Allow None when setting the state of a PureFluid

Allow None as an option when setting the temperature and quality or
pressure and quality of a PureFluid. This mimics similar functionality
for Solutions.

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3213 02a645c2-efd0-11dd-984d-ab748d24aa7e
[Cython] Allow None when setting the quality of a PureFluid

Allow None as an option for the quality as well as the
temperature and pressure when setting the state of a PureFluid.
Completes r3213.

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3214 02a645c2-efd0-11dd-984d-ab748d24aa7e
[Doc] Fix version number shown in Doxygen documentation

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3215 02a645c2-efd0-11dd-984d-ab748d24aa7e
[Doc] Fix errors in NASA9 formula documentation

Also, remove duplicate (erroneous) documentation from Nasa9PolyMultiTempRegion
and replace this with a reference to the docs for Nasa9Poly1.

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3216 02a645c2-efd0-11dd-984d-ab748d24aa7e
[Kinetics] Fix calculation of coverage-dependent reaction rates

The formula used was not consistent with the standard formulation for
coverage-dependent reaction rates, which uses 10 as the base for the
temperature-independent term with the coverage in the exponential (see
Eq. 11.113 of Kee et al.).

The impact of this change should be minor, as most coverage-dependent reaction
rates appear not to use this term of the parameterization.

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3217 02a645c2-efd0-11dd-984d-ab748d24aa7e
[Doc] Describe syntax for specifying coverage dependencies

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3218 02a645c2-efd0-11dd-984d-ab748d24aa7e
[Doc] Give better examples for using 'const_cp'

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3219 02a645c2-efd0-11dd-984d-ab748d24aa7e
[Kinetics] Deprecate unused methods of rate coefficient implementations

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3220 02a645c2-efd0-11dd-984d-ab748d24aa7e
[Kinetics] Deprecate unused methods for writing hard-coded mechanisms

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3221 02a645c2-efd0-11dd-984d-ab748d24aa7e
[SCons/Test] Re-run tests if shared library changes

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3222 02a645c2-efd0-11dd-984d-ab748d24aa7e
Remove CTML_VERSION macros

CTML_VERSION_1_4_1 was never used, and defining CTML_VERSION_1_4 broke reading
values written by the addInteger and addFloat functions with the getInteger and
getFloat functions, respectively.

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3223 02a645c2-efd0-11dd-984d-ab748d24aa7e
Add version of installVPThermoForSpecies without unused arguments

Deprecate the old version of SpeciesThermoFactory::installVPThermoForSpecies.

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3224 02a645c2-efd0-11dd-984d-ab748d24aa7e
[SCons] Remove unnecessary uses of pjoin

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3225 02a645c2-efd0-11dd-984d-ab748d24aa7e
[Test] Fix fileLog class used in DH_graph_1

The class was missing the implementation of writeendl, which caused the
base class method to be called, occasionally leading to confusing test failures.

Not setting the mode of the output file caused it not to be automatically created,
so the log file usually wasn't even being written.

git-svn-id: https://cantera.googlecode.com/svn/cantera/trunk@3226 02a645c2-efd0-11dd-984d-ab748d24aa7e