Commit graph

7000 commits

Author SHA1 Message Date
Ray Speth
cb31c297cf [Input] Parse YAML entries for falloff and chemically activated reactions 2019-06-25 22:30:59 -04:00
Ray Speth
8b502d4065 [Input] Parse YAML entries for three body reactions 2019-06-25 22:30:59 -04:00
Ray Speth
0220e11ef9 Allow conversion from long int to double in AnyValue.asMap 2019-06-25 22:30:59 -04:00
Ray Speth
de80f06887 [Input] Parse YAML entries for elementary reactions 2019-06-25 22:30:59 -04:00
Ray Speth
224c46ebbb Add functions for converting units from AnyValue instances 2019-06-25 22:30:59 -04:00
Ray Speth
65121becac Add special handling of activation energies to class Units 2019-06-25 22:30:59 -04:00
Ray Speth
da097631e3 UnitSystem class supports default source units for conversions 2019-06-25 22:30:59 -04:00
Ray Speth
c9b7de3b70 Add support for metric prefixes to class Units 2019-06-25 22:30:59 -04:00
Ray Speth
b8cb2c30f8 Add 'Units' class for doing conversions with dimensionality checks
Introduces a new, more natural notation for writing unit strings,
for use in YAML input files. Unlike 'toSI', conversions are checked for
dimensional consistency.
2019-06-25 22:30:59 -04:00
Ray Speth
ea88d4f9fb Add "get" functions to AnyMap
Simplify the common use case of checking for a key and using a default
value when it is missing.
2019-06-25 22:30:59 -04:00
Ray Speth
530adbb931 Add automatic conversions to vector<AnyValue> 2019-06-25 22:30:59 -04:00
Ray Speth
e5bd0b136f Allow AnyValue to convert implicitly from long int to double 2019-06-25 22:30:59 -04:00
Ray Speth
00f6b88fa4 [Input] Implement construction of AnyMap from YAML string/file 2019-06-25 22:30:59 -04:00
Ray Speth
e85e0e2108 Fix constness of some AnyMap functions 2019-06-25 22:30:59 -04:00
Ray Speth
ed24198e63 Add option to compile yaml-cpp or use system library 2019-06-25 22:30:59 -04:00
Ray Speth
4bd1ca1cde Add yaml-cpp submodule 2019-06-25 22:30:59 -04:00
Ray Speth
56cb190a64 Fix units of site density in sofc.cti 2019-06-25 22:30:59 -04:00
Bryan W. Weber
444ef91e0f Build the samples on the CI services
Requires libomp on macOS from homebrew. OpenMP with Visual C/C++ requires
the loop index to be a signed type (from OpenMP < 3.0).
2019-06-17 10:29:20 -04:00
Bryan W. Weber
142f533229 Correct flag and libs for OpenMP on macOS
Apple's clang on macOS requires the libomp to link. Apple symlinks gcc
to clang, so it can't be detected as clang by executable name
2019-06-17 10:29:20 -04:00
Bryan W. Weber
3588be16f3 CMake use Accelerate even if OpenMP is also used
For samples, make sure that OpenMP and Accelerate are not exclusive
options on macOS
2019-06-17 10:29:20 -04:00
Bryan W. Weber
007ecf0c7c Include boost_inc_dir when building the samples 2019-06-17 10:29:20 -04:00
Bryan W. Weber
857bb0a769 Include Func1.h in zerodim.h
zerodim.h used to have Func1.h included indirectly, so make it explicit.
2019-06-17 10:29:20 -04:00
Bryan W. Weber
9a5c2708e5 Replace the compiler variables during conda build
The build compilers should not be specified into the sample templates
2019-06-13 14:36:54 -04:00
Bryan W. Weber
265032da8f Remove build-system specific env vars on macOS
The isysroot and mmacosx-min-version flags are needed to build the
Cantera library, but not to actually use it on macOS. They should be
removed because users don't need these and should use the SDK installed
with XCode.
2019-06-13 14:36:54 -04:00
Steven DeCaluwe
ba8ac1d519 Mark ConstDensityThermo for deprecation.
The thermophase ConstDensityThermo instantiates a class with
constant density_mass  Such a model is of dubious physical
validity/applicability and has minimal foreseeable use cases.
This commit marks it for deprecation, and adds a message in
ctml_writer.py (where the model has the misleading alias
'incompressible_solid') refering the interested user to consider
appropriate alternate thermophase classes 'lattice' or
'IdealSolidSoln.'
2019-06-12 17:54:48 -04:00
Steven DeCaluwe
fb3dee36c5 Removing references to incompressible_solid in sofc.cti
Removes references to incompressible_solid phase in the codebase.
This phase type references ConstDensityThermo phase, which is a
non-physical model and is to be deprecated, with Cantera 2.5. In
order to enable deprecation, the following changes are hereby made:

