Create FUNDING.yml

Links to NumFOCUS donate page

.github/FUNDING.yml

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

.github/ISSUE_TEMPLATE/bug_report.md

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

.github/ISSUE_TEMPLATE/feature_request.md

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

.github/PULL_REQUEST_TEMPLATE.md

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

.github/SUPPORT.md

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

.gitignore

@@ -1,5 +1,6 @@
 doc/ctdeploy_key
 *~
+*#
 *.o
 *.so
 *.os

.gitmodules

@@ -10,3 +10,6 @@
 [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

@@ -1,18 +1,17 @@
 language: cpp
 sudo: false
-dist: trusty
+dist: xenial
 os:
   - linux
   - osx
 addons:
   apt:
     packages:
-      - python-dev
-      - python-numpy
-      - python-pip
+      - python3-pip
       - python3-dev
       - python3-numpy
       - python3-setuptools
+      - scons
       - gfortran
       - libsundials-serial-dev
       - liblapack-dev
@@ -31,31 +30,35 @@ env:
 before_script: |
   echo TRAVIS_OS_NAME: $TRAVIS_OS_NAME
   if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-      brew update > /dev/null
-      brew upgrade python  # Installs Python 3
-      brew install python@2  # Installs Python 2
-      brew install scons  # Install SCons which *should* use Python 3
-      pip3 install numpy cython  # Install numpy and Cython for Python 3
-      pip2 install numpy 3to2  # Install numpy and 3to2 for Python 2
-      brew install boost
+      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
-      pip2 install --user --install-option="--no-cython-compile" cython
-      pip2 install --user 3to2
+      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
-      pip2 install --user sphinx sphinxcontrib-matlabdomain
-      # These two packages have specific bug fixes from these branches
-      pip2 install --user https://github.com/Cantera/doxylink/archive/fix_relative_path_source_14.tar.gz
-      pip2 install --user https://github.com/bryanwweber/sphinxcontrib-katex/archive/fix-options-bug.tar.gz
+      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 [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-      set -e
-      scons build -j2 VERBOSE=y python2_package=full python3_package=full python3_cmd=/usr/bin/python3 blas_lapack_libs=lapack,blas optimize=n coverage=y
+      scons build -j2 python_cmd=/usr/bin/python3 VERBOSE=y python_package=full blas_lapack_libs=lapack,blas optimize=n coverage=y
       scons test
-      scons build sphinx_docs=y doxygen_docs=y
+      scons samples
+      scons build sphinx_docs=y doxygen_docs=y sphinx_cmd="/usr/bin/python3 `which sphinx-build`"
       if [[ "${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 "${ctdeploy_pass}" -in ./doc/ctdeploy_key.enc -out ./doc/ctdeploy_key -d
         chmod 0600 ./doc/ctdeploy_key
         RSYNC_OPTIONS=(
@@ -77,10 +80,11 @@ script: |
         echo "Skipping documentation upload from source other than Cantera/cantera:master"
       fi
   else
-      python3 `which scons` build -j2 VERBOSE=y python2_package=full python3_package=full python2_cmd=/usr/local/opt/python@2/bin/python2 blas_lapack_libs=lapack,blas optimize=n coverage=y
-      python3 `which scons` test
+      scons build -j2 python_cmd=python3 VERBOSE=y python_package=full blas_lapack_libs=lapack,blas optimize=n coverage=y extra_inc_dirs=$CONDA_PREFIX/include extra_lib_dirs=$CONDA_PREFIX/lib
+      scons test
+      scons samples
   fi
 after_success: |
-  if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+  if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
       bash <(curl -s https://codecov.io/bash)
   fi

AUTHORS

@@ -4,17 +4,42 @@ partial, alphabetical list of developers and contributors to Cantera over the
 years. If you've been left off, please report the omission on the Github issue
 tracker.
 
+Emil Atz
 Philip Berndt
+Wolfgang Bessler, Offenburg University of Applied Science
+Tilman Bremer
 Victor Brunini, Sandia National Laboratory
 Bang-Shiuh Chen, Purdue University
-Steven Decaluwe, Colorado School of Mines
+Ryan Crisanti
+Nicholas Curtis
+Steven DeCaluwe, Colorado School of Mines
+Vishesh Devgan
 Thomas Fiala, Technische Universität München
 David Fronczek
+@g3bk47
+Matteo Giani
 Dave Goodwin, California Institute of Technology
 John Hewson, Sandia National Laboratory
+Trevor Hickey
+Yuanjie Jiang
+Jon Kristofer
+Kyle Linevitch, Jr.
+Christopher Leuth
 Nicholas Malaya, University of Texas at Austin
+Thanasis Mattas, Aristotle University of Thessaloniki
+Evan McCorkle
+Ivan Mitrichev, Mendeleev University of Chemical Technology of Russia
 Harry Moffat, Sandia National Laboratory
+Christopher Neal
+Kyle Niemeyer, Oregon State University
+Paul Northrop
 Andreas Rücker
+Jeff Santner
+Satyam Saxena
+Ingmar Schoegl, Louisiana State University
 Santosh Shanbhogue, Massachusetts Institute of Technology
+David Sondak
 Raymond Speth, Massachusetts Institute of Technology
+Sergey Torokhov
 Bryan Weber, University of Connecticut
+Armin Wehrfritz

CONTRIBUTING.md

@@ -20,9 +20,9 @@
     followed by a blank line and a more detailed summary, if any)
   * Make related changes in a single commit, and unrelated changes in separate
     commits
-  * Make sure that your commits do not include any undesired files, e.g. files
+  * Make sure that your commits do not include any undesired files, e.g., files
     produced as part of the build process or other temporary files.
-  * Use Git's history-rewriting features (i.e. `git rebase -i`; see
+  * Use Git's history-rewriting features (i.e., `git rebase -i`; see
     https://help.github.com/articles/about-git-rebase/) to organize your commits
     and squash "fixup" commits and reversions.
   * Do not merge your branch with `master`. If needed, you should rebase your branch
@@ -33,7 +33,8 @@
   integration tests run using Travis and AppVeyor and resolve any issues that
   arise.
 * Additional discussion of good Git & Github workflow is provided at
-  http://matplotlib.org/devel/gitwash/development_workflow.html and https://docs.scipy.org/doc/numpy-dev/dev/index.html
+  http://matplotlib.org/devel/gitwash/development_workflow.html and
+  https://docs.scipy.org/doc/numpy-1.15.0/dev/gitwash/development_workflow.html
 * Cantera is licensed under a [BSD
   license](https://github.com/Cantera/cantera/blob/master/License.txt) which
   allows others to freely modify the code, and if your Pull Request is accepted,
@@ -52,8 +53,9 @@
 * Write comments to explain non-obvious operations
 
 ## C++
+
 * All classes, member variables, and methods should have Doxygen-style comments
-  (e.g. comment lines starting with `//!` or comment blocks starting with `/*!`)
+  (e.g., comment lines starting with `//!` or comment blocks starting with `/*!`)
 * Avoid defining non-trivial functions in header files
 * Header files should include an 'include guard'
 * Protected and private member variable names are generally prefixed with
@@ -73,7 +75,7 @@
   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.
+  `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
@@ -85,7 +87,7 @@
 ## Python
 
 * Style generally follows PEP8 (https://www.python.org/dev/peps/pep-0008/)
-* Code in .py files needs to be written to work with both Python 2
-  and Python 3. Code in Cython files (.pyx or .pxd) should automatically work with both.
-* Code in the Python examples should be written for Python 3. Python 2 versions
-  are automatically generated as part of the build process
+* Code in `.py` and `.pyx` files needs to be written to work with Python 3
+* The minimum Python version that Cantera supports is Python 3.4, so code should only use features added in Python 3.4 or earlier
+* Code in `ctml_writer.py` and `ck2cti.py` needs to be written to work with both Python 2 and Python 3
+* Code in the Python examples should be written for Python 3

ISSUE_TEMPLATE.md

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

PULL_REQUEST_TEMPLATE.md

@@ -1,8 +0,0 @@
-Please fill in the issue number this pull request is fixing:
-
-Fixes #
-
-Changes proposed in this pull request:
--
--
--

README.rst

@@ -9,8 +9,8 @@ What is Cantera?
 ================
 
 Cantera is an open-source collection of object-oriented software tools for
-problems involving chemical kinetics, thermodynamics, and transport
-processes. Among other things, it can be used to:
+problems involving chemical kinetics, thermodynamics, and transport processes.
+Among other things, it can be used to:
 
 * Evaluate thermodynamic and transport properties of mixtures
 * Compute chemical equilibrium
@@ -25,28 +25,27 @@ Cantera can be used from Python and Matlab, or in applications written in C++
 and Fortran 90. A number of `examples of Cantera's capabilities
 <https://github.com/Cantera/cantera-jupyter>`_ are available in the form of
 Jupyter notebooks. These examples can be tried interactively, in the cloud by
-using the following Binder link:
+using the following MyBinder link:
 
-.. image:: http://mybinder.org/badge.svg
-    :target: http://mybinder.org:/repo/cantera/cantera-jupyter
+.. image:: https://mybinder.org/badge.svg
+    :target: https://mybinder.org/repo/cantera/cantera-jupyter
 
 Installation
 ============
 
 `Installation instructions for the current release of Cantera
-<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.
+<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.
+Cantera, `compilation instructions <https://cantera.org/install/index.html>`_
+are also available.
 
 Documentation
 =============
@@ -71,7 +70,7 @@ Code of Conduct
 
 .. image:: https://img.shields.io/badge/code%20of%20conduct-contributor%20covenant-green.svg?style=flat-square
     :alt: conduct
-    :target: http://contributor-covenant.org/version/1/4/
+    :target: https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
 
 In order to have a more open and welcoming community, Cantera adheres to a
 `code of conduct <CODE_OF_CONDUCT.md>`_ adapted from the `Contributor Covenent
@@ -79,19 +78,19 @@ code of conduct <https://contributor-covenant.org/>`_.
 
 Please adhere to this code of conduct in any interactions you have in the
 Cantera community. It is strictly enforced on all official Cantera
-repositories, websites, users' group, and other resources.
-If you encounter someone violating these terms, please
-`contact the code of conduct team <mailto:conduct@cantera.org>`_
-(`@speth <https://github.com/speth>`_,
-`@bryanwweber <https://github.com/bryanwweber>`_, and
-`@kyleniemeyer <https://github.com/kyleniemeyer>`_)
-and we will address it as soon as possible.
+repositories, websites, users' group, and other resources. If you encounter
+someone violating these terms, please `contact the code of conduct team
+<mailto:conduct@cantera.org>`_ (`@speth <https://github.com/speth>`_,
+`@bryanwweber <https://github.com/bryanwweber>`_, and `@kyleniemeyer
+<https://github.com/kyleniemeyer>`_) and we will address it as soon as
+possible.
 
 Development Site
 ================
 
-The 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
+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.
@@ -99,25 +98,33 @@ enhancement requests, `downloads of Cantera releases and binary installers
 Users' Group
 ============
 
-The `Cantera Users' Group <http://groups.google.com/group/cantera-users>`_ is a
+The `Cantera Users' Group <https://groups.google.com/group/cantera-users>`_ is a
 message board / mailing list for discussions amongst Cantera users.
 
 Cantera Gitter Chat
-============
+===================
 
 .. image:: https://badges.gitter.im/org.png
    :target: https://gitter.im/Cantera/Lobby
 
 
-The `Cantera Gitter Chat <https://gitter.im/Cantera/Lobby>`_ is a public chat client that is linked to users' Github account. The developers do not closely monitor the discussion, so *any* discussion at all of Cantera functionality such as how to use certain function calls, syntax problems, input files, etc. should be directed the User's Group. All conversations in the Gitter room will be covered under the Cantera Code of Conduct, so please be nice.
+The `Cantera Gitter Chat <https://gitter.im/Cantera/Lobby>`_ is a public chat
+client that is linked to users' Github account. The developers do not closely
+monitor the discussion, so *any* discussion at all of Cantera functionality
+such as how to use certain function calls, syntax problems, input files, etc.
+should be directed the User's Group. All conversations in the Gitter room will
+be covered under the Cantera Code of Conduct, so please be nice.
 
-The chat room is a place to strengthen and develop the Cantera community, discuss tangentially-related topics such as how to model the underlying physics of a problem , share cool applications you’ve developed, etc.
+The chat room is a place to strengthen and develop the Cantera community,
+discuss tangentially-related topics such as how to model the underlying physics
+of a problem , share cool applications you’ve developed, etc.
 
 Summary:
 
 “How do I perform this Cantera function call?” --> User's Group
 
-"What do I do with the variables that a Cantera function call returns?” --> Chat
+"What do I do with the variables that a Cantera function call returns?” -->
+Chat
 
 
 Continuous Integration Status
@@ -134,19 +141,16 @@ Windows x64     Appveyor      |appveyor|
 NumFOCUS
 ========
 
-Cantera is a fiscally-sponsored project of NumFOCUS, a non-profit dedicated to
-supporting the open source scientific computing community.
+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.org
+    :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

SConstruct

@@ -65,10 +65,8 @@ if 'clean' in COMMAND_LINE_TARGETS:
     removeDirectory('include/cantera/ext')
     removeFile('interfaces/cython/cantera/_cantera.cpp')
     removeFile('interfaces/cython/cantera/_cantera.h')
-    removeFile('interfaces/cython/setup2.py')
-    removeFile('interfaces/cython/setup3.py')
-    removeFile('interfaces/python_minimal/setup2.py')
-    removeFile('interfaces/python_minimal/setup3.py')
+    removeFile('interfaces/cython/setup.py')
+    removeFile('interfaces/python_minimal/setup.py')
     removeFile('config.log')
     removeDirectory('doc/sphinx/matlab/examples')
     removeFile('doc/sphinx/matlab/examples.rst')
@@ -80,6 +78,7 @@ if 'clean' in COMMAND_LINE_TARGETS:
     for name in os.listdir('interfaces/cython/cantera/data/'):
         if name != '__init__.py':
             removeFile('interfaces/cython/cantera/data/' + name)
+    removeDirectory('interfaces/cython/cantera/test/data/test_subdir')
     for name in os.listdir('interfaces/cython/cantera/test/data/'):
         if name != '__init__.py':
             removeFile('interfaces/cython/cantera/test/data/' + name)
@@ -113,7 +112,7 @@ if 'clean' in COMMAND_LINE_TARGETS:
 if 'test-clean' in COMMAND_LINE_TARGETS:
     removeDirectory('build/test')
     removeDirectory('test/work')
-    removeDirectory('build/python_minimal')
+    removeDirectory('build/python_local')
 
 # ******************************************************
 # *** Set system-dependent defaults for some options ***
@@ -255,7 +254,15 @@ defaults.noDebugLinkFlags = ''
 defaults.warningFlags = '-Wall'
 defaults.buildPch = False
 env['pch_flags'] = []
-env['openmp_flag'] = '-fopenmp' # used to generate sample build scripts
+env['openmp_flag'] = ['-fopenmp'] # used to generate sample build scripts
+
+env['using_apple_clang'] = False
+# Check if this is actually Apple's clang on macOS
+if env['OS'] == 'Darwin':
+    result = subprocess.check_output([env.subst('$CC'), '--version']).decode('utf-8')
+    if 'clang' in result.lower() and result.startswith('Apple LLVM'):
+        env['using_apple_clang'] = True
+        env['openmp_flag'].insert(0, '-Xpreprocessor')
 
 if 'gcc' in env.subst('$CC') or 'gnu-cc' in env.subst('$CC'):
     defaults.optimizeCcFlags += ' -Wno-inline'
@@ -278,13 +285,13 @@ elif env['CC'] == 'cl': # Visual Studio
     defaults.warningFlags = '/W3'
     defaults.buildPch = True
     env['pch_flags'] = ['/FIpch/system.h']
-    env['openmp_flag'] = '/openmp'
+    env['openmp_flag'] = ['/openmp']
 
 elif 'icc' in env.subst('$CC'):
     defaults.cxxFlags = '-std=c++0x'
     defaults.ccFlags = '-vec-report0 -diag-disable 1478'
     defaults.warningFlags = '-Wcheck'
-    env['openmp_flag'] = '-openmp'
+    env['openmp_flag'] = ['-openmp']
 
