diff --git a/CMakeLists.txt b/CMakeLists.txt
index f7e49e1..49571d8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -5,35 +5,38 @@ set(CMAKE_CXX_STANDARD 11)
 
 
 # Define path to header files and libraries
-set(HOME /opt/scientific)
-set(CANTERA_DIR ${HOME}/cantera-2.4_gnu_blas)
-set(IDA_DIR ${HOME}/sundials-3.1.1_intel_mkl)
-set(GSL_DIR /usr/lib)
-set(COOLPROP_DIR /backup/weiye/CoolProp)
-set(FMT_DIR /backup/weiye/fmt)
+#set(HOME /opt/scientific)
+set(CANTERA_DIR /usr/local)
+set(IDA_DIR /usr/local)
+set(GSL_DIR /usr/local)
+set(COOLPROP_DIR /opt/CoolProp/shared_library/Linux)
+set(FMT_DIR /usr/local)
 
 set(CANTERA_INCLUDES ${CANTERA_DIR}/include)
 set(IDA_INCLUDES ${IDA_DIR}/include)
-set(GSL_INCLUDES /usr/include/gsl)
+set(GSL_INCLUDES ${GSL_DIR}/include/gsl)
 set(COOLPROP_INCLUDES ${COOLPROP_DIR}/include)
 set(FMT_INCLUDES ${FMT_DIR}/include)
-set(EIGEN_INCLUDES /backup/weiye/eigen-3.4.0)
+set(EIGEN_INCLUDES /opt/eigen-3.4.0)
 
 # Search for source files
 aux_source_directory(${PROJECT_SOURCE_DIR}/src SRC_LIST)
 add_executable(DropletCombustion ${SRC_LIST})
 
 # Set the RPATH parameter
-set(CMAKE_INSTALL_RPATH "${IDA_DIR}/lib;${CANTERA_DIR}/lib;${COOLPROP_DIR}/lib;${FMT_DIR}/lib")
+set(CMAKE_INSTALL_RPATH "${IDA_DIR}/lib;${CANTERA_DIR}/lib;${GSL_DIR}/lib;${COOLPROP_DIR}/lib;${FMT_DIR}/lib")
 
 # Link libraries
-target_link_directories(DropletCombustion PRIVATE ${CANTERA_DIR}/lib ${IDA_DIR}/lib ${GSL_DIR} ${COOLPROP_DIR}/lib ${FMT_DIR}/lib)
+target_link_directories(DropletCombustion PRIVATE ${CANTERA_DIR}/lib ${IDA_DIR}/lib ${GSL_DIR}/lib ${COOLPROP_DIR}/64bit ${FMT_DIR}/lib )
 target_link_libraries(DropletCombustion
     PRIVATE cantera_shared sundials_nvecopenmp sundials_ida sundials_sunlinsollapackband gsl gslcblas CoolProp fmt)
 
 # Include directories
 target_include_directories(DropletCombustion
-    PRIVATE ${PROJECT_SOURCE_DIR}/include ${CANTERA_INCLUDES} ${IDA_INCLUDES} ${GSL_INCLUDES} ${COOLPROP_INCLUDES} ${FMT_INCLUDES} ${EIGEN_INCLUDES})
+    PRIVATE ${PROJECT_SOURCE_DIR}/include ${CANTERA_INCLUDES} ${IDA_INCLUDES} ${GSL_INCLUDES} ${COOLPROP_INCLUDES} ${FMT_INCLUDES} ${EIGEN_INCLUDES} )
 
