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159 commits

Author SHA1 Message Date
Ray Speth
00cfa9c7bd Fixed compilation problems generated by merging 2012-02-10 03:29:20 +00:00
Ray Speth
7c171631af Merge branch 'scons' into 'trunk' 
Conflicts:
	Cantera/Makefile.in
	Cantera/clib/src/clib_defs.h
	Cantera/clib/src/ctreactor.cpp
	Cantera/clib/src/ctstagn.cpp
	Cantera/clib/src/ctstagn.h
	Cantera/cxx/Makefile.in
	Cantera/cxx/demos/combustor/combustor.cpp
	Cantera/cxx/demos/flamespeed/flamespeed.cpp
	Cantera/cxx/demos/kinetics1/example_utils.h
	Cantera/cxx/demos/kinetics1/kinetics1.cpp
	Cantera/cxx/include/Cantera.h
	Cantera/cxx/include/Cantera.mak.in
	Cantera/cxx/include/Cantera_bt.mak.in
	Cantera/cxx/include/Edge.h
	Cantera/cxx/include/GRI30.h
	Cantera/cxx/include/Interface.h
	Cantera/cxx/include/zerodim.h
	Cantera/fortran/f77demos/Makefile.in
	Cantera/fortran/src/Makefile.in
	Cantera/fortran/src/fct.cpp
	Cantera/fortran/src/fctxml.cpp
	Cantera/fortran/src/flib_defs.h
	Cantera/matlab/Makefile.in
	Cantera/matlab/cantera/Contents.m
	Cantera/matlab/setup_winmatlab.py
	Cantera/matlab/src/ctfunctions.cpp
	Cantera/matlab/src/ctmatutils.h
	Cantera/matlab/src/mixturemethods.cpp
	Cantera/matlab/src/mllogger.h
	Cantera/matlab/src/phasemethods.cpp
	Cantera/matlab/src/reactormethods.cpp
	Cantera/matlab/src/reactornetmethods.cpp
	Cantera/matlab/src/thermomethods.cpp
	Cantera/matlab/src/wallmethods.cpp
	Cantera/matlab/src/xmlmethods.cpp
	Cantera/python/Cantera/Edge.py
	Cantera/python/Cantera/Interface.py
	Cantera/python/Cantera/Phase.py
	Cantera/python/Cantera/importFromFile.py
	Cantera/python/Makefile.in
	Cantera/python/ctml_writer.py
	Cantera/python/setup.py.in
	Cantera/python/src/Makefile.in
	Cantera/python/src/ctkinetics_methods.cpp
	Cantera/python/src/ctonedim_methods.cpp
	Cantera/python/src/pylogger.h
	Cantera/src/Makefile.in
	Cantera/src/base/config.h.in
	Cantera/src/base/ctml.cpp
	Cantera/src/base/ctml.h
	Cantera/src/base/mdp_allo.cpp
	Cantera/src/base/mdp_allo.h
	Cantera/src/base/vec_functions.h
	Cantera/src/base/xml.cpp
	Cantera/src/base/xml.h
	Cantera/src/converters/CKParser.h
	Cantera/src/converters/Element.h
	Cantera/src/converters/Reaction.h
	Cantera/src/converters/RxnSpecies.h
	Cantera/src/converters/Species.h
	Cantera/src/converters/ckr_defs.h
	Cantera/src/converters/ckr_utils.h
	Cantera/src/equil/BasisOptimize.cpp
	Cantera/src/equil/Makefile.in
	Cantera/src/equil/MultiPhase.cpp
	Cantera/src/equil/vcs_MultiPhaseEquil.cpp
	Cantera/src/equil/vcs_VolPhase.cpp
	Cantera/src/equil/vcs_VolPhase.h
	Cantera/src/equil/vcs_linmaxc.cpp
	Cantera/src/equil/vcs_phaseStability.cpp
	Cantera/src/equil/vcs_rxnadj.cpp
	Cantera/src/equil/vcs_solve.cpp
	Cantera/src/equil/vcs_solve.h
	Cantera/src/equil/vcs_solve_TP.cpp
	Cantera/src/equil/vcs_util.cpp
	Cantera/src/equil/vcs_xerror.c
	Cantera/src/kinetics/GasKinetics.cpp
	Cantera/src/kinetics/GasKinetics.h
	Cantera/src/kinetics/InterfaceKinetics.cpp