 elif 'clang' in env.subst('$CC'):
     defaults.ccFlags = '-fcolor-diagnostics'
@@ -327,6 +334,14 @@ config_options = [
         'prefix',
         'Set this to the directory where Cantera should be installed.',
         defaults.prefix, PathVariable.PathAccept),
+    PathVariable(
+        'libdirname',
+        """Set this to the directory where Cantera libraries should be installed.
+           Some distributions (e.g. Fedora/RHEL) use 'lib64' instead of 'lib' on 64-bit systems
+           or could use some other library directory name instead of 'lib' depends
+           on architecture and profile (e.g. Gentoo 'libx32' on x32 profile).
+           If user didn't set 'libdirname' configuration variable set it to default value 'lib'""",
+        'lib', PathVariable.PathAccept),
     EnumVariable(
         'python_package',
         """If you plan to work in Python, then you need the ``full`` Cantera Python
@@ -345,15 +360,10 @@ config_options = [
         """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.""",
-        sys.executable),
-    PathVariable(
-        'python_array_home',
-        """If NumPy was installed using the '--home' option, set this to the home
-           directory for NumPy for Python 2.""",
-        '', PathVariable.PathAccept),
+        sys.executable, PathVariable.PathAccept),
     PathVariable(
         'python_prefix',
-        """Use this option if you want to install the Cantera Python 2 package to
+        """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 the 'python_prefix' option is set to
            the empty string or the 'prefix' option is not set, then the package
@@ -361,65 +371,22 @@ config_options = [
            To install to the current user's 'site-packages' directory, use
            'python_prefix=USER'.""",
         defaults.python_prefix, PathVariable.PathAccept),
-    EnumVariable(
-        'python2_package',
-        """Controls whether or not the Python 2 module will be built. By
-           default, the module will be built if the Python 2 interpreter
-           and the required dependencies (NumPy for Python 2 and Cython
-           for the version of Python for which SCons is installed) can be
-           found.""",
-        'default', ('full', 'minimal', 'y', 'n', 'none', 'default')),
-    PathVariable(
-        'python2_cmd',
-        """The path to the Python 2 interpreter. The default is
-           'python2'; if this executable cannot be found, this
-           value must be specified to build the Python 2 module.""",
-        'python2', PathVariable.PathAccept),
-    PathVariable(
-        'python2_array_home',
-        """If NumPy was installed using the '--home' option, set this to the home
-           directory for NumPy for Python 2.""",
-        '', PathVariable.PathAccept),
-    PathVariable(
-        'python2_prefix',
-        """Use this option if you want to install the Cantera Python 2 package to
-           an alternate location. On Unix-like systems, the default is the same
-           as the 'prefix' option. If the 'python_prefix' option is set to
-           the empty string or the 'prefix' option is not set, then the package
-           will be installed to the system default 'site-packages' directory.
-           To install to the current user's 'site-packages' directory, use
-           'python2_prefix=USER'.""",
-        defaults.python_prefix, PathVariable.PathAccept),
     EnumVariable(
         'python3_package',
-        """Controls whether or not the Python 3 module will be built. By
-           default, the module will be built if the Python 3 interpreter
-           and the required dependencies (NumPy for Python 3 and Cython
-           for the version of Python for which SCons is installed) can be
-           found.""",
+        """Deprecated synonym for the 'python_package' option. Will be overridden
+        if 'python_package' is set.""",
         'default', ('full', 'minimal', 'y', 'n', 'none', 'default')),
     PathVariable(
         'python3_cmd',
-        """The path to the Python 3 interpreter. The default is
-           'python3'; if this executable cannot be found, this
-           value must be specified to build the Python 3 module.""",
-        'python3', PathVariable.PathAccept),
-    PathVariable(
-        'python3_array_home',
-        """If NumPy was installed using the '--home' option, set this to the home
-           directory for NumPy for Python 3.""",
-        '', PathVariable.PathAccept),
+        """Deprecated synonym for the 'python_cmd' option. Will be overridden
+           if 'python_cmd' is set.""",
+        sys.executable, PathVariable.PathAccept),
     PathVariable(
         'python3_prefix',
-        """Use this option if you want to install the Cantera Python 3 package to
-           an alternate location. On Unix-like systems, the default is the same
-           as the 'prefix' option. If the 'python_prefix' option is set to
-           the empty string or the 'prefix' option is not set, then the package
-           will be installed to the system default 'site-packages' directory.
-           To install to the current user's 'site-packages' directory, use
-           'python3_prefix=USER'.""",
+        """Deprecated synonym for the 'python_prefix' option. Will be overridden
+           if 'python_prefix' is set.""",
         defaults.python_prefix, PathVariable.PathAccept),
-    EnumVariable(
+     EnumVariable(
         'matlab_toolbox',
         """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'
@@ -482,6 +449,14 @@ config_options = [
            ('y'), from a Git submodule ('n'), or to decide automatically
            ('default').""",
         'default', ('default', 'y', 'n')),
+    EnumVariable(
+        'system_yamlcpp',
+        """Select whether to use the yaml-cpp library from a system installation
+           ('y'), from a Git submodule ('n'), or to decide automatically
+           ('default'). If yaml-cpp is not installed directly into system
+           include and library directories, then you will need to add those
+           directories to 'extra_inc_dirs' and 'extra_lib_dirs'.""",
+        'default', ('default', 'y', 'n')),
     EnumVariable(
         'system_sundials',
         """Select whether to use SUNDIALS from a system installation ('y'), from
@@ -509,7 +484,8 @@ config_options = [
            Cantera will use Eigen for linear algebra support. To use BLAS
            and LAPACK, set 'blas_lapack_libs' to the the list of libraries
            that should be passed to the linker, separated by commas, e.g.,
-           "lapack,blas" or "lapack,f77blas,cblas,atlas".""",
+           "lapack,blas" or "lapack,f77blas,cblas,atlas". Eigen is required
+           whether or not BLAS/LAPACK are used.""",
         ''),
     PathVariable(
         'blas_lapack_dir',
@@ -655,11 +631,16 @@ config_options = [
     BoolVariable(
         'versioned_shared_library',
         """If enabled, create a versioned shared library, with symlinks to the
-           more generic library name, e.g. 'libcantera_shared.so.2.4.0' as the
+           more generic library name, e.g. 'libcantera_shared.so.2.5.0' as the
            actual library and 'libcantera_shared.so' and 'libcantera_shared.so.2'
            as symlinks.
            """,
         defaults.versionedSharedLibrary),
+    BoolVariable(
+        'use_rpath_linkage',
+        """If enabled, link to all shared libraries using 'rpath', i.e., a fixed
+           run-time search path for dynamic library loading.""",
+        True),
     EnumVariable(
         'layout',
         """The layout of the directory structure. 'standard' installs files to
@@ -669,13 +650,23 @@ config_options = [
            files in the subdirectory defined by 'prefix'. This layout is best
            with a prefix like '/opt/cantera'. 'debian' installs to the stage
            directory in a layout used for generating Debian packages.""",
-        defaults.fsLayout, ('standard','compact','debian')),
+        defaults.fsLayout, ('standard','compact','debian'))
 ]
 
 opts.AddVariables(*config_options)
 opts.Update(env)
 opts.Save('cantera.conf', env)
 
+# Expand ~/ and environment variables used in cantera.conf (variables used on
+# the command line will be expanded by the shell)
+for option in opts.keys():
+    original = env[option]
+    if isinstance(original, str):
+        modified = os.path.expandvars(os.path.expanduser(env[option]))
+        if original != modified:
+            print('INFO: Expanding {!r} to {!r}'.format(original, modified))
+            env[option] = modified
+
 if 'help' in COMMAND_LINE_TARGETS:
     ### Print help about configuration options and exit.
     print("""
@@ -717,7 +708,7 @@ for arg in ARGUMENTS:
         sys.exit(1)
 
 # Require a StrictVersion-compatible version
-env['cantera_version'] = "2.4.0"
+env['cantera_version'] = "2.5.0a3"
 ctversion = StrictVersion(env['cantera_version'])
 # For use where pre-release tags are not permitted (MSI, sonames)
 env['cantera_pure_version'] = '.'.join(str(x) for x in ctversion.version)
@@ -738,6 +729,11 @@ print()
 # *** Configure system-specific properties ***
 # ********************************************
 
+# Prevent setting prefix for Cantera installation to source directory
+if os.path.abspath(env['prefix']) == Dir('.').abspath:
+    print('ERROR: cannot install Cantera into source directory.')
+    exit(1)
+
 # Copy in external environment variables
 if env['env_vars'] == 'all':
     env['ENV'].update(os.environ)
@@ -762,6 +758,9 @@ env['extra_lib_dirs'] = [d for d in env['extra_lib_dirs'].split(':') if d]
 env.Append(CPPPATH=env['extra_inc_dirs'],
            LIBPATH=env['extra_lib_dirs'])
 
+if env['use_rpath_linkage']:
+    env.Append(RPATH=env['extra_lib_dirs'])
+
 if env['CC'] == 'cl':
     # embed manifest file
     env['LINKCOM'] = [env['LINKCOM'],
@@ -774,6 +773,8 @@ if env['boost_inc_dir']:
 
 if env['blas_lapack_dir']:
     env.Append(LIBPATH=[env['blas_lapack_dir']])
+    if env['use_rpath_linkage']:
+        env.Append(RPATH=env['blas_lapack_dir'])
 
 if env['system_sundials'] in ('y','default'):
     if env['sundials_include']:
@@ -782,6 +783,8 @@ if env['system_sundials'] in ('y','default'):
     if env['sundials_libdir']:
         env.Append(LIBPATH=[env['sundials_libdir']])
         env['system_sundials'] = 'y'
+        if env['use_rpath_linkage']:
+            env.Append(RPATH=env['sundials_libdir'])
 
 # BLAS / LAPACK configuration
 if env['blas_lapack_libs'] != '':
@@ -927,6 +930,33 @@ elif env['system_googletest'] == 'y':
 elif env['system_googletest'] == 'n':
     env['googletest'] = 'submodule'
 
+# Check for yaml-cpp library and checkout submodule if needed
+if env['system_yamlcpp'] in ('y', 'default'):
+    if conf.CheckCXXHeader('yaml-cpp/yaml.h', '""'):
+        env['system_yamlcpp'] = True
+        print("""INFO: Using system installation of yaml-cpp library.""")
+
+    elif env['system_yamlcpp'] == 'y':
+        config_error('Expected system installation of yaml-cpp library, but it '
+            'could not be found.')
+
+if env['system_yamlcpp'] in ('n', 'default'):
+    env['system_yamlcpp'] = False
+    print("""INFO: Using private installation of yaml-cpp library.""")
+    if not os.path.exists('ext/yaml-cpp/include/yaml-cpp/yaml.h'):
+        if not os.path.exists('.git'):
+            config_error('yaml-cpp is missing. Install source in ext/yaml-cpp.')
+
+        try:
+            code = subprocess.call(['git', 'submodule', 'update', '--init',
+                                    '--recursive', 'ext/yaml-cpp'])
+        except Exception:
+            code = -1
+        if code:
+            config_error('yaml-cpp submodule checkout failed.\n'
+                         'Try manually checking out the submodule with:\n\n'
+                         '    git submodule update --init --recursive ext/yaml-cpp\n')
+
 # Check for googletest and checkout submodule if needed
 if env['googletest'] in ('system', 'default'):
     has_gtest = conf.CheckCXXHeader('gtest/gtest.h', '""')
@@ -998,6 +1028,8 @@ print('INFO: Found Eigen version {}'.format(env['EIGEN_LIB_VERSION']))
 env['HAS_GLIBCXX'] = conf.CheckDeclaration('__GLIBCXX__', '#include <iostream>', 'C++')
 env['HAS_LIBCPP'] = conf.CheckDeclaration('_LIBCPP_VERSION', '#include <iostream>', 'C++')
 
+env['HAS_CLANG'] = conf.CheckDeclaration('__clang__', '', 'C++')
+
 boost_version_source = get_expression_value(['<boost/version.hpp>'], 'BOOST_LIB_VERSION')
 retcode, boost_lib_version = conf.TryRun(boost_version_source, '.cpp')
 env['BOOST_LIB_VERSION'] = '.'.join(boost_lib_version.strip().split('_'))
@@ -1005,26 +1037,35 @@ print('INFO: Found Boost version {0}'.format(env['BOOST_LIB_VERSION']))
 if not env['BOOST_LIB_VERSION']:
     config_error("Boost could not be found. Install Boost headers or set"
                  " 'boost_inc_dir' to point to the boost headers.")
+# demangle is availble in Boost 1.55 or newer
+env['has_demangle'] = conf.CheckDeclaration("boost::core::demangle",
+                                '#include <boost/core/demangle.hpp>', 'C++')
 
 import SCons.Conftest, SCons.SConf
 context = SCons.SConf.CheckContext(conf)
-ret = SCons.Conftest.CheckLib(context,
-                              ['sundials_cvodes'],
-                              header='#include "cvodes/cvodes.h"',
-                              language='C++',
-                              call='CVodeCreate(CV_BDF, CV_NEWTON);',
-                              autoadd=False,
-                              extra_libs=env['blas_lapack_libs'])
-if ret:
+
+# Check initially for Sundials<=3.2 and then for Sundials>=4.0
+for cvode_call in ['CVodeCreate(CV_BDF, CV_NEWTON);','CVodeCreate(CV_BDF);']:
+    ret = SCons.Conftest.CheckLib(context,
+                                  ['sundials_cvodes'],
+                                  header='#include "cvodes/cvodes.h"',
+                                  language='C++',
+                                  call=cvode_call,
+                                  autoadd=False,
+                                  extra_libs=env['blas_lapack_libs'])
     # CheckLib returns False to indicate success
+    if not ret:
+        if env['system_sundials'] == 'default':
+            env['system_sundials'] = 'y'
+        break
+
+# Execute if the cycle ends without 'break'
+else:
     if env['system_sundials'] == 'default':
         env['system_sundials'] = 'n'
     elif env['system_sundials'] == 'y':
         config_error('Expected system installation of Sundials, but it could '
                      'not be found.')
-elif env['system_sundials'] == 'default':
-    env['system_sundials'] = 'y'
-
 
 # Checkout Sundials submodule if needed
 if (env['system_sundials'] == 'n' and
@@ -1061,7 +1102,7 @@ if env['system_sundials'] == 'y':
 
     # Ignore the minor version, e.g. 2.4.x -> 2.4
     env['sundials_version'] = '.'.join(sundials_version.split('.')[:2])
-    if env['sundials_version'] not in ('2.4','2.5','2.6','2.7','3.0','3.1'):
+    if env['sundials_version'] not in ('2.4','2.5','2.6','2.7','3.0','3.1','3.2','4.0','4.1'):
         print("""ERROR: Sundials version %r is not supported.""" % env['sundials_version'])
         sys.exit(1)
     print("""INFO: Using system installation of Sundials version %s.""" % sundials_version)
@@ -1158,16 +1199,23 @@ if env['VERBOSE']:
 env['python_cmd_esc'] = quoted(env['python_cmd'])
 
 # Python Package Settings
+python_min_version = LooseVersion('3.3')
 cython_min_version = LooseVersion('0.23')
 numpy_min_test_version = LooseVersion('1.8.1')
 
-# If both python2_package and python3_package are set to something
-# other than the default ignore the python_package option
-if all([env['python{}_package'.format(p)] != 'default' for p in ['2', '3']]):
-    if env['python_package'] != 'default':
-        print("WARNING: Both version-specific pythonX_package options are set. Ignoring "
-              "non-version specific python_package options")
-    env['python_package'] = 'none'
+# Handle the version-specific Python package options
+python_options = (('package', 'default'),
+                  ('cmd', sys.executable),
+                  ('prefix', defaults.python_prefix))
+for option, default in python_options:
+    if env['python3_' + option] != default:
+        print("WARNING: Option 'python3_{0}' is deprecated."
+            " Use 'python_{0}' instead.".format(option))
+        if env['python_' + option] == default:
+            env['python_' + option] = env['python3_' + option]
+        else:
+            print("WARNING: Ignoring option 'python3_{0}'"
+                " because 'python_{0}' was also set.".format(option))
 
 if env['python_package'] == 'new':
     print("WARNING: The 'new' option for the Python package is "
@@ -1176,257 +1224,109 @@ if env['python_package'] == 'new':
     env['python_package'] = 'full'  # Allow 'new' as a synonym for 'full'
 elif env['python_package'] == 'y':
     env['python_package'] = 'full'  # Allow 'y' as a synonym for 'full'
-elif env['python_package'] in ['none', 'n']:
-    if env['python2_package'] == 'default':
-        env['python2_package'] = 'none'
-    if env['python3_package'] == 'default':
-        env['python3_package'] = 'none'
+elif env['python_package'] == 'n':
+  env['python_package'] = 'none'  # Allow 'n' as a synonym for 'none'
 
-for py_pkg in ['python2_package', 'python3_package']:
-    if env[py_pkg] == 'y':
-        env[py_pkg] = 'full'  # Allow 'y' as a synonym for 'full'
-    elif env[py_pkg] == 'n':
-        env[py_pkg] = 'none'  # Allow 'n' as a synonym for 'none'
+env['install_python_action'] = ''
+env['python_module_loc'] = ''
 
-if env['python_package'] in ('full', 'minimal', 'default'):
-    # If the non-specific python_package option is not none, check
-    # the version of the Python package we want to build using
-    # python_cmd
-    script = '\n'.join(["from __future__ import print_function",
-                        "import sys",
-                        "print('{v.major}.{v.minor}'.format(v=sys.version_info))"])
-
-    try:
-        env['python_version'] = getCommandOutput(env['python_cmd'], '-c', script)
-    except (OSError, subprocess.CalledProcessError) as err:
-        if env['python_package'] in ['full', 'minimal']:
-            print('ERROR: Problem checking for Python:')
-            print(err)
-            sys.exit(1)
-        else:
-            print('WARNING: Problem checking for Python:')
-            print(err)
-            print('Continuing with default parameters.')
-    else:
-        major = env['python_version'][0]
-        py_pkg = 'python{}_package'.format(major)
-        if env[py_pkg] != 'default':
-            if env['python_package'] != 'default':
-                # If python_package is default don't print a warning. If python_package has been
-                # set, warn the user that we're ignoring that option.
-                print("WARNING: The python{v}_package option has been set to {option}. All "
-                      "non-version-specific Python options (including python_cmd) have been "
-                      "ignored.".format(v=major, option=env[py_pkg]))
-        else:  # pythonX_package is 'default'
-            # This dictionary has the default values for the Python related variables
-            default_py_vars = {'python{}_array_home': '', 'python{}_cmd': 'python{}'.format(major),
-                       'python{}_prefix': '$prefix'}
-
-            env[py_pkg] = env['python_package']
-            # Check whether any Python related variables are different from the default
-            for key, value in default_py_vars.items():
-                if env[key.format(major)] != value:
-                    print("WARNING: The value for {0} has been set and will be used instead "
-                          "of {1}".format(key.format(major), key.format('')))
-                else:
-                    env[key.format(major)] = env[key.format('')]
-
-        del env['python_version']
-
-# Make sure everything gets converted to properly versioned variables by deleting
-# these so they don't get used accidentally
-del env['python_package']
-del env['python_array_home']
-del env['python_cmd']
-del env['python_prefix']
-
-require_python = any([env['python{}_package'.format(p)] == 'full' for p in ['2', '3']])
-want_python = any([env['python{}_package'.format(p)] == 'default' for p in ['2', '3']])
-
-if require_python or want_python:
-    # Check for Cython:
-    try:
-        import Cython
-        cython_version = LooseVersion(Cython.__version__)
-        assert cython_version >= cython_min_version
-    except ImportError:
-        message = "Cython could not be imported by the Python interpreter running SCons."
-        have_cython = False
-    except AssertionError:
-        message = ("Cython is an incompatible version: "
-                   "Found {0} but {1} or newer is required.".format(cython_version,
-                                                                    cython_min_version))
-        have_cython = False
-    else:
-        have_cython = True
-    finally:
-        if not have_cython:
-            if require_python:
-                print('ERROR: ' + message)
-                sys.exit(1)
-            elif want_python:
-                print('WARNING: ' + message)
-                for py_pkg in ['python{}_package'.format(p) for p in ['2', '3']]:
-                    if env[py_pkg] == 'default':
-                        env[py_pkg] = 'minimal-default'
-        else:
-            print('INFO: Using Cython version {0}.'.format(cython_version))
-
-def configure_minimal_python(py_ver):
-    # Test to see if we can run Python if the minimal interface is to be built
-    warn_no_python = False
+if env['python_package'] != 'none':
+    # Test to see if we can import numpy and Cython
     script = textwrap.dedent("""\
-        from __future__ import print_function
-        import sys
-        print('{v.major}.{v.minor}'.format(v=sys.version_info))
-    """)
-
-    try:
-        info = getCommandOutput(env['python{}_cmd'.format(py_ver)], '-c', script)
-    except OSError as err:
-        if env['VERBOSE']:
-            print('Error checking for Python {}:'.format(py_ver))
-            print(err)
-        warn_no_python = True
-    except subprocess.CalledProcessError as err:
-        if env['VERBOSE']:
-            print('Error checking for Python {}:'.format(py_ver))
-            print(err, err.output)
-        warn_no_python = True
-    else:
-        (env['python{}_version'.format(py_ver)],) = info.splitlines()[-1:]
-
-    if warn_no_python:
-        if 'default' in env['python{}_package'.format(py_ver)]:
-            print('WARNING: Not building the minimal Python {py_ver} package because the Python '
-                  '{py_ver} interpreter {interp!r} could not be '
-                  'found.'.format(py_ver=py_ver, interp=env['python{}_cmd'.format(py_ver)]))
-
-            env['python{}_package'.format(py_ver)] = 'none'
-        else:
-            print('ERROR: Could not execute the Python {py_ver} interpreter {interp!r}.'.format(
-                py_ver=py_ver, interp=env['python{}_cmd'.format(py_ver)]
-            ))
-
-            sys.exit(1)
-    else:
-        print('INFO: Building the minimal Python package for Python {0}'.format(env['python{}_version'.format(py_ver)]))
-        env['python{}_package'.format(py_ver)] = 'minimal'
-
-def configure_full_python(py_ver):
-    # Test to see if we can import numpy
-    warn_no_python = False
-    script = textwrap.dedent("""\
-        from __future__ import print_function
         import sys
         print('{v.major}.{v.minor}'.format(v=sys.version_info))
+        err = ''
         try:
             import numpy
             print(numpy.__version__)
-        except ImportError:
+        except ImportError as np_err:
             print('0.0.0')
+            err += str(np_err) + '\\n'
+        try:
+            import Cython
+            print(Cython.__version__)
+        except ImportError as cython_err:
+            print('0.0.0')
+            err += str(cython_err) + '\\n'
+        if err:
+            print(err)
     """)
 
