Updated #includes to reflect new header file locations

include/cantera/Cantera.h

@@ -7,25 +7,25 @@
 #ifndef CANTERA_H_INCL
 #define CANTERA_H_INCL
 
-#include "kernel/ct_defs.h"
+#include "base/ct_defs.h"
 
 // some useful functions
-#include "kernel/global.h"
+#include "base/global.h"
 
 // the CanteraError exception class
-#include "kernel/ctexceptions.h"
+#include "base/ctexceptions.h"
 
 // The Cantera logger class
-#include "kernel/logger.h"
+#include "base/logger.h"
 
 // Include the timer
-#include "kernel/clockWC.h"
+#include "base/clockWC.h"
 
 // Include routines for reading and writing XML files
-#include "kernel/xml.h"
+#include "base/xml.h"
 
 // Include string utility routines
-#include "kernel/stringUtils.h"
+#include "base/stringUtils.h"
 
 #endif
 

include/cantera/Edge.h

@@ -3,9 +3,9 @@
 
 #include <string>
 
-#include "kernel/EdgePhase.h"
-#include "kernel/EdgeKinetics.h"
-#include "kernel/importKinetics.h"
+#include "thermo/EdgePhase.h"
+#include "kinetics/EdgeKinetics.h"
+#include "kinetics/importKinetics.h"
 
 namespace Cantera
 {

include/cantera/GRI30.h

@@ -3,10 +3,10 @@
 
 #include <string>
 
-#include "kernel/IdealGasPhase.h"
-#include "kernel/GRI_30_Kinetics.h"
-#include "kernel/importKinetics.h"
-#include "kernel/stringUtils.h"
+#include "thermo/IdealGasPhase.h"
+#include "kinetics/GRI_30_Kinetics.h"
+#include "kinetics/importKinetics.h"
+#include "base/stringUtils.h"
 
 namespace Cantera
 {

include/cantera/IdealGasMix.h

@@ -3,10 +3,10 @@
 
 #include <string>
 
-#include "kernel/IdealGasPhase.h"
-#include "kernel/GasKinetics.h"
-#include "kernel/importKinetics.h"
-#include "kernel/stringUtils.h"
+#include "thermo/IdealGasPhase.h"
+#include "kinetics/GasKinetics.h"
+#include "kinetics/importKinetics.h"
+#include "base/stringUtils.h"
 
 namespace Cantera
 {

include/cantera/IncompressibleSolid.h

@@ -3,8 +3,8 @@
 
 #include <string>
 
-#include "kernel/ConstDensityThermo.h"
-#include "kernel/importKinetics.h"
+#include "thermo/ConstDensityThermo.h"
+#include "kinetics/importKinetics.h"
 
 namespace Cantera
 {

include/cantera/Metal.h

@@ -3,8 +3,8 @@
 
 #include <string>
 
-#include "kernel/MetalPhase.h"
-#include "kernel/importKinetics.h"
+#include "thermo/MetalPhase.h"
+#include "kinetics/importKinetics.h"
 
 namespace Cantera
 {

include/cantera/PureFluid.h

@@ -3,9 +3,9 @@
 
 #include <string>
 
-#include "kernel/PureFluidPhase.h"
+#include "thermo/PureFluidPhase.h"
 #include "kinetics.h"
-#include "kernel/stringUtils.h"
+#include "base/stringUtils.h"
 
 namespace Cantera
 {

include/cantera/electrolyteThermo.h

@@ -11,20 +11,20 @@
 
 
 #ifdef WITH_ELECTROLYTES
-#include "kernel/electrolytes.h"
-#include "kernel/MolalityVPSSTP.h"
-#include "kernel/VPStandardStateTP.h"
-#include "kernel/IdealMolalSoln.h"
-#include "kernel/WaterPropsIAPWS.h"
-#include "kernel/WaterProps.h"
-#include "kernel/PDSS.h"
-#include "kernel/PDSS_Water.h"
-#include "kernel/PDSS_HKFT.h"
-#include "kernel/HMWSoln.h"
-#include "kernel/DebyeHuckel.h"
-#include "kernel/WaterSSTP.h"
-#include "kernel/VPSSMgr_Water_HKFT.h"
-#include "kernel/VPSSMgr_Water_ConstVol.h"
+#include "thermo/electrolytes.h"
+#include "thermo/MolalityVPSSTP.h"
+#include "thermo/VPStandardStateTP.h"
+#include "thermo/IdealMolalSoln.h"
+#include "thermo/WaterPropsIAPWS.h"
+#include "thermo/WaterProps.h"
+#include "thermo/PDSS.h"
+#include "thermo/PDSS_Water.h"
+#include "thermo/PDSS_HKFT.h"
+#include "thermo/HMWSoln.h"
+#include "thermo/DebyeHuckel.h"
+#include "thermo/WaterSSTP.h"
+#include "thermo/VPSSMgr_Water_HKFT.h"
+#include "thermo/VPSSMgr_Water_ConstVol.h"
 #endif
 
