Create FUNDING.yml

Links to NumFOCUS donate page

.codecov.yml

@@ -0,0 +1,9 @@
+coverage:
+  range: "20...100"
+
+  ignore:
+  - ext/.*
+
+comment:
+  behavior: once
+  require_changes: yes

.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
@@ -7,7 +9,11 @@
 *.exe.manifest
 build/
 test/work/
+interfaces/cython/cantera/_cantera.h
 include/cantera/base/config.h
+include/cantera/base/config.h.build
+include/cantera/base/system.h.gch
+include/cantera/ext/
 interfaces/matlab/ctpath.m
 interfaces/matlab/Contents.m
 stage/
@@ -33,9 +39,14 @@ config.log
 .settings
 *.gcda
 *.gcno
+*.gch
 coverage/
 coverage.info
-doc/sphinx/cython/examples
+doc/sphinx/matlab/data.rst
-doc/sphinx/matlab/examples/
+doc/sphinx/matlab/importing.rst
-doc/sphinx/matlab/tutorials/
+doc/sphinx/matlab/kinetics.rst
-doc/sphinx/matlab/code-docs/
+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

@@ -0,0 +1,15 @@
+[submodule "ext/fmt"]
+	path = ext/fmt
+	url = https://github.com/fmtlib/fmt.git
+[submodule "ext/googletest"]
+	path = ext/googletest
+	url = https://github.com/google/googletest.git
+[submodule "ext/sundials"]
+	path = ext/sundials
+	url = https://github.com/Cantera/sundials-mirror
+[submodule "ext/eigen"]
+	path = ext/eigen
+	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

@@ -0,0 +1,90 @@
+language: cpp
+sudo: false
+dist: xenial
+os:
+  - linux
+  - osx
+addons:
+  apt:
+    packages:
+      - 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: |
+  echo TRAVIS_OS_NAME: $TRAVIS_OS_NAME
+  if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+      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 $HOME/miniconda/etc/profile.d/conda.sh && conda activate
+      conda config --set always_yes yes --set changeps1 no
+      conda install -q numpy cython scons boost ruamel_yaml
+      conda install -q -c conda-forge openmp
+  else
+      pip3 install --user --upgrade pip
+      pip3 install --user --upgrade setuptools wheel
+      pip3 install --user cython
+      pip3 install --user ruamel.yaml==0.15.94  # Need a version compatible with Python 3.4
+
+      # Install packages for the documentation
+      pip3 install --user sphinx sphinxcontrib-matlabdomain sphinxcontrib-doxylink
+      pip3 install --user https://github.com/hagenw/sphinxcontrib-katex/archive/master.tar.gz
+  fi
+  rm -f cantera.conf
+script: |
+  set -e
+  if [[ "$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" == "linux" ]]; then
+      bash <(curl -s https://codecov.io/bash)
+  fi

AUTHORS

@@ -1,17 +1,45 @@
-Cantera developers:
+Cantera was originally developed by Dave Goodwin, with its first public release
-
+in 2001. Since then, many people have contributed to Cantera. Below is a
-Dave Goodwin
+partial, alphabetical list of developers and contributors to Cantera over the
-Harry Moffat
+years. If you've been left off, please report the omission on the Github issue
-Raymond Speth
+tracker.
-
-Contributors:
 
+Emil Atz
 Philip Berndt
-Victor Brunini
+Wolfgang Bessler, Offenburg University of Applied Science
-Steven Decaluwe
+Tilman Bremer
-Thomas Fiala
+Victor Brunini, Sandia National Laboratory
+Bang-Shiuh Chen, Purdue University
+Ryan Crisanti
+Nicholas Curtis
+Steven DeCaluwe, Colorado School of Mines
+Vishesh Devgan
+Thomas Fiala, Technische Universität München
 David Fronczek
-John Hewson
+@g3bk47
-Nicholas Malaya
+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
-Bryan Weber
+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

CODE_OF_CONDUCT.md

@@ -0,0 +1,74 @@
+# Cantera Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers commit to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at conduct@cantera.org. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

CONTRIBUTING.md

@@ -0,0 +1,93 @@
+# Contributing to Cantera
+
+* For significant changes, consider starting a discussion on the Cantera
+  Users' Group to plan your modifications so that they can be implemented
+  efficiently and in a way that doesn't conflict with any other planned
+  future development
+* Fork the `Cantera/cantera` repository on Github
+* Clone your new repository or add it as a remote to an existing repository
+* Check out the existing `master` branch, then start a new feature branch for
+  your work
+* When making changes, write code that is consistent with the surrounding code
+  (see the [style guidelines](#style-guidelines) below)
+* Add tests for any new features that you are implementing to either the
+  GoogleTest-based test suite or the Python test suite.
+* Add examples that highlight new capabilities, or update existing
+  examples to make use of new features.
+* As you make changes, commit them to your feature branch
+  * Configure Git with your name and e-mail address before making any commits
+  * Use descriptive commit messages (summary line of no more than 72 characters,
+    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
+    produced as part of the build process or other temporary files.
+  * 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
+    onto the most recent `HEAD` commit of `master`.
+  * Periodically run the test suite (`scons test`) to make sure that your
+    changes are not causing any test failures.
+* Submit a Pull Request on Github. Check the results of the continuous-
+  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-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,
+  then that code will be release under this license as well. The copyright for
+  Cantera is held collectively by the contributors. If you have made a
+  significant contribution, please add your name to the `AUTHORS` file.
+
+# Style Guidelines
+
+* Try to follow the style of surrounding code, and use variable names that
+  follow existing patterns. Pay attention to indentation and spacing.
+* Configure your editor to use 4 spaces per indentation level, and **never to
+  use tabs**.
+* Avoid introducing trailing whitespace
+* Limit line lengths to 80 characters when possible
+* 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 `/*!`)
+* 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
+  `m_`. For most classes, member variables should not be public.
+* Class names use `InitialCapsNames`
+* Methods use `camelCaseNames`
+* Do not indent the contents of namespaces
+* Code may make use of most C++11 features, with the exceptions of delegating
+  constructors, inheriting constructors, and non-static data member
+  initializers. These limitations are needed to keep the minimum required
+  compiler versions at GCC 4.6, Clang 3.1, Visual Studio 2013 and Intel 14.0.
+* Avoid manual memory management (i.e. `new` and `delete`), preferring to use
+  standard library containers, as well as `std::unique_ptr` and
+  `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. 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
+  * http://geosoft.no/development/cppstyle.html
+* For any new code, do *not* use the `doublereal` and `integer` typedefs for the
+  basic types `double` and `int`, but also do not go out of your way to change
+  uses of these in otherwise unmodified code.
+
+## Python
+
+* Style generally follows PEP8 (https://www.python.org/dev/peps/pep-0008/)
+* 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
+See the instructions available at [online](https://cantera.org/install/index.html)
-available at http://cantera.github.com/docs/sphinx/html/compiling.html.

License.txt

@@ -6,6 +6,9 @@ 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) 2011-2018, Cantera Developers.
+All rights reserved.
+
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are
 met:
@@ -33,4 +36,3 @@ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-

README.rst

@@ -1,53 +1,174 @@
+.. Cantera
 
-*******
+|cantera|
-CANTERA
-*******
 
-Version 2.2.0b1 (development)
+|doi| |codecov| |travisci| |appveyor| |release|
 
-License Information
-===================
 
-See the file "License.txt" for information on the terms & conditions for usage,
+What is Cantera?
-and a DISCLAIMER OF ALL WARRANTIES.
+================
 
-All trademarks referenced herein are property of their respective holders.
+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:
 
-Web Resources
+* Evaluate thermodynamic and transport properties of mixtures
+* Compute chemical equilibrium
+* Evaluate species chemical production rates
+* Conduct kinetics simulations with large reaction mechanisms
+* Simulate one-dimensional flames
+* Conduct reaction path analysis
+* Create process simulations using networks of stirred reactors
+* Model non-ideal fluids
+
+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 MyBinder link:
+
+.. image:: https://mybinder.org/badge.svg
+    :target: https://mybinder.org/repo/cantera/cantera-jupyter
+
+Installation
+============
+
+`Installation instructions for the current release of Cantera
+<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 <https://cantera.org/install/index.html>`_
+are also available.
+
+Documentation
 =============
 
-1. *The Cantera Github site*
+The `documentation <https://cantera.org/documentation>`_
+offers a number of starting points:
 
-   https://github.com/Cantera/cantera
+- `Python tutorial
+  <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
+  <https://cantera.org/tutorials/input-files.html>`_
+- `Information about the Cantera community
+  <https://cantera.org/community.html>`_
 
-   This site contains the Cantera source code, the issue tracker for bugs and
+`Documentation for the development version of Cantera
-   enhancement requests, downloads of Cantera releases and binary installers,
+<https://cantera.org/documentation/dev-docs.html>`_ is also available.
-   and the Cantera wiki.
 
-2. *The Cantera SourceForge site*
+Code of Conduct
+===============
 
-   http://sourceforge.net/projects/cantera
+.. image:: https://img.shields.io/badge/code%20of%20conduct-contributor%20covenant-green.svg?style=flat-square
+    :alt: conduct
+    :target: https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
 
-   Alternative download location for Cantera releases and binary installers.
+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 <https://contributor-covenant.org/>`_.
 
-3. *Cantera Documentation*
+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.
 
-   http://cantera.github.com/docs/sphinx/html/index.html
+Development Site
+================
 
-   This site contains documentation for the current stable version of Cantera.
+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.
 
-   http://cantera.github.com/dev-docs/sphinx/html/index.html
+Users' Group
+============
 
-   This site contains documentation for the development version of Cantera.
+The `Cantera Users' Group <https://groups.google.com/group/cantera-users>`_ is a
+message board / mailing list for discussions amongst Cantera users.
 
-4. *The Cantera Users' Group*
+Cantera Gitter Chat
+===================
 
-   http://groups.google.com/group/cantera-users
+.. image:: https://badges.gitter.im/org.png
+   :target: https://gitter.im/Cantera/Lobby
 
-   This site has a message board for discussions amongst Cantera users.
 
-5. *The Cantera Developers Group*
+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.
 
-   http://groups.google.com/group/cantera-dev
+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.
 
-   Limited access site where developers can discuss development ideas.
+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
+=============================
+
+==============  ============  ===================
+Platform        Site          Status
+==============  ============  ===================
+Linux & OS X    Travis CI     |travisci|
+Windows x64     Appveyor      |appveyor|
+==============  ============  ===================
+
+
+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| 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

@@ -0,0 +1,27 @@
+version: 1.0.{build}
+install:
+- ps: |
+    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:\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:\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))
+    $wc.UploadFile("https://ci.appveyor.com/api/testresults/junit/$($env:APPVEYOR_JOB_ID)", (Resolve-Path .\test\work\gtest-thermo.xml))
+    $wc.UploadFile("https://ci.appveyor.com/api/testresults/junit/$($env:APPVEYOR_JOB_ID)", (Resolve-Path .\test\work\gtest-equil.xml))
+    $wc.UploadFile("https://ci.appveyor.com/api/testresults/junit/$($env:APPVEYOR_JOB_ID)", (Resolve-Path .\test\work\gtest-kinetics.xml))
+    $wc.UploadFile("https://ci.appveyor.com/api/testresults/junit/$($env:APPVEYOR_JOB_ID)", (Resolve-Path .\test\work\gtest-transport.xml))
+    if ( $sconsstatus ) { exit $sconsstatus }

bin/exp3to2.sh

@@ -1,20 +0,0 @@
-#/bin/sh
-#
-#  This sed script replaces 3 character exponents 
-#  starting with 0 with 2 characters
-#     e-0xx -> e-xx
-#     e0xx -> exx
-#     E-0xx -> E-xx
-#     E0xx -> Exx
-#         where
-#           x is a digit
-#
-#   It takes one argument, the file to be operated on.
-#   And, it writes to standard out. It may be used to do a 
-#   replacement in place.
-#
-cp $1 .exp.txt
-cat .exp.txt | sed 's/\([eE]-\)\(0\)\([0-9][0-9]\)/\1\3/g' | \
-               sed 's/\([eE]\)\(0\)\([0-9][0-9]\)/\1\3/g'  | \
-               sed 's/\([eE]+\)\(0\)\([0-9][0-9]\)/\1\3/g' 
-rm .exp.txt

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,
+          initial_state = state(
-                                pressure = 1.0e3,
+              temperature = 1200.0,
-                                mole_fractions = 'H:0.002, H2:1, CH4:0.01, CH3:0.0002'))
+              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',
+                     elements = 'C',
-           density = (3.52, 'g/cm3'),
+                     density = (3.52, 'g/cm3'),
-           species = 'C(d)')
+                     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'),
+        thermo = const_cp(h0 = (11.4, 'kcal/mol'),
-                          s0 = (21.0, 'cal/mol/K'))
+                          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('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* + H   <=> c6HH',        [1.0E13, 0.0, 0.0])  # b
-surface_reaction('c6H* + CH3 <=> c6HM',           [5.0e12,   0.0,  0.0]) # c
+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('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('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* + H2',  [2.8E7,  2.0, 7.7])  # f
-surface_reaction('c6HM* + H <=> c6HM',            [1.0e13,   0.0,  0.0]) # g
+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*      <=> 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  <=> c6H* + CH3',  [3.0E13, 0.0, 0.0])  # i
-surface_reaction('c6HM* + H <=> c6B + H2',        [1.3e14,   0.0,  7.3]) # k
+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('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('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('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('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   <=> 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 + 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** + 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('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('c6H*       <=> c6*H',        [1.0E8,  0.0, 0.0])  # t
-surface_reaction('c6B  => c6HH + C(d)',           [1.0e9,    0.0,  0.0])
+
+# 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
+!THERMO
-   300.000  1000.000  5000.000
+! Insert GRI-Mech thermodynamics here or use in default file
-O                 L 1/90O   1   00   00   00G   200.000  3500.000  1000.000    1
+!END
- 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
 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+CH2CHO                     2.920E+12     .000    1808.00
-O+CH3CHO=>OH+CH3+CO                      5.840E+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/gri30mod.inp