 # Set the output path
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/bin)
+
+
+
diff --git a/DropletCombustion11 b/DropletCombustion11
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diff --git a/DropletCombustionTest1 b/DropletCombustionTest1
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diff --git a/DropletCombustionTest7-Binary b/DropletCombustionTest7-Binary
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diff --git a/UserData.cpp b/UserData.cpp
deleted file mode 100644
index 8473e99..0000000
--- a/UserData.cpp
+++ /dev/null
@@ -1,499 +0,0 @@
-#include "UserData.h"
-#include "parse.h"
-
-void freeUserData(UserData data){
-	if(data!=NULL){
-		if(data->trmix!=NULL){
-			delete data->trmix;
-			printf("Transport Deleted!\n");
-
-		}
-		if(data->gas!=NULL){
-			delete data->gas;
-			printf("Gas Deleted!\n");
-
-		}
-		if(data->adaptiveGrid){
-			if(data->grid->xOld!=NULL){
-				delete[] data->grid->xOld;
-				printf("old grid array Deleted!\n");
-			}
-			if(data->grid->x!=NULL){
-				delete[] data->grid->x;
-				printf("current grid array Deleted!\n");
-			}
-			if(data->grid!=NULL){
-				free(data->grid);
-				printf("grid object Freed!\n");
-			}
-		}
-		else{
-			if(data->uniformGrid!=NULL){
-				delete[] data->uniformGrid;
-				printf("uniformGrid deleted!\n");
-			}
-		}
-		if(data->innerMassFractions!=NULL){
-			delete[] data->innerMassFractions;
-			printf("innerMassFractions array Deleted!\n");
-		}
-		if(data->output!=NULL){
-  			fclose(data->output);
-			printf("Output File Cleared from Memory!\n");
-		}
-		if(data->gridOutput!=NULL){
-  			fclose(data->gridOutput);
-			printf("Grid Output File Cleared from Memory!\n");
-		}
-		//if(data->ratesOutput!=NULL){
-  		//	fclose(data->ratesOutput);
-		//	printf("Rates Output File Cleared from Memory!\n");
-		//}
-		if(data->globalOutput!=NULL){
-  			fclose(data->globalOutput);
-			printf("Global Output File Cleared from Memory!\n");
-		}
-		if(data->timescaleOutput!=NULL){
-  			fclose(data->timescaleOutput);
-			printf("Characteristic Timescale Output File Cleared from Memory!\n");
-		}
-		//if(data->rxnROPOutput!=NULL){
-  		//	fclose(data->rxnROPOutput);
-		//	printf("Reactions Rate of Progress Output File Cleared from Memory!\n");
-		//}
-		//if(data->spROPOutput!=NULL){
-  		//	fclose(data->spROPOutput);
-		//	printf("Species Rate of Production Output File Cleared from Memory!\n");
-		//}
-	}
-  	free(data);             /* Free the user data */
-	printf("\n\n");
-}
-
-UserData allocateUserData(FILE *input){
-
-	UserData data;
-  	data = (UserData) malloc(sizeof *data);
-
-	if(!data){
-		printf("Allocation Failed!\n");
-		return(NULL);
-	}
-	setSaneDefaults(data);
-
-	int ier;
-
-	ier=parseNumber<size_t>(input, "basePts"	, MAXBUFLEN, &data->npts);
-	if(ier==-1 || data->npts<=0){
-		printf("Enter non-zero basePts!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<double>(input, "domainLength", MAXBUFLEN, &data->domainLength);
-	if(ier==-1 || data->domainLength<=0.0e0){
-		printf("domainLength error!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<double>(input, "Rd", MAXBUFLEN, &data->Rd);
-	if(ier==-1 || data->Rd<=0.0e0){
-		printf("Rd error!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>(input, "constantPressure"	, MAXBUFLEN, &data->constantPressure);
-	if(ier==-1 || (data->constantPressure!=0 && data->constantPressure!=1)){
-		printf("constantPressure error!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>(input, "problemType"	, MAXBUFLEN, &data->problemType);
-	if(ier==-1 || (data->problemType!=0 
-		       && data->problemType!=1
-			&& data->problemType!=2
-			&& data->problemType!=3)){
-		printf("include valid problemType!\n");
-		printf("0: premixed combustion with NO equilibrated ignition kernel\n");
-		printf("1: premixed combustion WITH equilibrated ignition kernel\n");
-		printf("2: arbitrary initial conditions\n");
-		printf("3: Restart\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>(input, "quasiSteady"	, MAXBUFLEN, &data->quasiSteady);
-	if(ier==-1 || (data->quasiSteady!=0 
-		       && data->quasiSteady!=1)){
-		printf("include valid quasiSteady!\n");
-		printf("0: The droplet surface recedes and the droplet losses mass\n");
-		printf("1: The droplet surface does not move and the droplet mass is constant\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<double>(input, "dPdt"		, MAXBUFLEN, &data->dPdt);
-
-	ier=parseNumber<double>(input, "Rg"		, MAXBUFLEN, &data->Rg);
-	if(data->Rg < 0.0){
-		printf("Rg must be greater than 0");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>   (input, "reflectProblem"	, MAXBUFLEN, &data->reflectProblem);
-	if(data->reflectProblem!=0 && data->reflectProblem!=1){
-		printf("Invalid entry for reflectProblem! Can be only 1 or 0.\n");
-		return(NULL);
-	}
-	
-	ier=parseNumber<double>(input, "mdot"		, MAXBUFLEN, &data->mdot);
-	
-	ier=parseNumber<double>(input, "initialTemperature", MAXBUFLEN,
-			&data->initialTemperature);
-	if(ier==-1 || data->initialTemperature<=0.0e0){
-		printf("Enter positive initialTemperature in K!\n");
-		return(NULL);
-	}
-
-
-	ier=parseNumber<double>(input, "initialPressure", MAXBUFLEN,
-			&data->initialPressure);
-	if(ier==-1 || data->initialTemperature<=0.0e0){
-		printf("Enter positive initialPressure in atm!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>   (input, "metric"	, MAXBUFLEN, &data->metric);
-	if(data->metric!=0 && data->metric!=1 && data->metric!=2){
-		printf("Invalid entry for metric!\n");
-		printf("0: Cartesian\n");
-		printf("1: Cylindrical\n");
-		printf("2: Spherical\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<double>(input, "QDot", MAXBUFLEN, &data->maxQDot);
-	if(ier==-1 && data->problemType==0){
-		printf("Need to specify QDot for problemType 0!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<double>(input, "kernelSize", MAXBUFLEN, &data->kernelSize);
-	if(ier==-1 && data->problemType==0){
-		printf("Need to specify kernelSize for problemType 0!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<double>(input, "ignTime", MAXBUFLEN, &data->ignTime);
-	if(ier==-1 && data->problemType==0){
-		printf("Need to specify ignTime for problemType 0!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<double>(input, "mixingWidth", MAXBUFLEN,
-			&data->mixingWidth);
-	if(ier==-1){
-		printf("Need to specify mixingWidth!\n");
-		return(NULL);
-	}
-	
-	ier=parseNumber<double>(input, "shift", MAXBUFLEN, &data->shift);
-
-	ier=parseNumber<double>(input, "firstRadius", MAXBUFLEN, &data->firstRadius);
-	
-	ier=parseNumber<double>(input, "wallTemperature", MAXBUFLEN, &data->wallTemperature);
-
-	ier=parseNumber<int>   (input, "dirichletInner"	, MAXBUFLEN,
-			&data->dirichletInner);
-	if(data->dirichletInner!=0 && data->dirichletInner!=1){
-		printf("dirichletInner can either be 0 or 1!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>   (input, "dirichletOuter"	, MAXBUFLEN,
-			&data->dirichletOuter);
-	if(data->dirichletOuter!=0 && data->dirichletOuter!=1){
-		printf("dirichletOuter can either be 0 or 1!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>   (input, "adaptiveGrid"	, MAXBUFLEN,
-			&data->adaptiveGrid);
-	if(ier==-1 || (data->adaptiveGrid!=0 && data->adaptiveGrid!=1)){
-		printf("specify adaptiveGrid as 0 or 1!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>   (input, "moveGrid"	, MAXBUFLEN,
-			&data->moveGrid);
-	if(ier==-1 || (data->moveGrid!=0 && data->moveGrid!=1)){
-		printf("specify moveGrid as 0 or 1!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<double>   (input, "isotherm"	, MAXBUFLEN,
-			&data->isotherm);
-	if(ier==-1){
-		printf("specify temperature of isotherm!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<double>(input, "gridOffset", MAXBUFLEN, &data->gridOffset);
-
-	ier=parseNumber<int>   (input, "nSaves"	, MAXBUFLEN, &data->nSaves);
-	if(data->nSaves<0 ){
-		printf("nSaves must be greater than 0!\n");
-		return(NULL);
-	}
-	
-	ier=parseNumber<int>   (input, "writeRates"	, MAXBUFLEN,
-			&data->writeRates);
-	if(data->writeRates!=0 && data->writeRates!=1){
-		printf("writeRates must either be 0 or 1!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>   (input, "writeEveryRegrid", MAXBUFLEN,
-			&data->writeEveryRegrid);
-	if(data->writeEveryRegrid!=0 && data->writeEveryRegrid!=1){
-		printf("writeEveryRegrid must either be 0 or 1!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>   (input, "setConstraints"	, MAXBUFLEN,
-			&data->setConstraints);
-	if(data->setConstraints!=0 && data->setConstraints!=1){
-		printf("setConstraints must either be 0 or 1!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>   (input, "suppressAlg"	, MAXBUFLEN,
-			&data->suppressAlg);
-	if(data->suppressAlg!=0 && data->suppressAlg!=1){
-		printf("suppressAlg must either be 0 or 1!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<int>   (input, "dryRun"	, MAXBUFLEN,
-			&data->dryRun);
-	if(data->dryRun!=0 && data->dryRun!=1){
-		printf("dryRun must either be 0 or 1!\n");
-		return(NULL);
-	}
-
-	ier=parseNumber<double>   (input, "finalTime"	, MAXBUFLEN,
-			&data->finalTime);
-
-	ier=parseNumber<double>   (input, "relativeTolerance"	, MAXBUFLEN,
-			&data->relativeTolerance);
-	ier=parseNumber<double>   (input, "radiusTolerance"	, MAXBUFLEN,
-			&data->radiusTolerance);
-	ier=parseNumber<double>   (input, "temperatureTolerance", MAXBUFLEN,
-			&data->temperatureTolerance);
-	ier=parseNumber<double>   (input, "pressureTolerance", MAXBUFLEN,
-			&data->pressureTolerance);
-	ier=parseNumber<double>   (input, "massFractionTolerance", MAXBUFLEN,
-			&data->massFractionTolerance);
-	ier=parseNumber<double>   (input, "bathGasTolerance", MAXBUFLEN,
-			&data->bathGasTolerance);
-	ier=parseNumber<double>   (input, "MdotTolerance", MAXBUFLEN,
-			&data->MdotTolerance);
-
-	char chem[MAXBUFLEN],mix[MAXBUFLEN],tran[MAXBUFLEN];
-
-	ier=parseNumber<char>(input, "chemistryFile"	, MAXBUFLEN, chem);
-	if(ier==-1){
-		printf("Enter chemistryFile!\n");
-		return(NULL);
-	}else{
-		try{
-			data->gas = new Cantera::IdealGasMix(chem);
-			data->nsp=data->gas->nSpecies(); //assign no: of species
-
-    		} catch (Cantera::CanteraError& err) {
-		    printf("Error:\n");
-		    printf("%s\n",err.what());
-		    return(NULL);
-    		}
-	}
-
-	ier=parseNumber<char>(input, "transportModel", MAXBUFLEN, tran);
-	if(ier==-1){
-		printf("Enter transportModel!\n");
-		return(NULL);
-	}else{
-		try{
-  			data->trmix = Cantera::newTransportMgr(tran, data->gas);
-		}catch (Cantera::CanteraError& err) {
-			printf("Error:\n");
-			printf("%s\n",err.what());
-			return(NULL);
-    		}
-	}
-
-	ier=parseNumber<char>(input, "mixtureComposition", MAXBUFLEN, mix);
-	if(ier==-1){
-		printf("Enter mixtureComposition!\n");
-		return(NULL);
-	}else{
-		if(data->gas!=NULL){
-			try{
-				data->gas->setState_TPX(data->initialTemperature,
-							data->initialPressure*Cantera::OneAtm,
-							mix);
-			}catch (Cantera::CanteraError& err) {
-		    		printf("Error:\n");
-		    		printf("%s\n",err.what());
-		    		return(NULL);
-    			}
-		}
-	}
-
-	//ier=parseNumber<char>(input, "dropletComposition", MAXBUFLEN, data->dropSpec);
-	//if(ier==-1){
-	//	printf("Enter composition of droplet!\n");
-	//	return(NULL);
-	//}
-
-    ier=parseDrop(input,"dropletComposition",data->dropSpec,data->dropMole,MAXBUFLEN);
-    ier=parseDrop(input,"dropletDensity",data->dropSpec,data->dropDens,MAXBUFLEN);
-
-
-	ier=parseNumber<int>   (input, "nThreads", MAXBUFLEN, &data->nThreads);
-	if(data->nThreads<0 ){
-		printf("nThreads must be greater than 0!\n");
-		return(NULL);
-	}
-    
-
-	ier=parseNumber<double>(input, "PCAD", MAXBUFLEN, &data->PCAD);
-    ier=parseNumber<double>(input,"RGTC", MAXBUFLEN, &data->RGTC);
-    ier=parseNumber<int>(input,"JJRG", MAXBUFLEN, &data->JJRG);
-    ier=parseNumber<double>(input,"deltaT", MAXBUFLEN, &data->deltaT);
-	
-    data->nr=0;
-	//data->np=data->nr+1;
-	data->nt=data->nr+1;
-	data->ny=data->nt+1;
-	data->np=data->ny+data->nsp;
-	data->nm=data->np+1;
-				
-	data->nvar=data->nsp+4;		 //assign no: of variables (R,T,P,Mdot,nsp species)
-
-
-    double MW[2]; 
-    for(int i=0;i<=1;i++){
-        int speciesIndex = data->gas->speciesIndex(data->dropSpec[i]);
-        double weight = data->gas->molecularWeight(speciesIndex);