	Cantera/src/kinetics/InterfaceKinetics.h
	Cantera/src/kinetics/Kinetics.h
	Cantera/src/kinetics/ReactionStoichMgr.h
	Cantera/src/kinetics/RxnRates.h
	Cantera/src/kinetics/StoichManager.h
	Cantera/src/numerics/BandMatrix.cpp
	Cantera/src/numerics/BandMatrix.h
	Cantera/src/numerics/DAE_Solver.h
	Cantera/src/numerics/DAE_solvers.cpp
	Cantera/src/numerics/DenseMatrix.cpp
	Cantera/src/numerics/DenseMatrix.h
	Cantera/src/numerics/FuncEval.h
	Cantera/src/numerics/IDA_Solver.cpp
	Cantera/src/numerics/IDA_Solver.h
	Cantera/src/numerics/Integrator.h
	Cantera/src/numerics/Makefile.in
	Cantera/src/numerics/NonlinearSolver.cpp
	Cantera/src/numerics/NonlinearSolver.h
	Cantera/src/numerics/ResidEval.h
	Cantera/src/numerics/ResidJacEval.cpp
	Cantera/src/numerics/ResidJacEval.h
	Cantera/src/numerics/SquareMatrix.cpp
	Cantera/src/numerics/SquareMatrix.h
	Cantera/src/numerics/ctlapack.h
	Cantera/src/oneD/Domain1D.h
	Cantera/src/oneD/OneDim.cpp
	Cantera/src/oneD/OneDim.h
	Cantera/src/oneD/Resid1D.h
	Cantera/src/oneD/Solid1D.cpp
	Cantera/src/oneD/Solid1D.h
	Cantera/src/oneD/StFlow.cpp
	Cantera/src/oneD/Surf1D.h
	Cantera/src/spectra/LineBroadener.h
	Cantera/src/thermo/Constituents.cpp
	Cantera/src/thermo/GibbsExcessVPSSTP.cpp
	Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp
	Cantera/src/thermo/IonsFromNeutralVPSSTP.h
	Cantera/src/thermo/LatticePhase.cpp
	Cantera/src/thermo/LatticeSolidPhase.cpp
	Cantera/src/thermo/LatticeSolidPhase.h
	Cantera/src/thermo/Makefile.in
	Cantera/src/thermo/MargulesVPSSTP.cpp
	Cantera/src/thermo/MargulesVPSSTP.h
	Cantera/src/thermo/NasaThermo.h
	Cantera/src/thermo/PDSS_IonsFromNeutral.cpp
	Cantera/src/thermo/PDSS_IonsFromNeutral.h
	Cantera/src/thermo/PDSS_SSVol.cpp
	Cantera/src/thermo/Phase.cpp
	Cantera/src/thermo/PseudoBinaryVPSSTP.cpp
	Cantera/src/thermo/PseudoBinaryVPSSTP.h
	Cantera/src/thermo/PureFluidPhase.cpp
	Cantera/src/thermo/ShomateThermo.h
	Cantera/src/thermo/SimpleThermo.h
	Cantera/src/thermo/SpeciesThermoFactory.cpp
	Cantera/src/thermo/State.h
	Cantera/src/thermo/StoichSubstance.h
	Cantera/src/thermo/ThermoFactory.cpp
	Cantera/src/thermo/ThermoPhase.cpp
	Cantera/src/thermo/ThermoPhase.h
	Cantera/src/transport/AqueousTransport.cpp
	Cantera/src/transport/AqueousTransport.h
	Cantera/src/transport/DustyGasTransport.cpp
	Cantera/src/transport/DustyGasTransport.h
	Cantera/src/transport/L_matrix.h
	Cantera/src/transport/LiquidTransport.cpp
	Cantera/src/transport/LiquidTransport.h
	Cantera/src/transport/LiquidTransportData.h
	Cantera/src/transport/MMCollisionInt.cpp
	Cantera/src/transport/MMCollisionInt.h
	Cantera/src/transport/Makefile.in
	Cantera/src/transport/MixTransport.cpp
	Cantera/src/transport/MixTransport.h
	Cantera/src/transport/MultiTransport.cpp
	Cantera/src/transport/MultiTransport.h
	Cantera/src/transport/SimpleTransport.cpp
	Cantera/src/transport/SimpleTransport.h
	Cantera/src/transport/SolidTransport.cpp
	Cantera/src/transport/SolidTransport.h
	Cantera/src/transport/TransportBase.h
