
-    >>> g = ct.Solution('gri30.xml')
-
-To get help on the Python class that this object is an instance of::
-
-    >>> help(g)
-
-For a simple list of the properties and methods of this object::
-
-    >>> dir(g)
-
-To get help on a specific method, e.g. the ``species_index`` method::
-
-    >>> help(g.species_index)
-
-For properties, getting the documentation is slightly trickier, as the usual
-method will give you the help for the *result*, e.g.::
-
-    >>> help(g.T)
-
-will provide help on Python's ``float`` class. To get the help for the
-temperature property, ask for the attribute of the class object itself::
-
-    >>> help(g.__class__.T)
-
-If you are using the IPython shell, help can also be obtained using the `?`
-syntax::
-
-    In[1]: g.species_index?
-
-Chemical Equilibrium
---------------------
-
-To set a gas mixture to a state of chemical equilibrium, use the equilibrate
-method::
-
-    >>> import cantera as ct
-    >>> g = ct.Solution('gri30.xml')
-    >>> g.TPX = 300.0, ct.one_atm, 'CH4:0.95,O2:2,N2:7.52'
-    >>> g.equilibrate('TP')
-
-The above statement sets the state of object ``g`` to the state of chemical
-equilibrium holding temperature and pressure fixed. Alternatively, the
-specific enthalpy and pressure can be held fixed::
-
-    >>> g.TPX = 300.0, ct.one_atm, 'CH4:0.95,O2:2,N2:7.52'
-    >>> g.equilibrate('HP')
-
-Other options are:
-
-    - 'UV'   fixed specific internal energy and specific volume
-    - 'SV'   fixed specific entropy and specific volume
-    - 'SP'   fixed specific entropy and pressure
-
-How can you tell if ``equilibrate`` has correctly found the chemical equilibrium
-state? One way is verify that the net rates of progress of all reversible
-reactions are zero. Here is the code to do this:
-
-    >>> g.TPX = 300.0, ct.one_atm, 'CH4:0.95,O2:2,N2:7.52'
-    >>> g.equilibrate('HP')
-
-    >>> rf = g.forward_rates_of_progress
-    >>> rr = g.reverse_rates_of_progress
-    >>> for i in range(g.n_reactions):
-    >>>     if g.is_reversible(i) and rf[i] != 0.0:
-    >>>         print(' %4i  %10.4g  ' % (i, (rf[i] - rr[i])/rf[i]))
-
-If the magnitudes of the numbers in this list are all very small, then each
-reversible reaction is very nearly equilibrated, which only occurs if the gas
-is in chemical equilibrium.
-
-You might be wondering how ``equilibrate`` works. (Then again, you might not).
-Method ``equilibrate`` invokes Cantera's chemical equilibrium solver, which uses
-an element potential method. The element potential method is one of a class of
-equivalent *nonstoichiometric* methods that all have the characteristic that
-the problem reduces to solving a set of M nonlinear algebraic equations, where
-M is the number of elements (not species). The so-called *stoichiometric*
-methods, on the other hand, (including Gibbs minimization), require solving K
-nonlinear equations, where K is the number of species (usually K >> M). See
-Smith and Missen, "Chemical Reaction Equilibrium Analysis" for more
-information on the various algorithms and their characteristics.
-
-Cantera uses a damped Newton method to solve these equations, and does a few
-other things to generate a good starting guess and to produce a reasonably
-robust algorithm. If you want to know more about the details, look at the on-
-line documented source code of Cantera C++ class 'ChemEquil.h'.
-
-Chemical Kinetics
------------------
-
-`Solution` objects are also `Kinetics` objects, and provide all of the methods
-necessary to compute the thermodynamic quantities associated with each reaction,
-reaction rates, and species creation and destruction rates. They also provide
-methods to inspect the quantities that define each reaction such as the rate
-constants and the stoichiometric coefficients. The rate calculation functions
-are used extensively within Cantera's :ref:`reactor network model
-<sec-cython-zerodim>` and :ref:`1D flame model <sec-cython-onedim>`.
-
-Information about individual reactions that is independent of the thermodynamic
-state can be obtained by accessing `Reaction` objects with the
-`Kinetics.reaction` method::
-
-    >>> g = ct.Solution('gri30.cti')
-    >>> r = g.reaction(2) # get a Reaction object
-    >>> r
-    <ElementaryReaction: H2 + O <=> H + OH>
-
-    >>> r.reactants
-    {'H2': 1.0, 'O': 1.0}
-    >>> r.products
-    {'H': 1.0, 'OH': 1.0}
-    >>> r.rate
-    Arrhenius(A=38.7, b=2.7, E=2.61918e+07)
-
-If we are interested in only certain types of reactions, we can use this
-information to filter the full list of reactions to find the just the ones of
-interest. For example, here we find the indices of just those reactions which
-convert `CO` into `CO2`::
-
-    >>> II = [i for i,r in enumerate(g.reactions())
-              if 'CO' in r.reactants and 'CO2' in r.products]
-    >>> for i in II:
-    ...     print(g.reaction(i).equation)
-    CO + O (+M) <=> CO2 (+M)
-    CO + O2 <=> CO2 + O
-    CO + OH <=> CO2 + H
-    CO + HO2 <=> CO2 + OH
-
-(Actually, we should also include reactions where the reaction is written such
-that ``CO2`` is a reactant and ``CO`` is a product, but for this example, we'll
-just stick to this smaller set of reactions.) Now, let's set the composition to
-an interesting equilibrium state::
-
-    >>> g.TPX = 300, 101325, {'CH4':0.6, 'O2':1.0, 'N2':3.76}
-    >>> g.equilibrate('HP')
-
-We can verify that this is an equilibrium state by seeing that the net reaction
-rates are essentially zero::
-
-    >>> g.net_rates_of_progress[II]
-    array([  4.06576e-20,  -5.50571e-21,   0.00000e+00,  -4.91279e-20])
-
-Now, let's see what happens if we decrease the temperature of the mixture::
-
-    >>> g.TP = g.T-100, None
-    >>> g.net_rates_of_progress[II]
-    array([  3.18645e-05,   5.00490e-08,   1.05965e-01,   2.89503e-06])
-
-All of the reaction rates are positive, favoring the formation of ``CO2`` from
-``CO``, with the third reaction, ``CO + OH <=> CO2 + H`` proceeding the fastest.
-If we look at the enthalpy change associated with each of these reactions::
-
-    >>> g.delta_enthalpy[II]
-    array([ -5.33035e+08,  -2.23249e+07,  -8.76650e+07,  -2.49170e+08])
-
-we see that the change is negative in each case, indicating a net release of
-thermal energy. The total heat release rate can be computed either from the
-reaction rates::
-
-    >>> np.dot(g.net_rates_of_progress, g.delta_enthalpy)
-    -58013370.720881931
-
-or from the species production rates::
-
-    >>> np.dot(g.net_production_rates, g.partial_molar_enthalpies)
-    -58013370.720881805
-
-The contribution from just the selected reactions is:
-
-    >>> np.dot(g.net_rates_of_progress[II], g.delta_enthalpy[II])
-    -9307123.2625651453
-
-Or about 16% of the total heat release rate.

doc/sphinx/faq.rst

@@ -1,152 +0,0 @@
-**************************
-Frequently Asked Questions
-**************************
-
-Installation & Compilation
---------------------------
-
-**How do I install Cantera on Windows?**
-
-    Download the MSI installer for Cantera and the corresponding Python module
-    from `SourceForge <https://sourceforge.net/projects/cantera/files/cantera/>`_.
-    Choose between x86 and x64 based on the versions of Python and/or Matlab
-    you want to work with. See :ref:`Windows Installation <sec-install-win>`
-    for details.
-
-**How do I install Cantera on Linux?**
-
-    For Ubuntu, packages for the current stable version of Cantera are available
-    in a PPA. See :ref:`Ubuntu Installation <sec-install-ubuntu>` for details.
-
-    For other Linux distributions, download the source code (e.g.
-    ``cantera-2.1.1.tar.gz``) from `SourceForge
-    <https://sourceforge.net/projects/cantera/files/cantera/>`_ and follow the
-    instructions in the :ref:`sec-compiling`.
-
-**How do I install Cantera on Mac OS X?**
-
-    Cantera can be installed using Homebrew. See :ref:`Mac OS X Installation
-    <sec-install-osx>` for details.
-
-**What do I do if compiling Cantera fails?**
-
-    - Examine the output of the ``scons build`` command, especially anything
-      identified as a       ``WARNING`` or ``ERROR``. Check for discrepancies
-      with your expected configuration (e.g. not finding SUNDIALS even though
-      you have it installed).
-    - Check the contents of ``cantera.conf`` to make sure they are correct.
-    - If any of the configuration tests (``Checking for...``) fail unexpectedly,
-      look at the contents of ``config.log`` to determine the reason.
-    - If none of these help identify the cause of the failure, consider asking
-      for help on the Cantera Users' Group. If you decide to make a post, please
-      include the following information:
-
-      * The contents of ``cantera.conf`` and ``config.log``
-      * The output of the ``scons build`` and ``scons build dump`` commands
-        (you can direct this output to a file by running ``scons build >buildlog.txt 2>&1``)
-      * The exact version of Cantera you are trying to compile, and how it was
-        obtained (i.e. downloaded source tarball or the specific Git commit)
-      * Your operating system, compiler versions, and the versions of any other
-        relevant software.
-
-**How do I debug issues with the SCons build system?**
-
-    Sometimes, it is helpful to see all of the internal variables defined by
-    SCons, either automatically or by the Cantera build scripts. To do this, add
-    ``dump`` to your SCons command line. For example::
-
-        $ scons build dump
-
-    will show the variables that would be set during the ``build`` step. Note
-    that in this case, the ``build`` step will not be executed.
-
-    Alternatively, it is also possible to run SCons through the Python debugger, and set a breakpoint in the ``SConstruct`` file. For example::
-
-        $ scons --debug=pdb build
-        (Pdb) b /full/path/to/SConstruct:33
-        (Pdb) cont
-
-General
--------
-
-**Which Cantera interface should I use?**
-
-    If you're new to Cantera, the best interface to get started with is
-    probably the Python interface. It offers most of the features of the
-    C++ core in a much more flexible environment. Since all of the
-    calculations are still done in C++, there is very little performance
-    penalty to using the high-level language interfaces.
-
-**Where can I find examples of how to use Cantera?**
-
-    Cantera is distributed with many examples for the Python and Matlab
-    interfaces, and a smaller number of examples for the C++ and Fortran
-    interfaces. The Matlab, C++, and Fortran examples should be
-    installed in the ``samples`` subdirectory of the Cantera installation
-    directory, or they can be found in the ``samples`` subdirectory of the
-    Cantera source directory.
-
-    Examples for the Python interface can be found in the ``examples``
-    subdirectory of the Cantera Python module installation directory, or in
-    the ``interfaces/cython/cantera/examples`` subdirectory of the Cantera
-    source directory.
-
-**How should I cite Cantera?**
-
-    The recommended citation for Cantera is as follows:
-
-    David G. Goodwin, Harry K. Moffat, and Raymond L. Speth. *Cantera: An object-
-    oriented software toolkit for chemical kinetics, thermodynamics, and
-    transport processes*. http://www.cantera.org, 2017. Version 2.3.0.
-    doi:10.5281/zenodo.170284
-
-    The following BibTeX entry may also be used::
-
-        @Misc{Cantera,
-           author = "David G. Goodwin and Harry K. Moffat and Raymond L. Speth",
-           title = "Cantera: An Object-oriented Software Toolkit for Chemical
-                    Kinetics, Thermodynamics, and Transport Processes",
-           year = 2017,
-           note = "Version 2.3.0",
-           howpublished = "\url{http://www.cantera.org}"
-           doi = {10.5281/zenodo.170284}
-        }
-
-    If you are using a different version of Cantera, update the ``version`` and
-    ``year`` fields accordingly.
-
-
-Support and Bug Reporting
--------------------------
-
-**What should I do if I think I've found a bug in Cantera?**
-
-    - Check to see if you're using the most recent version of Cantera, and
-      upgrade if not.
-    - Check the `Issue Tracker
-      <https://github.com/Cantera/cantera/issues>`_ to see if the issue
-      has already been reported.
-    - Try to generate a `minimal, complete, and verifiable example
-      <http://stackoverflow.com/help/mcve>`_ that demonstrates the observed bug.
-    - Create a new issue on the tracker. Include as much information as
-      possible about your system configuration (operating system, compiler
-      versions, Python versions, installation method, etc.)
-
-**What information should I include in my bug report?**
-
-    - The version of Cantera are you using, and how you installed it
-    - The operating system you are using
-    - If you compiled Cantera, what compiler you used, and what compilation
-      options you specified
-    - The version of Python or Matlab are you using, if applicable
-    - The necessary *input* to generate the reported behavior
-    - The full text of any error message you receive
-
-**What should I do if I need help using Cantera?**
-
-    You can join the `Cantera Users' Group
-    <https://groups.google.com/forum/#!forum /cantera-users>`_ on Google
-    Groups and ask a question there. Please use the search feature before
-    posting to see if your question has been answered before. This group is
-    moderated, so it may take some time for your posts to appear if you are a
-    new member.

doc/sphinx/flames.rst

@@ -1,213 +0,0 @@
-.. default-role:: math
-
-.. py:currentmodule:: cantera
-
-**********************
-One-Dimensional Flames
-**********************
-
-Cantera includes a set of models for representing steady-state, quasi-one-
-dimensional reacting flows, which can be used to simulate a number of common
-flames, such as:
-
-- freely-propagating premixed laminar flames
-- burner-stabilized premixed flames
-- counterflow diffusion flames
-- counterflow (strained) premixed flames
-
-Additional capabilities include simulation of surface reactions, which can be
-used to represent processes such as combustion on a catalytic surface or
-chemical vapor deposition processes.
-
-All of these configurations are simulated using a common set of governing
-equations within a 1D "flow" domain, with the differences between the models
-being represented by differences in the boundary conditions applied. Here, we
-describe the governing equations and the various boundary conditions which can
-be applied.
-
-Stagnation Flow Governing Equations
-===================================
-
-Cantera models flames which are stabilized in an axisymmetric stagnation flow,
-and computes the solution along the stagnation streamline (`r=0`), using a
-similarity solution to reduce the three-dimensional governing equations to a
-single dimension.
-
-The governing equations for a steady axisymmetric stagnation flow follow those
-derived in Section 6.2 of [KCG2003]_:
-
-*Continuity*:
-
-.. math::
-
-    \frac{\partial\rho u}{\partial z} + 2 \rho V = 0
-
-*Radial momentum*:
-
-.. math::
-
-    \rho u \frac{\partial V}{\partial z} + \rho V^2 =
-        - \Lambda
-        + \frac{\partial}{\partial z}\left(\mu \frac{\partial V}{\partial z}\right)
-
-
-*Energy*:
-
-.. math::
-
-    \rho c_p u \frac{\partial T}{\partial z} =
-        \frac{\partial}{\partial z}\left(\lambda \frac{\partial T}{\partial z}\right)
-        - \sum_k j_k c_{p,k} \frac{\partial T}{\partial z}
-        - \sum_k h_k W_k \dot{\omega}_k
-
-*Species*:
-
-.. math::
-
-    \rho u \frac{\partial Y_k}{\partial z} = - \frac{\partial j_k}{\partial z}
-        + W_k \dot{\omega}_k
-
-where `\rho` is the density, `u` is the axial velocity, `v` is the radial
-velocity, `V = v/r` is the scaled radial velocity, `\Lambda` is the pressure
-eigenvalue (independent of `z`), `\mu` is the dynamic viscosity, `c_p` is the
-heat capacity at constant pressure, `T` is the temperature, `\lambda` is the
-thermal conductivity, `Y_k` is the mass fraction of species `k`, `j_k` is the
-diffusive mass flux of species `k`, `c_{p,k}` is the specific heat capacity of
-species `k`, `h_k` is the enthalpy of species `k`, `W_k` is the molecular weight
-of species `k`, and `\dot{\omega}_k` is the molar production rate of species
-`k`.
-
-The tangential velocity `w` has been assumed to be zero, and the fluid has been
-assumed to behave as an ideal gas.
-
-To help in the solution of the discretized problem, it is convenient to write a
-differential equation for the scalar `\Lambda`:
-
-.. math::
-
-    \frac{d\Lambda}{dz} = 0
-
-Diffusive Fluxes
-----------------
-
-The species diffusive mass fluxes `j_k` are computed according to either a
-mixture-averaged or multicomponent formulation. If the mixture-averaged
-formulation is used, the calculation performed is:
-
-.. math::
-
-    j_k^* = \rho \frac{W_k}{\overline{W}} D_{k,m} \frac{\partial X_k}{\partial z}
-
-    j_k = j_k^* - Y_k \sum_i j_i^*
-
-where `\overline{W}` is the mean molecular weight of the mixture, `D_{k,m}` is the
-mixture-averaged diffusion coefficient for species `k`, and `X_k` is the mole
-fraction for species `k`. The diffusion coefficients used here are those
-computed by the method :ct:`GasTransport::getMixDiffCoeffs`. The correction
-applied by the second equation ensures that the sum of the mass fluxes is zero,
-a condition which is not inherently guaranteed by the mixture-averaged
-formulation.
-
-When using the multicomponent formulation, the mass fluxes are computed
-according to:
-
-.. math::
-
-    j_k = \frac{\rho W_k}{\overline{W}^2} \sum_i W_i D_{ki} \frac{\partial X_i}{\partial z}
-          - \frac{D_k^T}{T} \frac{\partial T}{\partial z}
-
-where `D_{ki}` is the multicomponent diffusion coefficient and `D_k^T` is the
-Soret diffusion coefficient (used only if calculation of this term is
-specifically enabled).
-
-Boundary Conditions
-===================
-
-Inlet boundary
---------------
-
-For a boundary located at a point `z_0` where there is an inflow, values are
-supplied for the temperature `T_0`, the species mass fractions `Y_{k,0}` the
-scaled radial velocity `V_0`, and the mass flow rate `\dot{m}_0` (except in the
-case of the freely-propagating flame).
-
-The following equations are solved at the point `z = z_0`:
-
-.. math::
-
-    T(z_0) = T_0
-
-    V(z_0) = V_0
-
-    \dot{m}_0 Y_{k,0} - j_k(z_0) - \rho(z_0) u(z_0) Y_k(z_0) = 0
-
-If the mass flow rate is specified, we also solve:
-
-.. math::
-
-    \rho(z_0) u(z_0) = \dot{m}_0
-
-Otherwise, we solve:
-
-.. math::
-
-    \Lambda(z_0) = 0
-
-Outlet boundary
----------------
-
-For a boundary located at a point `z_0` where there is an outflow, we solve:
-
-.. math::
-
-    \Lambda(z_0) = 0
-
-    \left.\frac{\partial T}{\partial z}\right|_{z_0} = 0
-
-    \left.\frac{\partial Y_k}{\partial z}\right|_{z_0} = 0
-
-    V(z_0) = 0
-
-
-Symmetry boundary
------------------
-
-For a symmetry boundary located at a point `z_0`, we solve:
-
-.. math::
-
-    \rho(z_0) u(z_0) = 0
-
-    \left.\frac{\partial V}{\partial z}\right|_{z_0} = 0
-
-    \left.\frac{\partial T}{\partial z}\right|_{z_0} = 0
-
-    j_k(z_0) = 0
-
-Reacting surface
-----------------
-
-For a surface boundary located at a point `z_0` on which reactions may occur,
-the temperature `T_0` is specified. We solve:
-
-.. math::
-
-    \rho(z_0) u(z_0) = 0
-
-    V(z_0) = 0
-
-    T(z_0) = T_0
-
-    j_k(z_0) + \dot{s}_k W_k = 0
-
-where `\dot{s}_k` is the molar production rate of the gas-phase species `k` on
-the surface. In addition, the surface coverages `\theta_i` for each surface
-species `i` are computed such that `\dot{s}_i = 0`.
-
-
-References
-==========
-
-.. [KCG2003] Kee, Coltrin, Glarborg: *Chemically Reacting Flow*.
-             Wiley-Interscience, 2003
-