@@ -1,692 +0,0 @@
-! GRI-Mech Version 3.0 3/12/99  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', 
-! for additional information, contacts, and disclaimer
-ELEMENTS
-O  H  C  N  AR
-END
-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
-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
-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/ 
-O+H+M<=>OH+M                             5.000E+17   -1.000        .00
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-O+H2<=>H+OH                              3.870E+04    2.700    6260.00
-O+HO2<=>OH+O2                            2.000E+13     .000        .00
-!% (O) + (H)(O2) = (O)(H) + (O2)
-O+H2O2<=>OH+HO2                          9.630E+06    2.000    4000.00
-O+CH<=>H+CO                              5.700E+13     .000        .00
-O+CH2<=>H+HCO                            8.000E+13     .000        .00
-O+CH2(S)<=>H2+CO                         1.500E+13     .000        .00
-O+CH2(S)<=>H+HCO                         1.500E+13     .000        .00
-O+CH3<=>H+CH2O                           5.060E+13     .000        .00
-O+CH4<=>OH+CH3                           1.020E+09    1.500    8600.00
-O+CO(+M)<=>CO2(+M)                       1.800E+10     .000    2385.00
-   LOW/ 6.020E+14     .000    3000.00/
-H2/2.00/ O2/6.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/3.50/ C2H6/3.00/ AR/ .50/ 
-O+HCO<=>OH+CO                            3.000E+13     .000        .00
-O+HCO<=>H+CO2                            3.000E+13     .000        .00
-O+CH2O<=>OH+HCO                          3.900E+13     .000    3540.00
-O+CH2OH<=>OH+CH2O                        1.000E+13     .000        .00
-O+CH3O<=>OH+CH2O                         1.000E+13     .000        .00
-O+CH3OH<=>OH+CH2OH                       3.880E+05    2.500    3100.00
-O+CH3OH<=>OH+CH3O                        1.300E+05    2.500    5000.00
-O+C2H<=>CH+CO                            5.000E+13     .000        .00
-O+C2H2<=>H+HCCO                          1.350E+07    2.000    1900.00
-O+C2H2<=>OH+C2H                          4.600E+19   -1.410   28950.00
-O+C2H2<=>CO+CH2                          6.940E+06    2.000    1900.00
-O+C2H3<=>H+CH2CO                         3.000E+13     .000        .00
-O+C2H4<=>CH3+HCO                         1.250E+07    1.830     220.00
-O+C2H5<=>CH3+CH2O                        2.240E+13     .000        .00
-O+C2H6<=>OH+C2H5                         8.980E+07    1.920    5690.00
-O+HCCO<=>H+2CO                           1.000E+14     .000        .00
-!% (O) + (H)(C)(C-O) = (H) + (C)(O) + (C-O)
-O+CH2CO<=>OH+HCCO                        1.000E+13     .000    8000.00
-O+CH2CO<=>CH2+CO2                        1.750E+12     .000    1350.00
-O2+CO<=>O+CO2                            2.500E+12     .000   47800.00
-O2+CH2O<=>HO2+HCO                        1.000E+14     .000   40000.00
-H+O2+M<=>HO2+M                           2.800E+18    -.860        .00
-O2/ .00/ H2O/ .00/ CO/ .75/ CO2/1.50/ C2H6/1.50/ N2/ .00/ AR/ .00/ 
-H+2O2<=>HO2+O2                           2.080E+19   -1.240        .00
-H+O2+H2O<=>HO2+H2O                       11.26E+18    -.760        .00
-H+O2+N2<=>HO2+N2                         2.600E+19   -1.240        .00
-H+O2+AR<=>HO2+AR                         7.000E+17    -.800        .00
-H+O2<=>O+OH                              2.650E+16    -.6707  17041.00
-2H+M<=>H2+M                              1.000E+18   -1.000        .00
-H2/ .00/ H2O/ .00/ CH4/2.00/ CO2/ .00/ C2H6/3.00/ AR/ .63/ 
-2H+H2<=>2H2                              9.000E+16    -.600        .00
-2H+H2O<=>H2+H2O                          6.000E+19   -1.250        .00
-2H+CO2<=>H2+CO2                          5.500E+20   -2.000        .00
-H+OH+M<=>H2O+M                           2.200E+22   -2.000        .00
-H2/ .73/ H2O/3.65/ CH4/2.00/ C2H6/3.00/ AR/ .38/ 
-H+HO2<=>O+H2O                            3.970E+12     .000     671.00
-H+HO2<=>O2+H2                            4.480E+13     .000    1068.00
-H+HO2<=>2OH                              0.840E+14     .000     635.00
-H+H2O2<=>HO2+H2                          1.210E+07    2.000    5200.00
-H+H2O2<=>OH+H2O                          1.000E+13     .000    3600.00
-!% (H) + (O-H)(O-H) = (H)(O-H) + (O-H)
-H+CH<=>C+H2                              1.650E+14     .000        .00
-H+CH2(+M)<=>CH3(+M)                      6.000E+14     .000        .00
-     LOW  /  1.040E+26   -2.760   1600.00/
-     TROE/   .5620  91.00  5836.00  8552.00/
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-H+CH2(S)<=>CH+H2                         3.000E+13     .000        .00
-H+CH3(+M)<=>CH4(+M)                      13.90E+15    -.534     536.00
-     LOW  /  2.620E+33   -4.760   2440.00/
-     TROE/   .7830   74.00  2941.00  6964.00 /
-H2/2.00/ H2O/6.00/ CH4/3.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-H+CH4<=>CH3+H2                           6.600E+08    1.620   10840.00
-H+HCO(+M)<=>CH2O(+M)                     1.090E+12     .480    -260.00
-     LOW  /  2.470E+24   -2.570    425.00/
-     TROE/   .7824  271.00  2755.00  6570.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-H+HCO<=>H2+CO                            7.340E+13     .000        .00
-H+CH2O(+M)<=>CH2OH(+M)                   5.400E+11     .454    3600.00
-     LOW  /  1.270E+32   -4.820   6530.00/
-     TROE/   .7187  103.00  1291.00  4160.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ 
-H+CH2O(+M)<=>CH3O(+M)                    5.400E+11     .454    2600.00
-     LOW  /  2.200E+30   -4.800   5560.00/
-     TROE/   .7580   94.00  1555.00  4200.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ 
-H+CH2O<=>HCO+H2                          5.740E+07    1.900    2742.00
-H+CH2OH(+M)<=>CH3OH(+M)                  1.055E+12     .500      86.00
-     LOW  /  4.360E+31   -4.650   5080.00/
-     TROE/   .600  100.00  90000.0  10000.0 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ 
-H+CH2OH<=>H2+CH2O                        2.000E+13     .000        .00
-H+CH2OH<=>OH+CH3                         1.650E+11     .650    -284.00
-!%    (H) + (H2-C)(O-H) = (H)(H2-C) + (O-H)
-H+CH2OH<=>CH2(S)+H2O                     3.280E+13    -.090     610.00
-H+CH3O(+M)<=>CH3OH(+M)                   2.430E+12     .515      50.00
-     LOW  /  4.660E+41   -7.440   14080.0/
-     TROE/   .700  100.00  90000.0 10000.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ 
-H+CH3O<=>H+CH2OH                         4.150E+07    1.630    1924.00
-H+CH3O<=>H2+CH2O                         2.000E+13     .000        .00
-H+CH3O<=>OH+CH3                          1.500E+12     .500    -110.00
-H+CH3O<=>CH2(S)+H2O                      2.620E+14    -.230    1070.00
-H+CH3OH<=>CH2OH+H2                       1.700E+07    2.100    4870.00
-H+CH3OH<=>CH3O+H2                        4.200E+06    2.100    4870.00
-H+C2H(+M)<=>C2H2(+M)                     1.000E+17   -1.000        .00
-     LOW  /  3.750E+33   -4.800   1900.00/
-     TROE/   .6464  132.00  1315.00  5566.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-H+C2H2(+M)<=>C2H3(+M)                    5.600E+12     .000    2400.00
-     LOW  /  3.800E+40   -7.270   7220.00/
-     TROE/   .7507   98.50  1302.00  4167.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-H+C2H3(+M)<=>C2H4(+M)                    6.080E+12     .270     280.00
-     LOW  /  1.400E+30   -3.860   3320.00/
-     TROE/   .7820  207.50  2663.00  6095.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-H+C2H3<=>H2+C2H2                         3.000E+13     .000        .00
-H+C2H4(+M)<=>C2H5(+M)                    0.540E+12     .454    1820.00
-     LOW  /  0.600E+42   -7.620   6970.00/
-     TROE/   .9753  210.00   984.00  4374.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-H+C2H4<=>C2H3+H2                         1.325E+06    2.530   12240.00
-H+C2H5(+M)<=>C2H6(+M)                    5.210E+17    -.990    1580.00
-     LOW  /  1.990E+41   -7.080   6685.00/
-     TROE/   .8422  125.00  2219.00  6882.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-H+C2H5<=>H2+C2H4                         2.000E+12     .000        .00
-H+C2H6<=>C2H5+H2                         1.150E+08    1.900    7530.00
-H+HCCO<=>CH2(S)+CO                       1.000E+14     .000        .00
-H+CH2CO<=>HCCO+H2                        5.000E+13     .000    8000.00
-H+CH2CO<=>CH3+CO                         1.130E+13     .000    3428.00
-H+HCCOH<=>H+CH2CO                        1.000E+13     .000        .00
-H2+CO(+M)<=>CH2O(+M)                     4.300E+07    1.500   79600.00
-     LOW  /  5.070E+27   -3.420  84350.00/
-     TROE/   .9320  197.00  1540.00 10300.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-OH+H2<=>H+H2O                            2.160E+08    1.510    3430.00
-2OH(+M)<=>H2O2(+M)                       7.400E+13    -.370        .00
-     LOW  /  2.300E+18    -.900  -1700.00/
-     TROE/   .7346   94.00  1756.00  5182.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-2OH<=>O+H2O                              3.570E+04    2.400   -2110.00
-OH+HO2<=>O2+H2O                          1.450E+13     .000    -500.00
- DUPLICATE
-OH+H2O2<=>HO2+H2O                        2.000E+12     .000     427.00
- DUPLICATE
-OH+H2O2<=>HO2+H2O                        1.700E+18     .000   29410.00
- DUPLICATE
-OH+C<=>H+CO                              5.000E+13     .000        .00
-OH+CH<=>H+HCO                            3.000E+13     .000        .00
-OH+CH2<=>H+CH2O                          2.000E+13     .000        .00
-OH+CH2<=>CH+H2O                          1.130E+07    2.000    3000.00
-OH+CH2(S)<=>H+CH2O                       3.000E+13     .000        .00
-OH+CH3(+M)<=>CH3OH(+M)                   2.790E+18   -1.430    1330.00
-     LOW  /  4.000E+36   -5.920   3140.00/
-     TROE/   .4120  195.0  5900.00  6394.00/ 
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ 
-OH+CH3<=>CH2+H2O                         5.600E+07    1.600    5420.00
-OH+CH3<=>CH2(S)+H2O                      6.440E+17   -1.340    1417.00
-OH+CH4<=>CH3+H2O                         1.000E+08    1.600    3120.00
-OH+CO<=>H+CO2                            4.760E+07    1.228      70.00
-OH+HCO<=>H2O+CO                          5.000E+13     .000        .00
-OH+CH2O<=>HCO+H2O                        3.430E+09    1.180    -447.00
-OH+CH2OH<=>H2O+CH2O                      5.000E+12     .000        .00
-OH+CH3O<=>H2O+CH2O                       5.000E+12     .000        .00
-OH+CH3OH<=>CH2OH+H2O                     1.440E+06    2.000    -840.00
-OH+CH3OH<=>CH3O+H2O                      6.300E+06    2.000    1500.00
-OH+C2H<=>H+HCCO                          2.000E+13     .000        .00
-OH+C2H2<=>H+CH2CO                        2.180E-04    4.500   -1000.00
-OH+C2H2<=>H+HCCOH                        5.040E+05    2.300   13500.00
-OH+C2H2<=>C2H+H2O                        3.370E+07    2.000   14000.00
-OH+C2H2<=>CH3+CO                         4.830E-04    4.000   -2000.00
-OH+C2H3<=>H2O+C2H2                       5.000E+12     .000        .00
-OH+C2H4<=>C2H3+H2O                       3.600E+06    2.000    2500.00
-OH+C2H6<=>C2H5+H2O                       3.540E+06    2.120     870.00
-OH+CH2CO<=>HCCO+H2O                      7.500E+12     .000    2000.00
-2HO2<=>O2+H2O2                           1.300E+11     .000   -1630.00
- DUPLICATE
-2HO2<=>O2+H2O2                           4.200E+14     .000   12000.00
- DUPLICATE
-HO2+CH2<=>OH+CH2O                        2.000E+13     .000        .00
-HO2+CH3<=>O2+CH4                         1.000E+12     .000        .00
-HO2+CH3<=>OH+CH3O                        3.780E+13     .000        .00
-HO2+CO<=>OH+CO2                          1.500E+14     .000   23600.00
-HO2+CH2O<=>HCO+H2O2                      5.600E+06    2.000   12000.00
-C+O2<=>O+CO                              5.800E+13     .000     576.00
-C+CH2<=>H+C2H                            5.000E+13     .000        .00
-C+CH3<=>H+C2H2                           5.000E+13     .000        .00
-CH+O2<=>O+HCO                            6.710E+13     .000        .00
-CH+H2<=>H+CH2                            1.080E+14     .000    3110.00
-CH+H2O<=>H+CH2O                          5.710E+12     .000    -755.00
-CH+CH2<=>H+C2H2                          4.000E+13     .000        .00
-!%     (H-C) + (H-C)(H) = (H-C)(H-C) + (H)  ! uncertain
-CH+CH3<=>H+C2H3                          3.000E+13     .000        .00
-!%     (H-C) + (H2-C)(H) = (H-C)(H2-C) + (H) ! uncertain
-CH+CH4<=>H+C2H4                          6.000E+13     .000        .00
-!%     (H-C) + (H3-C)(H) = (H-C)(H3-C) + (H) ! uncertain
-CH+CO(+M)<=>HCCO(+M)                     5.000E+13     .000        .00
-     LOW  /  2.690E+28   -3.740   1936.00/
-     TROE/   .5757  237.00  1652.00  5069.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-CH+CO2<=>HCO+CO                          1.900E+14     .000   15792.00
-CH+CH2O<=>H+CH2CO                        9.460E+13     .000    -515.00
-!%     (O-H2-C) + (C)(H) = (O-H2-C)(C) + (H) ! uncertain
-CH+HCCO<=>CO+C2H2                        5.000E+13     .000        .00
-CH2+O2=>OH+H+CO                          5.000E+12     .000    1500.00
-CH2+H2<=>H+CH3                           5.000E+05    2.000    7230.00
-2CH2<=>H2+C2H2                           1.600E+15     .000   11944.00
-CH2+CH3<=>H+C2H4                         4.000E+13     .000        .00
-!%     (H2-C) + (H2-C)(H) = (H2-C)(H2-C) + (H)
-CH2+CH4<=>2CH3                           2.460E+06    2.000    8270.00
-CH2+CO(+M)<=>CH2CO(+M)                   8.100E+11     .500    4510.00
-     LOW  /  2.690E+33   -5.110   7095.00/
-     TROE/   .5907  275.00  1226.00  5185.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-CH2+HCCO<=>C2H3+CO                       3.000E+13     .000        .00
-CH2(S)+N2<=>CH2+N2                       1.500E+13     .000     600.00
-CH2(S)+AR<=>CH2+AR                       9.000E+12     .000     600.00
-CH2(S)+O2<=>H+OH+CO                      2.800E+13     .000        .00
-CH2(S)+O2<=>CO+H2O                       1.200E+13     .000        .00
-CH2(S)+H2<=>CH3+H                        7.000E+13     .000        .00
-CH2(S)+H2O(+M)<=>CH3OH(+M)               4.820E+17   -1.160    1145.00
-     LOW  /  1.880E+38   -6.360   5040.00/
-     TROE/   .6027  208.00  3922.00  10180.0 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ 
-CH2(S)+H2O<=>CH2+H2O                     3.000E+13     .000        .00
-CH2(S)+CH3<=>H+C2H4                      1.200E+13     .000    -570.00
-CH2(S)+CH4<=>2CH3                        1.600E+13     .000    -570.00
-!%     (H2-C) + (H2-C)(H) = (H2-C)(H2-C) + (H)
-CH2(S)+CO<=>CH2+CO                       9.000E+12     .000        .00
-CH2(S)+CO2<=>CH2+CO2                     7.000E+12     .000        .00
-CH2(S)+CO2<=>CO+CH2O                     1.400E+13     .000        .00
