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1137 commits

Author SHA1 Message Date
Ray Speth
cd1f1fd5ac [Doc] Clean up Doxygen documentation for ThermoPhase classes 
Remove redundant documentation from overloaded methods which does not add any
additional information.

Reformat to to make indentation and line lengths more consistent.
 2015-11-09 17:59:22 -05:00
Ray Speth
75b0c71044 Clean up comments in Kinetics 2015-11-09 17:59:22 -05:00
Ray Speth
5bf3b0fc67 Clean up comments in other equilibrium-related classes 2015-11-09 17:59:22 -05:00
Ray Speth
618c485c55 Clean up comments in VCS equilibrium solver 2015-11-09 17:34:46 -05:00
Ray Speth
4382ae6c85 Clean up comments in Thermo class source files 2015-11-09 17:34:46 -05:00
Steven DeCaluwe
14864e840b Extend NoNorm option for setCoverages to the Matlab toolbox 
Because normalizing the species coverages leads to incorrect Jacobian
calculations, it is sometimes necessary to not normalize the coverages.
As for bulk species mass/mole fractions, this option is currently only
available when passing the coverages as a vector (i.e., not available
for string identifiers).
 2015-11-07 21:14:03 -05:00
Ray Speth
70fe821c19 Deprecate FuncEval::getInitialConditions and related functions 2015-11-06 14:40:48 -05:00
Thomas Fiala
16ab7dff51 [Reactor] Implement functions getState for reactors and reactor networks 
These are simpler forms of getInitialConditions.
 2015-11-03 14:34:28 -05:00
imitrichev
f7a0e14f3e Remove unused field m_logA from class SurfaceArrhenius 2015-10-25 15:41:59 -04:00
imitrichev
40e09043bc Added methods to InterfaceKinetics to get effective rate parameters 
Effective rate parameters are used in SurfaceArrhenius reactions.