-    if env['python{}_array_home'.format(py_ver)]:
-        script = "sys.path.append({})\n".format(env['python{}_array_home'.format(py_ver)]) + script
-
     try:
-        info = getCommandOutput(env['python{}_cmd'.format(py_ver)], '-c', script)
+        info = getCommandOutput(env['python_cmd'], '-c', script).splitlines()
     except OSError as err:
         if env['VERBOSE']:
-            print('Error checking for Python {}:'.format(py_ver))
+            print('Error checking for Python:')
             print(err)
         warn_no_python = True
     except subprocess.CalledProcessError as err:
         if env['VERBOSE']:
-            print('Error checking for Python {}:'.format(py_ver))
+            print('Error checking for Python:')
             print(err, err.output)
         warn_no_python = True
     else:
-        (env['python{}_version'.format(py_ver)], numpy_version) = info.splitlines()[-2:]
-        numpy_version = LooseVersion(numpy_version)
-        if numpy_version == LooseVersion('0.0.0'):
-            print("NumPy for Python {0} not found.".format(env['python{}_version'.format(py_ver)]))
-            warn_no_python = True
-        elif numpy_version < numpy_min_test_version:
-            print("WARNING: The installed version of Numpy for Python {0} is not tested and "
-                  "support is not guaranteed. Found {1} but {2} or newer is preferred".format(
-                      env['python{}_version'.format(py_ver)], numpy_version, numpy_min_test_version))
-        else:
-            print('INFO: Using NumPy version {0} for Python {1}.'.format(
-                numpy_version, env['python{}_version'.format(py_ver)]))
+        warn_no_python = False
+        python_version = LooseVersion(info[0])
+        numpy_version = LooseVersion(info[1])
+        cython_version = LooseVersion(info[2])
 
     if warn_no_python:
-        if env['python{}_package'.format(py_ver)] == 'default':
-            print('WARNING: Not building the full Python {py_ver} package because the Python '
-                  '{py_ver} interpreter {interp!r} could not be found or a required dependency '
-                  '(e.g. numpy) was not found.'.format(py_ver=py_ver, interp=env['python{}_cmd'.format(py_ver)]))
-
-            env['python{}_package'.format(py_ver)] = 'minimal-default'
+        if env['python_package'] == 'default':
+            print('WARNING: Not building the Python package because the Python '
+                  'interpreter {!r} could not be found'.format(env['python_cmd']))
+            env['python_package'] = 'none'
         else:
-            print('ERROR: Could not execute the Python {py_ver} interpreter {interp!r} or a required '
-                  'dependency (e.g. numpy) could not be found.'.format(py_ver=py_ver, interp=env['python{}_cmd'.format(py_ver)]))
-
+            print('ERROR: Could not execute the Python interpreter {!r}'.format(
+                env['python_cmd']))
             sys.exit(1)
+    elif env['python_package'] == 'minimal':
+        print('INFO: Building the minimal Python package for Python {}'.format(python_version))
     else:
-        print('INFO: Building the full Python package for Python {0}'.format(env['python{}_version'.format(py_ver)]))
-        env['python{}_package'.format(py_ver)] = 'full'
+        warn_no_full_package = False
+        if len(info) > 3:
+            print("WARNING: Unexpected output while checking Python / Numpy / Cython versions:")
+            print('| ' + '\n| '.join(info[3:]))
 
-for py_ver in [2, 3]:
-    env['install_python{}_action'.format(py_ver)] = ''
-    if env['python{}_package'.format(py_ver)] in ['full', 'default']:
-        configure_full_python(py_ver)
-    elif env['python{}_package'.format(py_ver)] == 'minimal':
-        configure_minimal_python(py_ver)
-        env['python{}_module_loc'.format(py_ver)] = ''
-    else:
-        env['python{}_module_loc'.format(py_ver)] = ''
+        if python_version < python_min_version:
+            print("WARNING: Python version is incompatible with the full Python module: "
+                "Found {0} but {1} or newer is required".format(
+                python_version, python_min_version))
+            warn_no_full_package = True
 
-# If we're building the full Python interface for one version of Python,
-# we probably don't want the minimal interface of the other version
-if env['python2_package'] == 'minimal-default' and env['python3_package'] == 'full':
-    env['python2_package'] = 'none'
-elif env['python3_package'] == 'minimal-default' and env['python2_package'] == 'full':
-    env['python3_package'] = 'none'
+        if numpy_version == LooseVersion('0.0.0'):
+            print("NumPy not found.")
+            warn_no_full_package = True
+        elif numpy_version < numpy_min_test_version:
+            print("WARNING: The installed version of Numpy is not tested and "
+                  "support is not guaranteed. Found {0} but {1} or newer is preferred".format(
+                  numpy_version, numpy_min_test_version))
+        else:
+            print('INFO: Using NumPy version {0}.'.format(numpy_version))
 
-# 'minimal-default' means that something was wrong with Python or NumPy
-# such that the full interface for that version of Python can't be built
-# and the pythonX_package option wasn't supplied by the user. Check to see
-# if the minimal package should be built
-if env['python2_package'] == 'minimal-default':
-    configure_minimal_python(2)
-if env['python3_package'] == 'minimal-default':
-    configure_minimal_python(3)
+        if cython_version == LooseVersion('0.0.0'):
+            print("Cython not found.")
+            warn_no_full_package = True
+        elif cython_version < cython_min_version:
+            print("WARNING: Cython is an incompatible version: "
+                  "Found {0} but {1} or newer is required.".format(
+                    cython_version, cython_min_version))
+            warn_no_full_package = True
+        else:
+            print('INFO: Using Cython version {0}.'.format(cython_version))
 
-for py_ver in [2, 3]:
-    if env['python{}_package'.format(py_ver)] != 'none':
-        # The directory within the source tree which will contain the Python module
-        env['pythonpath_build{}'.format(py_ver)] = Dir('build/python{}'.format(py_ver)).abspath
-        if 'PYTHONPATH' in env['ENV']:
-            env['pythonpath_build{}'.format(py_ver)] += os.path.pathsep + env['ENV']['PYTHONPATH']
-
-# Check for 3to2. See http://pypi.python.org/pypi/3to2
-# Only needed for Python 2 package
-if env['python2_package'] == 'full':
-    script = textwrap.dedent("""\
-        from lib3to2.main import main
-        print(main('lib3to2.fixes', ['-l']))
-    """)
-    try:
-        ret = getCommandOutput(env['python2_cmd'], '-c', script)
-    except (OSError, subprocess.CalledProcessError) as err:
-        if env['VERBOSE']:
-            print('Error checking for 3to2:')
-            print(err)
-        ret = ''
-    if 'print' in ret:
-        env['python_convert_examples'] = True
-    else:
-        env['python_convert_examples'] = False
-        print("WARNING: Couldn't find the 3to2 package. "
-              "Python 2 examples will not work correctly.")
-else:
-    env['python_convert_examples'] = False
+        if warn_no_full_package:
+            if env['python_package'] == 'default':
+                print('WARNING: Unable to build the full Python package because compatible '
+                    'versions of Python, Numpy, and Cython could not be found.')
+                print('INFO: Building the minimal Python package for Python {}'.format(python_version))
+                env['python_package'] = 'minimal'
+            else:
+                print('ERROR: Unable to build the full Python package because compatible '
+                    'versions of Python, Numpy, and Cython could not be found.')
+                sys.exit(1)
+        else:
+            print('INFO: Building the full Python package for Python {0}'.format(python_version))
+            env['python_package'] = 'full'
 
 # Matlab Toolbox settings
 if env['matlab_path'] != '' and env['matlab_toolbox'] == 'default':
@@ -1465,12 +1365,6 @@ if env['matlab_toolbox'] == 'y':
 # *** Set additional configuration variables ***
 # **********************************************
 
-# Some distributions (e.g. Fedora/RHEL) use 'lib64' instead of 'lib' on 64-bit systems
-if any(name.startswith('/usr/lib64/python') for name in sys.path):
-    env['libdirname'] = 'lib64'
-else:
-    env['libdirname'] = 'lib'
-
 # On Debian-based systems, need to special-case installation to
 # /usr/local because of dist-packages vs site-packages
 env['debian'] = any(name.endswith('dist-packages') for name in sys.path)
@@ -1518,12 +1412,11 @@ addInstallActions = ('install' in COMMAND_LINE_TARGETS or
 if env['stage_dir']:
     instRoot = pjoin(os.getcwd(), env['stage_dir'],
                      stripDrive(env['prefix']).strip('/\\'))
-    for k in ('python2_prefix', 'python3_prefix'):
-        if env[k]:
-            env[k] = pjoin(os.getcwd(), env['stage_dir'],
-                           stripDrive(env[k]).strip('/\\'))
-        else:
-            env[k] = pjoin(os.getcwd(), env['stage_dir'])
+    if env['python_prefix']:
+        env['python_prefix'] = pjoin(os.getcwd(), env['stage_dir'],
+                       stripDrive(env['python_prefix']).strip('/\\'))
+    else:
+        env['python_prefix'] = pjoin(os.getcwd(), env['stage_dir'])
 else:
     instRoot = env['prefix']
 
@@ -1544,8 +1437,7 @@ if env['layout'] == 'debian':
                                    env['libdirname'], 'cantera', 'matlab', 'toolbox')
 
     env['inst_python_bindir'] = pjoin(base, 'cantera-python', 'usr', 'bin')
-    env['python2_prefix'] = pjoin(base, 'cantera-python')
-    env['python3_prefix'] = pjoin(base, 'cantera-python3')
+    env['python_prefix'] = pjoin(base, 'cantera-python3')
 else:
     env['inst_libdir'] = pjoin(instRoot, env['libdirname'])
     env['inst_bindir'] = pjoin(instRoot, 'bin')
@@ -1586,7 +1478,9 @@ def cdefine(definevar, configvar, comp=True, value=1):
 # Need to test all of these to see what platform.system() returns
 configh['SOLARIS'] = 1 if env['OS'] == 'Solaris' else None
 configh['DARWIN'] = 1 if env['OS'] == 'Darwin' else None
-cdefine('NEEDS_GENERIC_TEMPL_STATIC_DECL', 'OS', 'Solaris')
+
+if env['OS'] == 'Solaris' or env['HAS_CLANG']:
+    configh['NEEDS_GENERIC_TEMPL_STATIC_DECL'] = 1
 
 configh['CT_SUNDIALS_VERSION'] = env['sundials_version'].replace('.','')
 
@@ -1602,6 +1496,8 @@ cdefine('LAPACK_NAMES_LOWERCASE', 'lapack_names', 'lower')
 cdefine('CT_USE_LAPACK', 'use_lapack')
 cdefine('CT_USE_SYSTEM_EIGEN', 'system_eigen')
 cdefine('CT_USE_SYSTEM_FMT', 'system_fmt')
+cdefine('CT_USE_SYSTEM_YAMLCPP', 'system_yamlcpp')
+cdefine('CT_USE_DEMANGLE', 'has_demangle')
 
 config_h_build = env.Command('build/src/config.h.build',
                              'include/cantera/base/config.h.in',
@@ -1667,20 +1563,58 @@ for cti in mglob(env, 'data/inputs', 'cti'):
     build(env.Command('build/data/%s' % outName, cti.path,
                       '$python_cmd_esc interfaces/cython/cantera/ctml_writer.py $SOURCE $TARGET'))
 
-
-# Copy input files which are not present as cti:
+# Copy XML input files which are not present as cti:
 for xml in mglob(env, 'data/inputs', 'xml'):
     dest = pjoin('build','data',xml.name)
     if xml.name not in convertedInputFiles:
         build(env.Command(dest, xml.path, Copy('$TARGET', '$SOURCE')))
 
+# Convert input files from Chemkin format to YAML
+ck_sources = [
+    dict(output='gri30.yaml', input='data/inputs/gri30.inp',
+         thermo='data/thermo/gri30_thermo.dat',
+         transport='data/transport/gri30_tran.dat',
+         phase='gri30'),
+    dict(output='air.yaml', input='data/inputs/air.inp',
+         transport='data/transport/gri30_tran.dat',
+         phase='air'),
+    dict(output='airNASA9.yaml', input='data/inputs/airNASA9.inp',
+         thermo='data/thermo/airDataNASA9.dat',
+         phase='airNASA9'),
+    dict(output='h2o2.yaml', input='data/inputs/h2o2.inp',
+         transport='data/transport/gri30_tran.dat',
+         phase='ohmech'),
+    dict(output='silane.yaml', input='data/inputs/silane.inp')
+]
+
+for mech in ck_sources:
+    convertedInputFiles.add(mech['output'])
+    cmd = ('$python_cmd_esc interfaces/cython/cantera/ck2yaml.py'
+           ' --quiet --no-validate --input=$SOURCE --output=$TARGET')
+    if 'thermo' in mech:
+        cmd += ' --thermo=' + mech['thermo']
+    if 'transport' in mech:
+        cmd += ' --transport=' + mech['transport']
+    if 'phase' in mech:
+        cmd += ' --name=' + mech['phase']
+    b = build(env.Command('build/data/{}'.format(mech['output']), mech['input'], cmd))
+    env.Depends(b, 'interfaces/cython/cantera/ck2yaml.py')
+
+# preprocess input files (cti -> yaml)
+for cti in mglob(env, 'data/inputs', 'cti'):
+    outName = os.path.splitext(cti.name)[0] + '.yaml'
+    if outName not in convertedInputFiles:
+        b = build(env.Command('build/data/{}'.format(outName), cti.path,
+                              '$python_cmd_esc interfaces/cython/cantera/cti2yaml.py $SOURCE $TARGET'))
+        env.Depends(b, 'interfaces/cython/cantera/cti2yaml.py')
+
 if addInstallActions:
     # Put headers in place
     headerBase = 'include/cantera'
     install(env.RecursiveInstall, '$inst_incdir', 'include/cantera')
 
     # Data files
-    install('$inst_datadir', mglob(env, 'build/data', 'cti', 'xml'))
+    install('$inst_datadir', mglob(env, 'build/data', 'cti', 'xml', 'yaml'))
 
 
 ### List of libraries needed to link to Cantera ###
@@ -1704,6 +1638,10 @@ else:
 linkLibs.extend(env['sundials_libs'])
 linkSharedLibs.extend(env['sundials_libs'])
 
+if env['system_yamlcpp']:
+    linkLibs.append('yaml-cpp')
+    linkSharedLibs.append('yaml-cpp')
+
 #  Add LAPACK and BLAS to the link line
 if env['blas_lapack_libs']:
     linkLibs.extend(env['blas_lapack_libs'])
@@ -1730,10 +1668,9 @@ if env['f90_interface'] == 'y':
 VariantDir('build/src', 'src', duplicate=0)
 SConscript('build/src/SConscript')
 
-if env['python3_package'] == 'full' or env['python2_package'] == 'full':
+if env['python_package'] == 'full':
     SConscript('interfaces/cython/SConscript')
-
-if env['python3_package'] == 'minimal' or env['python2_package'] == 'minimal':
+elif env['python_package'] == 'minimal':
     SConscript('interfaces/python_minimal/SConscript')
 
 if env['CC'] != 'cl':
@@ -1804,17 +1741,15 @@ def postInstallMessage(target, source, env):
           samples                     {ct_sampledir!s}
           data files                  {ct_datadir!s}""".format(**env_dict))
 
-    if env['python2_package'] == 'full':
-        env['python2_example_loc'] = pjoin(env['python2_module_loc'], 'cantera', 'examples')
+    if env['sphinx_docs'] or env['doxygen_docs']:
         install_message += indent(textwrap.dedent("""
-            Python 2 package (cantera)  {python2_module_loc!s}
-            Python 2 samples            {python2_example_loc!s}""".format(**env_dict)), '  ')
+            HTML documentation          {inst_docdir!s}""".format(**env_dict)), '  ')
 
-    if env['python3_package'] == 'full':
-        env['python3_example_loc'] = pjoin(env['python3_module_loc'], 'cantera', 'examples')
+    if env['python_package'] == 'full':
+        env['python_example_loc'] = pjoin(env['python_module_loc'], 'cantera', 'examples')
         install_message += indent(textwrap.dedent("""
-            Python 3 package (cantera)  {python3_module_loc!s}
-            Python 3 samples            {python3_example_loc!s}""".format(**env_dict)), '  ')
+            Python package (cantera)    {python_module_loc!s}
+            Python samples              {python_example_loc!s}""".format(**env_dict)), '  ')
 
     if env['matlab_toolbox'] == 'y':
         env['matlab_sample_loc'] = pjoin(env['ct_sampledir'], 'matlab')
@@ -1866,26 +1801,22 @@ def getParentDirs(path, top=True):
 # Files installed by SCons
 allfiles = FindInstalledFiles()
 
-# Files installed by the Python installer(s)
-pyFiles = ['build/python2-installed-files.txt',
-           'build/python3-installed-files.txt']
+# Files installed by the Python installer
+if os.path.exists('build/python-installed-files.txt'):
+    with open('build/python-installed-files.txt', 'r') as f:
+        file_list = f.readlines()
 
-for filename in pyFiles:
-    if os.path.exists(filename):
-        with open(filename, 'r') as f:
-            file_list = f.readlines()
-
-        install_base = os.path.dirname(file_list[0].strip())
-        if os.path.exists(install_base):
-            not_listed_files = [s for s in os.listdir(install_base) if not any(s in j for j in file_list)]
-            for f in not_listed_files:
-                f = pjoin(install_base, f)
-                if not os.path.isdir(f) and os.path.exists(f):
-                    allfiles.append(File(f))
-        for f in file_list:
-            f = f.strip()
+    install_base = os.path.dirname(file_list[0].strip())
+    if os.path.exists(install_base):
+        not_listed_files = [s for s in os.listdir(install_base) if not any(s in j for j in file_list)]
+        for f in not_listed_files:
+            f = pjoin(install_base, f)
             if not os.path.isdir(f) and os.path.exists(f):
                 allfiles.append(File(f))
+    for f in file_list:
+        f = f.strip()
+        if not os.path.isdir(f) and os.path.exists(f):
+            allfiles.append(File(f))
 
 # After removing files (which SCons keeps track of),
 # remove any empty directories (which SCons doesn't track)
@@ -1938,13 +1869,13 @@ if any(target.startswith('test') for target in COMMAND_LINE_TARGETS):
     env['testNames'] = []
     env['test_results'] = env.Command('test_results', [], testResults.printReport)
 
