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341 commits

Author SHA1 Message Date
Bryan W. Weber
fc2d7e4ce0 [Reactor] Change 'species' to 'component' in context of sensitivities 
Change the variable named *species* to be named *component*. This
better matches the utility of this variable, since it can be used to
retrieve any of the state variables. Also, update the corresponding
documentation.
 2013-12-16 23:22:04 +00:00
Ray Speth
e1a49487b7 [Kinetics] Remove deprecated getActivationEnergies function 
Resolves Issue 147.
 2013-12-16 23:21:52 +00:00
Ray Speth
f1b28158bf [Reactor] Fix behavior of componentIndex with ambigous names 
The name 'H' can mean either the species by that name or the entahlpy
of the reactor, in the case of ConstPressureReactor, and the previous
behavior always returned the index of the enthalpy.

This changes the behavior to preferentially return the species, and
adds alternative names for reactor state variables that are less
likely to generate namespace collisions: 'mass', 'volume',
'int_energy', 'enthalpy', 'temperature', 'distance', 'velocity'. The
single character names are still supported.

Resolves Issue 193.
 2013-12-14 00:18:12 +00:00
Ray Speth
5b7a8d1b4e [Python/Doc] Improved documentation of sensitivity parameters 2013-12-14 00:18:07 +00:00
Ray Speth
f63f8ae57e Remove deprecated HTML logging functionality 2013-12-09 01:36:11 +00:00
Ray Speth
e7e5d739a1 [Test] Fix some issues with PYTHONPATH 2013-12-09 01:36:03 +00:00
Ray Speth
b5e540c903 [Python] Remove the legacy Python module 2013-12-09 01:35:08 +00:00
Ray Speth
07739c4b1f [Cython] Move CTI/CTML converter tests from old Python module to Cython module 2013-12-09 01:34:50 +00:00
Ray Speth
57f1506d0b [Cython] Move reactor tests from old Python module to Cython module 2013-12-09 01:34:46 +00:00
Ray Speth
59564659b3 [Cython] Move equilibrium tests from old Python module to Cython module 2013-12-09 01:34:41 +00:00
Ray Speth
6ec7d04839 [Cython] Move pure fluid tests from old Python module to Cython module 2013-12-09 01:34:36 +00:00
Ray Speth
24e3f99da4 [Cython] Move kinetics tests from old Python module to Cython module 2013-12-09 01:34:30 +00:00
Ray Speth
70a728c8f7 [Cython] Move thermo tests from old Python module to Cython module 2013-12-09 01:34:25 +00:00
Ray Speth
9dd30c7116 [Test] Adjust integrator tolerances for some reactor tests 
Tests of the old-style ConstPressureReactor with surface reactions were
failing on Windows when using the old (non-Sundials) version of CVODE.
 2013-12-09 01:34:16 +00:00
Ray Speth
3e4ccd4027 [Thermo] Make modification of discontinuous NASA polynomials optional 
Adding the attribute allow_discontinuities="true" to a phase's
'thermo' node (CTML) or adding 'allow_discontinuous_thermo' to a
phase's 'options' argument (CTI) will disable the automatic adjustment
of the provided polynomials so that enthalpy and entropy are
continuous at the midpoint temperature.
 2013-12-09 01:34:06 +00:00
Ray Speth
9651b16b16 [ctml] Fix constructor for stoichiometric_solid phase 
Error introduced in r2579
 2013-12-06 23:45:22 +00:00
Ray Speth
a289e6f613 [ck2cti] Add support for species names containing '+' and '=' 2013-12-06 23:15:24 +00:00
Ray Speth
4107b268ce [ck2cti/Test] Eliminate confusing messages from expected errors 
Suppress error messages from tests of ck2cti that use bad input to
test that input validation is working correctly.
 2013-12-06 23:15:21 +00:00
Ray Speth
a786135f13 [ck2cti] Add support for truncated section header names 
Accept truncated section names such as 'REAC' for 'REACTIONS' and
'ELEM' for 'ELEMENTS'.
 2013-12-06 23:15:18 +00:00
Ray Speth
b29a6b1c7b [Cython] Direct log output to sys.stdout 
This fixes the problem of some output (notably from the 1D solver)
going to std::cout when that is not the primary output location,
e.g. when using IDLE or the IPython QtConsole.
 2013-12-06 23:15:14 +00:00
Ray Speth
025da8b4c0 [Matlab] Remove broken ck2ctml function 
There are three problems with this function. It does not work, since
it calls ctmethods with the wrong number of arguments. Even if that
were fixed, it wouldn't do what it claims, as the method it calls
generates a CTI file, not an XML file. Finally, it is redundant, as
the 'ck2cti' function can be used for generating the CTI file, and the
CTI to XML conversion is handled automatically when importing the
phase.