 #endif

include/cantera/equil/ChemEquil.h

@@ -13,11 +13,11 @@
 
 
 // Cantera includes
-#include "ct_defs.h"
-#include "vec_functions.h"
-#include "ctexceptions.h"
-#include "ThermoPhase.h"
-#include "DenseMatrix.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/vec_functions.h"
+#include "cantera/base/ctexceptions.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/numerics/DenseMatrix.h"
 
 #include "MultiPhaseEquil.h"
 

include/cantera/equil/MultiPhase.h

@@ -9,9 +9,9 @@
 #ifndef CT_MULTIPHASE_H
 #define CT_MULTIPHASE_H
 
-#include "ct_defs.h"
-#include "DenseMatrix.h"
-#include "ThermoPhase.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/numerics/DenseMatrix.h"
+#include "cantera/thermo/ThermoPhase.h"
 
 namespace Cantera
 {

include/cantera/equil/MultiPhaseEquil.h

@@ -1,7 +1,7 @@
 #ifndef CT_MULTIPHASE_EQUIL
 #define CT_MULTIPHASE_EQUIL
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "MultiPhase.h"
 
 namespace Cantera

include/cantera/equil/vcs_MultiPhaseEquil.h

@@ -5,7 +5,7 @@
 #ifndef VCS_MULTIPHASEEQUIL_H
 #define VCS_MULTIPHASEEQUIL_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "MultiPhase.h"
 #include "vcs_defs.h"
 

include/cantera/equilibrium.h

@@ -5,11 +5,11 @@
  */
 #ifndef CT_EQUIL_INCL
 #define CT_EQUIL_INCL
-#include "kernel/equil.h"
-#include "kernel/ChemEquil.h"
-#include "kernel/MultiPhaseEquil.h"
+#include "equil/equil.h"
+#include "equil/ChemEquil.h"
+#include "equil/MultiPhaseEquil.h"
 #ifdef WITH_VCSNONIDEAL
-#include "kernel/vcs_MultiPhaseEquil.h"
+#include "equil/vcs_MultiPhaseEquil.h"
 #endif
 #endif
 

include/cantera/integrators.h

@@ -5,8 +5,8 @@
 #ifndef CT_INTEG_H_INCL
 #define CT_INTEG_H_INCL
 
-#include "kernel/Integrator.h"
-#include "kernel/DAE_Solver.h"
-#include "kernel/IDA_Solver.h"
+#include "numerics/Integrator.h"
+#include "numerics/DAE_Solver.h"
+#include "numerics/IDA_Solver.h"
 
 #endif

include/cantera/kinetics.h

@@ -3,10 +3,10 @@
 
 #include "thermo.h"
 
-#include "kernel/Kinetics.h"
-#include "kernel/InterfaceKinetics.h"
-#include "kernel/GasKinetics.h"
-#include "kernel/KineticsFactory.h"
-#include "kernel/importKinetics.h"
+#include "kinetics/Kinetics.h"
+#include "kinetics/InterfaceKinetics.h"
+#include "kinetics/GasKinetics.h"
+#include "kinetics/KineticsFactory.h"
+#include "kinetics/importKinetics.h"
 
 #endif

include/cantera/kinetics/AqueousKinetics.h

@@ -12,10 +12,10 @@
 #include <fstream>
 #include <map>
 
-#include "mix_defs.h"
+#include "cantera/thermo/mix_defs.h"
 #include "Kinetics.h"
 
-#include "utilities.h"
+#include "cantera/base/utilities.h"
 
 #include "ReactionStoichMgr.h"
 #include "ThirdBodyMgr.h"

include/cantera/kinetics/FalloffFactory.h

@@ -9,9 +9,9 @@
 #ifndef CT_NEWFALLOFF_H
 #define CT_NEWFALLOFF_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "reaction_defs.h"
-#include "FactoryBase.h"
+#include "cantera/base/FactoryBase.h"
 
 #if defined(THREAD_SAFE_CANTERA)
 #include <boost/thread/mutex.hpp>

include/cantera/kinetics/GasKinetics.h

@@ -13,10 +13,10 @@
 #include <fstream>
 #include <map>
 
-#include "mix_defs.h"
+#include "cantera/thermo/mix_defs.h"
 #include "Kinetics.h"
 
-#include "utilities.h"
+#include "cantera/base/utilities.h"
 