	Cantera/src/transport/TransportFactory.cpp
	Cantera/src/transport/TransportFactory.h
	Cantera/src/transport/TransportParams.h
	Cantera/src/transport/WaterTransport.h
	Cantera/src/zeroD/FlowDevice.h
	Cantera/src/zeroD/Reactor.h
	Cantera/src/zeroD/ReactorBase.cpp
	Cantera/src/zeroD/ReactorBase.h
	Cantera/src/zeroD/ReactorNet.h
	Cantera/src/zeroD/Wall.h
	Cantera/user/Makefile.in
	License.rtf
	Makefile.in
	apps/bvp/stagnation.cpp
	configure
	configure.in
	data/transport/misc_tran.dat
	docs/Makefile.in
	docs/install_examples/README.txt
	docs/install_examples/cygwin_gcc434_dbg_f2c_numpy.sh
	docs/install_examples/linux_64_gcc424_dbg_python252_numpy
	docs/install_examples/linux_64_gcc424_opt_python252_numpy
	docs/install_examples/mac_gcc401_python251_numpy
	docs/python/.cvsignore
	ext/Makefile.in
	ext/blas/Makefile.in
	ext/cvode/Makefile.in
	ext/f2c_blas/Makefile.in
	ext/f2c_lapack/Makefile.in
	ext/f2c_math/Makefile.in
	ext/f2c_math/xersve.c
	ext/f2c_recipes/Makefile.in
	ext/lapack/Makefile.in
	ext/math/Makefile.in
	ext/recipes/Makefile.in
	ext/tpx/CarbonDioxide.cpp
	ext/tpx/Makefile.in
	ext/tpx/Sub.cpp
	ext/tpx/utils.cpp
	preconfig
	test_problems/ChemEquil_gri_matrix/gri_matrix.cpp
	test_problems/ChemEquil_gri_pairs/gri_pairs.cpp
	test_problems/ChemEquil_ionizedGas/ionizedGasEquil.cpp
	test_problems/ChemEquil_ionizedGas/runtest
	test_problems/ChemEquil_red1/basopt_red1.cpp
	test_problems/CpJump/CpJump.cpp
	test_problems/Makefile.in
	test_problems/VCSnonideal/Makefile.in
	test_problems/VCSnonideal/NaCl_equil/HMW_NaCl.xml
	test_problems/VCSnonideal/NaCl_equil/nacl_equil.cpp
	test_problems/VPsilane_test/silane_equil.cpp
	test_problems/cathermo/DH_graph_1/DH_graph_1.cpp
	test_problems/cathermo/DH_graph_NM/DH_graph_1.cpp
	test_problems/cathermo/DH_graph_Pitzer/DH_graph_1.cpp
	test_problems/cathermo/DH_graph_acommon/DH_graph_1.cpp
	test_problems/cathermo/DH_graph_bdotak/DH_graph_1.cpp
	test_problems/cathermo/HMW_dupl_test/HMW_NaCl_sp1977_alt.xml
	test_problems/cathermo/HMW_dupl_test/HMW_dupl_test.cpp
	test_problems/cathermo/HMW_dupl_test/TemperatureTable.h
	test_problems/cathermo/HMW_dupl_test/sortAlgorithms.cpp
	test_problems/cathermo/HMW_dupl_test/sortAlgorithms.h
	test_problems/cathermo/HMW_graph_CpvT/HMW_NaCl_sp1977_alt.xml
	test_problems/cathermo/HMW_graph_CpvT/HMW_graph_CpvT.cpp
	test_problems/cathermo/HMW_graph_CpvT/TemperatureTable.h
	test_problems/cathermo/HMW_graph_CpvT/sortAlgorithms.cpp
	test_problems/cathermo/HMW_graph_CpvT/sortAlgorithms.h
	test_problems/cathermo/HMW_graph_GvI/HMW_NaCl.xml
	test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp
	test_problems/cathermo/HMW_graph_GvI/TemperatureTable.h
	test_problems/cathermo/HMW_graph_GvI/sortAlgorithms.cpp
	test_problems/cathermo/HMW_graph_GvI/sortAlgorithms.h
	test_problems/cathermo/HMW_graph_GvT/HMW_NaCl_sp1977_alt.xml
	test_problems/cathermo/HMW_graph_GvT/HMW_graph_GvT.cpp
	test_problems/cathermo/HMW_graph_GvT/TemperatureTable.h
