[Doc] Update branch in git checkout instructions to 2.2

Taking the address of a dereferenced null pointer is still undefined
behavior. This was causing the test TestReactor.test_valve_errors to fail on
some versions of OS X.

.travis.yml

@@ -0,0 +1,7 @@
+language: cpp
+before_script:
+  - sudo apt-get update -qq
+  - sudo apt-get install -y python-dev python-numpy-dev cython gfortran libsundials-serial-dev liblapack-dev libblas-dev libboost-thread-dev python3-dev python3-numpy-dev
+script:
+  - scons build VERBOSE=y blas_lapack_libs=lapack,blas build_thread_safe=y boost_thread_lib=boost_thread optimize=n
+  - scons test

README.rst

@@ -3,7 +3,7 @@
 CANTERA
 *******
 
-Version 2.2.0 (stable)
+Version 2.2.1 (stable)
 
 License Information
 ===================
@@ -45,9 +45,3 @@ Web Resources
    http://groups.google.com/group/cantera-users
 
    This site has a message board for discussions amongst Cantera users.
-
-5. *The Cantera Developers Group*
-
-   http://groups.google.com/group/cantera-dev
-
-   Limited access site where developers can discuss development ideas.

SConstruct

@@ -590,7 +590,7 @@ config_options = [
            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')),
-    ('cantera_version', '', '2.2.0')
+    ('cantera_version', '', '2.2.1')
 ]
 
 opts.AddVariables(*config_options)
@@ -929,7 +929,7 @@ if env['VERBOSE']:
 env['python_cmd_esc'] = quoted(env['python_cmd'])
 
 # Python 2 Package Settings
-cython_min_version = LooseVersion('0.17')
+cython_min_version = LooseVersion('0.19')
 env['install_python2_action'] = ''
 if env['python_package'] == 'new':
     env['python_package'] = 'full' # Allow 'new' as a synonym for 'full'

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         = 2.2
+PROJECT_NUMBER         = 2.2.1
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.

doc/sphinx/compiling.rst

@@ -42,7 +42,7 @@ Linux
 * Checking out the source code from version control requires Git (install
   ``git``).
 
-* The minimum compatible Cython version is 0.17. If your distribution does not
+* The minimum compatible Cython version is 0.19. If your distribution does not
   contain a suitable version, you may be able to install a more recent version
   using `easy_install` or `pip`.
 
@@ -94,7 +94,7 @@ OS X
 
   and agree to the Xcode license agreement
 
-* If you don't have numpy version >= 1.3, you can install a recent version with::
+* If you don't have numpy version >= 1.4, you can install a recent version with::
 
     sudo easy_install -U numpy
 
@@ -126,7 +126,7 @@ Stable Release
 
     git clone https://github.com/Cantera/cantera.git
     cd cantera
-    git checkout 2.1
+    git checkout 2.2
 
 Development Version
 -------------------
@@ -437,13 +437,12 @@ Optional Programs
   * Required to build the Cantera Python module, and to run significant portions
     of the test suite.
   * http://sourceforge.net/projects/numpy/
-  * Known to work with versions 1.7 and 1.8; Expected to work with version >= 1.3
+  * Known to work with versions 1.7-1.9; Expected to work with version >= 1.4
 
 * `Cython <http://cython.org/>`_
 
-  * Required to build the Python module
-  * Known to work with versions 0.19 and 0.20. Expected to work with
-    versions >= 0.17.
+  * Required version >=0.19 to build the Python module
+  * Known to work with versions 0.19 and 0.20.
   * Tested with Python 2.7, 3.3, and 3.4. Expected to work with versions 2.6 and
     3.1+ as well.
 

doc/sphinx/conf.py

@@ -86,7 +86,7 @@ copyright = u'2012, Cantera Developers'
 # The short X.Y version.
 version = '2.2'
 # The full version, including alpha/beta/rc tags.
-release = '2.2.0'
+release = '2.2.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/sphinx/cti/input-files.rst

@@ -487,3 +487,221 @@ importing any species that contain undeclared elements, instead of flagging them
 as errors. You can also specify that reactions containing undeclared species
 (also usually an error) should be skipped. This allows you to very easily
 extract a portion of a large reaction mechanism, as described in :ref:`sec-phase-options`.
+
+.. _sec-ck-format-conversion:
+
+Converting CK-format files
+--------------------------
+
+Many existing reaction mechanism files are in "CK format," by which we mean
+the input file format developed for use with the Chemkin-II software package
+as specified in the report describing the Chemkin software [SAND89]_.
+
+Cantera comes with a converter utility program ``ck2cti`` (or ``ck2cti.py``)
+that converts CK format into Cantera format. This program should be run from
+the command line first to convert any CK files you plan to use into Cantera
+format (CTI format).
+
+Usage::
+
+    ck2cti [--input=<filename>]
+           [--thermo=<filename>]
+           [--transport=<filename>]
+           [--id=<phase-id>]
+           [--output=<filename>]
+           [--permissive]
+           [-d | --debug]
+
+Each of the terms in square brackets is an option that can be passed on the
+command line to ``ck2cti``. ``--input`` is the chemistry input file, containing
+a list of all the element names that are used, a list of all the species names,
+and a list of all the reactions to be considered between the species. This file
+can also optionally contain thermodynamic information for the species. If the
+``--input`` file does not contain the thermodynamic data, a separate file
+containing this information must be specified to the `--thermo`` option. Finally,
+the ``--input`` file can also optionally contain transport information for the
+species. If it does not, and the user wishes to use a part of Cantera that relies
+on some transport properties, the ``--transport`` option must be used to specify
+the file containing all the transport data for the species.
+
+Example::
+
+    ck2cti --input=chem.inp --thermo=therm.dat --transport=tran.dat
+
+If the output file name is not given, an output file with the same name as the
+input file, with the extension changed to '.cti'.
+
+An input file containing only species definitions (which can be referenced from
+phase definitions in other input files) can be created by specifying only a
+thermo file.
+
+Many existing CK format files cause errors in ``ck2cti`` when they are
+processed. Some of these errors may be avoided by specifying the
+``--permissive`` option. This option allows certain recoverable parsing errors
+(e.g. duplicate transport or thermodynamic data) to be ignored. Other errors
+may be caused by incorrect formatting of lines in one or more of the input files.
+
+Debugging common errors in CK files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+When ``ck2cti`` encounters an error, it attempts to print the surrounding
+information to help you to locate the error. Many of the most common errors
+are due to an inconsistency of the input files from their standard, as defined
+in the report for Chemkin referenced above. These errors include:
+
+  * Each section of the input files must be started with a keyword representing that
+    section and ending with the keyword ``END``. Keywords that may begin a section
+    include:
+
+    - ``ELEMENTS`` or ``ELEM``
+    - ``SPECIES`` or ``SPEC``
+    - ``THERMO`` or ``THERMO ALL``
+    - ``REACTIONS`` or ``REAC``
+    - ``TRANSPORT``
+
+  * The thermodynamic data is read in a fixed format. This means that each
+    column of the input has a particular meaning. *Many common errors are
+    generated because information is missing or in the wrong column. Check
+    thoroughly for extraneous or missing spaces.* The format for each
+    thermodynamic entry should be as follows::
+
+        N2                      N 2                 G200.000   6000.000  1000.00       1
+         2.95258000E+00 1.39690000E-03-4.92632000E-07 7.86010000E-11-4.60755000E-15    2
+        -9.23949000E+02 5.87189000E+00 3.53101000E+00-1.23661000E-04-5.02999000E-07    3
+         2.43531000E-09-1.40881000E-12-1.04698000E+03 2.96747000E+00                   4
+
+    The following table is adapted from the Chemkin manual [SAND89]_ to describe the
+    column positioning of each required part of the entry. Empty columns should be
+    filled with spaces.
+
+    +---------+-------------------------------------+--------+
+    |Line No. | Contents                            | Column |
+    +=========+=====================================+========+
+    | 1       | Species Name                        | 1--18  |
+    +---------+-------------------------------------+--------+
+    | 1       | Date (Optional)                     | 19--24 |
+    +---------+-------------------------------------+--------+
+    | 1       | Atomic Symbols and formula          | 25--44 |
+    +---------+-------------------------------------+--------+
+    | 1       | Phase of species (S, L, G)          | 45     |
+    +---------+-------------------------------------+--------+
+    | 1       | Low temperature                     | 46--55 |
+    +---------+-------------------------------------+--------+
+    | 1       | High temperature                    | 56--65 |
+    +---------+-------------------------------------+--------+
+    | 1       | Common temperature                  | 66--73 |
+    +---------+-------------------------------------+--------+
+    | 1       | Additional Atomic Symbols           | 74--78 |
+    +---------+-------------------------------------+--------+
+    | 1       | The integer ``1``                   | 80     |
+    +---------+-------------------------------------+--------+
+    | 2       | Coefficients :math:`a_1`            | 1--75  |
+    |         | to :math:`a_5` for the upper        |        |
+    |         | temperature interval                |        |
+    +---------+-------------------------------------+--------+
+    | 2       | The integer ``2``                   | 80     |
+    +---------+-------------------------------------+--------+
+    | 3       | Coefficients :math:`a_6,\ a_7`      | 1--75  |
+    |         | for the upper temperature interval, |        |
+    |         | and :math:`a_1,\ a_2,\ a_3` for     |        |
+    |         | the lower temperature interval      |        |
+    +---------+-------------------------------------+--------+
+    | 3       | The integer ``3``                   | 80     |
+    +---------+-------------------------------------+--------+
+    | 4       | Coefficients :math:`a_4` through    | 1--60  |
+    |         | :math:`a_7` for the lower           |        |
+    |         | temperature interval                |        |
+    +---------+-------------------------------------+--------+
+    | 4       | The integer ``4``                   | 80     |
+    +---------+-------------------------------------+--------+
+
+    The first 18 columns are reserved for the species name. The name assigned
+    to the species in the thermodynamic data must be the same as the species
+    name defined in the ``SPECIES`` section. If the species name is shorter
+    than 18 characters, the rest of the characters should be filled by spaces.
+    The next six columns (columns 19--24) are typically used to write a date;
+    they are not used further. The next 20 columns (25--44) are used to
+    specify the elemental composition of the species. In column 45, the phase
+    of the species (``S``, ``L``, or ``G`` for solid, liquid, or gas
+    respectively) should be specified. The next 28 columns are reserved for
+    the temperatures that delimit the ranges of the polynomials specified on
+    the next several lines. The first two temperatures have a width of 10
+    columns each (46--55 and 56--65), and represent the lowest temperature and
+    highest temperature for which the polynomials are valid. The last
+    temperature has a width of 8 columns (66--73) and is the "common"
+    temperature, where the switch from low to high occurs. The next 5 columns
+    (74--78) are reserved for atomic symbols and are usually left blank for
+    the default behavior. Column 79 is blank and finally, the row is ended in
+    column 80 with the integer ``1``.
+
+    The next three lines of the thermodynamic entry have a similar format.
+    They contain the coefficients of the polynomial described in
+    :ref:`sec-thermo-models` for the NASA 7-coefficient polynomial formulation.
+    The second row of the thermo entry (the first after the information row)
+    contains the first five coefficients that apply the the temperature range
+    between the midpoint and the upper limit. 15 columns are alloted for each
+    coefficient (for a total of 75 columns), with no spaces between them.
+    Although the entry above shows spaces between positive coefficients, it is
+    to be noted that this is done only for formatting consistency with other
+    lines that contain negative numbers. After the coefficients, four spaces
+    in columns 76--79 are followed by the integer ``2`` in column 80. On the
+    next line, the last two coefficients for the upper temperature range and
+    the first three coefficients for the lower temperature range are
+    specified. Once again, this takes up the first 75 columns, columns 76--79
+    are blank, and the integer ``3`` is in column 80. Finally, on the last
+    line of a particular entry, the last four coefficients of the lower
+    temperature range are specified in columns 1--60, 19 blank spaces are
+    present, and the integer ``4`` is in column 80. The 19 blank spaces in the
+    last line are part of the standard. However, since the original Chemkin
+    interpreter ignored those spaces, researchers began using that space to
+    store additional information that was not necessary for the input file.
+    Although these numbers create an error in ``ck2cti`` if present, they are
+    harmless and can be ignored by using the ``--permissive`` option.
+
+  * It may be the case that scientific formatted numbers are missing the ``E``.
+    In this case, numbers often show up as ``1.1+01``, when they should be
+    ``1.1E+01``. You can fix this with a simple Regular Expression find and
+    replace::
+
+        Find: (\d+\.\d+)([+-]\d+)
+        Replace: \1E\2
+
+  * The transport data file also has a specified format, as described in
+    [SAND98]_, although the format is not as strict as for the thermodynamic
+    entries. In particular, the first 15 columns of a line are reserved for
+    the species name. *One common source of errors is a species that is present
+    in the transport data file, but not in the thermodynamic data or in
+    the species list; or a species that is present in the species list but
+    not the transport data file.* The rest of the columns on a given line have
+    no particular format, but must be present in the following order:
+
+    +------------------+------------------------------------------------------+
+    | Parameter Number | Parameter Name                                       |
+    +==================+======================================================+
+    | 1                | An integer with value 0, 1, or 2 indicating          |
+    |                  | monatomic, linear, or non-linear molecular geometry. |
+    +------------------+------------------------------------------------------+
+    | 2                | The Lennerd-Jones potential well depth               |
+    |                  | :math:`\varepsilon/k_B` in Kelvin                    |
+    +------------------+------------------------------------------------------+
+    | 3                | The Lennerd-Jones collision diameter :math:`\sigma`  |
+    |                  | in Angstrom                                          |
+    +------------------+------------------------------------------------------+
+    | 4                | The dipole moment :math:`\mu` in Debye               |
+    +------------------+------------------------------------------------------+
+    | 5                | The polarizability :math:`\alpha` in Angstrom        |
+    +------------------+------------------------------------------------------+
+    | 6                | The rotational relaxation collision number           |
+    |                  | :math:`Z_{rot}` at 298 K                             |
+    +------------------+------------------------------------------------------+
+
+    Another common error is if all 6 of these numbers are not present for every
+    species.
+
+.. [SAND89] See R. J. Kee, F. M. Rupley, and J. A. Miller, Sandia National
+   Laboratories Report SAND89-8009 (1989).
+   http://www.osti.gov/scitech/biblio/5681118
+
+.. [SAND98] See R. J. Kee, G. Dixon-Lewis, J. Warnatz, M. E. Coltrin, J. A. Miller,
+   H. K. Moffat, Sandia National Laboratories Report SAND86-8246B (1998).
+   