 #include "ReactionStoichMgr.h"
 #include "ThirdBodyMgr.h"

include/cantera/kinetics/Group.h

@@ -7,7 +7,7 @@
 #ifndef CT_RXNPATH_GROUP
 #define CT_RXNPATH_GROUP
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 namespace Cantera
 {

include/cantera/kinetics/InterfaceKinetics.h

@@ -11,10 +11,10 @@
 #include <fstream>
 #include <map>
 
-#include "mix_defs.h"
+#include "cantera/thermo/mix_defs.h"
 #include "Kinetics.h"
 
-#include "utilities.h"
+#include "cantera/base/utilities.h"
 #include "RateCoeffMgr.h"
 #include "ReactionStoichMgr.h"
 

include/cantera/kinetics/Kinetics.h

@@ -10,9 +10,9 @@
 #ifndef CT_KINETICS_H
 #define CT_KINETICS_H
 
-#include "ctexceptions.h"
-#include "ThermoPhase.h"
-#include "mix_defs.h"
+#include "cantera/base/ctexceptions.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/thermo/mix_defs.h"
 
 namespace Cantera
 {

include/cantera/kinetics/KineticsFactory.h

@@ -8,8 +8,8 @@
 #define KINETICS_FACTORY_H
 
 #include "Kinetics.h"
-#include "xml.h"
-#include "FactoryBase.h"
+#include "cantera/base/xml.h"
+#include "cantera/base/FactoryBase.h"
 
 #if defined(THREAD_SAFE_CANTERA)
 #include <boost/thread/mutex.hpp>

include/cantera/kinetics/RateCoeffMgr.h

@@ -7,11 +7,11 @@
 #ifndef CT_RATECOEFF_MGR_H
 #define CT_RATECOEFF_MGR_H
 
-#include "utilities.h"
+#include "cantera/base/utilities.h"
 #include "RxnRates.h"
 
-#include "ct_defs.h"
-#include "ctexceptions.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/ctexceptions.h"
 
 
 namespace Cantera

include/cantera/kinetics/ReactionPath.h

@@ -10,8 +10,8 @@
 #define CT_RXNPATH_H
 
 // Cantera includes
-#include "ct_defs.h"
-#include "DenseMatrix.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/numerics/DenseMatrix.h"
 #include "Group.h"
 #include "Kinetics.h"
 

include/cantera/kinetics/ReactionStoichMgr.h

@@ -6,7 +6,7 @@
 #ifndef CT_RXN_STOICH
 #define CT_RXN_STOICH
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 namespace Cantera
 {

include/cantera/kinetics/RxnRates.h

@@ -9,7 +9,7 @@
 #define CT_RXNRATES_H
 
 #include "reaction_defs.h"
-#include "ctexceptions.h"
+#include "cantera/base/ctexceptions.h"
 
 namespace Cantera
 {

include/cantera/kinetics/ThirdBodyMgr.h

@@ -10,8 +10,8 @@
 
 #include <algorithm>
 
-#include "ct_defs.h"
-#include "utilities.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/utilities.h"
 #include "Enhanced3BConc.h"
 
 

include/cantera/kinetics/importKinetics.h

@@ -17,7 +17,7 @@
 
 #include <string>
 
-#include "ThermoPhase.h"
+#include "cantera/thermo/ThermoPhase.h"
 #include "Kinetics.h"
 
 namespace Cantera

include/cantera/kinetics/reaction_defs.h

@@ -8,7 +8,7 @@
 #ifndef CT_RXN_DEFS_H
 #define CT_RXN_DEFS_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 namespace Cantera
 {

include/cantera/numerics.h

@@ -1,9 +1,9 @@
 #ifndef CT_NUM_H_INCL
 #define CT_NUM_H_INCL
 
-#include "kernel/DenseMatrix.h"
-#include "kernel/BandMatrix.h"
-#include "kernel/SquareMatrix.h"
-#include "kernel/NonlinearSolver.h"
+#include "numerics/DenseMatrix.h"
+#include "numerics/BandMatrix.h"
+#include "numerics/SquareMatrix.h"
+#include "numerics/NonlinearSolver.h"
 
 #endif

include/cantera/numerics/ArrayViewer.h

@@ -9,10 +9,10 @@
 #ifndef CT_ARRAYVIEWER_H
 #define CT_ARRAYVIEWER_H
 
-#include "ct_defs.h"
-#include "ctexceptions.h"
-#include "stringUtils.h"
-#include "utilities.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/ctexceptions.h"
+#include "cantera/base/stringUtils.h"
+#include "cantera/base/utilities.h"
 
 namespace Cantera
 {

include/cantera/numerics/BandMatrix.h

@@ -11,10 +11,10 @@
 #ifndef CT_BANDMATRIX_H
 #define CT_BANDMATRIX_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "ctlapack.h"
-#include "utilities.h"
-#include "ctexceptions.h"
+#include "cantera/base/utilities.h"
+#include "cantera/base/ctexceptions.h"
 #include "GeneralMatrix.h"
 