doc/sphinx/glossary.rst

@@ -1,26 +0,0 @@
-********
-Glossary
-********
-
-The following abbreviations are used in Cantera, both in documentation and in
-the names of variables and classes:
-
-* **CK**: Chemkin
-* **CT**: Cantera
-* **CTI**: Cantera input
-* **CTML**: Cantera markup language
-* **HKFT**: Helgeson-Kirkham-Flowers-Tanger
-* **HMW**: Harvie, Møller, and Weare
-* **IAPWS**: International Association for the Properties of Water and Steam
-* **MFTP**: Mixture fugacity ThermoPhase
-* **PDSS**: Pressure-dependent standard state
-* **RT**: Product of the gas constant (R) and the temperature
-* **SHE**: Single half-electrode
-* **SP**: "Surface Problem"
-* **SS**: Standard state
-* **SSTP**: SingleSpeciesTP (ThermoPhase)
-* **STIT**: SpeciesThermoInterpType
-* **VCS**: Villars Cruise Smith
-* **VPSS**: Variable pressure standard state
-* **VPSSTP**: variable pressure standard state ThermoPhase
-* **wrt**: with respect to

doc/sphinx/index.rst

@@ -1,50 +1,17 @@
 .. Cantera documentation master file, created by
    sphinx-quickstart on Mon Mar 12 11:43:09 2012.
 
-*******
-Welcome
-*******
-
-Cantera is a suite of object-oriented software tools for problems involving
-chemical kinetics, thermodynamics, and/or transport processes.
-
-Cantera provides types (or classes) of objects representing phases of
-matter, interfaces between these phases, reaction managers, time-dependent
-reactor networks, and steady one-dimensional reacting flows. Cantera is
-currently used for applications including combustion, detonations,
-electrochemical energy conversion and storage, fuel cells, batteries, aqueous
-electrolyte solutions, plasmas, and thin film deposition.
-
-Cantera can be used from Python and Matlab, or in applications written
-in C++ and Fortran 90.
-
 Documentation
 =============
+
+These are the detailed API documentation pages for the Python and Matlab
+interfaces for Cantera. There is also documentation of the CTI input file
+format.
+
 .. toctree::
    :maxdepth: 2
 
-   faq
-   Installation Instructions <install>
-   Compiliation Instructions <compiling/index>
-   language-interfaces
-   cti/index
-   reactors
-   flames
+   yaml/index
+   cti/classes
    cython/index
    matlab/index
-   cxx-guide/index
-   glossary
-
-   Cantera Development Homepage <https://github.com/Cantera/cantera>
-
-* **C++ Documentation**
-
-  * `Module Organization <../../doxygen/html/modules.html>`_
-  * `Index of Classes <../../doxygen/html/classes.html>`_
-  * `Deprecation List <../../doxygen/html/deprecated.html>`_
-
-Indexes
-=======
-
-* :ref:`genindex`
-* :ref:`search`

doc/sphinx/install.rst

@@ -1,473 +0,0 @@
-.. _sec-install:
-
-******************
-Installing Cantera
-******************
-
-.. contents::
-   :local:
-   :depth: 2
-
-.. _sec-install-conda:
-
-Conda
-=====
-
-`Anaconda <https://www.continuum.io/downloads>`_ and `Miniconda
-<http://conda.pydata.org/miniconda.html>`_ are Python distributions for which
-Cantera is available through the `conda` package manager. Both distributions are
-available for Linux, OS X, and Windows. The base Anaconda distribution includes
-a large number of Python packages that are widely used in scientific
-applications. Miniconda is a minimal distribution, where all of the packages
-available in Anaconda can be installed using the package manager. Note that
-installing Cantera using conda will only provide the Cantera Python module. If
-you want to use the other Cantera interfaces, see the OS-specific installation
-options below.
-
-For more details on how to use conda, see the `conda documentation
-<http://conda.pydata.org/docs/intro.html>`_.
-
-**Option 1: Create a new environment for Cantera**
-
-If you have just installed Anaconda or Miniconda, the following instructions
-will create a conda environment where you can use Cantera. For this example, the
-environment is named ``spam``. From the command line, run::
-
-    conda create -n spam -c cantera cantera ipython matplotlib
-
-This will create an environment with Cantera, IPython, Matplotlib, and all their
-dependencies installed. Although conda can install a large set of packages by
-default, it is also possible to install packages such as Cantera that are
-maintained independently. These additional channels from which packages may be
-obtained are specified by adding the ``-c`` option in the ``install`` or
-``create`` commands. In this case, we want to install Cantera from the
-``cantera`` channel, so we add ``-c cantera`` and to tell conda to look at the
-``cantera`` channel in addition to the default channels.
-
-If you are running Linux or OS X, you can then activate this environment by
-running::
-
-    source activate spam
-
-If you are running Windows, the equivalent command is::
-
-    activate spam
-
-**Option 2: Install Cantera in an existing environment**
-
-First, activate your environment (assumed to be named ``baked_beans``; if you've
-forgotten the name of the conda environment you wanted to use, the command
-``conda env list`` can help). For Linux and OS X, this is done by running::
-
-    source activate baked_beans
-
-For Windows users, the command is::
-
-    activate baked_beans
-
-Then, install Cantera by running::
-
-    conda install -c cantera cantera
-
-**Option 3: Install the development version of Cantera**
-
-To install a recent development snapshot (i.e. an alpha or beta version) of
-Cantera in an existing environment, run::
-
-    conda install -c cantera/label/dev cantera
-
-If you later want to revert back to the stable version, first remove and then
-reinstall Cantera::
-
-    conda remove cantera
-    conda install -c cantera cantera
-
-.. _sec-install-win:
-
-Windows
-=======
-
-Windows installers are provided for stable versions of Cantera. These
-installation instructions are for Cantera 2.3.0. Use these installers if you
-want to work with a copy of Python downloaded from `Python.org
-<https://www.python.org/>`_. If you are using Anaconda / Miniconda, see the
-directions :ref:`above <sec-install-conda>`.
-
-1. **Choose your Python version and architecture**
-
-   - On Windows, Installers are provided for Python 2.7, Python 3.4, and Python
-     3.5. Python 3.5 is recommended unless you need to use legacy code that does
-     not work with Python 3. You can install multiple Cantera Python modules
-     simultaneously.
-
-   - Cantera supports both 32- and 64- bit Python installations.
-
-   - You need choose the matching Cantera installer for your Python version and
-     machine architecture.
-
-   - The rest of these instructions will refer to your chosen version of Python
-     as *X.Y*.
-
-   - If you are using Matlab, you must use the same architecture for Cantera and
-     Matlab. Matlab defaults to 64-bit if you are running a 64-bit operating
-     system.
-
-2. **Install Python**
-
-   - Go to `python.org <https://www.python.org/>`_.
-
-     - *64-bit*: Download the most recent "Windows X86-64 MSI Installer" for
-       Python *X.Y*.
-     - *32-bit*: Download the most recent "Windows x86 MSI Installer" for
-       Python *X.Y*.
-
-   - Run the installer. The default installation options should be fine.
-
-   - Python is required in order to work with `.cti` input files even if you are
-     not using the Python interface to Cantera.
-
-   - Cantera can also be used with alternative Python distributions such as the
-     Enthought `Canopy <https://www.enthought.com/products/canopy/>`_
-     distribution. These distributions will generally be based on the 64-bit
-     version of Python 2.7, and will include Numpy as well as many other
-     packages useful for scientific users.
-
-3. **Install the Visual C++ Redistributable for Visual Studio 2015**
-
-   - If you are using Python 3.5, you can skip this step as this will have
-     already been installed when you installed Python.
-
-   - Go to the `Microsoft Visual C++ Redistributable Download Page
-     <https://www.microsoft.com/en-us/download/details.aspx?id=48145>`_.
-
-     - *64-bit*: Download ``vc_redist.x64.exe``
-     - *32-bit*: Download ``vc_redist.x86.exe``
-
-   - Run the installer.
-
-   - If this package is not installed, you will encounter the following error
-     when importing the `cantera` module::
-
-         ImportError: DLL load failed: The specified module could not be found.
-
-4. **Install Numpy and optional Python packages**
-
-   - Go to the `Unofficial Windows Binaries for Python Extension Packages page
-     <http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy>`_.
-
-   - Download the most recent release (distributed as a "wheel" archive) of the
-     1.x series for Python *X.Y* that matches your Python architecture. In the
-     filename, the digits after "cp" indicate the Python version, e.g.
-     ``numpy‑1.11.2+mkl‑cp35‑none‑win_amd64.whl`` is the installer for 64-bit
-     Python 3.5. The Windows installers for Cantera 2.3.0 require Numpy 1.10 or
-     newer.
-
-   - From an administrative command prompt, install the downloaded wheel using
-     pip, e.g.::
-
-         c:\python35\scripts\pip.exe install "%USERPROFILE%\Downloads\numpy‑1.11.2+mkl‑cp35‑none‑win_amd64.whl"
-
-   - If you plan on using Cantera from Python, you may also want to install
-     IPython (an advanced interactive Python interpreter) and Matplotlib (a
-     plotting library), which are also available from the above link (note that
-     you may also need to download additional dependencies for each of these
-     packages). Matplotlib is required to run some of the Python examples.
-
-5. **Remove old versions of Cantera**
-
-   - Use The Windows "Add/Remove Programs" interface
-
-   - Remove both the main Cantera package and the Python module.
-
-   - The Python module will be listed as "Python *X.Y* Cantera ..."
-
-6. **Install Cantera**
-
-   - Go to the `Cantera Releases <https://github.com/Cantera/cantera/releases>`_
-     page.
-
-     - *64-bit*: Download **Cantera-2.3.0-x64.msi** and
-       **Cantera-Python-2.3.0-x64-pyX.Y.msi**.
-     - *32-bit*: Download **Cantera-2.3.0-x86.msi** and
-       **Cantera-Python-2.3.0-x86-pyX.Y.msi**.
-
-   - If you are only using the Python module, you do not need to download and
-     install the base package.
-
-   - Run the installer(s).
-
-7. **Configure Matlab** (optional)
-
-   - Set the environment variable ``PYTHON_CMD``
-
-     - From the *Start* menu (Windows 7) or the *Start* screen (Windows 8) type
-       "edit environment" and select "Edit environment variables for your
-       account".
-     - Add a *New* variable with ``PYTHON_CMD`` as the *name* and the full path
-       to the Python executable (e.g. ``C:\python35\python.exe``) as the
-       *value*.
-     - Setting ``PYTHON_CMD`` is not necessary if the path to ``python.exe`` is
-       in your ``PATH`` (which can be set from the same configuration dialog).
-
-   - Launch Matlab
-
-   - Go to *File->Set Path...*
-
-   - Select *Add with Subfolders*
-
-   - Browse to the folder ``C:\Program Files\Cantera\matlab\toolbox``
-
-   - Select *Save*, then *Close*.
-
-8. **Test the installation**
-
-   - Python::
-
-         import cantera
-         gas = cantera.Solution('gri30.cti')
-         h2o = cantera.PureFluid('liquidvapor.cti', 'water')
-
-   - Matlab::
-
-         gas = IdealGasMix('gri30.cti')
-         h2o = Solution('liquidvapor.cti','water')
-
-.. _sec-install-osx:
-
-Mac OS X
-========
-
-Cantera can be installed on OS X using either Homebrew, MacPorts, or Anaconda /
-Miniconda. If you are using Anaconda / Miniconda, see the directions
-:ref:`above <sec-install-conda>`. With Homebrew, the current stable, or
-development version of Cantera can be installed, and both the Python 2.7 and
-Python 3.x modules are available, as well as the Matlab toolbox. The MacPorts
-portfile supports the current stable version of Cantera and builds the Python
-2.7 module.
-
-Homebrew
----------
-These instructions have been tested on Mac OS X 10.9 (Mavericks) with Xcode 5.1
-and Mac OS X 10.10 (Yosemite) with Xcode 6.1. If you've used Homebrew before,
-you can skip any steps which have already been completed.
-
-1. **Install Xcode and Homebrew**
-
-   - Install Xcode from the App Store
-
-   - From a Terminal, run::
-
-         sudo xcode-select --install
-         sudo xcodebuild -license
-
-     and agree to the Xcode license agreement.
-
-   - Install `Homebrew <http://brew.sh/>`_ by running the following command in a
-     Terminal::
-
-         ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
-
-2. **Set up the compilation environment**
-
-   - Run the following commands::
-
-         brew tap homebrew/science
-         brew update
-         brew install python scons
-
-   - Verify that your path is set up to use Homebrew's version of Python by
-     running::
-
-         which python
-
-     If this command does not print ``/usr/local/bin/python``, add the following
-     to ``~/.bash_profile`` (creating this file if it doesn't already exist; you
-     can use the command line editor ``nano`` to edit this file)::
-
-         export PATH=/usr/local/bin:$PATH
-
-     and then run::
-
-         source ~/.bash_profile
-
-   - Install Python packages required to compile Cantera by running::
-
-         pip install numpy
-
-     Note that these packages are required even if you do not plan on using the
-     Cantera Python 2 module.
-
-   - If you plan on using Cantera from Python, you may also want to install
-     IPython (an advanced interactive Python interpreter) and Matplotlib (a
-     plotting library). Matplotlib is required to run some of the Python
-     examples::
-
-         pip install ipython matplotlib
-
-   - If you want to build the Cantera Python 3 module, run::
-
-         brew install python3
-         pip3 install numpy cython
-
-     and, optionally::
-
-         pip3 install ipython matplotlib
-
-3. **Compile and install Cantera**
-
-   * To compile and install Cantera using the default configuration, run::
-
-         brew install cantera
-
-   * The following options are supported:
-
-     ``--HEAD``
-         Installs the current development version of Cantera.
-
-     ``--with-python3``
-         Install the Python 3 module.
-
-     ``--with-matlab=/Applications/MATLAB_R2014a.app/``
-         Installs the Matlab toolbox (with the path modified to match your
-         installed Matlab version)
-
-     ``--without-sundials``
-         Do not use an external SUNDIALS version to build Cantera. This option
-         is set automatically when using Matlab.
-
-     ``--without-test``
-         NOT RECOMMENDED! Disable automatic testing of Cantera during the
-         installation process.
-
-   * These options are specified as additional arguments to the ``brew install``
-     command, e.g.::
-
-         brew install cantera --HEAD --with-python3
-
-   * If you are installing the Matlab toolbox, the recommended command is::
-
-         brew install cantera --with-matlab=/Applications/MATLAB_R2014a.app/
-
-   * If something goes wrong with the Homebrew install, re-run the command with
-     the ``-v`` flag to get more verbose output that may help identify the
-     source of the problem::
-
-         brew install -v cantera
-
-   * If Homebrew claims that it can't find a formula named ``cantera``, you may
-     be able to fix it by running the commands::
-
-         brew doctor
-         brew tap --repair
-
-4. **Test Cantera Installation (Python)**
-
-   * The Python examples will be installed in::
-
-         /usr/local/lib/pythonX.Y/site-packages/cantera/examples/
-
-     where ``X.Y`` is your Python version, e.g. ``2.7``.
-
-   * You may find it convenient to copy the examples to your Desktop::
-
-         cp -r /usr/local/lib/python2.7/site-packages/cantera/examples ~/Desktop/cantera_examples
-
-   * To run an example::
-
-         cd cantera_examples/reactors
-         python reactor1.py
-
-5. **Test Cantera Installation (Matlab)**
-
-   * The Matlab toolbox, if enabled, will be installed in::
-
-         /usr/local/lib/cantera/matlab
-
-   * To use the Cantera Matlab toolbox, run the following commands in Matlab
-     (each time you start Matlab), or add them to a ``startup.m`` file located
-     in ``/Users/$USER/Documents/MATLAB``, where ``$USER`` is your username::
-
-         addpath(genpath('/usr/local/lib/cantera/matlab'))
-         setenv('PYTHON_CMD', '/usr/local/bin/python')
-
-   * The Matlab examples will be installed in::
-
-         /usr/local/share/cantera/samples/matlab
-
-   * You may find it convenient to copy the examples to your user directory::
-
-         cp -r /usr/local/share/cantera/samples/matlab ~/Documents/MATLAB/cantera_examples
-
-MacPorts
---------
-
-If you have MacPorts installed (see https://www.macports.org/install.php), you
-can install Cantera by executing::
-
-    sudo port install cantera
-
-from the command line. All dependencies will be installed automatically.
-
-MacPorts installs its own Python interpreter. Be sure to be actually using it by
-checking::
-
-    sudo port select python python27
-
-.. _sec-install-ubuntu:
-
-Ubuntu
-======
-
-Ubuntu packages are provided for recent versions of Ubuntu using a Personal
-Package Archive (PPA). As of Cantera 2.3.0, packages are available for Ubuntu
-Ubuntu 16.04 (Xenial Xerus) and Ubuntu 16.10 (Yakkety Yak). To see which Ubuntu
-releases and Cantera versions are currently available, visit
-https://launchpad.net/~speth/+archive/ubuntu/cantera
-
-The available packages are:
-
-- ``cantera-python`` - The Cantera Python module for Python 2.
-
-- ``cantera-python3`` - The Cantera Python module for Python 3.
-
-- ``cantera-dev`` - Libraries and header files for compiling your own C++ and
-  Fortran 90 programs that use Cantera.
-
-To add the Cantera PPA::
-
-    sudo aptitude install python-software-properties
-    sudo apt-add-repository ppa:speth/cantera
-    sudo aptitude update
-
-To install all of the Cantera packages::
-
-    sudo aptitude install cantera-python cantera-python3 cantera-dev
-
-or install whichever subset you need by adjusting the above command.
-
-If you plan on using Cantera from Python, you may also want to install IPython
-(an advanced interactive Python interpreter) and Matplotlib (a plotting
-library), which are also available from the above link. Matplotlib is required
-to run some of the Python examples. For Python 2, these packages can be
-installed with::
-
-    pip2 install ipython matplotlib
-
-And for Python 3, these packages can be installed with::
-
-    pip3 install ipython matplotlib
-
-You may need to install ``pip`` first; instructions can be found on the
-`pip installation instructions.
-<https://pip.pypa.io/en/latest/installing.html#install-pip>`_
-You may need to have superuser access to install packages into the system
-directories. Alternatively, you can add ``--user`` after ``pip install`` but
-before the package names to install into your local user directory. An
-alternative method is to use the Ubuntu repositories, but these tend to
-be very out of date. For Python 2, the command is::
-
-    sudo aptitude install ipython python-matplotlib
-
-And for Python 3, these packages can be installed with::
-
-    sudo aptitude install ipython3 python3-matplotlib