doc/sphinx/cti/species.rst

@@ -141,9 +141,9 @@ polynomial:
     \frac{c_p^0(T)}{R} = a_0 + a_1 T + a_2 T^2 + a_3 T^3 + a_4 T^4
 
     \frac{h^0(T)}{RT} = a_0 + \frac{a1}{2}T + \frac{a_2}{3} T^2 +
-                        \frac{a_3}{4} T^3 + \frac{a_4}{5} T^4 + a_5
+                        \frac{a_3}{4} T^3 + \frac{a_4}{5} T^4 + \frac{a_5}{T}
 
-    \frac{s^0(T)}{R} = a_o \ln T + a_1 T + \frac{a_2}{2} T^2 + \frac{a_3}{3} T^3 +
+    \frac{s^0(T)}{R} = a_0 \ln T + a_1 T + \frac{a_2}{2} T^2 + \frac{a_3}{3} T^3 +
                        \frac{a_4}{4} T^4 + a_6
 
 Note that this is the "old" NASA polynomial form, used in the original NASA

doc/sphinx/cython/constants.rst

@@ -23,7 +23,7 @@ These values are the same as those in the Cantera C++ header file ct_defs.h.
 
 .. data:: planck
 
-   Planck constant (J/s)
+   Planck constant (J-s)
 
 .. data:: stefan_boltzmann
 

doc/sphinx/cython/tutorial.rst

@@ -227,19 +227,7 @@ surface reactions must also be passed as arguments to `Interface`.
 Converting CK-format files
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Many existing reaction mechanism files are in "CK format," by which we mean
-the input file format developed for use with the Chemkin-II software package.
-[See R. J. Kee, F. M. Rupley, and J. A. Miller, Sandia National Laboratories
-Report SAND89-8009 (1989).]
-
-Cantera comes with a converter utility program ``ck2cti`` (or ``ck2cti.py``)
-that converts CK format into Cantera format. This program should be run from
-the command line first to convert any CK files you plan to use into Cantera
-format. Here's an example of how to use it. The command::
-
-    $python ck2cti.py --input=mech.inp --thermo=therm.dat --transport=tran.dat
-
-will produce the file ``mech.cti`` in the current directory.
+See :ref:`sec-ck-format-conversion` in the :ref:`sec-input-files` documentation.
 
 
 Getting Help

doc/sphinx/faq.rst

@@ -97,7 +97,7 @@ General
 
     David G. Goodwin, Harry K. Moffat, and Raymond L. Speth. *Cantera: An object-
     oriented software toolkit for chemical kinetics, thermodynamics, and
-    transport processes*. http://www.cantera.org, 2015. Version 2.2.0.
+    transport processes*. http://www.cantera.org, 2016. Version 2.2.1.
 
     The following BibTeX entry may also be used::
 
@@ -105,8 +105,8 @@ General
            author = "David G. Goodwin and Harry K. Moffat and Raymond L. Speth",
            title = "Cantera: An Object-oriented Software Toolkit for Chemical
                     Kinetics, Thermodynamics, and Transport Processes",
-           year = 2015,
-           note = "Version 2.2.0",
+           year = 2016,
+           note = "Version 2.2.1",
            howpublished = "\url{http://www.cantera.org}"
         }
 
@@ -124,8 +124,8 @@ Support and Bug Reporting
     - Check the `Issue Tracker
       <https://github.com/Cantera/cantera/issues>`_ to see if the issue
       has already been reported.
-    - Try to generate a complete, minimal example that demonstrates the
-      observed bug.
+    - Try to generate a `minimal, complete, and verifiable example
+      <http://stackoverflow.com/help/mcve>`_ that demonstrates the observed bug.
     - Create a new issue on the tracker. Include as much information as
       possible about your system configuration (operating system, compiler
       versions, Python versions, installation method, etc.)

doc/sphinx/install.rst

@@ -14,7 +14,7 @@ Windows
 =======
 
 Windows installers are provided for stable versions of Cantera. These
-installation instructions are for Cantera 2.2.0.
+installation instructions are for Cantera 2.2.1.
 
 1. **Choose your Python version and architecture**
 
@@ -68,14 +68,14 @@ installation instructions are for Cantera 2.2.0.
 
          c:\python34\python.exe "%USERPROFILE%\Downloads\get-pip.py"
 
-4. **Install Numpy**
+4. **Install Numpy and optional Python packages**
 
    - Go to the `Unofficial Windows Binaries for Python Extension Packages page
      <http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy>`_.
 
    - Download the most recent release (distributed as a "wheel" archive) of the
      1.x series for Python *X.Y* that matches your Python architecture. The
-     binaries for Cantera 2.2.0 require Numpy 1.8.0 or newer, e.g. In the
+     binaries for Cantera 2.2.1 require Numpy 1.8.0 or newer, e.g. In the
      filename, the digits after "cp" indicate the Python version, e.g.
      ``numpy‑1.8.2+mkl‑cp34‑none‑win_amd64.whl`` is the installer for 64-bit
      Python 3.4.
@@ -85,6 +85,12 @@ installation instructions are for Cantera 2.2.0.
 
          c:\python34\scripts\pip.exe install "%USERPROFILE%\Downloads\numpy‑1.8.2+mkl‑cp34‑none‑win_amd64.whl"
 
+   - If you plan on using Cantera from Python, you may also want to install
+     IPython (an advanced interactive Python interpreter) and Matplotlib (a
+     plotting library), which are also available from the above link (note that
+     you may also need to download additional dependencies for each of these
+     packages). Matplotlib is required to run some of the Python examples.
+
 5. **Remove old versions of Cantera**
 
    - Use The Windows "Add/Remove Programs" interface
@@ -98,10 +104,10 @@ installation instructions are for Cantera 2.2.0.
    - Go to the `Cantera Releases <https://github.com/Cantera/cantera/releases>`_
      page.
 
-     - *64-bit*: Download **Cantera-2.2.0-x64.msi** and
-       **Cantera-Python-2.2.0-x64-pyX.Y.msi**.
-     - *32-bit*: Download **Cantera-2.2.0-x86.msi** and
-       **Cantera-Python-2.2.0-x86-pyX.Y.msi**.
+     - *64-bit*: Download **Cantera-2.2.1-x64.msi** and
+       **Cantera-Python-2.2.1-x64-pyX.Y.msi**.
+     - *32-bit*: Download **Cantera-2.2.1-x86.msi** and
+       **Cantera-Python-2.2.1-x86-pyX.Y.msi**.
 
    - If you are only using the Python module, you do not need to download and
      install the base package.
@@ -207,11 +213,22 @@ you can skip any steps which have already been completed.
      Note that these packages are required even if you do not plan on using the
      Cantera Python 2 module.
 
+   - If you plan on using Cantera from Python, you may also want to install
+     IPython (an advanced interactive Python interpreter) and Matplotlib (a
+     plotting library). Matplotlib is required to run some of the Python
+     examples::
+
+         pip install ipython matplotlib
+
    - If you want to build the Cantera Python 3 module, run::
 
          brew install python3
          pip3 install numpy cython
 
+     and, optionally::
+
+         pip3 install ipython matplotlib
+
 3. **Compile and install Cantera**
 
    * To compile and install Cantera using the default configuration, run::
@@ -223,14 +240,31 @@ you can skip any steps which have already been completed.
      ``--HEAD``
          Installs the current development version of Cantera.
 
+     ``--with-python3``
+         Install the Python 3 module.
+
      ``--with-matlab=/Applications/MATLAB_R2014a.app/``
          Installs the Matlab toolbox (with the path modified to match your
          installed Matlab version)
 
+     ``--without-sundials``
+         Do not use an external SUNDIALS version to build Cantera. Users
+         choosing this option will not be able to run sensitivity analysis
+         of Reactor Networks, but it may prevent errors when installing
+         the Matlab toolbox.
+
+     ``--without-check``
+         NOT RECOMMENDED! Disable automatic testing of Cantera during the
+         installation process.
+
    * These options are specified as additional arguments to the ``brew install``
      command, e.g.::
 
-         brew install cantera --HEAD --with-matlab=/Applications/MATLAB_R2014a.app/
+         brew install cantera --HEAD --with-python3
+
+   * If you are installing the Matlab toolbox, the recommended command is::
+
+         brew install cantera --with-matlab=/Applications/MATLAB_R2014a.app/ --without-sundials
 
    * If something goes wrong with the Homebrew install, re-run the command with
      the ``-v`` flag to get more verbose output that may help identify the
@@ -303,7 +337,7 @@ Ubuntu
 ======
 