 namespace Cantera

include/cantera/numerics/DAE_Solver.h

@@ -17,9 +17,9 @@
 
 #include <vector>
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "ResidJacEval.h"
-#include "global.h"
+#include "cantera/base/global.h"
 
 namespace Cantera
 {

include/cantera/numerics/DenseMatrix.h

@@ -11,8 +11,8 @@
 #ifndef CT_DENSEMATRIX_H
 #define CT_DENSEMATRIX_H
 
-#include "ct_defs.h"
-#include "Array.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/Array.h"
 
 namespace Cantera
 {

include/cantera/numerics/Func1.h

@@ -9,7 +9,7 @@
 
 #undef DEBUG_FUNC
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 #include <iostream>
 #include <string>

include/cantera/numerics/FuncEval.h

@@ -8,7 +8,7 @@
 #ifndef CT_FUNCEVAL_H
 #define CT_FUNCEVAL_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 namespace Cantera
 {

include/cantera/numerics/GeneralMatrix.h

@@ -18,7 +18,7 @@
 #ifndef CT_GENERALMATRIX_H
 #define CT_GENERALMATRIX_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 namespace Cantera
 {

include/cantera/numerics/IDA_Solver.h

@@ -19,7 +19,7 @@
 #include <vector>
 
 #include "DAE_Solver.h"
-#include "ctexceptions.h"
+#include "cantera/base/ctexceptions.h"
 
 #ifdef HAS_SUNDIALS
 

include/cantera/numerics/Integrator.h

@@ -12,8 +12,8 @@
 #define CT_INTEGRATOR_H
 #include "FuncEval.h"
 
-#include "ct_defs.h"
-#include "global.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/global.h"
 
 namespace Cantera
 {

include/cantera/numerics/ResidEval.h

@@ -16,8 +16,8 @@
 #pragma warning(disable:4503)
 #endif
 
-#include "ct_defs.h"
-#include "ctexceptions.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/ctexceptions.h"
 
 namespace Cantera
 {

include/cantera/numerics/ctlapack.h

@@ -11,7 +11,7 @@
 #undef NO_FTN_STRING_LEN_AT_END
 #endif
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 typedef double doublereal;
 typedef int     integer;

include/cantera/numerics/funcs.h

@@ -9,7 +9,7 @@
 #ifndef CT_FUNCS_H
 #define CT_FUNCS_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 namespace Cantera
 {

include/cantera/numerics/polyfit.h

@@ -11,7 +11,7 @@
 
 #include <vector>
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 namespace Cantera
 {

include/cantera/numerics/solveProb.h

@@ -21,7 +21,7 @@
 
 
 #include <vector>
-#include "Array.h"
+#include "cantera/base/Array.h"
 #include "ResidEval.h"
 
 //! Solution Methods

include/cantera/oneD/Domain1D.h

@@ -9,9 +9,9 @@
 #define CT_DOMAIN1D_H
 
 
-#include "xml.h"
-#include "stringUtils.h"
-#include "ctexceptions.h"
+#include "cantera/base/xml.h"
+#include "cantera/base/stringUtils.h"
+#include "cantera/base/ctexceptions.h"
 #include "refine.h"
 
 

include/cantera/oneD/Inlet1D.h

@@ -12,11 +12,11 @@
 #define CT_BDRY1D_H
 
 #include "Domain1D.h"
-#include "SurfPhase.h"
-#include "InterfaceKinetics.h"
+#include "cantera/thermo/SurfPhase.h"
+#include "cantera/kinetics/InterfaceKinetics.h"
 #include "StFlow.h"
 #include "OneDim.h"
-#include "ctml.h"
+#include "cantera/base/ctml.h"
 
 namespace Cantera
 {

include/cantera/oneD/MultiJac.h

@@ -9,7 +9,7 @@
 #ifndef CT_MULTIJAC_H
 #define CT_MULTIJAC_H
 
-#include "BandMatrix.h"
+#include "cantera/numerics/BandMatrix.h"
 #include "OneDim.h"
 #include "time.h"
 

include/cantera/oneD/Sim1D.h

@@ -6,7 +6,7 @@
 #define CT_SIM1D_H
 
 #include "OneDim.h"
-#include "funcs.h"
+#include "cantera/numerics/funcs.h"
 
 namespace Cantera
 {

include/cantera/oneD/StFlow.h

@@ -7,12 +7,12 @@
 #ifndef CT_STFLOW_H
 #define CT_STFLOW_H
 
-#include "TransportBase.h"
+#include "cantera/transport/TransportBase.h"
 #include "Domain1D.h"
-#include "Array.h"
-#include "IdealGasPhase.h"
-#include "Kinetics.h"
-#include "funcs.h"
+#include "cantera/base/Array.h"
+#include "cantera/thermo/IdealGasPhase.h"
+#include "cantera/kinetics/Kinetics.h"
+#include "cantera/numerics/funcs.h"
 //#include "../flowBoundaries.h"
 
