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152 commits

Author SHA1 Message Date
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
Ray Speth
2c58b7237a Moved the "checkFinite" function into the Cantera namespace 2013-04-29 18:05:22 +00:00
Ray Speth
0a059d406a Eliminated unnecessary empty destructors from derived classes 
See http://www.parashift.com/c++-faq-lite/virtual-dtors.html
 2013-04-29 18:04:23 +00:00
Ray Speth
59d615c8d2 Removed the useless SAFE_DELETE macro 2013-04-12 23:06:45 +00:00
Ray Speth
9a1d6532ba Fixed compilation error when using Sundials 2.3 2013-03-13 20:20:27 +00:00
Harry Moffat
3cc0aa1689 Fixed an overloaded operator error 
Fixed a compilation error that occurred in DEBUG_MODE
 2013-02-25 20:00:24 +00:00
Ray Speth
934010136d Removed unnecessary temporaries used for storing return values 2013-02-14 01:04:07 +00:00
Ray Speth
e04e59cdd3 Removed extraneous parentheses around arguments to 'return' 
'return' is a keyword, not a function, so these parens are unnecessary.
 2013-02-14 01:03:48 +00:00
Ray Speth
6d6e237f07 Removed unnecessary checks surrounding delete operations 2013-02-14 01:03:32 +00:00
Ray Speth
7da738d238 Re-applied consistent formatting to trunk 
Applied using: astyle -n --style=kr --add-brackets --indent=spaces=4
--indent-col1-comments --unpad-paren --pad-header --align-pointer=type
--lineend=linux
 2013-02-07 23:40:59 +00:00
Ray Speth
a5b1d1f7f6 [Reactor] Added ability to set the CVODES "MaxErrTestFails" variable 
Increasing this value (from the default of 7) will sometimes allow CVODES to
find solutions to problems that previously caused it to fail.
 2013-02-07 23:40:40 +00:00
Ray Speth
791c82b0c6 CVodesIntegrator now sets the minimum setp size when [re]initializing 2013-02-07 23:40:35 +00:00
Ray Speth
67a143f396 Refactored CVodesIntegrator to reduce redundancy when setting options 2013-02-07 23:40:31 +00:00
Ray Speth
15a45de820 Fixed some regressions in indentation consistency 
Problems with vcs_util.cpp were introduced in r1944. Problems with
NonLinearSolver.{h,cpp} were introduced in r1978.
 2013-02-01 23:40:07 +00:00
Ray Speth
9109888882 Fixed regressions in NonlinearSolver introduced in r1978 
Fixed signed/unsigned type consistency, spelling mistakes, and removed
unnecessary macros.
 2013-02-01 23:39:58 +00:00
Victor Brunini
64aef5fac7 Rename m_y_n_1 and m_ydot_n_1 to _trial to clarify their intent. 
Add setPreviousTimeStep function to set m_y_nm1 and m_ydot_nm1
so that time derivative calculations can be run for time-dependent
nonlinear solves.

Change m_ydot_nm1 to a std::vector.
 2013-01-15 20:17:00 +00:00
Victor Brunini
9b6b65fe04 Add function to DenseMatrix that multiplies two square matrices. 2013-01-07 18:18:10 +00:00
Ray Speth
382ad7ba80 Fixed compiler warnings about uninitialized values 2013-01-04 21:37:26 +00:00
Ray Speth
ee2697b4b8 Fixed a compiler error caused by ambiguous call to sqrt 2012-12-17 23:59:40 +00:00
Harry Moffat
ea25de7fe7 Continuing transfering LiquidTransport changes, doing bugfixes, and 
qualifying against our testsuite.
 2012-12-15 00:49:14 +00:00