Resolves #297.
 2015-10-25 15:41:31 -04:00
Ray Speth
87aaa6ad1e Use math functions from C++11 standard library 2015-10-19 13:14:40 -04:00
Ray Speth
0542e694a9 [Thermo] Merge classes StoichSubstance and StoichSubstanceSSTP 
Use the implementation of StoichSubstanceSSTP (descended from
SingleSpeciesTP) but change the name to StoichSubstance.
 2015-10-19 00:17:40 -04:00
Ray Speth
90b0ee152b Fix compilation with GCC 4.6 and 4.7 
The standard libraries for these versions of GCC do not have 'emplace'
methods for associative containers.
 2015-10-17 18:58:50 -04:00
Ray Speth
0647823ada Replace DATA_PTR macro with calls to data() 2015-10-17 18:58:50 -04:00
Ray Speth
8b16eb489f Eliminate unnecessary aliases for member variables in HMWSoln 2015-10-17 18:58:50 -04:00
Ray Speth
91d3002df1 Make use of "make_shared" where possible 2015-10-17 18:58:50 -04:00
Ray Speth
a945ef2c23 Make use of initializer lists where appropriate 2015-10-17 18:58:50 -04:00
Ray Speth
f9375e1a09 Use locks/mutexes from the standard library instead of Boost.Thread 
This eliminates the need to link against any of the compiled Boost libraries,
and means that we can always build in thread-safe mode
 2015-10-17 18:58:50 -04:00
Ray Speth
a03f370cfd Make use of emplace and emplace_back methods 2015-10-14 18:45:23 -04:00
Ray Speth
c3a16ec1fb Update AssertThrowMsg and AssertFinite to use cppformat 2015-10-14 18:45:23 -04:00
Ray Speth
fb4eece9f8 Use std::unique_ptr instead of raw pointers where appropriate 2015-10-14 18:45:23 -04:00
Ray Speth
0690626ab8 Make m_sub a regular member of WaterSSTP instead of a pointer 2015-10-14 18:45:23 -04:00
Ray Speth
ffc4ba07da Make m_phi a regular member of WaterPropsIAPWS instead of a pointer 2015-10-14 18:45:23 -04:00
Ray Speth
3c05e801a4 Remove unused variable MetalSHEelectrons::xdef_ 2015-10-14 18:45:23 -04:00
Ray Speth
3f6d8b0aca Use cppformat instead of int2str and fp2str 2015-10-14 18:45:23 -04:00
Ray Speth
78e2d13da7 Eliminate some special cases by using std::vector.data() 
Unlike &vec[0], vec.data() is a valid operation even when vec is empty,
removing the need to allocate space in vectors just so we can get an
address that won't be used.
 2015-10-14 18:45:23 -04:00
Ray Speth
2589a27b6c Use range-based for and auto to simplify some loops 2015-10-14 18:45:23 -04:00
Ray Speth
c2ba24c0c2 Fix possible memory leak in newPhase 
If importPhase threw an exception, then the ThermoPhase object allocated here
would not be deleted. Switching to a smart pointer fixes this problem.
 2015-10-14 18:45:23 -04:00
Ray Speth
f335350c35 Always use std::shared_ptr 
Since we compile as c++11, std::shared_ptr is guaranteed to exist.
 2015-10-14 18:45:23 -04:00
Ray Speth
e131766b71 Replace auto_ptr with unique_ptr 
auto_ptr is deprecated in c++11
 2015-10-14 18:45:23 -04:00
Ray Speth
0b2c7b59b8 Replace printf with writelogf in all library code 2015-10-14 18:45:23 -04:00
Ray Speth
71bb73b728 Eliminate unnecessary calles to std::string.c_str() 2015-10-14 18:45:22 -04:00
Ray Speth
e669f912a5 Use cppformat in Phase and ThermoPhase 2015-10-14 18:45:22 -04:00
Ray Speth
745db409a6 Add a constructor for CanteraError that uses format strings 2015-10-14 18:45:22 -04:00
Ray Speth
16143b47b6 Replace most uses of sprintf with cppformat 2015-10-14 18:45:22 -04:00
Ray Speth
1411419b0f [1D] Eliminate sprintf-style string formatting 2015-10-14 18:45:22 -04:00
Ray Speth
41527b1ea7 Rename two-argument version of writelog 'debuglog' 
This is a prerequisite to allowing writelog to take an arbitrary number
of arguments.
 2015-10-14 18:45:22 -04:00
Ray Speth
61a755ff51 Use cppformat to implement writelogf 
This represents the first use of variadic templates in Cantera.
 2015-10-14 18:45:22 -04:00
Ray Speth
caf9c6f062 Use cppformat in ThermoPhase::report and overrides 2015-10-14 18:45:22 -04:00
Ray Speth
3d27dfa1a1 [Reactor] Eliminate unused variable ReactorNet::m_iown 2015-10-05 18:48:14 -04:00
Ray Speth
a956f3904a [Thermo] Deprecate get/setReferenceComposition and xMol_Ref 2015-10-05 15:25:05 -04:00
Ray Speth
b38a9332e2 Treat duplicate keys in composition strings as errors 
For example, 'H2:0.5, O2:0.5, H2:0.1', which would previously have been treated
as equivalent to 'O2:0.5, H2:0.1'.
 2015-10-05 13:02:16 -04:00
Ray Speth
0e4b0cba0f [Matlab] Fix error handling for nAtoms to avoid false positives 
Species can have negative "atoms" of an "element" in the case where the element
is an electron and the species is a positive ion.
 2015-09-08 12:26:58 -04:00
Ray Speth
567a854377 Fix a compilation error when using '-std=c++11' 2015-09-04 18:37:55 -04:00
Ray Speth
6e138d0ae4 [Reactor] Always check that input/output are finite 
This causes problems to be caught early, where they can at least sometimes be
handled as recoverable intergrator errors, rather than letting NaN values
propagate through the solution.
 2015-08-24 12:27:07 -04:00
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
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
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