doc/sphinx/language-interfaces.rst

@@ -1,55 +0,0 @@
-
-*******************
-Language Interfaces
-*******************
-
-Although most of Cantera is written in C++, interfaces are provided to
-allow users to work with Cantera from several different languages or
-environments, including Fortran 90/95, Python, and MATLAB. Which
-language should you choose? The basic rule of thumb is this: use
-Python or MATLAB if possible; use C++ or Fortran if necessary.
-
-Python
-======
-
-Python is a free scripting language that is designed to be easy to use. If you
-are familiar with any other programming language, you can probably learn Python
-in a couple of hours. It is also an elegant language, and provides a
-user-friendly introduction to the concepts of object-oriented programming.
-Python is great for solving problems quickly, and Cantera provides example
-Python scripts to do calculations ranging from simple evaluation of
-thermodynamic or transport properties, on up to chemical equilibrium in
-multiphase mixtures, 1D laminar flames, reactor networks, and more.  If your
-problem can be solved by using Cantera from Python, you'll almost certainly
-solve it faster with Python than by writing programs in Fortran or C++.
-
-See http://www.python.org
-
-Matlab
-======
-
-The comments above for Python apply to MATLAB too, except hat Python is free and
-MATLAB isn't. If you have MATLAB already and are familiar with it, this is a
-good choice for an environment from which to run Cantera. It is probably the
-most popular Cantera application environment. http://www.mathworks.com.
-
-C++
-===
-
-If you find that you need full access to the internals of Cantera, or want to
-extend and customize Cantera, then C++ is the language for you. Most of Cantera
-is itself written in C++, and so C++ application programs have more direct
-access to Cantera's core functionality than do programs written in other
-languages, which access Cantera through a library of C-like functions. From C++,
-you can implement new equations of state, new models for transport properties,
-and many other things that simply can't be done through the other language
-interfaces. If you are doing substantial code development with Cantera, rather
-than simply using it to solve a few problems, then you will probably want to use
-it from C++.
-
-Fortran
-=======
-
-Cantera provides an interface to Fortran 90/95, and can even be used from
-Fortran 77 programs. Use this if you have existing Fortran code you want to port
-to Cantera.

