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239 commits

Author SHA1 Message Date
Ray Speth
e48bd48c4e [1D] General cleanup of class Refiner 2013-02-07 23:41:49 +00:00
Ray Speth
dc1ffee1a2 Fixed some compiler warnings 
(shadowed virtual functions, initialization order)
 2013-02-07 23:41:42 +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
7a4be4dcfd Use qualified names for math functions in RxnRates.h 
See Issue 136.
 2013-02-07 23:40:45 +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
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
Harry Moffat
8793fc3bcb Doxygen update 
Doxygen is currently broken. This commit starts to fix some issues.
 2013-02-01 18:59:17 +00:00
Ray Speth
78f6e61703 Combined the shared parts of AxiStagnFlow::eval and FreeFlame::eval 2013-01-17 15:31:36 +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
a709d5f816 Revert "Removed unused member variable ReactionData.rxn_number" 
This variable is used in some applications we build against
cantera.

This reverts commit 7d7b6dd39d12c2e2bdd2a9d2a959c0aee3c0c4c5.
 2013-01-15 20:16:42 +00:00
Ray Speth
d75bf72e65 Removed duplicated methods from IdealMolalSoln 
The class incorrectly had copies of the non-virtual methods 'electricPotential'
and 'setElectricPotential' from the base class ThermoPhase.
 2013-01-11 22:56:49 +00:00
Ray Speth
31f90fe32d Removed unnecessary typedef for 'index_t' 2013-01-11 22:56:44 +00:00
Ray Speth
50327a665f Moved some function implementations out of InterfaceKinetics.h 
This gets rid of some (mostly spurious) warnings generated by MSVC
 2013-01-11 22:56:33 +00:00
Ray Speth
33653e7f43 Removed unused member variable ReactionData.rxn_number 2013-01-11 22:56:30 +00:00
Ray Speth
83097b3860 Consolidated definitions of repeatedly-used constants 
"MIN_X" and "TINY" are replaced by "Tiny". "xxSmall" is replaced with
"SmallNumber".
 2013-01-11 22:55:46 +00:00
Victor Brunini
9b6b65fe04 Add function to DenseMatrix that multiplies two square matrices. 2013-01-07 18:18:10 +00:00
Ray Speth
205706f5dd [Reactor] Avoid a segfault when using phases with no Kinetics 2013-01-07 18:08:23 +00:00
Ray Speth
1e43e4f333 Added a version of writelog which takes the log level as an argument 2012-12-30 00:17:08 +00:00
Ray Speth
6b8986d0d0 Fixed const-ness of PecosTransport virtual functions 
These now match the function signatures in the base class.
 2012-12-26 23:56:10 +00:00
Ray Speth
46a8b3052f Use size_t instead of int in InterfaceKinetics 2012-12-26 23:56:07 +00:00
Harry Moffat
eab8781ea7 Added back ability to get transport parameters from transport objects. 
Added back read and write of named XML array blocks.
Fixed an error in IonsFromNeutralVPSSTP.
 2012-12-21 01:18:28 +00:00
Ray Speth
8587abf17f Fixed an uninitialized variable in Domain1D 2012-12-18 00:13:48 +00:00
Ray Speth
1e91bd59af [1D/Cython] Set pressure when restoring solution from XML file 
This partially addresses Issue 90.
 2012-12-18 00:10:48 +00:00
Ray Speth
14426bfc86 [1D] Added loglevel argument to control output from save and restore 
Passing loglevel=0 to Sim1D::save or Sim1D::restore will suppress all output
from these functions. The default loglevel maintains the normal level of output.
 2012-12-18 00:09:29 +00:00
Victor Brunini
95e66cd5ff Get rid of static variables in member functions. 2012-12-17 16:14:14 +00:00
Harry Moffat
ea25de7fe7 Continuing transfering LiquidTransport changes, doing bugfixes, and 
qualifying against our testsuite.
 2012-12-15 00:49:14 +00:00
Victor Brunini
bd653e357f Revert change to LiquidTransport. 2012-12-13 22:16:50 +00:00
Victor Brunini
749f988e52 Convert LiquidTransport to just store a pointer to the external 
gradient (T, X, V) values that it uses to compute fluxes. These
are never changed by the LiquidTransport object so there is no
reason to have them stored locally rather than just holding a pointer
to the data.
 2012-12-13 22:15:35 +00:00
Victor Brunini
2eba1ee7c8 PDSS_IonsFromNeutral does not own the neutralMoleculePhase_ pointer 
and the state of the neutralMoleculePhase_ is updated by the
VPSSIonsFromNeutral phase object that the PDSS_IonsFromNeutral
species object belongs to. Remove neutralMoleculePhase_->setState
calls from PDSS_IonsFromNeutral to avoid duplicate work, and make
it a const * to reflect that.
 2012-12-13 22:15:14 +00:00
Victor Brunini
d4d1093957 Performance improvements focused on Stefan-Maxwell liquid transport 
model for molten salts.

