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Author SHA1 Message Date
Ray Speth
2528df0f75 Reorganized source tree structure 
These changes make it unnecessary to copy header files around during
the build process, which tends to confuse IDEs and debuggers. The
headers which comprise Cantera's external C++ interface are now in
the 'include' directory.

All of the samples and demos are now in the 'samples' subdirectory.
 2012-02-12 02:27:14 +00:00
Ray Speth
a6f939c2fe Applied consistent formatting to all C++ code 
Done using astyle:
astyle --style=kr --add-brackets --indent=spaces=4 --indent-col1-comments --unpad-paren --pad-header --align-pointer=type --lineend=linux
 2012-02-10 17:24:00 +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
39f2e4786a Changed the default number of digits that are saved to an xml file. 
This crucial change is needed if xml files are to be used as restart files,
where we will need close to machine precision.
 2012-02-08 16:00:55 +00:00
Harry Moffat
fdd37f5f2d Added addNamedFloat Array() to ctml. Easy way to read and write float arrays. 
volt and coulomb added to units
added depth argument to several xml calls.
 2012-01-23 20:59:38 +00:00
Ray Speth
f23bb0365a Fixed more signed/unsigned/size_t warnings 
These were warnings that showed up when compiling with the Microsoft
Platform SDK.
 2012-01-20 23:13:54 +00:00
Ray Speth
afdf3fb2d1 Removed some empty comment lines 2012-01-19 20:30:04 +00:00
Ray Speth
aeb16e0bc9 Fixed some signed/unsigned comparison warnings 2012-01-17 04:13:04 +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
Harry Moffat
8c98b3560e Added an index lookup up capability. 
Added a depth gauge to findByAttr.
 2012-01-14 02:20:48 +00:00
Harry Moffat
8e1563b07d Added a recursive limit to the writes. 2012-01-13 02:24:48 +00:00
Harry Moffat
8c39c0307b Clarified the API for addChild. The function always mallocs a 
new copy of the child. Added a new function, mergeAsChild(XML_Node &), for
the case where a malloc is not wanted.

Made setRoot() a recursive function, as it should be.
 2012-01-09 22:32:55 +00:00
Ray Speth
9e1fdfe39a Eliminated CVS keyword cruft 2012-01-09 17:32:01 +00:00
Harry Moffat
5f9c515e03 Added a new function getNamedStringValue 2012-01-09 16:12:23 +00:00
Harry Moffat
f3bec02808 A reworking of the LatticePhase and LatticeSolidPhase classes. 2011-03-11 00:10:50 +00:00
Harry Moffat
fd62251e6f Added a capability to expose the comment field. 
nChildren now takes an argument (has a default) to ignore comments.
 2010-09-21 16:03:45 +00:00
Harry Moffat
b784726e08 Doxygen update 2010-08-10 15:34:05 +00:00
Harry Moffat
74b1c3c0a1 Added more constructor inits 2010-05-07 14:44:05 +00:00
Harry Moffat
7abb1dc33a Merged with the trunk. 2010-01-17 19:08:00 +00:00
Harry Moffat
66ea343cea Doxygen update 
- no code changed
  - All the easy warning messages are eliminated now from the trunk.
 2010-01-17 18:17:55 +00:00
Harry Moffat
e381001c95 Merged changes from the 1.8.0 branch ontl the main trunk. 2010-01-04 00:46:26 +00:00
Harry Moffat
9c6080e3c9 Turned on keyword substitution in the cpp files. 2009-12-09 17:50:27 +00:00
Harry Moffat
2c712b8c56 Merges from the Trunk. 2009-12-06 19:25:59 +00:00
Harry Moffat
ae22fd8aca Added more initializations 2009-12-06 17:54:24 +00:00
Harry Moffat
1922aa9fe0 Took executable prop off these files. 2009-12-05 22:42:07 +00:00
Harry Moffat
35e4c9ea45 Turned on Keyword substition in all files. 2009-11-09 23:36:49 +00:00
Harry Moffat
9593d2996e Another update aimed at getting a SimpleTransport model up and running. 
SimpleTransport now can read its XML file.
 2009-10-13 00:27:48 +00:00
Harry Moffat
d503c55864 Added a clear() function to the xml object. This will wipe 
out the current level and everything below it.
 2009-10-11 21:34:06 +00:00
Harry Moffat
70647c85ed Initial Import 2009-07-27 23:17:19 +00:00
Harry Moffat
e7078147b3 Changed xml constructors to make them simpler with less implicit 
conversion routines. Trying to figure out what the issue is with
the pc interface's /MD vs /MDd problems.
 2009-07-22 01:21:35 +00:00
Harry Moffat
7f5d7efd87 Eliminated a possible source of leaks. not sure about this one. 2009-05-13 21:47:45 +00:00
Harry Moffat
c20cf5ebfd Fixed an error in the xml writer, that occurred when two newlines 
appear next to each other.
 2009-03-17 15:12:16 +00:00
Harry Moffat
fb0ab374e0 Added headers for possible ubuntu compilation problems. 2009-03-13 03:18:08 +00:00
Harry Moffat
08cc65d5d4 Made the CanteraError exception inherit from std::exception 
Added in mdp_allo package. It's not really linked in anywhere except
for applications, so call it provisional.
 2009-02-11 19:55:56 +00:00
Harry Moffat
2dc2b21423 doxygen update - eliminated warnings 2009-01-06 21:30:08 +00:00
Harry Moffat
e16a74df83 doxygen updates 2009-01-05 23:52:43 +00:00
Harry Moffat
7ba6449978 Finished low lvl doxygen commenting XML_Node object 2009-01-05 23:33:44 +00:00
Harry Moffat
a879666984 Doxygen updates 2009-01-03 18:48:25 +00:00
Harry Moffat
09236f42f8 Doxygen updates 2009-01-02 21:46:31 +00:00
Harry Moffat
e8c33462c6 doxygen update 2008-12-29 21:19:28 +00:00
Harry Moffat
a44c7650c5 Added fpValueCheck and added doxygen info 2008-12-27 00:25:04 +00:00
Harry Moffat
dad3088736 Changed findByAttr to be a const function. 2008-12-04 02:11:51 +00:00
Harry Moffat
022f3da1da More doxygen updates. 
Started changing 'const std::string ggg' arguments into
                 'const std::string & ggg arguments.
Supposedly, the latter is faster, as it only passes a pointer instead
of going through an implicit copy constructor operation.
 2008-11-03 16:10:25 +00:00
Harry Moffat
e48f46cd1a Doxygen update. 
moved attribs() to be a private function.
 2008-11-01 00:55:22 +00:00
Harry Moffat
0cebba592f Doxygen update 2008-10-31 20:57:48 +00:00
Harry Moffat
8a740e53d8 Doxygen updates 2008-10-31 19:14:57 +00:00
Harry Moffat
3bd378733a Doxygen updates on these files 2008-10-31 17:51:09 +00:00
Harry Moffat
33f5767833 More documentation of XML_Node 2008-10-31 16:46:49 +00:00
Harry Moffat
75e56cf8d3 Added documentation. 
Made getFloat() more explicit. Took out the use of "-" for type. Now,
have to specify the type of units conversion.
 2008-10-31 15:45:00 +00:00