 Ubuntu packages are provided for recent versions of Ubuntu using a Personal
-Package Archive (PPA). As of Cantera 2.2.0, packages are available for Ubuntu
+Package Archive (PPA). As of Cantera 2.2.1, packages are available for Ubuntu
 Ubuntu 14.04 LTS (Trusty Tahr), Ubuntu 14.10 (Utopic Unicorn), and Ubuntu 15.04
 (Vivid Vervet). To see which Ubuntu releases and Cantera versions are currently
 available, visit https://launchpad.net/~speth/+archive/ubuntu/cantera
@@ -328,3 +362,30 @@ To install all of the Cantera packages::
     sudo aptitude install cantera-python cantera-python3 cantera-dev
 
 or install whichever subset you need by adjusting the above command.
+
+If you plan on using Cantera from Python, you may also want to install IPython
+(an advanced interactive Python interpreter) and Matplotlib (a plotting
+library), which are also available from the above link. Matplotlib is required
+to run some of the Python examples. For Python 2, these packages can be
+installed with::
+
+    pip2 install ipython matplotlib
+
+And for Python 3, these packages can be installed with::
+
+    pip3 install ipython matplotlib
+
+You may need to install ``pip`` first; instructions can be found on the
+`pip installation instructions.
+<https://pip.pypa.io/en/latest/installing.html#install-pip>`_
+You may need to have superuser access to install packages into the system
+directories. Alternatively, you can add ``--user`` after ``pip install`` but
+before the package names to install into your local user directory. An
+alternative method is to use the Ubuntu repositories, but these tend to
+be very out of date. For Python 2, the command is::
+
+    sudo aptitude install ipython python-matplotlib
+
+And for Python 3, these packages can be installed with::
+
+    sudo aptitude install ipython3 python3-matplotlib

doc/sphinx/matlab/input-tutorial.rst

@@ -59,17 +59,4 @@ must also be passed as arguments to importInterface.
 Converting CK-format files
 --------------------------
 
-Many existing reaction mechanism files are in "CK format," by which we mean the
-input file format developed for use with the Chemkin-II software package.  [See
-R. J. Kee, F. M. Rupley, and J. A. Miller, Sandia National Laboratories Report
-SAND89-8009 (1989).]
-
-Cantera comes with a converter utility program ``ck2cti`` (or ``ck2cti.exe``)
-that converts CK format into Cantera format. This program should be run from the
-command line first to convert any CK files you plan to use into Cantera format.
-
-Here's an example of how to use it:
-
-.. code-block:: bash
-
-    ck2cti -i mech.inp -t therm.dat -tr tran.dat -id mymech > mech.cti
+See :ref:`sec-ck-format-conversion` in the :ref:`sec-input-files` documentation.

doc/sphinx/scons-options.txt

@@ -1,5 +1,3 @@
-scons: Reading SConscript files ...
-
         **************************************************
         *   Configuration options for building Cantera   *
         **************************************************
@@ -9,11 +7,10 @@ build process. They should be given in the form:
 
     scons build option1=value1 option2=value2
 
-Variables set in this way will be stored in the 'cantera.conf' file
-and reused automatically on subsequent invocations of
-scons. Alternatively, the configuration options can be entered
-directly into 'cantera.conf' before running 'scons build'. The format
-of this file is:
+Variables set in this way will be stored in the 'cantera.conf' file and reused
+automatically on subsequent invocations of scons. Alternatively, the
+configuration options can be entered directly into 'cantera.conf' before
+running 'scons build'. The format of this file is:
 
     option1 = 'value1'
     option2 = 'value2'
@@ -21,13 +18,15 @@ of this file is:
         **************************************************
 
 * msvc_version: [ string ]
-    Version of Visual Studio to use. The default is the same version
-    that was used to compile the installed version of Python.
-    - default: '9.0'
+    Version of Visual Studio to use. The default is the newest installed
+    version. Specify '9.0' for Visual Studio 2008; '10.0' for Visual
+    Studio 2010; '11.0' for Visual Studio 2012; or '12.0' for Visual
+    Studio 2013.
+    - default: ''
 
 * target_arch: [ string ]
     Target architecture. The default is the same architecture as the
-    installed version of Python
+    installed version of Python.
     - default: 'amd64'
 
 * toolchain: [ msvc | mingw | intel ]
@@ -36,16 +35,15 @@ of this file is:
 
 * CXX: [ string ]
     The C++ compiler to use.
-    - default: 'g++'
+    - default: '$CC'
 
 * CC: [ string ]
-    The C compiler to use. This is only used to compile CVODE and the
-    Python extension module.
-    - default: 'gcc'
+    The C compiler to use. This is only used to compile CVODE.
+    - default: 'cl'
 
 * prefix: [ /path/to/prefix ]
     Set this to the directory where Cantera should be installed.
-    - default: '/usr/local'
+    - default: 'C:\\Program Files\\Cantera'
 
 * python_package: [ new | full | minimal | none | default ]
     If you plan to work in Python, or you want to use the graphical
@@ -53,7 +51,7 @@ of this file is:
     Package. If, on the other hand, you will only use Cantera from some
     other language (e.g. MATLAB or Fortran 90/95) and only need Python
     to process .cti files, then you only need a 'minimal' subset of the
-    package (actually, only one file). The default behavior is to build
+    package (actually, only two files). The default behavior is to build
     the Python package if the required prerequisites (numpy) are
     installed.
     - default: 'default'
@@ -62,7 +60,7 @@ of this file is:
     Cantera needs to know where to find the Python interpreter. If
     PYTHON_CMD is not set, then the configuration process will use the
     same Python interpreter being used by SCons.
-    - default: '/usr/bin/python'
+    - default: 'c:\\Python27\\python.exe'
 
 * python_array_home: [ /path/to/python_array_home ]
     If numpy was installed using the --home option, set this to the home
@@ -74,13 +72,14 @@ of this file is:
     an alternate location. On Unix-like systems, the default is the same
     as the $prefix option. If this option is set to the empty string
     (the default on Windows), then the Package will be installed to the
-    system default 'site-packages' directory.
-    - default: '$prefix'
+    system default 'site-packages' directory. To install to the current
+    user's site-packages directory, use 'python_prefix=USER'.
+    - default: ''
 
 * python3_package: [ y | n | default ]
     Controls whether or not the Python 3 module will be built. By
     default, the module will be built if the Python 3 interpreter can be
-    found
+    found.
     - default: 'default'
 
 * python3_cmd: [ /path/to/python3_cmd ]
@@ -90,7 +89,7 @@ of this file is:
 
 * python3_array_home: [ /path/to/python3_array_home ]
     "If numpy was installed to a custom location (e.g. using the --home
-    option, set this to the directory for numpy
+    option, set this to the directory for numpy.
     - default: ''
 
 * python3_prefix: [ /path/to/python3_prefix ]
@@ -98,8 +97,9 @@ of this file is:
     to an alternate location. On Unix-like systems, the default is the
     same as the $prefix option. If this option is set to the empty
     string (the default on Windows), then the Package will be installed
-    to the system default 'site-packages' directory.
-    - default: '$prefix'
+    to the system default 'site-packages' directory. To install to the
+    current user's site-packages directory, use 'python3_prefix=USER'.
+    - default: ''
 
 * matlab_toolbox: [ y | n | default ]
     This variable controls whether the Matlab toolbox will be built. If
@@ -123,13 +123,13 @@ of this file is:
     if one is found.
     - default: 'default'
 
-* F90: [ /path/to/F90 ]
-    The Fortran 90 compiler. If unspecified, the builder will look for a
-    compatible compiler (gfortran, ifort, g95) in the $PATH.
+* FORTRAN: [ /path/to/FORTRAN ]
+    The Fortran (90) compiler. If unspecified, the builder will look for
+    a compatible compiler (gfortran, ifort, g95) in the $PATH.
     - default: ''
 
-* F90FLAGS: [ string ]
-    Compilation options for the Fortran 90 compiler.
+* FORTRANFLAGS: [ string ]
+    Compilation options for the Fortran (90) compiler.
     - default: '-O3'
 
 * debug_verbose: [ yes | no ]
@@ -143,33 +143,17 @@ of this file is:
     - default: 'no'
 
 * doxygen_docs: [ yes | no ]
-    Build HTML documentation for the C++ interface using Doxygen
+    Build HTML documentation for the C++ interface using Doxygen.
     - default: 'no'
 
 * sphinx_docs: [ yes | no ]
-    Build HTML documentation for the Python module using Sphinx
+    Build HTML documentation for the Python module using Sphinx.
     - default: 'no'
 
-* with_lattice_solid: [ yes | no ]
-    Include thermodynamic model for lattice solids in the Cantera
-    kernel.
-    - default: 'yes'
 * sphinx_cmd: [ /path/to/sphinx_cmd ]
-    Command to use for building the Sphinx documentation
+    Command to use for building the Sphinx documentation.
     - default: 'sphinx-build'
 
-* with_h298modify_capability: [ yes | no ]
-    Enable changing the 298K heats of formation directly via the C++
-    layer.
-    - default: 'no'
-
-* with_html_log_files: [ yes | no ]
-    write HTML log files. Some multiphase equilibrium procedures can
-    write copious diagnostic log messages. Set this to 'n' to disable
-    this capability. (results in slightly faster equilibrium
-    calculations)
-    - default: 'yes'
-
 * use_sundials: [ default | y | n ]
     Cantera uses the CVODE or CVODES ODE integrator to time-integrate
     reactor network ODE's and for various other purposes. An older
@@ -182,8 +166,9 @@ of this file is:
     will be used if you have it, and if not the older CVODE will be
     used. Or set USE_SUNDIALS to 'y' or 'n' to force using it or not.
     Note that sensitivity analysis with Cantera requires use of
-    sundials. See: http://www.llnl.gov/CASC/sundials
+    sundials. See: http://www.llnl.gov/CASC/sundials.
     - default: 'default'
+    - actual: 'y'
 
 * sundials_include: [ /path/to/sundials_include ]
     The directory where the Sundials header files are installed. This
@@ -198,6 +183,16 @@ of this file is:
     /usr/lib.
     - default: ''
 
+* sundials_license: [ /path/to/sundials_license ]
+    Path to the sundials LICENSE file. Needed so that it can be included
+    when bundling Sundials.
+    - default: ''
+
+* install_sundials: [ yes | no ]
+    Determines whether Sundials library and header files are installed
+    alongside Cantera. Intended for use when installing on Windows.
+    - default: 'yes'
+
 * blas_lapack_libs: [ string ]
     Cantera comes with Fortran (or C) versions of those parts of BLAS
     and LAPACK it requires. But performance may be better if you use a
@@ -226,37 +221,37 @@ of this file is:
 * env_vars: [ string ]
     Environment variables to propagate through to SCons. Either the
     string "all" or a comma separated list of variable names, e.g.
-    'LD_LIBRARY_PATH,HOME'
-    - default: ''
+    'LD_LIBRARY_PATH,HOME'.
+    - default: 'LD_LIBRARY_PATH,PYTHONPATH'
 
 * cxx_flags: [ string ]
     Compiler flags passed to the C++ compiler only.
-    - default: '-ftemplate-depth-128'
+    - default: '/EHsc'
 
 * cc_flags: [ string ]
     Compiler flags passed to both the C and C++ compilers, regardless of
     optimization level
-    - default: '-Wall -Wno-deprecated-declarations'
+    - default: '/MD /nologo /D_SCL_SECURE_NO_WARNINGS /D_CRT_SECURE_NO_WARNINGS'
 
 * thread_flags: [ string ]
-    Compiler and linker flags for POSIX multithreading support
-    - default: '-pthread'
+    Compiler and linker flags for POSIX multithreading support.
+    - default: ''
 
 * optimize: [ yes | no ]
     Enable extra compiler optimizations specified by the
     "optimize_flags" variable, instead of the flags specified by the
-    "debug_flags" variable
+    "debug_flags" variable.
     - default: 'yes'
 
 * optimize_flags: [ string ]
     Additional compiler flags passed to the C/C++ compiler when
     optimize=yes.
-    - default: '-O3 -DNDEBUG -finline-functions -Wno-inline'
+    - default: '/O2'
 
 * no_optimize_flags: [ string ]
     Additional compiler flags passed to the C/C++ compiler when
     optimize=no.
-    - default: '-O0 -fno-inline'
+    - default: '/Od /Ob0'
 