-        MW[i]= weight;
-    }
-
-    double massSum = 0.0; 
-    for(int i=0;i<=1;i++){
-        massSum = massSum + data->dropMole[i] * MW[i];
-    }
-    data->dropRho = 0.0;
-    for(int i=0;i<=1;i++){
-        data->dropMassFrac[i] = data->dropMole[i]*MW[i]/massSum;
-        data->dropRho = data->dropRho + data->dropMassFrac[i]*data->dropDens[i];
-    }
-    printf("Density of droplet is: %.3f [kg/m^3]\n",data->dropRho);
-	//Mass of droplet
-	//data->massDrop=1.0/3.0*pow(data->Rd,3)*997.0; //TODO: The density of the droplet should be a user input
-    //data->massDrop=1.0/3.0*pow(data->Rd,3)*684.00; //TODO: The density of the droplet(n-heptane) should be a user input
-    data->massDrop=1.0/3.0*pow(data->Rd,3)*data->dropRho;
-
-	if(!data->adaptiveGrid){
-		data->uniformGrid = new double [data->npts];
-		data->neq=data->nvar*data->npts;
-	}
-	else{
-		data->grid=(UserGrid) malloc(sizeof *data->grid);
-		ier=getGridSettings(input,data->grid);
-		if(ier==-1)return(NULL);
-
-		ier=initializeGrid(data->grid);
-		if(ier==-1)return(NULL);
-
-		ier=reGrid(data->grid, data->grid->position);
-		if(ier==-1)return(NULL);
-
-
-//        /**************** TEST THE data->grid->xOld *******************/
-//        double* ptr = data->grid->xOld ; 
-//        printf("allocateUserData function is called,Start print the first 5 elements of the xOld array : \n");
-//        printf("1st:%.6f, 2nd:%.6f, 3rd:%.6f, 4th:%.6f, 5th:%.6f.\n",ptr[0],ptr[1],ptr[2],ptr[3],ptr[4]);
-
-		data->npts=data->grid->nPts;
-		data->neq=data->nvar*data->npts;
-	}
-
-	data->output=fopen("output.dat","w");
-	data->globalOutput=fopen("globalOutput.dat","w");
-	data->gridOutput=fopen("grid.dat","w");
-	data->timescaleOutput=fopen("timeScale.dat","w") ;
-    data->rxnROPOutput=fopen("rxnROP.dat","w");
-    data->spROPOutput=fopen("spROP.dat","w");
-	//data->ratesOutput=fopen("rates.dat","w");
-	
-	data->innerMassFractions = new double [data->nsp];
-	//data->wdot_mole = new double [data->nsp] ; 
-	//data->wdot_mass = new double [data->nsp] ; 
-	data->time_scale = new double [(data->npts) * (data->nsp)] ; 
-	//data->MW = new double [data->nsp] ; 
-
-	return(data);
-}
-
-void setSaneDefaults(UserData data){
-	data->domainLength=1.0e-02;
-	data->Rd=100.0e-06;
-	data->constantPressure=1;
-	data->problemType=1;
-	data->quasiSteady=1;
-	data->dPdt=0.0e0;
-	data->reflectProblem=0;
-	data->mdot=0.0;
-	data->initialTemperature=300.0;
-	data->initialPressure=1.0;
-	data->metric=0;
-	data->ignTime=1e-09;
-	data->maxQDot=0.0e0;
-	data->maxTemperature=300.0e0;
-	data->mixingWidth=1e-04;
-	data->shift=3.0e-03;
-	data->firstRadius=1e-04;
-	data->wallTemperature=298.0e0;
-	data->dirichletInner=0;
-	data->dirichletOuter=0;
-	data->adaptiveGrid=0;
-	data->moveGrid=0;
-	data->gridOffset=0.0e0;
-	data->Rg=1.0;
-	data->isotherm=1000.0;
-	data->nSaves=30;
-	data->writeRates=0;
-	data->writeEveryRegrid=0;
-	data->relativeTolerance=1e-06;
-	data->radiusTolerance=1e-08;
-	data->temperatureTolerance=1e-06;
-	data->pressureTolerance=1e-06;
-	data->massFractionTolerance=1e-09;
-	data->bathGasTolerance=1e-06;
-	data->finalTime=1e-02;
-	data->tNow=0.0e0;
-	data->setConstraints=0;
-	data->suppressAlg=1;
-	data->regrid=0;
-	data->gridDirection=1;
-	data->dryRun=0;
-	data->nThreads=1;
-
-	data->flamePosition[0]=0.0e0;
-	data->flamePosition[1]=0.0e0;
-	data->flameTime[0]=0.0e0;
-	data->flameTime[1]=0.0e0;
-	data->nTimeSteps=0;
-    data->PCAD=0.75;
-    data->RGTC=1.0;
-    data->JJRG=0;
-    data->deltaT=200.0;
-}
-
diff --git a/UserData.d b/UserData.d
deleted file mode 100644
index 7531ae1..0000000
--- a/UserData.d
+++ /dev/null
@@ -1,63 +0,0 @@
-UserData.o: UserData.cpp UserData.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/IdealGasMix.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/IdealGasPhase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/ThermoPhase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/Phase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ctexceptions.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/fmt.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ct_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/config.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/format.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/core.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/format-inl.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/format.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/printf.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/ostream.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/ostream.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/Elements.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ct_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/Species.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/AnyMap.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/global.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/AnyMap.inl.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ValueCache.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/MultiSpeciesThermo.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/SpeciesThermoInterpType.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/speciesThermoTypes.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/GasKinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/BulkKinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Kinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/ThermoPhase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/StoichManager.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/stringUtils.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Reaction.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/utilities.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/global.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/RxnRates.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/reaction_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Falloff.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/RateCoeffMgr.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/RxnRates.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/ThirdBodyCalc.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/FalloffMgr.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/reaction_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/FalloffFactory.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/FactoryBase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Reaction.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/importKinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/stringUtils.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportFactory.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportBase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LiquidTransportParams.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportParams.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/numerics/DenseMatrix.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/Array.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/utilities.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LiquidTranInteraction.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LiquidTransportData.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LTPspecies.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportData.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/xml.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ctexceptions.h \
- gridRoutines.h parse.h parse.hpp
diff --git a/UserData.h b/UserData.h
deleted file mode 100644
index ff713c4..0000000
--- a/UserData.h
+++ /dev/null
@@ -1,221 +0,0 @@
-#ifndef CANTERA_DEF
-#define CANTERA_DEF
-#include <cantera/IdealGasMix.h>
-#include <cantera/transport.h>
-#endif
-
-#include "gridRoutines.h"
-#include <string>
-
-#ifndef USER_DEF
-#define USER_DEF
-typedef struct UserDataTag{
-	/*An ideal gas object from Cantera. Contains thermodynamic and kinetic
-	 * info of all species.*/
-	Cantera::IdealGasMix* gas;
-	/*A Transport object from Cantera. Contains all transport info of all
-	 * species.*/
-	Cantera::Transport* trmix;
-	/* Droplet species composition */
-	//char dropSpec[MAXBUFLEN];
-    char dropSpec[2][10];
-    /* Droplet species mole fractions */
-    double dropMole[2];
-    /* Droplet species density at given initialTemperature*/
-    double dropDens[2];
-    /* Droplet species mass fractions*/
-    double dropMassFrac[2];
-    double dropRho; 
-	/*Length of the domain (in meters):*/			  
-	double domainLength;	  
-	/*Initial Droplet Radius (in meters)*/
-	double Rd;
-	/*Droplet Mass*/
-	double massDrop;
-	/*Mass of gas in domain (in kg):*/			  
-	double mass;		  
-	/*Parameter that indicates the symmetry of the problem;*/			  
-	/*metric=0:Planar*/			  
-	/*metric=1:Cylindrical*/			  
-	/*metric=2:Spherical*/			  
-	int metric;		  
-	/*No: of species:*/
-	size_t nsp;	  
-	/*No: of equations:*/
-	size_t neq;
-	/*No: of variables:*/
-	size_t nvar;
-	/*Pointer indices (see "macros.h" for aliases that use these):*/
-	/*Pointer index for temperature:*/
-	size_t nt;	  
-	/*Pointer index for species:*/
-	size_t ny;
-	/*Pointer index for spatial coordinate:*/
-	size_t nr;
-	/*Pointer index for pressure:*/
-	size_t np;
-	/*Pointer index for mass flow rate:*/
-	size_t nm;
-	/*Species index of bath gas:*/			  
-	size_t k_bath;		  
-	/*Species index of oxidizer:*/			  
-	size_t k_oxidizer;		  
-	size_t k_OH;
-	size_t k_HO2;
-	/*Species index of droplet composition*/
-    /*Index starts with 1 instead of 0*/
-	size_t k_drop[2];
-	/*User-defined mass flux (kg/m^2/s):*/			  
-	double mdot;
-	/*Flag to solve isobaric/isochoric problem;*/
-	/*constantPressure=1: isobaric*/
-	/*constantPressure=0: isochoric*/
-	int constantPressure;
-	/*User-defined dPdt (Pa/s), activates when problem is "isobaric":*/			  
-	double dPdt;	
-	/*Initial temperature of the gas (K):*/
-	double initialTemperature;
-	/*Initial Pressure of the gas (atm):*/
-	double initialPressure;
-	/*Classification of problem type;*/
-	/*problemType=0: Mixture is premixed and spatially uniform initially.
-	 * In order for mixture to ignite, an external heat source (finite
-	 * maxQDot) must be used.*/
-	/*problemType=1: Mixture is premixed but spatially non-uniform
-	 * initially. Equilibrium products are contained within a hot kernel of
-	 * size given by "shift" and a mixing length scale given by
-	 * "mixingWidth".*/
-	/*problemType=2: User specified initial condition. Use file
-	 * "initialCondition.dat".*/
-	int problemType;
-	/*Quasi-Steady Assumption:
-	 *quasiSteady=0: The droplet surface recedes and the droplet losses mass.
-	 *quasiSteady=1: The droplet surface does not move and the droplet mass is constant.*/
-	int quasiSteady;
-	/*Maximum External heat source (K/s):*/
-	double maxQDot;
-	/*Ignition kernel size:*/
-	double kernelSize;
-
-	double maxTemperature;
-	/*Maximum time for which the external heat source is applied (s):*/
-	double ignTime;
-	/*Vector of Mass Fractions used to impose Robin Boundary Condition for
-	 * species at the domain origin:*/
-	double* innerMassFractions;
-	/*Value of temperature to be used if Dirichlet Boundary Conditions are
-	 * imposed for temperature:*/
-	double innerTemperature;
-	double wallTemperature;
-	/*Isotherm chosen to find the location of a "burning" front (K):*/
-	double isotherm;
-	/*Interval of time integration:*/
-	double finalTime;
-	/*Current time:*/
-	double tNow;
-	/*Flag to reflect initial conditions across center of the domain:*/
-	int reflectProblem;
-	/*Parameters for initial conditions in setting up profiles:
-	increasing function of x: g=0.5*(erf(x-3*w-shift)/w)+1)
-	decreasing function of x: f=1-g*/
-	double mixingWidth;
-	double shift;
-	double firstRadius;
-	/*Flag to run program without time-integration i.e. simply layout the
-	 * initial conditions and quit:*/
-	int dryRun;
-	/*Relative Tolerance:*/
-	double relativeTolerance;
-	/*Absolute Tolerance for spatial coordinate:*/
-	double radiusTolerance;
-	/*Absolute Tolerance for Temperature:*/
-	double temperatureTolerance;
-	/*Absolute Tolerance for Pressure:*/
-	double pressureTolerance;
-	/*Absolute Tolerance for Mass Fractions:*/
-	double massFractionTolerance;
