Index: sm/trunk-jpl/src/c/modules/ParseToolkitsOptionsx/ParsePetscOptionsx.cpp
===================================================================
--- /issm/trunk-jpl/src/c/modules/ParseToolkitsOptionsx/ParsePetscOptionsx.cpp	(revision 14626)
+++ 	(revision )
@@ -1,131 +1,0 @@
-/*!\file ParsePetscOptionsx
- * * \brief: parse options present in a petsc file, and create petsc options 
- * objects accordingly. This will be used to drive the behaviour of Petsc for 
- * each analysis type.
- */
-
-#ifdef HAVE_CONFIG_H
-	#include <config.h>
-#else
-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
-#endif
-
-#include <cstring>
-
-#include "./ParsePetscOptionsx.h"
-#include "../../io/io.h"
-#include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
-
-void ParsePetscOptionsx(Parameters* parameters,FILE* fid){
-
-	char line [1000];
-	int my_rank;
-	int i;
-
-	/*intermediary: */
-	IssmDouble* analyses=NULL;
-	char** strings=NULL;
-	int numanalyses;
-	char* string=NULL;
-	char* newstring=NULL;
-	char* catstring=NULL;
-	int   stringlength;
-
-	/*Get my_rank:*/
-	my_rank=IssmComm::GetRank();
-
-	if(my_rank==0){
-
-		/*Now, go through lines and figure out how many analyses we have: */
-		numanalyses=0;
-		while ( fgets(line, sizeof line, fid) ){
-			/*skip comments and empty lines: */
-			if ((line[0]=='%') || (line[0]=='\n') || (line[0]==' ') || (line[0]=='\t') || (line[0]=='\r'))continue;
-			/*ok, first time, we should get an analysis enum, starting with a +: */
-			if (line[0]=='+')numanalyses++;
-			else continue;
-		}
-
-		/*Now, allocate analyses and strings: */
-		analyses=xNew<IssmDouble>(numanalyses);
-		strings=xNew<char*>(numanalyses);
-		for(i=0;i<numanalyses;i++)strings[i]=NULL; 
-
-		/*Go back to beginning of file:*/
-		fseek(fid,0,SEEK_SET);
-		numanalyses=0;
-		while ( fgets(line, sizeof line, fid) ){
-
-			/*skip comments and empty lines: */
-			if ((line[0]=='%') || (line[0]=='\n') || (line[0]==' ') || (line[0]=='\t') || (line[0]=='\r'))continue;
-
-			/*Get rid of end of line: */
-			line[strlen(line)-1]='\0';
-
-			if (line[0]=='+'){ /*this is the analysis line: */
-				analyses[numanalyses]=StringToEnumx(&line[1]);  //skip the '+'
-				numanalyses++;
-			}
-			else{ /*this is an option corresponding to analysis numanalyses-1. Add it 
-			to the already existing options*/
-				if(strings[numanalyses-1]==NULL){
-					string=xNew<char>((strlen(line)+1)); 
-					xMemCpy<char>(string,line,(strlen(line)+1));
-
-					strings[numanalyses-1]=string;
-				}
-				else{
-					string=strings[numanalyses-1];
-					newstring=xNew<char>((strlen(line)+1));
-					xMemCpy<char>(newstring,line,(strlen(line)+1));
-
-					/*concatenate:*/
-					catstring=xNew<char>(strlen(string)+1+strlen(newstring)+1+1); //fit in a space " "
-					xMemCpy<char>(catstring,string,(strlen(string)+1));
-
-					strcat(catstring," ");
-					strcat(catstring,newstring);
-					strings[numanalyses-1]=catstring;
-					xDelete<char>(newstring);
-					xDelete<char>(string);
-				}
-			}
-		}
-	}
-
-	/*Ok, broadcast to other cpus: */
- 	#ifdef _HAVE_MPI_
-	MPI_Bcast(&numanalyses,1,MPI_INT,0,IssmComm::GetComm());
-	if(my_rank!=0){
-		analyses=xNew<IssmPDouble>(numanalyses);
-		strings=xNew<char*>(numanalyses);
-	}
-	MPI_Bcast(analyses,numanalyses,MPI_DOUBLE,0,IssmComm::GetComm());
-	#endif
-	for(i=0;i<numanalyses;i++){
-		char* string=strings[i];
-		if(my_rank==0){