 * debug: [ yes | no ]
     Enable compiler debugging symbols.
@@ -265,7 +260,8 @@ of this file is:
 * debug_flags: [ string ]
     Additional compiler flags passed to the C/C++ compiler when
     debug=yes.
-    - default: '-g'
+    - default: '/Zi /Fd${TARGET}.pdb'
+    - actual: '/Zi /Fd.pdb'
 
 * no_debug_flags: [ string ]
     Additional compiler flags passed to the C/C++ compiler when
@@ -273,11 +269,27 @@ of this file is:
     - default: ''
 
 * debug_linker_flags: [ string ]
-    Additional options passed to the linker when debug=yes
-    - default: ''
+    Additional options passed to the linker when debug=yes.
+    - default: '/DEBUG'
 
 * no_debug_linker_flags: [ string ]
-    Additional options passed to the linker when debug=yes
+    Additional options passed to the linker when debug=no.
+    - default: ''
+
+* warning_flags: [ string ]
+    Additional compiler flags passed to the C/C++ compiler to enable
+    extra warnings. Used only when compiling source code that part of
+    Cantera (e.g. excluding code in the 'ext' directory).
+    - default: '/W3'
+
+* extra_inc_dirs: [ string ]
+    Additional directories to search for header files (colon-separated
+    list).
+    - default: ''
+
+* extra_lib_dirs: [ string ]
+    Additional directories to search for libraries (colon-separated
+    list).
     - default: ''
 
 * build_thread_safe: [ yes | no ]
@@ -289,16 +301,23 @@ of this file is:
     - default: 'no'
 
 * boost_inc_dir: [ /path/to/boost_inc_dir ]
-    Location of the Boost header files
-    - default: '/usr/include'
+    Location of the Boost header files.
+    - default: ''
 
 * boost_lib_dir: [ /path/to/boost_lib_dir ]
-    Directory containing the Boost.Thread library
-    - default: '/usr/lib'
+    Directory containing the Boost.Thread library.
+    - default: ''
 
 * boost_thread_lib: [ string ]
-    The name of the Boost.Thread library.
-    - default: 'boost_thread'
+    A comma-separated list containing the names of the libraries needed
+    to link to Boost.Thread.
+    - default: ''
+
+* boost_windows_libs: [ string ]
+    Comma-separated list containing the names of the Boost libraries
+    required to link Cantera programs on Windows. These libraries will
+    be copied to the Cantera installation directory.
+    - default: 'thread,system,date_time,chrono'
 
 * build_with_f2c: [ yes | no ]
     For external procedures written in Fortran 77, both the original F77
@@ -309,7 +328,7 @@ of this file is:
 
 * F77: [ string ]
     Compiler used to build the external Fortran 77 procedures from the
-    Fortran source code
+    Fortran source code.
     - default: 'gfortran'
 
 * F77FLAGS: [ string ]
@@ -325,6 +344,29 @@ of this file is:
     of installing into the local filesystem.
     - default: ''
 
-* cantera_version: [ string ]
-    - default: '2.0.0b1'
+* VERBOSE: [ yes | no ]
+    Create verbose output about what scons is doing.
+    - default: 'no'
+
+* renamed_shared_libraries: [ yes | no ]
+    If this option is turned on, the shared libraries that are created
+    will be renamed to have a "_shared" extension added to their base
+    name. If not, the base names will be the same as the static
+    libraries. In some cases this simplifies subsequent linking
+    environments with static libraries and avoids a bug with using
+    valgrind with the -static linking flag.
+    - default: 'yes'
+
+* layout: [ standard | compact | debian ]
+    The layout of the directory structure. 'standard' installs files to
+    several subdirectories under 'prefix', e.g. $prefix/bin,
+    $prefix/include/cantera, $prefix/lib. This layout is best used in
+    conjunction with 'prefix'='/usr/local'. 'compact' puts all installed
+    files in the subdirectory define by 'prefix'. This layout is best
+    for with a prefix like '/opt/cantera'. 'debian' installs to the
+    stage directory in a layout used for generating Debian packages.
+    - default: 'compact'
+
+* cantera_version: [ string ]
+    - default: '2.2.1'
 

include/cantera/Edge.h

@@ -9,6 +9,7 @@
 namespace Cantera
 {
 
+//! Convenience class which inherits from both EdgePhase and EdgeKinetics
 class Edge :
     public EdgePhase, public EdgeKinetics
 {

include/cantera/IdealGasMix.h

@@ -10,6 +10,7 @@
 namespace Cantera
 {
 
+//! Convenience class which inherits from both IdealGasPhase and GasKinetics
 class IdealGasMix :
     public IdealGasPhase,
     public GasKinetics

include/cantera/IncompressibleSolid.h

@@ -8,6 +8,7 @@
 namespace Cantera
 {
 
+//! Wrapper for ConstDensityThermo with constructor from file
 class IncompressibleSolid : public ConstDensityThermo
 {
 public:

include/cantera/Metal.h

@@ -8,6 +8,7 @@
 namespace Cantera
 {
 
+//! Wrapper for MetalPhase with constructor from file
 class Metal : public MetalPhase
 {
 public:

include/cantera/PureFluid.h

@@ -8,6 +8,7 @@
 namespace Cantera
 {
 
+//! Wrapper for PureFluidPhase with constructor from file
 class PureFluid : public PureFluidPhase
 {
 public:

include/cantera/kinetics/StoichManager.h

@@ -771,7 +771,7 @@ public:
         }
         bool frac = false;
         for (size_t n = 0; n < stoich.size(); n++) {
-            if (fmod(stoich[n], 1.0) || fmod(order[n], 1.0)) {
+            if (fmod(stoich[n], 1.0) || stoich[n] != order[n]) {
                 frac = true;
                 break;
             }

include/cantera/thermo/Phase.h

@@ -548,12 +548,16 @@ public:
     //! Elemental mole fraction of element m
     /*!
      *  The elemental mole fraction \f$Z_{\mathrm{mole},m}\f$ of element \f$m\f$
-     *  is defined as
+     *  is the number of atoms of element *m* divided by the total number of
+     *  atoms. It is defined as:
+     *
      *  \f[
-     *      Z_{\mathrm{mole},m} = \sum_k \frac{a_{m,k}}{\sum_j a_{j,k}} X_k
+     *      Z_{\mathrm{mole},m} = \frac{\sum_k a_{m,k} X_k}
+     *                                 {\sum_k \sum_j a_{j,k} X_k}
      *  \f]
      *  with \f$a_{m,k}\f$ being the number of atoms of element \f$m\f$ in
-     *  species \f$k\f$and \f$X_k\f$ the mole fraction of species \f$k\f$.
+     *  species \f$k\f$, \f$\sum_j\f$ being a sum over all elements, and
+     *  \f$X_k\f$ being the mole fraction of species \f$k\f$.
      *
      *  @param[in] m Index of the element within the phase. If m is outside the
      *               valid range, an exception will be thrown.
@@ -617,10 +621,12 @@ public:
     //! Note the density of a phase is an independent variable.
     //!     @param[in] density_ density (kg/m^3).
     virtual void setDensity(const doublereal density_) {
-        if (density_ <= 0.0) {
-            throw CanteraError("Phase::setDensity()", "density must be positive");
+        if (density_ > 0.0) {
+            m_dens = density_;
+        } else {
+            throw CanteraError("Phase::setDensity()",
+                               "density must be positive");
         }
-        m_dens = density_;
     }
 
     //! Set the internally stored molar density (kmol/m^3) of the phase.
@@ -630,11 +636,12 @@ public:
     //! Set the internally stored temperature of the phase (K).
     //!     @param temp Temperature in Kelvin
     virtual void setTemperature(const doublereal temp) {
-        if (temp <= 0) {
+        if (temp > 0) {
+            m_temp = temp;
+        } else {
             throw CanteraError("Phase::setTemperature",
                                "temperature must be positive");
         }
-        m_temp = temp;
     }
     //@}
 

include/cantera/zeroD/ReactorBase.h

@@ -133,10 +133,18 @@ public:
 
     //! return a reference to the contents.
     thermo_t& contents() {
+        if (!m_thermo) {
+            throw CanteraError("ReactorBase::contents",
+                               "Reactor contents not defined.");
+        }
         return *m_thermo;
     }
 
     const thermo_t& contents() const {
+        if (!m_thermo) {
+            throw CanteraError("ReactorBase::contents",
+                               "Reactor contents not defined.");
+        }
         return *m_thermo;
     }
 

include/cantera/zeroD/ReactorNet.h

@@ -167,6 +167,10 @@ public:
         if (!m_init) {
             initialize();
         }
+        if (p >= m_sensIndex.size()) {
+            throw IndexError("ReactorNet::sensitivity",
+                             "m_sensIndex", p, m_sensIndex.size()-1);
+        }
         return m_integ->sensitivity(k, m_sensIndex[p])/m_integ->solution(k);
     }
 

include/cantera/zeroD/flowControllers.h

@@ -54,7 +54,7 @@ public:
     }
 
     virtual bool ready() {
-        return FlowDevice::ready() && m_master != 0;
+        return FlowDevice::ready() && m_master != 0 && m_coeffs.size() == 1;
     }
 
     void setMaster(FlowDevice* master) {
@@ -62,6 +62,10 @@ public:
     }
 
     virtual void updateMassFlowRate(doublereal time) {
+        if (!ready()) {
+            throw CanteraError("PressureController::updateMassFlowRate",
+                "Device is not ready; some parameters have not been set.");
+        }
         doublereal master_mdot = m_master->massFlowRate(time);
         m_mdot = master_mdot + m_coeffs[0]*(in().pressure() -
                                             out().pressure());
@@ -72,7 +76,8 @@ protected:
     FlowDevice* m_master;
 };
 
-//! Supply a mass flow rate that is a function of the pressure drop across the valve. 
+//! Supply a mass flow rate that is a function of the pressure drop across the
+//! valve.
 /*!
  * The default behavior is a linearly proportional to the pressure difference.
  * Note that real valves do not have this behavior, so this class does not
@@ -86,11 +91,15 @@ public:
     }
 
     virtual bool ready() {
-        return FlowDevice::ready() && m_coeffs.size() >= 1;
+        return FlowDevice::ready() && (m_coeffs.size() == 1 || m_func);
     }
 
     /// Compute the currrent mass flow rate, based on the pressure difference.
     virtual void updateMassFlowRate(doublereal time) {
+        if (!ready()) {
+            throw CanteraError("Valve::updateMassFlowRate",
+                "Device is not ready; some parameters have not been set.");
+        }
         double delta_P = in().pressure() - out().pressure();
         if (m_func) {
             m_mdot = m_func->eval(delta_P);

interfaces/cython/SConscript

@@ -18,7 +18,7 @@ def configure_python(env, python_command):
                         "print(numpy.get_include())"))
     info = getCommandOutput(python_command, '-c', script)
     module_ext, inc, pylib, prefix, py_version, numpy_include = info.splitlines()[-6:]
-    env.Append(CPPPATH=[inc, numpy_include, Dir('#include')])
+    env.Prepend(CPPPATH=[Dir('#include'), inc, numpy_include])
     env.Prepend(LIBS=env['cantera_libs'])
     if env['OS'] == 'Darwin':
         env.Append(LINKFLAGS='-undefined dynamic_lookup')
@@ -137,7 +137,7 @@ if localenv['python3_package'] == 'y':
     obj = py3env.SharedObject('#build/temp-py/_cantera3', 'cantera/_cantera.cpp')
     ext = py3env.LoadableModule('#build/python3/cantera/_cantera%s' % module_ext,
                                 obj, LIBPREFIX='', SHLIBSUFFIX=module_ext,
-                                LIBSUFFIXES=[module_ext])
+                                SHLIBPREFIX='', LIBSUFFIXES=[module_ext])
     py3env['py_extension'] = ext[0].name
 
     py3env.SubstFile('setup3.py', 'setup.py.in')
@@ -161,7 +161,7 @@ if localenv['python_package'] == 'full':
     obj = py2env.SharedObject('#build/temp-py/_cantera2', 'cantera/_cantera.cpp')
     ext = py2env.LoadableModule('#build/python2/cantera/_cantera%s' % module_ext,
                                 obj, LIBPREFIX='', SHLIBSUFFIX=module_ext,
-                                LIBSUFFIXES=[module_ext])
+                                SHLIBPREFIX='', LIBSUFFIXES=[module_ext])
     py2env['py_extension'] = ext[0].name
     py2env.SubstFile('setup2.py', 'setup.py.in')
     build_cmd = ('cd interfaces/cython &&'

interfaces/cython/cantera/_cantera.pxd

@@ -512,8 +512,8 @@ cdef extern from "cantera/zeroD/Wall.h":
 cdef extern from "cantera/zeroD/flowControllers.h":
     cdef cppclass CxxFlowDevice "Cantera::FlowDevice":
         CxxFlowDevice()
-        double massFlowRate(double)
-        cbool install(CxxReactorBase&, CxxReactorBase&)
+        double massFlowRate(double) except +
+        cbool install(CxxReactorBase&, CxxReactorBase&) except +
         void setFunction(CxxFunc1*)
         void setParameters(int, double*)
 