-	/*Absolute Tolerance for bath gas mass fraction:*/
-	double bathGasTolerance;
-	/*Absolute Tolerance for Mdot:*/
-	double MdotTolerance;
-	/*Flag to set constraints on Mass fractions so they don't acquire
-	 * negative values:*/
-	int setConstraints;
-	/*Flag to suppress error checking on algebraic variables:*/
-	int suppressAlg;
-	/*Number of time-steps elapsed before saving the solution:*/
-	int nSaves;		  
-	/*Flag to set write for every regrid:*/
-	int writeEveryRegrid;
-	/*Solution output file:*/
-	FILE* output;
-	/*Flag to write the rates (ydot) of solution components into the
-	 * "ratesOutput" file:*/
-	int writeRates;
-	/*Grid output file:*/
-	FILE* gridOutput;
-	///*Rate of change (ydot) output file (see "writeRates"):*/
-	//FILE* ratesOutput;
-	/*Global properties (mdot, radius of flame, etc.) output file:*/
-	FILE* globalOutput;
-
-	/*Flag to adapt grid:*/
-	int adaptiveGrid;
-	/*Flag to move grid:*/
-	int moveGrid;
-	/*Flag to initiate regrid:*/
-	int regrid;
-	/*Integer that specifies grid movement direction:
-	 * gridDirection = -1: Move Left
-	 * gridDirection = +1: Move Right*/ 
-	int gridDirection;
-	
-	/*Grid Ratio: This replaces the uniform grid. dX0 and dXf are the grid
-	spacing at the droplet surface and right boundary, respectivly. The Grid
-	Ratio is equal to dXf/dX0. A Rg>1 focuses grid points on the droplet
-	surface while a Rg<1 focuses grid points at the right boundary. A Rg of 1
-	is a uniform grid.*/ 
-	double Rg;
-	/*Total number of points for grid:*/
-	size_t npts;
-
-	double gridOffset;
-
-	UserGrid grid;
-	double* uniformGrid;
-
-	int dirichletInner,dirichletOuter;
-
-	int nThreads;
-	double clockStart;
-	
-	/*These arrays are used to compute dr/dt, which in turn is used to
-	 * compute the flame speed S_u:*/
-	double flamePosition[2];
-	double flameTime[2];
-	size_t nTimeSteps;
-
-	/*Following arrays are used to compute the characteristic time scale of
-	species*/
-	//double* wdot_mole ; 
-	//double* wdot_mass ; 
-	double* time_scale ; 
-	//double* MW;
-	FILE* timescaleOutput;
-
-    /*Following parameters are used for REGRID function*/
-    double PCAD;
-    double RGTC;
-    int JJRG;
-    double deltaT;
-
-    FILE* rxnROPOutput;
-    FILE* spROPOutput;
-
-
-} *UserData;
-UserData allocateUserData(FILE *input);
-void setSaneDefaults(UserData data);
-void freeUserData(UserData data);
-#endif
-
diff --git a/UserData.o b/UserData.o
deleted file mode 100644
index ab3b26a..0000000
Binary files a/UserData.o and /dev/null differ
diff --git a/gridRoutines.cpp b/gridRoutines.cpp
deleted file mode 100644
index 6f6107b..0000000
--- a/gridRoutines.cpp
+++ /dev/null
@@ -1,293 +0,0 @@
-#include "gridRoutines.h"
-#include <stdio.h>
-
-inline double l(const double* x, 
-	 	const double* a,
-	 	const double* w,
-		const double* fac,
-		const int* refineLeft){
-	if(*refineLeft==0){
-		return(tanh(-*a*(*x+*w*100.0e0)));
-	}else{
-        double l ; 
-        l = tanh(-*a*(*x-*w*(*fac))) ;
-        
-        if(l>=0){
-            return l*10.0;
-        }else{
-		    //return(tanh(-*a*(*x-*w*(*fac))));
-            return l;
-        }
-	}
-}
-
-//inline double l(const double* x, 
-//	 	const double* a,
-//        const double* c,
-//	 	const double* w,
-//		const double* fac,
-//		const int* refineLeft){
-//	if(*refineLeft==0){
-//		return(tanh(-*a*(*x+*w*100.0e0)));
-//	}else{
-//        double l ; 
-//        //l = tanh(-*a*(*x-*w*(*fac))) ;
-//        l = tanh(-*a*(*x-*c));
-//
-//        if(l>=0){
-//            return l*10.0;
-//        }else{
-//		    //return(tanh(-*a*(*x-*w*(*fac))));
-//            return l;
-//        }
-//	}
-//}
-
-inline double r(const double* x, 
-		const double* a, 
-		const double* w,
-		const double* fac,
-		const int* refineRight){
-	if(*refineRight==0){
-		return(tanh(*a*(*x-(1.0e0+*w*100.0e0))));
-	}else{
-		return(tanh(*a*(*x-(1.0e0-*w*(*fac)))));
-	}
-}
-
-inline double f(const double* x,
-		const double* a,
-		const double* c,
-		const double* w){
-	return(tanh(-*a*(*x-(*c+*w)))
-		+tanh(-*a*((*x-1.0e0)-(*c+*w)))
-		+tanh(-*a*((*x+1.0e0)-(*c+*w))));
-}
-
-inline double g(const double* x, 
-		const double* a, 
-		const double* c, 
-		const double* w){
-	return(tanh(*a*(*x-(*c-*w)))
-	       +tanh(*a*((*x-1.0e0)-(*c-*w)))
-	       +tanh(*a*((*x+1.0e0)-(*c-*w))));
-}
-
-inline double rho(const double* x,
-	   	  const double* a,
-	   	  const double* c,
-	   	  const double* w,
-	   	  const double* mag,
-	   	  const double* leftFac,
-	   	  const double* rightFac,
-		  const int* refineLeft,
-		  const int* refineRight){
-
-	return(((2.0e0+f(x,a,c,w)
-		 +g(x,a,c,w)
-		 +l(x,a,w,leftFac,refineLeft)
-//         +l(x,a,c,w,leftFac,refineLeft)
-		 +r(x,a,w,rightFac,refineRight))*0.5e0)
-		  *(*mag-1.0e0)+1.0e0);
-}
-
-size_t maxPoints(const size_t basePts,
-	   	 const double* a,
-	   	 const double* w,
-	   	 const double* mag,
-	   	 const double* leftFac,
-	   	 const double* rightFac,
-	   	 const int* refineLeft,
-	   	 const int* refineRight){
-	double dx=1.0e0/((double)(basePts)-1.0e0);
-	double y=0.0e0;
-	size_t i=0;
-	double r=0.0e0;
-	double t=0.5e0;
-	while(y<=1.0e0){
-		r=rho(&y,a,&t,w,mag,leftFac,rightFac,refineLeft,refineRight);
-		y=y+(dx/r);
-		i++;
-	}
-	return(i);
-}
-
-void fillGrid(const size_t* basePts,
-	      const size_t* nPts,
-	      const double* a,
-	      const double* c,
-	      const double* w,
-	      const double* mag,
-	      const double* leftFac,
-	      const double* rightFac,
-	      const int* refineLeft,
-	      const int* refineRight,
-	      double x[]){
-
-	FILE* out;out=fopen("tmp.dat","w");
-
-	double y=0.0e0;
-	double r=0.0e0;
-	double dx=1.0e0/((double)(*basePts)-1.0e0);
-	for(size_t j=0;j<*nPts;j++){
-		r=rho(&y,a,c,w,mag,leftFac,rightFac,refineLeft,refineRight); // Point density?
-		fprintf(out, "%15.15e\n",dx/r); // writing number of points per section to tmp.dat
-		y=y+(dx/r); // y is the total number of points?
-	}
-	fclose(out);
-	
-	double dxp[*nPts-1];
-	for (size_t j = 0; j < *nPts; j++) {
-		dxp[j]=0.0e0;
-	}
-
-	FILE* tmp;tmp=fopen("tmp.dat","r");
-	char buf[MAXBUFLEN];
-	size_t i=0;
-	while (fgets(buf,MAXBUFLEN, tmp)!=NULL){
-		sscanf(buf, "%lf", &y);
-		dxp[i]=y;
-		i++;
-	}
-	fclose(tmp);
-
-	double sum=0.0e0;
-	double err=0.0e0;
-	double fix=0.0e0;
-    double arr[*nPts-1] ; 
-    size_t halfboundII  = 0;
-	for(size_t j=0;j<*nPts-1;j++){
-		sum+=dxp[j];
-        arr[j]=sum;
-	}
-    
-    for(size_t j=0;j<*nPts;j++){
-        if(arr[j] > 0.5e0){
-            halfboundII = j;
-            break;
-        }
-    }
-
-	err=1.0e0-sum;
-	printf("sum before correction: %15.6e\n",sum);
-	printf("err before correction: %15.6e\n",err);
-    
-	//fix=err/((double)(*nPts));
-    fix = err/((double)(*nPts-1-(halfboundII+1)));
-
-	sum=0.0e0;
-	for(size_t j=0;j<*nPts-1;j++){
-	//	dxp[j]+=fix;
-        if(j>halfboundII){
-            dxp[j]=dxp[j]+fix ; 
-        }
-		sum+=dxp[j];
-	}
-	err=1.0e0-sum;
-	printf("sum after correction:%15.6e\n",sum);
-	printf("err after correction: %15.6e\n",err);
-
-	x[0]=0.0e0;
-	for(size_t j=0;j<*nPts-1;j++){
-		x[j+1]=x[j]+dxp[j];
-	}
-	x[*nPts-1]=1.0e0;
-
-}
-
-double safePosition(double c, double w){
-	if(c<w){
-		return(w);
-	}
-	else if(c>1.0e0-w){
-		return(1.0e0-w);
-	}
-	else{
-		return(c);
-	}
-}
-
-int reGrid(UserGrid grid, double position){
-
-	printf("before regrid: %ld\n", grid->nPts);
-	double xx[grid->nPts];
-
-	fillGrid(&grid->basePts,
-		 &grid->nPts,
-		 &grid->a,
-		 &position,
-		 &grid->w,
-		 &grid->mag,
-		 &grid->leftFac,
-		 &grid->rightFac,
-		 &grid->refineLeft,
-		 &grid->refineRight,
-		 xx);
-
-	for (size_t i = 0; i < grid->nPts; i++) {
-		grid->x[i]=xx[i];
-	}
-	return(0);
-}
-
-void storeGrid(const double* x, double *y, const size_t nPts){
-	for(size_t i=0;i<nPts;i++){
-		y[i]=x[i];
-	}
-}
-
-int initializeGrid(UserGrid grid){
-	grid->nPts=maxPoints(grid->basePts,
-			     &grid->a,
-			     &grid->w,
-			     &grid->mag,
-			     &grid->leftFac,
-			     &grid->rightFac,
-			     &grid->refineLeft,
-			     &grid->refineRight);
-	printf("nPts: %ld\n",grid->nPts);
-	grid->leastMove=grid->w;
-
-	grid->x    = new double [grid->nPts];
-	grid->xOld = new double [grid->nPts];
-	for (size_t i = 0; i < grid->nPts; i++) {
-		grid->x[i]=0.0e0;
-		grid->xOld[i]=0.0e0;
-	}
-	return(0);
-}
-
-int getGridSettings(FILE *input, UserGrid grid){
-
-	int ier=0;
-
-	ier=parseNumber<size_t>(input, "basePts"	, MAXBUFLEN, &grid->basePts);
-	if(ier==-1)return(-1);
-
-	ier=parseNumber<double>(input, "gridDensitySlope", MAXBUFLEN, &grid->a);
-	if(ier==-1)return(-1);
-
-	ier=parseNumber<double>(input, "fineGridHalfWidth", MAXBUFLEN, &grid->w);
-	if(ier==-1)return(-1);
-
-	ier=parseNumber<double>(input, "gridRefinement", MAXBUFLEN, &grid->mag);
-	if(ier==-1)return(-1);
-
-	ier=parseNumber<double>(input, "leftRefineFactor", MAXBUFLEN, &grid->leftFac);
-	if(ier==-1)return(-1);
-
-	ier=parseNumber<double>(input, "rightRefineFactor", MAXBUFLEN, &grid->rightFac);
-	if(ier==-1)return(-1);
-
-	ier=parseNumber<int>(input, "refineLeft"	, MAXBUFLEN, &grid->refineLeft);
-	if(ier==-1)return(-1);
-
-	ier=parseNumber<int>(input, "refineRight"	, MAXBUFLEN, &grid->refineRight);
-	if(ier==-1)return(-1);
-
-	ier=parseNumber<double>(input, "position"	, MAXBUFLEN, &grid->position);
-	if(ier==-1)return(-1);
-
-	return(0);
-}
-
diff --git a/gridRoutines.d b/gridRoutines.d
deleted file mode 100644
index 80fc6ad..0000000
--- a/gridRoutines.d
+++ /dev/null
@@ -1 +0,0 @@
-gridRoutines.o: gridRoutines.cpp gridRoutines.h parse.h parse.hpp
diff --git a/gridRoutines.h b/gridRoutines.h
deleted file mode 100644
index 9352fd7..0000000
--- a/gridRoutines.h
+++ /dev/null
@@ -1,89 +0,0 @@
-#include "parse.h"
-
-#ifndef GSL_DEF
-#define GSL_DEF
-#include <gsl/gsl_math.h>
-#include <gsl/gsl_spline.h>
-#endif
-
-#ifndef GRID_DEF
-#define GRID_DEF
-
-typedef struct gridTag{
-
-	size_t basePts;
-	size_t nPts;
-	double position;
-	double leastMove;
-	double a;
-	double w;
-	double mag;
-	double leftFac;
-	double rightFac;
-	int refineLeft;
-	int refineRight;
-	double* x;
-	double* xOld;
-
-} *UserGrid;
-
-inline double l(const double* x, 
-	 	const double* a,
-	 	const double* w,
-		const double* fac,
-		const int* refineLeft);
-
-//inline double l(const double* x, 
-//	 	const double* a,
-//        const double* c,
-//	 	const double* w,
-//		const double* fac,
-//		const int* refineLeft);
-
-inline double r(const double* x, 
-		const double* a, 
-		const double* w,
-		const double* fac,
-		const int* refineRight);
-
-inline double f(const double* x,
-		const double* a,
-		const double* c,
-		const double* w);
-
-inline double g(const double* x, 
-		const double* a, 
-		const double* c, 
-		const double* w);
-
-inline double rho(const double* x,
-	   	  const double* a,
-	   	  const double* c,
-	   	  const double* w,
-	   	  const double* mag,
-	   	  const double* leftFac,
-	   	  const double* rightFac,
-		  const int* refineLeft,
-		  const int* refineRight);
-
-size_t maxPoints(const size_t basePts,
-	   	 const double* a,
-	   	 const double* w,
-	   	 const double* mag,
-	   	 const double* leftFac,
-	   	 const double* rightFac,
-	   	 const int* refineLeft,
-	   	 const int* refineRight);
-
-
-double safePosition(double c, double w);
-
-int reGrid(UserGrid grid, double position);
-
-void storeGrid(const double* x, double *y, const size_t nPts);
-
-int initializeGrid(UserGrid grid);
-
-int getGridSettings(FILE *input, UserGrid grid);
-
-#endif
diff --git a/gridRoutines.o b/gridRoutines.o
deleted file mode 100644
index b397aa2..0000000
Binary files a/gridRoutines.o and /dev/null differ
diff --git a/include/UserData.h b/include/UserData.h
index a5b8acb..5f21874 100644
--- a/include/UserData.h
+++ b/include/UserData.h
@@ -34,11 +34,13 @@ typedef struct UserDataTag{
 	/* Current version only support single and binary component(s) droplet */
 	int dropType;
 	/* Droplet species gamma using UNIFAC method */
-	double gamma[2]; 
-	/* Droplet species composition */
+	std::vector<double> gamma; 
+	/* Droplet species composition, C3H8,n-C7H16,etc.*/
 	std::vector<std::string> dropSpec;
+	/*droplet initial species mole fractions*/
 	std::vector<double> dropMole; 
-    //char dropSpec[2][10] = {"propane","n-heptane"};
+	/*droplet species molecular weight*/
+	std::vector<double> MW;
 
