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58 commits

Author SHA1 Message Date
Ray Speth
c57f9b644f Conversion of Chemkin mechanisms in Python and Matlab now uses ck2cti.py 2012-07-26 20:49:37 +00:00
Ray Speth
0e21bfd0e0 Introduced a test suite for Chemkin-format mechanism conversions 2012-07-26 20:49:01 +00:00
Ray Speth
b29438eb6d ck2cti.py supports extended format for large molecule compositions 
This extension places extra elemental composition data at the end of the first
line of the thermo data. See 'soot.inp' for an example.
 2012-07-26 20:48:58 +00:00
Ray Speth
a0c4da3e44 Updated ck2cti.py to handle non-integer stoichiometric coefficients 2012-07-26 20:48:55 +00:00
Ray Speth
2b9bbddf36 ck2cti.py can now parse 9-coefficient NASA polynomials 2012-07-26 20:48:52 +00:00
Ray Speth
5c041b51cf ck2cti.py now checks for undefined elements 2012-07-26 20:48:49 +00:00
Ray Speth
d3218d4dfa ck2cti.py now preserves order of chemical elements 2012-07-26 20:48:44 +00:00
Ray Speth
27950730ef [Python] More flexible interface to Phase.selectSpecies and Phase.SelectElement 
Allow specification of a single component when extracting a single value,
instead of requiring a sequence. This in turn provides the same capability to a
number of functions which previously only accepted sequences of element or
species names.
 2012-06-22 22:36:27 +00:00
Ray Speth
ac54d63782 Fixed some documentation issues with the Python Flame classes 
Docstrings for undocumented methods of child classes are automatically copied
from the corresponding method of the parent class. This works both for
docstrings as shown in the Python interpreter as well as the Sphinx-generated
documentation.