-			if(string==NULL) _error_("PETSc options for analysis " << EnumToStringx(reCast<int>(analyses[i])) << " have been declared but were not found");
-		}
-		if(my_rank==0)stringlength=(strlen(string)+1)*sizeof(char);
-		#ifdef _HAVE_MPI_
-		MPI_Bcast(&stringlength,1,MPI_INT,0,IssmComm::GetComm());
-		if(my_rank!=0)string=xNew<char>(stringlength);
-		MPI_Bcast(string,stringlength,MPI_CHAR,0,IssmComm::GetComm());
-		if(my_rank!=0)strings[i]=string;
-		#endif
-	}
-
-	/*Ok, out of strings and analyses and numanalyses, create parameters, and plug them into parameters container: */
-	parameters->AddObject(new StringArrayParam(PetscOptionsStringsEnum,strings,numanalyses));
-	parameters->AddObject(new DoubleVecParam(PetscOptionsAnalysesEnum,analyses,numanalyses));
-
-	/*Clean up and return*/
-	for(i=0;i<numanalyses;i++) xDelete<char>(strings[i]);
-	xDelete<char*>(strings);
-	xDelete<IssmDouble>(analyses);
-	return;
-}
Index: sm/trunk-jpl/src/c/modules/ParseToolkitsOptionsx/ParsePetscOptionsx.h
===================================================================
--- /issm/trunk-jpl/src/c/modules/ParseToolkitsOptionsx/ParsePetscOptionsx.h	(revision 14626)
+++ 	(revision )
@@ -1,14 +1,0 @@
-/*!\file:  ParsePetscOptionsx.h
- * \brief header file for parsing petsc options file
- */ 
-
-#ifndef _PARSEPETSCOPTIONSX_H
-#define _PARSEPETSCOPTIONSX_H
-
-#include "../../Container/Container.h"
-#include "../../classes/objects/objects.h"
-
-/* local prototypes: */
-void ParsePetscOptionsx(Parameters* parameters, FILE* petscoptionsfid);
-
-#endif  /* _PARSEPETSCOPTIONSX_H */
Index: /issm/trunk-jpl/src/c/modules/ParseToolkitsOptionsx/ParseToolkitsOptionsx.cpp
===================================================================
--- /issm/trunk-jpl/src/c/modules/ParseToolkitsOptionsx/ParseToolkitsOptionsx.cpp	(revision 14627)
+++ /issm/trunk-jpl/src/c/modules/ParseToolkitsOptionsx/ParseToolkitsOptionsx.cpp	(revision 14627)
@@ -0,0 +1,131 @@
+/*!\file ParseToolkitsOptionsx
+ * * \brief: parse options present in a petsc file, and create petsc options 
+ * objects accordingly. This will be used to drive the behaviour of Toolkits for 
+ * each analysis type.
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include <config.h>
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include <cstring>
+
+#include "./ParseToolkitsOptionsx.h"
+#include "../../io/io.h"
+#include "../../shared/shared.h"
+#include "../../include/include.h"
+#include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+
+void ParseToolkitsOptionsx(Parameters* parameters,FILE* fid){
+
+	char line [1000];
+	int my_rank;
+	int i;
+
+	/*intermediary: */
+	IssmDouble* analyses=NULL;
+	char** strings=NULL;
+	int numanalyses;
+	char* string=NULL;
+	char* newstring=NULL;
+	char* catstring=NULL;
+	int   stringlength;
+
+	/*Get my_rank:*/
+	my_rank=IssmComm::GetRank();
+
+	if(my_rank==0){
+
+		/*Now, go through lines and figure out how many analyses we have: */
+		numanalyses=0;
+		while ( fgets(line, sizeof line, fid) ){
+			/*skip comments and empty lines: */
+			if ((line[0]=='%') || (line[0]=='\n') || (line[0]==' ') || (line[0]=='\t') || (line[0]=='\r'))continue;
+			/*ok, first time, we should get an analysis enum, starting with a +: */
+			if (line[0]=='+')numanalyses++;
+			else continue;
+		}
+
+		/*Now, allocate analyses and strings: */
+		analyses=xNew<IssmDouble>(numanalyses);