-    if env['python2_package'] == 'none' and env['python3_package'] == 'none':
+    if env['python_package'] == 'none':
         # copy scripts from the full Cython module
-        test_py_int = env.Command('#build/python_minimal/cantera/__init__.py',
+        test_py_int = env.Command('#build/python_local/cantera/__init__.py',
                                   '#interfaces/python_minimal/cantera/__init__.py',
                                   Copy('$TARGET', '$SOURCE'))
         for script in ['ctml_writer', 'ck2cti']:
-            s = env.Command('#build/python_minimal/cantera/{}.py'.format(script),
+            s = env.Command('#build/python_local/cantera/{}.py'.format(script),
                             '#interfaces/cython/cantera/{}.py'.format(script),
                             Copy('$TARGET', '$SOURCE'))
             env.Depends(test_py_int, s)
@@ -1952,6 +1883,11 @@ if any(target.startswith('test') for target in COMMAND_LINE_TARGETS):
         env.Depends(env['test_results'], test_py_int)
 
         env['python_cmd'] = sys.executable
+        env.PrependENVPath('PYTHONPATH', Dir('build/python_local').abspath)
+    else:
+        env.PrependENVPath('PYTHONPATH', Dir('build/python').abspath)
+
+    env['ENV']['PYTHON_CMD'] = env.subst('$python_cmd')
 
     # Tests written using the gtest framework, the Python unittest module,
     # or the Matlab xunit package.

appveyor.yml

@@ -1,23 +1,22 @@
 version: 1.0.{build}
 install:
 - ps: |
-    C:\Python27-x64\python.exe -m pip install --no-cache-dir --upgrade pip
-    C:\Python27-x64\python.exe -m pip install --upgrade setuptools
-    C:\Python27-x64\python.exe -m pip install --upgrade --no-warn-script-location wheel
-    C:\Python27-x64\Scripts\pip.exe install scons
-    C:\Python27-x64\Scripts\pip.exe install --no-cache-dir --no-warn-script-location numpy
-    C:\Python27-x64\Scripts\pip.exe install --no-warn-script-location cython
-    C:\Python27-x64\Scripts\pip.exe install 3to2
-    C:\Python27-x64\Scripts\pip.exe install pypiwin32
-    C:\Python35-x64\python.exe -m pip install --no-cache-dir --upgrade pip
-    C:\Python35-x64\Scripts\pip.exe install --no-cache-dir --no-warn-script-location numpy
+    C:\Python37-x64\python.exe -m pip install --no-cache-dir --upgrade pip
+    C:\Python37-x64\python.exe -m pip install --upgrade setuptools
+    C:\Python37-x64\python.exe -m pip install --upgrade --no-warn-script-location wheel
+    C:\Python37-x64\Scripts\pip.exe install scons==3.0.1
+    C:\Python37-x64\Scripts\pip.exe install --no-cache-dir --no-warn-script-location numpy
+    C:\Python37-x64\Scripts\pip.exe install --no-warn-script-location cython
+    C:\Python37-x64\Scripts\pip.exe install pypiwin32
+    C:\Python37-x64\Scripts\pip.exe install ruamel.yaml
 
 build_script:
-- cmd: C:\Python27-x64\Scripts\scons build -j2 boost_inc_dir=C:\Libraries\boost_1_62_0 debug=n VERBOSE=y python3_cmd=C:\Python35-x64\python.exe
+- cmd: C:\Python37-x64\Scripts\scons build -j2 boost_inc_dir=C:\Libraries\boost_1_62_0 debug=n VERBOSE=y python_package=full
+- cmd: C:\Python37-x64\Scripts\scons samples
 
 test_script:
 - ps: |
-    C:\Python27-x64\Scripts\scons test
+    C:\Python37-x64\Scripts\scons test
     $sconsstatus = $lastexitcode
     $wc = New-Object 'System.Net.WebClient'
     $wc.UploadFile("https://ci.appveyor.com/api/testresults/junit/$($env:APPVEYOR_JOB_ID)", (Resolve-Path .\test\work\gtest-general.xml))

data/inputs/air.inp

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

data/inputs/airNASA9.xml

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

data/inputs/diamond.cti

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

data/inputs/gri30.cti

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

data/inputs/gri30.inp

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

data/inputs/gri30_highT.cti

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

data/inputs/gri30_ion.cti

@@ -57,7 +57,7 @@ species(name = "O2",
              ),
     transport = gas_transport(
                      geom = "linear",
-                     diam =     3.46,
+                     diam =     3.458,
                      well_depth =   107.40,
                      polar =     1.131,
                      rot_relax =     3.80),
@@ -76,9 +76,9 @@ species(name = "H2O",
              ),
     transport = gas_transport(
                      geom = "nonlinear",
-                     diam =     2.60,
+                     diam =     2.605,
                      well_depth =   572.40,
-                     dipole =     1.84,
+                     dipole =     1.844,
                      polar = 1.053,
                      rot_relax =     4.00),
     note = "L 8/89"
@@ -96,7 +96,7 @@ 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),
@@ -134,7 +134,7 @@ 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),
@@ -153,7 +153,7 @@ 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),

data/inputs/lithium_ion_battery.cti

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

data/inputs/sofc.cti

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

data/thermo/gri30_thermo.dat

@@ -0,0 +1,222 @@
+THERMO
+   300.000  1000.000  5000.000
+! GRI-Mech Version 3.0 Thermodynamics released 7/30/99
+! NASA Polynomial format for CHEMKIN-II
+! see README file for disclaimer
+O                 L 1/90O   1               G   200.000  3500.000  1000.000    1
+ 2.56942078E+00-8.59741137E-05 4.19484589E-08-1.00177799E-11 1.22833691E-15    2
+ 2.92175791E+04 4.78433864E+00 3.16826710E+00-3.27931884E-03 6.64306396E-06    3
+-6.12806624E-09 2.11265971E-12 2.91222592E+04 2.05193346E+00                   4
+O2                TPIS89O   2               G   200.000  3500.000  1000.000    1
+ 3.28253784E+00 1.48308754E-03-7.57966669E-07 2.09470555E-10-2.16717794E-14    2
+-1.08845772E+03 5.45323129E+00 3.78245636E+00-2.99673416E-03 9.84730201E-06    3
+-9.68129509E-09 3.24372837E-12-1.06394356E+03 3.65767573E+00                   4
+H                 L 7/88H   1               G   200.000  3500.000  1000.000    1
+ 2.50000001E+00-2.30842973E-11 1.61561948E-14-4.73515235E-18 4.98197357E-22    2
+ 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               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          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          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          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          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               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          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          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          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          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          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          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          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     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     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     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   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     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          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          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          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          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          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          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     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   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   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   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     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     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               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          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          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          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          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          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          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          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
+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     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          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   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
+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          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          G   300.000  5000.000  1000.000    1
+ 0.77026987E+01 0.16044203E-01-0.52833220E-05 0.76298590E-09-0.39392284E-13    2
+ 0.82984336E+04-0.15480180E+02 0.10515518E+01 0.25991980E-01 0.23800540E-05    3
+-0.19609569E-07 0.93732470E-11 0.10631863E+05 0.21122559E+02                   4
+CH3CHO            L 8/88C   2H   4O   1     G   200.000  6000.000  1000.000    1
+ 0.54041108E+01 0.11723059E-01-0.42263137E-05 0.68372451E-09-0.40984863E-13    2
+-0.22593122E+05-0.34807917E+01 0.47294595E+01-0.31932858E-02 0.47534921E-04    3
+-0.57458611E-07 0.21931112E-10-0.21572878E+05 0.41030159E+01                   4
+CH2CHO            SAND86O   1H   3C   2     G   300.000  5000.000  1000.000    1
+ 0.05975670E+02 0.08130591E-01-0.02743624E-04 0.04070304E-08-0.02176017E-12    2
+ 0.04903218E+04-0.05045251E+02 0.03409062E+02 0.10738574E-01 0.01891492E-04    3
+-0.07158583E-07 0.02867385E-10 0.15214766E+04 0.09558290E+02                   4
+END
+
+
+
+

doc/SConscript

@@ -144,8 +144,7 @@ if localenv['sphinx_docs']:
         '1D/@Domain1D': ['1D/AxiStagnFlow.m', '1D/AxisymmetricFlow.m',
                          '1D/Inlet.m', '1D/Outlet.m', '1D/OutletRes.m',
                          '1D/Surface.m', '1D/SymmPlane.m'],
-        '1D/@Stack': ['1D/FreeFlame.m', '1D/npflame_init.m',
-                      '1D/CounterFlowDiffusionFlame.m'],
+        '1D/@Stack': ['1D/FreeFlame.m', '1D/CounterFlowDiffusionFlame.m'],
         '@Interface': ['importEdge.m', 'importInterface.m'],
         '@Data': ['gasconstant.m', 'oneatm.m'],
         '@Utilities': ['adddir.m', 'ck2cti.m', 'cleanup.m', 'geterr.m',
@@ -206,3 +205,5 @@ if localenv['sphinx_docs']:
         localenv.Depends(sphinxdocs, c)
 
     localenv.AlwaysBuild(sphinxdocs)
+    install(localenv.RecursiveInstall, '$inst_docdir/sphinx/html',
+            '#/build/docs/sphinx/html')

doc/doxygen/Doxyfile

@@ -34,7 +34,7 @@ PROJECT_NAME           = Cantera
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 2.4.0
+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.

doc/sphinx/_templates/layout.html

@@ -10,20 +10,24 @@ 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 %}
-    <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
+    {%- 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" integrity="sha384-Smlep5jCw/wG7hdkwQ/Z5nLIefveQRIY9nfy6xoR1uRYBtpZgI6339F5dgvm/e9B" crossorigin="anonymous" />
+  <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) }}" type="text/css"{% if css.title is not none %} title="{{ css.title }}"{% endif %} />
+  <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) }}" type="text/css" />
+  <link rel="stylesheet" href="{{ pathto(css, 1) }}" media="none" onload="this.media='all'" type="text/css" />
     {%- endif %}
   {%- endfor %}
 {%- endmacro %}
@@ -90,10 +94,10 @@ lang="en">
                 <a href="/install/index.html" class="nav-link">Install</a>
               </li>
               <li class="nav-item">
-                <a href="/examples/index.html" class="nav-link">Examples</a>
+                <a href="/tutorials/index.html" class="nav-link">Tutorials</a>
               </li>
               <li class="nav-item">
-                <a href="/about.html" class="nav-link">About</a>
+                <a href="/examples/index.html" class="nav-link">Examples</a>
               </li>
               <li class="nav-item">
                 <a href="/community.html" class="nav-link">Community</a>
@@ -152,7 +156,7 @@ lang="en">
       </div>
   </div>
 
-  <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.3/umd/popper.min.js" integrity="sha256-98vAGjEDGN79TjHkYWVD4s87rvWkdWLHPs5MC3FvFX4=" crossorigin="anonymous"></script>
-  <script 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>
+  <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

@@ -1,5 +1,5 @@
 <div id="numfocus">
 <h3>Donate to Cantera</h3>
-<a href="https://www.flipcause.com/secure/cause_pdetails/Mjk3MjU=">
+<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/conf.py

@@ -16,10 +16,7 @@ import sys, os, re
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-if sys.version_info[0] == 3:
-    sys.path.insert(0, os.path.abspath('../../build/python3'))
-else:
-    sys.path.insert(0, os.path.abspath('../../build/python2'))
+sys.path.insert(0, os.path.abspath('../../build/python'))
 
 sys.path.append(os.path.abspath('.'))
 sys.path.append(os.path.abspath('./exts'))
@@ -99,9 +96,6 @@ release = re.search('CANTERA_VERSION "(.*?)"', configh).group(1)
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = []
-if sys.version_info[0] == 3:
-    exclude_patterns.append('python/*')
-
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 default_role = 'py:obj'

doc/sphinx/cti/classes.rst

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

doc/sphinx/index.rst

@@ -11,6 +11,7 @@ format.
 .. toctree::
    :maxdepth: 2
 
+   yaml/index
    cti/classes
    cython/index
    matlab/index

doc/sphinx/yaml/elements.rst

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

doc/sphinx/yaml/general.rst

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

doc/sphinx/yaml/index.rst

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

doc/sphinx/yaml/phases.rst

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

doc/sphinx/yaml/reactions.rst

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

doc/sphinx/yaml/species.rst

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

ext/SConscript

@@ -82,10 +82,29 @@ if env['system_sundials'] == 'n':
         libraryTargets.extend(localenv.SharedObject(
             [f for f in mglob(localenv, 'sundials/src/'+subdir, 'c')]))
 
+if not env['system_yamlcpp']:
+    localenv = prep_default(env)
+    localenv.Prepend(CPPPATH=Dir('#include/cantera/ext'))
+    license_files.append(('YAML-CPP', 'yaml-cpp/LICENSE'))
+
+    # Copy header files into common include directory
+    for subdir in ('', 'contrib', 'node', 'node/detail'):
+        for header in mglob(env, 'yaml-cpp/include/yaml-cpp/'+subdir, 'h'):
+            h = build(localenv.Command('#include/cantera/ext/yaml-cpp/{}/{}'.format(subdir, header.name),
+                                       '#ext/yaml-cpp/include/yaml-cpp/{}/{}'.format(subdir, header.name),
+                                       Copy('$TARGET', '$SOURCE')))
+
+    # Compile yaml-cpp source files
+    for subdir in ('', 'contrib'):
+        libraryTargets.extend(localenv.SharedObject(
+            [f for f in mglob(localenv, 'yaml-cpp/src/'+subdir, 'cpp')]))
+
+
 if not env['system_eigen']:
     license_files.append(('Eigen', 'eigen/COPYING.MPL2'))
-    build(copyenv.Command('#include/cantera/ext/Eigen', '#ext/eigen/Eigen',
-                          Copy('$TARGET', '$SOURCE')))
+    h = build(copyenv.Command('#include/cantera/ext/Eigen', '#ext/eigen/Eigen',
+                              Copy('$TARGET', '$SOURCE')))
+    copyenv.Depends(copyenv['config_h_target'], h)
 
 # Google Test: Used internally for Cantera unit tests.
 if env['googletest'] == 'submodule':

ext/yaml-cpp

@@ -0,0 +1 @@
+Subproject commit 012269756149ae99745b6dafefd415843d7420bb

include/cantera/Edge.h

@@ -1,11 +1,13 @@
 //! @file Edge.h
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CXX_EDGE
 #define CXX_EDGE
 
+#pragma message("warning: Edge.h is deprecated and will be removed after Cantera 2.5.0.")
+
 #include "thermo/ThermoFactory.h"
 #include "kinetics/importKinetics.h"
 #include "kinetics/EdgeKinetics.h"
@@ -15,6 +17,10 @@ namespace Cantera
 {
 
 //! Convenience class which inherits from both EdgePhase and EdgeKinetics
+/*!
+ * @deprecated To be removed after Cantera 2.5.0.
+ *             Replaceable with Solution and/or EdgePhase/EdgeKinetics.
+ */
 class Edge :
     public EdgePhase, public EdgeKinetics
 {
@@ -22,6 +28,9 @@ public:
     Edge(const std::string& infile, std::string id, std::vector<ThermoPhase*> phases)
         : m_ok(false), m_r(0)
     {
+        warn_deprecated("class Metal",
+            "To be removed after Cantera 2.5.0. "
+            "Replaceable with Solution and/or EdgePhase/EdgeKinetics.");
         m_r = get_XML_File(infile);
         if (id == "-") {
             id = "";

include/cantera/IdealGasMix.h

@@ -1,11 +1,13 @@
 //! @file IdealGasMix.h
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CXX_IDEALGASMIX
 #define CXX_IDEALGASMIX
 
+#pragma message("warning: IdealGasMix.h is deprecated and will be removed after Cantera 2.5.")
+
 #include "thermo/IdealGasPhase.h"
 #include "kinetics/GasKinetics.h"
 #include "kinetics/importKinetics.h"
@@ -15,6 +17,10 @@ namespace Cantera
 {
 
 //! Convenience class which inherits from both IdealGasPhase and GasKinetics
+/*!
+ * @deprecated To be removed after Cantera 2.5.
+ *             Replaceable with Solution and/or IdealGasPhase/GasKinetics.
+ */
 class IdealGasMix :
     public IdealGasPhase,
     public GasKinetics
@@ -25,6 +31,9 @@ public:
     IdealGasMix(const std::string& infile, std::string id_="") :
         m_ok(false), m_r(0)
     {
+        warn_deprecated("class IdealGasMix",
+            "To be removed after Cantera 2.5. "
+            "Replaceable with Solution and/or IdealGasPhase/GasKinetics.");
         m_r = get_XML_File(infile);
         m_id = id_;
         if (id_ == "-") {
@@ -38,12 +47,18 @@ public:
 
     IdealGasMix(XML_Node& root,
                 std::string id_) : m_ok(false), m_r(&root), m_id(id_) {
+        warn_deprecated("class IdealGasMix",
+            "To be removed after Cantera 2.5. "
+            "Replaceable with Solution and/or IdealGasPhase/GasKinetics.");
         m_ok = buildSolutionFromXML(root, id_, "phase", this, this);
     }
 
     IdealGasMix(const IdealGasMix& other) : m_ok(false),
         m_r(other.m_r),
         m_id(other.m_id) {
+        warn_deprecated("class IdealGasMix",
+            "To be removed after Cantera 2.5. "
+            "Replaceable with Solution and/or IdealGasPhase/GasKinetics.");
         m_ok = buildSolutionFromXML(*m_r, m_id, "phase", this, this);
     }
 

include/cantera/IncompressibleSolid.h

@@ -1,11 +1,13 @@
 //! @file IncompressibleSolid.h
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CXX_INCOMPRESSIBLE
 #define CXX_INCOMPRESSIBLE
 
+#pragma message("warning: IncompressibleSolid.h is deprecated and will be removed after Cantera 2.5.0.")
+
 #include "thermo/ConstDensityThermo.h"
 #include "kinetics/importKinetics.h"
 
@@ -13,19 +15,26 @@ namespace Cantera
 {
 
 //! Wrapper for ConstDensityThermo with constructor from file
+/*!
+ * @deprecated To be removed after Cantera 2.5.0.
+ *             Replaceable with Solution and/or LatticePhase/IdealSolidSolnPhase.
+ */
 class IncompressibleSolid : public ConstDensityThermo
 {
 public:
     IncompressibleSolid(const std::string& infile,
                         std::string id="") : m_ok(false), m_r(0)
     {
+        warn_deprecated("class IncompressibleSolid",
+            "To be removed after Cantera 2.5.0. "
+            "Replaceable with Solution and/or LatticePhase/IdealSolidSolnPhase.");
         m_r = get_XML_File(infile);
         if (id == "-") {
             id = "";
         }
         m_ok = buildSolutionFromXML(*m_r, id, "phase", this, 0);
         if (!m_ok) throw CanteraError("IncompressibleSolid",
-                                          "buildSolutionFromXML returned false");
+                                      "buildSolutionFromXML returned false");
     }
 
     bool operator!() {

include/cantera/Interface.h

@@ -4,11 +4,13 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CXX_INTERFACE
 #define CXX_INTERFACE
 
