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Author SHA1 Message Date
Ray Speth
8591a7ee5c [Python] Fix handling of bad input to 'stringify' 
Cases where a string is required but a non-string is provided will now generate
an exception instead of substituting the empty string.
 2015-10-14 12:58:08 -04:00
Ray Speth
512dffe859 [Test] Fix csv test comparisons to work with Numpy 1.10 
Drop support for Numpy 1.3 (which lacks the skip_header argument to genfromtxt).
 2015-10-08 13:20:07 -04:00
Ray Speth
fbf93bf270 [Doc] Add Doxygen docstrings for wrapper classes 
Without at least a basic docstring, these classes are excluded from the Doxygen
documentation.
 2015-10-07 13:54:47 -04:00
Ray Speth
3914ede44a [Test/Python] Fix warnings about unclosed files 2015-10-07 12:59:46 -04:00
Ray Speth
58110351af [Test] Fix deprecation warnings in Python tests 
This also fixes support for Numpy 1.10, which removes the 'skiprows' keyword.
 2015-10-07 12:59:27 -04:00
Ray Speth
92d3ba0bf7 [Test] Enable DeprecationWarning in Python test suite 2015-10-07 11:45:55 -04:00
Ray Speth
3d27dfa1a1 [Reactor] Eliminate unused variable ReactorNet::m_iown 2015-10-05 18:48:14 -04:00
Ray Speth
a956f3904a [Thermo] Deprecate get/setReferenceComposition and xMol_Ref 2015-10-05 15:25:05 -04:00
Ray Speth
5926d2db7c [ck2cti] Handle reactions containing 'hv' pseudospecies 
Convert to an irreversible reaction and ignore the photon.
 2015-10-05 14:59:35 -04:00
Ray Speth
b38a9332e2 Treat duplicate keys in composition strings as errors 
For example, 'H2:0.5, O2:0.5, H2:0.1', which would previously have been treated
as equivalent to 'O2:0.5, H2:0.1'.
 2015-10-05 13:02:16 -04:00
Ray Speth
0e4b0cba0f [Matlab] Fix error handling for nAtoms to avoid false positives 
Species can have negative "atoms" of an "element" in the case where the element
is an electron and the species is a positive ion.
 2015-09-08 12:26:58 -04:00
Ray Speth
54a71b8f68 Remove unused exp3to2 script 2015-09-08 12:26:58 -04:00
Ray Speth
5ed6d9a2af [Test] Fix compilation errors with VS2015 2015-09-08 12:26:58 -04:00
Ray Speth
67172cd478 [Test] Disable problematic test with old CVODE 2015-09-08 12:26:55 -04:00
Ray Speth
567a854377 Fix a compilation error when using '-std=c++11' 2015-09-04 18:37:55 -04:00
Ray Speth
d69daab39f [Test] Fix error in test comparison when numbers disappear 2015-09-04 18:37:43 -04:00
Ray Speth
62730b1ff7 Remove unimplemented derivative calculation functions 2015-08-28 15:51:13 -04:00
Ray Speth
ab4add0ba2 Cantera does not write temporary files 2015-08-27 23:38:55 -04:00
Ray Speth
a77b79b00c [Python] Check for compatibility before adding Quantities 2015-08-24 17:31:04 -04:00
Ray Speth
25b1dc90f2 [Python] Set default constant property pair in Quantity.equilibrate 2015-08-24 17:31:04 -04:00
Ray Speth
8299646059 [Python] Add example demonstrating use of class Quantity 2015-08-24 17:31:04 -04:00
Ray Speth
032537710f [Python] Quantity.equilibrate updates the Quantity's state 2015-08-24 17:31:04 -04:00
Ray Speth
d559af9d38 [Python] Add docs for class Quantity 2015-08-24 17:31:04 -04:00
Ray Speth
94f94dd0e6 [Python] Basic implementation of class Quantity 2015-08-24 17:31:04 -04:00
Ray Speth
6e138d0ae4 [Reactor] Always check that input/output are finite 
This causes problems to be caught early, where they can at least sometimes be
handled as recoverable intergrator errors, rather than letting NaN values
propagate through the solution.
 2015-08-24 12:27:07 -04:00
Ray Speth
86835a5eeb [Thermo] Show large negative species concentrations in phase report 
Non-trivial negative concentrations generally indicate a problem, and shouldn't
be hidden.
 2015-08-23 19:35:23 -04:00
Ray Speth
60b98b362c [Kinetics] Prevent positive feedback in negative species concentrations 
For binary (or higher order) reactions, multiple negative (but small, i.e. with
respect to integration tolerances) species concentrations should not produce
positive reaction rates that would drive those concentrations to even more
negative values.
 2015-08-23 19:29:49 -04:00
Ray Speth
bb2d1c0993 [Thermo] Prevent setting thermodynamic state variables to NaN 
Throwing an exception when a state variable is being set to NaN transforms some
reactor network integration errors from unrecoverable errors into recoverable
errors.
 2015-08-23 17:09:17 -04:00
Ray Speth
2b7bcf2b3e [Python] Prevent renaming of Python extension module 
In Cygwin, some versions of SCons append a 'cyg' prefix to DLL names, which
breaks the Python extension module that is supposed to be named just
'_cantera.dll'.
 2015-08-13 22:22:33 -04:00
Ray Speth
7bcbbaafd9 [Thermo] Use consistent implementation for convenience constructors 
The constructor with the signature (inputFile, [id]) just calls initThermoFile.
The constructor with the signature (phase XML node, [id]) just calls importPhase
(note that the id argument is unused, since the correct XML node must already be
given).
 2015-08-05 12:34:22 -04:00
Ray Speth
7fe8f0f3b7 [Thermo] Refactor common initialization out of constructors 2015-08-05 12:09:02 -04:00
Ray Speth
ff60328ecd [Thermo] Fix IdealGasPhase constructor from XML_Node 2015-08-04 12:01:45 -04:00
Ray Speth
78412b3d72 Increase number of points used in multiprocessing example 
This helps average out some performance variability to make the effect of
multiprocessing more clear.
 2015-08-03 23:15:07 -04:00
Ray Speth
6514f7a8e1 Fix multiprocessing example when using Python 3 
In Python 3, 'map' returns an object which evalutes the function as it is
consumed, not when 'map' is called. Therefore, the correct comparison to
pool.map(...) is list(map(...)).
 2015-08-03 23:00:54 -04:00
Ray Speth
7ca9327f7d Fix multiprocessing example to actually get the indicated property 2015-08-03 22:57:03 -04:00
Ray Speth
ea1f7c015b Deprecate PDSS construction directly from XML files 
The constructors from existing XML_Nodes are the ones that are actually used.
 2015-08-03 17:16:38 -04:00
Bryan W. Weber
2334410b5b Uninstall all files properly 2015-08-02 23:06:16 -04:00
Bryan W. Weber
19f4468728 Clean up after setuptools builds 2015-08-02 23:06:16 -04:00
Bryan W. Weber
ca3a09a3d4 Add setuptools directories to python_minimal .gitignore 2015-08-02 23:06:16 -04:00
Bryan W. Weber
1174de9232 Reformat Cython setup.py.in and add metadata 
Conform to 4 space tabs. Add classifiers about Cantera. Add long
description.
 2015-08-02 23:06:16 -04:00
Bryan W. Weber
b979cea3d2 Switch Cython and python interfaces to setuptools 
Replace distutils with setuptools in the Cython and python_minimal
interfaces. Add console_scripts option to generate OS specific scripts to run
ck2cti, mixmaster, and ctml_writer