doc/sphinx/mathjax.py

@@ -1,68 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-    sphinx.ext.mathjax
-    ~~~~~~~~~~~~~~~~~~
-
-    Allow `MathJax <http://mathjax.org/>`_ to be used to display math 
-    in Sphinx's HTML writer - requires the MathJax JavaScript library
-    on your webserver/computer.
-
-    Kevin Dunn, kgdunn@gmail.com, 3-clause BSD license.
-    
-
-    For background, installation details and support: 
-    
-        https://bitbucket.org/kevindunn/sphinx-extension-mathjax
-
-"""
-from docutils import nodes
-from sphinx.application import ExtensionError
-from sphinx.ext.mathbase import setup_math as mathbase_setup
-
-def html_visit_math(self, node):
-    self.body.append(self.starttag(node, 'span', '', CLASS='math'))
-    self.body.append(self.builder.config.mathjax_inline[0] + \
-                     self.encode(node['latex']) +\
-                     self.builder.config.mathjax_inline[1] + '</span>')
-    raise nodes.SkipNode
-
-def html_visit_displaymath(self, node):
-    self.body.append(self.starttag(node, 'div', CLASS='math'))
-    if node['nowrap']:
-        self.body.append(self.builder.config.mathjax_display[0] + \
-                         node['latex'] +\
-                         self.builder.config.mathjax_display[1])
-        self.body.append('</div>')
-        raise nodes.SkipNode
-
-    parts = [prt for prt in node['latex'].split('\n\n') if prt.strip() != '']
-    for i, part in enumerate(parts):
-        part = self.encode(part)
-        if i == 0:
-            # necessary to e.g. set the id property correctly
-            if node['number']:
-                self.body.append('<span class="eqno">(%s)</span>' %
-                                 node['number'])
-        if '&' in part or '\\\\' in part:
-            self.body.append(self.builder.config.mathjax_display[0] + \
-                             '\\begin{split}' + part + '\\end{split}' + \
-                             self.builder.config.mathjax_display[1])
-        else:
-            self.body.append(self.builder.config.mathjax_display[0] + part + \
-                             self.builder.config.mathjax_display[1])
-    self.body.append('</div>\n')
-    raise nodes.SkipNode
-
-def builder_inited(app):
-    if not app.config.mathjax_path:
-        raise ExtensionError('mathjax_path config value must be set for the '
-                             'mathjax extension to work')
-    app.add_javascript(app.config.mathjax_path)
-
-def setup(app):
-    mathbase_setup(app, (html_visit_math, None), (html_visit_displaymath, None))
-    app.add_config_value('mathjax_path', '', False)
-    app.add_config_value('mathjax_inline', [r'\(', r'\)'], 'html')
-    app.add_config_value('mathjax_display', [r'\[', r'\]'], 'html')
-    app.connect('builder-inited', builder_inited)
-

doc/sphinx/matlab/example-script.rst.in

@@ -1,9 +0,0 @@
-:orphan:
-
-.. _matlab-example-@script_name@:
-
-@script_name@
-=======================================================================
-
-.. literalinclude:: @script_path@
-   :language: matlab

doc/sphinx/matlab/examples.rst.in

@@ -1,16 +0,0 @@
-.. _sec-matlab-examples:
-
-Index of Examples
-=================
-
-This is an index of the examples included with the Cantera Matlab Toolbox.
-
-Tutorials
----------
-
-@matlab_tutorials@
-
-Examples
---------
-
-@matlab_examples@

doc/sphinx/matlab/index.rst

@@ -6,14 +6,11 @@ Matlab Interface User's Guide
 .. toctree::
    :maxdepth: 2
 
-   input-tutorial
-   code-docs/importing
-   code-docs/interface
-   code-docs/thermodynamics
-   code-docs/kinetics
-   code-docs/transport
-   code-docs/zero-dim
-   code-docs/one-dim
-   code-docs/data
-   code-docs/utilities
-   examples
+   importing
+   thermodynamics
+   kinetics
+   transport
+   zero-dim
+   one-dim
+   data
+   utilities

doc/sphinx/matlab/input-tutorial.rst

@@ -1,62 +0,0 @@
-
-**********************************
-Tutorial: Working with input files
-**********************************
-
-.. highlight:: matlab
-
-CTI files
----------
-
-This is the typical way to create a Cantera "phase" object in Matlab::
-
-    gas1 = Solution('gri30.cti', 'gri30');
-
-This statement constructs a ``Solution`` object representing a phase of matter by
-reading in attributes of the phase from a file, which in this case is
-``gri30.cti``. This file contains several phase specifications; the one we want
-here is ``gri30``, which is specified by the second argument. This file contains
-a complete specification of the GRI-Mech 3.0 reaction mechanism, including
-element data (name, atomic weight), species data (name, elemental composition,
-coefficients to compute thermodynamic and transport properties), and reaction
-data (stoichiometry, rate coefficient parameters). The file is written in a
-format understood by Cantera, which is described in :ref:`sec-defining-phases`.
-
-CTI files distributed with Cantera
-----------------------------------
-
-Several reaction mechanism files in this format are included in the Cantera
-distribution, including ones that model high-temperature air, a hydrogen/oxygen
-reaction mechanism, and a few surface reaction mechanisms.  These files are kept
-in the ``data`` subdirectory within the Cantera installation directory.
-
-If for some reason Cantera has difficulty finding where these files are on your
-system, set environment variable ``CANTERA_DATA`` to the directory or
-directories (separated using ``;`` on Windows or ``:`` on other operating
-systems) where they are located. Alternatively, you can call function
-`add_directory` to add a directory to the Cantera search path::
-
-    addDirectory('/usr/local/cantera/my_data_files');
-
-Cantera input files are plain text files, and can be created with any text
-editor. See :ref:`sec-defining-phases` for more information.
-
-Importing multiple phases or interfaces
----------------------------------------
-
-A Cantera input file may contain more than one phase specification, or may
-contain specifications of interfaces (surfaces). Here we import definitions of
-two bulk phases and the interface between them from file ``diamond.cti``::
-
-    gas2 = Solution('diamond.cti', 'gas');                   % a gas
-    diamond = Solution('diamond.cti', 'diamond');             % bulk diamond
-    diamond_surf = importInterface('diamond.cti', 'diamond_100', ...
-                                   gas2, diamond);
-
-Note that the bulk (i.e., 3D) phases that participate in the surface reactions
-must also be passed as arguments to importInterface.
-
-Converting CK-format files
---------------------------
-
-See :ref:`sec-ck-format-conversion` in the :ref:`sec-input-files` documentation.

doc/sphinx/reactors.rst

@@ -1,625 +0,0 @@
-.. default-role:: math
-
-.. py:currentmodule:: cantera
-
-*****************************
-Reactors and Reactor Networks
-*****************************
-
-A Cantera Reactor represents the simplest form of a chemically reacting system.
-It corresponds to an extensive thermodynamic control volume `V`, in which all
-state variables are homogeneously distributed. The system is generally unsteady,
-i.e. all states are functions of time. In particular, transient state changes
-due to chemical reactions are possible. However, thermodynamic (but not
-chemical) equilibrium is assumed to be present throughout the reactor at all
-instants of time.
-
-Reactors can interact with the surrounding environment in multiple ways:
-
-- Expansion/compression work: By moving the walls of the reactor, its volume can
-  be changed and expansion or compression work can be done by or on the system,
-  i.e., the Reactor.
-- Heat transfer: An arbitrary heat transfer rate can be defined to cross the
-  boundaries of the reactor.
-- Mass transfer: The reactor can have multiple inlets and outlets. For the
-  inlets, arbitrary states can be defined. Through the outlets, fluid with the
-  current state of the reactor exits the reactor.
-- Surface interaction: One or multiple walls can influence the chemical
-  reactions in the reactor. This is not just restricted to catalytic reactions,
-  but mass transfer between the surface and the fluid can also be modeled.
-
-All of these interactions do not have to be constant, but can vary as a function
-of time or state. For example, heat transfer can be described as a function of
-the temperature difference between the reactor and the environment, or the wall
-movement can be modeled depending on the pressure difference. Typically,
-interactions of the reactor with the environment are defined on one or multiple
-*walls*, *inlets*, and *outlets*.
-
-In addition to single reactors, Cantera is also able to interconnect reactors
-into a *Reactor Network*. Each reactor in a network may be connected so that
-the contents of one reactor flow into another. Reactors may also be in contact
-with one another or the environment via walls which move or conduct heat.
-
-Governing Equations for Single Reactors
-=======================================
-
-The state variables for Cantera's general reactor model are
-
-- `m`, the mass of the reactor's contents (in kg)
-- `V`, the reactor volume (in m\ :sup:`3`) (not a state variable for
-  *Constant Pressure Reactor* and *Ideal Gas Constant Pressure Reactor*)
-- A state variable describing the energy of the system, depending on the
-  configuration (see `Energy Conservation`_ for further explanation):
-
-  - General *Reactor*: `U`, the total internal energy of the reactors
-    contents (in J)
-  - *Constant Pressure Reactor*: `H`, the total enthalpy of the reactors
-    contents (in J)
-  - *Ideal Gas Reactor* and *Ideal Gas Constant Pressure Reactor*: `T`, the
-    temperature (in K)
-
-- `Y_k`, the mass fractions for each species (dimensionless)
-
-Mass Conservation
------------------
-
-The total mass of the reactor's contents changes as a result of flow through
-the reactor's inlets and outlets, and production of homogeneous phase species
-on the reactor walls:
-
-.. math::
-
-    \frac{dm}{dt} = \sum_{in} \dot{m}_{in} - \sum_{out} \dot{m}_{out} +
-                    \dot{m}_{wall}
-
-Species Conservation
---------------------
-
-The rate at which species `k` is generated through homogeneous phase reactions
-is `V \dot{\omega}_k W_k`, and the total rate at which species `k` is generated
-is:
-
-.. math::
-
-    \dot{m}_{k,gen} = V \dot{\omega}_k W_k + \dot{m}_{k,wall}
-
-The rate of change in the mass of each species is:
-
-.. math::
-
-    \frac{d(mY_k)}{dt} = \sum_{in} \dot{m}_{in} Y_{k,in} -
-                         \sum_{out} \dot{m}_{out} Y_k +
-                         \dot{m}_{k,gen}
-
-Expanding the derivative on the left hand side and substituting the equation
-for `dm/dt`, the equation for each homogeneous phase species is:
-
-.. math::
-
-    m \frac{dY_k}{dt} = \sum_{in} \dot{m}_{in} (Y_{k,in} - Y_k)+
-                      \dot{m}_{k,gen} - Y_k \dot{m}_{wall}
-
-
-Reactor Volume
---------------
-
-The reactor volume changes as a function of time due to the motion of one or
-more walls:
-
-.. math::
-
-    \frac{dV}{dt} = \sum_w f_w A_w v_w(t)
-
-where `f_w = \pm 1` indicates the facing of the wall, `A_w` is the surface
-area of the wall, and `v_w(t)` is the velocity of the wall as a function of
-time.
-
-For *Constant Pressure Reactor* and *Ideal Gas Constant Pressure Reactor*, the
-volume is not a state variable, but instead takes on whatever value is
-consistent with holding the pressure constant.
-
-Energy Conservation
--------------------
-
-The solution of the energy equation can be enabled or disabled by changing the
-``energy_enabled`` flag. It is enabled by default.
-
-The implemented formulation of the energy equation depends on which reactor
-model is used.
-
-Standard Reactor
-****************
-
-The equation for the total internal energy is found by writing the first law
-for an open system:
-
-.. math::
-
-    \frac{dU}{dt} = - p \frac{dV}{dt} - \dot{Q} +
-                    \sum_{in} \dot{m}_{in} h_{in} - h \sum_{out} \dot{m}_{out}
-
-
-Constant Pressure Reactor
-*************************
-
-For this reactor model, the pressure is held constant. The volume is not a
-state variable, but instead takes on whatever value is consistent with holding
-the pressure constant. The total enthalpy replaces the total internal energy
-as a state variable. Using the definition of the total enthalpy:
-
-.. math::
-
-    H = U + pV
-
-    \frac{d H}{d t} = \frac{d U}{d t} + p \frac{dV}{dt} + V \frac{dp}{dt}
-
-Noting that `dp/dt = 0` and substituting into the energy equation yields:
-
-.. math::
-
-   \frac{dH}{dt} = - \dot{Q} + \sum_{in} \dot{m}_{in} h_{in}
-                   - h \sum_{out} \dot{m}_{out}
-
-
-Ideal Gas Reactor
-*****************
-
-In case of the Ideal Gas Reactor Model, the reactor temperature `T` is used
-instead of the total internal energy `U` as a state variable. For an ideal gas,
-we can rewrite the total internal energy in terms of the mass fractions and
-temperature:
-
-.. math::
-
-    U = m \sum_k Y_k u_k(T)
-
-    \frac{dU}{dt} = u \frac{dm}{dt}
-                    + m c_v \frac{dT}{dt}
-                    + m \sum_k u_k \frac{dY_k}{dt}
-
-Substituting the corresponding derivatives yields an equation for the
-temperature:
-
-.. math::
-
-    m c_v \frac{dT}{dt} = - p \frac{dV}{dt} - \dot{Q}
-        + \sum_{in} \dot{m}_{in} \left( h_{in} - \sum_k u_k Y_{k,in} \right)
-        - \frac{p V}{m} \sum_{out} \dot{m}_{out} - \sum_k \dot{m}_{k,gen} u_k
-
-While this form of the energy equation is somewhat more complicated, it
-significantly reduces the cost of evaluating the system Jacobian, since the
-derivatives of the species equations are taken at constant temperature instead
-of constant internal energy.
-
-
-Ideal Gas Constant Pressure Reactor
-***********************************
-
-As for the Ideal Gas Reactors, we replace the total enthalpy as a state
-variable with the temperature by writing the total enthalpy in terms of the
-mass fractions and temperature:
-
-.. math::
-
-    H = m \sum_k Y_k h_k(T)
-
-    \frac{dH}{dt} = h \frac{dm}{dt} + m c_p \frac{dT}{dt}
-                    + m \sum_k h_k \frac{dY_k}{dt}
-
-Substituting the corresponding derivatives yields an equation for the
-temperature:
-
-.. math::
-
-    m c_p \frac{dT}{dt} = - \dot{Q} - \sum_k h_k \dot{m}_{k,gen}
-        + \sum_{in} \dot{m}_{in} \left(h_{in} - \sum_k h_k Y_{k,in} \right)
-
-
-Wall Interactions
------------------
-
-The total rate of heat transfer through all walls is:
-
-.. math::
-
-    \dot{Q} = \sum_w f_w \dot{Q}_w
-
-where `f_w = \pm 1` indicates the facing of the wall (+1 for the reactor on the
-left, -1 for the reactor on the right). The heat flux `\dot{Q}_w` through a wall
-`k` connecting reactors "left" and "right" is computed as:
-
-.. math::
-
-    \dot{Q}_w = U A (T_{\rm left} - T_{\rm right})
-              + \epsilon\sigma A (T_{\rm left}^4 - T_{\rm right}^4)
-              + A q_0(t)
-
-where `U` is a user-specified heat transfer coefficient (W/m^2-K), `A` is the
-wall area (m^2), `\epsilon` is the user-specified emissivity, `\sigma` is the
-Stefan-Boltzmann radiation constant, and `q_0(t)` is a user-specified,
-time-dependent heat flux (W/m^2). This definition is such that positive `q_0(t)`
-implies heat transfer from the "left" reactor to the "right" reactor. Each of
-the user-specified terms defaults to 0.
-
-In case of surface reactions, there can be a net generation (or destruction) of
-homogeneous (gas) phase species at the wall. The molar rate of production for
-each homogeneous phase species `k` on wall `w` is `\dot{s}_{k,w}` (in
-kmol/s/m^2). The total (mass) production rate for homogeneous phase species `k`
-on all walls is:
-
-.. math::
-
-    \dot{m}_{k,wall} = W_k \sum_w A_w \dot{s}_{k,w}
-
-where `W_k` is the molecular weight of species `k` and `A_w` is the area of
-each wall. The net mass flux from all walls is then:
-
-.. math::
-
-    \dot{m}_{wall} = \sum_k \dot{m}_{k,wall}
-
-
-For each surface species `i`, the rate of change of the site fraction
-`\theta_{i,w}` on each wall `w` is integrated with time:
-
-.. math::
-
-    \frac{d\theta_{i,w}}{dt} = \frac{\dot{s}_{i,w} n_i}{\Gamma_w}
-
-where `\Gamma_w` is the total surface site density on wall `w` and `n_i` is the
-number of surface sites occupied by a molecule of species `i` (sometimes
-referred to within Cantera as the molecule's "size").
-
-Reactor Networks and Devices
-============================
-
-While reactors by themselves just define the above governing equations of the
-reactor, the time integration is performed in reactor networks. A reactor
-network is therefore necessary even if only a single reactor is considered.
-
-The advantage of reactor networks obviously is that multiple reactors can be
-interconnected. Not only mass flow from one reactor into another can be
-realized, but also heat can be transferred, or the wall between reactors can
-move. To set up a network, the following components can be defined in addition
-to the reactors previously mentioned:
-
-- **Reservoir**: A reservoir can be thought of as an infinitely large volume, in
-  which all states are predefined and never change from their initial values.
-  Typically, it represents a vessel to define temperature and composition of a
-  stream of mass flowing into a reactor, or the ambient fluid surrounding the
-  reactor network. Besides, the fluid flow finally finally exiting a reactor
-  network has to flow into a reservoir. In the latter case, the state of the
-  reservoir (except pressure) is irrelevant.
-
-- **Wall**: A wall separates two reactors, or a reactor and a reservoir. A wall
-  has a finite area, may conduct or radiate heat between the two reactors on
-  either side, and may move like a piston.
-
-  Walls are stateless objects in Cantera, meaning that no differential equation
-  is integrated to determine any wall property. Since it is the wall (piston)
-  velocity that enters the energy equation, this means that it is the velocity,
-  not the acceleration or displacement, that is specified. The wall velocity is
-  computed from
-
-  .. math:: v = K(P_{\rm left} - P_{\rm right}) + v_0(t),
-
-  where :math:`K` is a non-negative constant, and :math:`v_0(t)` is a specified
-  function of time. The velocity is positive if the wall is moving to the right.
-
-  The heat flux through the wall is computed from
-
-  .. math:: q = U(T_{\rm left} - T_{\rm right}) + \epsilon\sigma (T_{\rm left}^4
-                - T_{\rm right}^4) + q_0(t),
-
-  where :math:`U` is the overall heat transfer coefficient for
-  conduction/convection, and :math:`\epsilon` is the emissivity. The function
-  :math:`q_0(t)` is a specified function of time. The heat flux is positive when
-  heat flows from the reactor on the left to the reactor on the right.
-
-  A heterogeneous reaction mechanism may be specified for one or both of the
-  wall surfaces. The mechanism object (typically an instance of class Interface)
-  must be constructed so that it is properly linked to the object representing
-  the fluid in the reactor the surface in question faces. The surface
-  temperature on each side is taken to be equal to the temperature of the