+#pragma message("warning: Interface.h is deprecated and will be removed after Cantera 2.5.")
+
 #include "thermo.h"
 #include "kinetics.h"
 #include "cantera/thermo/SurfPhase.h"
@@ -22,6 +24,9 @@ namespace Cantera
  * and InterfaceKinetics. It therefore represents a surface phase, and also acts
  * as the kinetics manager to manage reactions occurring on the surface,
  * possibly involving species from other phases.
+ *
+ * @deprecated To be removed after Cantera 2.5.
+ *             Replaceable with Solution and/or SurfPhase/InterfaceKinetics.
  */
 class Interface :
     public SurfPhase,
@@ -42,6 +47,10 @@ public:
               std::vector<ThermoPhase*> otherPhases) :
         m_ok(false),
         m_r(0) {
+        warn_deprecated("class Interface",
+            "To be removed after Cantera 2.5. "
+            "Replaceable with Solution and/or SurfPhase/InterfaceKinetics.");
+
         m_r = get_XML_File(infile);
         if (id == "-") {
             id = "";
@@ -79,11 +88,15 @@ protected:
 //! Import an instance of class Interface from a specification in an input file.
 /*!
  *  This is the preferred method to create an Interface instance.
+ *
+ * @deprecated To be removed after Cantera 2.5. Replaceable with Solution.
  */
 inline Interface* importInterface(const std::string& infile,
                                   const std::string& id,
                                   std::vector<ThermoPhase*> phases)
 {
+    warn_deprecated("importInterface", "To be removed after Cantera 2.5. "
+                    "Replaceable with Solution.");
     return new Interface(infile, id, phases);
 }
 

include/cantera/Metal.h

@@ -1,11 +1,13 @@
 //! @file Metal.h
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CXX_METAL
 #define CXX_METAL
 
+#pragma message("warning: Metal.h is deprecated and will be removed after Cantera 2.5.0.")
+
 #include "thermo/MetalPhase.h"
 #include "kinetics/importKinetics.h"
 
@@ -13,18 +15,25 @@ namespace Cantera
 {
 
 //! Wrapper for MetalPhase with constructor from file
+/*!
+ * @deprecated To be removed after Cantera 2.5.0.
+ *             Replaceable with Solution and/or MetalPhase.
+ */
 class Metal : public MetalPhase
 {
 public:
     Metal(const std::string& infile, std::string id="") : m_ok(false), m_r(0)
     {
+        warn_deprecated("class Metal",
+            "To be removed after Cantera 2.5.0. "
+            "Replaceable with Solution and/or MetalPhase.");
         m_r = get_XML_File(infile);
         if (id == "-") {
             id = "";
         }
         m_ok = buildSolutionFromXML(*m_r, id, "phase", this, 0);
         if (!m_ok) throw CanteraError("Metal::Metal",
-                                          "buildSolutionFromXML returned false");
+                                      "buildSolutionFromXML returned false");
     }
 
     bool operator!() {

include/cantera/PureFluid.h

@@ -1,11 +1,13 @@
 //! @file PureFluid.h
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CXX_PUREFLUID
 #define CXX_PUREFLUID
 
+#pragma message("warning: PureFluid.h is deprecated and will be removed after Cantera 2.5.0.")
+
 #include "thermo/PureFluidPhase.h"
 #include "kinetics.h"
 
@@ -13,12 +15,20 @@ namespace Cantera
 {
 
 //! Wrapper for PureFluidPhase with constructor from file
+/*!
+ * @deprecated To be removed after Cantera 2.5.0. Replaceable with PureFluidPhase.
+ */
 class PureFluid : public PureFluidPhase
 {
 public:
-    PureFluid() : m_ok(false), m_r(0) {}
+    PureFluid() : m_ok(false), m_r(0) {
+        warn_deprecated("class PureFluid", "To be removed after Cantera 2.5.0. "
+            "Replaceable with PureFluidPhase.");
+    }
 
     PureFluid(const std::string& infile, std::string id="") : m_ok(false), m_r(0) {
+        warn_deprecated("class PureFluid", "To be removed after Cantera 2.5.0. "
+            "Replaceable with PureFluidPhase::initThermoFile.");
         m_r = get_XML_File(infile);
         if (id == "-") {
             id = "";
@@ -51,10 +61,18 @@ protected:
     XML_Node* m_r;
 };
 
+
+//! Water definition from liquidvapor input file
+/*!
+ * @deprecated To be removed after Cantera 2.5.0. Replaceable with PureFluidPhase.
+ */
 class Water : public PureFluid
 {
 public:
-    Water() : PureFluid(std::string("liquidvapor.cti"),std::string("water")) {}
+    Water() : PureFluid(std::string("liquidvapor.cti"),std::string("water")) {
+        warn_deprecated("class Water", "To be removed after Cantera 2.5.0. "
+        "Replaceable with PureFluidPhase.");
+    }
     virtual ~Water() {}
 };
 

include/cantera/base/AnyMap.h

@@ -1,16 +1,21 @@
 //! @file AnyMap.h
 
+// This file is part of Cantera. See License.txt in the top-level directory or
+// at https://cantera.org/license.txt for license and copyright information.
+
 #ifndef CT_ANYMAP_H
 #define CT_ANYMAP_H
 
 #include "cantera/base/ct_defs.h"
 #include "cantera/base/global.h"
+#include "cantera/base/Units.h"
 #include "cantera/base/ctexceptions.h"
 
 #include <string>
 #include <vector>
 #include <memory>
 #include <unordered_map>
+#include <functional>
 
 namespace boost
 {
@@ -21,6 +26,7 @@ namespace Cantera
 {
 
 class AnyMap;
+class InputFile;
 
 //! A wrapper for a variable whose type is determined at runtime
 /*!
@@ -30,7 +36,13 @@ class AnyMap;
  *
  * Elements are set using assignment, and the assignment operator has been
  * overloaded for specific types so that only those types are allowed to be
- * used in an AnyValue.
+ * used in an AnyValue. The allowed types are:
+ * - AnyMap
+ * - `double`
+ * - `long int`
+ * - `bool`
+ * - `std::string`
+ * - `std::vector` of any of the above
  */
 class AnyValue
 {
@@ -42,46 +54,87 @@ public:
     AnyValue& operator=(AnyValue const& other);
     AnyValue& operator=(AnyValue&& other);
 
+    //! If this AnyValue is an AnyMap, return the value stored in `key`.
     AnyValue& operator[](const std::string& key);
+    const AnyValue& operator[](const std::string& key) const;
 
+    //! Returns `true` if this AnyValue is an AnyMap and that map contains
+    //! a key with the given name.
     bool hasKey(const std::string& key) const;
 
-    // The value knows the name of its corresponding key in order to provide
-    // comprehensible error messages.
+    //! Set the name of the key storing this value in an AnyMap. Used for
+    //! providing informative error messages in class InputFileError.
     void setKey(const std::string& key);
 
+    //! For values which are derived from an input file, set the line and column
+    //! of this value in that file. Used for providing context for some error
+    //! messages.
+    void setLoc(int line, int column);
+
+    //! Set information about the file used to create this value. Recursively
+    //! sets the information on any child elements.
+    void setFile(shared_ptr<InputFile>& file);
+
+    //! Get the value of this key as the specified type.
     template<class T>
     const T& as() const;
 
     template<class T>
     T& as();
 
-    const std::type_info& type();
+    //! Returns the type of the held value.
+    const std::type_info& type() const;
 
+    //! Returns a string specifying the type of the held value.
+    std::string type_str() const;
+
+    //! Returns `true` if the held value is of the specified type.
     template<class T>
     bool is() const;
 
+    //! Returns `true` if the held value is a scalar type (e.g. `double`, `long
+    //! int`, `string`, or `bool`).
+    bool isScalar() const;
+
+    explicit AnyValue(const std::string& value);
+    explicit AnyValue(const char* value);
     AnyValue& operator=(const std::string& value);
     AnyValue& operator=(const char* value);
+    //! Return the held value, if it is a string
     const std::string& asString() const;
 
+    explicit AnyValue(double value);
     AnyValue& operator=(double value);
-    double asDouble() const;
+    //! Return the held value as a `double`, if it is a `double` or a `long
+    //! int`.
+    double& asDouble();
+    const double& asDouble() const;
 
+    explicit AnyValue(bool value);
     AnyValue& operator=(bool value);
-    bool asBool() const;
+    //! Return the held value, if it is a `bool`.
+    bool& asBool();
+    const bool& asBool() const;
 
+    explicit AnyValue(long int value);
     AnyValue& operator=(long int value);
     AnyValue& operator=(int value);
-    long int asInt() const;
+    //! Return the held value, if it is a `long int`.
+    long int& asInt();
+    const long int& asInt() const;
 
     template<class T>
     AnyValue& operator=(const std::vector<T>& value);
+    //! Return the held value, if it is a vector of type `T`. If called with one
+    //! argument, requires the vector to be of the specified size. If called
+    //! with two arguments, requires the vector to be within the range specified
+    //! by the two values, inclusive.
     template<class T>
-    const std::vector<T>& asVector() const;
+    const std::vector<T>& asVector(size_t nMin=npos, size_t nMax=npos) const;
     template<class T>
-    std::vector<T>& asVector();
+    std::vector<T>& asVector(size_t nMin=npos, size_t nMax=npos);
 
+    explicit AnyValue(const AnyMap& value);
     AnyValue& operator=(const AnyMap& value);
     AnyValue& operator=(AnyMap&& value);
 
@@ -91,17 +144,81 @@ public:
     template<class T>
     AnyValue& operator=(const std::map<std::string, T> items);
 
+    //! Return the held `AnyMap` as a `std::map` where all of the values have
+    //! the specified type.
     template<class T>
-    std::map<std::string, T> asMap();
+    std::map<std::string, T> asMap() const;
+
+    //! Access a `vector<AnyMap>` as a mapping using the value of `name` from
+    //! each item as the key in the new mapping.
+    /*!
+     * For example, for the list:
+     * ```
+     * [{name: O2, weight: 32}, {name: CH4, weight: 16}]
+     * ```
+     * calling `asMap("name")` will create a map with keys ``O2`` and ``CH4``.
+     */
+    std::unordered_map<std::string, const AnyMap*> asMap(const std::string& name) const;
+    std::unordered_map<std::string, AnyMap*> asMap(const std::string& name);
+
+    //! For objects of type `vector<AnyMap>`, return the item where the given
+    //! key has the specified value. If value is the empty string, returns the
+    //! first item in the list.
+    AnyMap& getMapWhere(const std::string& key, const std::string& value);
+
+    //! @see AnyMap::applyUnits
+    void applyUnits(const UnitSystem& units);
 
 private:
     std::string demangle(const std::type_info& type) const;
 
+    template<class T>
+    void checkSize(const std::vector<T>& v, size_t nMin, size_t nMax) const;
+
+    //! Line where this value occurs in the input file
+    int m_line;
+
+    //! Column where this value occurs in the input file
+    int m_column;
+
+    //! Information about the input file used to create this object
+    shared_ptr<InputFile> m_file;
+
+    //! Key of this value in a parent `AnyMap`
     std::string m_key;
+
+    //! The held value
     std::unique_ptr<boost::any> m_value;
+
+    //! Human-readable names for some common types, for use when
+    //! `boost::demangle` is not available.
     static std::map<std::string, std::string> s_typenames;
+
+    friend class InputFileError;
 };
 
+//! Implicit conversion to vector<AnyValue>
+template<>
+const std::vector<AnyValue>& AnyValue::asVector<AnyValue>(size_t nMin, size_t nMax) const;
+
+template<>
+std::vector<AnyValue>& AnyValue::asVector<AnyValue>(size_t nMin, size_t nMax);
+
+//! Implicit conversion of long int to double if accessed as a vector<double>
+template<>
+const std::vector<double>& AnyValue::asVector<double>(size_t nMin, size_t nMax) const;
+
+template<>
+std::vector<double>& AnyValue::asVector<double>(size_t nMin, size_t nMax);
+
+//! Implicit conversion of long int to double if accessed as a vector<vector<double>>
+template<>
+const std::vector<vector_fp>& AnyValue::asVector<vector_fp>(size_t nMin, size_t nMax) const;
+
+template<>
+std::vector<vector_fp>& AnyValue::asVector<vector_fp>(size_t nMin, size_t nMax);
+
+
 //! A map of string keys to values whose type can vary at runtime
 /*!
  * Values in an AnyMap are held by instances of AnyValue. Instances of AnyMap
@@ -117,8 +234,6 @@ private:
  * // Create a nested AnyMap named "beans" which has a key named "baked"
  * // whose value is a vector<double>
  * std::vector<double> v{3.14, 1.59, 2.65};
- * breakfast["beans/baked"] = v;
- * // Equivalently:
  * breakfast["beans"]["baked"] = v;
  *
  * // Create a nested AnyMap with values of the same type
@@ -146,7 +261,8 @@ private:
  *     breakfast["waffle"].asDouble();
  * } except (std::exception& err) {
  *     // Exception will be thrown.
- *     // 'breakfast' will have an empty key named "waffle"
+ *     // 'breakfast' will have an empty key named "waffle" unless `breakfast`
+ *     // is a `const AnyMap`.
  * }
  *
  * try {
@@ -173,17 +289,209 @@ private:
 class AnyMap
 {
 public:
-    AnyMap() {};
+    AnyMap(): m_units() {};
 
+    //! Create an AnyMap from a YAML file.
+    /*!
+     *  Searches the directory containing the optionally-specified parent file
+     *  first, followed by the current working directory and the Cantera include
+     *  path.
+     */
+    static AnyMap fromYamlFile(const std::string& name,
+                               const std::string& parent_name="");
+
+    //! Create an AnyMap from a string containing a YAML document
+    static AnyMap fromYamlString(const std::string& yaml);
+
+    //! Get the value of the item stored in `key`.
     AnyValue& operator[](const std::string& key);
+    const AnyValue& operator[](const std::string& key) const;
 
-    AnyValue& at(const std::string& key);
+    //! Get the value of the item stored in `key`. Raises an exception if the
+    //! value does not exist.
+    const AnyValue& at(const std::string& key) const;
 
+    //! Returns `true` if the map contains an item named `key`.
     bool hasKey(const std::string& key) const;
 
+    //! Erase the value held by `key`.
+    void erase(const std::string& key);
+
+    //! Return a string listing the keys in this AnyMap, e.g. for use in error
+    //! messages
+    std::string keys_str() const;
+
+    //! For AnyMaps which are derived from an input file, set the line and
+    //! column of this AnyMap in that file. Used for providing context for some
+    //! error messages.
+    void setLoc(int line, int column);
+
+    //! Set information about the file used to create this AnyMap. Recursively
+    //! sets the information on any child elements.
+    void setFile(shared_ptr<InputFile>& file);
+
+    //! Set the name of the file used to create this AnyMap. Recursively sets
+    //! the information on any child elements.
+    void setFileName(const std::string& filename);
+
+    //! Set the contents of the file used to create this AnyMap. Used in the
+    //! case where the AnyMap is created from an input string rather than a
+    //! file. Recursively sets the information on any child elements.
+    void setFileContents(const std::string& contents);
+
+    //! If `key` exists, return it as a `bool`, otherwise return `default_`.
+    bool getBool(const std::string& key, bool default_) const;
+
+    //! If `key` exists, return it as a `long int`, otherwise return `default_`.
+    long int getInt(const std::string& key, long int default_) const;
+
+    //! If `key` exists, return it as a `double`, otherwise return `default_`.
+    double getDouble(const std::string& key, double default_) const;
+
+    //! If `key` exists, return it as a `string`, otherwise return `default_`.
+    const std::string& getString(const std::string& key,
+                                 const std::string& default_) const;
+
+    //! Convert the item stored by the given `key` to the units specified in
+    //! `units`. If the stored value is a double, convert it using the default
+    //! units. If the input is a string, treat this as a dimensioned value, e.g.
+    //! '988 kg/m^3' and convert from the specified units.
+    double convert(const std::string& key, const std::string& units) const;
+    double convert(const std::string& key, const Units& units) const;
+
+    //! Convert the item stored by the given `key` to the units specified in
+    //! `units`. If the stored value is a double, convert it using the default
+    //! units. If the input is a string, treat this as a dimensioned value, e.g.
+    //! '988 kg/m^3' and convert from the specified units. If the key is
+    //! missing, the `default_` value is returned.
+    double convert(const std::string& key, const std::string& units,
+                   double default_) const;
+
+    //! Convert a vector of dimensional values
+    /*!
+     * For each item in the vector, if the stored value is a double, convert it
+     * using the default units. If the value is a string, treat it as a
+     * dimensioned value, e.g. '988 kg/m^3', and convert from the specified
+     * units.
+     *
+     * @param key    Location of the vector in this AnyMap
+     * @param units  Units to convert to
+     * @param nMin   Minimum allowed length of the vector. If `nMax` is not
+     *     specified, this is also taken to be the maximum length. An exception
+     *     is thrown if this condition is not met.
+     * @param nMax   Maximum allowed length of the vector. An exception is
+     *     thrown if this condition is not met.
+     */
+    vector_fp convertVector(const std::string& key, const std::string& units,
+                            size_t nMin=npos, size_t nMax=npos) const;
+
+    using const_iterator = std::unordered_map<std::string, AnyValue>::const_iterator;
+
+    //! Defined to allow use with range-based for loops
+    const_iterator begin() const {
+        return m_data.begin();
+    }
+
+    //! Defined to allow use with range-based for loops
+    const_iterator end() const {
+        return m_data.end();
+    }
+
+    //! Returns the number of elements in this map
+    size_t size() {
+        return m_data.size();
+    };
+
+    //! Return the default units that should be used to convert stored values
+    const UnitSystem& units() const { return m_units; }
+
+    //! Use the supplied UnitSystem to set the default units, and recursively
+    //! process overrides from nodes named `units`.
+    /*!
+     * If a `units` node is present in a map that contains other keys, the
+     * specified units are taken to be the defaults for that map. If the map
+     * contains only a `units` node, and is the first item in a list of maps,
+     * then the specified units are taken to be the defaults for all the maps in
+     * the list.
+     *
+     * After being processed, the `units` nodes are removed, so this function
+     * should be called only once, on the root AnyMap. This function is called
+     * automatically by the fromYamlFile() and fromYamlString() constructors.
+     */
+    void applyUnits(const UnitSystem& units);
+
 private:
+    //! The stored data
     std::unordered_map<std::string, AnyValue> m_data;
+
+    //! The default units that are used to convert stored values
+    UnitSystem m_units;
+
+    //! Starting line for this map in the input file
+    int m_line;
+
+    //! Starting column for this map in the input file
+    int m_column;
+
+    //! Information about the file used to create this map
+    shared_ptr<InputFile> m_file;
+
+    //! Cache for previously-parsed input (YAML) files. The key is the full path
+    //! to the file, and the second element of the value is the last-modified
+    //! time for the file, which is used to enable change detection.
+    static std::unordered_map<std::string, std::pair<AnyMap, int>> s_cache;
+
     friend class AnyValue;
+    friend class InputFileError;
+};
+
+// Define begin() and end() to allow use with range-based for loops
+AnyMap::const_iterator begin(const AnyValue& v);
+AnyMap::const_iterator end(const AnyValue& v);
+
+//! Error thrown for problems processing information contained in an AnyMap or
+//! AnyValue.
+/*!
+ *  This class uses the file, line, and column information stored in an AnyMap
+ *  or AnyValue to provide an error message including context lines for the
+ *  original user input.
+ */
+class InputFileError : public CanteraError
+{
+public:
+    //! Indicate an error occurring in `procedure` while using information from
+    //! `node`. The `message` and `args` are processed as in the CanteraError
+    //! class.
+    template <typename... Args>
+    InputFileError(const std::string& procedure, const AnyValue& node,
+                   const std::string& message, const Args&... args)
+        : CanteraError(
+            procedure,
+            formatError(fmt::format(message, args...),
+                        node.m_line, node.m_column, node.m_file))
+        {
+        }
+
+    //! Indicate an error occurring in `procedure` while using information from
+    //! `node`. The `message` and `args` are processed as in the CanteraError
+    //! class.
+    template <typename... Args>
+    InputFileError(const std::string& procedure, const AnyMap& node,
+                   const std::string& message, const Args&... args)
+        : CanteraError(
+            procedure,
+            formatError(fmt::format(message, args...),
+                        node.m_line, node.m_column, node.m_file))
+        {
+        }
+
+    virtual std::string getClass() const {
+        return "InputFileError";
+    }
+protected:
+    static std::string formatError(const std::string& message,
+                                   int line, int column,
+                                   const shared_ptr<InputFile>& file);
 };
 