	test_problems/cathermo/HMW_graph_GvT/sortAlgorithms.cpp
	test_problems/cathermo/HMW_graph_GvT/sortAlgorithms.h
	test_problems/cathermo/HMW_graph_HvT/HMW_NaCl_sp1977_alt.xml
	test_problems/cathermo/HMW_graph_HvT/HMW_graph_HvT.cpp
	test_problems/cathermo/HMW_graph_HvT/TemperatureTable.h
	test_problems/cathermo/HMW_graph_HvT/sortAlgorithms.cpp
	test_problems/cathermo/HMW_graph_HvT/sortAlgorithms.h
	test_problems/cathermo/HMW_graph_VvT/HMW_NaCl_sp1977_alt.xml
	test_problems/cathermo/HMW_graph_VvT/HMW_graph_VvT.cpp
	test_problems/cathermo/HMW_graph_VvT/TemperatureTable.h
	test_problems/cathermo/HMW_graph_VvT/sortAlgorithms.cpp
	test_problems/cathermo/HMW_graph_VvT/sortAlgorithms.h
	test_problems/cathermo/HMW_test_1/HMW_test_1.cpp
	test_problems/cathermo/HMW_test_3/HMW_test_3.cpp
	test_problems/cathermo/Makefile.in
	test_problems/cathermo/VPissp/ISSPTester.cpp
	test_problems/cathermo/ims/IMSTester.cpp
	test_problems/cathermo/issp/ISSPTester.cpp
	test_problems/cathermo/stoichSubSSTP/TemperatureTable.h
	test_problems/cathermo/stoichSubSSTP/sortAlgorithms.cpp
	test_problems/cathermo/stoichSubSSTP/sortAlgorithms.h
	test_problems/cathermo/stoichSubSSTP/stoichSubSSTP.cpp
	test_problems/cathermo/testIAPWS/testIAPWSphi.cpp
	test_problems/cathermo/testWaterPDSS/testWaterPDSS.cpp
	test_problems/cathermo/testWaterTP/testWaterSSTP.cpp
	test_problems/cathermo/wtWater/wtWater.cpp
	test_problems/ck2cti_test/Makefile.in
	test_problems/ck2cti_test/runtest.in
	test_problems/cxx_ex/Makefile.in
	test_problems/cxx_ex/equil_example1.cpp
	test_problems/cxx_ex/example_utils.h
	test_problems/cxx_ex/kinetics_example1.cpp
	test_problems/cxx_ex/kinetics_example2.cpp
	test_problems/cxx_ex/kinetics_example3.cpp
	test_problems/cxx_ex/runtest
	test_problems/cxx_ex/rxnpath_example1.cpp
	test_problems/cxx_ex/transport_example1.cpp
	test_problems/cxx_ex/transport_example2.cpp
	test_problems/min_python/Makefile.in
	test_problems/min_python/minDiamond/Makefile.in
	test_problems/min_python/negATest/negATest.cpp
	test_problems/mixGasTransport/runtest
	test_problems/nasa9_reader/Makefile.in
	test_problems/nasa9_reader/runtest.in
	test_problems/negATest/negATest.cpp
	test_problems/printUtilUnitTest/pUtest.cpp
	test_problems/pureFluidTest/testPureWater.cpp
	test_problems/silane_equil/silane_equil.cpp
	test_problems/surfkin/surfdemo.cpp
	tools/Makefile.in
	tools/bin/cvs2cl.pl
	tools/src/ck2cti.cpp
	tools/templates/f77/demo_ftnlib.cpp
	win32/vc7/Sundials/sundials/sundials_config.h
	win32/vc9/Sundials/SUNDIALS_SHARED/sundials_config.h
	winconfig.h
 2012-02-10 03:21:33 +00:00
Harry Moffat
cb4048249c Added a way to specify weighting norms for the residuals. 2012-02-08 15:59:11 +00:00
Ray Speth
c708682e56 Removed 'using namespace std' from all header files 2012-01-23 03:36:42 +00:00
Ray Speth
f922a9c348 Removed unnecessary TRUE and FALSE macros 
Replaced with built-in true and false values, and the variables
these were assigned to have been converted from int to bool.