-CH2(S)+C2H6<=>CH3+C2H5                   4.000E+13     .000    -550.00
-CH3+O2<=>O+CH3O                          3.560E+13     .000   30480.00
-CH3+O2<=>OH+CH2O                         2.310E+12     .000   20315.00
-CH3+H2O2<=>HO2+CH4                       2.450E+04    2.470    5180.00
-2CH3(+M)<=>C2H6(+M)                      6.770E+16   -1.180     654.00
-     LOW  /  3.400E+41   -7.030   2762.00/
-     TROE/   .6190  73.20  1180.00  9999.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-2CH3<=>H+C2H5                            6.840E+12     .100   10600.00
-CH3+HCO<=>CH4+CO                         2.648E+13     .000        .00
-CH3+CH2O<=>HCO+CH4                       3.320E+03    2.810    5860.00
-CH3+CH3OH<=>CH2OH+CH4                    3.000E+07    1.500    9940.00
-CH3+CH3OH<=>CH3O+CH4                     1.000E+07    1.500    9940.00
-CH3+C2H4<=>C2H3+CH4                      2.270E+05    2.000    9200.00
-CH3+C2H6<=>C2H5+CH4                      6.140E+06    1.740   10450.00
-HCO+H2O<=>H+CO+H2O                       1.500E+18   -1.000   17000.00
-HCO+M<=>H+CO+M                           1.870E+17   -1.000   17000.00
-H2/2.00/ H2O/ .00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ 
-HCO+O2<=>HO2+CO                          13.45E+12     .000     400.00
-CH2OH+O2<=>HO2+CH2O                      1.800E+13     .000     900.00
-CH3O+O2<=>HO2+CH2O                       4.280E-13    7.600   -3530.00
-C2H+O2<=>HCO+CO                          1.000E+13     .000    -755.00
-C2H+H2<=>H+C2H2                          5.680E+10    0.900    1993.00
-C2H3+O2<=>HCO+CH2O                       4.580E+16   -1.390    1015.00
-C2H4(+M)<=>H2+C2H2(+M)                   8.000E+12     .440   86770.00
-     LOW  /  1.580E+51   -9.300  97800.00/
-     TROE/   .7345  180.00  1035.00  5417.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-C2H5+O2<=>HO2+C2H4                       8.400E+11     .000    3875.00
-HCCO+O2<=>OH+2CO                         3.200E+12     .000     854.00
-!% (H)(C)(C-O) + (O)(O) = (O)(H) + (C)(O) + (C-O)
-2HCCO<=>2CO+C2H2                         1.000E+13     .000        .00
-!% (H-C)(C-O) + (H-C)(C-O) = (C-O) + (C-O) + (H-C)(H-C)
-N+NO<=>N2+O                              2.700E+13     .000     355.00
-N+O2<=>NO+O                              9.000E+09    1.000    6500.00
-N+OH<=>NO+H                              3.360E+13     .000     385.00
-N2O+O<=>N2+O2                            1.400E+12     .000   10810.00
-N2O+O<=>2NO                              2.900E+13     .000   23150.00
-N2O+H<=>N2+OH                            3.870E+14     .000   18880.00
-N2O+OH<=>N2+HO2                          2.000E+12     .000   21060.00
-N2O(+M)<=>N2+O(+M)                       7.910E+10     .000   56020.00
-     LOW  /  6.370E+14     .000  56640.00/
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .625/ 
-HO2+NO<=>NO2+OH                          2.110E+12     .000    -480.00
-NO+O+M<=>NO2+M                           1.060E+20   -1.410        .00
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-NO2+O<=>NO+O2                            3.900E+12     .000    -240.00
-NO2+H<=>NO+OH                            1.320E+14     .000     360.00
-NH+O<=>NO+H                              4.000E+13     .000        .00
-NH+H<=>N+H2                              3.200E+13     .000     330.00
-NH+OH<=>HNO+H                            2.000E+13     .000        .00
-NH+OH<=>N+H2O                            2.000E+09    1.200        .00
-NH+O2<=>HNO+O                            4.610E+05    2.000    6500.00
-NH+O2<=>NO+OH                            1.280E+06    1.500     100.00
-NH+N<=>N2+H                              1.500E+13     .000        .00
-NH+H2O<=>HNO+H2                          2.000E+13     .000   13850.00
-NH+NO<=>N2+OH                            2.160E+13    -.230        .00
-NH+NO<=>N2O+H                            3.650E+14    -.450        .00
-NH2+O<=>OH+NH                            3.000E+12     .000        .00
-NH2+O<=>H+HNO                            3.900E+13     .000        .00
-NH2+H<=>NH+H2                            4.000E+13     .000    3650.00
-NH2+OH<=>NH+H2O                          9.000E+07    1.500    -460.00
-NNH<=>N2+H                               3.300E+08     .000        .00
-NNH+M<=>N2+H+M                           1.300E+14    -.110    4980.00
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-NNH+O2<=>HO2+N2                          5.000E+12     .000        .00
-NNH+O<=>OH+N2                            2.500E+13     .000        .00
-NNH+O<=>NH+NO                            7.000E+13     .000        .00
-NNH+H<=>H2+N2                            5.000E+13     .000        .00
-NNH+OH<=>H2O+N2                          2.000E+13     .000        .00
-NNH+CH3<=>CH4+N2                         2.500E+13     .000        .00
-H+NO+M<=>HNO+M                           4.480E+19   -1.320     740.00
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-HNO+O<=>NO+OH                            2.500E+13     .000        .00
-HNO+H<=>H2+NO                            9.000E+11     .720     660.00
-HNO+OH<=>NO+H2O                          1.300E+07    1.900    -950.00
-HNO+O2<=>HO2+NO                          1.000E+13     .000   13000.00
-CN+O<=>CO+N                              7.700E+13     .000        .00
-CN+OH<=>NCO+H                            4.000E+13     .000        .00
-CN+H2O<=>HCN+OH                          8.000E+12     .000    7460.00
-CN+O2<=>NCO+O                            6.140E+12     .000    -440.00
-CN+H2<=>HCN+H                            2.950E+05    2.450    2240.00
-NCO+O<=>NO+CO                            2.350E+13     .000        .00
-!%      (O) + (N)(O-C) = (O)(N) + (O-C)
-NCO+H<=>NH+CO                            5.400E+13     .000        .00
-NCO+OH<=>NO+H+CO                         0.250E+13     .000        .00
-!% (N)(C-O) + (O)(H) = (N)(O) + (C-O) + (H)
-NCO+N<=>N2+CO                            2.000E+13     .000        .00
-NCO+O2<=>NO+CO2                          2.000E+12     .000   20000.00
-NCO+M<=>N+CO+M                           3.100E+14     .000   54050.00
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-NCO+NO<=>N2O+CO                          1.900E+17   -1.520     740.00
-NCO+NO<=>N2+CO2                          3.800E+18   -2.000     800.00
-HCN+M<=>H+CN+M                           1.040E+29   -3.300  126600.00
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-HCN+O<=>NCO+H                            2.030E+04    2.640    4980.00
-HCN+O<=>NH+CO                            5.070E+03    2.640    4980.00
-HCN+O<=>CN+OH                            3.910E+09    1.580   26600.00
-HCN+OH<=>HOCN+H                          1.100E+06    2.030   13370.00
-!%     (O-H) + (C-N)(H) = (O-H)(C-N) + (H)
-HCN+OH<=>HNCO+H                          4.400E+03    2.260    6400.00
-!%     (H-C-N) + (O)(H) = (H-C-N)(O) + (H)
-HCN+OH<=>NH2+CO                          1.600E+02    2.560    9000.00
-H+HCN(+M)<=>H2CN(+M)                     3.300E+13     .000        .00
-      LOW /  1.400E+26   -3.400    1900.00/
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-H2CN+N<=>N2+CH2                          6.000E+13     .000     400.00
-C+N2<=>CN+N                              6.300E+13     .000   46020.00
-CH+N2<=>HCN+N                            3.120E+09    0.880   20130.00
-CH+N2(+M)<=>HCNN(+M)                     3.100E+12     .150        .00
-     LOW  /  1.300E+25   -3.160    740.00/
-     TROE/   .6670  235.00  2117.00  4536.00 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ 1.0/ 
-CH2+N2<=>HCN+NH                          1.000E+13     .000   74000.00
-CH2(S)+N2<=>NH+HCN                       1.000E+11     .000   65000.00
-C+NO<=>CN+O                              1.900E+13     .000        .00
-C+NO<=>CO+N                              2.900E+13     .000        .00
-CH+NO<=>HCN+O                            4.100E+13     .000        .00
-CH+NO<=>H+NCO                            1.620E+13     .000        .00
-CH+NO<=>N+HCO                            2.460E+13     .000        .00
-CH2+NO<=>H+HNCO                          3.100E+17   -1.380    1270.00
-CH2+NO<=>OH+HCN                          2.900E+14    -.690     760.00
-CH2+NO<=>H+HCNO                          3.800E+13    -.360     580.00
-CH2(S)+NO<=>H+HNCO                       3.100E+17   -1.380    1270.00
-CH2(S)+NO<=>OH+HCN                       2.900E+14    -.690     760.00
-CH2(S)+NO<=>H+HCNO                       3.800E+13    -.360     580.00
-CH3+NO<=>HCN+H2O                         9.600E+13     .000   28800.00
-CH3+NO<=>H2CN+OH                         1.000E+12     .000   21750.00
-HCNN+O<=>CO+H+N2                         2.200E+13     .000        .00
-HCNN+O<=>HCN+NO                          2.000E+12     .000        .00
-HCNN+O2<=>O+HCO+N2                       1.200E+13     .000        .00
-HCNN+OH<=>H+HCO+N2                       1.200E+13     .000        .00
-!% (H)(C)(N2) + (O-H) = (H) + (C)(O-H) + (N2)  
-HCNN+H<=>CH2+N2                          1.000E+14     .000        .00
-HNCO+O<=>NH+CO2                          9.800E+07    1.410    8500.00
-HNCO+O<=>HNO+CO                          1.500E+08    1.570   44000.00
-!%     (O) + (H-N)(O-C) = (O)(H-N) + (O-C)
-HNCO+O<=>NCO+OH                          2.200E+06    2.110   11400.00
-HNCO+H<=>NH2+CO                          2.250E+07    1.700    3800.00
-HNCO+H<=>H2+NCO                          1.050E+05    2.500   13300.00
-HNCO+OH<=>NCO+H2O                        3.300E+07    1.500    3600.00
-HNCO+OH<=>NH2+CO2                        3.300E+06    1.500    3600.00
-HNCO+M<=>NH+CO+M                         1.180E+16     .000   84720.00
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-HCNO+H<=>H+HNCO                          2.100E+15    -.690    2850.00
-HCNO+H<=>OH+HCN                          2.700E+11     .180    2120.00
-!%     (H) + (C-N)(O-H) = (H)(C-N) + (O-H)
-HCNO+H<=>NH2+CO                          1.700E+14    -.750    2890.00
-HOCN+H<=>H+HNCO                          2.000E+07    2.000    2000.00
-HCCO+NO<=>HCNO+CO                        0.900E+13     .000        .00
-CH3+N<=>H2CN+H                           6.100E+14    -.310     290.00
-CH3+N<=>HCN+H2                           3.700E+12     .150     -90.00
-NH3+H<=>NH2+H2                           5.400E+05    2.400    9915.00
-NH3+OH<=>NH2+H2O                         5.000E+07    1.600     955.00
-NH3+O<=>NH2+OH                           9.400E+06    1.940    6460.00
-NH+CO2<=>HNO+CO                          1.000E+13     .000   14350.00
-CN+NO2<=>NCO+NO                          6.160E+15   -0.752     345.00
-NCO+NO2<=>N2O+CO2                        3.250E+12     .000    -705.00
-!% (N)(C-O) + (N-O)(O) = (N)(N-O) + (C-O)(O)
-N+CO2<=>NO+CO                            3.000E+12     .000   11300.00
-O+CH3=>H+H2+CO                           3.370E+13     .000        .00
-O+C2H4<=>H+CH2CHO                        6.700E+06    1.830     220.00
-O+C2H5<=>H+CH3CHO                        1.096E+14     .000        .00
-OH+HO2<=>O2+H2O                          0.500E+16     .000   17330.00
-  DUPLICATE
-OH+CH3=>H2+CH2O                          8.000E+09     .500   -1755.00
-CH+H2(+M)<=>CH3(+M)                      1.970E+12     .430    -370.00
-   LOW/ 4.820E+25  -2.80  590.0 /
-   TROE/ .578  122.0  2535.0  9365.0 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-CH2+O2=>2H+CO2                           5.800E+12     .000    1500.00
-CH2+O2<=>O+CH2O                          2.400E+12     .000    1500.00
-CH2+CH2=>2H+C2H2                         2.000E+14     .000   10989.00
-!% (H)(C-H) + (H)(C-H) = (H) + (H) + (C-H)(C-H)
-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) + (C-H3)(C-O)(H) = (H)(O) + (C-O) + (C-H3)
-O2+CH3CHO=>HO2+CH3+CO                    3.010E+13     .000   39150.00
-!% (O2) + (C-H3)(C-O)(H) = (H)(O2) + (C-O) + (C-H3)
-H+CH3CHO<=>CH2CHO+H2                     2.050E+09    1.160    2405.00
-H+CH3CHO=>CH3+H2+CO                      2.050E+09    1.160    2405.00
-!% (H) + (C-H3)(H)(C-O) = (H)(H) + (C-O) + (C-H3)
-OH+CH3CHO=>CH3+H2O+CO                    2.343E+10    0.730   -1113.00
-!% (O-H) + (C-H3)(H)(C-O) = (H)(O-H) + (C-O) + (C-H3)
-HO2+CH3CHO=>CH3+H2O2+CO                  3.010E+12     .000   11923.00
-!% (O-H2) + (C-H3)(H)(C-O) = (H)(O-H2) + (C-O) + (C-H3)
-CH3+CH3CHO=>CH3+CH4+CO                   2.720E+06    1.770    5920.00
-!% (C-H3) + (C-H3)(H)(C-O) = (H)(C-H3) + (C-O) + (C-H3)
-H+CH2CO(+M)<=>CH2CHO(+M)                 4.865E+11    0.422   -1755.00
-    LOW/ 1.012E+42  -7.63  3854.0/
-    TROE/ 0.465  201.0  1773.0  5333.0 /
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-O+CH2CHO=>H+CH2+CO2                      1.500E+14     .000       .00
-O2+CH2CHO=>OH+CO+CH2O                    1.810E+10     .000       .00
-!% (O)(O) + (C-H2)(C-O)(H) = (O)(H) + (C-H2)(O) + (C-O)
-O2+CH2CHO=>OH+2HCO                       2.350E+10     .000       .00
-!% (O)(O) + (C-H)(C-H-O)(H) = (O)(H) + (C-H)(O) + (C-H-O)
-H+CH2CHO<=>CH3+HCO                       2.200E+13     .000       .00
-H+CH2CHO<=>CH2CO+H2                      1.100E+13     .000       .00
-OH+CH2CHO<=>H2O+CH2CO                    1.200E+13     .000       .00
-OH+CH2CHO<=>HCO+CH2OH                    3.010E+13     .000       .00
-!%     (O-H) + (H2-C)(O-H-C) = (O-H)(H2-C) + (O-H-C)
-CH3+C2H5(+M)<=>C3H8(+M)                  .9430E+13     .000       .00
-     LOW/ 2.710E+74  -16.82  13065.0 /
-     TROE/ .1527  291.0  2742.0  7748.0 / 
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-O+C3H8<=>OH+C3H7                         1.930E+05    2.680   3716.00
-H+C3H8<=>C3H7+H2                         1.320E+06    2.540   6756.00
-OH+C3H8<=>C3H7+H2O                       3.160E+07    1.800    934.00
-C3H7+H2O2<=>HO2+C3H8                     3.780E+02    2.720   1500.00
-CH3+C3H8<=>C3H7+CH4                      0.903E+00    3.650   7154.00
-CH3+C2H4(+M)<=>C3H7(+M)                  2.550E+06    1.600   5700.00
-      LOW/ 3.00E+63  -14.6  18170./
-      TROE/ .1894  277.0  8748.0  7891.0 / 
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-O+C3H7<=>C2H5+CH2O                       9.640E+13     .000       .00
-H+C3H7(+M)<=>C3H8(+M)                    3.613E+13     .000       .00
-      LOW/ 4.420E+61  -13.545  11357.0/
-      TROE/ .315  369.0  3285.0  6667.0 / 
-H2/2.00/ H2O/6.00/ CH4/2.00/ CO/1.50/ CO2/2.00/ C2H6/3.00/ AR/ .70/ 
-H+C3H7<=>CH3+C2H5                        4.060E+06    2.190    890.00
-OH+C3H7<=>C2H5+CH2OH                     2.410E+13     .000       .00
-HO2+C3H7<=>O2+C3H8                       2.550E+10    0.255   -943.00
-HO2+C3H7=>OH+C2H5+CH2O                   2.410E+13     .000       .00
-!% (O-H)(O) + (C2-H5)(C-H2) = (O-H) + (C2-H5) + (O)(C-H2)
-CH3+C3H7<=>2C2H5                         1.927E+13   -0.320       .00
-END