 	/* Droplet species mole fractions */
     //double dropMoleFrac[2];
@@ -55,8 +57,10 @@ typedef struct UserDataTag{
 	/*metric=0:Planar*/			  
 	/*metric=1:Cylindrical*/			  
 	/*metric=2:Spherical*/			  
-	int metric;		  
-	/*No: of species:*/
+	int metric;	
+	/* Gas phase relevent #s and Pointer index */	
+	/* Variables to be solved in the gas phase: T,Yi,r,P,mdot */  
+	/*No: of species in the gas phase:*/
 	size_t nsp;	  
 	/*No: of equations:*/
 	size_t neq;
@@ -73,6 +77,25 @@ typedef struct UserDataTag{
 	size_t np;
 	/*Pointer index for mass flow rate:*/
 	size_t nm;
+
+	/*No: of species in the liquid phase:*/
+//	size_t l_nsp;
+	// /*No: of equations:*/
+	// size_t l_neq;
+	// /*No: of variables:*/
+	// size_t l_nvar;
+	// /*Pointer indices (see "macros.h" for aliases that use these):*/
+	// /*Pointer index for temperature:*/
+	// size_t l_nt;	  
+	// /*Pointer index for species:*/
+	// size_t l_ny;
+	// /*Pointer index for spatial coordinate:*/
+	// size_t l_nr;
+	// /*Pointer index for pressure:*/
+	// size_t l_np;
+	// /*Pointer index for mass flow rate:*/
+	// size_t l_nm;
+
 	/*Species index of bath gas:*/			  
 	size_t k_bath;		  
 	/*Species index of oxidizer:*/			  
@@ -81,7 +104,8 @@ typedef struct UserDataTag{
 	size_t k_HO2;
 	/*Species index of droplet composition*/
     /*Index starts with 1 instead of 0*/
-	size_t k_drop[2];
+	/*Similar to dropMole and dropSpec,size of k_drop should be based on droplet type*/
+	std::vector<size_t> k_drop;
 	/*User-defined mass flux (kg/m^2/s):*/			  
 	double mdot;
 	/*Flag to solve isobaric/isochoric problem;*/
@@ -195,6 +219,10 @@ typedef struct UserDataTag{
 	double Rg;
 	/*Total number of points for grid:*/
 	size_t npts;
+	/*Number of points for liquid phase:*/
+	size_t l_npts; 
+	/*Number of points for gas phase:*/
+	size_t g_npts;
 