 2012-01-20 23:13:32 +00:00
Ray Speth
4e2a48c4e5 Fixed erroneous inequality comparisons between size_t and 0 2012-01-20 23:13:17 +00:00
Ray Speth
6589eb7f7c Removed some unused numerical integration utilities 2012-01-18 23:44:50 +00:00
Ray Speth
4cdac9a90f Eliminated "heapsort" function in favor of using std::sort 2012-01-18 03:42:52 +00:00
Ray Speth
de7d58805e Removed unused variables identified by compiler warnings 2012-01-17 23:58:38 +00:00
Ray Speth
aeb16e0bc9 Fixed some signed/unsigned comparison warnings 2012-01-17 04:13:04 +00:00
Ray Speth
e8d895ac26 Fixed MSVC warning LNK4221 by removing a few "empty" source files 2012-01-17 04:12:23 +00:00
Ray Speth
bc9ec48516 Fixing compiler warnings, part 5 2012-01-17 04:11:51 +00:00
Ray Speth
9470103bb2 Fixing compiler warnings, part 4 2012-01-17 04:11:20 +00:00
Ray Speth
255f1f9b9f Fixing compiler warnings, part 3 2012-01-17 04:10:43 +00:00
Ray Speth
4babd5898b Fixing compiler warnings, part 1 2012-01-17 04:10:08 +00:00
Ray Speth
453576f0ad Removed MSVC-specific compiler warning suppression 2012-01-17 04:09:18 +00:00
Ray Speth
9e1fdfe39a Eliminated CVS keyword cruft 2012-01-09 17:32:01 +00:00
Harry Moffat
701bcc53b1 Added a print statement. 2012-01-03 16:24:09 +00:00
Ray Speth
71588d307d Remove files for Autotools and Visual Studio build systems 2011-12-14 19:38:10 +00:00
Ray Speth
99a0dc5f0f Removed incomplete CMake build scripts 2011-12-14 03:54:19 +00:00
Ray Speth
b6bfca8e94 SCons now builds the Cantera kernel 2011-12-14 03:03:57 +00:00
Harry Moffat
b9c9f81761 Made the BandMatrix class and SquareMatrix inherit from a common 
parent so that they can be used interchangeably in other software.

Removed PsuedBinaryVPSSTP in favor of MolarityIonicVPSSTP
 2011-10-19 20:45:06 +00:00
Harry Moffat
e8d6649c7b Doxygen updates 
-> Also moved implementation functions for BandMatrix into the cpp file
 2011-10-13 21:16:06 +00:00
Harry Moffat
6cf9c46630 Worked on lvl 4 printouts 2011-10-10 16:51:52 +00:00
Harry Moffat
7d63cd24d4 Fixed the trust region calculation 2011-10-08 01:02:29 +00:00
Harry Moffat
a510731dca Fixed a column scaling error for the dogleg method 2011-10-05 17:30:08 +00:00
Harry Moffat
9197a283b6 Stable intermediate step. Working on a new test problem where 
the Newton direction is fouled up by a large condition number.