-  reactor it faces.
-
-  Source: `Python <cython/zerodim.html#wall>`_ | :ct:`C++ <Wall>`
-
-- **Valve**: A valve is a flow devices with mass flow rate that is a function of
-  the pressure drop across it. The default behavior is linear:
-
-  .. math:: \dot m = K_v (P_1 - P_2)
-
-  if :math:`P_1 > P_2.` Otherwise, :math:`\dot m = 0`. However, an arbitrary
-  function can also be specified, such that
-
-  .. math:: \dot m = F(P_1 - P_2)
-
-  if :math:`P_1 > P_2`, or :math:`\dot m = 0` otherwise. It is never possible
-  for the flow to reverse and go from the downstream to the upstream
-  reactor/reservoir through a line containing a Valve object.
-
-  Valve objects are often used between an upstream reactor and a downstream
-  reactor or reservoir to maintain them both at nearly the same pressure. By
-  setting the constant :math:`K_v` to a sufficiently large value, very small
-  pressure differences will result in flow between the reactors that counteracts
-  the pressure difference.
-
-- **Mass Flow Controller**: A mass flow controller maintains a specified mass
-  flow rate independent of upstream and downstream conditions. The equation used
-  to compute the mass flow rate is
-
-  .. math:: \dot m = \max(\dot m_0, 0.0)
-
-  where :math:`\dot m_0` is either a constant value or a function of time. Note
-  that if :math:`\dot m_0 < 0`, the mass flow rate will be set to zero, since
-  reversal of the flow direction is not allowed.
-
-  Unlike a real mass flow controller, a MassFlowController object will maintain
-  the flow even if the downstream pressure is greater than the upstream
-  pressure. This allows simple implementation of loops, in which exhaust gas
-  from a reactor is fed back into it through an inlet. But note that this
-  capability should be used with caution, since no account is taken of the work
-  required to do this.
-
-- **Pressure Controller**: A pressure controller is designed to be used in
-  conjunction with another 'master' flow controller, typically a
-  MassFlowController. The master flow controller is installed on the inlet of
-  the reactor, and the corresponding PressureController is installed on on
-  outlet of the reactor. The PressureController mass flow rate is equal to the
-  master mass flow rate, plus a small correction dependent on the pressure
-  difference:
-
-  .. math:: \dot m = \dot m_{\rm master} + K_v(P_1 - P_2).
-
-Time Integration
-----------------
-
-Cantera provides an ODE solver for solving the stiff equations of reacting
-systems. If installed in combination with SUNDIALS, their optimized solver is
-used. Starting off the current state of the system, it can be advanced in time
-by one of the following methods:
-
-- ``step()``: The step method computes the state of the system at the a priori
-  unspecified time `t_{\rm new}`. The time `t_{\rm new}` is internally computed
-  so that all states of the system only change within a (specifiable) band of
-  absolute and relative tolerances. Additionally, the time step must not be
-  larger than a predefined maximum time step `\Delta t_{\rm max}`. The new time
-  `t_{\rm new}` is returned by this function.
-
-- ``advance``\ `(t_{\rm new})`: This method computes the state of the system at
-  time `t_{\rm new}`. `t_{\rm new}` describes the absolute time from the initial
-  time of the system. By calling this method in a for loop for pre-defined
-  times, the state of the system is obtained for exactly the times specified.
-  Internally, several ``step()`` calls are typically performed to reach the
-  accurate state at time `t_{\rm new}`.
-
-- ``advance_to_steady_state(max_steps, residual_threshold, atol,
-  write_residuals)`` [Python interface only]: If the steady state solution of a
-  reactor network is of interest, this method can be used. Internally, the
-  steady state is approached by time stepping. The network is considered to be
-  at steady state if the feature-scaled residual of the state vector is below a
-  given threshold value (which by default is 10 times the time step rtol).
-
-The use of the ``advance`` method in a loop has the advantage that it produces
-results corresponding to a predefined time series. These are associated with a
-predefined memory consumption and well comparable between simulation runs with
-different parameters. However, some detail (e.g. a fast ignition process) might
-not be resolved in the output data due to the typically large time steps.
-
-The ``step`` method results in much more data points because of the small
-timesteps needed. Additionally, the absolute time has to be kept tracked of
-manually.
-
-Even though Cantera comes pre-defined with typical parameters for tolerances
-and the maximum internal time step, the solution sometimes diverges. To solve
-this problem, three parameters can be tuned: The absolute time stepping
-tolerances, the relative time stepping tolerances, and the maximum time step. A
-reduction of the latter value is particularly useful when dealing with abrupt
-changes in the boundary conditions (e.g. opening/closing valves, see also
-example :ref:`py-example-ic_engine.py`).
-
-General Usage in Cantera
-========================
-
-In Cantera, the following steps are typically necessary to investigate a
-reactor network:
-
-1. Define ``Solution`` objects for the fluids to be flowing through your reactor
-   network.
-
-2. Define the reactor type(s) and reservoir(s) that describe your system. Chose
-   Ideal Gas (Constant Pressure) Reactor(s) if you only consider ideal gas
-   phases.
-
-3. *Optional:* Set up the boundary conditions and flow devices between reactors
-   or reservoirs.
-
-4. Define a reactor network which contains all the reactors previously created.
-
-5. Advance the simulation in time, typically in a for- or while-loop. Note that
-   only the current state is stored in Cantera by default. If you want to
-   observe the transient states, you manually have to keep track of them.
-
-6. Analyze the data.
-
-Note that Cantera always solves a transient problem. If you are interested in
-steady-state conditions, you can run your simulation for a long time until the
-states are converged (see e.g. example :ref:`py-example-surf_pfr.py`,
-:ref:`py-example-combustor.py`).
-
-Cantera comes with a broad variety of well-commented example scrips for reactor
-networks. Please refer to them for further information (:ref:`Python <sec-cython-examples>`, :ref:`Matlab <sec-matlab-examples>`).
-
-Common Reactor Types and their Implementation in Cantera
-========================================================
-
-Batch Reactor at Constant Volume or at Constant Pressure
---------------------------------------------------------
-
-If you are interested in how a homogeneous chemical composition changes in time
-when it is left to its own, a simple batch reactor can be used. Two versions
-are commonly considered: A rigid vessel with fixed volume but variable
-pressure, or a system idealized at constant pressure but varying volume.
-
-In Cantera, such a simulation can be performed very easily. The initial state
-of the solution can be specified by composition and a set of thermodynamic
-parameters (like temperature and pressure) as a standard Cantera solution
-object. Upon its base, a general (Ideal Gas) Reactor or an (Ideal Gas) Constant
-Pressure Reactor can be created, depending on if a constant volume or constant
-pressure batch reactor should be considered, respectively. The behavior of the
-solution in time can be simulated as a very simple Reactor Network containing
-only the formerly created reactor.
-
-An example for such a Batch Reactor is :ref:`py-example-reactor1.py`.
-
-Continuously Stirred Tank Reactor
----------------------------------
-
-A Continuously Stirred Tank Reactor (CSTR), also often referred to as
-Well-Stirred Reactor (WSR), Perfectly Stirred Reactor (PSR), or Longwell
-Reactor, is essentially a single Cantera reactor with an inlet, an outlet, and
-constant volume. Therefore, the `Governing Equations for Single Reactors`_
-defined above apply accordingly.
-
-Steady state solutions to CSTRs are often of interest. In this case, the mass
-flow rate `\dot{m}` is constant and equal at inlet and outlet. The mass
-contained in the confinement `m` divided by `\dot{m}` defines the mean
-residence time of the fluid in the confinement.
-
-At steady state, the time derivatives in the governing equations become zero,
-and the system of ordinary differential equations can be reduced to a set of
-coupled nonlinear algebraic equations. A Newton solver could be used to solve
-this system of equations. However, a sophisticated implementation might be
-required to account for the strong nonlinearities and the presence of multiple
-solutions.
-
-Cantera does not have such a Newton solver implemented. Instead, steady CSTRs
-are simulated by considering a time-dependent constant volume reactor with
-specified in- and outflow conditions. Starting off at an initial solution, the
-reactor network containing this reactor is advanced in time until the state of
-the solution is converged. An example for this procedure is
-:ref:`py-example-combustor.py`.
-
-A problem can be the ignition of a CSTR: If the reactants are not reactive
-enough, the simulation can result in the trivial solution that inflow and
-outflow states are identical. To solve this problem, the reactor can be
-initialized with a high temperature and/or radical concentration. A good
-approach is to use the equilibrium composition of the reactants (which can be
-computed using Cantera's ``equilibrate`` function) as an initial guess.
-
-
-Plug-Flow Reactor
------------------
-
-A Plug-Flow Reactor (PFR) represents a steady-state channel with a
-cross-sectional area `A`. Typically an ideal gas flows through it at a constant
-mass flow rate `\dot{m}`. Perpendicular to the flow direction, the gas is
-considered to be completely homogeneous. In the axial direction `z`, the states
-of the gas is allowed to change. However, all diffusion processes are neglected.
-
-Plug-Flow Reactors are often used to simulate ignition delay times, emission
-formation, and catalytic processes.
-
-The governing equations of Plug-Flow Reactors are [KCG2003]_:
-
-- Mass conservation:
-
-  .. math:: \frac{d(\rho u A)}{dz} =  P' \sum_k \dot{s}_k W_k
-
-  where `u` is the axial velocity in (m/s) and `P'` is the chemically active
-  channel perimeter in (m) (chemically active perimeter per unit length).
-
-- Continuity equation of species `k`:
-
- .. math:: \rho u \frac{d Y_k}{dz} + Y_k P' \sum_k \dot{s}_k W_k =
-      \dot{\omega}_k W_k + P' \dot{s}_k W_k
-
-- Energy conservation:
-
-  .. math:: \rho u A c_p \frac{d T}{d z} =
-     - A \sum_k h_k \dot{\omega}_k W_k
-     - P' \sum_k h_k \dot{s}_k W_k
-     + U P (T_w - T)
-
-  where `U` is the heat transfer coefficient in (W/m/K), `P` is the perimeter of
-  the duct in (m), and `T_w` is the wall temperature in (K). Kinetic and
-  potential energies are neglected.
-
-- Momentum conservation in the axial direction:
-
-  .. math:: \rho u A \frac{d u}{d z} + u P' \sum_k \dot{s}_k W_k =
-     - \frac{d (p A)}{dz} - \tau_w P
-
-  where `\tau_w` is the wall friction coefficient (which might be computed from
-  Reynolds number based correlations).
-
-Even though this problem extends geometrically in one direction, it can be
-modeled via zero-dimensional reactors: Due to the neglecting of diffusion,
-downstream parts of the reactor have no influence on upstream parts. Therefore,
-PFRs can be modeled by marching from the beginning to the end of the reactor.
-
-Cantera does not (yet) provide dedicated class to solve the PFR equations (The
-``FlowReactor`` class is currently under development). However, there are two
-ways to simulate a PFR with the reactor elements previously presented. Both
-rely on the assumption that pressure is approximately constant throughout the
-Plug-Flow Reactor and that there is no friction. The momentum conservation
-equation is thus neglected.
-
-
-PFR Modeling by Considering a Lagrangian Reactor
-************************************************
-
-A Plug-Flow Reactor can also be described from a Lagrangian point of view: An
-unsteady fluid particle is considered which travels along the axial streamline
-through the PFR. Since there is no information traveling upstream, the state
-change of the fluid particle can be computed by a forward (upwind) integration
-in time. Using the continuity equation, the speed of the particle can be
-derived. By integrating the velocity in time, the temporal information can be
-translated into the spatial resolution of the PFR.
-
-An example for this procedure can be found in :ref:`py-example-pfr.py`.
-
-
-PFR Modeling as a Series of CSTRs
-*********************************
-
-The Plug-Flow Reactor is spatially discretized into a large number of axially
-distributed volumes. These volumes are modeled to be steady-state CSTRs.
-
-The only reason to use this approach as opposed to the Lagrangian one is if you
-need to include surface reactions, because the system of equations ends up
-being a DAE system instead of an ODE system.
-
-In Cantera, it is sufficient to consider a single reactor and march it forward
-in time, because there is no information traveling upstream. The mass flow rate
-`\dot{m}` through the PFR enters the reactor from an upstream reservoir. For
-the first reactor, the reservoir conditions are the inflow boundary conditions
-of the PFR. By performing a time integration as described in `Continuously
-Stirred Tank Reactor`_ until the state of the reactor is converged, the
-steady-state CSTR solution is computed. The state of the CSTR is the inlet
-boundary condition for the next CSTR downstream.
-
-An example for this procedure can be found in :ref:`py-example-pfr.py` and
-:ref:`py-example-surf_pfr.py`.
-
-
-Advanced Concepts
-=================
-
-In some cases, Cantera's solver is insufficient to describe a certain
-configuration. In this situation, Cantera can still be used to provide chemical
-and thermodynamic computations, but external ODE solvers can be applied. See
-example :ref:`py-example-custom.py`.
-
-
-Literature
-==========
-
-For further reading, the following books are recommended:
-
-.. [KCG2003] Kee, Coltrin, Glarborg: *Chemically Reacting Flow*.
-             Wiley-Interscience, 2003
-
-.. [Tur2000] Turns: *An Introduction to Combustion: Concepts and Applications*,
-             McGraw Hill, 2000

doc/sphinx/yaml/elements.rst

@@ -0,0 +1,25 @@
+.. highlight:: yaml
+
+.. _sec-yaml-elements:
+
+********
+Elements
+********
+
+``element`` entries are needed only when defining custom elements that are not
+standard chemical elements, or defining specific isotopes.
+
+The fields of an ``element`` entry are:
+
+``symbol``
+    The symbol used for the element, as used when specifying the composition of
+    species.
+
+``atomic-weight``
+    The atomic weight of the element, in unified atomic mass units (dalton).
+
+``atomic-number``
+    The atomic number of the element. Optional.
+
+``entropy298``
+    The standard molar entropy of the element at 298.15 K. Optional.

doc/sphinx/yaml/general.rst

@@ -0,0 +1,97 @@
+.. highlight:: yaml
+
+*****************
+General Structure
+*****************
+
+Sections
+--------
+
+The top level of a Cantera `YAML <https://yaml.org/spec/1.2/spec.html#Introduction>`__
+input file is a mapping that defines different input file sections. Each
+section consists of a list of mappings that define objects of the same type,
+e.g., reactions, species, phases, or elements. The ``phases`` section of an input
+file contains all of the phase definitions. Multiple sections containing
+reaction, species, or element definitions can be used. The specific names
+``reactions``, ``species``, and ``elements`` are used as defaults when looking
+for :ref:`sec-yaml-reactions`, :ref:`sec-yaml-species`, and
+:ref:`sec-yaml-elements` to add to a phase. A simple input file has the
+following structure::
+
+    phases:
+    - name: spam
+      thermo: ideal-gas
+      # Additional fields come after this
+    - name: green-eggs
+      thermo: model-name
+      # Additional fields come after this
+
+    species:
+    - name: A
+      # Additional fields come after this
+    - name: B
+      # Additional fields come after this
+    - name: C
+      # Additional fields come after this
+
+    reactions:
+    - equation: A + B <=> C + D
+      # Additional fields come after this
+    - equation: A + C <=> 2 D
+      # Additional fields come after this
+
+Units
+-----
+
+While Cantera generally works internally in SI units, input values can be
+provided using a number of different units.
+
+Compound units are written using the asterisk (``*``) to indicate
+multiplication, the forward slash (``/``) to indicate division, and the caret
+(``^``) to indicate exponentiation. Exponents can include negative and decimal
+values. Standard one-letter metric prefixes can be applied to any unit.
+Supported base units are:
+
+- Mass: ``g``
+- Length: ``m``, ``micron``, ``angstrom``, ``Å``
+- Time: ``s``, ``min``, ``hr``
+- Temperature: ``K``, ``C``
+- Current: ``A``
+- Quantity: ``mol`` (gram mole), ``gmol``, ``mole``, ``kmol``, ``kgmol``, ``molec``
+
+Supported compound units are:
+
+- Energy: ``J``, ``cal``, ``erg``, ``eV``
+- Activation Energy: ``K``, or any unit of energy per quantity (``J/kmol``,
+  ``cal/mol``, etc.)
+- Force: ``N``, ``dyn``
+- Pressure: ``Pa``, ``atm``, ``bar``, ``dyn/cm^2``
+- Volume: ``m^3``, ``liter``, ``L``, ``l``, ``cc``
+- Other electrical units: ``ohm``, ``V``, ``coulomb``
+
+Units can be specified on individual input values by placing them after the
+value, separated by a space::
+
+    {A: 1.45e9 cm^3/kmol, b: 0.4, Ea: 21033 kJ/kmol}
+
+or by using a ``units`` mapping::
+
+    units: {mass: g, quantity: mol, pressure: atm, activation-energy: cal/mol}
+
+A ``units`` mapping will set the default units for all values within the same
+YAML list or mapping, including any nested lists and mappings. Units not
+specified by a mapping use the values from higher level mappings, or the Cantera
+defaults if no ``units`` mapping specifies applicable units. If a ``units``
+mapping appears in a list, it must be the first item in that list.
+
+Default units may be set for ``mass``, ``length``, ``time``, ``temperature``,
+``current``, ``quantity``, ``pressure``, ``energy``, and ``activation-energy``.
+The units ``pressure`` and ``energy`` are used when these units appear
+explicitly in the units that a value is being converted to within Cantera. For
+example, a conversion to ``N/m^2`` will use the default units for mass, length,
+and time, while a conversion to ``Pa`` will use the default units for pressure.
+
+Conversions of activation energies implicitly include scaling by the gas
+constant where necessary. Setting default units for ``energy`` and ``quantity``
+will determine the default units of ``activation-energy``, which can be
+overridden by explicitly giving the desired units of ``activation-energy``.

doc/sphinx/yaml/index.rst

@@ -0,0 +1,13 @@
+
+*************************