@@ -977,7 +977,7 @@ cdef class ReactionPathDiagram:
     cdef CxxStringStream* _log
 
 # free functions
-cdef string stringify(x)
+cdef string stringify(x) except *
 cdef pystr(string x)
 cdef np.ndarray get_species_array(Kinetics kin, kineticsMethod1d method)
 cdef np.ndarray get_reaction_array(Kinetics kin, kineticsMethod1d method)

interfaces/cython/cantera/ck2cti.py

@@ -70,16 +70,17 @@ if sys.version_info[0] == 2:
     def strip_nonascii(s):
         return s.decode('ascii', 'ignore')
 
-    def open(filename, *args):
-        return _open(filename, *args)
+    def open(filename, mode, *args):
+        return _open(filename, mode, *args)
 
 else:
     string_types = (str,)
     def strip_nonascii(s):
         return s.encode('ascii', 'ignore').decode()
 
-    def open(filename, *args):
-        return _open(filename, *args, errors='ignore')
+    def open(filename, mode, *args):
+        mode = mode.replace('U', '')
+        return _open(filename, mode, *args, errors='ignore')
 
 
 def compatible_quantities(quantity_basis, units):

interfaces/cython/cantera/examples/kinetics/extract_submechanism.py

@@ -38,7 +38,7 @@ print('Species: {0}'.format(', '.join(S.name for S in species)))
 all_reactions = ct.Reaction.listFromFile('gri30.xml')
 reactions = []
 
-print '\nReactions:'
+print('\nReactions:')
 for R in all_reactions:
     if not all(reactant in species_names for reactant in R.reactants):
         continue

interfaces/cython/cantera/examples/transport/multiprocessing_viscosity.py

@@ -40,7 +40,7 @@ def get_viscosity(args):
     mech, T, P, X = args
     gas = gases[mech]
     gas.TPX = T, P, X
-    return gas.enthalpy_mass
+    return gas.viscosity
 
 def parallel(mech, predicate, nProcs, nTemps):
     """
@@ -64,13 +64,13 @@ def serial(mech, predicate, nTemps):
     P = ct.one_atm
     X = 'CH4:1.0, O2:1.0, N2:3.76'
     init_process(mech)
-    y = map(predicate, 
-            zip(itertools.repeat(mech),
-                np.linspace(300, 900, nTemps),
-                itertools.repeat(P),
-                itertools.repeat(X)))
+    y = list(map(predicate,
+                 zip(itertools.repeat(mech),
+                     np.linspace(300, 900, nTemps),
+                     itertools.repeat(P),
+                     itertools.repeat(X))))
     return y
-    
+
 if __name__ == '__main__':
     # For functions where the work done in each subprocess is substantial,
     # significant speedup can be obtained using the multiprocessing module.

interfaces/cython/cantera/onedim.py

@@ -1,5 +1,6 @@
 import numpy as np
 from ._cantera import *
+import csv as _csv
 
 try:
     # Python 2.7 or 3.2+
@@ -265,7 +266,7 @@ class FlameBase(Sim1D):
         V = self.V
 
         csvfile = open(filename, 'w')
-        writer = csv.writer(csvfile)
+        writer = _csv.writer(csvfile)
         writer.writerow(['z (m)', 'u (m/s)', 'V (1/s)',
                          'T (K)', 'rho (kg/m3)'] + self.gas.species_names)
         for n in range(self.flame.n_points):

interfaces/cython/cantera/test/test_kinetics.py

@@ -426,8 +426,8 @@ class ExplicitForwardOrderTest(utilities.CanteraTest):
     def test_irreversibility(self):
         # Reactions are irreversible
         Rr = self.gas.reverse_rate_constants
-        self.assertEqual(Rr[0], 0.0)
-        self.assertEqual(Rr[1], 0.0)
+        for i in range(3):
+            self.assertEqual(Rr[i], 0.0)
 
     def test_rateConstants(self):
         # species order: [H, AR, R1A, R1B, P1]
@@ -436,6 +436,7 @@ class ExplicitForwardOrderTest(utilities.CanteraTest):
         kf = self.gas.forward_rate_constants
         self.assertNear(Rf[0], kf[0] * C[2]**1.5 * C[3]**0.5)
         self.assertNear(Rf[1], kf[1] * C[0]**1.0 * C[4]**0.2)
+        self.assertNear(Rf[2], kf[2] * C[2]**3.0)
 
     def test_ratio1(self):
         rop1 = self.gas.forward_rates_of_progress
@@ -445,6 +446,7 @@ class ExplicitForwardOrderTest(utilities.CanteraTest):
         ratio = rop2/rop1
         self.assertNear(ratio[0], 2**1.5) # order of R1A is 1.5
         self.assertNear(ratio[1], 2**1.0) # order of H is 1.0
+        self.assertNear(ratio[2], 2**3) # order of R1A is 3
 
     def test_ratio2(self):
         rop1 = self.gas.forward_rates_of_progress
@@ -454,6 +456,7 @@ class ExplicitForwardOrderTest(utilities.CanteraTest):
         ratio = rop2/rop1
         self.assertNear(ratio[0], 2**0.5) # order of R1B is 0.5
         self.assertNear(ratio[1], 2**0.2) # order of P1 is 1.0
+        self.assertNear(ratio[2], 2**0.0) # order of R1B is 0
 
 
 class TestSofcKinetics(utilities.CanteraTest):

interfaces/cython/cantera/test/test_onedim.py

@@ -241,7 +241,7 @@ class TestFreeFlame(utilities.CanteraTest):
 
         self.create_sim(p, Tin, reactants)
         self.solve_fixed_T()
-        filename = 'onedim-fixed-T.xml'
+        filename = 'onedim-fixed-T{0}.xml'.format(utilities.python_version)
         if os.path.exists(filename):
             os.remove(filename)
 
@@ -302,7 +302,7 @@ class TestFreeFlame(utilities.CanteraTest):
         p = 2 * ct.one_atm
         Tin = 400
 
-        filename = 'onedim-add-species.xml'
+        filename = 'onedim-add-species{0}.xml'.format(utilities.python_version)
         if os.path.exists(filename):
             os.remove(filename)
 
@@ -330,7 +330,7 @@ class TestFreeFlame(utilities.CanteraTest):
         p = 2 * ct.one_atm
         Tin = 400
 
-        filename = 'onedim-add-species.xml'
+        filename = 'onedim-add-species{0}.xml'.format(utilities.python_version)
         if os.path.exists(filename):
             os.remove(filename)
 
@@ -353,6 +353,19 @@ class TestFreeFlame(utilities.CanteraTest):
             k1 = gas1.species_index(species)
             self.assertArrayNear(Y1[k1], Y2[k2])
 
+    def test_write_csv(self):
+        filename = 'onedim-write_csv{0}.csv'.format(utilities.python_version)
+        if os.path.exists(filename):
+            os.remove(filename)
+
+        self.create_sim(2e5, 350, 'H2:1.0, O2:2.0', mech='h2o2.xml')
+        self.sim.write_csv(filename)
+        data = np.genfromtxt(filename, delimiter=',', skip_header=1)
+        self.assertArrayNear(data[:,0], self.sim.grid)
+        self.assertArrayNear(data[:,3], self.sim.T)
+        k = self.gas.species_index('H2')
+        self.assertArrayNear(data[:,5+k], self.sim.X[k,:])
+
     def test_refine_criteria_boundscheck(self):
         self.create_sim(ct.one_atm, 300.0, 'H2:1.1, O2:1, AR:5')
         good = [3.0, 0.1, 0.2, 0.05]

interfaces/cython/cantera/test/test_purefluid.py

@@ -76,6 +76,14 @@ class TestPureFluid(utilities.CanteraTest):
         self.check_fd_properties(self.water.max_temp*(1-1e-5), 101325,
                               self.water.max_temp*(1-1e-4), 101325, 1e-2)
 
+    def test_TPX(self):
+        self.water.TX = 400, 0.8
+        T,P,X = self.water.TPX
+        self.assertNear(T, 400)
+        self.assertNear(X, 0.8)
+        with self.assertRaises(AttributeError):
+            self.water.TPX = 500, 101325, 0.3
+
 
 # To minimize errors when transcribing tabulated data, the input units here are:
 # T: K, P: MPa, rho: kg/m3, v: m3/kg, (u,h): kJ/kg, s: kJ/kg-K

interfaces/cython/cantera/test/test_reactor.py

@@ -433,6 +433,19 @@ class TestReactor(utilities.CanteraTest):
             self.assertNear(speciesMass(kAr), mAr)
             self.assertNear(speciesMass(kO2), mO2)
 
+    def test_valve_errors(self):
+        self.make_reactors()
+        res = ct.Reservoir()
+
+        with self.assertRaises(RuntimeError):
+            # Must assign contents of both reactors before creating Valve
+            v = ct.Valve(self.r1, res)
+
+        v = ct.Valve(self.r1, self.r2)
+        with self.assertRaises(RuntimeError):
+            # inlet and outlet cannot be reassigned
+            v._install(self.r2, self.r1)
+
     def test_pressure_controller(self):
         self.make_reactors(n_reactors=1)
         g = ct.Solution('h2o2.xml')
@@ -456,6 +469,25 @@ class TestReactor(utilities.CanteraTest):
             dP = self.r1.thermo.P - outlet_reservoir.thermo.P
             self.assertNear(mdot(t) + 1e-5 * dP, pc.mdot(t))
 
+    def test_pressure_controller_errors(self):
+        self.make_reactors()
+        res = ct.Reservoir(self.gas1)
+        mfc = ct.MassFlowController(res, self.r1, mdot=0.6)
+
+        p = ct.PressureController(self.r1, self.r2, master=mfc, K=0.5)
+
+        with self.assertRaises(RuntimeError):
+            p = ct.PressureController(self.r1, self.r2, K=0.5)
+            p.mdot(0.0)
+
+        with self.assertRaises(RuntimeError):
+            p = ct.PressureController(self.r1, self.r2, master=mfc)
+            p.mdot(0.0)
+
+        with self.assertRaises(RuntimeError):
+            p = ct.PressureController(self.r1, self.r2)
+            p.mdot(0.0)
+
     def test_set_initial_time(self):
         self.make_reactors(P1=10*ct.one_atm, X1='AR:1.0', X2='O2:1.0')
         self.net.rtol = 1e-12

interfaces/cython/cantera/test/test_thermo.py

@@ -65,8 +65,8 @@ class TestThermoPhase(utilities.CanteraTest):
 
         mO = self.phase.element_index('O')
         self.assertEqual(Zo, self.phase.elemental_mole_fraction(mO))
-        self.assertNear(Zo, 0.5/3 + 0.5)
-        self.assertNear(Zh, 0.5*2/3)
+        self.assertNear(Zo, (0.5 + 1) / (0.5*3 + 0.5*2))
+        self.assertNear(Zh, (2*0.5) / (0.5*3 + 0.5*2))
         self.assertEqual(Zar, 0.0)
 
         with self.assertRaises(ValueError):
@@ -74,6 +74,22 @@ class TestThermoPhase(utilities.CanteraTest):
         with self.assertRaises(ValueError):
             self.phase.elemental_mole_fraction(5)
 