 

include/cantera/oneD/Surf1D.h

@@ -4,11 +4,11 @@ dep
 #define CT_SURF1D_H
 
 #include "Domain1D.h"
-#include "SurfPhase.h"
-#include "InterfaceKinetics.h"
+#include "cantera/thermo/SurfPhase.h"
+#include "cantera/kinetics/InterfaceKinetics.h"
 #include "StFlow.h"
 #include "OneDim.h"
-#include "ctml.h"
+#include "cantera/base/ctml.h"
 
 namespace Cantera
 {

include/cantera/onedim.h

@@ -1,13 +1,13 @@
 #ifndef CT_INCL_ONEDIM_H
 #define CT_INCL_ONEDIM_H
 
-#include "kernel/Sim1D.h"
-#include "kernel/OneDim.h"
-#include "kernel/Domain1D.h"
-#include "kernel/Inlet1D.h"
-#include "kernel/Surf1D.h"
-#include "kernel/MultiNewton.h"
-#include "kernel/MultiJac.h"
-#include "kernel/StFlow.h"
+#include "oneD/Sim1D.h"
+#include "oneD/OneDim.h"
+#include "oneD/Domain1D.h"
+#include "oneD/Inlet1D.h"
+#include "oneD/Surf1D.h"
+#include "oneD/MultiNewton.h"
+#include "oneD/MultiJac.h"
+#include "oneD/StFlow.h"
 #endif
 

include/cantera/radiation.h

@@ -1,8 +1,8 @@
 #ifndef CT_RAD_H_INCL
 #define CT_RAD_H_INCL
 
-#include "kernel/rotor.h"
-#include "kernel/LineBroadener.h"
+#include "spectra/rotor.h"
+#include "spectra/LineBroadener.h"
 //#include "kernel/AbsorptionLine.h"
 
 #endif

include/cantera/reactionpaths.h

@@ -1,6 +1,6 @@
 #ifndef CT_RXNPATHS_H
 #define CT_RXNPATHS_H
 
-#include "kernel/ReactionPath.h"
+#include "kinetics/ReactionPath.h"
 
 #endif

include/cantera/solvers.h

@@ -5,8 +5,8 @@
 #ifndef CT_SOLVERS_H_INCL
 #define CT_SOLVERS_H_INCL
 
-#include "kernel/ResidEval.h"
+#include "numerics/ResidEval.h"
 
-#include "kernel/solveProb.h"
+#include "numerics/solveProb.h"
 
 #endif

include/cantera/spectra.h

@@ -1,8 +1,8 @@
 #ifndef CT_SPECTRA_H_INCL
 #define CT_SECTRA_H_INCL
 
-#include "kernel/LineBroadener.h"
-#include "kernel/rotor.h"
+#include "spectra/LineBroadener.h"
+#include "spectra/rotor.h"
 //#include "kernel/AbsorptionLine.h"
 
 #endif

include/cantera/spectra/LineBroadener.h

@@ -4,8 +4,8 @@
  * @ingroup spectroscopy
  */
 
-#include "ct_defs.h"
-#include "ctexceptions.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/ctexceptions.h"
 
 namespace Cantera
 {

include/cantera/spectra/rotor.h

@@ -13,7 +13,7 @@
  * molecules.
  */
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 /**
  * Namespace for spectroscopic functions and classes.

include/cantera/surface.h

@@ -1,7 +1,7 @@
 #ifndef CT_SURFACE_INCL
 #define CT_SURFACE_INCL
 
-#include "SurfPhase.h"
-#include "InterfaceKinetics.h"
+#include "thermo/SurfPhase.h"
+#include "kinetics/InterfaceKinetics.h"
 
 #endif

include/cantera/thermo.h

@@ -9,15 +9,15 @@
 #ifndef CT_THERMO_INCL
 #define CT_THERMO_INCL
 
-#include "kernel/ThermoFactory.h"
-#include "kernel/SurfPhase.h"
-#include "kernel/EdgePhase.h"
+#include "thermo/ThermoFactory.h"
+#include "thermo/SurfPhase.h"
+#include "thermo/EdgePhase.h"
 
 
 #ifdef WITH_IDEAL_SOLUTIONS
 
-#include "kernel/GibbsExcessVPSSTP.h"
-#include "kernel/MargulesVPSSTP.h"
+#include "thermo/GibbsExcessVPSSTP.h"
+#include "thermo/MargulesVPSSTP.h"
 
 #endif
 
@@ -30,8 +30,8 @@
 
 #ifdef WITH_LATTICE_SOLID
 
-#include "kernel/LatticePhase.h"
-#include "kernel/LatticeSolidPhase.h"
+#include "thermo/LatticePhase.h"
+#include "thermo/LatticeSolidPhase.h"
 
