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372 commits

Author SHA1 Message Date
Ray Speth
df908229b1 [ctml_writer] Fix handling of units in some fields 
When using Python 3, using -1 as the dummy value for density and site_density
causes probems, because the (ordered) comparison between a density specified
with units (as a tuple) and 0 is not allowed. Instead, use None as the
placeholder value.
 2014-03-13 02:19:28 +00:00
Ray Speth
755164397d [ctml_writer] Improve error reporting 
Print a more useful traceback for cases where exceptions are raised in ctml_writer.
 2014-03-13 02:19:23 +00:00
Ray Speth
ec6b65513b [Python] Add multiprocessing example 2014-03-08 21:47:14 +00:00
Ray Speth
98c480c7c7 [Python] Fix docstring of Sim1D.restore 
Resolves Issue 210.
 2014-03-08 21:47:09 +00:00
Ray Speth
c5eb2f57dd [Python] Make Cantera objects explicitly non-picklable and uncopyable. 
Attempting to copy or pickle Cantera objects with an underlying C++ object
previously led to unexpected errors. These operations will not raise excptions
indicating the unimplemented feature.

Resolves Issue 205.
 2014-03-04 17:39:21 +00:00
Ray Speth
6e72f8930f [SCons] Fix Cython module compilation with MinGW 2014-02-24 03:25:30 +00:00
Ray Speth
3e073aae27 [SCons] Force relink of Python extension when necessary 2014-02-21 19:07:58 +00:00
Ray Speth
aad284cce7 [SCons] Fix library linking issues under Cygwin 2014-02-20 03:01:01 +00:00
Bryan W. Weber
3de3842e3c [MixMaster] Fix variable ambiguity in DataFrame.py. 
Fix file not closed bug in importCSV. Import from XML is broken due
to missing XML module.
 2014-02-19 22:45:00 +00:00
Ray Speth
771ff96e86 [MixMaster] Fixes to use Cython function names 
DataFrame.importCSV and dataFrame.importData were still using function names
from the old Python module.
 2014-02-14 16:40:58 +00:00
Ray Speth
377d3877f7 [MixMaster] Fix usage of numpy.zeros and numpy.ones 2014-02-14 16:40:54 +00:00
Ray Speth
03be898300 [ck2cti] Skip non-ASCII characters in input files 2014-02-06 22:58:53 +00:00
Ray Speth
eaceaf7b86 [SCons] Use SCons to compile the Cython extension 
Fixes issues with mismatched compilers between the Cython extension and the
cantera library, especially on OS X. Improves build dependency resolution to
eliminate unnecessary recompilation of _cantera.cpp.
 2014-01-31 23:15:17 +00:00
Ray Speth
d4a9ca0847 [SCons] Fix simultaneous compilation of Python 2 and Python 3 modules 
Use separate SCons Environments so the 'py_include_dirs' variable (which
contains the Numpy include directory) can be distinct for each Python module.
 2014-01-30 00:48:03 +00:00
Ray Speth
e59a7a7eeb [1D] Eliminate deprecated methods of Domain1D 2014-01-30 00:47:52 +00:00
Ray Speth
ff9584105b Do implicit CTI to XML conversions without generating .xml files 
When instantiating a phase from a .cti file, do the conversion in memory,
without writing the XML representation to disk. This eliminates the unrequrested
XML files that Cantera normally generates, and also avoids errors when running
Cantera from a directory where the user does not have write permissons.
 2014-01-30 00:47:37 +00:00
Ray Speth
3c703eb4ed [Cython/1D] Use 'Mix' transport if no transport model is provided 2014-01-24 20:40:32 +00:00
Ray Speth
c34877a96f [ck2cti] Fix support for species names containing '+' and '=' 
This addesses a parsing error that would occur if a mechanism contained both
'foo' and 'foo+', where reactions written as 'foo+bar' would be parsed as a
reaction with 'foo+' and 'bar'.

See Issue 182.
 2014-01-24 20:40:26 +00:00
Ray Speth
a3d8684d94 [Samples] Explicitly set transport model to 'Mix' for clarity 2014-01-11 00:20:27 +00:00
Ray Speth
f3b1555a6b [Cython] By default, use same interpreter for mechanism conversions 
Fixes failures when only the Python 3 module is present.
 2014-01-09 23:12:03 +00:00
Bryan W. Weber
a689717a7a [Matlab] Add isothermalCompressibility and thermalExpansionCoeff functions 
Resolves Issue 157.
 2014-01-08 17:10:41 +00:00
Ray Speth
908b63fccd [Cython] Fix compilation issue when using Clang 2014-01-08 17:10:29 +00:00
Bryan W. Weber
1d1ad21840 [ck2cti] Fix for support of unterminated thermo sections 
Fixes the case where the next section header contains a modifier, e.g. 'thermo
all' or 'reactions <units>'.

See Issue 199.
 2014-01-06 18:47:02 +00:00
Bryan W. Weber
b5c2881f64 [ck2cti] Add extra info about handling of extra thermo parameters 
See Issue 199.
 2014-01-06 18:46:55 +00:00
Bryan W. Weber
e3ab2dbf8a [ck2cti] Improve handling of duplicate species 
Warn when a species is given multiple times in the input list. Do not add the
duplicate species to speciesList.

Resolves Issue 199.
 2014-01-06 18:46:49 +00:00
Bryan W. Weber
7deb45a840 [Matlab] Check for sparse arrays in the Solution 'set' function 
Resolves Issue 140.
 2014-01-06 18:46:43 +00:00
Bryan W. Weber
120c6e742c [Matlab] Add fwdRateConstants and revRateConstants functions 
Resolves Issue 125.
 2014-01-06 18:46:36 +00:00
Bryan W. Weber
16335a0932 [Matlab] Allow nAtoms to take string inputs for species and elements 
Resolves Issue 159.
 2014-01-06 18:46:30 +00:00
Ray Speth
3a308a041f [Matlab] Remove broken rxnEqs function 
"ReactionEqn" is the working alternative. See Issue 118.
 2014-01-06 18:46:25 +00:00
Bryan W. Weber
f8850963a0 Use b instead of n for temperature exponent 
Resolves Issue 198.
 2014-01-02 22:23:38 +00:00
Bryan W. Weber
b02bb4287a [Doc] Update docstrings in ctml_writer for the NASA thermo classes 
See Issue 196.
 2013-12-18 17:46:27 +00:00
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