+    def test_elemental_mass_mole_fraction(self):
+        # expected relationship between elmental mass and mole fractions
+        comps = ['H2O:0.5, O2:0.5', 'H2:0.1, O2:0.4, H2O2:0.3, AR:0.2',
+                 'O2:0.1, H2:0.9']
+        for comp in comps:
+            self.phase.X = comp
+
+            denom = sum(self.phase.elemental_mole_fraction(i)
+                        * self.phase.atomic_weight(i)
+                        for i in range(self.phase.n_elements))
+
+            for i in range(self.phase.n_elements):
+                self.assertNear(self.phase.elemental_mass_fraction(i),
+                                self.phase.elemental_mole_fraction(i)
+                                * self.phase.atomic_weight(i) / denom)
+
     def test_weights(self):
         atomic_weights = self.phase.atomic_weights
         molecular_weights = self.phase.molecular_weights

interfaces/cython/cantera/test/utilities.py

@@ -4,6 +4,8 @@ import os
 import warnings
 
 _ver = sys.version_info[:2]
+python_version = str(_ver[0])
+
 if  _ver < (2,7) or (3,0) <= _ver < (3,2):
     # unittest2 is a backport of the new features added to the unittest
     # testing framework in Python 2.7 and Python 3.2. See

interfaces/cython/cantera/thermo.pyx

@@ -557,13 +557,15 @@ cdef class ThermoPhase(_SolutionBase):
     def elemental_mole_fraction(self, m):
         r"""
         Get the elemental mole fraction :math:`Z_{\mathrm{mole},m}` of element
-        :math:`m` as defined by:
+        :math:`m` (the number of atoms of element m divided by the total number
+        of atoms) as defined by:
 
-        .. math:: Z_{\mathrm{mole},m} = \sum_k \frac{a_{m,k}}{\sum_j a_{j,k}} X_k
+        .. math:: Z_{\mathrm{mole},m} = \frac{\sum_k a_{m,k} X_k}
+                                             {\sum_k \sum_j a_{j,k} X_k}
 
         with :math:`a_{m,k}` being the number of atoms of element :math:`m` in
-        species :math:`k` and :math:`X_k` the mole fraction of species
-        :math:`k`.
+        species :math:`k`, :math:`\sum_j` being a sum over all elements, and
+        :math:`X_k` being the mole fraction of species :math:`k`.
 
         :param m:
             Base element, may be specified by name or by index.
@@ -1200,3 +1202,51 @@ cdef class PureFluid(ThermoPhase):
             P = values[0] if values[0] is not None else self.P
             X = values[1] if values[1] is not None else self.X
             self.thermo.setState_Psat(P, X)
+
+    property TDX:
+        """
+        Get the temperature [K], density [kg/m^3 or kmol/m^3], and vapor
+        fraction.
+        """
+        def __get__(self):
+            return self.T, self.density, self.X
+
+    property TPX:
+        """Get the temperature [K], pressure [Pa], and vapor fraction."""
+        def __get__(self):
+            return self.T, self.P, self.X
+
+    property UVX:
+        """
+        Get the internal energy [J/kg or J/kmol], specific volume
+        [m^3/kg or m^3/kmol], and vapor fraction.
+        """
+        def __get__(self):
+            return self.u, self.v, self.X
+
+    property DPX:
+        """Get the density [kg/m^3], pressure [Pa], and vapor fraction."""
+        def __get__(self):
+            return self.density, self.P, self.X
+
+    property HPX:
+        """
+        Get the enthalpy [J/kg or J/kmol], pressure [Pa] and vapor fraction.
+        """
+        def __get__(self):
+            return self.h, self.P, self.X
+
+    property SPX:
+        """
+        Get the entropy [J/kg/K or J/kmol/K], pressure [Pa], and vapor fraction.
+        """
+        def __get__(self):
+            return self.s, self.P, self.X
+
+    property SVX:
+        """
+        Get the entropy [J/kg/K or J/kmol/K], specific volume [m^3/kg or
+        m^3/kmol], and vapor fraction.
+        """
+        def __get__(self):
+            return self.s, self.v, self.X

interfaces/cython/cantera/utils.pyx

@@ -4,7 +4,7 @@ cdef int _pythonMajorVersion = sys.version_info[0]
 cdef CxxPythonLogger* _logger = new CxxPythonLogger()
 CxxSetLogger(_logger)
 
-cdef string stringify(x):
+cdef string stringify(x) except *:
     """ Converts Python strings to std::string. """
     # This method works with both Python 2.x and 3.x.
     if isinstance(x, bytes):

interfaces/matlab/toolbox/@ThermoPhase/setState_Psat.m

@@ -1,10 +1,15 @@
 function setState_Psat(tp, px)
-% SETSTATE_PSAT  Set the fluid to a saturated state at a given pressure.
+% SETSTATE_PSAT  Set the fluid state using the given pressure and quality.
 % setState_Psat(tp,px)
+% The fluid state will be set to a saturated liquid-vapor state using the
+% input pressure and vapor fraction (quality) as the independent,
+% intensive variables.
 % :param tp:
 %     Instance of class :mat:func:`ThermoPhase` (or another
 %     class derived from ThermoPhase)
 % :param px:
-%     Pressure. Units: Pa
+%     Vector of length 2 containing the desired values for the pressure (Pa)
+%     and the vapor fraction
 %
+
 thermo_set(tp.tp_id, 24, px);

interfaces/matlab/toolbox/@ThermoPhase/setState_Tsat.m

@@ -1,11 +1,15 @@
 function setState_Tsat(tp, tx)
-% SETSTATE_TSAT  Set the fluid to a saturated state at a given temperature.
+% SETSTATE_TSAT  Set the fluid state using the given temperature and quality.
 % setState_Tsat(tp,tx)
+% The fluid state will be set to a saturated liquid-vapor state using the
+% input temperature and vapor fraction (quality) as the independent,
+% intensive variables.
 % :param tp:
 %     Instance of class :mat:func:`ThermoPhase` (or another
 %     class derived from ThermoPhase)
 % :param tx:
-%     Temperature. Units: K
+%     Vector of length 2 containing the desired values for the temperature (K)
+%     and the vapor fraction (quality)
 %
 
 thermo_set(tp.tp_id, 25, tx);

interfaces/matlab/toolbox/@ThermoPhase/setState_satLiquid.m

@@ -6,4 +6,4 @@ function setState_satLiquid(tp)
 %     class derived from ThermoPhase)
 %
 
-thermo_set(tp.tp_id, 2, 0);
+set(tp, 'T', temperature(tp), 'Liquid', 1.0)

interfaces/matlab/toolbox/@ThermoPhase/setState_satVapor.m

@@ -6,4 +6,4 @@ function setState_satVapor(tp)
 %     class derived from ThermoPhase)
 %
 
-thermo_set(tp.tp_id, 3, 0);
+set(tp, 'T', temperature(tp), 'Vapor', 1.0)

platform/posix/Cantera.mak.in

@@ -64,15 +64,7 @@ CANTERA_SUNDIALS_LIBS=@mak_sundials_libdir@ @mak_sundials_libs@
 #         BLAS LAPACK LINKAGE
 ###############################################################################
 
-CANTERA_have_blas_lapack_dir=@mak_have_blas_lapack_dir@
-
-ifeq ($(CANTERA_have_blas_lapack_dir), 1)
-CANTERA_BLAS_LAPACK_LIBS=@blas_lapack_dir@ @mak_blas_lapack_libs@
-CANTERA_BLAS_LAPACK_LIBS_DEP=  @mak_blas_lapack_libs_dep@
-else
-CANTERA_BLAS_LAPACK_LIBS=@mak_blas_lapack_libs@
-CANTERA_BLAS_LAPACK_LIBS_DEP=$(CANTERA_INSTALL_DIR)/lib/libctlapack.a $(CANTERA_INSTALL_DIR)/lib/libctblas.a
-endif
+CANTERA_BLAS_LAPACK_LIBS=-L@blas_lapack_dir@ @mak_blas_lapack_libs@
 
 ###############################################################################
 #      COMBINATIONS OF INCLUDES AND LIBS
@@ -94,9 +86,7 @@ CANTERA_LIBS=$(CANTERA_CORE_LIBS) \
 CANTERA_TOTAL_LIBS=$(CANTERA_LIBS)
 
 CANTERA_TOTAL_LIBS_DEP= $(CANTERA_CORE_LIBS_DEP) \
-                        $(CANTERA_SUNDIALS_LIBS_DEP) \
-                        $(CANTERA_BLAS_LAPACK_LIBS_DEP)
-
+                        $(CANTERA_SUNDIALS_LIBS_DEP)
 
 CANTERA_FORTRAN_LIBS=$(CANTERA_CORE_FTN) \
                      $(CANTERA_EXTRA_LIBDIRS) $(CANTERA_SUNDIALS_LIBS) \

platform/posix/SConscript

@@ -32,10 +32,10 @@ pc_cflags = []
 
 localenv['mak_corelibs'] = '-lcantera'
 
-localenv['mak_extra_includes'] = ['-I%s' % s for s in localenv['extra_inc_dirs']]
+localenv['mak_extra_includes'] = ' '.join('-I%s' % s for s in localenv['extra_inc_dirs'])
 pc_incdirs.extend(localenv['extra_inc_dirs'])
 
-localenv['mak_extra_libdirs'] = ['-L%s' % s for s in localenv['extra_lib_dirs']]
+localenv['mak_extra_libdirs'] = ' '.join('-L%s' % s for s in localenv['extra_lib_dirs'])
 pc_libdirs.extend(localenv['extra_lib_dirs'])
 
 if env['use_sundials'] == 'n':
@@ -74,14 +74,7 @@ localenv['mak_boost_libs'] = ' '.join('-l%s' % s for s in localenv['boost_libs']
 pc_libs += localenv['boost_libs']
 
 # Handle BLAS/LAPACK linkage
-localenv['mak_have_blas_lapack_dir'] = '1' if localenv['blas_lapack_dir'] else '0'
-
-if localenv['blas_lapack_dir']:
-    localenv['mak_blas_lapack_libs'] = ' '.join('-l%s' % s for s in localenv['blas_lapack_libs'])
-    localenv['mak_blas_lapack_libs_dep'] = ''
-else:
-    localenv['mak_blas_lapack_libs'] = ''
-    localenv['mak_blas_lapack_libs_dep'] = ''
+localenv['mak_blas_lapack_libs'] = ' '.join('-l%s' % s for s in localenv['blas_lapack_libs'])
 
 if 'Accelerate' in localenv['FRAMEWORKS']:
     localenv['mak_blas_lapack_libs'] += ' -framework Accelerate'

samples/cxx/bvp/BoundaryValueProblem.h

@@ -6,6 +6,7 @@
 #define BVP_H
 
 #include "cantera/onedim.h"
+#include <fstream>
 
 /// Namespace for the boundary value problem package.
 namespace BVP
@@ -113,18 +114,19 @@ public:
      *  @param n Component number.
      *  @param c Component parameter values
      */
-    void setComponent(int n, Component& c) {
+    void setComponent(size_t n, Component& c) {
         if (m_sim == 0) {
             start();
         }
-        if (n < 0 || n >= m_nv) {
+        if (n >= m_nv) {
             throw Cantera::CanteraError("BoundaryValueProblem::setComponent",
                                         "Illegal solution component number");
         }
         // set the upper and lower bounds for this component
         setBounds(n, c.lower, c.upper);
         // set the error tolerances
-        setTolerances(n, c.rtol, c.atol);
+        setSteadyTolerances(c.rtol, c.atol, n);
+        setTransientTolerances(c.rtol, c.atol, n);
         // specify whether this component should be considered in
         // refining the grid
         m_refiner->setActive(n, c.refine);
@@ -209,7 +211,7 @@ protected:
      * True if n is the index of the left-most grid point (zero),
      * false otherwise.
      */
-    bool isLeft(int n) const {
+    bool isLeft(size_t n) const {
         return (n == 0);
     }
 