 #endif
 

include/cantera/thermo/ConstDensityThermo.h

@@ -10,11 +10,11 @@
 #ifndef CT_CONSTRHOTHERMO_H
 #define CT_CONSTRHOTHERMO_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "mix_defs.h"
 #include "ThermoPhase.h"
 #include "SpeciesThermo.h"
-#include "utilities.h"
+#include "cantera/base/utilities.h"
 
 namespace Cantera
 {

include/cantera/thermo/Constituents.h

@@ -10,12 +10,12 @@
 #define CT_CONSTIT_H
 
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 #include "SpeciesThermo.h"
-#include "ctexceptions.h"
-#include "stringUtils.h"
-#include "xml.h"
+#include "cantera/base/ctexceptions.h"
+#include "cantera/base/stringUtils.h"
+#include "cantera/base/xml.h"
 #include "Elements.h"
 
 namespace Cantera

include/cantera/thermo/Crystal.h

@@ -4,7 +4,7 @@
 #ifndef CT_CRYSTAL_H
 #define CT_CRYSTAL_H
 
-#include "MultiPhase.h"
+#include "cantera/equil/MultiPhase.h"
 
 namespace Cantera
 {

include/cantera/thermo/DebyeHuckel.h

@@ -18,7 +18,7 @@
 
 #include "MolalityVPSSTP.h"
 #include "electrolytes.h"
-#include "Array.h"
+#include "cantera/base/Array.h"
 
 namespace Cantera
 {

include/cantera/thermo/Elements.h

@@ -12,7 +12,7 @@
 
 #undef USE_DGG_CODE
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 
 namespace Cantera

include/cantera/thermo/GeneralSpeciesThermo.h

@@ -9,7 +9,7 @@
 #ifndef CT_GENERALSPECIESTHERMO_H
 #define CT_GENERALSPECIESTHERMO_H
 #include <string>
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "SpeciesThermoMgr.h"
 #include "NasaPoly1.h"
 #include "Nasa9Poly1.h"

include/cantera/thermo/IdealGasPhase.h

@@ -10,11 +10,11 @@
 #ifndef CT_IDEALGASPHASE_H
 #define CT_IDEALGASPHASE_H
 
-//#include "ct_defs.h"
+//#include "cantera/base/ct_defs.h"
 #include "mix_defs.h"
 #include "ThermoPhase.h"
 #include "SpeciesThermo.h"
-#include "utilities.h"
+#include "cantera/base/utilities.h"
 
 namespace Cantera
 {

include/cantera/thermo/LatticePhase.h

@@ -10,15 +10,15 @@
 #ifndef CT_LATTICE_H
 #define CT_LATTICE_H
 
-#include "config.h"
+#include "cantera/base/config.h"
 
 #ifdef WITH_LATTICE_SOLID
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "mix_defs.h"
 #include "ThermoPhase.h"
 #include "SpeciesThermo.h"
-#include "utilities.h"
+#include "cantera/base/utilities.h"
 
 namespace Cantera
 {

include/cantera/thermo/LatticeSolidPhase.h

@@ -11,17 +11,17 @@
 #ifndef CT_LATTICESOLID_H
 #define CT_LATTICESOLID_H
 
-#include "config.h"
+#include "cantera/base/config.h"
 
 #ifdef WITH_LATTICE_SOLID
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 #include "mix_defs.h"
 #include "ThermoPhase.h"
 #include "SpeciesThermo.h"
 #include "LatticePhase.h"
-#include "utilities.h"
+#include "cantera/base/utilities.h"
 
 
 

include/cantera/thermo/MixtureFugacityTP.h

@@ -20,7 +20,7 @@
 
 #include "ThermoPhase.h"
 #include "VPSSMgr.h"
-#include "ResidEval.h"
+#include "cantera/numerics/ResidEval.h"
 
 namespace Cantera
 {

include/cantera/thermo/Nasa9Poly1.h

@@ -17,7 +17,7 @@
 
 #ifndef CT_NASA9POLY1_H
 #define CT_NASA9POLY1_H
-#include "global.h"
+#include "cantera/base/global.h"
 #include "SpeciesThermoInterpType.h"
 
 namespace Cantera

include/cantera/thermo/NasaPoly1.h

@@ -15,7 +15,7 @@
 // Copyright 2001  California Institute of Technology
 
 
-#include "global.h"
+#include "cantera/base/global.h"
 #include "SpeciesThermoInterpType.h"
 
 namespace Cantera

include/cantera/thermo/PDSS.h

@@ -11,7 +11,7 @@
  */
 #ifndef CT_PDSS_H
 #define CT_PDSS_H
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "mix_defs.h"
 
 class WaterPropsIAPWS;

include/cantera/thermo/PDSS_Water.h

@@ -12,7 +12,7 @@
 #ifndef CT_PDSS_WATER_H
 #define CT_PDSS_WATER_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "PDSS.h"
 #include "VPStandardStateTP.h"
 

include/cantera/thermo/Phase.h

@@ -13,9 +13,9 @@
 
 #include "State.h"
 #include "Constituents.h"
-#include "vec_functions.h"
+#include "cantera/base/vec_functions.h"
 
