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1101 commits

Author SHA1 Message Date
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
Bryan W. Weber
0b5a46fe03 Remove execute bit from files that don't need it 2015-08-02 23:06:16 -04:00
Ray Speth
bfb20e1f50 Consistently use vector_fp and vector_int typedefs 2015-08-02 23:06:16 -04:00
Ray Speth
ceefc5ecb0 Consistently use ThermoPhase::RT() 2015-08-02 23:06:16 -04:00
Ray Speth
9cdfd12172 Move definition of polyfit to polyfit.cpp 2015-08-02 23:06:16 -04:00
Ray Speth
acdf9cf0ed Clean up interstitial whitespace 
Remove extra space around operators, between words, etc.
 2015-08-02 23:06:16 -04:00
Ray Speth
6a04193646 Fix un-bracketed if, for, and else statements 2015-08-02 23:06:15 -04:00
Ray Speth
02f9497b20 Remove functions which just explicitly call base class functions 2015-08-02 23:06:15 -04:00
Ray Speth
801334c84e Merge nested if statements 2015-08-02 23:06:15 -04:00
Ray Speth
546eede80c Fix pointer logic errors in initThermoXML 
Affects DebyeHuckel and HMWSoln
 2015-08-02 23:06:15 -04:00
Ray Speth
f90bf978df Use += and -= where appropriate 2015-08-02 23:06:15 -04:00
Ray Speth
e4c45b6429 General whitespace cleanup 
Remove unnecessary blank lines and trailing whitespace. Replace tabs with
spaces.
 2015-08-02 23:06:15 -04:00
Ray Speth
619cd20f14 Fix badly-formatted else/else if/catch clauses 2015-08-02 23:06:15 -04:00
Ray Speth
d24dfea036 Remove unnecessary public/private/protected labels 2015-08-02 23:06:15 -04:00
Ray Speth
f219b49e63 Remove unnecessary newlines in function signatures 2015-08-02 23:06:15 -04:00
Ray Speth
d086be8d3d Eliminate do-while loops in favor of regular while loops 2015-08-02 23:06:15 -04:00
Ray Speth
a6e390dfc5 Standardize always-true while loop condition to "true" 2015-08-02 23:06:15 -04:00
Ray Speth
187fd27cef Remove unnecessary use of (void) 2015-08-02 23:06:14 -04:00
Ray Speth
09207eacfb Eliminate use of 'memset' 2015-08-02 23:06:14 -04:00
Ray Speth
c3c80f79fb Remove extraneous parentheses 2015-08-02 23:06:14 -04:00
Ray Speth
89c751f217 Fix compilation problems when debug_verbose=y 2015-08-02 23:06:14 -04:00
Ray Speth
d8772f261b [Reactor] Cannot add sensitivity reactions to initialized ReactorNet 
Before, the attempt to add the reaction was silently ignored. Now, this raises
an exception.
 2015-07-21 14:54:13 -04:00
Ray Speth
6cc5652de6 Remove commented-out code 2015-07-20 17:20:46 -04:00
Ray Speth
de005c083e Eliminate VCS_DATA_PTR macro 2015-07-20 16:17:31 -04:00
Ray Speth
bf2ceed60e Remove some leftover debugging ifdefs 2015-07-20 15:47:17 -04:00
Ray Speth
c49c969184 [Kinetics] Remove unused code for reactant and product "groups" 2015-07-20 14:04:53 -04:00
Ray Speth
4f1250ef53 [Kinetics] Remove unneeded variables for reaction equation 
Extract this data from the reaction objects directly as needed.
 2015-07-20 13:53:47 -04:00
Ray Speth
62f2af5534 [Kinetics] Eliminate unnecessary variable m_rxntype 2015-07-20 13:01:05 -04:00
Ray Speth
f623e44d32 [Kinetics] Eliminate unnecessary m_rrxn and m_prxn variables 
This information can be extracted from the Reaction objects as-needed.
 2015-07-20 12:56:56 -04:00
Ray Speth
761f54f241 Eliminate unnecessary counter variable Kinetics::m_ii 2015-07-16 15:37:41 -04:00
Ray Speth
e21a7ce7d7 Fix incorrect index check in GeneralSpeciesThermo::reportParams 
The SpeciesThermoInterpType no longer knows the species index, so
it isn't actually returned by the reportParameters function.
 2015-07-16 12:28:46 -04:00
Ray Speth
c08c365ebb Remove unimplemented option to use QR factorization in BandMatrix 2015-07-16 10:52:42 -04:00
Ray Speth
e8292d387e Fix definition of elemental mole fraction 
The elemental mole fractions should be invariant under composition changes which
conserve atoms.
 2015-07-16 10:41:39 -04:00
Ray Speth
97b32069cf Remove leftover "fenv" cruft 2015-07-15 12:46:48 -04:00
Ray Speth
6a9dd7f9d6 Remove unused 'csvdiff' application 2015-07-15 12:20:22 -04:00
Ray Speth
f1f10b6526 Remove unused, deprecated code marked for removal after Cantera 2.2 2015-07-15 12:08:50 -04:00
Ray Speth
ad4ed9e065 Remove unnecessary printing from SurfPhase::setCoverages 2015-07-15 11:40:13 -04:00