@@ -217,7 +219,7 @@ protected:
      * True if \a n is the index of the right-most grid point, false
      * otherwise.
      */
-    bool isRight(int n) const {
+    bool isRight(size_t n) const {
         return (n == nPoints() - 1);
     }
 

samples/cxx/combustor/combustor.cpp

@@ -19,7 +19,6 @@ void runexample()
 
     // use reaction mechanism GRI-Mech 3.0
     IdealGasMix gas("gri30.cti", "gri30");
-    int nsp = gas.nSpecies();
 
     // create a reservoir for the fuel inlet, and set to pure methane.
     Reservoir fuel_in;
@@ -105,7 +104,6 @@ void runexample()
     double tfinal = 1.0;
     double tnow = 0.0;
     double tres;
-    int k;
 
     std::ofstream f("combustor_cxx.csv");
     std::vector<size_t> k_out;

samples/cxx/demo.cpp

@@ -13,6 +13,7 @@
 
 #include "cantera/IdealGasMix.h"    // defines class IdealGasMix
 #include "cantera/transport.h"      // transport properties
+#include <cstdio>
 
 // All Cantera kernel names are in namespace Cantera. You can either
 // reference everything as Cantera::<name>, or include the following

samples/cxx/kinetics1/kinetics1.cpp

@@ -48,7 +48,7 @@ int kinetics1(int np, void* p)
     // create a container object to run the simulation
     // and add the reactor to it
     ReactorNet sim;
-    sim.addReactor(&r);
+    sim.addReactor(r);
 
     // main loop
     clock_t t0 = clock();        // save start time

site_scons/buildutils.py

@@ -235,15 +235,20 @@ def compareTextFiles(env, file1, file2):
                 # String representations match, so replacement is unnecessary
                 continue
 
-            delta = max(getPrecision(floats1[j][1]), getPrecision(floats2[j][1]))
-            num1 = float(floats1[j][1])
-            num2 = float(floats2[j][1])
-            abserr = abs(num1-num2)
-            relerr = abserr / (0.5 * abs(num1 + num2) + atol)
-            if abserr > (1.1*delta + atol) and relerr > rtol:
-                print 'Values differ: {0: 14g} {1: 14g}; rel. err = {2:.3e}; abs. err = {3:.3e}'.format(num1, num2, relerr, abserr)
-                allMatch = False
-                break
+            try:
+                delta = max(getPrecision(floats1[j][1]), getPrecision(floats2[j][1]))
+                num1 = float(floats1[j][1])
+                num2 = float(floats2[j][1])
+                abserr = abs(num1-num2)
+                relerr = abserr / (0.5 * abs(num1 + num2) + atol)
+                if abserr > (1.1*delta + atol) and relerr > rtol:
+                    print 'Values differ: {0: 14g} {1: 14g}; rel. err = {2:.3e}; abs. err = {3:.3e}'.format(num1, num2, relerr, abserr)
+                    allMatch = False
+                    break
+            except Exception as e:
+                # Something went wrong -- one of the strings isn't actually a number,
+                # so just ignore this line and let the test fail
+                pass
 
         # All the values are sufficiently close, so replace the string
         # so that the diff of this line will succeed
@@ -307,7 +312,6 @@ def compareCsvFiles(env, file1, file2):
     """
     try:
         import numpy as np
-        hasSkipHeader = tuple(np.version.version.split('.')[:2]) >= ('1','4')
     except ImportError:
         print 'WARNING: skipping .csv diff because numpy is not installed'
         return 0
@@ -323,12 +327,8 @@ def compareCsvFiles(env, file1, file2):
             break
 
     try:
-        if hasSkipHeader:
-            data1 = np.genfromtxt(file1, skip_header=headerRows, delimiter=',')
-            data2 = np.genfromtxt(file2, skip_header=headerRows, delimiter=',')
-        else:
-            data1 = np.genfromtxt(file1, skiprows=headerRows, delimiter=',')
-            data2 = np.genfromtxt(file2, skiprows=headerRows, delimiter=',')
+        data1 = np.genfromtxt(file1, skip_header=headerRows, delimiter=',')
+        data2 = np.genfromtxt(file2, skip_header=headerRows, delimiter=',')
     except (IOError, StopIteration) as e:
         print e
         return 1

site_scons/wxsgen.py

@@ -76,7 +76,7 @@ class WxsGenerator(object):
                                      UpgradeCode='2340BEE1-279D-11E1-A4AA-001FBC085391',
                                      Language='1033',
                                      Codepage='1252',
-                                     Version='2.2.0',
+                                     Version='2.2.1',
                                      Manufacturer='Cantera Developers'))
 
         fields = {'Platform': 'x64'} if self.x64 else {}

src/base/checkFinite.cpp

@@ -28,14 +28,14 @@
     #include <float.h>
     #define isnan(x) _isnan(x)
     #define finite(x) _finite(x)
-#elif defined(USE_STD_ISNAN)
-    // From C++11
-    using std::isnan;
-    #define finite(x) std::isfinite(x)
 #elif defined(USE_GLOBAL_ISNAN)
     // From C99
     using ::isnan;
     using ::finite;
+#elif defined(USE_STD_ISNAN)
+    // From C++11
+    using std::isnan;
+    #define finite(x) std::isfinite(x)
 #endif
 
 namespace Cantera {

src/clib/ct.cpp

@@ -327,7 +327,7 @@ extern "C" {
         try {
             return ThermoCabinet::item(n).nAtoms(k,m);
         } catch (...) {
-            return handleAllExceptions(-1, ERR);
+            return handleAllExceptions(ERR, ERR);
         }
     }
 

src/kinetics/ImplicitSurfChem.cpp

@@ -155,13 +155,12 @@ void ImplicitSurfChem::eval(doublereal time, doublereal* y,
 {
     updateState(y);   // synchronize the surface state(s) with y
     doublereal rs0, sum;
-    size_t loc, kstart;
+    size_t loc = 0, kstart;
     for (size_t n = 0; n < m_nsurf; n++) {
         rs0 = 1.0/m_surf[n]->siteDensity();
         m_vecKinPtrs[n]->getNetProductionRates(DATA_PTR(m_work));
         kstart = m_vecKinPtrs[n]->kineticsSpeciesIndex(0,m_surfindex[n]);
         sum = 0.0;
-        loc = 0;
         for (size_t k = 1; k < m_nsp[n]; k++) {
             ydot[k + loc] = m_work[kstart + k] * rs0 * m_surf[n]->size(k);
             sum -= ydot[k];

src/matlab/phasemethods.cpp

@@ -119,24 +119,46 @@ void phasemethods(int nlhs, mxArray* plhs[],
             // floating-point attributes
         case 1:
             vv = phase_temperature(ph);
+            if (vv == DERR) {
+                reportError();
+            }
             break;
         case 2:
             vv = phase_density(ph);
+            if (vv == DERR) {
+                reportError();
+            }
             break;
         case 3:
             vv = phase_molarDensity(ph);
+            if (vv == DERR) {
+                reportError();
+            }
             break;
         case 4:
             vv = phase_meanMolecularWeight(ph);
+            if (vv == DERR) {
+                reportError();
+            }
             break;
         case 8:
-            vv = 1.0/phase_density(ph);
+            vv = phase_density(ph);
+            if (vv == DERR) {
+                reportError();
+            }
+            vv = 1.0/vv;
             break;
         case 10:
             vv = static_cast<int>(phase_nElements(ph));
+            if (vv == -1) {
+                reportError();
+            }
             break;
         case 11:
             vv = static_cast<int>(phase_nSpecies(ph));
+            if (vv == -1) {
+                reportError();
+            }
             break;
         case 12:
             input_buf = getString(prhs[3]);
@@ -150,18 +172,21 @@ void phasemethods(int nlhs, mxArray* plhs[],
             k = getInt(prhs[3]);
             m = getInt(prhs[4]);
             vv = phase_nAtoms(ph,k-1,m-1);
+            if (vv == ERR) {
+                reportError();
+            }
             break;
         case 15:
             show_thermo = getInt(prhs[3]);
             threshold = getDouble(prhs[4]);
             vv = write_phase(ph,show_thermo,threshold);
+            if (vv == -1 || vv == ERR) {
+                reportError();
+            }
             break;
         default:
             mexErrMsgTxt("Unknown job number");
         }
-        if (vv == DERR || vv == -1 || vv == ERR) {
-            reportError();
-        }
         plhs[0] = mxCreateNumericMatrix(1,1,mxDOUBLE_CLASS,mxREAL);
         double* h = mxGetPr(plhs[0]);
         *h = vv;

src/thermo/DebyeHuckel.cpp

@@ -1037,7 +1037,7 @@ void DebyeHuckel::initThermoXML(XML_Node& phaseNode, const std::string& id_)
     for (size_t k = 0; k < m_kk; k++) {
         std::string kname = speciesName(k);
         const XML_Node* spPtr = xspecies[k];
-        if (!spPtr) {
+        if (spPtr) {
             if (spPtr->hasChild("electrolyteSpeciesType")) {
                 std::string est = getChildValue(*spPtr, "electrolyteSpeciesType");
                 if ((m_electrolyteSpeciesType[k] = interp_est(est)) == -1) {

src/thermo/GeneralSpeciesThermo.cpp

@@ -173,10 +173,6 @@ void GeneralSpeciesThermo::reportParams(size_t index, int& type,
     if (sp) {
         sp->reportParameters(n, type, minTemp_, maxTemp_,
                              refPressure_, c);
-        if (n != index) {
-            throw CanteraError("GeneralSpeciesThermo::reportParams",
-                               "Internal error encountered");
-        }
     } else {
         type = -1;
     }

src/thermo/HMWSoln_input.cpp

@@ -1533,7 +1533,7 @@ void HMWSoln::initThermoXML(XML_Node& phaseNode, const std::string& id_)
     std::vector<const XML_Node*> xspecies = speciesData();
     for (size_t k = 0; k < m_kk; k++) {
         const XML_Node* spPtr = xspecies[k];
-        if (!spPtr) {
+        if (spPtr) {
             if (spPtr->hasChild("electrolyteSpeciesType")) {
                 string est = getChildValue(*spPtr, "electrolyteSpeciesType");
                 if ((m_electrolyteSpeciesType[k] = interp_est(est)) == -1) {

src/thermo/IdealGasPhase.cpp

@@ -7,6 +7,7 @@
 
 #include "cantera/thermo/IdealGasPhase.h"
 #include "cantera/base/vec_functions.h"
+#include "cantera/thermo/ThermoFactory.h"
 
 using namespace std;
 
@@ -30,7 +31,7 @@ IdealGasPhase::IdealGasPhase(XML_Node& phaseRef, const std::string& id_) :
     m_p0(-1.0),
     m_logc0(0.0)
 {
-    initThermoXML(phaseRef, id_);
+    importPhase(phaseRef, this);
 }
 
