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31 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
Ray Speth
9439615c71 Fixed signed/unsigned comparison warnings in Thermo 2012-01-17 04:12:27 +00:00
Ray Speth
255f1f9b9f Fixing compiler warnings, part 3 2012-01-17 04:10:43 +00:00
Ray Speth
69bffa3800 Fixing compiler warnings, part 2 2012-01-17 04:10:26 +00:00
Ray Speth
9e1fdfe39a Eliminated CVS keyword cruft 2012-01-09 17:32:01 +00:00
Harry Moffat
89497de369 Moved the getActivityConcentration() function and related 
functions up to the parent level, GibbsExcessVPSSTP
 2012-01-03 16:59:02 +00:00
Harry Moffat
5f01cc30bb Worked on MolarityIonicVPSSTP, filling it in a little bit. 
Changed GibbsExcessVPSSTP so that getLnActivityCoefficient() is central.
The straight activity coefficients may not be representable within
machine limits.
 2011-11-01 21:09:58 +00:00
Harry Moffat
6a3c7eabd4 Added a getMoleFraction to GibbsExcess at the start of the 
calculation. Want the mole fraction to be synched at all times.
 2011-10-04 23:33:58 +00:00
Harry Moffat
ab9ca908c2 Changed the name dlnActCoeffdN to dlnActCoeffdlnN to reflect what its actually 
doing.
Fixed an error in dlnActCoeffdlnN_diag() for MargulesVPSSTP.
 2010-08-04 17:04:46 +00:00
Harry Moffat
7b063f3fc8 changed the name of getdlnActcoeffdlnX to getdlnActCoeffdlnX_diag to 
reflect what it is really doing.
 2010-08-04 16:06:14 +00:00
Harry Moffat
3b8b18e72d Changed the name of getdactcoeffdlnN to getdactcoeffdlnN_diag to reflect what it's actually doing. 2010-08-04 15:50:37 +00:00
Harry Moffat
b6cf6b3139 Fleshed out the gradient of actcoeff wrt mole number. 2010-08-03 21:07:28 +00:00
Christopher Lueth
42e2dd0c0b added enthalpy_mole(), entropy_mole().... capabilities to MargulesVPSSTP 2010-05-26 23:15:29 +00:00
Harry Moffat
ef7728b1d3 Merged thermo directory with the LiquidTransportDevelop 
thermo directory. 
  The biggest change is the addition of the derivative routines
of the activity wrt mole fraction and mole number.
Also There is an addition of reportCSV() routine, which is 
a method to create a comma separated file from ThermoPhase routines.
The rest are small issues.
 2010-05-09 03:18:33 +00:00
Christopher Lueth
1f6fe73076 Changed output format of reportCSV...still need to implement it properly in MolalityVPSSTP and PureFluidPhase 2010-04-02 23:11:47 +00:00
Christopher Lueth
58719349cb added reportCSV method to ThermoPhase class and all other derived classes that currently contain the report method. reportCSV will output phase data to a text file and a comma separated file that are passed in. 2010-04-01 23:05:39 +00:00
Harry Moffat
263aeb6b35 Added a new way to specify the kinetics reaction rate coefficient 
when dealing with electron transfer surface reactions.
This way specifies an exchange current density reaction rate coefficient
in units of amps / m2.  This is slightly more informative for 
electrode reactions. 

The new also preserves the correct treatment of activity coefficients
for these reactions. 

A memo describing this new capability is in the works.
 2010-03-01 18:14:07 +00:00
Christopher Lueth
d9b4031614 Added excess volume capability for GibbsExcessVPSSTP and children 
Corrected activity coefficients calculation for >2 species
 2010-02-27 00:47:47 +00:00
Harry Moffat
1a3af47eb9 took out checkMFSum() which is inappropriate in that context. 2009-12-06 17:55:43 +00:00
Harry Moffat
7b3b9b186a Transfering bugfixes from liquidTransport to the main branch. 
This mainly involved fixing the copy and assignment operators
for the IonsFromNeutralVPSSTP operator.

Added docs for PDSS_SSVol

Turned on keyword substitution
 2009-12-05 19:08:43 +00:00
Harry Moffat
1f9d937d15 Fixed errors in the copy and assignment operator functions 
for the IonsFromNeutralVPSSTP object.
 2009-12-02 18:06:09 +00:00
John Hewson
aae7d0b440 Added method 
virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const;
to ThermoPhase, GibbsExcessVPSSTP, VPStandardStateTP and 
MargulesVPSSTP classes (i.e. the whole thermo tree).  
In GibbsExcessVPSSTP and above, these methods are not yet implemented.

In MargulesVPSSTP, the internal method 
void s_update_dlnActCoeff_dlnX() const;
does the work and stores the result in the member dlnActCoeffdlnX_Scaled_.
 2009-11-15 04:40:37 +00:00
Harry Moffat
35e4c9ea45 Turned on Keyword substition in all files. 2009-11-09 23:36:49 +00:00
Harry Moffat
d5b74320ac Doxygen updates 
Started to document new PDSS formulations
 2009-10-21 01:02:44 +00:00
Harry Moffat
7e6f2a1775 Latest version of the IonsFromNeutral object. Hopefully, this 
clears up the linking errors that VC9 was experiencing.
 2009-09-10 22:51:40 +00:00
Harry Moffat
06276fba6d Added a new thermo object in. 
IonsFromNeutralVPSSTP : This is initially used for molten salts.
        Molten salt thermo is treated via the neutral molecule
        molten salt expressions. However, ions migrate by themselves.
        therefore, you must treat ions within the transport equations.
        This thermophase object treats the ions as species, and is
        made to be consistent with the neutral molecules thermophase
        object that is used to express the non-ideal thermodynamics
        of the molten salt solution. Currently, MargulesVPSSTP
        is used for this as the LiKCl system is parameterized using
        this excess Gibbs free energy formulation.

    MargulesVPSSTP
        Various upgrades and fillers. It now reads and is initiated
        from the input file.

    setState_TP(), setTemperature(), and setPressure() within 
    VPStandardStateTP() formulations
        There was some circular logic, previously. Now setTemperature() and setPressure()
        are subserviant to setState_TP(). Basically, it doesn't make
        sense to calculate the standard state without first getting
        both the temperature and pressure (not just one and then the other)
        before you calculate the standard state for VPStandardStateTP derivatives.
        Think about the water EOS, which is a real fluid. You don't want
        to be trying to calculate the standard state within the enveloppe where
        neither gas nor liquid is stable.

     PseudoBinaryVPSSTP
        Deprecated.
 2009-09-02 17:17:52 +00:00
Harry Moffat
70647c85ed Initial Import 2009-07-27 23:17:19 +00:00
Harry Moffat
49b413e61e Added an initial attempt at a Margules excess gibbs free energy 
model. It's just hard coded to match the Eutectic of LiKCl at the
moment.
 2009-03-03 21:08:31 +00:00
Harry Moffat
201c32bea6 A further iteration, where I've added an interface that maintains a 
current mole fraction vector.
 2009-02-23 21:06:38 +00:00
Harry Moffat
07bcac001b Started coding up general excess gibbs free energy thermo formulations 
based on mole fraction expansions.
 2009-02-23 20:41:03 +00:00