-#include "ctml.h"
+#include "cantera/base/ctml.h"
 
 namespace Cantera
 {

include/cantera/thermo/SpeciesThermo.h

@@ -10,7 +10,7 @@
 #ifndef CT_SPECIESTHERMO_H
 #define CT_SPECIESTHERMO_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
 namespace Cantera
 {

include/cantera/thermo/SpeciesThermoFactory.h

@@ -11,8 +11,8 @@
 #define SPECIESTHERMO_FACTORY_H
 
 #include "SpeciesThermo.h"
-#include "ctexceptions.h"
-#include "FactoryBase.h"
+#include "cantera/base/ctexceptions.h"
+#include "cantera/base/FactoryBase.h"
 
 
 namespace Cantera

include/cantera/thermo/SpeciesThermoMgr.h

@@ -12,9 +12,9 @@
 #ifndef CT_SPECIESTHERMO_MGR_H
 #define CT_SPECIESTHERMO_MGR_H
 
-#include "ct_defs.h"
-#include "ctexceptions.h"
-#include "stringUtils.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/ctexceptions.h"
+#include "cantera/base/stringUtils.h"
 #include "SpeciesThermo.h"
 #include <map>
 

include/cantera/thermo/State.h

@@ -13,8 +13,8 @@
 #ifndef CT_STATE2_H
 #define CT_STATE2_H
 
-#include "ct_defs.h"
-#include "utilities.h"
+#include "cantera/base/ct_defs.h"
+#include "cantera/base/utilities.h"
 
 namespace Cantera
 {

include/cantera/thermo/ThermoFactory.h

@@ -11,13 +11,13 @@
 #define THERMO_FACTORY_H
 
 #include "ThermoPhase.h"
-#include "xml.h"
+#include "cantera/base/xml.h"
 
 #if defined(THREAD_SAFE_CANTERA)
 #include <boost/thread/mutex.hpp>
 #endif
 
-#include "FactoryBase.h"
+#include "cantera/base/FactoryBase.h"
 
 namespace Cantera
 {

include/cantera/thermo/VPSSMgr.h

@@ -15,7 +15,7 @@
 #ifndef CT_VPSSMGR_H
 #define CT_VPSSMGR_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "mix_defs.h"
 
 namespace Cantera

include/cantera/thermo/VPSSMgr_ConstVol.h

@@ -14,7 +14,7 @@
 #ifndef CT_VPSSMGR_CONSTVOL_H
 #define CT_VPSSMGR_CONSTVOL_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "VPSSMgr.h"
 
 namespace Cantera

include/cantera/thermo/VPSSMgr_General.h

@@ -15,7 +15,7 @@
 #ifndef CT_VPSSMGR_GENERAL_H
 #define CT_VPSSMGR_GENERAL_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "VPSSMgr.h"
 
 namespace Cantera

include/cantera/thermo/VPSSMgr_IdealGas.h

@@ -15,7 +15,7 @@
 #ifndef CT_VPSSMGR_IDEALGAS_H
 #define CT_VPSSMGR_IDEALGAS_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "PDSS.h"
 #include "VPSSMgr.h"
 

include/cantera/thermo/WaterProps.h

@@ -14,7 +14,7 @@
 #define CT_WATERPROPS_H
 
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 namespace Cantera
 {
 class WaterPropsIAPWS;

include/cantera/thermo/WaterPropsIAPWS.h

@@ -13,7 +13,7 @@
 #define WATERPROPSIAPWS_H
 
 #include "WaterPropsIAPWSphi.h"
-#include "config.h"
+#include "cantera/base/config.h"
 
 typedef double doublereal;
 

include/cantera/thermo/WaterPropsIAPWSphi.h

@@ -13,7 +13,7 @@
 #ifndef WATERPROPSIAPWSPHI_H
 #define WATERPROPSIAPWSPHI_H
 
-#include "config.h"
+#include "cantera/base/config.h"
 
 typedef double doublereal;
 

include/cantera/thermo/speciesThermoTypes.h

@@ -68,10 +68,10 @@
 //! A general object is called with the pressure set at the reference state.
 #define PDSS_TYPE 37
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 
-#include "stringUtils.h"
-#include "global.h"
+#include "cantera/base/stringUtils.h"
+#include "cantera/base/global.h"
 