+YAML Input File Reference
+*************************
+
+.. toctree::
+   :maxdepth: 2
+
+   general
+   phases
+   elements
+   species
+   reactions

doc/sphinx/yaml/phases.rst

@@ -0,0 +1,808 @@
+.. highlight:: yaml
+
+*****************
+Phase Definitions
+*****************
+
+A ``phase`` is a mapping that contains definitions for the elements, species,
+and optionally reactions that can take place in that phase. The fields of a
+``phase`` entry are:
+
+``name``
+    String identifier used for the phase. Required.
+
+``elements``
+    Specification for the elements present in the phase. This can be:
+
+    - Omitted, in which case the standard elements will be added as needed by
+      the species included in the phase.
+    - A list of element symbols, which can be either defined in the ``elements``
+      section of the file or taken from the standard elements.
+    - A list of single-key mappings of section names to lists of element
+      symbols. These sections can be in the same file as the phase definition,
+      or from another file if written as ``file-path/sectionname``. If a
+      relative path is specified, the directory containing the current file is
+      searched first, followed by the Cantera data path. Standard elements can
+      be included by referencing the fictitious section ``default``.
+
+``species``
+    Specification for the species present in the phase. This can be:
+
+    - a list of species that appear in the ``species`` section of the file.
+    - The string ``all``, to indicate that all species in the ``species``
+      section should be included. This is the default if no ``species`` entry
+      is present.
+    - A list of single-key mappings of section names to either the string
+      ``all`` or a list of species names. These sections can be in the same
+      file as the phase definition, or from another file if written as
+      ``file-path/sectionname``. If a relative path is specified, the directory
+      containing the current file is searched first, followed by the Cantera
+      data path.
+
+    Species may be skipped depending on the setting of the
+    ``skip-undeclared-elements`` option.
+
+``skip-undeclared-elements``
+    If set to ``true``, do not add species that contain elements that are not
+    explicitly included in the phase. The default is ``false``, where the
+    presence of such species is considered an error.
+
+``skip-undeclared-third-bodies``
+   If set to ``true``, ignore third body efficiencies for species that are not
+   defined in the phase. The default is ``false``, where the presence of
+   such third body specifications is considered an error.
+
+``state``
+    A mapping specifying the thermodynamic state. See
+    :ref:`sec-yaml-setting-state`.
+
+``thermo``
+    String specifying the phase thermodynamic model to be used. Supported model
+    strings are:
+
+    - :ref:`binary-solution-tabulated <sec-yaml-binary-solution-tabulated>`
+    - :ref:`compound-lattice <sec-yaml-compound-lattice>`
+    - :ref:`constant-density <sec-yaml-constant-density>`
+    - :ref:`Debye-Huckel <sec-yaml-Debye-Huckel>`
+    - :ref:`edge <sec-yaml-edge>`
+    - :ref:`fixed-chemical-potential <sec-yaml-fixed-chemical-potential>`
+    - :ref:`fixed-stoichiometry <sec-yaml-fixed-stoichiometry>`
+    - :ref:`HMW-electrolyte <sec-yaml-HMW-electrolyte>`
+    - :ref:`ideal-gas <sec-yaml-ideal-gas>`
+    - :ref:`ideal-gas-VPSS <sec-yaml-ideal-gas-VPSS>`
+    - :ref:`ideal-molal-solution <sec-yaml-ideal-molal-solution>`
+    - :ref:`ideal-condensed <sec-yaml-ideal-condensed>`
+    - :ref:`ideal-solution-VPSS <sec-yaml-ideal-solution-VPSS>`
+    - :ref:`ideal-surface <sec-yaml-ideal-surface>`
+    - :ref:`ions-from-neutral-molecule <sec-yaml-ions-from-neutral-molecule>`
+    - :ref:`lattice <sec-yaml-lattice>`
+    - :ref:`liquid-water-IAPWS95 <sec-yaml-liquid-water-IAPWS95>`
+    - :ref:`Margules <sec-yaml-Margules>`
+    - :ref:`Maskell-solid-solution <sec-yaml-Maskell-solid-solution>`
+    - :ref:`electron-cloud <sec-yaml-electron-cloud>`
+    - :ref:`pure-fluid <sec-yaml-pure-fluid>`
+    - :ref:`Redlich-Kister <sec-yaml-Redlich-Kister>`
+    - :ref:`Redlich-Kwong <sec-yaml-Redlich-Kwong>`
+
+``kinetics``
+    String specifying the kinetics model to be used. Supported model strings
+    are:
+
+    - none
+    - `gas <https://cantera.org/documentation/dev/doxygen/html/de/dae/classCantera_1_1GasKinetics.html#details>`__
+    - `surface <https://cantera.org/documentation/dev/doxygen/html/d1/d72/classCantera_1_1InterfaceKinetics.html#details>`__
+    - `edge <https://cantera.org/documentation/dev/doxygen/html/d0/df0/classCantera_1_1EdgeKinetics.html#details>`__
+
+``reactions``
+    Source of reactions to include in the phase, if a kinetics model has been
+    specified. This can be:
+
+    - The string ``all``, which indicates that all reactions from the
+      ``reactions`` section of the file should be included. This is the default
+      if no ``reactions`` entry is present.
+    - The string ``declared-species``, which indicates that all reactions from
+      the ``reactions`` section involving only species present in the phase
+      should be included.
+    - The string ``none``, which indicates that no reactions should be added.
+      This can be used if reactions will be added programmatically after
+      the phase is constructed.
+    - A list of sections from which to include reactions. These sections can be
+      in the same file as the phase definition, or from another file if written
+      as ``file-path/sectionname``. If a relative path is specified, the
+      directory containing the current file is searched first, followed by the
+      Cantera data path.
+    - A list of single-key mappings of section names to rules for adding
+      reactions, where for each section name, that rule is either ``all`` or
+      ``declared-species`` and is applied as described above.
+
+``Motz-Wise``
+    Boolean indicating whether the Motz-Wise correction should be applied to
+    sticking reactions. Applicable only to interface phases. The default is
+    ``false``. The value set at the phase level may be overridden on individual
+    reactions.
+
+``transport``
+    String specifying the transport model to be used. Supported model strings
+    are:
+
+    - none
+    - `high-pressure <https://cantera.org/documentation/dev/doxygen/html/d9/d63/classCantera_1_1HighPressureGasTransport.html#details>`__
+    - `ionized-gas <https://cantera.org/documentation/dev/doxygen/html/d4/d65/classCantera_1_1IonGasTransport.html#details>`__
+    - `mixture-averaged <https://cantera.org/documentation/dev/doxygen/html/d9/d17/classCantera_1_1MixTransport.html#details>`__
+    - `mixture-averaged-CK <https://cantera.org/documentation/dev/doxygen/html/d9/d17/classCantera_1_1MixTransport.html#details>`__
+    - `multicomponent <https://cantera.org/documentation/dev/doxygen/html/df/d7c/classCantera_1_1MultiTransport.html#details>`__
+    - `multicomponent-CK <https://cantera.org/documentation/dev/doxygen/html/df/d7c/classCantera_1_1MultiTransport.html#details>`__
+    - `unity-Lewis-number <https://cantera.org/documentation/dev/doxygen/html/d3/dd6/classCantera_1_1UnityLewisTransport.html#details>`__
+    - `water <https://cantera.org/documentation/dev/doxygen/html/df/d1f/classCantera_1_1WaterTransport.html#details>`__
+
+
+
+.. _sec-yaml-setting-state:
+
+Setting the state
+=================
+
+The state of a ``phase`` can be set using two properties to set the
+thermodynamic state, plus the composition.
+
+The composition can be set using one of the following fields, depending on the
+phase type. The composition is specified as a mapping of species names to
+values. Where necessary, the values will be automatically normalized.
+
+- ``mass-fractions`` or ``Y``
+- ``mole-fractions`` or ``X``
+- ``coverages``
+- ``molalities`` or ``M``
+
+The thermodynamic state can be set using the following property pairs, with some
+exceptions for phases where setting that property pair is not implemented. All
+properties are on a per unit mass basis where relevant:
+
+- ``T`` and ``P``
+- ``T`` and ``D``
+- ``T`` and ``V``
+- ``H`` and ``P``
+- ``U`` and ``V``
+- ``S`` and ``V``
+- ``S`` and ``P``
+- ``S`` and ``T``
+- ``P`` and ``V``
+- ``U`` and ``P``
+- ``V`` and ``H``
+- ``T`` and ``H``
+- ``S`` and ``H``
+- ``D`` and ``P``
+
+The following synonyms are also implemented for use in any of the pairs:
+
+- ``temperature``, ``T``
+- ``pressure``, ``P``
+- ``enthalpy``, ``H``
+- ``entropy``, ``S``
+- ``int-energy``, ``internal-energy``, ``U``
+- ``specific-volume``, ``V``
+- ``density``, ``D``
+
+
+.. _sec-phase-thermo-models:
+
+Phase thermodynamic models
+==========================
+
+.. _sec-yaml-binary-solution-tabulated:
+
+``binary-solution-tabulated``
+-----------------------------
+
+A phase implementing tabulated standard state thermodynamics for one species in
+a binary solution, as `described here <https://cantera.org/documentation/dev/doxygen/html/de/ddf/classCantera_1_1BinarySolutionTabulatedThermo.html#details>`__.
+
+Includes the fields of :ref:`sec-yaml-ideal-molal-solution`, plus:
+
+``tabulated-species``
+    The name of the species to which the tabulated enthalpy and entropy is
+    added.
+
+``tabulated-thermo``
+    A mapping containing three lists of equal lengths:
+
+    ``mole-fractions``
+        A list of mole fraction values for the tabulated species.
+
+    ``enthalpy``
+        The extra molar enthalpy to be added to the tabulated species at these
+        mole fractions.
+
+    ``entropy``
+        The extra molar entropy to be added to the tabulated species at these
+        mole fractions.
+
+
+.. _sec-yaml-compound-lattice:
+
+``compound-lattice``
+--------------------
+
+A phase that is comprised of a fixed additive combination of other lattice
+phases, as `described here <https://cantera.org/documentation/dev/doxygen/html/de/de1/classCantera_1_1LatticeSolidPhase.html#details>`__.
+
+Additional fields:
+
+``composition``
+    A mapping of component phase names to their relative stoichiometries.
+
+Example::
+
+    thermo: compound-lattice
+    composition: {Li7Si3(s): 1.0, Li7Si3-interstitial: 1.0}
+
+
+.. _sec-yaml-constant-density:
+
+``constant-density``
+--------------------
+
+An incompressible phase with constant density, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d9/de4/classCantera_1_1ConstDensityThermo.html#details>`__.
+
+Additional fields:
+
+``density``
+    The density of the phase
+
+Example::
+
+    thermo: constant-density
+    density: 0.7 g/cm^3
+
+
+.. _sec-yaml-Debye-Huckel:
+
+``Debye-Huckel``
+----------------
+
+The Debye-Hückel model as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d8/d9a/classCantera_1_1DebyeHuckel.html#details>`__.
+
+Additional parameters for this model are contained in the ``activity-data``
+field:
+
+``activity-data``
+    The activity data field contains the following fields:
+
+    ``model``
+        One of ``dilute-limit``, ``B-dot-with-variable-a``,
+        ``B-dot-with-common-a``, ``beta_ij``, or ``Pitzer-with-beta_ij``
+
+    ``A_Debye``
+        The value of the Debye "A" parameter, or the string ``variable`` to use
+        a calculation based on the water equation of state.
+
+    ``B_Debye``
+        The Debye "B" parameter
+
+    ``max-ionic-strength``
+        The maximum ionic strength
+
+    ``use-Helgeson-fixed-form``
+        Boolean, ``true`` or ``false``
+
+    ``default-ionic-radius``
+        Ionic radius to use for species where the ionic radius has not been
+        specified.
+
+    ``B-dot``
+        The value of B-dot.
+
+    ``beta``
+        List of mappings providing values of :math:`\beta_{ij}` for different
+        species pairs. Each mapping contains a ``species`` key that contains a
+        list of two species names, and a ``beta`` key that contains the
+        corresponding value of :math:`\beta_{ij}`.
+
+Example::
+
+    thermo: Debye-Huckel
+    activity-data:
+      model: beta_ij
+      max-ionic-strength: 3.0
+      use-Helgeson-fixed-form: true
+      default-ionic-radius: 3.042843 angstrom
+      beta:
+      - species: [H+, Cl-]
+        beta: 0.27
+      - species: [Na+, Cl-]
+        beta: 0.15
+      - species: [Na+, OH-]
+        beta: 0.06
+
+
+.. _sec-yaml-edge:
+
+``edge``
+--------
+
+A one-dimensional edge between two surfaces, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d9/d17/classCantera_1_1EdgePhase.html#details>`__.
+
+Additional fields:
+
+``site-density``
+    The molar density of sites per unit length along the edge
+
+Example::
+
+    thermo: edge
+    site-density: 5.0e-17 mol/cm
+
+
+.. _sec-yaml-fixed-chemical-potential:
+
+``fixed-chemical-potential``
+----------------------------
+
+A phase defined by a fixed value of the chemical potential, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d6/db0/classCantera_1_1FixedChemPotSSTP.html#details>`__.
+
+Additional fields:
+
+``chemical-potential``
+    The molar chemical potential of the phase
+
+Example::
+
+    thermo: fixed-chemical-potential
+    chemical-potential: -2.3e7 J/kmol
+
+
+.. _sec-yaml-fixed-stoichiometry:
+
+``fixed-stoichiometry``
+-----------------------
+
+A phase with fixed composition, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d3/d50/classCantera_1_1StoichSubstance.html#details>`__.
+
+
+.. _sec-yaml-HMW-electrolyte:
+
+``HMW-electrolyte``
+-------------------
+
+A dilute or concentrated liquid electrolyte phase that obeys the Pitzer
+formulation for nonideality, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/de/d1d/classCantera_1_1HMWSoln.html#details>`__.
+
+Additional parameters for this model are contained in the ``activity-data``
+field:
+
+``activity-data``
+    The activity data field contains the following fields:
+
+    ``temperature-model``
+        The form of the Pitzer temperature model. One of ``constant``,
+        ``linear`` or ``complex``.
+
+    ``A_Debye``
+        The value of the Debye "A" parameter, or the string ``variable`` to use
+        a calculation based on the water equation of state.
+
+    ``max-ionic-strength``
+        The maximum ionic strength
+
+    ``interactions``
+        A list of mappings, where each mapping describes a binary or ternary
+        interaction among species. Fields of this mapping include:
+
+        ``species``
+            A list of one to three species names
+
+        ``beta0``
+            The :math:`\beta^{(0)}` parameters for an cation/anion interaction.
+            1, 2, or 5 values depending on the value of ``temperature-model``.
+
+        ``beta1``
+            The :math:`\beta^{(1)}` parameters for an cation/anion interaction.
+            1, 2, or 5 values depending on the value of ``temperature-model``.
+
+        ``beta2``
+            The :math:`\beta^{(2)}` parameters for an cation/anion interaction.
+            1, 2, or 5 values depending on the value of ``temperature-model``.
+
+        ``Cphi``
+            The :math:`C^\phi` parameters for an cation/anion interaction.
+            1, 2, or 5 values depending on the value of ``temperature-model``.
+
+        ``alpha1``
+            The :math:`\alpha^{(1)}` parameter for an cation/anion interaction.
+
+        ``alpha2``
+            The :math:`\alpha^{(2)}` parameter for an cation/anion interaction.
+
+        ``theta``
+            The :math:`\theta` parameters for a like-charged binary interaction.
+            1, 2, or 5 values depending on the value of ``temperature-model``.
+
+        ``lambda``
+            The :math:`\lambda` parameters for binary interactions involving at
+            least one neutral species. 1, 2, or 5 values depending on the value
+            of ``temperature-model``.
+
+        ``psi``
+            The :math:`\Psi` parameters for ternary interactions involving three
+            charged species. 1, 2, or 5 values depending on the value of
+            ``temperature-model``.
+
+        ``zeta``
+            The :math:`\zeta` parameters for ternary interactions involving one
+            neutral species. 1, 2, or 5 values depending on the value of
+            ``temperature-model``.
+
+        ``mu``
+            The :math:`\mu` parameters for a neutral species self-interaction.
+            1, 2, or 5 values depending on the value of ``temperature-model``.
+
+    ``cropping-coefficients``
+
+        ``ln_gamma_k_min``
+            Default -5.0.
+
+        ``ln_gamma_k_max``
+            Default 15.0.
+
+        ``ln_gamma_o_min``
+            Default -6.0.
+
+        ``ln_gamma_o_max``
+            Default 3.0.
+
+Example::
+
+    thermo: HMW-electrolyte
+    activity-data:
+      temperature-model: complex
+      A_Debye: 1.175930 kg^0.5/gmol^0.5
+      interactions:
+      - species: [Na+, Cl-]
+        beta0: [0.0765, 0.008946, -3.3158E-6, -777.03, -4.4706]
+        beta1: [0.2664, 6.1608E-5, 1.0715E-6, 0.0, 0.0]
+        beta2: [0.0, 0.0, 0.0, 0.0, 0.0]
+        Cphi: [0.00127, -4.655E-5, 0.0, 33.317, 0.09421]
+        alpha1: 2.0
+      - species: [H+, Cl-]
+        beta0: [0.1775]
+        beta1: [0.2945]
+        beta2: [0.0]
+        Cphi: [0.0008]
+        alpha1: 2.0
+      - species: [Na+, OH-]
+        beta0: 0.0864
+        beta1: 0.253
+        beta2: 0.0
+        Cphi: 0.0044
+        alpha1: 2.0
+        alpha2: 0.0
+      - {species: [Cl-, OH-], theta: -0.05}
+      - {species: [Na+, Cl-, OH-], psi: -0.006}
+      - {species: [Na+, H+], theta: 0.036}
+      - {species: [Cl-, Na+, H+], psi: [-0.004]}
+
+
+.. _sec-yaml-ideal-gas:
+
+``ideal-gas``
+-------------
+
+The ideal gas model as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d7/dfa/classCantera_1_1IdealGasPhase.html#details>`__.
+
+.. _sec-yaml-ideal-gas-VPSS:
+
+``ideal-gas-VPSS``
+------------------
+
+The ideal gas model, using variable pressure standard state methods as
+`described here <https://cantera.org/documentation/dev/doxygen/html/dc/ddb/classCantera_1_1IdealSolnGasVPSS.html#details>`__.
+
+
+.. _sec-yaml-ideal-molal-solution:
+
+``ideal-molal-solution``
+------------------------
+
+A phase based on the mixing-rule assumption that all molality-based activity
+coefficients are equal to one, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/da/d5c/classCantera_1_1IdealMolalSoln.html#details>`__.
+
+Additional fields:
+
+``standard-concentration-basis``
+    A string specifying the basis for the standard concentration. One of
+    ``unity``, ``species-molar-volume``, or ``solvent-molar-volume``.
+
+``cutoff``
+    Parameters for cutoff treatments of activity coefficients
+
+    ``model``
+        ``poly`` or ``polyExp``
+
+    ``gamma_o``
+        gamma_o value for the cutoff process at the zero solvent point
+
+    ``gamma_k``
+        gamma_k minimum for the cutoff process at the zero solvent point
+
+    ``X_o``
+        value of the solute mole fraction that centers the cutoff polynomials
+        for the cutoff = 1 process
+
+    ``c_0``
+        Parameter in the polyExp cutoff treatment having to do with rate of
+        exponential decay
+
+    ``slope_f``