 }

include/cantera/base/AnyMap.inl.h

@@ -16,15 +16,20 @@ namespace Cantera
 template<class T>
 const T &AnyValue::as() const {
     try {
+        if (typeid(T) == typeid(double) && m_value->type() == typeid(long int)) {
+            // Implicit conversion of long int to double
+            *m_value = static_cast<double>(as<long int>());
+        }
         return boost::any_cast<const T&>(*m_value);
     } catch (boost::bad_any_cast&) {
         if (m_value->type() == typeid(void)) {
             // Values that have not been set are of type 'void'
-            throw CanteraError("AnyValue::as", "Key '{}' not found", m_key);
+            throw InputFileError("AnyValue::as", *this,
+                "Key '{}' not found", m_key);
         } else {
-            throw CanteraError("AnyValue::as",
-                               "Key '{}' contains a '{}',\nnot a '{}'.",
-                               m_key, demangle(m_value->type()), demangle(typeid(T)));
+            throw InputFileError("AnyValue::as", *this,
+                "Key '{}' contains a '{}',\nnot a '{}'",
+                m_key, demangle(m_value->type()), demangle(typeid(T)));
         }
     }
 }
@@ -32,15 +37,20 @@ const T &AnyValue::as() const {
 template<class T>
 T &AnyValue::as() {
     try {
+        if (typeid(T) == typeid(double) && m_value->type() == typeid(long int)) {
+            // Implicit conversion of long int to double
+            *m_value = static_cast<double>(as<long int>());
+        }
         return boost::any_cast<T&>(*m_value);
     } catch (boost::bad_any_cast&) {
         if (m_value->type() == typeid(void)) {
             // Values that have not been set are of type 'void'
-            throw CanteraError("AnyValue::as", "Key '{}' not found", m_key);
+            throw InputFileError("AnyValue::as", *this,
+                "Key '{}' not found", m_key);
         } else {
-            throw CanteraError("AnyValue::as",
-                               "Key '{}' contains a '{}',\nnot a '{}'.",
-                               m_key, demangle(m_value->type()), demangle(typeid(T)));
+            throw InputFileError("AnyValue::as", *this,
+                "Key '{}' contains a '{}',\nnot a '{}'",
+                m_key, demangle(m_value->type()), demangle(typeid(T)));
         }
     }
 }
@@ -57,13 +67,17 @@ AnyValue &AnyValue::operator=(const std::vector<T> &value) {
 }
 
 template<class T>
-const std::vector<T> &AnyValue::asVector() const {
-    return as<std::vector<T>>();
+const std::vector<T> &AnyValue::asVector(size_t nMin, size_t nMax) const {
+    const auto& v = as<std::vector<T>>();
+    checkSize(v, nMin, nMax);
+    return v;
 }
 
 template<class T>
-std::vector<T> &AnyValue::asVector() {
-    return as<std::vector<T>>();
+std::vector<T> &AnyValue::asVector(size_t nMin, size_t nMax) {
+    auto& v = as<std::vector<T>>();
+    checkSize(v, nMin, nMax);
+    return v;
 }
 
 template<class T>
@@ -96,27 +110,36 @@ inline AnyMap& AnyValue::as<AnyMap>() {
         }
         return boost::any_cast<AnyMap&>(*m_value);
     } catch (boost::bad_any_cast&) {
-        throw CanteraError("AnyValue::as",
+        throw InputFileError("AnyValue::as", *this,
             "value of key '{}' is a '{}',\nnot an 'AnyMap'.",
             m_key, demangle(m_value->type()));
     }
 }
 
 template<class T>
-std::map<std::string, T> AnyValue::asMap()
+std::map<std::string, T> AnyValue::asMap() const
 {
     std::map<std::string, T> dest;
     for (const auto& item : as<AnyMap>().m_data) {
-        try {
-            dest[item.first] = boost::any_cast<T>(*item.second.m_value);
-        } catch (boost::bad_any_cast&) {
-            throw CanteraError("AnyValue::asMap",
-                "Value of key '{}' is not a '{}'",
-                item.first, demangle(typeid(T)));
-        }
+        dest[item.first] = item.second.as<T>();
     }
     return dest;
 }
 
+template<class T>
+void AnyValue::checkSize(const std::vector<T>& v, size_t nMin, size_t nMax) const
+{
+    if (nMin != npos && nMax == npos && v.size() != nMin) {
+        throw InputFileError("AnyValue::checkSize", *this,
+            "Expected array '{}' to have length {}, but found "
+            "an array of length {}.", m_key, nMin, v.size());
+    } else if (nMin != npos && nMax != npos
+               && (v.size() < nMin || v.size() > nMax)) {
+        throw InputFileError("AnyValue::checkSize", *this,
+            "Expected array '{}' to have from {} to {} elements, but found "
+            "an array of length {}.", m_key, nMin, nMax, v.size());
+    }
+}
+
 }
 #endif

include/cantera/base/Array.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_ARRAY_H
 #define CT_ARRAY_H

include/cantera/base/FactoryBase.h

@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_FACTORY_BASE
 #define CT_FACTORY_BASE

include/cantera/base/Solution.h

@@ -0,0 +1,88 @@
+//! @file Solution.h
+
+// This file is part of Cantera. See License.txt in the top-level directory or
+// at https://cantera.org/license.txt for license and copyright information.
+
+#ifndef CT_SOLUTION_H
+#define CT_SOLUTION_H
+
+#include "cantera/base/ctexceptions.h"
+
+namespace Cantera
+{
+
+class ThermoPhase;
+class Kinetics;
+class Transport;
+
+//! A container class holding managers for all pieces defining a phase
+class Solution : public std::enable_shared_from_this<Solution>
+{
+private:
+    Solution();
+
+public:
+    ~Solution() {}
+    Solution(const Solution&) = delete;
+    Solution& operator=(const Solution&) = delete;
+
+    //! Create an empty Solution object
+    static shared_ptr<Solution> create() {
+        return shared_ptr<Solution>( new Solution );
+    }
+
+    //! Return the name of this Solution object
+    std::string name() const;
+
+    //! Set the name of this Solution object
+    void setName(const std::string& name);
+
+    //! Set the ThermoPhase object
+    void setThermo(shared_ptr<ThermoPhase> thermo);
+
+    //! Set the Kinetics object
+    void setKinetics(shared_ptr<Kinetics> kinetics);
+
+    //! Set the Transport object
+    void setTransport(shared_ptr<Transport> transport);
+
+    //! Accessor for the ThermoPhase pointer
+    shared_ptr<ThermoPhase> thermo() {
+        return m_thermo;
+    }
+
+    //! Accessor for the Kinetics pointer
+    shared_ptr<Kinetics> kinetics() {
+        return m_kinetics;
+    }
+
+    //! Accessor for the Transport pointer
+    shared_ptr<Transport> transport() {
+        return m_transport;
+    }
+
+protected:
+    shared_ptr<ThermoPhase> m_thermo;  //!< ThermoPhase manager
+    shared_ptr<Kinetics> m_kinetics;  //!< Kinetics manager
+    shared_ptr<Transport> m_transport;  //!< Transport manager
+};
+
+//! Create and initialize a new Solution manager from an input file
+/*!
+ * This constructor wraps newPhase(), newKinetics() and
+ * newTransportMgr() routines for initialization.
+ *
+ * @param infile name of the input file
+ * @param name   name of the phase in the file.
+ *               If this is blank, the first phase in the file is used.
+ * @param transport name of the transport model.
+ * @param adjacent vector containing adjacent solution objects.
+ * @returns an initialized Solution object.
+ */
+shared_ptr<Solution> newSolution(const std::string& infile,
+                                 const std::string& name="",
+                                 const std::string& transport="",
+                                 const std::vector<shared_ptr<Solution>>& adjacent={});
+
+}
+#endif

include/cantera/base/Units.h

@@ -0,0 +1,208 @@
+/**
+ * @file Units.h
+ * Header for unit conversion utilities, which are used to translate
+ * user input from input files (See \ref inputfiles and
+ * class \link Cantera::Units Units\endlink).
+ */
+
+// This file is part of Cantera. See License.txt in the top-level directory or
+// at https://cantera.org/license.txt for license and copyright information.
+
+#ifndef CT_UNITS_H
+#define CT_UNITS_H
+
+#include "cantera/base/ct_defs.h"
+
+namespace Cantera
+{
+
+class AnyValue;
+class AnyMap;
+
+//! A representation of the units associated with a dimensional quantity.
+/*!
+ * Used for converting quantities between unit systems and checking for
+ * dimensional consistency. Units objects are mainly used within UnitSystem
+ * class to convert values from a user-specified Unit system to Cantera's
+ * base units (SI + kmol).
+ */
+class Units
+{
+public:
+    //! Create a Units object with the specified dimensions.
+    explicit Units(double factor=1.0, double mass=0, double length=0,
+                   double time=0, double temperature=0, double current=0,
+                   double quantity=0);
+
+    //! Create an object with the specified dimensions
+    explicit Units(const std::string& name);
+
+    //! Returns `true` if the specified Units are dimensionally consistent
+    bool convertible(const Units& other) const;
+
+    //! Return the factor for converting from this unit to Cantera's base
+    //! units.
+    double factor() const { return m_factor; }
+
+    //! Multiply two Units objects, combining their conversion factors and
+    //! dimensions
+    Units& operator*=(const Units& other);
+
+    //! Provide a string representation of these Units
+    std::string str() const;
+
+    //! Raise these Units to a power, changing both the conversion factor and
+    //! the dimensions of these Units.
+    Units pow(double expoonent) const;
+
+private:
+    //! Scale the unit by the factor `k`
+    void scale(double k) { m_factor *= k; }
+
+    double m_factor; //!< conversion factor to Cantera base units
+    double m_mass_dim;
+    double m_length_dim;
+    double m_time_dim;
+    double m_temperature_dim;
+    double m_current_dim;
+    double m_quantity_dim;
+    double m_pressure_dim; //!< pseudo-dimension to track explicit pressure units
+    double m_energy_dim; //!< pseudo-dimension to track explicit energy units
+
+    friend class UnitSystem;
+};
+
+
+//! Unit conversion utility
+/*!
+ * Provides functions for converting dimensional values from a given unit system.
+ * The main use is for converting values specified in input files to Cantera's
+ * native unit system, which is SI units except for the use of kmol as the base
+ * unit of quantity, i.e. kilogram, meter, second, kelvin, ampere, and kmol.
+ *
+ * String representations of units can be written using multiplication,
+ * division, and exponentiation. Spaces are ignored. Positive, negative, and
+ * decimal exponents are permitted. Examples:
+ *
+ *     kg*m/s^2
+ *     J/kmol
+ *     m*s^-2
+ *     J/kg/K
+ *
+ * Metric prefixes are recognized for all units, e.g. nm, hPa, mg, EJ, mL, kcal.
+ *
+ * Special functions for converting activation energies allow these values to be
+ * expressed as either energy per quantity, energy (e.g. eV), or temperature by
+ * applying a factor of the Avogadro number or the gas constant where needed.
+ *
+ * @ingroup inputfiles
+ */
+class UnitSystem
+{
+public:
+    //! Create a unit system with the specified default units
+    UnitSystem(std::initializer_list<std::string> units);
+
+    //! Default constructor for unit system (needed as VS2019 does not
+    //! recognize an optional argument with a default value)
+    UnitSystem() : UnitSystem({}) {}
+
+    //! Set the default units to convert from when explicit units are not
+    //! provided. Defaults can be set for mass, length, time, quantity, energy,
+    //! and pressure. Conversion using the pressure or energy units is done only
+    //! when the target units explicitly contain pressure or energy units.
+    //!
+    //! * To use SI+kmol: `setDefaults({"kg", "m", "s", "Pa", "J", "kmol"});`
+    //! * To use CGS+mol: `setDefaults({"cm", "g", "dyn/cm^2", "erg", "mol"});`
+    void setDefaults(std::initializer_list<std::string> units);
+
+    //! Set the default units using a map of dimension to unit pairs.
+    //!
+    //! Defaults for dimensions not specified will be left unchanged. To use
+    //! Cantera's default units:
+    //! ```
+    //! UnitSystem system;
+    //! std::map<string, string> defaults{
+    //!     {"length", "m"}, {"mass", "kg"}, {"time", "s"},
+    //!     {"quantity", "kmol"}, {"pressure", "Pa"}, {"energy", "J"},
+    //!     {"activation-energy", "J/kmol"}
+    //! };
+    //! setDefaults(defaults);
+    //! ```
+    void setDefaults(const std::map<std::string, std::string>& units);
+
+    //! Set the default units to convert from when using the
+    //! `convertActivationEnergy` function.
+    void setDefaultActivationEnergy(const std::string& e_units);
+
+    //! Convert `value` from the units of `src` to the units of `dest`.
+    double convert(double value, const std::string& src,
+                   const std::string& dest) const;
+    double convert(double value, const Units& src, const Units& dest) const;
+
+    //! Convert `value` from this unit system (defined by `setDefaults`) to the
+    //! specified units.
+    double convert(double value, const std::string& dest) const;
+    double convert(double value, const Units& dest) const;
+
+    //! Convert a generic AnyValue node to the units specified in `dest`. If the
+    //! input is a double, convert it using the default units. If the input is a
+    //! string, treat this as a dimensioned value, e.g. '988 kg/m^3' and convert
+    //! from the specified units.
+    double convert(const AnyValue& val, const std::string& dest) const;
+    double convert(const AnyValue& val, const Units& dest) const;
+
+    //! Convert an array of AnyValue nodes to the units specified in `dest`. For
+    //! each node, if the value is a double, convert it using the default units,
+    //! and if it is a string, treat it as a value with the given dimensions.
+    vector_fp convert(const std::vector<AnyValue>& vals,
+                      const std::string& dest) const;
+    vector_fp convert(const std::vector<AnyValue>& vals,
+                      const Units& dest) const;
+
+    //! Convert `value` from the units of `src` to the units of `dest`, allowing
+    //! for the different dimensions that can be used for activation energies
+    double convertActivationEnergy(double value, const std::string& src,
+                                   const std::string& dest) const;
+
+    //! Convert `value` from the default activation energy units to the
+    //! specified units
+    double convertActivationEnergy(double value, const std::string& dest) const;
+
+    //! Convert a generic AnyValue node to the units specified in `dest`. If the
+    //! input is a double, convert it using the default units. If the input is a
+    //! string, treat this as a dimensioned value, e.g. '2.7e4 J/kmol' and
+    //! convert from the specified units.
+    double convertActivationEnergy(const AnyValue& val,
+                                   const std::string& dest) const;
+
+private:
+    //! Factor to convert mass from this unit system to kg
+    double m_mass_factor;
+
+    //! Factor to convert length from this unit system to meters
+    double m_length_factor;
+
+    //! Factor to convert time from this unit system to seconds
+    double m_time_factor;
+
+    //! Factor to convert pressure from this unit system to Pa
+    double m_pressure_factor;
+
+    //! Factor to convert energy from this unit system to J
+    double m_energy_factor;
+
+    //! Factor to convert activation energy from this unit system to J/kmol
+    double m_activation_energy_factor;
+
+    //! Factor to convert quantity from this unit system to kmol
+    double m_quantity_factor;
+
+    //! True if activation energy units are set explicitly, rather than as a
+    //! combination of energy and quantity units
+    bool m_explicit_activation_energy;
+};
+
+}
+
+#endif

include/cantera/base/ValueCache.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_VALUECACHE_H
 #define CT_VALUECACHE_H

include/cantera/base/clockWC.h

@@ -5,7 +5,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_CLOCKWC_H
 #define CT_CLOCKWC_H

include/cantera/base/config.h.in

@@ -44,6 +44,8 @@ typedef int ftnlen;       // Fortran hidden string length type
 
 %(CT_USE_SYSTEM_EIGEN)s
 %(CT_USE_SYSTEM_FMT)s
+%(CT_USE_SYSTEM_YAMLCPP)s
+%(CT_USE_DEMANGLE)s
 
 //--------- operating system --------------------------------------
 

include/cantera/base/ct_defs.h

@@ -10,7 +10,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_DEFS_H
 #define CT_DEFS_H
@@ -35,6 +35,8 @@ namespace Cantera
 
 using std::shared_ptr;
 using std::make_shared;
+using std::unique_ptr;
+using std::isnan; // workaround for bug in libstdc++ 4.8
 
 /*!
  * All physical constants are stored here.
@@ -42,68 +44,89 @@ using std::make_shared;
  * @defgroup physConstants Physical Constants
  * %Cantera uses the MKS system of units. The unit for moles
  * is defined to be the kmol. All values of physical constants
- * are consistent with the 2010 CODATA recommendations.
+ * are consistent with the 2018 CODATA recommendations.
  * @ingroup globalData
  * @{
  */
 
 //! Pi
-const doublereal Pi = 3.14159265358979323846;
+const double Pi = 3.14159265358979323846;
 
 /*!
- *   @name Variations of the Gas Constant
- * %Cantera uses the MKS system of units. The unit for moles
- * is defined to be the kmol.
+ * @name Defined Constants
+ * These constants are defined by CODATA to have a particular value.
+ * https://physics.nist.gov/cuu/Constants/index.html
  */
 //@{
 
-//! Avogadro's Number [number/kmol]
-const doublereal Avogadro = 6.02214129e26;
+//! Avogadro's Number \f$ N_{\mathrm{A}} $\f [number/kmol]
+const double Avogadro = 6.02214076e26;
 
-/// Universal Gas Constant. [J/kmol/K]
-const doublereal GasConstant = 8314.4621;
+//! Boltzmann constant \f$ k $\f [J/K]
+const double Boltzmann = 1.380649e-23;
 
-const doublereal logGasConstant = std::log(GasConstant);
+//! Planck constant \f$ h $\f [J-s]
+const double Planck = 6.62607015e-34;
+
+//! Elementary charge \f$ e $\f [C]
+const double ElectronCharge = 1.602176634e-19;
+
+/// Speed of Light in a vacuum \f$ c $\f [m/s]
+const double lightSpeed = 299792458.0;
 
