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121 commits

Author SHA1 Message Date
Ray Speth
1c878c16de Fix issues indicated by compiler warnings 2015-05-26 11:42:20 -04:00
Ray Speth
341b137766 [Doc] Capitalize proper nouns and acronyms 2015-05-25 20:58:44 -04:00
Ray Speth
51c8d7365a [Doc] Fix spelling errors 2015-05-25 20:57:19 -04:00
Ray Speth
eb74329d1b Deprecate some unused/unfinished classes 2015-05-24 18:23:22 -04:00
Ray Speth
4049bb4bb2 Fix out-of-bounds memory access in CvodesIntegrator::getErrorInfo 
Out-of-bounds memory was being accessed in cases where the system had fewer
state variables than the specified maximum number of error estimates to display.
 2015-04-28 17:13:11 -04:00
Ray Speth
ecb6242b79 Fix spelling errors 2015-04-08 19:36:55 -04:00
Ray Speth
2e53890adf Minor cleanup of constructors and destructors 2015-02-26 21:58:42 +00:00
Ray Speth
004798aef4 Remove unused header files 2015-02-12 04:04:15 +00:00
Ray Speth
efb80dfe05 Remove unnecessary delimiter lines between functions 
A single line of white space is sufficient and consistent. Also moved a couple
Doxygen strings out of source files.
 2015-01-22 00:04:24 +00:00
Ray Speth
b8a99b4b83 Remove unnecessary explicit calls to default constructors 2015-01-22 00:04:12 +00:00
Ray Speth
d830012340 Remove unnecessary explicit calls to operator() and operator= 2014-12-05 23:33:15 +00:00
Ray Speth
eb71d8cdd0 Deprecate "copyData" method of array classes 2014-11-08 00:53:30 +00:00
Ray Speth
91f3a2b073 Fix statements that called the assignment operator twice 2014-10-03 01:45:41 +00:00
Ray Speth
0886de8650 Include CVodes error text in resulting CanteraErrors 
Failures in 'integrate' and 'advance' now include the error text provided by
CVodes directly, rather than just the numerical error code. This is especially
helpful in cases where the direct output from CVodes to stderr is lost
(e.g. when running from the Matlab GUI).
 2014-08-28 16:55:41 +00:00
Ray Speth
002c158761 Cleanup include statements 
Move includes from header to implementation files where possible, and remove
unnecessary includes.
 2014-08-28 16:54:13 +00:00
Harry Moffat
cdec2e90c7 Fixes need to restore capability to solve banded systems with nonlinear solver 2014-08-05 23:11:58 +00:00
Ray Speth
1cd82d40af Remove 'SQUARE' and 'DSIGN' macros 2014-07-25 18:32:29 +00:00
Ray Speth
83e38480d6 Throw exceptions instead of calling std::exit after an error 
By throwing an exception, Cantera is better behaved when used within other
applications, e.g. as in the case of the Matlab and Python interfaces.
 2014-06-06 00:17:58 +00:00
Ray Speth
dbfe428437 Fix compiler warnings 
These were mostly related to changes from r2957.
 2014-06-03 16:53:40 +00:00
Ray Speth
b5396837b2 Make use of std::min, std::max, and clip 2014-06-03 16:52:43 +00:00
Ray Speth
712293e415 Change debug code to avoid ifdefs where possible 
Use "if (DEBUG_MODE_ENABLED)" instead of "#ifdef DEBUG_MODE". This makes
it easier to see the flow control logic, and the compiler will optimize
out the always-false conditionals when DEBUG_MODE_ENABLED is 0, so there
isn't any speed penalty.
 2014-05-27 02:53:22 +00:00
Ray Speth
6c0cea5ee4 Standardize function used for writing a line of repeated characters 2014-05-27 02:53:06 +00:00
Ray Speth
789574ac80 Remove commented-out code 2014-05-27 02:52:21 +00:00
Ray Speth
54ded64e4b Miscellaneous whitespace cleanup 2014-05-08 23:01:12 +00:00
Ray Speth
95eb7ab3ba Remove newline after '::' in member function definitions 
This inconsistency makes it hard to directly search the code for a specific
member function definition.
