modified source files for rearranged directories

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/reorg@7310 1feff8c3-07ed-0310-ac33-dd36852eb9cd

Makefile.am

@@ -80,59 +80,59 @@ phreeqc_SOURCES=\
 	Use.h\
 	Utils.cxx\
 	Utils.h\
-	phreeqc/advection.cpp\
-	phreeqc/basicsubs.cpp\
-	phreeqc/cl1.cpp\
-	phreeqc/cvdense.cpp\
-	phreeqc/cvdense.h\
-	phreeqc/cvode.cpp\
-	phreeqc/cvode.h\
-	phreeqc/dense.cpp\
-	phreeqc/dense.h\
-	phreeqc/dw.cpp\
-	phreeqc/gases.cpp\
-	phreeqc/global_structures.h\
-	phreeqc/input.cpp\
-	phreeqc/integrate.cpp\
-	phreeqc/inverse.cpp\
-	phreeqc/isotopes.cpp\
-	phreeqc/kinetics.cpp\
-	phreeqc/mainsubs.cpp\
-	phreeqc/model.cpp\
-	phreeqc/NA.h\
-	phreeqc/nvector.cpp\
-	phreeqc/nvector.h\
-	phreeqc/nvector_serial.cpp\
-	phreeqc/nvector_serial.h\
-	phreeqc/parse.cpp\
-	phreeqc/phqalloc.cpp\
-	phreeqc/phqalloc.h\
-	phreeqc/PHRQ_io_output.cpp\
-	phreeqc/phrqtype.h\
-	phreeqc/pitzer.cpp\
-	phreeqc/pitzer_structures.cpp\
-	phreeqc/prep.cpp\
-	phreeqc/print.cpp\
-	phreeqc/read.cpp\
-	phreeqc/readtr.cpp\
-	phreeqc/sit.cpp\
-	phreeqc/smalldense.cpp\
-	phreeqc/smalldense.h\
-	phreeqc/spread.cpp\
-	phreeqc/step.cpp\
-	phreeqc/structures.cpp\
-	phreeqc/sundialsmath.cpp\
-	phreeqc/sundialsmath.h\
-	phreeqc/sundialstypes.h\
-	phreeqc/tally.cpp\
-	phreeqc/tidy.cpp\
-	phreeqc/transport.cpp\
-	phreeqc/utilities.cpp
+	advection.cpp\
+	basicsubs.cpp\
+	cl1.cpp\
+	cvdense.cpp\
+	cvdense.h\
+	cvode.cpp\
+	cvode.h\
+	dense.cpp\
+	dense.h\
+	dw.cpp\
+	gases.cpp\
+	global_structures.h\
+	input.cpp\
+	integrate.cpp\
+	inverse.cpp\
+	isotopes.cpp\
+	kinetics.cpp\
+	mainsubs.cpp\
+	model.cpp\
+	NA.h\
+	nvector.cpp\
+	nvector.h\
+	nvector_serial.cpp\
+	nvector_serial.h\
+	parse.cpp\
+	phqalloc.cpp\
+	phqalloc.h\
+	PHRQ_io_output.cpp\
+	phrqtype.h\
+	pitzer.cpp\
+	pitzer_structures.cpp\
+	prep.cpp\
+	print.cpp\
+	read.cpp\
+	readtr.cpp\
+	sit.cpp\
+	smalldense.cpp\
+	smalldense.h\
+	spread.cpp\
+	step.cpp\
+	structures.cpp\
+	sundialsmath.cpp\
+	sundialsmath.h\
+	sundialstypes.h\
+	tally.cpp\
+	tidy.cpp\
+	transport.cpp\
+	utilities.cpp
 
 if BUILD_GMP
 
 phreeqc_SOURCES+=\
-	phreeqc/cl1mp.cpp
+	cl1mp.cpp
 
 endif
 

basicsubs.cpp

@@ -2,10 +2,10 @@
 #include "phqalloc.h"
 
 #include "Utils.h"
-#include "../NameDouble.h"
-#include "../PBasic.h"
-#include "../Exchange.h"
-#include "../GasPhase.h"
+#include "NameDouble.h"
+#include "PBasic.h"
+#include "Exchange.h"
+#include "GasPhase.h"
 #include "PPassemblage.h"
 #include "SSassemblage.h"
 #include "cxxKinetics.h"

class_main.cpp

@@ -61,7 +61,7 @@ unsigned int cwOriginal = _controlfp(cw, MCW_EM); //Set it.
                             //_controlfp(cwOriginal, MCW_EM);
 #endif
 	Phreeqc phreeqc_instance;
-	phreeqc_instance.main_method(argc, argv);
+	return phreeqc_instance.main_method(argc, argv);
 }
 
 

readtr.cpp

@@ -1,8 +1,8 @@
 #include <iostream>				/* std::cout std::cerr */
 #include <sstream>
 #include <fstream>
-#include "../StorageBin.h"
-#include "../SS.h"
+#include "StorageBin.h"
+#include "SS.h"
 
 typedef unsigned char boolean;
 #include "Phreeqc.h"

structures.cpp

@@ -3615,7 +3615,7 @@ copier_init(struct copier *copier_ptr)
 		(int *) PHRQ_malloc((size_t) (copier_ptr->max * sizeof(int)));
 	return (OK);
 }
-#include "../StorageBin.h"
+#include "StorageBin.h"
 
 void Phreeqc::
 Use2cxxStorageBin(cxxStorageBin & sb)