 //! One atmosphere [Pa]
-const doublereal OneAtm = 1.01325e5;
-const doublereal OneBar = 1.0E5;
+const double OneAtm = 1.01325e5;
+
+//! One bar [Pa]
+const double OneBar = 1.0E5;
+
+//@}
+
+/*!
+ * @name Measured Constants
+ * These constants are measured and reported by CODATA
+ */
+//@{
+
+//! Fine structure constant \f$ \alpha $\f []
+const double fineStructureConstant = 7.2973525693e-3;
+
+//! Electron Mass \f$ m_e $\f [kg]
+const double ElectronMass = 9.1093837015e-31;
+
+//@}
+
+/*!
+ * @name Derived Constants
+ * These constants are found from the defined and measured constants
+ */
+//@{
+
+//! Reduced Planck constant \f$ \hbar $\f [m2-kg/s]
+const double Planck_bar = Planck / (2 * Pi);
+
+//! Universal Gas Constant \f$ R_u $\f [J/kmol/K]
+const double GasConstant = Avogadro * Boltzmann;
+
+const double logGasConstant = std::log(GasConstant);
 
 //! Universal gas constant in cal/mol/K
-const doublereal GasConst_cal_mol_K = GasConstant / 4184.0;
+const double GasConst_cal_mol_K = GasConstant / 4184.0;
 
-//! Boltzmann's constant [J/K]
-const doublereal Boltzmann = GasConstant / Avogadro;
+//! log(k_b/h)
+const double logBoltz_Planck = std::log(Boltzmann / Planck);
 
-/// Planck's constant. [J-s]
-const doublereal Planck = 6.62607009e-34; // J-s
-const doublereal Planck_bar = Planck / (2 * Pi); // m2-kg/s
+//! Stefan-Boltzmann constant \f$ \sigma $\f [W/m2/K4]
+const double StefanBoltz = Pi * Pi * std::pow(Boltzmann, 4.0) / (60.0 * std::pow(Planck_bar, 3.0) * lightSpeed * lightSpeed); // 5.670374419e-8
 
-/// log(k/h)
-const doublereal logBoltz_Planck = std::log(Boltzmann / Planck); // ln(k_B/h)
-/// Stefan-Boltzmann constant
-const doublereal StefanBoltz = 5.670373e-8;
+//! Faraday constant \f$ F $\f [C/kmol]
+const double Faraday = ElectronCharge * Avogadro;
 
-//@}
-/// @name Electron Properties
-//@{
-const doublereal ElectronCharge = 1.602176565e-19; // C
-const doublereal ElectronMass = 9.10938291e-31; // kg
-const doublereal Faraday = ElectronCharge * Avogadro;
-//@}
+//! Permeability of free space \f$ \mu_0 $\f [N/A2]
+const double permeability_0 = 2 * fineStructureConstant * Planck / (ElectronCharge * ElectronCharge * lightSpeed);
 
-/// @name Electromagnetism
-/// %Cantera uses the MKS unit system.
-//@{
-
-/// Speed of Light (m/s).
-const doublereal lightSpeed = 299792458.0;
-
-/// Permeability of free space \f$ \mu_0 \f$ in N/A^2.
-const doublereal permeability_0 = 4.0e-7*Pi;
-
-/// Permittivity of free space \f$ \epsilon_0 \f$ in F/m.
-const doublereal epsilon_0 = 1.0 / (lightSpeed*lightSpeed*permeability_0);
+//! Permittivity of free space \f$ \varepsilon_0 $\f [F/m]
+const double epsilon_0 = 1.0 / (lightSpeed * lightSpeed * permeability_0);
 
 //@}
 //@}
@@ -123,15 +146,15 @@ const int VT = -100, PH = -101, PS = -102, VP = -103, PT = -104,
 //@}
 
 //! smallest number to compare to zero.
-const doublereal SmallNumber = 1.e-300;
+const double SmallNumber = 1.e-300;
 //! largest number to compare to inf.
-const doublereal BigNumber = 1.e300;
+const double BigNumber = 1.e300;
 //! largest x such that exp(x) is valid
-const doublereal MaxExp = 690.775527898;
+const double MaxExp = 690.775527898;
 
 //! Fairly random number to be used to initialize variables against
 //! to see if they are subsequently defined.
-const doublereal Undef = -999.1234;
+const double Undef = -999.1234;
 
 //! Small number to compare differences of mole fractions against.
 /*!
@@ -140,17 +163,17 @@ const doublereal Undef = -999.1234;
  * used for the matrix inversion of transport properties when mole fractions
  * must be positive.
  */
-const doublereal Tiny = 1.e-20;
+const double Tiny = 1.e-20;
 
 //! Map connecting a string name with a double.
 /*!
  * This is used mostly to assign concentrations and mole fractions to species.
  */
-typedef std::map<std::string, doublereal> compositionMap;
+typedef std::map<std::string, double> compositionMap;
 
 //! Map from string names to doubles. Used for defining species mole/mass
 //! fractions, elemental compositions, and reaction stoichiometries.
-typedef std::map<std::string, doublereal> Composition;
+typedef std::map<std::string, double> Composition;
 
 //! Turn on the use of stl vectors for the basic array type within cantera
 //! Vector of doubles.

include/cantera/base/ctexceptions.h

@@ -6,7 +6,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_CTEXCEPTIONS_H
 #define CT_CTEXCEPTIONS_H
@@ -31,11 +31,6 @@ namespace Cantera
  * Any exceptions which are not caught cause a fatal error exit from the
  * program.
  *
- * Below is an example of how to catch errors that throw the CanteraError class.
- * In general, all Cantera C++ programs will have this basic structure.
- *
- * \include demo1a.cpp
- *
  * A group of defines may be used during debugging to assert conditions which
  * should be true. These are named AssertTrace(), AssertThrow(), and
  * AssertThrowMsg(). Examples of their usage is given below.

include/cantera/base/ctml.h

@@ -6,7 +6,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_CTML_H
 #define CT_CTML_H

include/cantera/base/global.h

@@ -14,7 +14,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_GLOBAL_H
 #define CT_GLOBAL_H
@@ -187,6 +187,26 @@ void warn_deprecated(const std::string& method, const std::string& extra="");
 //! @copydoc Application::suppress_deprecation_warnings
 void suppress_deprecation_warnings();
 
+//! helper function passing user warning to global handler
+void _warn_user(const std::string& method, const std::string& extra);
+
+/*!
+ * Print a user warning raised from *method*.
+ *
+ * @param method  method name
+ * @param msg  Python-style format string with the following arguments
+ * @param args  arguments for the format string
+ */
+template <typename... Args>
+void warn_user(const std::string& method, const std::string& msg,
+               const Args&... args) {
+    if (sizeof...(args) == 0) {
+        _warn_user(method, msg);
+    } else {
+        _warn_user(method, fmt::format(msg, args...));
+    }
+}
+
 //! @copydoc Application::make_deprecation_warnings_fatal
 void make_deprecation_warnings_fatal();
 

include/cantera/base/logger.h

@@ -5,7 +5,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_LOGGER_H
 #define CT_LOGGER_H

include/cantera/base/plots.h

@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_PLOTS_H
 #define CT_PLOTS_H

include/cantera/base/stringUtils.h

@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_STRINGUTILS_H
 #define CT_STRINGUTILS_H

include/cantera/base/utilities.h

@@ -5,7 +5,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 /**
  * @defgroup utils Templated Utility Functions
@@ -29,6 +29,8 @@ namespace Cantera
 /*!
  * The form of this operator is designed for use by std::transform.
  * @see @ref  scale().
+ *
+ * @deprecated To be removed after Cantera 2.5. Replaceable with C++11 lambda.
  */
 template<class T> struct timesConstant : public std::unary_function<T, double> {
     //! Constructor
@@ -36,7 +38,10 @@ template<class T> struct timesConstant : public std::unary_function<T, double> {
      * @param c  Constant of templated type T that will be stored internally
      *           within the object and used in the multiplication operation
      */
-    timesConstant(T c) : m_c(c) {}
+    timesConstant(T c) : m_c(c) {
+        warn_deprecated("class timesConstant",
+            "To be removed after Cantera 2.5. Replaceable with C++11 lambda.");
+    }
 
     //! Parenthesis operator returning a double
     /*!
@@ -107,7 +112,7 @@ template<class InputIter, class InputIter2>
 inline doublereal dot(InputIter x_begin, InputIter x_end,
                       InputIter2 y_begin)
 {
-    return inner_product(x_begin, x_end, y_begin, 0.0);
+    return std::inner_product(x_begin, x_end, y_begin, 0.0);
 }
 
 //! Multiply elements of an array by a scale factor.
@@ -130,7 +135,8 @@ template<class InputIter, class OutputIter, class S>
 inline void scale(InputIter begin, InputIter end,
                   OutputIter out, S scale_factor)
 {
-    std::transform(begin, end, out, timesConstant<S>(scale_factor));
+    std::transform(begin, end, out,
+        [scale_factor](double x) { return x * scale_factor; });
 }
 
 //! Multiply each entry in x by the corresponding entry in y.
@@ -157,11 +163,13 @@ inline void scale(InputIter begin, InputIter end,
  *                  begin determines the loop length
  * @param y_begin   Iterator pointing to the beginning of the vector y,
  *                  belonging to the iterator class outputIter.
+ * @deprecated      Unused. To be removed after Cantera 2.5.
  */
 template<class InputIter, class OutputIter>
 inline void multiply_each(OutputIter x_begin, OutputIter x_end,
                           InputIter y_begin)
 {
+    warn_deprecated("multiply_each", "To be removed after Cantera 2.5.");
     for (; x_begin != x_end; ++x_begin, ++y_begin) {
         *x_begin *= *y_begin;
     }
@@ -190,10 +198,12 @@ inline void multiply_each(OutputIter x_begin, OutputIter x_end,
  * @param end       Iterator pointing to the end of the x vector, belonging to
  *                  the iterator class InputIter. The difference between end and
  *                  begin determines the loop length
+ * @deprecated      Unused. To be removed after Cantera 2.5.
  */
 template<class InputIter>
 inline doublereal absmax(InputIter begin, InputIter end)
 {
+    warn_deprecated("absmax", "To be removed after Cantera 2.5.");
     doublereal amax = 0.0;
     for (; begin != end; ++begin) {
         amax = std::max(fabs(*begin), amax);
@@ -229,12 +239,14 @@ inline doublereal absmax(InputIter begin, InputIter end)
  *                  begin determines the loop length
  * @param out       Iterator pointing to the beginning of the output vector,
  *                  belonging to the iterator class OutputIter.
+ * @deprecated      Unused. To be removed after Cantera 2.5.
  */
 template<class InputIter, class OutputIter>
 inline void normalize(InputIter begin, InputIter end,
                       OutputIter out)
 {
-    doublereal sum = accumulate(begin, end, 0.0);
+    warn_deprecated("normalize", "To be removed after Cantera 2.5.");
+    doublereal sum = std::accumulate(begin, end, 0.0);
     for (; begin != end; ++begin, ++out) {
         *out = *begin/sum;
     }
@@ -264,11 +276,13 @@ inline void normalize(InputIter begin, InputIter end,
  *                  and begin determines the number of inner iterations.
  * @param y_begin   Iterator pointing to the beginning of the yvector, belonging
  *                  to the iterator class InputIter.
+ * @deprecated      Unused. To be removed after Cantera 2.5.
  */
 template<class InputIter, class OutputIter>
 inline void divide_each(OutputIter x_begin, OutputIter x_end,
                         InputIter y_begin)
 {
+    warn_deprecated("divide_each", "To be removed after Cantera 2.5.");
     for (; x_begin != x_end; ++x_begin, ++y_begin) {
         *x_begin /= *y_begin;
     }
@@ -285,11 +299,13 @@ inline void divide_each(OutputIter x_begin, OutputIter x_end,
  *                  and begin determines the number of inner iterations.
  * @param y_begin   Iterator pointing to the beginning of the yvector, belonging
  *                  to the iterator class InputIter.
+ * @deprecated      Unused. To be removed after Cantera 2.5.
  */
 template<class InputIter, class OutputIter>
 inline void sum_each(OutputIter x_begin, OutputIter x_end,
                      InputIter y_begin)
 {
+    warn_deprecated("sum_each", "To be removed after Cantera 2.5.");
     for (; x_begin != x_end; ++x_begin, ++y_begin) {
         *x_begin += *y_begin;
     }
@@ -325,11 +341,13 @@ inline void sum_each(OutputIter x_begin, OutputIter x_end,
  *                belonging to the iterator class outputIter.
  * @param index   Iterator pointing to the beginning of the index vector, belonging to the
  *                iterator class IndexIter.
+ * @deprecated      Unused. To be removed after Cantera 2.5.
  */
 template<class InputIter, class OutputIter, class IndexIter>
 inline void scatter_copy(InputIter begin, InputIter end,
                          OutputIter result, IndexIter index)
 {
+    warn_deprecated("scatter_copy", "To be removed after Cantera 2.5.");
     for (; begin != end; ++begin, ++index) {
         *(result + *index) = *begin;
     }
@@ -362,11 +380,13 @@ inline void scatter_copy(InputIter begin, InputIter end,
  *                     be selectively multiplied.
  * @param index        Iterator pointing to the beginning of the index vector,
  *                     belonging to the iterator class IndexIter.
+ * @deprecated      Unused. To be removed after Cantera 2.5.
  */
 template<class InputIter, class RandAccessIter, class IndexIter>
 inline void scatter_mult(InputIter mult_begin, InputIter mult_end,
                          RandAccessIter data, IndexIter index)
 {
+    warn_deprecated("scatter_mult", "To be removed after Cantera 2.5.");
     for (; mult_begin != mult_end; ++mult_begin, ++index) {
         *(data + *index) *= *mult_begin;
     }
@@ -377,17 +397,19 @@ inline void scatter_mult(InputIter mult_begin, InputIter mult_end,
  * The template arguments are:  template<class InputIter>
  *
  * A small number (1.0E-20) is added before taking the log. This templated
- * class does the indicated sun. The template must be an iterator.
+ * class does the indicated sum. The template must be an iterator.
  *
  * @param begin  Iterator pointing to the beginning, belonging to the
  *               iterator class InputIter.
  * @param end    Iterator pointing to the end, belonging to the
  *               iterator class InputIter.
  * @return The return from this class is a double.
+ * @deprecated      Unused. To be removed after Cantera 2.5.
  */
 template<class InputIter>
 inline doublereal sum_xlogx(InputIter begin, InputIter end)
 {
+    warn_deprecated("sum_xlogx", "To be removed after Cantera 2.5.");
     doublereal sum = 0.0;
     for (; begin != end; ++begin) {
         sum += (*begin) * std::log(*begin + Tiny);
@@ -410,11 +432,13 @@ inline doublereal sum_xlogx(InputIter begin, InputIter end)
  * @param Q_begin Iterator pointing to the beginning of Q_k, belonging to the
  *               iterator class InputIter2.
  * @return The return from this class is hard coded to a doublereal.
+ * @deprecated      Unused. To be removed after Cantera 2.5.
  */
 template<class InputIter1, class InputIter2>
 inline doublereal sum_xlogQ(InputIter1 begin, InputIter1 end,
                             InputIter2 Q_begin)
 {
+    warn_deprecated("sum_xlogQ", "To be removed after Cantera 2.5.");
     doublereal sum = 0.0;
     for (; begin != end; ++begin, ++Q_begin) {
         sum += (*begin) * std::log(*Q_begin + Tiny);

include/cantera/base/xml.h

@@ -6,7 +6,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_XML_H
 #define CT_XML_H
@@ -109,13 +109,12 @@ public:
     XML_Node& operator=(const XML_Node& right);
     virtual ~XML_Node();
 
-    //! Add a child node to the current node containing a comment
+    //! Clear the current node and everything under it
     /*!
-     *  Child node will have the name, comment.
-     *
-     *  @param comment    Content of the comment
+     * The value, attributes and children are all zeroed. The name and the
+     * parent information is kept.
      */
-    void addComment(const std::string& comment);
+    void clear();
 
     //! Merge an existing node as a child node to the current node
     /*!
@@ -190,6 +189,14 @@ public:
      *               isn't modified in any way.
      */
     void removeChild(const XML_Node* const node);
+    
+    //! Add a child node to the current node containing a comment
+    /*!
+     *  Child node will have the name, comment.
+     *
+     *  @param comment    Content of the comment
+     */
+    void addComment(const std::string& comment);
 
     //! Modify the value for the current node
     /*!
@@ -306,18 +313,10 @@ public:
      *
      * @param attr  String containing the attribute to be searched for.
      * @return  If a match is found, the attribute value is returned as a
-     *                  string. If no match is found, the empty string is
-     *                  returned.
+     *          string. If no match is found, the empty string is returned.
      */
     std::string attrib(const std::string& attr) const;
 
-    //! Clear the current node and everything under it
-    /*!
-     * The value, attributes and children are all zeroed. The name and the
-     * parent information is kept.
-     */
-    void clear();
-
 private:
     //! Returns a changeable value of the attributes map for the current node
     /*!
@@ -364,9 +363,6 @@ public:
     bool hasAttrib(const std::string& a) const;
 
     //! Returns the name of the XML node
-    /*!
-     * The name is the XML node is the XML node name
-     */
     std::string name() const {
         return m_name;
     }
@@ -393,7 +389,7 @@ public:
 
     //! Return an unchangeable reference to the vector of children of the current node
     /*!
-     * Each of the individual XML_Node child pointers, however, is to a
+     * Each of the individual XML_Node child pointers, however, is pointing to a
      * changeable XML node object.
      */
     const std::vector<XML_Node*>& children() const;
@@ -408,9 +404,9 @@ public:
     //!  Boolean function indicating whether a comment
     bool isComment() const;
 
-    //! Require that the current XML node have an attribute named by the first
-    //! argument, a, and that this attribute have the the string value listed
-    //! in the second argument, v.
+    //! Require that the current XML node has an attribute named by the first
+    //! argument, a, and that this attribute has the string value listed in
+    //! the second argument, v.
     /*!
      * @param a  attribute name
      * @param v  required value of the attribute
@@ -440,15 +436,15 @@ public:
     XML_Node* findNameID(const std::string& nameTarget,
                          const std::string& idTarget) const;
 
-    //! This routine carries out a search for an XML node based
-    //! on both the XML element name and the attribute ID and an integer index.
+    //! This routine carries out a search for an XML node based on the XML
+    //! element name, the attribute ID and an integer index.
     /*!
      * If exact matches are found for all fields, the pointer
      * to the matching XML Node is returned. The search is only carried out on
      * the current element and the child elements of the current element.
      *
      * The "id" attribute may be defaulted by setting it to "". In this case the
-     * pointer to the first XML element matching the name only is returned.
+     * pointer to the first XML element matching the name and the Index is returned.
      *
      * @param nameTarget  Name of the XML Node that is being searched for
      * @param idTarget    "id" attribute of the XML Node that the routine
@@ -461,14 +457,11 @@ public:
                               const std::string& idTarget, const int index) const;
 
     //! This routine carries out a recursive search for an XML node based
-    //! on the XML element attribute, "id"
+    //! on the XML element attribute "id"
     /*!
      * If exact match is found, the pointer to the matching XML Node is
      * returned. If not, 0 is returned.
      *
-     * The ID attribute may be defaulted by setting it to "". In this case the
-     * pointer to the first XML element matching the name only is returned.
-     *
      * @param id       "id" attribute of the XML Node that the routine looks for
      * @param depth    Depth of the search.
      * @returns the pointer to the XML node that fits the criteria
@@ -704,14 +697,14 @@ protected:
 