 	double gridOffset;
 
@@ -236,5 +264,5 @@ void setSaneDefaults(UserData data);
 void freeUserData(UserData data);
 #endif
 
-void getGamma(const double mole[],double gamma[]) ;
+void getGamma(const std::vector<double>& mole,std::vector<double>& gamma) ;
 
diff --git a/include/parse.h b/include/parse.h
index 92aebf0..ff42390 100644
--- a/include/parse.h
+++ b/include/parse.h
@@ -1,3 +1,5 @@
+#pragma once
+
 #ifndef PRINT_DEF
 #define PRINT_DEF
 #include <string.h>	//for strings
@@ -12,7 +14,7 @@
 #include <vector>
 #include <sstream>
 
-#ifndef PARSE_DEF	```
+#ifndef PARSE_DEF
 #define PARSE_DEF
 #define MAXBUFLEN 200
 
@@ -30,12 +32,101 @@ template<typename T>
 int parseArray(FILE* input, const char* keyword, const size_t bufLen,
 		const size_t arrLen, T y[]);
 
+//
+///*template function for parsing initial mole fraction in the droplet*/
+//template<typename T>
+//int parseDropSpec(FILE* input, const char* keyword, const size_t bufLen,const int* dropType, std::vector<T>& dropPara){
+//    char buf[bufLen];
+//    char buf1[bufLen];
+//    char comment[1];
+//    char *ret;
+//
+//    while (fgets(buf,bufLen, input)!=NULL){
+//        comment[0]=buf[0];
+//        if(strncmp(comment,"#",1)==0){
+//            //printf("Comment!:%s\n",buf);
+//        }
+//        else{
+//            ret=strtok(buf,"=");
+//            if(strcmp(ret,keyword)==0){
+//                /*offset buf by keyword size + 1 for the "="*/
+//                /* Second argument in the strncpy function is the address !!! */
+//                /* Note: current version of code can only take dropType =0 or 1 */
+//                strncpy(buf1, buf+strlen(keyword)+1, bufLen);
+//                printf("%10s: ",keyword);
+//                if(*dropType ==0){
+//                    /* Convert from char* to double */
+////                    std::string str(buf1);
+////                    dropPara.push_back(str);
+//                    T temp_num = std::stod(buf1) ;
+//                    dropPara.push_back(temp_num) ;
+//                    printf("%.3f\n",dropPara[0]);
+//                }else{
+//                    std::istringstream iss(buf1) ;
+//                    std::string token;
+//                    while(std::getline(iss,token,',')){
+//                        T temp_num = std::stod(token);
+//                        dropPara.push_back(temp_num);
+//                    }
+//                    printf("%.3f,%.3f\n",dropPara[0],dropPara[1]);
+//                }
+//                rewind(input);
+//                return(0);
+//            }
+//        }
+//    }
+//    rewind(input);
+//    return(-1);
+//}
 
-template<typename T> 
-int parseDropSpec(FILE* input, const char* keyword, const size_t bufLen,int* dropType, std::vector<T>& dropPara);
+/* Extract the droplet species and molefractions from input file using template */
+/* Generic template function */
+//template<typename T>
+//int parseDropSpec(FILE* input, const char* keyword, const size_t bufLen,const int* dropType, std::vector<T>& dropPara){
+//    char buf[bufLen];
+//    char buf1[bufLen];
+//    char comment[1];
+//    char *ret;
+//    T* n;
+//
+//    while (fgets(buf,bufLen, input)!=NULL){
+//        comment[0]=buf[0];
+//        if(strncmp(comment,"#",1)==0){
+//            //printf("Comment!:%s\n",buf);
+//        }
+//        else{
+//            ret=strtok(buf,"=");
+//            if(strcmp(ret,keyword)==0){
+//                /*offset buf by keyword size + 1 for the "="*/
+//                /* Second argument in the strncpy function is the address !!! */
+//                /* Note: current version of code can only take dropType =0 or 1 */
+//                strncpy(buf1, buf+strlen(keyword)+1, bufLen);
+//                printf("%10s: ",keyword);
+//                if(*dropType ==0){
+//                    getFromString(buf1,n);
+//                    dropPara.push_back(*n);
+//                }else{
+//                    std::istringstream iss(buf1) ;
+//                    std::string token;
+//                    while(std::getline(iss,token,',')){
+//                        T arg = std::stod(token);
+//                        dropPara.push_back(arg);
+//                    }
+//                    printf("%15.6e,%15.6e\n",dropPara[0],dropPara[1]);
+//                }
+//                rewind(input);
+//                return(0);
+//            }
+//        }
+//    }
+//    rewind(input);
+//    return(-1);
+//}
 
-template<> 
-int parseDropSpec<std::string>(FILE* input, const char* keyword, const size_t bufLen,int* dropType, std::vector<std::string>& dropPara);
+//
+///* Specialization for string */
+//template<>
+//int parseDropSpec<std::string>(FILE* input, const char* keyword, const size_t bufLen,const int* dropType, std::vector<std::string>& dropPara);
 
 int parseDrop(FILE* input, const char* keyword,char dropSpec[][10],double dropMole[],const size_t bufLen);
 
diff --git a/include/parse.hpp b/include/parse.hpp
index 247ab60..52363ca 100644
--- a/include/parse.hpp
+++ b/include/parse.hpp
@@ -1,3 +1,5 @@
+#pragma once
+
 template<typename T>
 int parseNumber(FILE* input, const char* keyword, const size_t bufLen, T* n){
 
@@ -83,7 +85,7 @@ int parseDropSpec(FILE* input, const char* keyword, const size_t bufLen,const in
     char buf1[bufLen];
     char comment[1];
     char *ret;
-    T* n;
+    T n;
 
     while (fgets(buf,bufLen, input)!=NULL){
         comment[0]=buf[0];
@@ -99,8 +101,8 @@ int parseDropSpec(FILE* input, const char* keyword, const size_t bufLen,const in
                 strncpy(buf1, buf+strlen(keyword)+1, bufLen);
                 printf("%10s: ",keyword);
                 if(*dropType ==0){
-                    getFromString(buf1,n);
-                    dropPara.push_back(*n);
+                    getFromString(buf1,&n);
+                    dropPara.push_back(n);
                 }else{
                     std::istringstream iss(buf1) ;
                     std::string token;
@@ -108,7 +110,7 @@ int parseDropSpec(FILE* input, const char* keyword, const size_t bufLen,const in
                         T arg = std::stod(token);
                         dropPara.push_back(arg);
                     }
-                    printf("%15.6e,%15.6e\n",dropPara[0],dropPara[1]);
+                    printf("%.3f,%.3f\n",dropPara[0],dropPara[1]);
                 }
                 rewind(input);
                 return(0);
@@ -121,5 +123,52 @@ int parseDropSpec(FILE* input, const char* keyword, const size_t bufLen,const in
 
 /* Specialization for string */
 template<>
-int parseDropSpec<std::string>(FILE* input, const char* keyword, const size_t bufLen,const int* dropType, std::vector<std::string>& dropPara);
+inline int parseDropSpec<std::string>(FILE* input, const char* keyword, const size_t bufLen,const int* dropType, std::vector<std::string>& dropPara){
+    char buf[bufLen];
+    char buf1[bufLen];
+    char comment[1];
+    char *ret;
 
+    while (fgets(buf,bufLen, input)!=NULL){
+        buf[strlen(buf)-1] = '\0' ;
+        comment[0]=buf[0];
+        if(strncmp(comment,"#",1)==0){
+            //printf("Comment!:%s\n",buf);
+        }
+        else{
+            ret=strtok(buf,"=");
+            if(strcmp(ret,keyword)==0){
+                /*offset buf by keyword size + 1 for the "="*/
+                /* Second argument in the strncpy function is the address !!! */
+                /* Note: current version of code can only take dropType =0 or 1 */
+                strncpy(buf1, buf+strlen(keyword)+1, bufLen);
+                printf("%10s: ",keyword);
+                if(*dropType ==0){
+                    /* Convert from char* to string */
+                    //printf("buf1 is %s!\n",buf1) ;
+                    std::string str;
+                    for(int i=0;i< strlen(buf1);i++){
+                        if(buf1[i] != ' '){
+                            str += buf1[i] ;
+                        }
+                    }
+//                    printf("str is :%s!\n",str.c_str()) ;
+                    dropPara.push_back(str);
+                    printf("%s.\n",dropPara[0].c_str());
+                }else{
+                    std::istringstream iss(buf1) ;
+                    std::string token;
+                    while(std::getline(iss,token,',')){
+                        //std::stod(token);
+                        dropPara.push_back(token);
+                    }
+                    printf("%s!,%s!\n",dropPara[0].c_str(),dropPara[1].c_str());
+                }
+                rewind(input);
+                return(0);
+            }
+        }
+    }
+    rewind(input);
+    return(-1);
+}
diff --git a/include/residue.h b/include/residue.h
index b4e325f..bb122d1 100644
--- a/include/residue.h
+++ b/include/residue.h
@@ -28,6 +28,7 @@
 
 #include "UserData.h"
 #include <vector> //add the vector module
+#include <algorithm>
 
 void REGRID(double* ydata,double* ydotdata,UserData data);
 
@@ -67,11 +68,14 @@ inline double calc_area(double x,int* i);
 void updateSolution(double* y, double* ydot, const size_t nvar,
 		    const double xOld[],const double xNew[],const size_t npts);
 
-void readInitialCondition(FILE* input, double* ydata, const size_t nvar, const size_t nr, const size_t nPts);
+//void readInitialCondition(FILE* input, double* ydata, const size_t nvar, const size_t nr, const size_t nPts);
+
+void readInitialCondition(FILE* input, double* ydata, const size_t nvar, const size_t nr, const size_t nPts, const size_t l_nPts, double Rg);
 
 double systemMass(double* ydata, UserData data);
 
 int initializePsiGrid(double* ydata, double* psidata, UserData data);
+int initializePsiEtaGrid(double* ydata, double* psidata, UserData data);
 
 int setInitialCondition(N_Vector* y, 
 	    		N_Vector* ydot, 
@@ -86,7 +90,10 @@ void getTransport(UserData data,
 		  double *rho,
 		  double *lambda,
 		  double *YV);
-
+void getGasMassFlux(UserData data,
+                    double *ydata,
+                    size_t gridPoint,
+                    double* YV) ;
 int residue(double t, 
 	    N_Vector y, 
 	    N_Vector ydot, 
@@ -97,6 +104,7 @@ void trackFlameOH(N_Vector y,UserData data);
 void trackFlame(N_Vector y,UserData data);
 size_t BathGasIndex(UserData data);
 size_t oxidizerIndex(UserData data);
+size_t specIndex(UserData data,const char *specName); 
 
 inline double Qdot(double* t, 
 	           double* x, 
@@ -123,7 +131,34 @@ void resetTolerance(UserData data, N_Vector* y,N_Vector* atolv);
 void getReactions(UserData data,N_Vector* y,FILE* output);
 void getSpecies(UserData data,N_Vector* y,FILE* output);
 