 2014-03-24 04:03:09 +00:00
Ray Speth
90c2d58973 [Numerics] move 'm_factored' up to GeneralMatrix 2014-03-24 04:03:01 +00:00
Ray Speth
4467b898a5 [Numerics] Remove unused BandMatrix::err method 2014-03-24 04:02:56 +00:00
Ray Speth
7fef1b0051 [Numerics] BandMatrix does not silently do LU when QR is specified 
Change GeneralMatrix to allow derived classes to not implement QR
factorization. BandMatrix does not implement QR because this LAPACK
does not contain a QR algorithm for this matrix type.
 2014-03-24 04:02:51 +00:00
Ray Speth
150a7845f8 [Numerics] Simplify solving DenseMatrix with multiple RHS 2014-03-24 04:02:41 +00:00
Ray Speth
e2dc48e45e Remove unnecessary includes of ctlapack.h 2014-03-24 04:02:34 +00:00
Ray Speth
44c53a6f27 [Kinetics] Abstract use of LAPACK in solveSP and solveProb 2014-03-24 04:02:18 +00:00
Ray Speth
8933203a20 [Numerics] Fix invalid dereference in SquareMatrix::factor 
The work array hasn't always been allocated, so taking its address isn't
necessarily valid. Also, dlange doesn't use the work array in the '1' norm
case anyway.
 2014-03-24 04:02:12 +00:00
Ray Speth
4e72cf0334 [Numerics] BandMatrix and SquareMatrix support solving multiple RHS 2014-03-24 04:02:06 +00:00
Ray Speth
c7ba8bfb84 Remove abandoned autotools build system 2014-03-04 17:38:53 +00:00
Bryan W. Weber
4badbd1fb3 [SCons/0D] Update to enable Sundials linked with external BLAS/LAPACK. 
With help from Nick Curtis and Ray Speth.
 2014-01-20 15:19:53 +00:00
Ray Speth
38532f800f Fix linker error in IDA_Solver 2013-12-20 19:21:36 +00:00
Ray Speth
54d11a016a Remove support for old Sundials versions 
Supported Sundials versions are 2.4 and 2.5.
 2013-12-14 00:18:17 +00:00
Ray Speth
cf0a418027 [Reactor] Fix segfault when requesting sensitivities at t = 0 2013-09-01 00:33:19 +00:00
Victor Brunini
e17d099b96 Fix lower_bound not found build error. 2013-06-11 19:41:30 +00:00
Ray Speth
a6614b87bb [Doxygen] Fix some incorrect/missing "@file" commands 2013-06-06 15:32:30 +00:00
Ray Speth
64bfdcc952 Deprecate support for Sundials 2.2 and 2.3. 2013-06-05 17:09:30 +00:00
Ray Speth
d253fc0d63 Eliminate redundant standard library includes 2013-06-05 17:08:13 +00:00
Ray Speth
e059b5c60c Eliminate unnecessary use of reinterpret_cast 2013-05-31 15:55:48 +00:00
Ray Speth
e43a4a8b3c Remove unnecessary "APPROACH" macro 2013-05-31 15:55:43 +00:00
Ray Speth
190c4bf8ce Cleaned up Doxygen documentation in other "numerics" classes 2013-05-29 00:11:40 +00:00
Ray Speth
eadf4e3fdd Cleaned up Doxygen documentation for Sundials wrapper classes 2013-05-29 00:11:32 +00:00
Ray Speth
e9daef3313 Cleaned up Doxygen Documentation for matrix classes 
BandMatrix, DenseMatrix, SquareMatrix, and GeneralMatrix
 2013-05-29 00:11:22 +00:00
Ray Speth
7e8276809f Cleaned up Doxygen documentation for class BEulerInt 2013-05-29 00:11:17 +00:00
Ray Speth
09def59948 Eliminated use of mdp functions in BEulerInt 2013-04-29 18:05:31 +00:00
Ray Speth
5205a7a530 Eliminated use of mdp functions in NonlinearSolver 2013-04-29 18:05:27 +00:00