+        Parameter in the ``polyExp`` cutoff treatment
+
+    ``slope_g``
+        Parameter in the ``polyExp`` cutoff treatment
+
+Example::
+
+    thermo: ideal-molal-solution
+    standard-concentration-basis: solvent-molar-volume
+    cutoff:
+      model: polyexp
+      gamma_o: 0.0001
+      gamma_k: 10.0
+      X_o: 0.2
+      c_0: 0.05
+      slope_f: 0.6
+      slope_g: 0.0
+
+
+.. _sec-yaml-ideal-condensed:
+
+``ideal-condensed``
+-------------------
+
+A condensed phase ideal solution as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d3/d4c/classCantera_1_1IdealSolidSolnPhase.html#details>`__.
+
+Additional fields:
+
+``standard-concentration-basis``
+    A string specifying the basis for the standard concentration. One of
+    ``unity``, ``species-molar-volume``, or ``solvent-molar-volume``.
+
+
+.. _sec-yaml-ideal-solution-VPSS:
+
+``ideal-solution-VPSS``
+-----------------------
+
+An ideal solution model using variable pressure standard state methods as
+`described here <https://cantera.org/documentation/dev/doxygen/html/dc/ddb/classCantera_1_1IdealSolnGasVPSS.html#details>`__.
+
+Additional fields:
+
+``standard-concentration-basis``
+    A string specifying the basis for the standard concentration. One of
+    ``unity``, ``species-molar-volume``, or ``solvent-molar-volume``.
+
+
+.. _sec-yaml-ideal-surface:
+
+``ideal-surface``
+-----------------
+
+An ideal surface phase, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d2/d95/classCantera_1_1SurfPhase.html#details>`__.
+
+Additional fields:
+
+``site-density``
+    The molar density of surface sites
+
+
+.. _sec-yaml-ions-from-neutral-molecule:
+
+``ions-from-neutral-molecule``
+------------------------------
+
+A model that handles the specification of the chemical potentials for ionic
+species, given a specification of the chemical potentials for the same phase
+expressed in terms of combinations of the ionic species that represent neutral
+molecules, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d7/d4a/classCantera_1_1IonsFromNeutralVPSSTP.html#details>`__.
+
+Additional fields:
+
+``neutral-phase``
+    The ``name`` of the phase definition for the phase containing the neutral
+    molecules.
+
+Example::
+
+    - name: KCl-ions
+      thermo: ions-from-neutral-molecule
+      neutral-phase: KCl-neutral
+      species: [K+, Cl-]
+    - name: KCl-neutral
+      species: [KCl(l)]
+      thermo: Margules
+
+
+.. _sec-yaml-lattice:
+
+``lattice``
+-----------
+
+A simple thermodynamic model for a bulk phase, assuming a lattice of solid
+atoms, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d1/da0/classCantera_1_1LatticePhase.html#details>`__.
+
+Additional fields:
+
+``site-density``
+    The molar density of lattice sites
+
+
+.. _sec-yaml-liquid-water-IAPWS95:
+
+``liquid-water-IAPWS95``
+------------------------
+
+An equation of state for liquid water, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/dc/d86/classCantera_1_1WaterSSTP.html#details>`__.
+
+
+.. _sec-yaml-Margules:
+
+``Margules``
+------------
+
+A phase employing the Margules approximation for the excess Gibbs free energy, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d7/dfe/classCantera_1_1MargulesVPSSTP.html#details>`__.
+
+Additional fields:
+
+``interactions``
+    A list of mappings, where each mapping has the following fields:
+
+    ``species``
+        A list of two species names
+
+    ``excess-enthalpy``
+        A list of two values specifying the first and second excess enthalpy
+        coefficients for the interaction of the specified species. Defaults to
+        [0, 0].
+
+    ``excess-entropy``
+        A list of two values specifying the first and second excess entropy
+        coefficients for the interaction of the specified species. Defaults to
+        [0, 0].
+
+    ``excess-volume-enthalpy``
+        A list of two values specifying the first and second enthalpy
+        coefficients for the excess volume interaction of the specified species.
+        Defaults to [0, 0].
+
+    ``excess-volume-entropy``
+        A list of two values specifying the first and second entropy
+        coefficients for the excess volume interaction of the specified species.
+        Defaults to [0, 0].
+
+Example::
+
+  thermo: Margules
+  interactions:
+  - species: [KCl(l), LiCl(l)]
+    excess-enthalpy: [-17570, -377]
+    excess-entropy: [-7.627, 4.958]
+
+
+.. _sec-yaml-Maskell-solid-solution:
+
+``Maskell-solid-solution``
+--------------------------
+
+A condensed phase non-ideal solution with two species, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/dd/d3a/classCantera_1_1MaskellSolidSolnPhase.html#details>`__.
+
+Additional fields:
+
+``excess-enthalpy``
+    The molar excess enthalpy
+
+``product-species``
+    String specifying the "product" species
+
+Example::
+
+    thermo: Maskell-solid-solution
+    excess-enthalpy: 5 J/mol
+    product-species: H(s)
+
+
+.. _sec-yaml-electron-cloud:
+
+``electron-cloud``
+------------------
+
+A phase representing an electron cloud, such as conduction electrons in a metal,
+as `described here <https://cantera.org/documentation/dev/doxygen/html/d9/d13/classCantera_1_1MetalPhase.html#details>`__.
+
+Additional fields:
+
+``density``
+    The density of the bulk metal
+
+
+.. _sec-yaml-pure-fluid:
+
+``pure-fluid``
+--------------
+
+A phase representing a pure fluid equation of state for one of several species,
+as `described here <https://cantera.org/documentation/dev/doxygen/html/d1/d29/classCantera_1_1PureFluidPhase.html#details>`__.
+
+Additional fields:
+
+``pure-fluid-name``
+    Name of the pure fluid model to use:
+    - ``carbondioxide``
+    - ``heptane``
+    - ``hfc134a``
+    - ``hydrogen``
+    - ``methane``
+    - ``nitrogen``
+    - ``oxygen``
+    - ``water``
+
+
+.. _sec-yaml-Redlich-Kister:
+
+``Redlich-Kister``
+------------------
+
+A phase employing the Redlich-Kister approximation for the excess Gibbs free
+energy, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d0/d23/classCantera_1_1RedlichKisterVPSSTP.html#details>`__.
+
+Additional fields:
+
+``interactions``
+    A list of mappings, where each mapping has the following fields:
+
+    ``species``
+        A list of two species names
+
+    ``excess-enthalpy``
+        A list of polynomial coefficients for the excess enthalpy of the
+        specified binary interaction
+
+    ``excess-entropy``
+        A list of polynomial coefficients for the excess entropy of the
+        specified binary interaction
+
+Example::
+
+  thermo: Redlich-Kister
+  interactions:
+  - species: [Li(C6), V(C6)]
+    excess-enthalpy: [-3.268e+06, 3.955e+06, -4.573e+06, 6.147e+06, -3.339e+06,
+                      1.117e+07, 2.997e+05, -4.866e+07, 1.362e+05, 1.373e+08,
+                      -2.129e+07, -1.722e+08, 3.956e+07, 9.302e+07, -3.280e+07]
+    excess-entropy: [0.0]
+
+
+.. _sec-yaml-Redlich-Kwong:
+
+``Redlich-Kwong``
+-----------------
+
+A multi-species Redlich-Kwong phase as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d6/d29/classCantera_1_1RedlichKwongMFTP.html#details>`__.
+
+The parameters for each species are contained in the corresponding species
+entries.

doc/sphinx/yaml/reactions.rst

@@ -0,0 +1,323 @@
+.. highlight:: yaml
+
+.. _sec-yaml-reactions:
+
+*********
+Reactions
+*********
+
+The fields common to all ``reaction`` entries are:
+
+``equation``
+    The stoichiometric equation for the reaction. Each term (i.e.,
+    stoichiometric coefficient, species name, ``+`` or ``<=>``) in the equation
+    must be separated by a space.
+
+    Reversible reactions may be written using ``<=>`` or ``=`` to separate
+    reactants and products. Irreversible reacions are written using ``=>``.
+
+``type``
+    A string specifying the type of reaction or rate coefficient
+    parameterization. The default is ``elementary``. Reaction types are:
+
+    - :ref:`elementary <sec-elementary>`
+    - :ref:`three-body <sec-three-body>`
+    - :ref:`falloff <sec-falloff>`
+    - :ref:`chemically-activated <sec-chemically-activated>`
+    - :ref:`pressure-dependent-Arrhenius <sec-pressure-dependent-Arrhenius>`
+    - :ref:`Chebyshev <sec-Chebyshev>`
+
+    Reactions on surfaces or edges are automatically treated as
+    :ref:`interface <sec-interface-reaction>` reactions, and reactions that
+    involve charge transfer between phases are automatically treated as
+    :ref:`electrochemical <sec-electrochemical-reaction>` reactions, without the
+    need to specify the ``type``.
+
+``duplicate``
+    Boolean indicating whether the reaction is a known duplicate of another
+    reaction. The default is ``false``.
+
+``orders``
+    An optional mapping of species to explicit reaction orders to use. Reaction
+    orders for reactant species not explicitly mentioned are taken to be their
+    respective stoichiometric coefficients. See
+    `Reaction orders <https://cantera.org/science/reactions.html#reaction-orders>`__
+    for additional information.
+
+``negative-orders``
+    Boolean indicating whether negative reaction orders are allowed. The
+    default is ``false``.
+
+``nonreactant-orders``
+    Boolean indicating whether orders for non-reactant species are allowed.
+    The default is ``false``.
+
+Depending on the reaction ``type``, other fields may be necessary to specify
+the rate of the reaction.
+
+.. _sec-arrhenius:
+
+Arrhenius expression
+====================
+
+Arrhenius expressions can be specified as either a three-element list containing
+the pre-exponential factor :math:`A`, the temperature exponent :math:`b`, and
+the activation energy :math:`E_a`, or a mapping containing the fields ``A``,
+``b``, and ``Ea``. The following are equivalent::
+
+    {A: -2.70000E+13 cm^3/mol/s, b: 0, Ea: 355 cal/mol}
+    [-2.70000E+13 cm^3/mol/s, 0, 355 cal/mol]
+
+
+.. _sec-efficiencies:
+
+Efficiencies
+============
+
+Some reaction types include parameters for the "efficiency" of different species
+as third-body colliders. For these reactions, the following additional fields
+are supported:
+
+``efficiencies``
+    A mapping of species names to efficiency values
+
+``default-efficiency``
+    The efficiency for use for species not included in the ``efficiencies``
+    mapping. Defaults to 1.0.
+
+
+Reaction types
+==============
+
+.. _sec-elementary:
+
+``elementary``
+--------------
+
+A homogeneous reaction with a pressure-independent rate coefficient and mass
+action kinetics, as
+`described here <https://cantera.org/science/reactions.html#reactions-with-a-pressure-independent-rate>`__.
+
+Additional fields are:
+
+``rate-constant``
+    An :ref:`Arrhenius-type <sec-arrhenius>` list or mapping.
+
+``negative-A``
+    A boolean indicating whether a negative value for the pre-exponential factor
+    is allowed. The default is ``false``.
+
+Example::
+
+    equation: N + NO <=> N2 + O
+    rate-constant: {A: -2.70000E+13 cm^3/mol/s, b: 0, Ea: 355 cal/mol}
+    negative-A: true
+
+
+.. _sec-three-body:
+
+``three-body``
+--------------
+
+A three body reaction as
+`described here <https://cantera.org/science/reactions.html#three-body-reactions>`__.
+
+The reaction equation should include the third body collision partner ``M``.
+
+Includes the fields of an ``elementary`` reaction, plus the fields for
+specifying :ref:`efficiencies <sec-efficiencies>`.
+
+Example::
+
+    equation: 2 O + M = O2 + M
+    type: three-body
+    rate-constant: [1.20000E+17 cm^6/mol^2/s, -1, 0]
+    efficiencies: {AR: 0.83, H2O: 5}
+
+
+.. _sec-falloff:
+
+``falloff``
+-----------
+
+A falloff reaction as
+`described here <https://cantera.org/science/reactions.html#falloff-reactions>`__.
+
+The reaction equation should include the pressure-dependent third body collision
+partner ``(+M)`` or ``(+name)`` where ``name`` is the name of a species. The
+latter case is equivalent to setting the efficiency for ``name`` to 1 and the
+efficiency for all other species to 0.
+
+Includes field for specifying :ref:`efficiencies <sec-efficiencies>` as well
+as:
+
+``high-P-rate-constant``
+    An :ref:`sec-arrhenius` expression for the high-pressure limit
+
+``low-P-rate-constant``
+    An :ref:`sec-arrhenius` expression for the low-pressure limit
+
+``Troe``
+    Parameters for the
+    `Troe <https://cantera.org/science/reactions.html#the-troe-falloff-function>`__
+    falloff function. A mapping containing the keys ``A``, ``T3``, ``T1`` and
+    optionally ``T2``. The default value for ``T2`` is 0.
+
+``SRI``
+    Parameters for the
+    `SRI <https://cantera.org/science/reactions.html#the-sri-falloff-function>`__
+    falloff function. A mapping containing the keys ``A``, ``B``, ``C``, and
+    optionally ``D`` and ``E``. The default values for ``D`` and ``E`` are 1.0
+    and 0.0, respectively.
+
+Example::
+
+    equation: H + CH2 (+ N2) <=> CH3 (+N2)
+    type: falloff
+    high-P-rate-constant: [6.00000E+14 cm^3/mol/s, 0, 0]
+    low-P-rate-constant: {A: 1.04000E+26 cm^6/mol^2/s, b: -2.76, Ea: 1600}
+    Troe: {A: 0.562, T3: 91, T1: 5836}
+
+
+.. _sec-chemically-activated:
+
+``chemically-activated``
+------------------------
+
+A chemically activated reaction as
+`described here <https://cantera.org/science/reactions.html#chemically-activated-reactions>`__.
+
+The parameters are the same as for :ref:`sec-falloff` reactions.
+
+Example::
+
+    equation: CH3 + OH (+M) <=> CH2O + H2 (+M)
+    type: chemically-activated
+    high-P-rate-constant: [5.88E-14, 6.721, -3022.227]
+    low-P-rate-constant: [282320.078, 1.46878, -3270.56495]
+
+.. _sec-pressure-dependent-Arrhenius:
+
+``pressure-dependent-Arrhenius``
+--------------------------------
+
+A pressure-dependent reaction using multiple Arrhenius expressions as
+`described here <https://cantera.org/science/reactions.html#pressure-dependent-arrhenius-rate-expressions-p-log>`__.
+
+The only additional field in this reaction type is:
+
+``rate-constants``
+    A list of mappings, where each mapping is the mapping form of an
+    :ref:`sec-arrhenius` expression with the addition of a pressure ``P``.
+
+Example::
+
+    equation: H + CH4 <=> H2 + CH3
+    type: pressure-dependent-Arrhenius
+    rate-constants:
+    - {P: 0.039474 atm, A: 2.720000e+09 cm^3/mol/s, b: 1.2, Ea: 6834.0}
+    - {P: 1.0 atm, A: 1.260000e+20, b: -1.83, Ea: 15003.0}
+    - {P: 1.0 atm, A: 1.230000e+04, b: 2.68, Ea: 6335.0}
+    - {P: 1.01325 MPa, A: 1.680000e+16, b: -0.6, Ea: 14754.0}
+
+
+.. _sec-Chebyshev:
+
+``Chebyshev``
+-------------
+
+A reaction parameterized as a bivariate Chebyshev polynomial as
+`described here <https://cantera.org/science/reactions.html#chebyshev-reaction-rate-expressions>`__.
+
+Additional fields are:
+
+``temperature-range``
+    A list of two values specifying the minimum and maximum temperatures at
+    which the rate constant is valid
+
+``pressure-range``
+    A list of two values specifying the minimum and maximum pressures at
+    which the rate constant is valid
+
+``data``
+    A list of lists containing the Chebyshev coefficients
+
+Example::
+
+    equation: CH4 <=> CH3 + H
+    type: Chebyshev
+    temperature-range: [290, 3000]
+    pressure-range: [0.0098692326671601278 atm, 98.692326671601279 atm]
+    data: [[-1.44280e+01,  2.59970e-01, -2.24320e-02, -2.78700e-03],
+           [ 2.20630e+01,  4.88090e-01, -3.96430e-02, -5.48110e-03],
+           [-2.32940e-01,  4.01900e-01, -2.60730e-02, -5.04860e-03],
+           [-2.93660e-01,  2.85680e-01, -9.33730e-03, -4.01020e-03],
+           [-2.26210e-01,  1.69190e-01,  4.85810e-03, -2.38030e-03],
+           [-1.43220e-01,  7.71110e-02,  1.27080e-02, -6.41540e-04]]
+
+
+.. _sec-interface-reaction:
+
+``interface``
+-------------
+
+A reaction occuring on a surface between two bulk phases, or along an edge
+at the intersection of two surfaces, as
+`described here <https://cantera.org/science/reactions.html#surface-reactions>`__.
+
+Includes the fields of an :ref:`sec-elementary` reaction plus:
+
+``sticking-coefficient``
+    An :ref:`Arrhenius-type <sec-arrhenius>` expression for the sticking coefficient
+
+``Motz-Wise``
+    A boolean applicable to sticking reactions, indicating whether to use the
+    Motz-Wise correction factor for sticking coefficients near unity. Defaults
+    to ``false``.
+
+``sticking-species``
+    The name of the sticking species. Required for sticking reactions only if
+    the reaction includes multiple non-surface species.
+
+``coverage-dependencies``
+    A mapping of species names to coverage dependence parameters, where these
+    parameters are contained in a mapping with the fields:
+
+    ``a``
+        Coefficient for exponential dependence on the coverage
+
+    ``m``
+        Power-law exponent of coverage dependence
+
+    ``E``
+        Activation energy dependence on coverage
+
+Example::
+
+    equation: 2 H(s) => H2 + 2 Pt(s)
+    rate-constant: {A: 3.7e21 cm^2/mol/s, b: 0, Ea: 67400 J/mol}
+    coverage-dependencies: {H(s): {a: 0, m: 0, E: -6000 J/mol}}
+
+
+.. _sec-electrochemical-reaction:
+
+``electrochemical``
+-------------------
+
+Interface reactions involving charge transfer between phases,
+as `described here <https://cantera.org/documentation/dev/doxygen/html/d6/ddd/classCantera_1_1ElectrochemicalReaction.html#details>`__.
+
+Includes the fields of an :ref:`sec-interface-reaction` reaction, plus:
+
+``beta``
+    The symmetry factor for the reaction. Default is 0.5.
+
+``exchange-current-density-formulation``
+    Set to ``true`` if the rate constant parameterizes the exchange current
+    density. Default is ``false``.
+
+Example::
+
+    equation: LiC6 <=> Li+(e) + C6
+    rate-constant: [5.74, 0.0, 0.0]
+    beta: 0.4

doc/sphinx/yaml/species.rst

@@ -0,0 +1,471 @@
+.. highlight:: yaml
+
+.. _sec-yaml-species:
+
+*******
+Species
+*******
+
+The fields of a ``species`` entry are:
+
+``name``
+    String identifier used for the species. Required.
+
+``composition``
+    Mapping that specifies the elemental composition of the species,
+    e.g., ``{C: 1, H: 4}``. Required.
+
+``thermo``
+    Mapping containing the reference state thermodynamic model specification
+    and parameters. See :ref:`sec-yaml-species-thermo`.
+
+``equation-of-state``
+    Mapping containing the equation of state model specification for the
+    species, any parameters for that model, and any parameters for interactions
+    with other species. :ref:`sec-yaml-species-eos`. If this field is absent,
+    the ``ideal-gas`` model is assumed.
+
+``transport``
+    Mapping containing the species transport model specification and
+    parameters. See :ref:`sec-yaml-species-transport`.
+
+``sites``
+    The number of sites occupied by a surface or edge species. Default is 1.
+
+``ionic-radius``
+    Size of the species. Used in the Debye-Hückel model.
+
+``electrolyte-species-type``
+    One of ``solvent``, ``charged-species``, ``weak-acid-associated``,
+    ``strong-acid-associated``, ``polar-neutral``, or ``nonpolar-neutral``.
+    The types ``solvent``, ``charged-species``, and ``nonpolar-neutral`` can be
+    inferred automatically. Used in the Debye-Hückel model.
+
+``weak-acid-charge``
+    Charge to use for species can break apart into charged species. Used in the
