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Author SHA1 Message Date
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
Ray Speth
02f9497b20 Remove functions which just explicitly call base class functions 2015-08-02 23:06:15 -04:00
Ray Speth
801334c84e Merge nested if statements 2015-08-02 23:06:15 -04:00
Ray Speth
546eede80c Fix pointer logic errors in initThermoXML 
Affects DebyeHuckel and HMWSoln
 2015-08-02 23:06:15 -04:00
Ray Speth
f90bf978df Use += and -= where appropriate 2015-08-02 23:06:15 -04:00
Ray Speth
e4c45b6429 General whitespace cleanup 
Remove unnecessary blank lines and trailing whitespace. Replace tabs with
spaces.
 2015-08-02 23:06:15 -04:00
Ray Speth
619cd20f14 Fix badly-formatted else/else if/catch clauses 2015-08-02 23:06:15 -04:00
Ray Speth
d24dfea036 Remove unnecessary public/private/protected labels 2015-08-02 23:06:15 -04:00
Ray Speth
f219b49e63 Remove unnecessary newlines in function signatures 2015-08-02 23:06:15 -04:00
Ray Speth
d086be8d3d Eliminate do-while loops in favor of regular while loops 2015-08-02 23:06:15 -04:00
Ray Speth
a6e390dfc5 Standardize always-true while loop condition to "true" 2015-08-02 23:06:15 -04:00
Ray Speth
187fd27cef Remove unnecessary use of (void) 2015-08-02 23:06:14 -04:00
Ray Speth
09207eacfb Eliminate use of 'memset' 2015-08-02 23:06:14 -04:00
Ray Speth
c3c80f79fb Remove extraneous parentheses 2015-08-02 23:06:14 -04:00
Ray Speth
89c751f217 Fix compilation problems when debug_verbose=y 2015-08-02 23:06:14 -04:00
Ray Speth
65741171f4 [Doc] Fix typos in NASA polynomial formulas 2015-07-23 16:46:08 -04:00
Ray Speth
d8772f261b [Reactor] Cannot add sensitivity reactions to initialized ReactorNet 
Before, the attempt to add the reaction was silently ignored. Now, this raises
an exception.
 2015-07-21 14:54:13 -04:00
Ray Speth
6cc5652de6 Remove commented-out code 2015-07-20 17:20:46 -04:00
Ray Speth
de005c083e Eliminate VCS_DATA_PTR macro 2015-07-20 16:17:31 -04:00
Ray Speth
bf2ceed60e Remove some leftover debugging ifdefs 2015-07-20 15:47:17 -04:00
Ray Speth
c49c969184 [Kinetics] Remove unused code for reactant and product "groups" 2015-07-20 14:04:53 -04:00
Ray Speth
4f1250ef53 [Kinetics] Remove unneeded variables for reaction equation 
Extract this data from the reaction objects directly as needed.
 2015-07-20 13:53:47 -04:00
Ray Speth
62f2af5534 [Kinetics] Eliminate unnecessary variable m_rxntype 2015-07-20 13:01:05 -04:00
Ray Speth
f623e44d32 [Kinetics] Eliminate unnecessary m_rrxn and m_prxn variables 
This information can be extracted from the Reaction objects as-needed.
 2015-07-20 12:56:56 -04:00
Ray Speth
ca90c671ac [Thermo/Doc] Fix description of Shomate temperature polynomial 
The docstring for this function was incorrectly copied from NasaPoly1.
 2015-07-17 18:21:25 -04:00
Ray Speth
b7a5aff900 [Thermo] Convert Shomate coefficients when creating objects 
Do conversion to nondimensional units once when creating the ShomatePoly object,
instead of every time that properties are calculated.
 2015-07-17 18:18:03 -04:00