 namespace Cantera
 {

include/cantera/transport.h

@@ -9,9 +9,9 @@
 #ifndef CT_TRANSPORT_INCL
 #define CT_TRANSPORT_INCL
 
-#include "kernel/TransportFactory.h"
-#include "kernel/DustyGasTransport.h"
-#include "kernel/MultiTransport.h"
-#include "kernel/MixTransport.h"
-#include "kernel/LiquidTransport.h"
+#include "transport/TransportFactory.h"
+#include "transport/DustyGasTransport.h"
+#include "transport/MultiTransport.h"
+#include "transport/MixTransport.h"
+#include "transport/LiquidTransport.h"
 #endif

include/cantera/transport/AqueousTransport.h

@@ -11,7 +11,7 @@
 
 // Cantera includes
 #include "TransportBase.h"
-#include "DenseMatrix.h"
+#include "cantera/numerics/DenseMatrix.h"
 #include "TransportParams.h"
 #include "LiquidTransportParams.h"
 

include/cantera/transport/DustyGasTransport.h

@@ -13,7 +13,7 @@
 
 // Cantera includes
 #include "TransportBase.h"
-#include "DenseMatrix.h"
+#include "cantera/numerics/DenseMatrix.h"
 
 
 namespace Cantera

include/cantera/transport/LTPspecies.h

@@ -13,9 +13,9 @@
 #define CT_LTPSPECIES_H
 
 // Cantera includes
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "TransportBase.h"
-#include "FactoryBase.h"
+#include "cantera/base/FactoryBase.h"
 
 // STL includes
 #include <vector>

include/cantera/transport/LiquidTranInteraction.h

@@ -12,12 +12,12 @@
 #ifndef CT_LIQUIDTRANINTERACTION_H
 #define CT_LIQUIDTRANINTERACTION_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "TransportBase.h"
 #include "TransportParams.h"
 #include "LiquidTransportData.h"
-#include "xml.h"
-#include "XML_Writer.h"
+#include "cantera/base/xml.h"
+#include "cantera/base/XML_Writer.h"
 
 namespace Cantera
 {

include/cantera/transport/LiquidTransport.h

@@ -16,7 +16,7 @@
 
 // Cantera includes
 #include "TransportBase.h"
-#include "DenseMatrix.h"
+#include "cantera/numerics/DenseMatrix.h"
 #include "TransportParams.h"
 #include "LiquidTransportParams.h"
 

include/cantera/transport/LiquidTransportData.h

@@ -11,9 +11,9 @@
 #include <string>
 
 // Cantera includes
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "TransportBase.h"
-#include "FactoryBase.h"
+#include "cantera/base/FactoryBase.h"
 #include "LTPspecies.h"
 
 namespace Cantera

include/cantera/transport/LiquidTransportParams.h

@@ -13,13 +13,13 @@
 #ifndef CT_LIQUIDTRANSPORTPARAMS_H
 #define CT_LIQUIDTRANSPORTPARAMS_H
 
-#include "ct_defs.h"
+#include "cantera/base/ct_defs.h"
 #include "TransportBase.h"
 #include "TransportParams.h"
 #include "LiquidTransportData.h"
 #include "LiquidTranInteraction.h"
-#include "xml.h"
-#include "XML_Writer.h"
+#include "cantera/base/xml.h"
+#include "cantera/base/XML_Writer.h"
 
 
 #include <vector>

include/cantera/transport/MixTransport.h

@@ -19,7 +19,7 @@
 
 // Cantera includes
 #include "TransportBase.h"
-#include "DenseMatrix.h"
+#include "cantera/numerics/DenseMatrix.h"
 
 namespace Cantera
 {

include/cantera/transport/MultiTransport.h

@@ -14,7 +14,7 @@
 
 // Cantera includes
 #include "TransportBase.h"
-#include "DenseMatrix.h"
+#include "cantera/numerics/DenseMatrix.h"
 
 namespace Cantera
 {

include/cantera/transport/SimpleTransport.h

@@ -18,7 +18,7 @@
 
 // Cantera includes
 #include "TransportBase.h"
-#include "DenseMatrix.h"
+#include "cantera/numerics/DenseMatrix.h"
 #include "TransportParams.h"
 #include "LiquidTransportParams.h"
 

include/cantera/transport/SolidTransport.h

@@ -19,7 +19,7 @@
 
 // Cantera includes
 #include "TransportBase.h"
-#include "DenseMatrix.h"
+#include "cantera/numerics/DenseMatrix.h"
 
 namespace Cantera
 {

include/cantera/transport/TransportBase.h

@@ -21,8 +21,8 @@
 #ifndef CT_TRANSPORTBASE_H
 #define CT_TRANSPORTBASE_H
 
-#include "ThermoPhase.h"
-#include "DenseMatrix.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/numerics/DenseMatrix.h"
 
 namespace Cantera
 {