- Changes oxide_bulk phase type from incompressible_solid to lattice in sofc.cti
- Changes test_convert.py so that it interrogates the density_mole of the bulk_oxide, rather than density_mass
2019-06-12 17:54:48 -04:00
Steven DeCaluwe
813d5064ae Enabling Lattice thermo phase via cti interface. 2019-06-12 17:54:48 -04:00
Steven DeCaluwe
0ed2b38594 Adding faradayconstant.m to Matlab toolbox 2019-06-08 17:33:30 -04:00
Thanasis Mattas
6a42e5942e rearranging methods to aid src reading 2019-06-08 17:25:55 -04:00
Thanasis Mattas
ea3bb0af90 Some documentation corrections at xml.h 2019-06-08 17:25:55 -04:00
Ingmar Schoegl
5d62f3bacc added factories for FlowDevice and Wall objects 2019-05-28 19:21:28 -04:00
Ingmar Schoegl
751afa3c2b addresses issue #615 2019-05-09 22:21:35 -04:00
CyberDrudge
fbe4ce5c1b Remove Unnecessary comments 2019-05-09 12:22:44 -04:00
Ingmar Schoegl
f078f53f39 Enable additional states / equations in onedim 2019-04-17 00:06:26 -04:00
Nick
848a3bf0e3 Add InterfaceKinetics.advance_coverages integrator options to the cython interface, and test 2019-04-10 22:14:27 -04:00
Nick
d2cb02f254 add integrator parameters to the InterfaceKinetics::advanceCoverages & ImplicitSurfChem constructor to allow users to modfiy 2019-04-10 22:14:27 -04:00
Bryan W. Weber
654e582bc0
Add NumFOCUS donation link to README
Also update some URLs to HTTPS
2019-03-20 09:28:59 -04:00
Bryan W. Weber
d25637d0ea
Update NumFOCUS donation link in docs sidebar 2019-03-20 09:15:39 -04:00
g3bk47
471041a27a Additional check for Troe coefficients being zero
This will prevent floating point exceptions (sometimes enabled by third-party
codes) in case c[1] or c[2] are zero but will not change the current behaviour
if c[1] and c[2] are not zero.
2019-03-18 14:39:50 -04:00
Bryan W. Weber
4026c17915 Add /usr/local/include to cmake incdirs
By default, CMake uses the system SDK on macOS as the system root by
setting the isysroot flag to clang. This setting removes /usr/local from
the include search path.
2019-03-15 14:44:43 -04:00
Bryan W. Weber
cb008a95d7 Add the Accelerate framework to the CMake builds of the samples 2019-03-15 14:44:43 -04:00
Ray Speth
337f33baad [CI] Use Travis Homebrew addon instead of manual brew commands
This should reduce the time needed to set up the build environment and avoid
build failures associated with errors while updating irrelevant homebrew
packages.
2019-03-14 14:08:54 -04:00
Ray Speth
968dc24925 [Python] Fix compatibility with Cython < 0.27
After setting the "language_level" directive (6c0866ef), nested comprehension
expressions erroneously triggered an error message from the Cython compiler
saying "local variable 's' referenced before assignment". While the problem has
been fixed in Cython 0.27 and newer, this commit restores compatibility with
older Cython versions as well.
2019-03-14 14:03:51 -04:00
Ray Speth
5e226535de Fix regression in compatibility with Sundials 2.4.0
Regression was introduced in 9c50f752 when adding compatibility with
Sundials 3.x.

Fixes #613
2019-03-14 14:03:51 -04:00
Bryan W. Weber
6c0866efb8 Add Cython language_level directive to _cantera.pyx
This fixes the warnings generated by recent versions of Cython that
the language_level will be changed in the future. By setting this
directive, all the code in the .pyx files should be written in
Python 3 syntax. This required several changes to the import
syntax in the files to fix relative vs. absolute imports
2019-03-11 17:00:13 -04:00
Ray Speth
d6d91f4d98 [Thermo] Fix updating state of PDSS_IonsFromNeutral objects
Setting T and P now updates the state of the underlying "neutral
molecule phase".

Also removed the unimplemented setState_TR method.
2019-03-06 19:50:16 -05:00
Ray Speth
bdc81684b1 [Thermo] Fix BinarySolutionTabulatedThermo initial mole fraction thermo
The value of m_xlast should only be set to a valid value by _updateThermo,
after it has calculated values for the tabulated enthalpy and entropy.
2019-03-06 19:48:45 -05:00
Ray Speth
aceb896f62 [Thermo] Fix BinarySolutionTabulatedThermo updates when only T changes
In the case where temperature changes but the mole fractions are the same, we
still need to apply the enthalpy and entropy offsets to the tabulated species.
2019-03-06 19:48:45 -05:00
Ray Speth
47005a5008 [Thermo] Fix overriding of IdealSolidSolnPhase::_updateThermo
Since IdealSolidSolnPhase::_updateThermo wasn't a virtual method, and
the signatures didn't match (const vs non-const), calls to this method
from IdealSolidSolnPhase weren't being overridden by
BinarySolutionTabulatedThermo::_updateThermo as expected.
2019-03-06 19:48:45 -05:00
Ray Speth
1f70f7751c Move sofc.cti from examples to main data directory 2019-03-05 16:09:55 -05:00