data/inputs/h2o2_noch.inp

@@ -1,48 +0,0 @@
-ELEMENTS
-O  H  AR
-END
-SPECIES
-H2      H       O       O2      OH      H2O     HO2     H2O2    
-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
-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
-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
-END

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/methane_pox_on_pt.cti

@@ -317,11 +317,11 @@ surface_reaction( "CO + PT(S) => CO(S)",
 # Desorption reactions
 
 surface_reaction( "2 H(S) => H2 + 2 PT(S)",
-		  Arrhenius(3.70000E+21, 0, 67400,
+                  Arrhenius(3.70000E+21, 0, 67400,
                             coverage = ['H(S)', 0.0, 0.0, -10000.0]))
 
 surface_reaction( "2 O(S) => O2 + 2 PT(S)",
-		  Arrhenius(3.70000E+21, 0, 235500,
+                  Arrhenius(3.70000E+21, 0, 235500,
                             coverage = ['O(S)', 0.0, 0.0, -188300.0]) )
 
 surface_reaction( "H2O(S) => H2O + PT(S)",   [4.50000E+12, 0, 41800])

data/inputs/mkxml.in

@@ -1,10 +0,0 @@
-#!/bin/sh
-# run ck2cti to convert Chemkin-format files to Cantera format
-#
-BUILDBIN="@buildbin@"
-#
-$BUILDBIN/ck2cti -i gri30.inp -id gri30              -tr ../transport/gri30_tran.dat > gri30.cti
-$BUILDBIN/ck2cti -i air.inp -id air -t gri30.inp     -tr ../transport/gri30_tran.dat > air.cti
-$BUILDBIN/ck2cti -i h2o2.inp -id ohmech              -tr ../transport/gri30_tran.dat > h2o2.cti
-$BUILDBIN/ck2cti -i silane.inp -id silane            -tr ../transport/misc_tran.dat  > silane.cti
-$BUILDBIN/ck2cti -i argon.inp -id argon -t gri30.inp -tr ../transport/gri30_tran.dat > argon.cti

data/inputs/ptcombust.cti

@@ -215,7 +215,7 @@ surface_reaction("H2 + 2 PT(S) => 2 H(S)", [4.45790E+10, 0.5, 0],
 
 #  Reaction 2
 surface_reaction( "2 H(S) => H2 + 2 PT(S)",
-		  Arrhenius(3.70000E+21, 0, 67400,
+                  Arrhenius(3.70000E+21, 0, 67400,
                             coverage = ['H(S)', 0.0, 0.0, -6000.0]))
 
 #  Reaction 3
@@ -231,7 +231,7 @@ surface_reaction( "O2 + 2 PT(S) => 2 O(S)",   stick(2.30000E-02, 0, 0),
 
 #  Reaction 6
 surface_reaction( "2 O(S) => O2 + 2 PT(S)",
-		  Arrhenius(3.70000E+21, 0, 213200,
+                  Arrhenius(3.70000E+21, 0, 213200,
                             coverage = ['O(S)', 0.0, 0.0, -60000.0]) )
 
 #  Reaction 7
@@ -273,7 +273,7 @@ surface_reaction( "CO(S) + O(S) => CO2(S) + PT(S)",   [3.70000E+21, 0, 105000])
 
 #  Reaction 19
 surface_reaction( "CH4 + 2 PT(S) => CH3(S) + H(S)",   [4.63340E+20, 0.5, 0],
-		  order = "PT(S):2.3")
+                  order = "PT(S):2.3")
 
 #  Reaction 20
 surface_reaction( "CH3(S) + PT(S) => CH2(S)s + H(S)",
@@ -290,11 +290,3 @@ surface_reaction( "C(S) + O(S) => CO(S) + PT(S)",   [3.70000E+21, 0, 62800])
 
 #  Reaction 24
 surface_reaction( "CO(S) + PT(S) => C(S) + O(S)",   [1.00000E+18, 0, 184000])
-
-#  Reaction 25 (12/28/2009 HKM added: This is a fictious rxn that is added for numerical stability.
-#               The issue is that if multiple surface species have a negative concentration, the
-#               Jacobian for the surface problem will go singular due to the way negative concentrations
-#               are truncated within Cantera. Adding in unimolecular desorption rxns with neglibigle real 
-#               effects alleviates the problem.)
-surface_reaction( "C(S)  => C + PT(S)",   [3.7E7, 0, 62800])
-

data/inputs/sofc.cti

@@ -17,12 +17,8 @@ units(length = "cm", time = "s", quantity = "mol", act_energy = "kJ/mol")
 # Turn on mechanism validation to detect unbalanced reactions, if any
 validate()
 
-
-
 #------------------------------------------------------------------
-#
 #    parameters
-#
 #------------------------------------------------------------------
 
 # a few numeric parameters are collected here to allow easy modification.
@@ -33,7 +29,6 @@ validate()
 tc = 800.0           # temperature in C
 tt = tc + 273.15     # temperature in K
 
-
 # these values are defined here only so they may be easily changed to
 # assess the effects of the oxide thermochemistry. For work at a
 # single temperature, all that we really need is g = h -
@@ -46,18 +41,13 @@ sox = (50.0, 'J/K/mol')             # entropy of an oxygen ion
 hhydrox = (-220.0, 'kJ/mol')        # enthalpy of a surface hydroxyl group
 shydrox = (87.0, 'J/mol/K')         # entropy of a surface hydroxyl group
 
-
-
-
 ####################### BULK PHASES ####################################
 
 # First we'll define the bulk (i.e. 3D) phases - a gas, a metal, and
 # an oxide.
 
 #------------------------------------------------------------------
-#
 #    Gas phase.
-#
 #------------------------------------------------------------------
 
 # The gas contains only the minimum number of species needed to model
@@ -73,11 +63,8 @@ ideal_gas(name = "gas",
                              pressure = OneAtm,
                              mole_fractions = 'H2:0.95, H2O:0.05'))
 
-
 #------------------------------------------------------------------
-#
 #    Bulk solid metal phase.
-#
 #------------------------------------------------------------------
 #
 #   This phase will be used for the electrodes. All we need is
@@ -113,28 +100,23 @@ species( name = "electron",   atoms = "E:1",
 # h0 + cp0*(t - t0), s = s0 + cp0*ln(t/t0). For work at a single
 # temperature, it is sufficient to specify only h0.
 
-
-
 #-------------------------------------------------------------------
-#
 #   Bulk solid oxide electrolyte
-#
 #--------------------------------------------------------------------
 
 # Here too, we create a very simple model for the bulk phase. We only
 # 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")
       )
 
-
 # The vacancy will be modeled as truly vacant - it contains no atoms,
 # has no charge, and has zero enthalpy and entropy.  This is different
 # from the usual convention in which the vacancy properties are are
@@ -152,14 +134,10 @@ species( name = "VO**",    atoms = "",
 species( name = "Ox",    atoms = "O:1 E:2",
         thermo = const_cp(h0 = hox, s0 = sox))
 
-
-
 ####################### SURFACE PHASES ####################################
 
 #--------------------------------------------------
-#
 #  Metal surface
-#
 #--------------------------------------------------
 
 # The surface of a bulk phase must be treated like a separate phase, with its
@@ -209,7 +187,6 @@ species( name = "H2O(m)", atoms = "H:2, O:1",
          thermo = const_cp(h0 = (-281.0, 'kJ/mol'),
                            s0 = (123.0, 'J/mol/K')))
 
-
 # Surface reactions on the metal. We assume three dissociative
 # adsorption reactions, and three reactions on the surface
 # among adsorbates. All reactions are treated as reversible.
@@ -231,11 +208,8 @@ surface_reaction( "H(m) + OH(m) <=> H2O(m) + (m)",
 surface_reaction( "OH(m) + OH(m) <=> H2O(m) + O(m)",
                   [5.00000E+21, 0, 100.0], id = 'metal-rxn6')
 
-
 #--------------------------------------------------------
-#
 #  Oxide surface.
-#
 #--------------------------------------------------------
 #H
 # On the oxide surface, we consider four species:
@@ -249,7 +223,7 @@ ideal_interface(name = "oxide_surface",
                 species = "(ox) O''(ox) OH'(ox) H2O(ox)",
                 site_density = 2.0e-9,
                 phases = 'gas oxide_bulk',
-		reactions = 'oxide-*',
+                reactions = 'oxide-*',
                 initial_state = state( temperature = tt,
                         coverages = "O''(ox):2.0, (ox):0.0") )
 
@@ -275,7 +249,6 @@ species( name = "H2O(ox)", atoms = "H:2, O:1",
         thermo = const_cp(h0 = (-265.0, 'kJ/mol'),
                           s0 = (98.0,'J/mol/K')))
 
-
 # This reaction represents the exchange of a surface oxygen vacancy and
 # a subsurface vacancy. The concentration of subsurface vacancies is
 # fixed by the doping level. If this reaction is given a large rate,
@@ -284,7 +257,6 @@ species( name = "H2O(ox)", atoms = "H:2, O:1",
 surface_reaction("(ox) + Ox <=> VO** + O''(ox)",
                  [5.0e8, 0.0, 0.0], id = "oxide-vac")
 
-
 # Desorption of physisorbed water. This is made fast.
 surface_reaction("H2O(ox) <=> H2O + (ox)",
                  [1.0e14, 0.0, (0.0, 'kJ/mol')], id = "oxide-water")
@@ -294,10 +266,8 @@ surface_reaction("H2O(ox) <=> H2O + (ox)",
 surface_reaction("H2O(ox) + O''(ox) <=> OH'(ox) + OH'(ox)",
                  [1.0e14, 0.0, (0.0, 'kJ/mol')], id = "oxide-oh")
 
-
 ####################### TRIPLE PHASE BOUNDARY #########################
 
-
 # The triple phase boundary between the metal, oxide, and gas. A
 # single species is specified, but it is not used, since all reactions
 # only involve species on either side of the tpb. Note that the site
@@ -316,8 +286,6 @@ edge(name = "tpb",
 # dummy species
 species( name = "(tpb)", atoms = "")
 
-
-
 # Here we define two charge transfer reactions. Both reactions are
 # reversible, and can be used to model either anodes or cathodes
 # (although real anodes and cathodes would usually have different
@@ -334,7 +302,6 @@ edge_reaction("H(m) + O''(ox) <=> (m) + electron + OH'(ox)",
 edge_reaction("O(m) + (ox) + 2 electron <=> (m) + O''(ox)",
               [5.0e13, 0.0, 120.0], beta = 0.5, id="edge-f3")
 
-
 # this reaction is commented out, but you can explore its effects by
 # uncommenting it. Be careful, if you are not solving for the OH'
 # concentration that the system does not become overdetermined
@@ -343,9 +310,3 @@ edge_reaction("O(m) + (ox) + 2 electron <=> (m) + O''(ox)",
 
 #edge_reaction("H(m) + OH'(ox) <=> H2O(ox) + (m) + electron",
 #              [5.0e13, 0.0, 120.0], beta = 0.5, id="edge-f")
-
-
-
-
-
-

data/thermo/gri30_thermo.dat

@@ -1,177 +1,169 @@
-! GRI-Mech Version 3.0 3/12/99  CHEMKIN-II format
+THERMO
-! 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', 
-! for additional information, contacts, and disclaimer
-ELEMENTS
-O  H  N  
-END
-SPECIES
-H2      H       O       O2      OH      H2O    N2
-END
-THERMO ALL
    300.000  1000.000  5000.000
-O                 L 1/90O   1   00   00   00G   200.000  3500.000  1000.000    1
+! 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   00   00   00G   200.000  3500.000  1000.000    1
+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   00   00   00G   200.000  3500.000  1000.000    1
+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
  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
+H2                TPIS78H   2               G   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
+OH                RUS 78O   1H   1          G   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
+H2O               L 8/89H   2O   1          G   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
+HO2               L 5/89H   1O   2          G   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
+H2O2              L 7/88H   2O   2          G   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
+C                 L11/88C   1               G   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
+CH                TPIS79C   1H   1          G   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
+CH2               L S/93C   1H   2          G   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
+CH2(S)            L S/93C   1H   2          G   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
+CH3               L11/89C   1H   3          G   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
+CH4               L 8/88C   1H   4          G   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
+CO                TPIS79C   1O   1          G   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
+CO2               L 7/88C   1O   2          G   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
+HCO               L12/89H   1C   1O   1     G   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
+CH2O              L 8/88H   2C   1O   1     G   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
+CH2OH             GUNL93C   1H   3O   1     G   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
+CH3O              121686C   1H   3O   1     G   300.00   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
+CH3OH             L 8/88C   1H   4O   1     G   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
+C2H               L 1/91C   2H   1          G   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
+C2H2              L 1/91C   2H   2          G   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
+C2H3              L 2/92C   2H   3          G   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
+C2H4              L 1/91C   2H   4          G   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
+C2H5              L12/92C   2H   5          G   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
+C2H6              L 8/88C   2H   6          G   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
+CH2CO             L 5/90C   2H   2O   1     G   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
+HCCO              SRIC91H   1C   2O   1     G   300.00   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
+HCCOH              SRI91C   2O   1H   2     G   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
+H2CN               41687H   2C   1N   1     G   300.00   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
+HCN               GRI/98H   1C   1N   1     G   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
+HNO               And93 H   1N   1O   1     G   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
+N                 L 6/88N   1               G   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
+NNH               T07/93N   2H   1          G   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
+N2O               L 7/88N   2O   1          G   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
+NH                And94 N   1H   1          G   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
+NH2               And89 N   1H   2          G   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
+NH3               J 6/77N   1H   3          G   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
+NO                RUS 78N   1O   1          G   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
+NO2               L 7/88N   1O   2          G   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
@@ -187,15 +179,15 @@ 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
+NCO               EA 93 N   1C   1O   1     G   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
+CN                HBH92 C   1N   1          G   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
+HCNN              SRI/94C   1N   2H   1     G   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
@@ -207,22 +199,24 @@ 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
+C3H8              L 4/85C   3H   8          G   300.000  5000.000  1000.000    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
+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    0G   200.000  6000.000  1000.00     1
+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   300.00   5000.00   1000.00     1
+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
-REACTIONS
+
-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