 2011-10-04 21:48:11 +00:00
Harry Moffat
9af9a3e702 Made the double dogleg capability operational. It can now be used by users reliably. 2011-09-29 23:11:12 +00:00
Harry Moffat
d251da7a84 Revamped the rootfinder algorithm. 
Behavior is substantially different.
A summary table is now written out at the end of the solve for
some print levels.
 2011-09-23 20:31:17 +00:00
Harry Moffat
445adce8fc Doxygen changes 2011-09-21 16:40:51 +00:00
Harry Moffat
cf730962a6 Protected against sundials not being compiled in 2011-09-13 23:32:29 +00:00
Harry Moffat
d2272b3707 Initialization for trust regions firmed up. 
Same results for the second time into the function as the first.
 2011-09-12 15:59:52 +00:00
Harry Moffat
93d5d43a19 More cleanup 2011-09-09 21:32:50 +00:00
Harry Moffat
4d2e6b65bb Updates to the internals, trying to simplify 2011-09-09 19:16:36 +00:00
Harry Moffat
2703130a7a Started working on the documentation and cleanup of the dogleg method. 
Now possible to run the algorithm without the DEBUG_DOGLEG block on.
 2011-09-08 02:07:02 +00:00
Harry Moffat
6fca9189da Added back conditional printing 2011-08-30 15:56:00 +00:00
Harry Moffat
36a56093d1 Buf fixes for handling boundaries. 2011-08-15 03:57:40 +00:00
Harry Moffat
d617f43013 Added a capability to turn off writing separate log files 2011-08-15 00:54:18 +00:00
Harry Moffat
efd58ec5b7 Tweaked the algorithm in several ways. The amount of unusual behavior 
should be reduced.
 2011-08-15 00:45:16 +00:00
Harry Moffat
78eb7b4127 More integration of IDA into Cantera. 
added cj parameter to some existing routines.
  Added correct delta_t to the parameter list of  ResidJacEval object
 2011-08-01 15:26:20 +00:00
Harry Moffat
2f97180753 Fixed an error in the IDA_Solver class. 
Added an analytical jacobian capability to IDA_Solver.
Added column pointers as a member to DenseMatrix
 2011-07-31 23:44:45 +00:00
Harry Moffat
82e194a2b0 Added column pointers as a member to this object. This is 
needed for linking in sundance more closely.
 2011-07-31 18:58:19 +00:00
Harry Moffat
2082b57699 Worked on getting the IDA_Solver interface operable. Previously, 
it hadn't been. It now works on one test problem.
 2011-07-30 03:08:10 +00:00
Harry Moffat
ff7e66e5a3 This update adds in a Multicomponent Real Gas capability to Cantera. 
The Object is called RedlichKwongMFTP, and it implements a multicomponent real gas approximation.
Most of the functionality has been verified against sample problems involving the CO2-H2O system.
 2011-07-23 00:30:35 +00:00
John Hewson
1982d0c928 Changed return flags for errors to be unique to each return condition. 
Hopefully this will help track down convergence problems.
 2011-07-15 23:27:45 +00:00
Harry Moffat
68ed8ad548 Guarded against a divide by zero that occurred when the cauchy step 
size and residual were exactly zero.
 2011-05-30 22:19:39 +00:00
Harry Moffat
4d245501cf Update on the NonlinearSolver: 
Update to :calcSolnToResNormVector() to align it with documentation.
 2011-05-30 17:57:53 +00:00
Harry Moffat
8710440a1f Another incremental update 
- decideStep() has been documented and checked out
 2011-05-28 02:51:49 +00:00
Harry Moffat
425085627b Incremental work. Fixed one error in an output variable. 2011-05-28 00:18:33 +00:00
Harry Moffat
6eccfa16ed Worked on getting the Affine solve capability working. 
This is now working, so that we can switch to a Hessian with junk on the
diagonal when there is a condition number problem.
 2011-05-17 00:45:08 +00:00