Summary:
- Division is expensive, replace repeated division with multiplication
  by stored 1/x.
- New and delete are expensive, make working vectors in some functions
  static so that they are not repeatedly instantiated and deleted.
- Reorder a few loops to reduce computation and hopefully cache misses.
 2012-12-13 22:14:36 +00:00
Victor Brunini
4f41718e5b Make all ThermoPhase setState functions virtual. 2012-12-13 22:14:02 +00:00
Ray Speth
b4f34045a8 [1D] Added a minimum grid spacing parameter 2012-12-06 17:31:44 +00:00
Ray Speth
347029d06a [1D] Added loglevel for saving residual components 
At loglevel 8, the residual after each Newton step, set of time steps, or grid
refinement is saved to 'debug_sim1D.xml'.
 2012-12-06 17:31:35 +00:00
Ray Speth
ecb930e9f7 [1D] Added a nSpecies() method to Bdry1D 2012-12-04 20:28:43 +00:00
Harry Moffat
c6f7abbf2f Fixed a serious error in InterfaceKinetics that had crept into this branch. 
Started upgrade/update of equilibrium solver
       - Fixed numerical jacobian calculation of the ln activity coefficients.
 2012-11-29 02:18:05 +00:00
Victor Brunini
c3233c1355 Update TransportFactory to allow the specification of the number of 
dimensions in the problem and default it to 1. At present this is
only passed through to the LiquidTransport constructor.

Remove LiquidTransport member m_nDim since the base Transport class
already stores m_nDim.

Don't set m_nDim to 1 in LiquidTransport constructor, it is set by
the Transport constructor.
 2012-11-26 20:19:57 +00:00
Ray Speth
7ed2a02953 StFlow::_getInitialSoln now sets the solution to a valid thermodynamic state 
This fixes errors that occured when the "showSolution" method was called before
explicitly setting the initial solution profile.
 2012-11-14 21:07:13 +00:00
Victor Brunini
7d8a61baf1 Clean up function prototypes to avoid 'a is hidden by b' warnings 
where the subclass prototype had an int and the super had a size_t
for a virtual function of the same name.
 2012-11-14 00:04:05 +00:00
Victor Brunini
28171eeece Update the definition of getSpeciesFluxesES to use all size_t 
instead of int to match the definition for the base Transport class.
Prior to this LiquidTransport::getSpeciesFluxesES was not overriding
the virtual Transport::getSpeciesFluxesES because the prototypes
differed.
 2012-11-13 21:59:11 +00:00
Harry Moffat
08a41f191c Added back constructPhaseFile() and constructPhaseXML(). 
All molten salt problems were broken and some brine problems were broken.
 2012-11-07 23:51:30 +00:00
Harry Moffat
83391db4fe Added back Cantera.h 
Note in the near future, we'll require that all Cantera code include this file so that the environment may be set up correctly.
 2012-11-07 23:41:58 +00:00
Victor Brunini
7c70568bb3 Clean up compiler warnings. 2012-11-07 21:08:56 +00:00
Ray Speth
fe6b5d3c0b Changed the ordering of Reactor sensitivity coefficients 
The order now matches the order in which the corresponding sensitivity reactions
are added to the ReactorNet, regardless of the order in which Reactors and Walls
are added to the network.

Sensitivity parameter names can be accessed using the "sensitivityParameterName"
method of ReactorNet, and the "sensParamID" methods of Reactor and Wall have
been removed as they no longer meaningful.
 2012-11-02 20:07:25 +00:00
Ray Speth
e34ac55f4f [Cython] Added sensitivity analysis to Reactor / ReactorNet 2012-11-02 20:07:15 +00:00
Ray Speth
845b73405e Merge bug fixes from 2.0 maintenance branch 2012-10-30 15:46:10 +00:00
Ray Speth
86e7723c26 Fixed sign error in isothermalCompressibility of ideal phases 2012-10-30 15:30:27 +00:00
Ray Speth
af10c288b4 Removed some unused member variables from PDSS classes 2012-10-24 15:46:57 +00:00
Ray Speth
436f38c6a6 Removed some unused member variables from Transport classes 2012-10-24 15:46:45 +00:00