+    Debye-Hückel model.
+
+
+.. _sec-yaml-species-thermo:
+
+Species thermo models
+=====================
+
+Fields of a species ``thermo`` entry used by all models are:
+
+``model``
+    String specifying the model to be used. Required. Supported model strings
+    are:
+
+    - :ref:`NASA7 <sec-yaml-nasa7>`
+    - :ref:`NASA9 <sec-yaml-nasa9>`
+    - :ref:`Shomate <sec-yaml-shomate>`
+    - :ref:`constant-cp <sec-yaml-constcp>`
+    - :ref:`piecewise-Gibbs <sec-yaml-piecewise-gibbs>`
+
+``reference-pressure``
+    The reference pressure at which the given thermodynamic properties apply.
+    Defaults to 1 atm.
+
+
+.. _sec-yaml-nasa7:
+
+NASA 7-coefficient polynomials
+------------------------------
+
+The polynomial form `described here <https://cantera.org/science/science-species.html#the-nasa-7-coefficient-polynomial-parameterization>`__,
+given for one or two temperature regions. Additional fields of a ``NASA7``
+thermo entry are:
+
+``temperature-ranges``
+    A list giving the temperature intervals on which the polynomials are valid.
+    For one temperature region, this list contains the minimum and maximum
+    temperatures for the polynomial. For two temperature regions, this list
+    contains the minimum, intermediate, and maximum temperatures.
+
+``data``
+    A list with one item per temperature region, where that item is a 7 item
+    list of polynomial coefficients. The temperature regions are arranged in
+    ascending order. Note that this is different from the standard CHEMKIN
+    formulation that uses two temperature regions listed in descending order.
+
+Example::
+
+    thermo:
+      model: NASA7
+      temperature-ranges: [300.0, 1000.0, 5000.0]
+      data:
+      - [3.298677, 0.0014082404, -3.963222e-06, 5.641515e-09,
+        -2.444854e-12, -1020.8999, 3.950372]
+      - [2.92664, 0.0014879768, -5.68476e-07, 1.0097038e-10,
+        -6.753351e-15, -922.7977, 5.980528]
+
+
+.. _sec-yaml-nasa9:
+
+NASA 9-coefficient polynomials
+------------------------------
+
+The polynomial form `described here <https://cantera.org/science/science-species.html#the-nasa-9-coefficient-polynomial-parameterization>`__,
+given for any number of temperature regions. Additional fields of a ``NASA9``
+thermo entry are:
+
+``temperature-ranges``
+    A list giving the temperature intervals on which the polynomials are valid.
+    This list contains the minimum temperature, the intermediate temperatures
+    between each set pair of regions, and the maximum temperature.
+
+``data``
+    A list with one item per temperature region, where that item is a 9 item
+    list of polynomial coefficients. The temperature regions are arranged in
+    ascending order.
+
+Example::
+
+    thermo:
+      model: NASA9
+      temperature-ranges: [200.00, 1000.00, 6000.0, 20000]
+      reference-pressure: 1 bar
+      data:
+      - [2.210371497E+04, -3.818461820E+02, 6.082738360E+00, -8.530914410E-03,
+         1.384646189E-05, -9.625793620E-09, 2.519705809E-12, 7.108460860E+02,
+         -1.076003744E+01]
+      - [5.877124060E+05, -2.239249073E+03, 6.066949220E+00, -6.139685500E-04,
+         1.491806679E-07,  -1.923105485E-11, 1.061954386E-15, 1.283210415E+04,
+         -1.586640027E+01]
+      - [8.310139160E+08, -6.420733540E+05, 2.020264635E+02, -3.065092046E-02,
+         2.486903333E-06, -9.705954110E-11, 1.437538881E-15, 4.938707040E+06,
+         -1.672099740E+03]
+
+.. _sec-yaml-shomate:
+
+Shomate polynomials
+-------------------
+
+The polynomial form `described here <https://cantera.org/science/science-species.html#the-shomate-parameterization>`__,
+given for one or two temperature regions. Additional fields of a ``Shomate``
+thermo entry are:
+
+``temperature-ranges``
+    A list giving the temperature intervals on which the polynomials are valid.
+    For one temperature region, this list contains the minimum and maximum
+    temperatures for the polynomial. For two temperature regions, this list
+    contains the minimum, intermediate, and maximum temperatures.
+
+``data``
+    A list with one item per temperature region, where that item is a 7 item
+    list of polynomial coefficients. The temperature regions are arranged in
+    ascending order.
+
+Example::
+
+    thermo:
+      model: Shomate
+      temperature-ranges: [298, 1300, 6000]
+      data:
+      - [25.56759, 6.096130, 4.054656, -2.671301, 0.131021,
+        -118.0089, 227.3665]
+      - [35.15070, 1.300095, -0.205921, 0.013550, -3.282780,
+        -127.8375, 231.7120]
+
+
+.. _sec-yaml-constcp:
+
+Constant heat capacity
+----------------------
+
+The constant heat capacity model `described here <https://cantera.org/science/science-species.html#constant-heat-capacity>`__.
+Additional fields of a ``constant-cp`` thermo entry are:
+
+``T0``
+    The reference temperature. Defaults to 298.15 K.
+
+``h0``
+    The molar enthalpy at the reference temperature. Defaults to 0.0.
+
+``s0``
+    The molar entropy at the reference temperature. Defaults to 0.0.
+
+``cp0``
+    The heat capacity at constant pressure. Defaults to 0.0.
+
+Example::
+
+    thermo:
+      model: constant-cp
+      T0: 1000 K
+      h0: 9.22 kcal/mol
+      s0: -3.02 cal/mol/K
+      cp0: 5.95 cal/mol/K
+
+.. _sec-yaml-piecewise-gibbs:
+
+Piecewise Gibbs
+---------------
+
+A model based on piecewise interpolation of the Gibbs free energy as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d4/d9e/classCantera_1_1Mu0Poly.html#details>`__
+Additional fields of a ``piecewise-Gibbs`` entry are:
+
+``h0``
+    The molar enthalpy at the reference temperature of 298.15 K. Defaults to
+    0.0.
+
+``dimensionless``
+    A boolean flag indicating whether the values of the Gibbs free energy are
+    given in a dimensionless form, i.e., divided by :math:`RT`. Defaults to
+    ``false``.
+
+``data``
+    A mapping of temperatures to values of the Gibbs free energy. The Gibbs free
+    energy can be either in molar units (if ``dimensionless`` is ``false``) or
+    nondimensionalized by the corresponding temperature (if ``dimensionless`` is
+    ``true``). A value must be provided at :math:`T^\circ = 298.15` K.
+
+Example::
+
+    thermo:
+      model: piecewise-Gibbs
+      h0: -230.015 kJ/mol
+      dimensionless: true
+      data: {298.15: -91.50963, 333.15: -85.0}
+
+
+.. _sec-yaml-species-eos:
+
+Species equation of state models
+================================
+
+``model``
+    String specifying the model to be used. Required. Supported model strings
+    are:
+
+    - :ref:`constant-volume <sec-yaml-eos-constant-volume>`
+    - :ref:`density-temperature-polynomial <sec-yaml-eos-density-temperature-polynomial>`
+    - :ref:`HKFT <sec-yaml-eos-hkft>`
+    - :ref:`ideal-gas <sec-yaml-eos-ideal-gas>`
+    - :ref:`ions-from-neutral-molecule <sec-yaml-eos-ions-from-neutral>`
+    - :ref:`liquid-water-IAPWS95 <sec-yaml-eos-liquid-water-iapws95>`
+    - :ref:`molar-volume-temperature-polynomial <sec-yaml-eos-molar-volume-temperature-polynomial>`
+    - :ref:`Redlich-Kwong <sec-yaml-eos-redlich-kwong>`
+
+
+.. _sec-yaml-eos-constant-volume:
+
+Constant volume
+---------------
+
+A constant volume model as
+`described here <https://cantera.org/documentation/dev/doxygen/html/da/d33/classCantera_1_1PDSS__ConstVol.html#details>`__.
+
+Any one of the following may be specified:
+
+``molar-volume``
+    The molar volume of the species.
+
+``molar-density``
+    The molar density of the species.
+
+``density``
+    The mass density of the species.
+
+Example::
+
+    equation-of-state:
+      model: constant-volume
+      molar-volume: 1.3 cm^3/mol
+
+
+.. _sec-yaml-eos-density-temperature-polynomial:
+
+Density temperature polynomial
+------------------------------
+
+A model in which the density varies with temperature as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d0/d2f/classCantera_1_1PDSS__SSVol.html#details>`__.
+
+Additional fields:
+
+``data``
+    Vector of 4 coefficients for a cubic polynomial in temperature
+
+Example::
+
+    equation-of-state:
+      model: density-temperature-polynomial
+      units: {mass: g, length: cm}
+      data: [0.536504, -1.04279e-4, 3.84825e-9, -5.2853e-12]
+
+
+.. _sec-yaml-eos-hkft:
+
+HKFT
+----
+
+The Helgeson-Kirkham-Flowers-Tanger model as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d9/d18/classCantera_1_1PDSS__HKFT.html#details>`__.
+
+Additional fields:
+
+``h0``
+    Enthalpy of formation at the reference temperature and pressure
+
+``s0``
+    Entropy of formation at the reference temperature and pressure
+
+``a``
+    4-element vector containing the coefficients :math:`a_1, \ldots , a_4`
+
+``c``
+    2-element vector containing the coefficients :math:`c_1` and :math:`c_2`
+
+``omega``
+    The :math:`\omega` parameter at the reference temperature and pressure
+
+Example::
+
+    equation-of-state:
+      model: HKFT
+      h0: -57433. cal/gmol
+      s0: 13.96 cal/gmol/K
+      a: [0.1839 cal/gmol/bar, -228.5 cal/gmol,
+         3.256 cal*K/gmol/bar, -27260. cal*K/gmol]
+      c: [18.18 cal/gmol/K, -29810. cal*K/gmol]
+      omega: 33060 cal/gmol
+
+
+.. _sec-yaml-eos-ideal-gas:
+
+Ideal gas
+---------
+
+A species using the ideal gas equation of state, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/df/d31/classCantera_1_1PDSS__IdealGas.html#details>`__.
+This model is the default if no ``equation-of-state`` section is included.
+
+
+.. _sec-yaml-eos-ions-from-neutral:
+
+Ions from neutral molecule
+--------------------------
+
+A species equation of state model used with the ``ions-from-neutral-molecule``
+phase model, as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d5/df4/classCantera_1_1PDSS__IonsFromNeutral.html#details>`__.
+
+Additional fields:
+
+``special-species``
+    Boolean indicating whether the species is the "special species" in the
+    phase. Default is ``false``.
+
+``multipliers``
+    A dictionary mapping species to neutral species multiplier values.
+
+Example::
+
+    equation-of-state:
+      model: ions-from-neutral-molecule
+      multipliers: {KCl(l): 1.2}
+
+
+.. _sec-yaml-eos-liquid-water-iapws95:
+
+Liquid Water IAPWS95
+--------------------
+
+A detailed equation of state for liquid water as
+`described here <https://cantera.org/documentation/dev/doxygen/html/de/d64/classCantera_1_1PDSS__Water.html#details>`__.
+
+
+.. _sec-yaml-eos-molar-volume-temperature-polynomial:
+
+Molar volume temperature polynomial
+-----------------------------------
+
+A model in which the molar volume varies with temperature as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d0/d2f/classCantera_1_1PDSS__SSVol.html#details>`__.
+
+Additional fields:
+
+``data``
+    Vector of 4 coefficients for a cubic polynomial in temperature
+
+
+.. _sec-yaml-eos-redlich-kwong:
+
+Redlich-Kwong
+-------------
+
+A model where species follow the Redlich-Kwong equation of state as
+`described here <https://cantera.org/documentation/dev/doxygen/html/d6/d29/classCantera_1_1RedlichKwongMFTP.html#details>`__.
+
+Additional fields:
+
+``a``
+    Pure-species ``a`` coefficient. Scalar or list of two values for a
+    temperature-dependent expression.
+
+``b``
+    Pure-species ``b`` coefficient.
+
+``binary-a``
+    Mapping where the keys are species and the values are the ``a``
+    coefficients for binary interactions between the two species.
+
+
+.. _sec-yaml-species-transport:
+
+Species transport models
+========================
+
+``model``
+    String specifying the model type. The only model that is specifically
+    handled is ``gas``.
+
+Gas transport
+-------------
+
+Species transport properties are a rare exception to Cantera's use of SI units,
+and use the units in which these properties are customarily reported. No
+conversions are supported.
+
+The additional fields of a ``gas`` transport entry are:
+
+``geometry``
+    A string specifying the geometry of the molecule. One of ``atom``,
+    ``linear``, or ``nonlinear``.
+
+``diameter``
+    The Lennard-Jones collision diameter [Å]
+
+``well-depth``
+    The Lennard-Jones well depth [K]
+
+``dipole``
+    The permanent dipole moment [Debye]. Default 0.0.
+
+``polarizability``
+    The dipole polarizability [Å^3]. Default 0.0.
+
+``rotational-relaxation``
+    The rotational relaxation collision number at 298 K [-]. Default 0.0.
+
+``acentric-factor``
+    Pitzer's acentric factor [-]. Default 0.0.
+
+``dispersion-coefficient``
+    The dispersion coefficient, normalized by :math:`e^2` [Å^5]. Default 0.0.
+
+``quadrupole-polarizability``
+    The quadrupole polarizability [Å^5]. Default 0.0.
+
+Example::
+
+    transport:
+      model: gas
+      geometry: linear
+      well-depth: 107.4
+      diameter: 3.458
+      polarizability: 1.6
+      rotational-relaxation: 3.8

ext/SConscript

@@ -2,6 +2,7 @@ from buildutils import *
 
 Import('env', 'build', 'install', 'libraryTargets')
 localenv = env.Clone()
+copyenv = localenv.Clone() # no CPPPATH addition, to avoid circular dependencies
 
 license_files = [('Cantera', '#License.txt'),
                  ('Libexecstream', 'libexecstream/doc/license.txt')]
@@ -18,30 +19,36 @@ def prep_default(env):
 
 def prep_gtest(env):
     localenv = prep_default(env)
-    localenv.Prepend(CPPPATH=[Dir('#ext/googletest'),
-                              Dir('#ext/googletest/include')],
-                    CPPDEFINES={'GTEST_HAS_PTHREAD': 0})
+    localenv.Prepend(CPPPATH=[Dir('#ext/googletest/googletest'),
+                              Dir('#ext/googletest/googletest/include')],
+                     CPPDEFINES={'GTEST_HAS_PTHREAD': 0})
     return localenv
 
-def prep_fmt(env):
+
+def prep_gmock(env):
     localenv = prep_default(env)
-    if not env['system_fmt']:
-        license_files.append(('fmtlib', 'fmt/LICENSE.rst'))
-        for name in ('format.h', 'ostream.h'):
-            build(localenv.Command("#include/cantera/ext/fmt/" + name,
-                                   "#ext/fmt/fmt/" + name,
-                                    Copy('$TARGET', '$SOURCE')))
+    localenv.Prepend(CPPPATH=[Dir('#ext/googletest/googletest/include'),
+                              Dir('#ext/googletest/googlemock'),
+                              Dir('#ext/googletest/googlemock/include')],
+                     CPPDEFINES={'GTEST_HAS_PTHREAD': 0})
     return localenv
 
+
 # each element of libs is: (subdir, (file extensions), prepfunction)
-libs = [('libexecstream', ['cpp'], prep_default),
-        ('fmt/fmt', ['cc'], prep_fmt)]
+libs = [('libexecstream', ['cpp'], prep_default)]
 
 for subdir, extensions, prepFunction in libs:
     localenv = prepFunction(env)
     objects = localenv.SharedObject(mglob(localenv, subdir, *extensions))
     libraryTargets.extend(objects)
 
+if not env['system_fmt']:
+    license_files.append(('fmtlib', 'fmt/LICENSE.rst'))
+    for name in ('format.h', 'ostream.h', 'printf.h', 'core.h', 'format-inl.h'):
+        build(copyenv.Command("#include/cantera/ext/fmt/" + name,
+                              "#ext/fmt/include/fmt/" + name,
+                              Copy('$TARGET', '$SOURCE')))
+
 if env['system_sundials'] == 'n':
     localenv = prep_default(env)
     localenv.Prepend(CPPPATH=Dir('#include/cantera/ext'))
@@ -58,31 +65,55 @@ if env['system_sundials'] == 'n':
                                      ConfigBuilder(sundials_configh)))
 
     # Copy sundials header files into common include directory
-    for subdir in ('sundials', 'nvector', 'cvodes', 'ida'):
+    for subdir in ('sundials', 'nvector', 'cvodes', 'ida', 'sunmatrix', 'sunlinsol'):
         for header in mglob(env, 'sundials/include/'+subdir, 'h'):
-            build(localenv.Command('#include/cantera/ext/%s/%s' % (subdir, header.name),
-                                   '#ext/sundials/include/%s/%s' % (subdir, header.name),
-                                   Copy('$TARGET', '$SOURCE')))
+            build(copyenv.Command('#include/cantera/ext/%s/%s' % (subdir, header.name),
+                                  '#ext/sundials/include/%s/%s' % (subdir, header.name),
+                                  Copy('$TARGET', '$SOURCE')))
 
     # Compile Sundials source files
-    exclude = ['_klu', '_superlumt']
-    if not env['use_lapack']:
-        exclude.append('_lapack')
-    for subdir in ('sundials', 'nvec_ser', 'cvodes', 'ida'):
+    subdirs = ['sundials', 'nvec_ser', 'cvodes', 'ida', 'sunmat_band',
+               'sunmat_dense', 'sunmat_sparse', 'sunlinsol_dense',
+               'sunlinsol_band','sunlinsol_spgmr']
+    if env['use_lapack']:
+        subdirs.extend(('sunlinsol_lapackdense', 'sunlinsol_lapackband'))
+
+    for subdir in subdirs:
         libraryTargets.extend(localenv.SharedObject(
-            [f for f in mglob(localenv, 'sundials/src/'+subdir, 'c')
-             if not any(pattern in f.name for pattern in exclude)]))
+            [f for f in mglob(localenv, 'sundials/src/'+subdir, 'c')]))
+
+if not env['system_yamlcpp']:
+    localenv = prep_default(env)
+    localenv.Prepend(CPPPATH=Dir('#include/cantera/ext'))
+    license_files.append(('YAML-CPP', 'yaml-cpp/LICENSE'))
+
+    # Copy header files into common include directory
+    for subdir in ('', 'contrib', 'node', 'node/detail'):
+        for header in mglob(env, 'yaml-cpp/include/yaml-cpp/'+subdir, 'h'):
+            h = build(localenv.Command('#include/cantera/ext/yaml-cpp/{}/{}'.format(subdir, header.name),
+                                       '#ext/yaml-cpp/include/yaml-cpp/{}/{}'.format(subdir, header.name),
+                                       Copy('$TARGET', '$SOURCE')))
+
+    # Compile yaml-cpp source files
+    for subdir in ('', 'contrib'):
+        libraryTargets.extend(localenv.SharedObject(
+            [f for f in mglob(localenv, 'yaml-cpp/src/'+subdir, 'cpp')]))
+
 
 if not env['system_eigen']:
     license_files.append(('Eigen', 'eigen/COPYING.MPL2'))
-    build(localenv.Command('#include/cantera/ext/Eigen', '#ext/eigen/Eigen',
-                           Copy('$TARGET', '$SOURCE')))
+    h = build(copyenv.Command('#include/cantera/ext/Eigen', '#ext/eigen/Eigen',
+                              Copy('$TARGET', '$SOURCE')))
+    copyenv.Depends(copyenv['config_h_target'], h)
 
 # Google Test: Used internally for Cantera unit tests.
-if not env['system_googletest']:
+if env['googletest'] == 'submodule':
     localenv = prep_gtest(env)
     gtest = build(localenv.Library('../lib/gtest',
-                                   source=['googletest/src/gtest-all.cc']))
+                                   source=['googletest/googletest/src/gtest-all.cc']))
+    localenv = prep_gmock(env)
+    gmock = build(localenv.Library('../lib/gmock',
+                                   source=['googletest/googlemock/src/gmock-all.cc']))
 
 # Create license file containing licenses for Cantera and all included packages
 def generate_license(target, source, env):

ext/eigen

@@ -1 +1 @@
-Subproject commit c6ef117db0a5d72ad0b0239ab1f6dfc3291c398e
+Subproject commit dde02fceedfc1ba09d4d4f71a2b5dafcfcb85491

ext/fmt

@@ -1 +1 @@
-Subproject commit 7fa8f8fa48b0903deab5bb42e6760477173ac485
+Subproject commit 5386f1df20392a08844f5034e8436c6ec7ce0b03