 IdealGasPhase::IdealGasPhase(const IdealGasPhase& right) :

src/thermo/Phase.cpp

@@ -645,15 +645,19 @@ doublereal Phase::elementalMassFraction(const size_t m) const
 doublereal Phase::elementalMoleFraction(const size_t m) const
 {
     checkElementIndex(m);
-    doublereal Z_n = 0.0;
-    for (size_t k = 0; k != m_kk; ++k) {
-        double nTotalAtoms = 0;
-        for (size_t l = 0; l != m_mm; ++l) {
-            nTotalAtoms += nAtoms(k, l);
+    double denom = 0;
+    for (size_t k = 0; k < m_kk; k++) {
+        double atoms = 0;
+        for (size_t j = 0; j < nElements(); j++) {
+            atoms += nAtoms(k, j);
         }
-        Z_n += nAtoms(k, m) / nTotalAtoms * moleFraction(k);
+        denom += atoms * moleFraction(k);
     }
-    return Z_n;
+    doublereal numerator = 0.0;
+    for (size_t k = 0; k != m_kk; ++k) {
+        numerator += nAtoms(k, m) * moleFraction(k);
+    }
+    return numerator / denom;
 }
 
 doublereal Phase::molarDensity() const

src/transport/GasTransport.cpp

@@ -465,23 +465,28 @@ void GasTransport::getTransportData()
 {
     for (size_t k = 0; k < m_thermo->nSpecies(); k++) {
         shared_ptr<Species> s = m_thermo->species(m_thermo->speciesName(k));
-        const GasTransportData& sptran =
-            dynamic_cast<GasTransportData&>(*s->transport.get());
-        if (sptran.geometry == "atom") {
+        const GasTransportData* sptran =
+            dynamic_cast<GasTransportData*>(s->transport.get());
+        if (!sptran) {
+            throw CanteraError("GasTransport::getTransportData",
+                "Missing gas-phase transport data for species '" + s->name + "'");
+        }
+
+        if (sptran->geometry == "atom") {
             m_crot[k] = 0.0;
-        } else if (sptran.geometry == "linear") {
+        } else if (sptran->geometry == "linear") {
             m_crot[k] = 1.0;
-        } else if (sptran.geometry == "nonlinear") {
+        } else if (sptran->geometry == "nonlinear") {
             m_crot[k] = 1.5;
         }
 
-        m_sigma[k] = sptran.diameter;
-        m_eps[k] = sptran.well_depth;
-        m_dipole(k,k) = sptran.dipole;
-        m_polar[k] = (sptran.dipole > 0);
-        m_alpha[k] = sptran.polarizability;
-        m_zrot[k] = sptran.rotational_relaxation;
-        m_w_ac[k] = sptran.acentric_factor;
+        m_sigma[k] = sptran->diameter;
+        m_eps[k] = sptran->well_depth;
+        m_dipole(k,k) = sptran->dipole;
+        m_polar[k] = (sptran->dipole > 0);
+        m_alpha[k] = sptran->polarizability;
+        m_zrot[k] = sptran->rotational_relaxation;
+        m_w_ac[k] = sptran->acentric_factor;
     }
 }
 

src/zeroD/FlowDevice.cpp

@@ -9,7 +9,7 @@ namespace Cantera
 bool FlowDevice::install(ReactorBase& in, ReactorBase& out)
 {
     if (m_in || m_out) {
-        return false;
+        throw CanteraError("FlowDevice::install", "Already installed");
     }
     m_in =  ∈
     m_out = &out;
@@ -19,9 +19,6 @@ bool FlowDevice::install(ReactorBase& in, ReactorBase& out)
     // construct adapters between inlet and outlet species
     ThermoPhase* mixin = &m_in->contents();
     ThermoPhase* mixout = &m_out->contents();
-    if (mixin == 0 || mixout == 0) {
-        return false;
-    }
 
     m_nspin = mixin->nSpecies();
     m_nspout = mixout->nSpecies();

src/zeroD/ReactorNet.cpp

@@ -234,6 +234,11 @@ size_t ReactorNet::globalComponentIndex(const string& component, size_t reactor)
 void ReactorNet::registerSensitivityReaction(void* reactor,
         size_t reactionIndex, const std::string& name, int leftright)
 {
+    if (m_integrator_init) {
+        throw CanteraError("ReactorNet::registerSensitivityReaction",
+                           "Sensitivity reactions cannot be added after the"
+                           "integrator has been initialized.");
+    }
     std::pair<void*, int> R = std::make_pair(reactor, leftright);
     if (m_sensOrder.count(R) &&
             m_sensOrder[R].count(reactionIndex)) {

test/SConscript

@@ -28,12 +28,8 @@ localenv['ENV']['CANTERA_DATA'] = Dir('#build/data').abspath
 
 PASSED_FILES = {}
 
-# Needed for Intel runtime libraries when compiling with ICC
 # Add build/lib in order to find Cantera shared library
-if localenv['ENV'].get('LD_LIBRARY_PATH'):
-    localenv['ENV']['LD_LIBRARY_PATH'] += os.pathsep + Dir('#build/lib').abspath
-else:
-    localenv['ENV']['LD_LIBRARY_PATH'] = Dir('#build/lib').abspath
+localenv.PrependENVPath('LD_LIBRARY_PATH', Dir('#build/lib').abspath)
 
 def addTestProgram(subdir, progName, env_vars={}):
     """

test/data/explicit-forward-order.inp

@@ -13,8 +13,14 @@ REACTIONS
 R1A+R1B=>H+P1              1e12  0.0   20000.0
   FORD / R1A 1.5 /
   FORD / R1B 0.5 /
+  DUPLICATE
 
 H+P1=>R1A+R1B             5e13 -2.0 5000.0
   FORD / P1 0.2 /
 
+R1A+R1B=>H+P1              1e12  0.0   20000.0
+  FORD / R1A 3.0 /
+  FORD / R1B 0.0 /
+  DUPLICATE
+
 END

test/data/explicit-forward-order.xml

@@ -108,7 +108,7 @@
   <reactionData id="reaction_data">
 
     <!-- reaction 0001    -->
-    <reaction reversible="no" id="0001">
+    <reaction duplicate="yes" reversible="no" id="0001">
       <equation>R1A + R1B =] H + P1</equation>
       <order species="R1B">0.5</order>
       <order species="R1A">1.5</order>
@@ -138,5 +138,21 @@
       <reactants>H:1.0 P1:1</reactants>
       <products>R1B:1 R1A:1.0</products>
     </reaction>
+
+    <!-- reaction 0003    -->
+    <reaction duplicate="yes" reversible="no" id="0003">
+      <equation>R1A + R1B =] H + P1</equation>
+      <order species="R1B">0.0</order>
+      <order species="R1A">3.0</order>
+      <rateCoeff>
+        <Arrhenius>
+           <A>1.000000E+06</A>
+           <b>0.0</b>
+           <E units="cal/mol">20000.000000</E>
+        </Arrhenius>
+      </rateCoeff>
+      <reactants>R1B:1 R1A:1.0</reactants>
+      <products>H:1.0 P1:1</products>
+    </reaction>
   </reactionData>
 </ctml>

test/thermo/ThermoPhase_Test.cpp

@@ -91,4 +91,15 @@ TEST_F(TestThermoMethods, getMassFractionsByName)
     EXPECT_EQ(Y.size(), (size_t) 3);
 }
 
+TEST_F(TestThermoMethods, setState_nan)
+{
+    double nan = std::numeric_limits<double>::quiet_NaN();
+    thermo->setState_TP(500, 12345);
+    EXPECT_THROW(thermo->setState_TP(nan, 55555), CanteraError);
+    EXPECT_THROW(thermo->setState_TP(555, nan), CanteraError);
+    EXPECT_THROW(thermo->setState_HP(nan, 55555), CanteraError);
+    EXPECT_THROW(thermo->setState_SV(1234, nan), CanteraError);
+    EXPECT_THROW(thermo->setState_TR(555, nan), CanteraError);
+}
+
 }

test_problems/ChemEquil_ionizedGas/ionizedGasEquil.cpp

@@ -7,7 +7,7 @@ using namespace Cantera;
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
 #ifdef DEBUG_CHEMEQUIL

test_problems/CpJump/CpJump.cpp

@@ -9,7 +9,7 @@ using namespace Cantera;
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     try {

test_problems/SConscript

@@ -33,10 +33,7 @@ else:
 localenv['ENV']['CANTERA_DATA'] = pjoin(os.getcwd(), '..', 'build', 'data')
 
 # Add build/lib in order to find Cantera shared library
-if localenv['ENV'].get('LD_LIBRARY_PATH'):
-    localenv['ENV']['LD_LIBRARY_PATH'] += os.pathsep + Dir('#build/lib').abspath
-else:
-    localenv['ENV']['LD_LIBRARY_PATH'] = Dir('#build/lib').abspath
+localenv.PrependENVPath('LD_LIBRARY_PATH', Dir('#build/lib').abspath)
 
 PASSED_FILES = {}
 

test_problems/VCSnonideal/NaCl_equil/nacl_equil.cpp

@@ -25,7 +25,7 @@ void printUsage()
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     suppress_deprecation_warnings();

test_problems/VPsilane_test/silane_equil.cpp

@@ -11,7 +11,7 @@ using namespace Cantera;
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     try {

test_problems/cathermo/HMW_test_1/HMW_test_1.cpp

@@ -30,7 +30,7 @@ void pAtable(HMWSoln* HMW)
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     int retn = 0;

test_problems/cathermo/HMW_test_3/HMW_test_3.cpp

@@ -30,7 +30,7 @@ void pAtable(HMWSoln* HMW)
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
 

test_problems/cathermo/VPissp/ISSPTester.cpp

@@ -24,7 +24,7 @@ using namespace Cantera;
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
 

test_problems/cathermo/ims/IMSTester.cpp

@@ -23,7 +23,7 @@ using namespace Cantera;
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
 

test_problems/cathermo/issp/ISSPTester.cpp

@@ -24,7 +24,7 @@ using namespace Cantera;
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
 

test_problems/cathermo/testIAPWS/testIAPWSphi.cpp

@@ -8,7 +8,7 @@ using namespace Cantera;
 
 int main()
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     WaterPropsIAPWSphi* phi = new WaterPropsIAPWSphi();

test_problems/cathermo/testIAPWSPres/testPress.cpp

@@ -20,7 +20,7 @@ double numdpdt(WaterPropsIAPWS* water, double T, double pres)
 
 int main()
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     double dens, u, s, h;

test_problems/cathermo/testIAPWSTripP/testTripleP.cpp

@@ -9,7 +9,7 @@ using namespace Cantera;
 
 int main()
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     double dens, u, s, h, cv, cp, pres;

test_problems/cathermo/testWaterPDSS/testWaterPDSS.cpp

@@ -18,7 +18,7 @@ double tvalue(double val, double atol = 1.0E-9)
 
 int main()
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     double pres;

test_problems/cathermo/testWaterTP/testWaterSSTP.cpp

@@ -17,7 +17,7 @@ double tvalue(double val, double atol = 1.0E-9)
 
 int main()
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     double pres;

test_problems/cxx_ex/examples.cpp

@@ -33,7 +33,7 @@ exfun fex[] = {kinetics_example1, kinetics_example3,
 // main program
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     int example_num = 0;

test_problems/diamondSurf/runDiamond.cpp

@@ -26,7 +26,7 @@ void printDbl(double val)
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     if (argc != 2) {

test_problems/mixGasTransport/mixGasTransport.cpp

@@ -26,7 +26,7 @@ using namespace Cantera;
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     string infile = "diamond.xml";

test_problems/multiGasTransport/multiGasTransport.cpp

@@ -36,7 +36,7 @@ static double cutoff(double val, double atol=1.0E-15)
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     string infile = "diamond.xml";

test_problems/pureFluidTest/testPureWater.cpp

@@ -17,7 +17,7 @@ double tvalue(double val, double atol = 1.0E-9)
 
 int main()
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     double pres;

test_problems/rankine_democxx/rankine.cpp

@@ -77,7 +77,7 @@ int openRankine(int np, void* p)
 
 int main()
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     try {

test_problems/silane_equil/silane_equil.cpp

@@ -9,7 +9,7 @@ using namespace Cantera;
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     try {

test_problems/surfSolverTest/surfaceSolver.cpp

@@ -151,7 +151,7 @@ void printSurf(ostream& oooo,
 
 int main(int argc, char** argv)
 {
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
     _set_output_format(_TWO_DIGIT_EXPONENT);
 #endif
     string infile;