@@ -1,3 +1,4 @@
+from __future__ import print_function
 from buildutils import *
 
 Import('env', 'build', 'install')
@@ -7,6 +8,7 @@ localenv = env.Clone()
 from collections import namedtuple
 Page = namedtuple('Page', ['name', 'title', 'objects'])
 
+
 # Set up functions to pseudo-autodoc the MATLAB toolbox
 def extract_matlab_docstring(mfile, level):
     """
@@ -27,7 +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
@@ -66,9 +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 '):
@@ -76,7 +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
@@ -97,8 +100,8 @@ if localenv['doxygen_docs']:
                       mglob(env, '#src/cantera/*', 'h', 'cpp'))
 
     env.Alias('doxygen', docs)
-    install('$inst_docdir/doxygen/html',
+    install(localenv.RecursiveInstall, '$inst_docdir/doxygen/html',
-            mglob(localenv, '#/build/docs/doxygen/html', 'html', 'svg', 'css', 'png'))
+            '#/build/docs/doxygen/html', exclude=['\\.map', '\\.md5'])
 
 if localenv['sphinx_docs']:
     localenv['SPHINXBUILD'] = Dir('#build/docs/sphinx')
@@ -109,65 +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
-    for subdir in subdirs(example_root):
-        for f in mglob(env, pjoin(example_root, subdir), 'py'):
-            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/examples/%s_%s.rst' % (subdir, f.name[:-3]),
-                                 '#doc/sphinx/cython/example-script.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',
+        Page('importing', 'Objects Representing Phases',
-             ['@Solution', '@Mixture',]
+             ['@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']
+             ['@Func', '@Reactor', '@ReactorNet', '@FlowDevice', '@Wall']),
-        ),
+        Page('one-dim', 'One-Dimensional Reacting Flows', ['1D/@Domain1D', '1D/@Stack']),
-        Page('one-dim', 'One-Dimensional Reacting Flows',
+        Page('data', 'Physical Constants', ['@Data']),
-             ['1D/@Domain1D', '1D/@Stack']
+        Page('utilities', 'Utility Functions', ['@Utilities', '@XML_Node']),
-         ),
-        Page('data', 'Built-In Thermochemical Data',
-             ['@Data']
-        ),
-        Page('utilities', 'Utility Functions',
-             ['@Utilities', '@XML_Node']
-        ),
-        Page('interface', 'Interfaces', ['@Interface']),
     ]
 
     # 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',
+                     'FlowReactor.m', 'IdealGasConstPressureReactor.m',
-                  'IdealGasReactor.m', 'Reservoir.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/Inlet.m', '1D/Outlet.m', '1D/OutletRes.m',
-                      '1D/Surface.m', '1D/SymmPlane.m'],
+                         '1D/Surface.m', '1D/SymmPlane.m'],
-        '1D/@Stack': ['1D/FreeFlame.m', '1D/npflame_init.m'],
+        '1D/@Stack': ['1D/FreeFlame.m', '1D/CounterFlowDiffusionFlame.m'],
         '@Interface': ['importEdge.m', 'importInterface.m'],
-        '@Data': ['air.m', 'constants.m', 'gasconstant.m', 'GRI30.m',
+        '@Data': ['gasconstant.m', 'oneatm.m'],
-             'Hydrogen.m', 'Methane.m', 'Nitrogen.m', 'oneatm.m',
+        '@Utilities': ['adddir.m', 'ck2cti.m', 'cleanup.m', 'geterr.m',
-             'Oxygen.m', 'Water.m'],
+                       'getDataDirectories.m', 'canteraVersion.m',
-        '@Utilities': ['adddir.m', 'ck2cti.m', 'cleanup.m', 'geterr.m',]
+                       'canteraGitCommit.m']
     }
 
     # These files do not need to be documented in the MATLAB classes because they
@@ -182,7 +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
@@ -217,24 +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,
+        c = tempenv.SubstFile('#doc/sphinx/matlab/%s.rst' % page.name,
-                          '#doc/sphinx/matlab/matlab-template.rst.in')
+                              '#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
-    for f in mglob(env, '#samples/matlab', 'm'):
-        tmpenv = env.Clone()
-        tmpenv['script_name'] = f.name
-        tmpenv['script_path'] = '../../../../samples/matlab/%s' % f.name
-        if f.name.startswith('tut'):
-            b = tmpenv.SubstFile('#doc/sphinx/matlab/tutorials/%s.rst' % f.name[:-2],
-                                 '#doc/sphinx/matlab/example-script.rst.in')
-        else:
-            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)
-
     localenv.AlwaysBuild(sphinxdocs)
+    install(localenv.RecursiveInstall, '$inst_docdir/sphinx/html',
+            '#/build/docs/sphinx/html')

doc/doxygen/Cantera.txt

@@ -3,7 +3,4 @@
 
 Use the menu at the top to view detailed documentation of the code.
 
-\ref thermopage
-
-
 */

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         = 2.2a
+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.
-# 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.
-
 
 # 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
@@ -571,8 +565,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = src/apps \
+INPUT                  = src/base \
-                         src/base \
                          src/equil \
                          src/kinetics \
                          src/numerics \
@@ -611,7 +604,7 @@ RECURSIVE              = YES
 # excluded from the INPUT source files. This way you can easily exclude a
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                =
+EXCLUDE                = include/cantera/ext
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or
 # directories that are symbolic links (a Unix filesystem feature) are excluded
@@ -625,7 +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
@@ -641,8 +634,7 @@ EXCLUDE_SYMBOLS        = std::*
 
 EXAMPLE_PATH           = samples \
                          data/inputs \
-                         doc/doxygen \
+                         doc/doxygen
-                         doc/sphinx/cxx-guide
 
 # 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
@@ -1171,7 +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
@@ -1179,18 +1171,6 @@ GENERATE_XML           = NO
 
 XML_OUTPUT             = xml
 
-# The XML_SCHEMA tag can be used to specify an XML schema,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_SCHEMA             =
-
-# The XML_DTD tag can be used to specify an XML DTD,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_DTD                =
-
 # If the XML_PROGRAMLISTING tag is set to YES Doxygen will
 # dump the program listings (including syntax highlighting
 # and cross-referencing information) to the XML output. Note that
@@ -1397,17 +1377,6 @@ HIDE_UNDOC_RELATIONS   = YES
 
 HAVE_DOT               = YES
 
-# By default doxygen will write a font called FreeSans.ttf to the output
-# directory and reference it in all dot files that doxygen generates. This
-# font does not include all possible unicode characters however, so when you need
-# these (or just want a differently looking font) you can specify the font name
-# using DOT_FONTNAME. You need need to make sure dot is able to find the font,
-# which can be done by putting it in a standard location or by setting the
-# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
-# containing the font.
-
-DOT_FONTNAME           = FreeSans
-
 # The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
 # The default size is 10pt.
 

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
+ *   species are all derived from the PDSS virtual base class. In turn, these
- *   standard state, which coordinate the calculation for all of the species
+ *   standard states may employ reference state calculation to aid in their
- *   in a phase, are all derived from the virtual base class VPSSMgr.
+ *   calculations. However, there are some PDSS objects which do not employ
- *   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
  *   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
@@ -140,7 +136,7 @@
  *   phase density or the phase pressure.
  *   Lists of classes in this group are given below.
  *
- *   - StoichSubstanceSSTP  in StoichSubstanceSSTP.h
+ *   - StoichSubstance      in StoichSubstance.h
  *   - WaterSSTP            in WaterSSTP.h
  *
  *   The reader may note that there are duplications in functionality in 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,
+ *  Within installSpecies(), for standard states, derived PDSS object is created
- *  SpeciesThermoFactory::installVPThermoForSpecies() is
+ *  and installed into the VPStandardStateTP list containing all of the PDSS
- *  called. However, this is just a shell routine for calling
+ *  objects for that phase.
- *  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.
  *
  *  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/_static/site.css

@@ -1,507 +0,0 @@
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- * Alternate Sphinx design
- * Originally created by Armin Ronacher for Werkzeug, adapted by Georg Brandl.
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-
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-    font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva', 'Verdana', sans-serif;
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-    text-align: center;
-    /*background-color: #AFC1C4; */
-    background-color: #BFD1D4;
-    color: black;
-    padding: 0;
-    border: 1px solid #aaa;
-
-    margin: 0px 80px 0px 80px;
-    min-width: 740px;
-}
-
-a {
-    color: #CA7900;
-    text-decoration: none;
-}
-
-a:hover {
-    color: #2491CF;
-}
-
-pre {
-    font-family: 'Consolas', 'Deja Vu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
-    font-size: 0.95em;
-    letter-spacing: 0.015em;
-    padding: 0.5em;
-    border: 1px solid #ccc;
-    background-color: #f8f8f8;
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-
-td.linenos pre {
-    padding: 0.5em 0;
-    border: 0;
-    background-color: transparent;
-    color: #aaa;
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-table.highlighttable {
-    margin-left: 0.5em;
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-    padding: 0 0.5em 0 0.5em;
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-    font-size: 0.95em;
-    letter-spacing: 0.01em;
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-    background-color: #f2f2f2;
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-    padding: 0;
-}
-
-h3 {
-    margin: 1em 0 -0.3em 0;
-    font-size: 1.2em;
-}
-
-h1 a, h2 a, h3 a, h4 a, h5 a, h6 a {
-    color: black!important;
-}
-
-h1 a.anchor, h2 a.anchor, h3 a.anchor, h4 a.anchor, h5 a.anchor, h6 a.anchor {
-    display: none;
-    margin: 0 0 0 0.3em;
-    padding: 0 0.2em 0 0.2em;
-    color: #aaa!important;
-}
-
-h1:hover a.anchor, h2:hover a.anchor, h3:hover a.anchor, h4:hover a.anchor,
-h5:hover a.anchor, h6:hover a.anchor {
-    display: inline;
-}
-
-h1 a.anchor:hover, h2 a.anchor:hover, h3 a.anchor:hover, h4 a.anchor:hover,
-h5 a.anchor:hover, h6 a.anchor:hover {
-    color: #777;
-    background-color: #eee;
-}
-
-table {
-    border-collapse: collapse;
-    margin: 0 -0.5em 0 -0.5em;
-}
-
-table td, table th {
-    padding: 0.2em 0.5em 0.2em 0.5em;
-}
-
-div.footer {
-    background-color: #E3EFF1;
-    color: #86989B;
-    padding: 3px 8px 3px 0;
-    clear: both;
-    font-size: 0.8em;
-    text-align: right;
-}
-
-div.footer a {
-    color: #86989B;
-    text-decoration: underline;
-}
-
-div.pagination {
-    margin-top: 2em;
-    padding-top: 0.5em;
-    border-top: 1px solid black;
-    text-align: center;
-}
-
-div.sphinxsidebar ul.toc {
-    margin: 1em 0 1em 0;
-    padding: 0 0 0 0.5em;
-    list-style: none;
-}
-
-div.sphinxsidebar ul.toc li {
-    margin: 0.5em 0 0.5em 0;
-    font-size: 0.9em;
-    line-height: 130%;
-}
-
-div.sphinxsidebar ul.toc li p {
-    margin: 0;
-    padding: 0;
-}
-
-div.sphinxsidebar ul.toc ul {
-    margin: 0.2em 0 0.2em 0;
-    padding: 0 0 0 1.8em;
-}
-
-div.sphinxsidebar ul.toc ul li {
-    padding: 0;
-}
-
-div.admonition, div.warning {
-    font-size: 0.9em;
-    margin: 1em 0 0 0;
-    border: 1px solid #86989B;
-    background-color: #f7f7f7;
-}
-
-div.admonition p, div.warning p {
-    margin: 0.5em 1em 0.5em 1em;
-    padding: 0;
-}
-
-div.admonition pre, div.warning pre {
-    margin: 0.4em 1em 0.4em 1em;
-}
-
-div.admonition p.admonition-title,
-div.warning p.admonition-title {
-    margin: 0;
-    padding: 0.1em 0 0.1em 0.5em;
-    color: white;
-    border-bottom: 1px solid #86989B;
-    font-weight: bold;
-    background-color: #AFC1C4;
-}
-
-div.warning {
-    border: 1px solid #940000;
-}
-
-div.warning p.admonition-title {
-    background-color: #CF0000;
-    border-bottom-color: #940000;
-}
-
-div.admonition ul, div.admonition ol,
-div.warning ul, div.warning ol {
-    margin: 0.1em 0.5em 0.5em 3em;
-    padding: 0;
-}
-
-div.versioninfo {
-    margin: 1em 0 0 0;
-    border: 1px solid #ccc;
-    background-color: #DDEAF0;
-    padding: 8px;
-    line-height: 1.3em;
-    font-size: 0.9em;
-}
-
-
-a.headerlink {
-    color: #c60f0f!important;
-    font-size: 1em;
-    margin-left: 6px;
-    padding: 0 4px 0 4px;
-    text-decoration: none!important;
-    visibility: hidden;
-}
-
-h1:hover > a.headerlink,
-h2:hover > a.headerlink,
-h3:hover > a.headerlink,
-h4:hover > a.headerlink,
-h5:hover > a.headerlink,
-h6:hover > a.headerlink,
-dt:hover > a.headerlink {
-    visibility: visible;
-}
-
-a.headerlink:hover {
-    background-color: #ccc;
-    color: white!important;
-}
-
-table.indextable td {
-    text-align: left;
-    vertical-align: top;
-}
-
-table.indextable dl, table.indextable dd {
-    margin-top: 0;
-    margin-bottom: 0;
-}
-
-table.indextable tr.pcap {
-    height: 10px;
-}
-
-table.indextable tr.cap {
-    margin-top: 10px;
-    background-color: #f2f2f2;
-}
-
-img.toggler {
-    margin-right: 3px;
-    margin-top: 3px;
-    cursor: pointer;
-}
-
-img.inheritance {
-    border: 0px
-}
-
-form.pfform {
-    margin: 10px 0 20px 0;
-}
-
-table.contentstable {
-    width: 90%;
-}
-
-table.contentstable p.biglink {
-    line-height: 150%;
-}
-
-a.biglink {
-    font-size: 1.3em;
-}
-
-span.linkdescr {
-    font-style: italic;
-    padding-top: 5px;
-    font-size: 90%;
-}
-
-ul.search {
-    margin: 10px 0 0 20px;
-    padding: 0;
-}
-
-ul.search li {
-    padding: 5px 0 5px 20px;
-    background-image: url(file.png);
-    background-repeat: no-repeat;
-    background-position: 0 7px;
-}
-
-ul.search li a {
-    font-weight: bold;
-}
-
-ul.search li div.context {
-    color: #888;
-    margin: 2px 0 0 30px;
-    text-align: left;
-}
-
-ul.keywordmatches li.goodmatch a {
-    font-weight: bold;
-}

doc/sphinx/_templates/layout.html

@@ -1,10 +1,162 @@
-{% extends "!layout.html" %}
+{%- set render_sidebar = (not embedded) and (not theme_nosidebar|tobool) and (sidebars != []) %}
-
+{% block doctype %}
-
+<!DOCTYPE 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() }}
 {% 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.rst