Removed manually duplicated docstrings from setProfile(), solve() and
setRefineCriteria() methods.
 2012-06-19 16:34:16 +00:00
Ray Speth
1a22835ad4 Added support for specifying forward reaction orders in ck2cti.py 2012-06-15 21:56:56 +00:00
Ray Speth
0da94ea0c2 Added support for explicit reverse rate constants to ck2cti.py 2012-06-15 21:56:53 +00:00
Ray Speth
1a60d55135 Added support for SRI falloff parameterization to ck2cti.py 2012-06-15 21:56:49 +00:00
Ray Speth
aab72379fe Updated physical constants to be consistent with 2010 CODATA recommendations 2012-06-12 22:48:32 +00:00
Ray Speth
96114edb46 Fixed names of some executable scripts 
Also added shebang line to ctml_writer
 2012-06-05 19:56:21 +00:00
Ray Speth
7709978392 Cleanup of MixMaster/Units package 2012-06-05 19:56:10 +00:00
Ray Speth
2f9f2abf5e Fixed setting the _initialized flag on restored Python OneD objects 2012-05-30 16:02:48 +00:00
Ray Speth
bdac195cb0 Added input file documentation for Chebyshev and P-log rate expressions 2012-05-29 18:03:31 +00:00
Ray Speth
176d8ecfe0 Updated the rxnpath1.py sample 
This sample now uses a locally installed copy of Graphviz to produce an image,
instead of relying on a public 'webdot' server which no longer exists.
 2012-05-29 18:03:27 +00:00
Ray Speth
3df5c60e8f Eliminated trailing commas from some CSV files used in regression tests 2012-05-25 23:13:42 +00:00
Ray Speth
a78755b971 Fixed some undefined references in the CTI documentation 2012-05-18 22:42:03 +00:00
Ray Speth
754faa3b13 Added option to ignore third-body efficiencies for undeclared species 
To enable this option, in the phase definition, add
'skip_undeclared_third_bodies' to the list passed as the 'options'
argument.
 2012-05-18 22:41:58 +00:00
Ray Speth
eb6c7659b8 ctml_writer accepts 'id' argument as lower case 
This maintains compatibility with existing (<=1.8) input files, at the
cost of being poor Python style since it overloads the built-in 'id'
function.
 2012-05-13 22:41:17 +00:00
Ray Speth
34cffd0135 Fixed issues generating version-dependent installer for Windows Python module 
Passing the '--target-version' option to bdist_msi will generate an
installer that requires the right version of Python without distutils
needing to be able to find a working compiler.
 2012-04-19 16:45:15 +00:00
Ray Speth
02ccf4f715 Improved formatting of TypeErrors encountered in ctml_writer.py 2012-04-04 18:45:07 +00:00
Ray Speth
47f3bac7ae Added documentation for the classes used in CTI files 2012-04-04 18:45:03 +00:00
Ray Speth
d16f70ab44 Fixed some spelling issues 2012-04-04 18:44:24 +00:00
Ray Speth
bb54b13997 Removed RMG-specific code from ck2cti.py 2012-03-30 23:48:47 +00:00
Ray Speth
382c4bd02e Fixed some parsing issues in ck2cti.py 2012-03-30 23:48:44 +00:00
Ray Speth
e4b804b208 Added command line interface to ck2cti.py 2012-03-30 23:48:40 +00:00
Ray Speth
938d767fde Replaced deprecated syntax in ctml_writer.py 2012-03-30 23:48:29 +00:00
Ray Speth
8386df50b9 ctml_writer now handles Chebyshev and P-log rate expressions 2012-03-30 23:47:27 +00:00
Ray Speth
126dc9e04c Print error message when missing species thermo 2012-03-30 23:47:24 +00:00
Ray Speth
d456284b8e Implemented writing the parsed mechanism to a .cti file in ck2cti.py 2012-03-30 23:47:15 +00:00
Ray Speth
a7ae602612 ck2cti.py parses elemental compositions from thermo entries 2012-03-30 23:47:12 +00:00
Ray Speth
dddfd857db Python ck2cti can read transport properties 2012-03-30 23:47:09 +00:00
Ray Speth
6a4cce979c Fixed string representations of Species in ck2cti 2012-03-30 23:47:05 +00:00
Ray Speth
cee19f67a6 Fixed handling of reaction delimiters 2012-03-30 23:47:01 +00:00
Ray Speth
c80113d767 Imported a trimmed-down version of the RMG-py Chemkin reader 2012-03-30 23:46:58 +00:00
Ray Speth
80b723cfe7 Python: Fixed reference counting issues with Func objects used by Reactors 
The C++ Reactor class doesn't own a reference to the Func object. To make
borrowing the reference safe, the Python Reactor class now owns a reference,
which is guaranteed to be valid for the lifetime of the C++ Reactor object.
 2012-03-25 23:25:45 +00:00
Ray Speth
c56bfab0ed Matlab: Allow simpler syntax for creating ReactorNets with one reactor 
A network with a single reactor can be created with either:
    ReactorNet({reactor}), i.e. a single element cell array
or, the new way:
    ReactorNet(reactor)
 2012-03-24 01:33:54 +00:00
Ray Speth
6c29c0fe84 Syntax errors in CTI files now show more context lines 2012-03-16 14:44:31 +00:00
Ray Speth
4506ee2f8a Fixed some compiler warning issues 2012-03-15 19:55:18 +00:00
Ray Speth
e4f2acaf3d Fixed issues with Matlab toolbox identified by the code analyzer 2012-03-15 19:54:41 +00:00
Ray Speth
790d40b00c Normalized whitespace and indentation in the matlab toolbox 2012-03-15 19:52:58 +00:00
Ray Speth
b4ceb7da2e Reformatted the Python docstrings to work better with Sphinx 
This means that the docstrings are now parsed as reStructuredText.
 2012-03-13 17:34:47 +00:00
Ray Speth
7676097b4a Removed execute permission from nonexecutable files 2012-03-13 17:32:41 +00:00
Ray Speth
bac65b26a1 Added machinery for unit testing of the Matlab toolbox 
Unit tests are written using the Matlab xUnit Test Framework
 2012-03-13 17:32:10 +00:00
Ray Speth
45eae5b351 Matlab: fixed importing files from paths containing periods 
This includes handling relative paths specified with '..'
 2012-03-13 17:32:02 +00:00
Ray Speth
32de9a8b27 Fixed some problems printing error messages in Matlab 2012-03-10 21:25:22 +00:00
Ray Speth
82d467944f Eliminated temporary files from the ct2ctml conversion process 
Added libstringstream, which maps stdin and stdout to std::iostream.
Using this library means we no longer create either the temporary .py
file or the ct2ctml.log file.

This also eliminates the synchronization problems that motivated the
sleep commands around the system call, so cti to ctml conversions are
significantly faster now.
 2012-03-09 22:59:21 +00:00