Therefore, this function is being removed.
 2013-12-06 23:15:08 +00:00
Ray Speth
1a291b47fe [CTI] Add optional 'note' field to Phase definitions 
The note field is preserved when converting to XML, and can be used to
store extra information used by applications other than Cantera.
 2013-12-05 20:54:08 +00:00
Ray Speth
7f35228e3f [Cython] Expose global 'appdelete' method 
Occasionally useful for debugging memory leaks
 2013-12-05 20:54:06 +00:00
Ray Speth
681a08fc8d Fix issues with pure fluids near temperature limits 
Fixes Issue 186.
 2013-11-12 23:44:51 +00:00
Ray Speth
81a8274e99 [Cython] Add 'atomic_weight' method and 'atomic_weights' property 
Resolves Issue 185.
 2013-11-12 23:44:46 +00:00
Ray Speth
904e3e66e9 [ck2cti] Accept reaction units declared in either order 
That is, energy followed by quantity or quantity followed by energy.
 2013-10-21 22:13:00 +00:00
Ray Speth
94f1b35b79 [ck2cti] Partial support for scientific notation in stoichiometric coefficients 
This won't work for positive exponents, because the '+' will still be
interpreted as a delimiter between terms of the reaction expression.
 2013-10-21 01:55:18 +00:00
Ray Speth
6d5b7999de [SCons] Use specified 'python_compiler' to link Python module 
Fixes Issue 179.
 2013-10-15 17:06:35 +00:00
Ray Speth
f871dd8cf0 [SCons] Add 'python_compiler' option for Cython module compilation 2013-10-15 14:59:31 +00:00
Ray Speth
2de0ae6350 [SCons/Cython] Fix library_dirs to include BLAS/LAPACK directory 2013-09-30 01:54:12 +00:00
Ray Speth
8498123689 [ck2cti] Show line number for some parsing errors 2013-09-30 01:54:00 +00:00
Ray Speth
a6f4c111e7 [Cython] Add declarations for free functions to _cantera.pxd 2013-09-30 01:53:40 +00:00
Ray Speth
0458eb736f [Cython] Add __init__.pxd to allow 'from cantera cimport ...' 2013-09-28 18:18:23 +00:00
Ray Speth
a6ce399374 [Cython] Move extra Cython-related headers to main include directory 2013-09-28 18:18:12 +00:00
Ray Speth
332569114e [Cython] Install headers needed for derived Cython modules 2013-09-25 23:05:21 +00:00
Ray Speth
7520170f30 [Cython] Improve support for building derived Cython modules 
The .pxd file now contains declarations for all of the cdef classes,
and is installed with the module.
 2013-09-25 22:57:36 +00:00
Ray Speth
717a2367b1 [Transport] Add electricalConductivity method to all language interfaces 
Thanks to user 'hencken' for the patch.

Resolves Issue 171.
 2013-08-23 17:43:55 +00:00
Ray Speth
1cedf904df [Doc] Add all Python examples to the Sphinx docs 2013-08-22 21:46:27 +00:00
Ray Speth
8d7f48d031 [Cython] Minor reorganization of examples 2013-08-22 21:46:17 +00:00
Ray Speth
3d5ac35c6f [Test] Avoid exact comparisons of floating point numbers 2013-08-21 19:49:37 +00:00
Ray Speth
32ea4fd924 [SCons] Fix to skip Python startup messages 
This fixes an issue when the Python interpreter prints startup messages that
appear before the expected output lines. Known to be a problem with the Anaconda
Python distribution.
 2013-08-16 17:25:04 +00:00
Ray Speth
d60629ead5 [Cython] Fix syntax errors in MixMaster for Python 3 
Backticks are not allowed in Python 3 (equivalent to repr)
 2013-08-14 17:56:05 +00:00
Ray Speth
a22ceda566 [Scons] Fix build order dependencies for python modules 2013-08-14 17:55:51 +00:00
Ray Speth
dfe5945cd6 [Matlab] Add access to class FlowReactor 2013-08-02 23:17:54 +00:00
Ray Speth
ea3ac2fc91 [Test] Fix file name used for Cython pdep tests 2013-08-02 23:17:49 +00:00
Ray Speth
3fe2cd9bbb [Cython] Fix format strings for compatibility with Python 2.6 2013-08-02 23:17:45 +00:00
Ray Speth
c32b54a47d [ck2cti] Fix for reading files with no final 'END' keyword 2013-08-02 23:17:38 +00:00
Ray Speth
cc75faf402 [Matlab] Add support for additional reactor types 
Matlab interface now supports ConstPressureReactor, IdealGasReactor, and
IdealGasConstPressureReactor.
 2013-07-31 18:14:47 +00:00
Ray Speth
03786fd07b [Python] Add support for IdealGasReactor and IdealGasConstPressureReactor 2013-07-31 18:14:45 +00:00
Ray Speth
9b6354b0c0 [SCons] Fix generation of ctpath.m 
Was failing because of dependency on dynamically-generated 'python_module_loc'
variable.
 2013-07-31 18:14:42 +00:00