@@ -1,523 +0,0 @@
-.. _sec-compiling:
-
-*************************
-Cantera Compilation Guide
-*************************
-
-.. toctree::
-   :hidden:
-
-   SCons Configuration Options <configuring>
-
-This guide contains instructions for compiling Cantera on the following
-operating systems:
-
-* Linux
-
-  * Ubuntu 12.04 LTS (Lucid Lynx) or newer
-  * Debian 6.0 (Squeeze) or newer
-
-* Windows Vista, Windows 7, or Windows 8 (32-bit or 64-bit versions)
-* OS X 10.9 (Mavericks) or OS X 10.10 (Yosemite).
-
-In addition to the above operating systems, Cantera should work on any
-Unix-like system where the necessary prerequisites are available, but some
-additional configuration may be required.
-
-Installation Prerequisites
-==========================
-
-Linux
------
-
-* For Ubuntu or Debian users, the following packages should be installed using
-  your choice of package manager::
-
-      g++ python scons libboost-all-dev libsundials-serial-dev
-
-* Building the python module also requires::
-
-      cython python-dev python-numpy python-numpy-dev
-
-* Checking out the source code from version control requires Git (install
-  ``git``).
-
-* The minimum compatible Cython version is 0.17. If your distribution does not
-  contain a suitable version, you may be able to install a more recent version
-  using `easy_install` or `pip`.
-
-* Building the Fortran interface also requires gfortran or another supported
-  Fortran compiler.
-* Users of other distributions should install the equivalent packages, which
-  may have slightly different names.
-
-Windows
--------
-
-There are a number of requirements for the versions of software to install
-depending on which interfaces (Python, Matlab) you want to build and what
-architecture (32-bit or 64-bit) you want to use. See :ref:`sec-dependencies` for
-the full list of dependencies.
-
-* 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.
-* 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.
-* There is no 64-bit installer for SCons under Windows, so you will need to
-  download the ZIP version. After extracting it, start a command prompt in the
-  unzipped folder and run::
-
-     python setup.py install
-
-* It is generally helpful to have SCons and Python in your PATH. This can
-  usually be accomplished by adding the top-level Python directory
-  (e.g. ``C:\Python27``) to your PATH. This is accessible from::
-
-      Control Panel > System and Security > System > Advanced System Settings > Environment Variables
-* 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.
-
-OS X
-----
-
-* Download and install Xcode from the App Store
-
-* From a Terminal, run::
-
-      sudo xcode-select --install
-
-  and agree to the Xcode license agreement
-
-* If you don't have numpy version >= 1.3, you can install a recent version with::
-
-    sudo easy_install -U numpy
-
-* If you want to build Cantera with Fortran 90 support, download gfortran from::
-
-    http://gcc.gnu.org/wiki/GFortranBinaries#MacOS
-
-* Download scons-2.x.y.tar.gz from scons.org and extract the contents. Install with either::
-
-      sudo python setup.py install
-
-  to install for all users, or::
-
-     python setup.py install --user
-
-  to install to a location in your home directory.
-
-Downloading the Cantera source code
-===================================
-
-Stable Release
---------------
-
-* Option 1: Download the most recent source tarball from `SourceForge
-  <https://sourceforge.net/projects/cantera/files/cantera/>`_ and extract the
-  contents.
-
-* Option 2: Check out the code using Git::
-
-    git clone https://github.com/Cantera/cantera.git
-    cd cantera
-    git checkout 2.1
-
-Development Version
--------------------
-
-* Check out the code using Git::
-
-    git clone https://github.com/Cantera/cantera.git
-
-Determine configuration options
-===============================
-
-General
--------
-
-* 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 build -j4 blas_lapack_libs=lapack,blas
-
-* If the prerequisites are installed in standard locations, the default values
-  should work.
-* If you installed Sundials to a non-standard location (e.g. the libraries
-  aren't in /usr/lib), you will need to specify the options::
-
-    sundials_include=/path/to/sundials/include
-    sundials_libdir=/path/to/sundials/lib
-
-* If you want to build the Matlab toolbox, you will need to specify the path
-  to the Matlab installation, e.g.::
-
-    matlab_path=/opt/MATLAB/R2011a
-    matlab_path="C:\Program Files\MATLAB\R2011a"
-    matlab_path=/Applications/MATLAB_R2011a.app
-
-  The above paths are typical defaults on Linux, Windows, and OS X,
-  respectively.
-* 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::
-
-    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``.
-
-
-Python Module
--------------
-
-Cantera 2.1 introduces a new Python module implemented using Cython. This new
-module provides support for both Python 2.x and Python 3.x. It also features a
-redesigned API that simplifies many operations and aims to provide a more
-"Pythonic" interface to Cantera.
-
-Building the new Python module requires the Cython package for Python.
-
-The Cython module is compatible with the following Python versions: 2.6, 2.7,
-3.1, 3.2, and 3.3. Support for Python 2.6 and Python 3.1 requires the ``scipy``
-and ``unittest2`` packages to be installed as well (see :ref:`sec-dependencies`)
-to provide certain features that are included in the standard
-library in more recent versions.
-
-Building for Python 2
-.....................
-
-By default, SCons will attempt to build the Cython-based Python module for
-Python 2, if both Numpy and Cython are installed.
-
-Building for Python 3
-.....................
-
-If SCons detects a Python 3 interpreter installed in a default location
-(i.e. ``python3`` is on the path), it will try to build the new Python module
-for Python 3. The following SCons options control how the Python 3 module is
-built::
-
-    python3_package=[y|n]
-    python3_cmd=/path/to/python3/interpreter
-    python3_array_home=/path/to/numpy
-    python3_prefix=/path/to/cantera/module
-
-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 (MSVC)
---------------
-
-* 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``.
-
-.. 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.
-
-
-Windows (MinGW)
----------------
-
-* To compile with MinGW, use the SCons command line option::
-
-    toolchain=mingw
-
-* The version of MinGW from http://www.mingw.org is 32-bit only, and therefore
-  cannot be used to build a 64-bit Python module. Versions of MinGW that provide
-  a 64-bit compiler are available from http://mingw-w64.sourceforge.net/ .
-
-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.
-
-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=$(MKLROOT)/lib/intel64
-
-  Your final SCons call might then look something like::
-
-    scons build env_vars=all CC=icc CXX=icpc F90=ifort F77=ifort blas_lapack_libs=mkl_rt blas_lapack_dir=$(MKLROOT)/lib/intel64
-
-  When installing Cantera after building with the Intel compiler, the normal
-  method of using ``sudo`` to install Cantera 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
-
-Compile Cantera & Test
-======================
-
-* Run scons with the list of desired configuration options, e.g.::
-
-    scons build optimize=n blas_lapack_libs=blas,lapack prefix=/opt/cantera
-
-* 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
-
-MinGW Compilation problems
---------------------------
-
-* If you get a compiler error while compiling some of the "f2c" code, then your
-  version of MinGW has a problem with the order of its internal include paths,
-  such that it sees the GCC float.h before its own special version. To fix this
-  problem edit the GCC float.h located at (roughly)::
-
-    c:\MinGW\lib\gcc\mingw32\4.6.1\include\float.h
-
-  and add the following just before the end (before the final #endif)
-
-  .. code-block:: c++
-
-      #ifndef _MINGW_FLOAT_H_
-      #include_next <float.h>
-      #endif
-
-.. _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 use Cantera from a Fortran
-program.
-
-* GNU compilers (C/C++/Fortran)
-
-  * Known to work with version 4.8; Expected to work with version >= 4.4
-
-* Clang/LLVM (C/C++)
-
-  * Known to work with versions 3.3 through 3.5. Expected to work with version
-    >= 2.9.
-  * Works with the versions included with Xcode 5.1 and Xcode 6.1.
-
-* Intel compilers (C/C++/Fortran)
-
-  * Known to work with version 11.0 and 12.1; Expected to work with
-    versions >= 11.0
-
-* Microsoft compilers (C/C++)
-
-  * Known to work with versions 9.0 (Visual Studio 2008) through 12.0 (Visual
-    Studio 2013).
-  * The "Express" editions of Visual Studio 2008 and 2010 do not include a
-    64-bit compiler. To compile Cantera with 64-bit support, you must install
-    the corresponding version of the Windows SDK, available as a free download.
-  * Windows SDK, equivalent to Visual Studio 2008:
-    http://www.microsoft.com/download/en/details.aspx?id=3138
-  * Windows SDK, equivalent to Visual Studio 2010:
-    http://www.microsoft.com/en-us/download/details.aspx?id=8279
-
-* MinGW (C/C++/Fortran)
-
-  * http://www.mingw.org (32-bit only)
-  * http://mingw-w64.sourceforge.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.
-
-Other Required Software
------------------------
-
-* SCons:
-
-  * http://www.scons.org/download.php
-  * Known to work with SCons 2.3.0; Expected to work with versions >= 1.0.0
-  * Version 2.3.2 or newer is required to use Visual Studio 2013.
-
-* Python:
-
-  * http://python.org/download/
-  * Known to work with 2.6 and 2.7; Expected to work with versions >= 2.6.
-  * The Cython module supports Python 2.x and 3.x. However, SCons requires
-    Python 2.x, 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 >= 1.41
-  * Only the "header-only" portions of Boost are required. Cantera does not
-    currently depend on any of the compiled Boost libraries.
-  * The compiled Boost.Thread library is required to build a thread-safe version
-    of Cantera (using the ``build_thread_safe`` option to SCons.
-  * Pre-built Binaries for Windows are available from http://boost.teeks99.com/ .
-    Make sure to download the file corresponding to your architecture and
-    Visual Studio version.
-
-Optional Programs
------------------
-
-* Numpy
-
-  * Required to build the Cantera Python module, and to run significant portions
-    of the test suite.
-  * http://sourceforge.net/projects/numpy/
-  * Known to work with versions 1.7 and 1.8; Expected to work with version >= 1.3
-
-* `Cython <http://cython.org/>`_
-
-  * Required to build the Python module
-  * Known to work with versions 0.19 and 0.20. Expected to work with
-    versions >= 0.17.
-  * Tested with Python 2.7, 3.3, and 3.4. Expected to work with versions 2.6 and
-    3.1+ as well.
-
-* `3to2 <http://pypi.python.org/pypi/3to2>`_
-
-  * Used to convert Cython examples to Python 2 syntax.
-  * Known to work with version 1.0
-
-* `Scipy <http://scipy.org/install.html>`_
-
-  * Required in order to use the Python module with Python 2.6 or 3.1.
-
-* Unittest2
-
-  * Required in order to run the test suite for the Python module with
-    Python 2.6 or Python 3.1.
-  * https://pypi.python.org/pypi/unittest2 (Python 2.6)
-  * https://pypi.python.org/pypi/unittest2py3k (Python 3.1)
-
-* Matlab
-
-  * Required to build the Cantera Matlab toolbox.
-  * Known to work with 2009a and 2014b. Expected to work with versions >= 2009a.
-
-* Sundials
-
-  * Required to enable some features such as sensitivity analysis.
-  * Strongly recommended if using reactor network or 1D simulation capabilities.
-  * https://computation.llnl.gov/casc/sundials/download/download.html
-  * Known to work with versions 2.4, 2.5 and 2.6.
-  * 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::
-
-          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.
-
-
-* `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.
-
-* `Distribute <http://pypi.python.org/pypi/distribute>`_ (Python)
-
-  * Provides the ``easy_install`` 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 ``easy_install -U Sphinx``)
-  * `Pygments <http://pygments.org/>`_ (install with ``easy_install -U pygments``)
-  * `pyparsing <http://sourceforge.net/projects/pyparsing/>`_ (install with ``easy_install -U pyparsing``)
-  * `doxylink <http://pypi.python.org/pypi/sphinxcontrib-doxylink/>`_ (install with ``easy_install sphinxcontrib-doxylink``)
-  * `matlabdomain <https://pypi.python.org/pypi/sphinxcontrib-matlabdomain>`_ (install with ``easy_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/conf.py

@@ -11,15 +11,12 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
+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/python'))
-    sys.path.insert(0, os.path.abspath('../../build/python3'))
-else:
-    sys.path.insert(0, os.path.abspath('../../build/python2'))
 
 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
+katex_version = '0.10.0-beta'
-#        custom extension for that once that version becomes more standard
 
 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'),
+        'ct': (os.path.abspath('../../build/docs/Cantera.tag'),
-                '../../doxygen/html/')
+               '../../doxygen/html/')
 }
 
 # Ensure that the primary domain is the Python domain, since we've added the
@@ -76,17 +70,18 @@ source_suffix = '.rst'
 master_doc = 'index'
 
 # General information about the project.
-project = u'Cantera'
+project = 'Cantera'
-copyright = u'2012, 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
 # built documents.
-#
+
+configh = open('../../include/cantera/base/config.h').read()
 # The short X.Y version.
-version = '2.2'
+version = re.search('CANTERA_SHORT_VERSION "(.*?)"', configh).group(1)
 # The full version, including alpha/beta/rc tags.
-release = '2.2.0b1'
+release = re.search('CANTERA_VERSION "(.*?)"', configh).group(1)
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -101,9 +96,6 @@ release = '2.2.0b1'
 # 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'
@@ -130,15 +122,47 @@ pygments_style = 'sphinx'
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinxdoc'
+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 = []
+html_theme_path = ['.']
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
@@ -154,14 +178,13 @@ 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,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
-html_style = 'site.css'
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
 #html_last_updated_fmt = '%b %d, %Y'
@@ -218,8 +241,8 @@ htmlhelp_basename = 'Canteradoc'
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'Cantera.tex', u'Cantera Documentation',
+  ('index', 'Cantera.tex', 'Cantera Documentation',
-   u'Cantera Developers', 'manual'),
+   'Cantera Developers', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -251,6 +274,6 @@ latex_documents = [
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'cantera', u'Cantera Documentation',
+    ('index', 'cantera', 'Cantera Documentation',
-     [u'Cantera Developers'], 1)
+     ['Cantera Developers'], 1)
 ]

doc/sphinx/configuring.rst

@@ -1,15 +0,0 @@
-.. _scons-config:
-
-*******************
-Configuring Cantera
-*******************
-
-This document lists the options available for compiling Cantera with SCons.
-
-These options may be seen by running the command::
-
-    scons help
-
-from the command prompt.
-
-.. literalinclude:: scons-options.txt

doc/sphinx/cti/classes.rst

@@ -50,9 +50,6 @@ Phases of Matter
 .. autoclass:: liquid_vapor
    :no-undoc-members:
 
-.. autoclass:: redlich_kwong
-   :no-undoc-members:
-
 .. autoclass:: ideal_interface
    :no-undoc-members:
 
@@ -83,9 +80,6 @@ Thermodynamic Properties
 .. autoclass:: Shomate
    :no-undoc-members:
 
-.. autoclass:: Adsorbate
-   :no-undoc-members:
-
 .. autoclass:: const_cp
    :no-undoc-members:
 
@@ -125,6 +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

@@ -1,489 +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 function like importPhase 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`.