-double getLiquidRho(double dropMole[],double temp,double pres);
-double getLiquidCp(double dropMole[],double temp,double pres);
-double getLiquidHv(double dropMole[],double temp,double pres);
-double getLiquidMaxT(double dropMole[],double pres);
\ No newline at end of file
+//double getLiquidRho(double dropMole[],double temp,double pres);
+//double getLiquidCp(double dropMole[],double temp,double pres);
+//double getLiquidHv(double dropMole[],double temp,double pres);
+//double getLiquidMaxT(double dropMole[],double pres);
+
+double getLiquidDensity(const double temp,const double pres, const std::vector<std::string>& composition);
+double getLiquidDensity(const double temp,const double pres, std::vector<std::string>& composition,const std::vector<double>& mole);
+
+double getLiquidCond(const double temp,const double pres, const std::vector<std::string>& composition);
+double getLiquidCond(const double temp,const double pres, std::vector<std::string>& composition,const std::vector<double>& mole);
+
+double getLiquidCpb(const double temp,const double pres, const std::vector<std::string>& composition);
+double getLiquidCpb(const double temp,const double pres, const std::vector<std::string>& composition,const std::vector<double>& mole);
+
+std::vector<double> getLiquidCp(const double temp, const double pres, const std::vector<std::string> &composition);
+double getGasCond(UserData data, double *ydata, size_t gridPoint);
+std::vector<double> getLiquidVH(const double pres,const int dropType);
+
+void mass2mole(const std::vector<double>& mass,std::vector<double>& mole, UserData data);
+
+double getLiquidmassdiff(UserData data, double* ydata, size_t gridPoint,const double temp);
+std::vector<double> getLiquidmassvec(UserData data,double* ydata,int gridPoint);
+std::vector<double> getLiquidmolevec(UserData data,double* ydata,int gridPoint);
+std::vector<std::string> components(int dropType);
+
+std::vector<double> getVapPressure(UserData data, double* ydata,int gridPoint,const std::vector<double> mole_);
+
+double dropletmass(UserData data,double* ydata);
+
+void printIddata(UserData data, double* iddata);
+void printPsidata(UserData data,double* psidata);
diff --git a/include/timing.hpp b/include/timing.hpp
index e07e3eb..18a8d9b 100644
--- a/include/timing.hpp
+++ b/include/timing.hpp
@@ -39,6 +39,7 @@ double get_wall_time(){
     }
     return (double)time.tv_sec + (double)time.tv_usec * .000001;
 }
+
 double get_cpu_time(){
     return (double)clock() / CLOCKS_PER_SEC;
 }
diff --git a/lagrangianCombustion2 b/lagrangianCombustion2
deleted file mode 100755
index 78125e7..0000000
Binary files a/lagrangianCombustion2 and /dev/null differ
diff --git a/macros.h b/macros.h
deleted file mode 100644
index bcfbc8c..0000000
--- a/macros.h
+++ /dev/null
@@ -1,80 +0,0 @@
-#ifndef MACRO_DEF
-#define MACRO_DEF
-//#define SUNDIALS_DOUBLE_PRECISION 1
-//#define SUNDIALS_SINGLE_PRECISION 1
-
-#define ZERO  RCONST(0.0)
-#define HALF  RCONST(0.5)
-#define ONE   RCONST(1.0)
-#define TWO   RCONST(2.0)
-#define THREE RCONST(3.0)
-#define FOUR  RCONST(4.0)
-#define TEN   RCONST(10.0)
-
-/* In order to keep begin the index numbers from 1 instead of 0, we define
- * macros here. Also, we define macros to ease referencing various variables in
- * the sundials nvector.
- */
-#define WORK(i) WORK[i-1]
-#define XNEW(i) XNEW[i-1]
-
-#define psi(i)   psidata[i-1]
-
-#define T(i)    ydata[((i-1)*data->nvar)+data->nt]
-#define Y(i,k)  ydata[((i-1)*data->nvar)+data->ny+k-1]
-#define R(i)    ydata[((i-1)*data->nvar)+data->nr]
-#define P(i)    ydata[((i-1)*data->nvar)+data->np]
-#define Mdot(i) ydata[((i-1)*data->nvar)+data->nm]
-
-#define Tdot(i)    ydotdata[((i-1)*data->nvar)+data->nt]
-#define Ydot(i,k)  ydotdata[((i-1)*data->nvar)+data->ny+k-1]
-#define Rdot(i)    ydotdata[((i-1)*data->nvar)+data->nr]
-#define Pdot(i)    ydotdata[((i-1)*data->nvar)+data->np]
-#define Mdotdot(i) ydotdata[((i-1)*data->nvar)+data->nm]
-
-#define Tres(i)    resdata[((i-1)*data->nvar)+data->nt]
-#define Yres(i,k)  resdata[((i-1)*data->nvar)+data->ny+k-1]
-#define Rres(i)    resdata[((i-1)*data->nvar)+data->nr]
-#define Pres(i)    resdata[((i-1)*data->nvar)+data->np]
-#define Mdotres(i) resdata[((i-1)*data->nvar)+data->nm]
-
-#define Tid(i)    iddata[((i-1)*data->nvar)+data->nt]
-#define Yid(i,k)  iddata[((i-1)*data->nvar)+data->ny+k-1]
-#define Rid(i)    iddata[((i-1)*data->nvar)+data->nr]
-#define Pid(i)    iddata[((i-1)*data->nvar)+data->np]
-#define Mdotid(i) iddata[((i-1)*data->nvar)+data->nm]
-
-#define Yav(i) Yav[i-1]
-#define YAvg(i) YAvg[i-1]
-#define YVmhalf(i) YVmhalf[i-1]
-#define YVphalf(i) YVphalf[i-1]
-#define X(i) X[i-1]
-#define Xp(i) Xp[i-1]
-#define Xgradhalf(i) Xgradhalf[i-1]
-#define XLeft(i) XLeft[i-1]
-#define XRight(i) XRight[i-1]
-#define gradX(i) gradX[i-1]
-#define wdot(i) wdot[i-1]
-#define enthalpy(i) enthalpy[i-1]
-#define energy(i) energy[i-1]
-#define Cp(i) Cp[i-1]
-
-#define atolT(i)   atolvdata[((i-1)*data->nvar)+data->nt]
-#define atolY(i,k)   atolvdata[((i-1)*data->nvar)+data->ny+k-1]
-#define atolR(i)   atolvdata[((i-1)*data->nvar)+data->nr]
-#define atolP(i)   atolvdata[((i-1)*data->nvar)+data->np]
-#define atolMdot(i)   atolvdata[((i-1)*data->nvar)+data->nm]
-
-
-#define constraintsY(i,k)   constraintsdata[((i-1)*data->nvar)+data->ny+k-1]
-#define constraintsR(i)   constraintsdata[((i-1)*data->nvar)+data->nr]
-
-/*Following marcos are defined to calculate the characteristic time-scale */
-#define wdot_mole(i)    wdot_mole[i-1]
-#define wdot_mass(i)    wdot_mass[i-1]
-#define MW(i)         MW[i-1]
-#define time_scale(i,k)    time_scale[(i-1)*data->nsp+k-1]
-#define concentra(i)     concentra[i-1]
-
-
-#endif
diff --git a/main.cpp b/main.cpp
deleted file mode 100644
index ab0e15f..0000000
--- a/main.cpp
+++ /dev/null
@@ -1,491 +0,0 @@
-/*
- _____ ___  ____   ____ 
-|_   _/ _ \|  _ \ / ___|
-  | || | | | |_) | |    
-  | || |_| |  _ <| |___ 
-  |_| \___/|_| \_\\____|
-                        
-*/
-
-#include "UserData.h"
-#include "solution.h"
-#include "residue.h"
-#include "macros.h"
-#include "timing.h"
-
-#include <ida/ida.h>
-#include <ida/ida_direct.h>
-#include <sunmatrix/sunmatrix_band.h>
-#include <sunlinsol/sunlinsol_lapackband.h>
-//#include <ida/ida_band.h>
-
-static int check_flag(void *flagvalue, 
-		      const char *funcname, 
-		      int opt);
-
-void freeAtLast(void* mem, N_Vector *y, 
-		N_Vector *ydot, 
-		N_Vector *res, 
-		N_Vector *id, 
-		N_Vector *atolv,
-		N_Vector *constraints,UserData data);
-
-int main(){
-
-	// Read input file specifying the details of the case and store them
-  	FILE *input;input=fopen("input.dat","r");
-  	UserData data;data=NULL;data=allocateUserData(input);
-	fclose(input);
-	data->clockStart=get_wall_time();
-
-
-//     /**************** TEST THE xOld *******************/
-//     double* ptr1 = data->grid->xOld ; 
-//     printf("After allocateUserData in main.cpp,Start print the first 5 elements of the xOld array : \n");
-//     printf("1st:%.6f, 2nd:%.6f, 3rd:%.6f, 4th:%.6f, 5th:%.6f.\n",ptr1[0],ptr1[1],ptr1[2],ptr1[3],ptr1[4]);
-
-	if(data==NULL){
-		printf("check input file!\n");
-  		freeUserData(data);
-		return(-1);
-	}
-
-	// Allocate solution variables
-	long int ier,mu,ml,count,netf,ncfn,njevals,nrevals;
-	realtype tNow,*atolvdata,*constraintsdata,finalTime,dtMax,tolsfac;
-
-
-  	N_Vector y,ydot,id,res,atolv,constraints;
-  	y=ydot=id=res=atolv=constraints=NULL;
- 	ier=allocateSolution(data->neq,data->nThreads,&y,&ydot,&id,&res,&atolv,&constraints);
-	ier=setAlgebraicVariables(&id,data);
-
-
-//     /**************** TEST THE xOld *******************/
-//     double* ptr2 = data->grid->xOld ; 
-//     printf("Before setInitialCondition in main.cpp,Start print the first 5 elements of the xOld array : \n");
-//     printf("1st:%.6f, 2nd:%.6f, 3rd:%.6f, 4th:%.6f, 5th:%.6f.\n",ptr2[0],ptr2[1],ptr2[2],ptr2[3],ptr2[4]);
-
-	ier=setInitialCondition(&y,&ydot,data);
-	if(ier==-1)return(-1);
-	tNow=data->tNow;
-	finalTime=data->finalTime;
-	//TODO: dtMax should be a user input
-	dtMax = 1e-4;
-
-	double* ydata;
-	double* ydotdata;
-  	ydata    = N_VGetArrayPointer_OpenMP(y);
-  	ydotdata = N_VGetArrayPointer_OpenMP(ydot);
-	////////// DEBUG ///////////////////
-	//double* resdata;
-	//double* iddata;
-	//resdata = N_VGetArrayPointer_OpenMP(res);
-	//iddata = N_VGetArrayPointer_OpenMP(id);
-	///////////////////////////////////
-
-	void *mem;mem=NULL;mem = IDACreate();
-  	ier = IDASetUserData(mem, data);
-  	ier = IDASetId(mem, id);
-  	ier = IDAInit(mem, residue, tNow, y, ydot);
-
-        // Atol array
-        atolvdata = N_VGetArrayPointer_OpenMP(atolv);
-	for (size_t i = 1; i <=data->npts; i++) {
-             atolT(i) = data->temperatureTolerance;
-             for (size_t k = 1; k <=data->nsp; k++) {
-		     	if(k!=data->k_bath){
-                		atolY(i,k) = data->massFractionTolerance;
-			}
-			else{
-                		atolY(i,k) = data->bathGasTolerance;
-			}
-
-             }
-             atolR(i) = data->radiusTolerance;
-             atolP(i) = data->pressureTolerance;
-			 atolMdot(i) = data->MdotTolerance;
-	}
-  	ier = IDASVtolerances(mem, data->relativeTolerance, atolv);
-
-  	mu = 2*data->nvar; ml = mu;
-	SUNMatrix A; A=NULL;
-	A=SUNBandMatrix(data->neq,mu,ml,mu+ml);
-	SUNLinearSolver LS; LS=NULL;
-	//LS=SUNBandLinearSolver(y,A);
-	LS=SUNLapackBand(y,A);
-	ier=IDADlsSetLinearSolver(mem,LS,A);
-  	//ier = IDABand(mem, data->neq, mu, ml);
-
-        constraintsdata = N_VGetArrayPointer_OpenMP(constraints);
-	if(data->setConstraints){
-		for (size_t i = 1; i <=data->npts; i++) {
-             		for (size_t k = 1; k <=data->nsp; k++) {
-             		   constraintsY(i,k) = ONE;
-             		}
-		}
-  		ier=IDASetConstraints(mem, constraints);
-	}
-	
-	if(!data->quasiSteady){
-		constraintsR(1) = ONE;
-		ier=IDASetConstraints(mem, constraints);
-	}
-
-	ier = IDASetSuppressAlg(mem, data->suppressAlg);
-  	if(check_flag(&ier, "IDASetSuppressAlg", 1)) return(1);
-
-	//ier= IDASetMaxNumStepsIC(mem, 1);
-	//ier= IDASetMaxNumJacsIC(mem,8);
-	//ier= IDASetMaxNumItersIC(mem,100);
-	//ier= IDASetMaxBacksIC(mem,2000);
-	//ier = IDASetLineSearchOffIC(mem,SUNTRUE);
-
-	//////// DEBUG ///////////
-	//if(data->dryRun){
-    //	ier = residue(tNow,y, ydot, res, data);
-	//	for(size_t k=0; k < data->nvar*data->npts; k++){
-	//		printf("%i: %15.6e\n",k,resdata[k]);
-	//	}
-	//	for(size_t k=0; k < data->nvar*data->npts; k++){
-	//		if(iddata[k] == 1){
-	//			ydotdata[k] = -resdata[k];
-	//		}
-	//	}
-    //	ier = residue(tNow,y, ydot, res, data);
-	//	for(size_t k=0; k < data->nvar*data->npts; k++){
-	//		printf("%i: %15.6e\n",k,resdata[k]);
-	//	}
-	//}
-	//for(size_t k=0; k < data->neq; k++){
-	//	if(iddata[k] == 1){
-	//		ydotdata[k] = -resdata[k];
-	//	}
-	//}
-	//////////////////////////
-	
-	if(!data->dryRun){
-		printf("Calculating Initial Conditions:\n");
-		printf("Cross your fingers...\n");
-
-  		ier = IDACalcIC(mem, IDA_YA_YDP_INIT, 1e-5*finalTime);
-
-		//If at first IDACalcIC doesn't succeed, try, try, try again:
-		for (int i = 0; i < 10; i++) {
-  			ier = IDACalcIC(mem, IDA_YA_YDP_INIT, (1e-01+pow(10,i)*finalTime));
-
-            /*************  Print the #of iterations ************/
-            //printf("This the %dth try of calculating initial conditions. \n",i);
-
-			if(ier==0){
-				break;
-			}
-		}
-
-		//...or else cry again :(
-  		if(check_flag(&ier, "IDACalcIC", 1)){
-			freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
-		       	return(-1);
-		}else{
-			printf("Initial (Consistent) Conditions Calculated!\n");
-		}
-		ier = IDASetInitStep(mem,1e-12);
-	}
-
-	printSpaceTimeHeader(data);
-	printGlobalHeader(data);
-	printTimescaleHeader(data);
-	printSpaceTimeOutput(tNow, &y, data->output, data);
-	printSpaceTimeOutput(tNow, &y, data->gridOutput, data);
-
-//    getTimescale(data,&y) ; 
-//	printTimescaleOutput(tNow, &y, data->timescaleOutput,data);
-	
-
-	if(!data->dryRun){
-		count=0;
-		double dt=1e-08;
-		double t1=0.0e0;
-		double xOld=0.0e0;
-		double x=0.0e0;
-		double dx=0.0e0;
-		double dxMin=1.0e0;
-		double dxRatio=dx/dxMin;
-		int move=0;
-		int kcur=0;
-        int RGCOUNT=0;
-        size_t ii=0;
-		if(data->adaptiveGrid){
-			dxMin=data->grid->leastMove;
-			xOld=maxCurvPosition(ydata, data->nt, data->nvar,
-					     data->grid->x, data->npts);
-			//xOld=isothermPosition(ydata, data->isotherm, data->nt, 
-	        //        		   data->nvar, data->grid->x, data->npts);
-		}
-		while (tNow<=finalTime && R(1)>100e-9) {
-			t1=tNow;
-            
-            /*Floor small value to zero*/
-            floorSmallValue(data, &y);
-            
-
-			if(data->quasiSteady){
-  				ier = IDASolve(mem, finalTime, &tNow, y, ydot, IDA_ONE_STEP);
-			}else{
-				/*This prevents the solver from taking a step so large that
-				 *the droplet radius becomes negative.
-				 *TODO:Try adding the constraint that the droplet radius must
-				 *     be a positive number*/
-  				ier = IDASolve(mem, tNow+dtMax, &tNow, y, ydot, IDA_ONE_STEP);
-  				//ier = IDASolve(mem, tNow+dtMax, &tNow, y, ydot, IDA_NORMAL);
-			}
-
-  			if(check_flag(&ier, "IDASolve", 1)){
-				freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
-		       		return(-1);
-			}
-			dt=tNow-t1;
-  			ier = IDAGetCurrentOrder(mem, &kcur);
-
-            /******** Print the max Temperature *********/
-            double maxT = 0.00; 
-            maxT = maxTemperature(ydata,data->nt,data->nvar,data->npts);
-            printf("Maximum temperature is : %.3f[K] \n",maxT);
-
-			if(data->adaptiveGrid==1 && data->moveGrid==1){
-				x=maxCurvPosition(ydata, data->nt, data->nvar,
-						  data->grid->x, data->npts);
-				//x=isothermPosition(ydata, data->isotherm, data->nt, 
-	            //    			   data->nvar, data->grid->x, data->npts);
-
-				//x=maxGradPosition(ydata, data->nt, data->nvar,
-				//		  data->grid->x, data->npts);
-				dx=x-xOld;
-
-				if(dx*dxMin>0.0e0){
-					move=1;
-				}else{
-					move=-1;
-				}
-
-				//if(fabs(dx)>=dxMin && x+(double)(move)*0.5e0*dxMin<=1.0e0){
-				dxRatio=fabs(dx/dxMin);
-                
-                /************ Print xOld, x,dx,dxMin,dxRatio ******************/
-                printf("xOld = %.6f, x = %.6f,",xOld,x);
-                printf("dx = %.6f, dxMin = %.6f, dxRatio = %.3f\n",dx,dxMin,dxRatio); 
-
-				if(dxRatio>=1.0e0 && dxRatio<=2.0e0){
-					printf("Regridding!\n");
-
-					data->regrid=1;
-					printSpaceTimeOutput(tNow, &y, data->gridOutput, data);
-
-					ier=reGrid(data->grid, x+(double)(move)*0.5e0*dxMin);
-					if(ier==-1){
-						freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
-						return(-1);
-					}
-
-					updateSolution(ydata, ydotdata, data->nvar,
-					               data->grid->xOld,data->grid->x,data->npts);
-					storeGrid(data->grid->x,data->grid->xOld,data->npts);
-					xOld=x;
-
-					printf("Regrid Complete! Restarting Problem at %15.6e s\n",tNow);
-					ier = IDAReInit(mem, tNow, y, ydot);
-  					if(check_flag(&ier, "IDAReInit", 1)){
-						freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
-		       				return(-1);
-					}
-					ier = IDASetInitStep(mem,1e-01*dt);
-					printf("Reinitialized! Calculating Initial Conditions:\n");
-					printf("Cross your fingers...\n");
-  					ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+1e-01*dt);
-  					if(check_flag(&ier, "IDACalcIC", 1)){
-  						ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+1e+01*dt);
-					}
-					//Every once in a while, for reasons
-					//that befuddle this mathematically
-					//lesser author, IDACalcIC fails. Here,
-					//I desperately try to make it converge
-					//again by sampling increasingly larger
-					//time-steps:
-					for (int i = 0; i < 10; i++) {
-  						ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+(1e-01+pow(10,i)*dt));
-						if(ier==0){
-							break;
-						}
-					}
-					//Failure :( Back to the drawing board:
-  					if(check_flag(&ier, "IDACalcIC", 1)){
-						freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
-		       				return(-1);
-					}
-					printf("Initial (Consistent) Conditions Calculated!\n");
-					printf("------------------------------------------\n\n");
-					if(data->writeEveryRegrid){
-						printSpaceTimeOutput(tNow, &y, data->output, data);
-						FILE* fp;
-						fp=fopen("restart.bin","w");
-						writeRestart(tNow, &y, &ydot, fp, data);
-						fclose(fp);
-					}
-
-				}
-			}
-            
-            /*reset the tolerance after ignition*/
-            //resetTolerance(data,&y,&atolv);
-            
-            /*regrid and update the solution based on R,re-initialize the problem*/
-            /*For the time being,we only allow TORC to REGRID once for each run*/
-            
-            if(data->JJRG ==1 && (maxT >= data->initialTemperature+data->deltaT)){
-               if(RGCOUNT<1){
-                RGCOUNT = RGCOUNT +1;
-                REGRID(ydata,ydotdata,data);
-                initializePsiGrid(ydata,data->uniformGrid,data);
-                printf("REGRID Complete!Restarting Problem at %15.6e s\n",tNow);
-                ier = IDAReInit(mem,tNow,y,ydot);
-                
-                if(check_flag(&ier,"IDAReInit",1)){