+		strings=xNew<char*>(numanalyses);
+		for(i=0;i<numanalyses;i++)strings[i]=NULL; 
+
+		/*Go back to beginning of file:*/
+		fseek(fid,0,SEEK_SET);
+		numanalyses=0;
+		while ( fgets(line, sizeof line, fid) ){
+
+			/*skip comments and empty lines: */
+			if ((line[0]=='%') || (line[0]=='\n') || (line[0]==' ') || (line[0]=='\t') || (line[0]=='\r'))continue;
+
+			/*Get rid of end of line: */
+			line[strlen(line)-1]='\0';
+
+			if (line[0]=='+'){ /*this is the analysis line: */
+				analyses[numanalyses]=StringToEnumx(&line[1]);  //skip the '+'
+				numanalyses++;
+			}
+			else{ /*this is an option corresponding to analysis numanalyses-1. Add it 
+			to the already existing options*/
+				if(strings[numanalyses-1]==NULL){
+					string=xNew<char>((strlen(line)+1)); 
+					xMemCpy<char>(string,line,(strlen(line)+1));
+
+					strings[numanalyses-1]=string;
+				}
+				else{
+					string=strings[numanalyses-1];
+					newstring=xNew<char>((strlen(line)+1));
+					xMemCpy<char>(newstring,line,(strlen(line)+1));
+
+					/*concatenate:*/
+					catstring=xNew<char>(strlen(string)+1+strlen(newstring)+1+1); //fit in a space " "
+					xMemCpy<char>(catstring,string,(strlen(string)+1));
+
+					strcat(catstring," ");
+					strcat(catstring,newstring);
+					strings[numanalyses-1]=catstring;
+					xDelete<char>(newstring);
+					xDelete<char>(string);
+				}
+			}
+		}
+	}
+
+	/*Ok, broadcast to other cpus: */
+ 	#ifdef _HAVE_MPI_
+	MPI_Bcast(&numanalyses,1,MPI_INT,0,IssmComm::GetComm());
+	if(my_rank!=0){
+		analyses=xNew<IssmPDouble>(numanalyses);
+		strings=xNew<char*>(numanalyses);
+	}
+	MPI_Bcast(analyses,numanalyses,MPI_DOUBLE,0,IssmComm::GetComm());
+	#endif
+	for(i=0;i<numanalyses;i++){
+		char* string=strings[i];
+		if(my_rank==0){
+			if(string==NULL) _error_("PETSc options for analysis " << EnumToStringx(reCast<int>(analyses[i])) << " have been declared but were not found");
+		}
+		if(my_rank==0)stringlength=(strlen(string)+1)*sizeof(char);
+		#ifdef _HAVE_MPI_
+		MPI_Bcast(&stringlength,1,MPI_INT,0,IssmComm::GetComm());
+		if(my_rank!=0)string=xNew<char>(stringlength);
+		MPI_Bcast(string,stringlength,MPI_CHAR,0,IssmComm::GetComm());
+		if(my_rank!=0)strings[i]=string;
+		#endif
+	}
+
+	/*Ok, out of strings and analyses and numanalyses, create parameters, and plug them into parameters container: */
+	parameters->AddObject(new StringArrayParam(ToolkitsOptionsStringsEnum,strings,numanalyses));
+	parameters->AddObject(new DoubleVecParam(ToolkitsOptionsAnalysesEnum,analyses,numanalyses));
+
+	/*Clean up and return*/
+	for(i=0;i<numanalyses;i++) xDelete<char>(strings[i]);
+	xDelete<char*>(strings);
+	xDelete<IssmDouble>(analyses);
+	return;
+}
Index: /issm/trunk-jpl/src/c/modules/ParseToolkitsOptionsx/ParseToolkitsOptionsx.h
===================================================================
--- /issm/trunk-jpl/src/c/modules/ParseToolkitsOptionsx/ParseToolkitsOptionsx.h	(revision 14627)
+++ /issm/trunk-jpl/src/c/modules/ParseToolkitsOptionsx/ParseToolkitsOptionsx.h	(revision 14627)
@@ -0,0 +1,14 @@
+/*!\file:  ParseToolkitsOptionsx.h
+ * \brief header file for parsing petsc options file
+ */ 
+
+#ifndef _PARSEPETSCOPTIONSX_H
+#define _PARSEPETSCOPTIONSX_H
+
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+
+/* local prototypes: */
+void ParseToolkitsOptionsx(Parameters* parameters, FILE* petscoptionsfid);
+
+#endif  /* _PARSEPETSCOPTIONSX_H */