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

@@ -1,501 +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 and/or
-commas. 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::
-
-    >>> gas = importPhase('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::
-
-    # commas are optional
-    species = 'AR SI Si2 SiH SiH2 SiH3 SiH4'
-    species = 'H, O, OH, H2O, HO2, H2O2, H2, O2'
-
-    # 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 assiging 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 = importPhase('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 bounday 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

@@ -1,520 +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'))
-
-Note: the usage of ``n`` as the temperature exponent has been deprecated. It is
-still available in version 2.2 but will be removed.
-
-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]]))
-
-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.
-
-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'])
-
-
-.. 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-!8", 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 + a_5
-
-    \frac{s^0(T)}{R} = a_o \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

@@ -0,0 +1,19 @@
+@import url('./alabaster.css');
+
+dl.method, dl.attribute, dl.staticmethod, dl.classmethod {
+     border-top: 1px solid #aaa;
+     padding-top: 4px;
+ }
+
+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

@@ -0,0 +1,3 @@
+[theme]
+inherit = alabaster
+stylesheet = cantera.css

doc/sphinx/cxx-guide/compiling.rst

@@ -1,117 +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>`_.
-
-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 referincing 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

@@ -1,38 +0,0 @@
-#include "cantera/thermo.h"
-
-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
-    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;
-
-    //  Clean up
-    delete gas;
-}
-
-// 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/demoequil.cpp

@@ -1,21 +0,0 @@
-#include "cantera/thermo.h"
-
-using namespace Cantera;
-
-void equil_demo()
-{
-    std::auto_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/headers.rst

@@ -1,38 +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``
-    Chemical kinetics.
-
-``numerics.h``
-    Classes for matrices.
-
-``onedim.h``
-    One-dimensional reacting flows.
-
-``reactionpaths.h``
-    Reaction path diagrams.
-
-``transport.h``
-    Transport properties.
-
-``zerodim.h``
-    Zero-dimensional reactor networks.

doc/sphinx/cxx-guide/index.rst

@@ -1,13 +0,0 @@
-
-**************************
-C++ Interface User's Guide
-**************************
-
-.. toctree::
-   :maxdepth: 2
-  
-   compiling
-   headers
-   thermo
-   simple-example
-   equil-example

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

@@ -1,64 +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++
-
-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. In
-the ``catch`` block, function :ct:`showErrors` may be called to print the error
-message associated with the exception.
-
-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

@@ -1,125 +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)
-    {
-	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
-<ThermoPhase::temperature>` that returns the current temperature, a method
-:ct:`setTemperature(double T) <ThermoPhase::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 polynomoial
-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 *r*+1 independent thermodynamic properties, where
-*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)
-{
-    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/constants.rst

@@ -7,48 +7,48 @@ These values are the same as those in the Cantera C++ header file ct_defs.h.
 
 .. data:: avogadro
 
-   Avogadro's Number, /kmol
+   Avogadro's Number, kmol\ :sup:`-1`
 
 .. data:: gas_constant
 
-   The ideal gas constant in J/kmol-K
+   The ideal gas constant, J kmol\ :sup:`-1` K\ :sup:`-1`
 
 .. data:: one_atm
 
-   One atmosphere in Pascals
+   One atmosphere, Pa
 
 .. data:: boltzmann
 
-   Boltzmann constant
+   Boltzmann constant, m\ :sup:`2` kg s\ :sup:`-2` K\ :sup:`-1`
 
 .. data:: planck
 
-   Planck constant (J/s)
+   Planck constant, J s
 
 .. data:: stefan_boltzmann
 
-   The Stefan-Boltzmann constant, W/m^2K^4
+   The Stefan-Boltzmann constant, W m\ :sup:`-2` K\ :sup:`-4`
 
 .. data:: electron_charge
 
-   The charge on an electron (C)
+   The charge on an electron, C
 
 .. data:: electron_mass
 
-   The mass of an electron (kg)
+   The mass of an electron, kg
 
 .. data:: faraday
 
-   Faraday constant, C/kmol
+   Faraday constant, C kmol\ :sup:`-1`
 
 .. data:: light_speed
 
-   Speed of Light (m/s).
+   Speed of Light, m s\ :sup:`-1`
 
 .. data:: permeability_0
 
-   Permeability of free space :math:`\mu_0` in N/A^2.
+   Permeability of free space, m kg s\ :sup:`-2` A\ :sup:`-2`
 
 .. data:: epsilon_0
 
-   Permittivity of free space (Farads/m = C^2/N/m^2)
+   Permittivity of free space, s\ :sup:`4` A\ :sup:`2` m\ :sup:`-3` kg\ :sup:`-1`

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

@@ -1,6 +0,0 @@
-.. _py-example-@script_name@:
-
-@script_name@
-=======================================================================
-
-.. literalinclude:: @script_path@

doc/sphinx/cython/examples.rst

@@ -1,62 +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
---------------
-.. toctree::
-   :glob:
-
-   examples/thermo*
-
-Kinetics
---------
-.. toctree::
-   :glob:
-
-   examples/kinetics*
-
-Transport
----------
-.. toctree::
-   :glob:
-
-   examples/transport*
-
-Reactor Networks
-----------------
-.. toctree::
-   :glob:
-
-   examples/reactors*
-
-One-dimensional Flames
-----------------------
-.. toctree::
-   :glob:
-
-   examples/onedim*
-
-Multiphase Mixtures
--------------------
-.. toctree::
-   :glob:
-
-   examples/multiphase*
-
-Surface Chemistry
------------------
-.. toctree::
-   :glob:
-
-   examples/surface_chemistry*

doc/sphinx/cython/importing.rst

@@ -1,7 +1,13 @@
 .. py:currentmodule:: cantera
 
-Creating Phase Objects
+Objects Representing Phases
-======================
+===========================
+
+.. contents::
+   :local:
+
+Composite Phase Objects
+-----------------------
 
 These classes are composite representations of a substance which has
 thermodynamic, chemical kinetic, and (optionally) transport properties.
@@ -12,7 +18,33 @@ thermodynamic, chemical kinetic, and (optionally) transport properties.
 
 .. autoclass:: DustyGas(infile, phaseid='')
 
+Pure Fluid Phases
+-----------------
+
+The following convenience functions can be used to create `PureFluid` objects
+with the indicated equation of state:
+
+.. autofunction:: CarbonDioxide
+.. autofunction:: Heptane
+.. autofunction:: Hfc134a
+.. autofunction:: Hydrogen
+.. autofunction:: Methane
+.. autofunction:: Nitrogen
+.. autofunction:: Oxygen
+.. autofunction:: Water
+
+Representing Quantities of Phases
+---------------------------------
+
+.. autoclass:: Quantity
+
+Representing Multiple States
+----------------------------
+
+.. autoclass:: SolutionArray
+
 Utility Functions
 -----------------
 
 .. autofunction:: add_directory
+.. autofunction:: get_data_directories

doc/sphinx/cython/index.rst

@@ -8,8 +8,6 @@ Contents:
 .. toctree::
    :maxdepth: 2
 
-   migrating
-   tutorial
    importing
    thermo
    kinetics
@@ -17,4 +15,3 @@ Contents:
    zerodim
    onedim
    constants
-   examples

doc/sphinx/cython/kinetics.rst

@@ -3,53 +3,91 @@
 Chemical Kinetics
 =================
 
+.. contents::
+   :local:
+
+Kinetics Managers
+-----------------
+
+Kinetics
+^^^^^^^^
 .. autoclass:: Kinetics(infile='', phaseid='', phases=())
 
+InterfaceKinetics
+^^^^^^^^^^^^^^^^^
+.. autoclass:: InterfaceKinetics
+
 Reactions
 ---------
 
 These classes contain the definition of a single reaction and its associated
-rate expression, indepenent of a specific `Kinetics` object.
+rate expression, independent of a specific `Kinetics` object.
 
+Reaction
+^^^^^^^^
 .. autoclass:: Reaction(reactants='', products='')
    :no-undoc-members:
 
+ElementaryReaction
+^^^^^^^^^^^^^^^^^^
 .. autoclass:: ElementaryReaction(reactants='', products='')
    :no-undoc-members:
 
+ThreeBodyReaction
+^^^^^^^^^^^^^^^^^
 .. autoclass:: ThreeBodyReaction(reactants='', products='')
    :no-undoc-members:
 
+FalloffReaction
+^^^^^^^^^^^^^^^
 .. autoclass:: FalloffReaction(reactants='', products='')
    :no-undoc-members:
 
+ChemicallyActivatedReaction
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 .. autoclass:: ChemicallyActivatedReaction(reactants='', products='')
    :no-undoc-members:
 
+PlogReaction
+^^^^^^^^^^^^
 .. autoclass:: PlogReaction(reactants='', products='')
    :no-undoc-members:
 
+ChebyshevReaction
+^^^^^^^^^^^^^^^^^
 .. autoclass:: ChebyshevReaction(reactants='', products='')
    :no-undoc-members:
 
+InterfaceReaction
+^^^^^^^^^^^^^^^^^
 .. autoclass:: InterfaceReaction(reactants='', products='')
    :no-undoc-members:
 
 Auxilliary Reaction Data
 ------------------------
 
+Arrhenius
+^^^^^^^^^
 .. autoclass:: Arrhenius(A, b, E)
 
+Falloff
+^^^^^^^
 .. autoclass:: Falloff(coeffs=(), init=True)
    :no-undoc-members:
 
+TroeFalloff
+^^^^^^^^^^^
 .. autoclass:: TroeFalloff(coeffs=(), init=True)
    :no-undoc-members:
 
+SriFalloff
+^^^^^^^^^^
 .. autoclass:: SriFalloff(coeffs=(), init=True)
    :no-undoc-members:
 
 Reaction Path Analysis
 ----------------------
 
+ReactionPathDiagram
+^^^^^^^^^^^^^^^^^^^
 .. autoclass:: ReactionPathDiagram(Kinetics kin, str element)

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 Thermodyamic 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 enbale 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

@@ -1,5 +1,7 @@
 .. py:currentmodule:: cantera
 
+.. _sec-cython-onedim:
+
 One-dimensional Reacting Flows
 ==============================
 
@@ -11,28 +13,59 @@ Composite Domains
 
 FreeFlame
 ^^^^^^^^^
-.. autoclass:: FreeFlame(gas, grid=None)
+.. autoclass:: FreeFlame(gas, grid=None, width=None)
 
 BurnerFlame
 ^^^^^^^^^^^
-.. autoclass:: BurnerFlame(gas, grid=None)
+.. autoclass:: BurnerFlame(gas, grid=None, width=None)
 
 CounterflowDiffusionFlame
 ^^^^^^^^^^^^^^^^^^^^^^^^^
-.. autoclass:: CounterflowDiffusionFlame(gas, grid=None)
+.. autoclass:: CounterflowDiffusionFlame(gas, grid=None, width=None)
+
+CounterflowPremixedFlame
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. autoclass:: CounterflowPremixedFlame(gas, grid=None, width=None)
+
+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/thermo.rst

@@ -1,15 +1,27 @@
 .. py:currentmodule:: cantera
 
+
 Thermodynamic Properties
 ========================
 
+.. contents::
+   :local:
+
 Phases
 ------
 
 These classes are used to describe the thermodynamic state of a system.
 
+ThermoPhase
+^^^^^^^^^^^
 .. autoclass:: ThermoPhase(infile='', phaseid='')
+
+InterfacePhase
+^^^^^^^^^^^^^^
 .. autoclass:: InterfacePhase(infile='', phaseid='')
+
+PureFluid
+^^^^^^^^^
 .. autoclass:: PureFluid(infile='', phaseid='')
 
 Mixture
@@ -28,12 +40,31 @@ Species Thermodynamic Properties
 These classes are used to describe the reference-state thermodynamic properties
 of a pure species.
 
+SpeciesThermo
+^^^^^^^^^^^^^
 .. autoclass:: SpeciesThermo(T_low, T_high, P_ref, coeffs)
+
+ConstantCp
+^^^^^^^^^^
 .. autoclass:: ConstantCp(T_low, T_high, P_ref, coeffs)
     :no-undoc-members:
 
+NasaPoly2
+^^^^^^^^^
 .. autoclass:: NasaPoly2(T_low, T_high, P_ref, coeffs)
     :no-undoc-members:
 
+ShomatePoly2
+^^^^^^^^^^^^
 .. autoclass:: ShomatePoly2(T_low, T_high, P_ref, coeffs)
     :no-undoc-members:
+
+Element
+-------
+
+.. autoclass:: Element
+    :no-undoc-members:
+
+    .. autoattribute:: num_elements_defined
+    .. autoattribute:: element_symbols
+    .. autoattribute:: element_names

doc/sphinx/cython/tutorial.rst

@@ -1,339 +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 by running::
-
-    >>> import cantera as ct
-
-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'
-
-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 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
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-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.
-[See R. J. Kee, F. M. Rupley, and J. A. Miller, Sandia National Laboratories
-Report SAND89-8009 (1989).]
-
-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. Here's an example of how to use it. The command::
-
-    $python ck2cti.py --input=mech.inp --thermo=therm.dat --transport=tran.dat
-
-will produce the file ``mech.cti`` in the current directory.
-
-
-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'.

doc/sphinx/cython/zerodim.rst

@@ -1,5 +1,7 @@
 .. py:currentmodule:: cantera
 
+.. _sec-cython-zerodim:
+
 Zero-Dimensional Reactor Networks
 =================================
 
@@ -54,14 +56,27 @@ FlowReactor
 ^^^^^^^^^^^
 .. autoclass:: FlowReactor(contents=None, *, name=None, energy='on')
 
-
+Walls
-Flow Controllers
+-----
-----------------
 
 Wall
 ^^^^
 .. autoclass:: Wall(left, right, *, name=None, A=None, K=None, U=None, Q=None, velocity=None, kinetics=(None,None))
 
+WallSurface
+^^^^^^^^^^^
+.. autoclass:: WallSurface(wall, side)
+
+Surfaces
+--------
+
+ReactorSurface
+^^^^^^^^^^^^^^
+.. autoclass:: ReactorSurface(kin=None, r=None, *, A=None)
+
+Flow Controllers
+----------------
+
 MassFlowController
 ^^^^^^^^^^^^^^^^^^
 .. autoclass:: MassFlowController(upstream, downstream, *, name=None, mdot=None)

doc/sphinx/faq.rst

@@ -1,150 +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 "new" 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 legacy Python 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 new 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, 2014. Version 2.2.0.
-
-    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 = 2014,
-           note = "Version 2.2.0",
-           howpublished = "\url{http://www.cantera.org}"
-        }
-
-    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 complete, minimal example 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/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

@@ -1,49 +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
+   yaml/index
-   Installation Instructions <install>
+   cti/classes
-   Compiliation Instructions <compiling>
-   language-interfaces
-   cti/index
-   reactors
    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