 //! Search an XML_Node tree for a named phase XML_Node
 /*!
- *  Search for a phase Node matching a name.
+ *  Search for a phase Node matching an id.
  *
  *  @param root         Starting XML_Node* pointer for the search
- *  @param phaseName    Name of the phase to search for
+ *  @param phaseId      id of the phase to search for
  *  @returns the XML_Node pointer if the phase is found. If the phase is not
- *          found, it returns 0
+ *           found, it returns 0
  */
-XML_Node* findXMLPhase(XML_Node* root, const std::string& phaseName);
+XML_Node* findXMLPhase(XML_Node* root, const std::string& phaseId);
 
 }
 

include/cantera/base/yaml.h

@@ -0,0 +1,6 @@
+#include "cantera/base/ct_defs.h"
+#if CT_USE_SYSTEM_YAMLCPP
+#include "yaml-cpp/yaml.h"
+#else
+#include "cantera/ext/yaml-cpp/yaml.h"
+#endif

include/cantera/clib/clib_defs.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CTC_DEFS_H
 #define CTC_DEFS_H

include/cantera/clib/ct.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CTC_CT_H
 #define CTC_CT_H
@@ -16,6 +16,7 @@ extern "C" {
 
     CANTERA_CAPI int ct_appdelete();
 
+    CANTERA_CAPI int thermo_newFromFile(const char* filename, const char* phasename);
     CANTERA_CAPI int thermo_newFromXML(int mxml);
     CANTERA_CAPI int thermo_del(int n);
     CANTERA_CAPI size_t thermo_nElements(int n);
@@ -72,7 +73,6 @@ extern "C" {
     CANTERA_CAPI double thermo_thermalExpansionCoeff(int n);
     CANTERA_CAPI double thermo_isothermalCompressibility(int n);
     CANTERA_CAPI int thermo_chemPotentials(int n, size_t lenm, double* murt);
-    CANTERA_CAPI int thermo_elementPotentials(int n, size_t lenm, double* lambda);
     CANTERA_CAPI int thermo_getEnthalpies_RT(int n, size_t lenm, double* h_rt);
     CANTERA_CAPI int thermo_getEntropies_R(int n, size_t lenm, double* s_r);
     CANTERA_CAPI int thermo_getCp_R(int n, size_t lenm, double* cp_r);
@@ -102,9 +102,12 @@ extern "C" {
     CANTERA_CAPI int thermo_setState_Psat(int n, double p, double x);
     CANTERA_CAPI int thermo_setState_Tsat(int n, double t, double x);
 
-    CANTERA_CAPI size_t kin_newFromXML(int mxml, int iphase,
-                                       int neighbor1, int neighbor2, int neighbor3,
-                                       int neighbor4);
+    CANTERA_CAPI int kin_newFromFile(const char* filename, const char* phasename,
+                                     int reactingPhase, int neighbor1, int neighbor2,
+                                     int neighbor3, int neighbor4);
+    CANTERA_CAPI int kin_newFromXML(int mxml, int iphase,
+                                    int neighbor1, int neighbor2, int neighbor3,
+                                    int neighbor4);
     CANTERA_CAPI int kin_del(int n);
     CANTERA_CAPI size_t kin_nSpecies(int n);
     CANTERA_CAPI size_t kin_nReactions(int n);
@@ -137,7 +140,8 @@ extern "C" {
     CANTERA_CAPI int kin_advanceCoverages(int n, double tstep);
     CANTERA_CAPI size_t kin_phase(int n, size_t i);
 
-    CANTERA_CAPI size_t trans_new(const char* model, int th, int loglevel);
+    CANTERA_CAPI int trans_newDefault(int th, int loglevel);
+    CANTERA_CAPI int trans_new(const char* model, int th, int loglevel);
     CANTERA_CAPI int trans_del(int n);
     CANTERA_CAPI double trans_viscosity(int n);
     CANTERA_CAPI double trans_electricalConductivity(int n);

include/cantera/clib/ctfunc.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CTC_FUNC1_H
 #define CTC_FUNC1_H

include/cantera/clib/ctmultiphase.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CTC_MULTIPHASE_H
 #define CTC_MULTIPHASE_H

include/cantera/clib/ctonedim.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CTC_ONEDIM_H
 #define CTC_ONEDIM_H

include/cantera/clib/ctreactor.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CTC_REACTOR_H
 #define CTC_REACTOR_H
@@ -14,7 +14,8 @@
 extern "C" {
 #endif
 
-    CANTERA_CAPI int reactor_new(int type);
+    CANTERA_CAPI int reactor_new2(const char* type);
+    CANTERA_CAPI int reactor_new(int type); //!< @deprecated To be changed after Cantera 2.5.
     CANTERA_CAPI int reactor_del(int i);
     CANTERA_CAPI int reactor_setInitialVolume(int i, double v);
     CANTERA_CAPI int reactor_setChemistry(int i, int cflag);
@@ -47,16 +48,23 @@ extern "C" {
     CANTERA_CAPI double reactornet_atol(int i);
     CANTERA_CAPI double reactornet_sensitivity(int i, const char* v, int p, int r);
 
-    CANTERA_CAPI int flowdev_new(int type);
+    CANTERA_CAPI int flowdev_new2(const char* type);
+    CANTERA_CAPI int flowdev_new(int type); //!< @deprecated To be changed after Cantera 2.5.
     CANTERA_CAPI int flowdev_del(int i);
     CANTERA_CAPI int flowdev_install(int i, int n, int m);
     CANTERA_CAPI int flowdev_setMaster(int i, int n);
     CANTERA_CAPI double flowdev_massFlowRate(int i, double time);
     CANTERA_CAPI int flowdev_setMassFlowRate(int i, double mdot);
-    CANTERA_CAPI int flowdev_setParameters(int i, int n, const double* v);
-    CANTERA_CAPI int flowdev_setFunction(int i, int n);
+    CANTERA_CAPI int flowdev_setParameters(int i, int n, const double* v);  //!< @deprecated To be removed after Cantera 2.5.
+    CANTERA_CAPI int flowdev_setMassFlowCoeff(int i, double v);
+    CANTERA_CAPI int flowdev_setValveCoeff(int i, double v);
+    CANTERA_CAPI int flowdev_setPressureCoeff(int i, double v);
+    CANTERA_CAPI int flowdev_setFunction(int i, int n); //!< @deprecated To be removed after Cantera 2.5.
+    CANTERA_CAPI int flowdev_setPressureFunction(int i, int n);
+    CANTERA_CAPI int flowdev_setTimeFunction(int i, int n);
 
-    CANTERA_CAPI int wall_new(int type);
+    CANTERA_CAPI int wall_new2(const char* type);
+    CANTERA_CAPI int wall_new(int type); //!< @deprecated To be changed after Cantera 2.5.
     CANTERA_CAPI int wall_del(int i);
     CANTERA_CAPI int wall_install(int i, int n, int m);
     CANTERA_CAPI double wall_vdot(int i, double t);

include/cantera/clib/ctrpath.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CTC_RXNPATH_H
 #define CTC_RXNPATH_H

include/cantera/clib/ctsurf.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CTC_SURF_H
 #define CTC_SURF_H

include/cantera/clib/ctxml.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CTC_XML_H
 #define CTC_XML_H

include/cantera/cython/funcWrapper.h

@@ -1,5 +1,5 @@
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_CYTHON_FUNC_WRAPPER
 #define CT_CYTHON_FUNC_WRAPPER

include/cantera/cython/wrappers.h

@@ -1,5 +1,5 @@
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #include "cantera/base/logger.h"
 #include "cantera/thermo/ThermoPhase.h"
@@ -112,6 +112,7 @@ TRANSPORT_1D(getMixDiffCoeffsMass)
 TRANSPORT_1D(getMixDiffCoeffsMole)
 TRANSPORT_1D(getThermalDiffCoeffs)
 TRANSPORT_1D(getSpeciesViscosities)
+TRANSPORT_1D(getMobilities)
 
 TRANSPORT_2D(getMultiDiffCoeffs)
 TRANSPORT_2D(getBinaryDiffCoeffs)

include/cantera/equil/ChemEquil.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_CHEM_EQUIL_H
 #define CT_CHEM_EQUIL_H
@@ -124,11 +124,6 @@ public:
     int equilibrate(thermo_t& s, const char* XY, vector_fp& elMoles,
                     int loglevel = 0);
 
-    //! @deprecated To be removed after Cantera 2.4.
-    const vector_fp& elementPotentials() const {
-        return m_lambda;
-    }
-
     /**
      * Options controlling how the calculation is carried out.
      * @see EquilOptions
@@ -267,10 +262,6 @@ protected:
     //! Current value of the mole fractions in the single phase. length = #m_kk.
     vector_fp m_molefractions;
 
-    //! Current value of the dimensional element potentials. length = #m_mm
-    //! @deprecated To be removed after Cantera 2.4.
-    vector_fp m_lambda;
-
     //! Current value of the sum of the element abundances given the current
     //! element potentials.
     doublereal m_elementTotalSum;

include/cantera/equil/MultiPhase.h

@@ -5,7 +5,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_MULTIPHASE_H
 #define CT_MULTIPHASE_H

include/cantera/equil/MultiPhaseEquil.h

@@ -1,7 +1,7 @@
 //! @file MultiPhaseEquil.h
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_MULTIPHASE_EQUIL
 #define CT_MULTIPHASE_EQUIL

include/cantera/equil/vcs_MultiPhaseEquil.h

@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef VCS_MULTIPHASEEQUIL_H
 #define VCS_MULTIPHASEEQUIL_H

include/cantera/equil/vcs_SpeciesProperties.h

@@ -1,7 +1,7 @@
 //! @file vcs_SpeciesProperties.h
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef VCS_SPECIES_PROPERTIES_H
 #define VCS_SPECIES_PROPERTIES_H

include/cantera/equil/vcs_VolPhase.h

@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef VCS_VOLPHASE_H
 #define VCS_VOLPHASE_H

include/cantera/equil/vcs_defs.h

@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef VCS_DEFS_H
 #define VCS_DEFS_H

include/cantera/equil/vcs_internal.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef _VCS_INTERNAL_H
 #define _VCS_INTERNAL_H

include/cantera/equil/vcs_solve.h

@@ -5,7 +5,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef _VCS_SOLVE_H
 #define _VCS_SOLVE_H

include/cantera/equil/vcs_species_thermo.h

@@ -1,7 +1,7 @@
 //! @file vcs_species_thermo.h
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef VCS_SPECIES_THERMO_H
 #define VCS_SPECIES_THERMO_H

include/cantera/kinetics/AqueousKinetics.h

@@ -1,61 +0,0 @@
-/**
- * @file AqueousKinetics.h
- * @ingroup chemkinetics
- */
-
-// This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
-
-#ifndef CT_AQUEOUSKINETICS_H
-#define CT_AQUEOUSKINETICS_H
-
-#include "BulkKinetics.h"
-
-namespace Cantera
-{
-
-/**
- * Kinetics manager for elementary aqueous-phase chemistry. This kinetics
- * manager implements standard mass-action reaction rate expressions for liquids
- *
- * @attention This class currently does not have any test cases or examples. Its
- *     implementation may be incomplete, and future changes to Cantera may
- *     unexpectedly cause this class to stop working. If you use this class,
- *     please consider contributing examples or test cases. In the absence of
- *     new tests or examples, this class may be deprecated and removed in a
- *     future version of Cantera. See
- *     https://github.com/Cantera/cantera/issues/267 for additional information.
- *
- * @deprecated To be removed after Cantera 2.4
- *
- * @ingroup kinetics
- */
-class AqueousKinetics : public BulkKinetics
-{
-public:
-    /// Constructor. Creates an empty reaction mechanism.
-    AqueousKinetics(thermo_t* thermo = 0);
-
-    virtual std::string kineticsType() const {
-        return "Aqueous";
-    }
-
-    virtual void getEquilibriumConstants(doublereal* kc);
-    virtual void getFwdRateConstants(doublereal* kfwd);
-    void updateROP();
-
-    //! Update temperature-dependent portions of reaction rates
-    void _update_rates_T();
-
-    //! Update properties that depend on concentrations.
-    void _update_rates_C();
-
-    //! Update the equilibrium constants in molar units.
-    void updateKc();
-
-    virtual bool addReaction(shared_ptr<Reaction> r);
-    virtual void modifyReaction(size_t i, shared_ptr<Reaction> rNew);
-};
-}
-
-#endif

include/cantera/kinetics/BulkKinetics.h

@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_BULKKINETICS_H
 #define CT_BULKKINETICS_H

include/cantera/kinetics/EdgeKinetics.h

@@ -6,7 +6,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_EDGEKINETICS_H
 #define CT_EDGEKINETICS_H

include/cantera/kinetics/Falloff.h

@@ -1,10 +1,11 @@
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_FALLOFF_H
 #define CT_FALLOFF_H
 
 #include "cantera/kinetics/reaction_defs.h"
+#include "cantera/base/global.h"
 
 namespace Cantera
 {
@@ -74,8 +75,18 @@ public:
         return 0;
     }
 
+    //! Return a string representing the type of the Falloff parameterization.
+    virtual std::string type() const {
+        return "Lindemann";
+    }
+
     //! Return an integer representing the type of the Falloff parameterization.
+    /*!
+     * @deprecated To be removed after Cantera 2.5.
+     */
     virtual int getType() const {
+        warn_deprecated("Falloff::getType()",
+            "Replaced by Falloff::type(). To be removed after Cantera 2.5.");
         return SIMPLE_FALLOFF;
     }
 
@@ -146,7 +157,13 @@ public:
         return 1;
     }
 
+    virtual std::string type() const {
+        return "Troe";
+    }
+
     virtual int getType() const {
+        warn_deprecated("Troe::getType()",
+            "Replaced by Troe::type(). To be removed after Cantera 2.5.");
         return TROE_FALLOFF;
     }
 
@@ -181,9 +198,9 @@ protected:
  *  \f[ P_r = \frac{k_0 [M]}{k_{\infty}} \f]
  *
  *  \f[ F = {\left( a \; exp(\frac{-b}{T}) + exp(\frac{-T}{c})\right)}^n
- *              \;  d \; exp(\frac{-e}{T}) \f]
+ *              \;  d \; T^e \f]
  *      where
- *  \f[ n = \frac{1.0}{1.0 + {\log_{10} P_r}^2} \f]
+ *  \f[ n = \frac{1.0}{1.0 + (\log_{10} P_r)^2} \f]
  *
  *  \f$ c \f$ s required to greater than or equal to zero. If it is zero, then
  *  the corresponding term is set to zero.
@@ -220,7 +237,13 @@ public:
         return 2;
     }
 
+    virtual std::string type() const {
+        return "SRI";
+    }
+
     virtual int getType() const {
+        warn_deprecated("SRI::getType()",
+            "Replaced by SRI::type(). To be removed after Cantera 2.5.");
         return SRI_FALLOFF;
     }
 

include/cantera/kinetics/FalloffFactory.h

@@ -6,7 +6,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_NEWFALLOFF_H
 #define CT_NEWFALLOFF_H
@@ -58,9 +58,23 @@ public:
      * @param c    input vector of doubles which populates the falloff
      *             parameterization.
      * @returns    a pointer to a new Falloff class.
+     *
+     * @deprecated To be removed after Cantera 2.5.
      */
     virtual Falloff* newFalloff(int type, const vector_fp& c);
 
+    //! Return a pointer to a new falloff function calculator.
+    /*!
+     * @param type String identifier specifying the type of falloff function.
+     *             The standard types match class names defined in Falloff.h.
+     *             A factory class derived from FalloffFactory may define
+     *             other types as well.
+     * @param c    input vector of doubles which populates the falloff
+     *             parameterization.
+     * @returns    a pointer to a new Falloff class.
+     */
+    virtual Falloff* newFalloff(const std::string& type, const vector_fp& c);
+
 private:
     //! Pointer to the single instance of the factory
     static FalloffFactory* s_factory;
@@ -73,7 +87,13 @@ private:
 };
 
 //! @copydoc FalloffFactory::newFalloff
+/*!
+ * @deprecated To be removed after Cantera 2.5.
+ */
 shared_ptr<Falloff> newFalloff(int type, const vector_fp& c);
 
+//! @copydoc FalloffFactory::newFalloff
+shared_ptr<Falloff> newFalloff(const std::string& type, const vector_fp& c);
+
 }
 #endif

include/cantera/kinetics/FalloffMgr.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_FALLOFFMGR_H
 #define CT_FALLOFFMGR_H

include/cantera/kinetics/GasKinetics.h

@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_GASKINETICS_H
 #define CT_GASKINETICS_H

include/cantera/kinetics/Group.h

@@ -3,7 +3,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_RXNPATH_GROUP
 #define CT_RXNPATH_GROUP

include/cantera/kinetics/ImplicitSurfChem.h

@@ -6,7 +6,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_IMPSURFCHEM_H
 #define CT_IMPSURFCHEM_H
@@ -61,8 +61,19 @@ public:
      * @param k  Vector of pointers to InterfaceKinetics objects Each object
      *           consists of a surface or an edge containing internal degrees of
      *           freedom representing the concentration of surface adsorbates.
+     * @param rtol   The relative tolerance for the integrator
+     * @param atol   The absolute tolerance for the integrator
+     * @param maxStepSize   The maximum step-size the integrator is allowed to take.
+     *                      If zero, this option is disabled.
+     * @param maxSteps   The maximum number of time-steps the integrator can take.
+     *                   If not supplied, uses the default value in the CVodesIntegrator (20000).
+     * @param maxErrTestFails   the maximum permissible number of error test failures
+     *                           If not supplied, uses the default value in CVODES (7).
      */
-    ImplicitSurfChem(std::vector<InterfaceKinetics*> k);
+    ImplicitSurfChem(std::vector<InterfaceKinetics*> k,
+                     double rtol=1.e-7, double atol=1.e-14,
+                     double maxStepSize=0, size_t maxSteps=20000,
+                     size_t maxErrTestFails=7);
 
     virtual ~ImplicitSurfChem() {};
 
@@ -71,6 +82,27 @@ public:
      */
     virtual void initialize(doublereal t0 = 0.0);
 
+    /*!
+     *  Set the maximum integration step-size.  Note, setting this value to zero
+     *  disables this option
+     */
+    virtual void setMaxStepSize(double maxstep = 0.0);
+
+    /*!
+     *  Set the relative and absolute integration tolerances.
+     */
+    virtual void setTolerances(double rtol=1.e-7, double atol=1.e-14);
+
+    /*!
+     *  Set the maximum number of CVODES integration steps.
+     */
+    virtual void setMaxSteps(size_t maxsteps = 20000);
+
+    /*!
+     *  Set the maximum number of CVODES error test failures
+     */
+    virtual void setMaxErrTestFails(size_t maxErrTestFails = 7);
+
     //! Integrate from t0 to t1. The integrator is reinitialized first.
     /*!
      *   This routine does a time accurate solve from t = t0 to t = t1.
@@ -230,6 +262,8 @@ protected:
     std::unique_ptr<Integrator> m_integ;
     doublereal m_atol, m_rtol; // tolerances
     doublereal m_maxstep; //!< max step size
+    size_t m_nmax; //!< maximum number of steps allowed
+    size_t m_maxErrTestFails; //!< maximum number of error test failures allowed
     vector_fp m_work;
 
     /**