Remove script files that are obsoleted by console_scripts from
setuptools. Remove installation of the script modules from SConstruct.

Fix Python installers so that when a prefix directory is specified on the
command line, setuptools doesn't throw an error. The setuptools documentation at
[1] prefers setting PYTHONUSERBASE rather than PYTHONPATH. Use normpath to avoid
bugs in setuptools on Windows [2].  Specify an empty "--prefix" if the compiler
is clang to fix a bug with Homebrew Python on Mac OSX [3].

[1]: https://pythonhosted.org/setuptools/easy_install.html#custom-installation-locations
[2]: http://stackoverflow.com/q/31629398
[3]: https://github.com/Homebrew/homebrew-python/issues/187
 2015-08-02 23:06:16 -04:00
Bryan W. Weber
5f8bd40c0d Add functions to main scripts to be entry_points 
Add functions to ck2cti, ctml_writer, and a new file __main__.py to
mixmaster to be the entry_points locations that setuptools scripts
will call.
 2015-08-02 23:06:16 -04:00
Bryan W. Weber
c6ccffe44f Move imports in ck2cti to the top of the file 2015-08-02 23:06:16 -04:00
Bryan W. Weber
eb2df78260 Fix syntax error in a Python example 2015-08-02 23:06:16 -04:00
Bryan W. Weber
0b5a46fe03 Remove execute bit from files that don't need it 2015-08-02 23:06:16 -04:00
Ray Speth
bfb20e1f50 Consistently use vector_fp and vector_int typedefs 2015-08-02 23:06:16 -04:00
Ray Speth
ceefc5ecb0 Consistently use ThermoPhase::RT() 2015-08-02 23:06:16 -04:00
Ray Speth
9cdfd12172 Move definition of polyfit to polyfit.cpp 2015-08-02 23:06:16 -04:00
Ray Speth
acdf9cf0ed Clean up interstitial whitespace 
Remove extra space around operators, between words, etc.
 2015-08-02 23:06:16 -04:00
Ray Speth
6a04193646 Fix un-bracketed if, for, and else statements 2015-08-02 23:06:15 -04:00