@@ -1,330 +0,0 @@
-.. _sec-install:
-
-******************
-Installing Cantera
-******************
-
-.. contents::
-   :local:
-   :depth: 2
-
-.. _sec-install-win:
-
-Windows
-=======
-
-Windows installers are provided for stable versions of Cantera. These
-installation instructions are for Cantera 2.1.1.
-
-1. **Choose your Python version and architecture**
-
-   - On Windows, Cantera supports Python 2.7 and Python 3.3. Python 3.3 is
-     recommended unless you need to use legacy code that does not work with
-     Python 3. You can install both 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* (i.e. prefer 3.3.5 to 3.3.4, but not 3.4.1).
-     - *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
-     `Anaconda <https://store.continuum.io/cshop/anaconda/>`_ or 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 pip**
-
-   - Go to the `pip installation instructions
-     <https://pip.pypa.io/en/latest/installing.html#install-pip>`_ and download
-     `get-pip.py` (You may need to right click the link and select *Save target
-     as...*).
-
-   - From a administrative command prompt, run `get-pip.py` with the copy of
-     Python you plan on use with Cantera, e.g.::
-
-         c:\python33\python.exe "%USERPROFILE%\Downloads\get-pip.py"
-
-4. **Install Numpy**
-
-   - 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. The
-     binaries for Cantera 2.1.1 require Numpy 1.8.0 or newer, e.g. In the
-     filename, the digits after "cp" indicate the Python version, e.g.
-     ``numpy‑1.8.2+mkl‑cp33‑none‑win_amd64.whl`` is the installer for 64-bit
-     Python 3.3.
-
-   - From an administrative command prompt, install the downloaded wheel using
-     pip, e.g.::
-
-         c:\python33\scripts\pip.exe install "%USERPROFILE%\Downloads\numpy‑1.8.2+mkl‑cp33‑none‑win_amd64.whl"
-
-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 Downloads
-     <https://sourceforge.net/projects/cantera/files/cantera/2.1.1/>`_ page.
-
-     - *64-bit*: Download **Cantera-2.1.1-x64.msi** and
-       **Cantera-Python-2.1.1-x64-pyX.Y.msi**.
-     - *32-bit*: Download **Cantera-2.1.1-x86.msi** and
-       **Cantera-Python-2.1.1-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:\python27\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 = importPhase('liquidvapor.cti','water')
-
-.. _sec-install-osx:
-
-Mac OS X
-========
-
-Cantera can be installed on OS X using either Homebrew or MacPorts. With
-Homebrew, the current stable, maintenance, or development versions 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 "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
-
-2. **Set up the compilation environment**
-
-   - Run the following commands::
-
-         brew tap homebrew/science
-         brew update
-         brew install python scons sundials
-
-   - Verify that your path is set up to use Homebrew's version of Python by
-     running::
-
-         which python
-
-     If this command does not print ``/usr/local/bin/python``, add the following
-     to ``~/.bash_profile`` (creating this file if it doesn't already exist; you
-     can use the command line editor ``nano`` to edit this file)::
-
-         export PATH=/usr/local/bin:$PATH
-
-     and then run::
-
-         source ~/.bash_profile
-
-   - Install Python packages required to compile Cantera by running::
-
-         pip install cython numpy
-
-     Note that these packages are required even if you do not plan on using the
-     Cantera Python 2 module.
-
-   - If you want to build the Cantera Python 3 module, run::
-
-         brew install python3
-         pip3 install numpy cython
-
-3. **Compile and install Cantera**
-
-   * To compile and install Cantera using the default configuration, run::
-
-         brew install cantera
-
-   * The following options are supported:
-
-     ``--devel``
-         Installs Cantera with additional patches that will be included in the
-         next maintenance release.
-
-     ``--HEAD``
-         Installs the current development version of Cantera.
-
-     ``--with-matlab=/Applications/MATLAB_R2014a.app/``
-         Installs the Matlab toolbox (with the path modified to match your
-         installed Matlab version)
-
-   * These options are specified as additional arguments to the ``brew install``
-     command, e.g.::
-
-         brew install cantera --devel --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
-
-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 2.1.2, packages are available for Ubuntu
-12.04 LTS (Precise Pangolin), Ubuntu 14.04 LTS (Trusty Tahr), and Ubuntu 14.10
-(Utopic Unicorn). 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. For Ubuntu 12.04,
-  this is the "legacy" Python module. For Ubuntu 14.04 and newer, this is the
-  "new" Python module.
-
-- ``cantera-python3`` - The Cantera Python module for Python 3. Only available
-  for Ubuntu 14.04 and newer.
-
-- ``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.

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

@@ -1,7 +0,0 @@
-.. _matlab-example-@script_name@:
-
-@script_name@
-=======================================================================
-
-.. literalinclude:: @script_path@
-   :language: matlab

doc/sphinx/matlab/examples.rst

@@ -1,21 +0,0 @@
-.. _sec-matlab-examples:
-
-Index of Examples
-=================
-
-This is an index of the examples included with the Cantera Matlab Toolbox.
-
-Tutorials
----------
-.. toctree::
-   :glob:
-
-   tutorials/*
-
-Examples
---------
-
-.. toctree::
-   :glob:
-
-   examples/*

doc/sphinx/matlab/index.rst

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

doc/sphinx/matlab/input-tutorial.rst

@@ -1,75 +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 = importPhase('gri30.cti', 'gri30');
-
-Function ``importPhase`` constructs an 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 = importPhase('diamond.cti', 'gas');                   % a gas
-    diamond = importPhase('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
---------------------------
-
-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.  [See
-R. J. Kee, F. M. Rupley, and J. A. Miller, Sandia National Laboratories Report
-SAND89-8009 (1989).]
-
-Cantera comes with a converter utility program ``ck2cti`` (or ``ck2cti.exe``)
-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.
-
-Here's an example of how to use it:
-
-.. code-block:: bash
-
-    ck2cti -i mech.inp -t therm.dat -tr tran.dat -id mymech > mech.cti

doc/sphinx/reactors.rst

@@ -1,197 +0,0 @@
-.. default-role:: math
-
-****************
-Reactor Networks
-****************
-
-Cantera's Reactor Network module is designed to simulate networks of
-interconnected reactors. The contents of each reactor in the network are
-assumed to be homogeneous, a model variously referred to as the Continuously
-Stirred Tank Reactor (CSTR), Well-Stirred Reactor (WSR), or Perfectly Stirred
-Reactor (PSR) model. Cantera solves the time-dependent governing equations
-that describe the evolution of the chemical and thermodynamic state of the
-reactors.
-
-The contents of each reactor can undergo chemical reactions according to a
-specified kinetic mechanism, and surface reactions may occur on the reactor
-walls. Each reactor in a network may be connected so that the contents of one
-reactor flow into another. Reactors may be also be in contact with one another
-or the environment via walls which move or conduct heat.
-
-The purpose of this document is to describe the governing equations of reactor
-models as implemented in Cantera.
-
-Wall Interactions
-=================
-
-At each wall where there are surface reactions, there is a net generation (or
-destruction) of homogeneous phase species. The molar rate of production for
-each species `k` on wall `w` is `\dot{s}_{k,w}`. The total (mass) production
-rate for 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}
-
-The total rate of heat transfer through all walls is:
-
-.. math::
-
-    \dot{Q} = \sum_w f_w \dot{Q}_w
-
-General Reactor
-===============
-
-The state variables for Cantera's general reactor model are
-
-    - `m`, the mass of the reactor's contents
-    - `V`, the reactor volume
-    - `U`, the total internal energy of the reactors contents
-    - `Y_k`, the mass fractions for each species
-
-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.
-
-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}{dt} = \sum_{in} \dot{m}_{in} (Y_{k,in} - Y_k)+
-                      \dot{m}_{k,gen} - Y_k \dot{m}_{wall}
-
-Energy Conservation
--------------------
-
-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}
-
-Ideal Gas Reactor
-=================
-
-The Ideal Gas Reactor model is similar to the General Reactor model, with the
-reactor temperature `T` replacing 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.
-
-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{dH}{dt} = 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}
-
-The species and continuity equations are the same as for the general reactor
-model.
-
-Ideal Gas Constant Pressure Reactor
-===================================
-
-As for the Ideal Gas Reactor, 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)

doc/sphinx/scons-options.txt

@@ -1,330 +0,0 @@
-scons: Reading SConscript files ...
-
-        **************************************************
-        *   Configuration options for building Cantera   *
-        **************************************************
-
-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'
-
-        **************************************************
-
-* msvc_version: [ string ]
-    Version of Visual Studio to use. The default is the same version
-    that was used to compile the installed version of Python.
-    - default: '9.0'
-
-* target_arch: [ string ]
-    Target architecture. The default is the same architecture as the
-    installed version of Python
-    - default: 'amd64'
-
-* toolchain: [ msvc | mingw | intel ]
-    The preferred compiler toolchain.
-    - default: 'msvc'
-
-* CXX: [ string ]
-    The C++ compiler to use.
-    - default: 'g++'
-
-* CC: [ string ]
-    The C compiler to use. This is only used to compile CVODE and the
-    Python extension module.
-    - default: 'gcc'
-
-* prefix: [ /path/to/prefix ]
-    Set this to the directory where Cantera should be installed.
-    - default: '/usr/local'
-
-* python_package: [ new | full | minimal | none | default ]
-    If you plan to work in Python, or you want to use the graphical
-    MixMaster application, 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 (actually, only one file). The default behavior is to build
-    the Python package if the required prerequisites (numpy) are
-    installed.
-    - default: 'default'
-
-* python_cmd: [ /path/to/python_cmd ]
-    Cantera needs to know where to find the Python interpreter. If
-    PYTHON_CMD is not set, then the configuration process will use the
-    same Python interpreter being used by SCons.
-    - default: '/usr/bin/python'
-
-* python_array_home: [ /path/to/python_array_home ]
-    If numpy was installed using the --home option, set this to the home
-    directory for numpy.
-    - default: ''
-
-* python_prefix: [ /path/to/python_prefix ]
-    Use this option if you want to install the Cantera Python package to
-    an alternate location. On Unix-like systems, the default is the same
-    as the $prefix option. If this option is set to the empty string
-    (the default on Windows), then the Package will be installed to the
-    system default 'site-packages' directory.
-    - default: '$prefix'
-
-* 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 can be
-    found
-    - default: 'default'
-
-* python3_cmd: [ /path/to/python3_cmd ]
-     The name (full path if necessary) of the Python 3 interpreter.
-    Required to build the Python 3 module.
-    - default: 'python3'
-
-* python3_array_home: [ /path/to/python3_array_home ]
-    "If numpy was installed to a custom location (e.g. using the --home
-    option, set this to the directory for numpy
-    - default: ''
-
-* 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 $prefix option. If this option is set to the empty
-    string (the default on Windows), then the Package will be installed
-    to the system default 'site-packages' directory.
-    - default: '$prefix'
-
-* 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 set to 'default', the Matlab toolbox will be built if
-    'matlab_path' is set.
-    - default: 'default'
-
-* 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: [ 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, and compile the Fortran 90 interface
-    if one is found.
-    - default: 'default'
-
-* F90: [ /path/to/F90 ]
-    The Fortran 90 compiler. If unspecified, the builder will look for a
-    compatible compiler (gfortran, ifort, g95) in the $PATH.
-    - default: ''
-
-* F90FLAGS: [ string ]
-    Compilation options for the Fortran 90 compiler.
-    - default: '-O3'
-
-* debug_verbose: [ yes | no ]
-    Enable extra printing to aid in debugging. This code is marked by
-    the preprocessor macros DEBUG_MODE and DEBUG_MODE_ENABLED.
-    - default: 'no'
-
-* coverage: [ yes | no ]
-    Enable collection of code coverage information with gcov. Available
-    only when compiling with gcc.
-    - default: 'no'
-
-* doxygen_docs: [ yes | no ]
-    Build HTML documentation for the C++ interface using Doxygen
-    - default: 'no'
-
-* sphinx_docs: [ yes | no ]
-    Build HTML documentation for the Python module using Sphinx
-    - default: 'no'
-
-* with_lattice_solid: [ yes | no ]
-    Include thermodynamic model for lattice solids in the Cantera
-    kernel.
-    - default: 'yes'
-* sphinx_cmd: [ /path/to/sphinx_cmd ]
-    Command to use for building the Sphinx documentation
-    - default: 'sphinx-build'
-
-* with_h298modify_capability: [ yes | no ]
-    Enable changing the 298K heats of formation directly via the C++
-    layer.
-    - default: 'no'
-
-* with_html_log_files: [ yes | no ]
-    write HTML log files. Some multiphase equilibrium procedures can
-    write copious diagnostic log messages. Set this to 'n' to disable
-    this capability. (results in slightly faster equilibrium
-    calculations)
-    - default: 'yes'
-
-* use_sundials: [ default | y | n ]
-    Cantera uses the CVODE or CVODES ODE integrator to time-integrate
-    reactor network ODE's and for various other purposes. An older
-    version of CVODE comes with Cantera, but it is possible to use the
-    latest version as well, which now supports sensitivity analysis
-    (CVODES). CVODES is a part of the 'sundials' package from Lawrence
-    Livermore National Laboratory. Sundials is not distributed with
-    Cantera, but it is free software that may be downloaded and
-    installed separately. If you leave USE_SUNDIALS = 'default', then it
-    will be used if you have it, and if not the older CVODE will be
-    used. Or set USE_SUNDIALS to 'y' or 'n' to force using it or not.
-    Note that sensitivity analysis with Cantera requires use of
-    sundials. See: http://www.llnl.gov/CASC/sundials
-    - default: 'default'
-
-* 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: [ /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: [ string ]
-    Cantera comes with Fortran (or C) versions of those parts of BLAS
-    and LAPACK it requires. But performance may be better if you use a
-    version of these libraries optimized for your machine hardware. If
-    you want to use your own libraries, 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: [ /path/to/blas_lapack_dir ]
-    Directory containing the libraries specified by 'blas_lapack_libs'.
-    - default: ''
-
-* 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: [ yes | no ]
-    - default: 'yes'
-
-* lapack_ftn_string_len_at_end: [ yes | no ]
-    - default: 'yes'
-
-* 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: ''
-
-* cxx_flags: [ string ]
-    Compiler flags passed to the C++ compiler only.
-    - default: '-ftemplate-depth-128'
-
-* cc_flags: [ string ]
-    Compiler flags passed to both the C and C++ compilers, regardless of
-    optimization level
-    - default: '-Wall -Wno-deprecated-declarations'
-
-* thread_flags: [ string ]
-    Compiler and linker flags for POSIX multithreading support
-    - default: '-pthread'
-
-* optimize: [ yes | no ]
-    Enable extra compiler optimizations specified by the
-    "optimize_flags" variable, instead of the flags specified by the
-    "debug_flags" variable
-    - default: 'yes'
-
-* optimize_flags: [ string ]
-    Additional compiler flags passed to the C/C++ compiler when
-    optimize=yes.
-    - default: '-O3 -DNDEBUG -finline-functions -Wno-inline'
-
-* no_optimize_flags: [ string ]
-    Additional compiler flags passed to the C/C++ compiler when
-    optimize=no.
-    - default: '-O0 -fno-inline'
-
-* debug: [ yes | no ]
-    Enable compiler debugging symbols.
-    - default: 'yes'
-
-* debug_flags: [ string ]
-    Additional compiler flags passed to the C/C++ compiler when
-    debug=yes.
-    - default: '-g'
-
-* no_debug_flags: [ string ]
-    Additional compiler flags passed to the C/C++ compiler when
-    debug=no.
-    - default: ''
-
-* debug_linker_flags: [ string ]
-    Additional options passed to the linker when debug=yes
-    - default: ''
-
-* no_debug_linker_flags: [ string ]
-    Additional options passed to the linker when debug=yes
-    - default: ''
-
-* build_thread_safe: [ yes | no ]
-    Cantera can be built so that it is thread safe. Doing so requires
-    using procedures from the Boost library, so if you want thread
-    safety then you need to get and install Boost (http://www.boost.org)
-    if you don't have it. This is turned off by default, in which case
-    Boost is not required to build Cantera.
-    - default: 'no'
-
-* boost_inc_dir: [ /path/to/boost_inc_dir ]
-    Location of the Boost header files
-    - default: '/usr/include'
-
-* boost_lib_dir: [ /path/to/boost_lib_dir ]
-    Directory containing the Boost.Thread library
-    - default: '/usr/lib'
-
-* boost_thread_lib: [ string ]
-    The name of the Boost.Thread library.
-    - default: 'boost_thread'
-
-* build_with_f2c: [ yes | no ]
-    For external procedures written in Fortran 77, both the original F77
-    source code and C source code generated by the 'f2c' program are
-    included. Set this to "n" if you want to build Cantera using the F77
-    sources in the ext directory.
-    - default: 'yes'
-
-* F77: [ string ]
-    Compiler used to build the external Fortran 77 procedures from the
-    Fortran source code
-    - default: 'gfortran'
-
-* F77FLAGS: [ string ]
-    Fortran 77 Compiler flags. Note that the Fortran compiler flags must
-    be set to produce object code compatible with the C/C++ compiler you
-    are using.
-    - default: '-O3'
-
-* 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/...' instead
-    of installing into the local filesystem.
-    - default: ''
-
-* cantera_version: [ string ]
-    - default: '2.0.0b1'
-

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