-                    freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
-                    return(-1);
-                }
-
-                ier= IDASetInitStep(mem,1e-01*dt);
-                //ier= IDASetInitStep(mem,0.0);
-                printf("Reinitialized!Calculating Initial Conditions:\n");
-                printf("Cross your fingers...\n");
-  			    ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+1e-01*dt);
-  			    if(check_flag(&ier, "IDACalcIC", 1)){
-  			    	ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+1e+01*dt);
-			    }
-			    //Every once in a while, for reasons
-			    //that befuddle this mathematically
-			    //lesser author, IDACalcIC fails. Here,
-			    //I desperately try to make it converge
-			    //again by sampling increasingly larger
-			    //time-steps:
-			    for (int i = 0; i < 10; i++) {
-  			    	ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+(1e-01+pow(10,i)*dt));
-			    	if(ier==0){
-			    		break;
-			    	}
-			    }
-			    //Failure :( Back to the drawing board:
-  			    if(check_flag(&ier, "IDACalcIC", 1)){
-			    	freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
-		        		return(-1);
-			    }
-			    printf("Initial (Consistent) Conditions Calculated!\n");
-			    printf("------------------------------------------\n\n");
-
-                }
-            }
-
-            /*Floor small value to zero*/
-            floorSmallValue(data, &y);
-
-			if(count%data->nSaves==0 && !data->writeEveryRegrid){
-				printSpaceTimeOutput(tNow, &y, data->output, data);
-				//if(data->writeRates){
-				//	printSpaceTimeRates(tNow, ydot, data);
-				//}
-			}
-           
-           /*Get and Print Rxns Rate of Progress and Specie Rate of Production data*/ 
-           /*Following code snippet will be executed only once*/
-           if(ii==0 && maxT >=(data->initialTemperature+data->deltaT)){
-                getReactions(data,&y,data->rxnROPOutput);
-                getSpecies(data,&y,data->spROPOutput);
-                ii++; 
-           }
-//            getTimescale(data,&y);
-//			if(count%data->nSaves==0){
-//				printTimescaleOutput(tNow,&y, data->timescaleOutput,data);
-//				//printSpaceTimeOutput(tNow, &y, data->output, data);
-//				//if(data->writeRates){
-//				//	printSpaceTimeRates(tNow, ydot, data);
-//				//}
-//			}
-
-			/*Print global variables only if time-step is of high order!*/
-			if(data->nTimeSteps==0){
-				data->flamePosition[0]=0.0e0;
-				data->flamePosition[1]=0.0e0;
-				data->flameTime[0]=tNow;
-				data->flameTime[1]=tNow;
-			}
-
-  			ier = IDAGetNumErrTestFails(mem, &netf);
-  			ier = IDAGetNumNonlinSolvConvFails(mem, &ncfn);
-  			ier = IDADlsGetNumJacEvals(mem, &njevals);
-  			ier = IDADlsGetNumResEvals(mem, &nrevals);
-  			printf("etf = %ld ,"
-			       "nlsf= %ld ," 
-			       "J=%ld ,"
-			       "R=%ld ,"
-			       "o=%d ,",netf, ncfn, njevals, nrevals, kcur);
-			printf("Time=%15.6e s,",tNow);
-            printf("dt=%15.6e s,",dt);
-			printf("frac: %15.6e\n",dxRatio);
-			count++;
-			data->nTimeSteps=count;
-		}
-	}
-
-	SUNLinSolFree(LS);
-	SUNMatDestroy(A);
-	freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
-
-	return(0);
-}
-
-void freeAtLast(void* mem, 
-		N_Vector *y, 
-		N_Vector *ydot, 
-		N_Vector *res, 
-		N_Vector *id, 
-		N_Vector *atolv,
-		N_Vector *constraints,UserData data){
-
-  	IDAFree(&mem);
-	freeSolution(y,ydot,res,id,atolv,constraints);
-  	freeUserData(data);
-}
-
-static int check_flag(void *flagvalue, const char *funcname, int opt)
-{
-  int *errflag;
-
-  /* Check if SUNDIALS function returned NULL pointer - no memory allocated */
-  if (opt == 0 && flagvalue == NULL) {
-    fprintf(stderr, 
-            "\nSUNDIALS_ERROR: %s() failed - returned NULL pointer\n\n",
-	    funcname);
-    return(1);
-  }
-
-  /* Check if flag < 0 */
-  else if (opt == 1) {
-    errflag = (int *) flagvalue;
-    if (*errflag < 0) {
-      fprintf(stderr,
-              "\nSUNDIALS_ERROR: %s() failed with flag = %d\n\n",
-	      funcname, *errflag);
-      return(1); 
-    }
-  }
-
-  /* Check if function returned NULL pointer - no memory allocated */
-  else if (opt == 2 && flagvalue == NULL) {
-    fprintf(stderr,
-            "\nMEMORY_ERROR: %s() failed - returned NULL pointer\n\n",
-	    funcname);
-    return(1);
-  }
-
-  return(0);
-}
diff --git a/main.d b/main.d
deleted file mode 100644
index d585097..0000000
--- a/main.d
+++ /dev/null
@@ -1,77 +0,0 @@
-main.o: main.cpp UserData.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/IdealGasMix.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/IdealGasPhase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/ThermoPhase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/Phase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ctexceptions.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/fmt.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ct_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/config.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/format.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/core.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/format-inl.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/format.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/printf.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/ostream.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/ostream.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/Elements.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ct_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/Species.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/AnyMap.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/global.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/AnyMap.inl.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ValueCache.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/MultiSpeciesThermo.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/SpeciesThermoInterpType.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/speciesThermoTypes.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/GasKinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/BulkKinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Kinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/ThermoPhase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/StoichManager.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/stringUtils.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Reaction.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/utilities.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/global.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/RxnRates.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/reaction_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Falloff.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/RateCoeffMgr.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/RxnRates.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/ThirdBodyCalc.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/FalloffMgr.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/reaction_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/FalloffFactory.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/FactoryBase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Reaction.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/importKinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/stringUtils.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportFactory.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportBase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LiquidTransportParams.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportParams.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/numerics/DenseMatrix.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/Array.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/utilities.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LiquidTranInteraction.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LiquidTransportData.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LTPspecies.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportData.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/xml.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ctexceptions.h \
- gridRoutines.h parse.h parse.hpp solution.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_types.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_config.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/nvector/nvector_openmp.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_nvector.h \
- residue.h macros.h timing.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/ida/ida.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/ida/ida_direct.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_direct.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_matrix.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_linearsolver.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_iterative.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sunmatrix/sunmatrix_band.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sunlinsol/sunlinsol_lapackband.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_lapack.h
diff --git a/main.o b/main.o
deleted file mode 100644
index ba7f899..0000000
Binary files a/main.o and /dev/null differ
diff --git a/parse.cpp b/parse.cpp
deleted file mode 100644
index d2e6e9f..0000000
--- a/parse.cpp
+++ /dev/null
@@ -1,79 +0,0 @@
-#include "parse.h"
-void getFromString (const char* buf, int* n){
-	*n=atoi(buf);
-	printf("%d\n",*n);
-}
-
-void getFromString (const char* buf, size_t* n){
-	*n=(size_t)(atoi(buf));
-	printf("%lu\n",*n);
-}
-
-void getFromString (const char* buf, double* n){
-	*n=(double)(atof(buf));
-	printf("%15.6e\n",*n);
-}
-
-void getFromString (const char* buf, char* n){
-	sscanf(buf,"%s",n);
-	printf("%s\n",n);
-}
-
-/*Extract droplet species and mole fractions*/
-int parseDrop(FILE* input, const char* keyword,char dropSpec[][10],double dropMole[],const size_t bufLen){
-	char buf[bufLen];
-    char buf1[bufLen];
-	char comment[1];
-	char *ret;
-	while (fgets(buf,bufLen, input)!=NULL){
-		comment[0]=buf[0];
-		if(strncmp(comment,"#",1)==0){
-		}
-		else{
-            strcpy(buf1,buf); 
-			ret=strtok(buf,"=");
-            //DEBUG
-            //printf("Current KEYWORD in input: %20s \n",ret);
-			if(strcmp(ret,keyword)==0){
-                    char* modifiedFuel = NULL;
-                    char* equalSign = strstr(buf1,"=");
-                    if(equalSign!= NULL){
-                        modifiedFuel = new char [strlen(equalSign)+1];
-                        strcpy(modifiedFuel,equalSign+1);
-                        //DEBUG
-                        //printf("modifiedFuel:%20s \n",modifiedFuel);
-                        char* token = strtok(modifiedFuel,",");
-                        int index = 0 ; 
-                        char* list[2]; 
-                        while(token!= NULL){
-                            //DEBUG
-                            //printf("TOKEN :%20s \n",token);
-                            list[index] = token; 
-                            token = strtok(NULL,",");
-                            index++;
-                        }
-                        //for (int i=0;i<2;i++){
-                        //    printf("%20s",list[i]);
-                        //}
-                        for(int i=0;i<2;i++){
-                            char* name= strtok(list[i],":"); 
-                            char* value = strtok(NULL,":");
-                            //DEBUG
-                           // printf("Name:%10s,Value:%10s \n",name,value);
-                            strcpy(dropSpec[i],name);
-                            dropMole[i]=std::stod(value);
-                           // printf("In the dropArray,Name:%10s,Value:%.3f\n",dropSpec[i],dropMole[i]);
-                        }
-                        delete[] modifiedFuel;
-                   } 
-                   printf("%10s:%10s:%.3f,%10s:%.3f\n",keyword,dropSpec[0],dropMole[0],dropSpec[1],dropMole[1]);
-                   //printf("IF statement is execuated. \n");
-		           rewind(input);
-                   //delete[] modifiedFuel;
-			       return(0);
-            }
-		}
-	}
-	rewind(input);
-	return(-1);
-}
diff --git a/parse.d b/parse.d
deleted file mode 100644
index 7abe434..0000000
--- a/parse.d
+++ /dev/null
@@ -1 +0,0 @@
-parse.o: parse.cpp parse.h parse.hpp
diff --git a/parse.h b/parse.h
deleted file mode 100644
index 894bd12..0000000
--- a/parse.h
+++ /dev/null
@@ -1,36 +0,0 @@
-#ifndef PRINT_DEF
-#define PRINT_DEF
-#include <string.h>	//for strings
-#include <stdio.h>	//for printf,scanf
-#include <stdlib.h>	//for atoi, atof
-#include <string>
-#include <cstring>
-#include <iostream>
-#include <stdexcept>
-#endif
-
-#ifndef PARSE_DEF
-#define PARSE_DEF
-#define MAXBUFLEN 200
-
-void getFromString (const char* buf, int* n);
-void getFromString (const char* buf, size_t* n);
-void getFromString (const char* buf, double* n);
-void getFromString (const char* buf, char* n);
-
-int parseString(FILE* input, const char* keyword, const size_t bufLen, char* n);
-
-template<typename T>
-int parseNumber(FILE* input, const char* keyword, const size_t bufLen, T* n);
-
-template<typename T>
-int parseArray(FILE* input, const char* keyword, const size_t bufLen,
-		const size_t arrLen, T y[]);
-
-int parseDrop(FILE* input, const char* keyword,char dropSpec[][10],double dropMole[],const size_t bufLen);
-
-#include "parse.hpp"
-
-#endif
-
-
diff --git a/parse.hpp b/parse.hpp
deleted file mode 100644
index 6c10a9a..0000000
--- a/parse.hpp
+++ /dev/null
@@ -1,75 +0,0 @@
-template<typename T>
-int parseNumber(FILE* input, const char* keyword, const size_t bufLen, T* n){
-
-	char buf[bufLen];
-	char buf1[bufLen];
-	char comment[1];
-	char *ret;
-
-	while (fgets(buf,bufLen, input)!=NULL){
-		comment[0]=buf[0];
-		if(strncmp(comment,"#",1)==0){
-			//printf("Comment!:%s\n",buf);
-		}
-		else{
-			ret=strtok(buf,"=");
-			if(strcmp(ret,keyword)==0){
-				/*offset buf by keyword size + 1 for the "="*/
-				strncpy (buf1, buf+strlen(keyword)+1, bufLen);	
-       				printf("%30s: ",keyword);
-				getFromString(buf1,n);
-				rewind(input);
-				return(0);
-			}
-		}
-	}
-	rewind(input);
-	return(-1);
-}
-
-template<typename T>
-int parseArray(FILE* input, const char* keyword, const size_t bufLen,
-		const size_t arrLen, T y[]){
-
-	char buf[bufLen];
-	char buf1[bufLen];
-	char comment[1];
-	char *ret;
-
-	while (fgets(buf,bufLen, input)!=NULL){
-		comment[0]=buf[0];
-		if(strncmp(comment,"#",1)==0){
-			//printf("Comment!:%s\n",buf);
-		}
-		else{
-			ret=strtok(buf,"=");
-
-			if(strcmp(ret,keyword)==0){
-				/*offset buf by keyword size + 1 for the "="*/
-				strncpy (buf1, buf+strlen(keyword)+1, bufLen);	
-       				printf("%30s:\n",keyword);
-				ret=strtok(buf1,",");
-				size_t j=0;
-				while(ret!=NULL){
-					if(j<arrLen){
-						//y[j]=atof(ret);
-						getFromString(ret,&y[j]);
-					}
-   		  			ret=strtok(NULL,",");
-					j++;
-				}
-				rewind(input);
-				if(j!=arrLen){
-					printf("Check no: of values entered for %s\n",keyword);
-					printf("%lu values required!\n",arrLen);
-					return(-1);
-				}
-				else{
-					return(0);
-				}
-			}
-		}
-	}
-	rewind(input);
-	return(-1);
-}
diff --git a/parse.o b/parse.o
deleted file mode 100644
index 37e06cf..0000000
Binary files a/parse.o and /dev/null differ
diff --git a/residue.cpp b/residue.cpp
deleted file mode 100644
index 724caec..0000000
--- a/residue.cpp
+++ /dev/null
@@ -1,1983 +0,0 @@
-#ifndef GSL_DEF
-#define GSL_DEF
-#include <gsl/gsl_math.h>
-#include <gsl/gsl_spline.h>
-#endif
-#include "residue.h"
-#include "macros.h"
-#include <cmath>
-#include <stdio.h>
-#include "timing.hpp"
-
-void REGRID(double* ydata,double* ydotdata,UserData data){
-    size_t nPts = data->npts;
-    size_t nvar = data->nvar;
-    double WORK[nPts],XNEW[nPts],XOLD[nPts]; 
-    double P,R,R0,R1,R2,TV1,TV2,XLEN,B1,B2;
-    double DX,DDX;
-    double DETA,ETAJ,DEL;
-    size_t ISTART; 
-    P = data->PCAD;
-    R = data->RGTC;
-    R0 =1.0 - P;
-    R1 =P*R/(R+1.0);
-    R2 =P - R1 ; 
-    TV1 = 0.0; 
-    TV2 = 0.0;
-
-    for(size_t i=2;i<=nPts;i++){
-        TV1 = TV1 + fabs(T(i)-T(i-1));
-    }
-    
-    for(size_t i=2;i<=nPts-1;i++){
-        TV2 = TV2 +  fabs( (T(i+1)-T(i))/(R(i+1)-R(i)) - (T(i)-T(i-1))/(R(i)-R(i-1)) );
-    }
-    
-    XLEN = R(nPts) - R(1); 
-    B1 = R1* XLEN/ ( (1.0-P)*TV1);
-    B2 = R2* XLEN/ ( (1.0-P)*TV2);
-
-    //Compute partial sum of weight function
-    WORK(1) =0.0;
-    DX = 0.0;
-    for(size_t i=2;i<=nPts-1;i++){
-        DX = R(i) - R(i-1) ; 
-        WORK(i) = DX + B1*fabs(T(i)-T(i-1)) + WORK(i-1)+B2*fabs( (T(i+1)-T(i))/(R(i+1)-R(i)) - (T(i)-T(i-1))/(R(i)-R(i-1)) );
-    }
-    
-    DDX = R(nPts) - R(nPts-1); 
-    WORK(nPts) = WORK(nPts-1) +DDX ; 
-    
-    for(size_t i=2;i<=nPts;i++){
-        WORK(i) = WORK(i)/WORK(nPts); 
-    }
-        
-    XNEW(1)=R(1); 
-    XNEW(nPts)=R(nPts); 
-    ISTART =2;
-    //double DETA;
-    DETA = 1.0/(nPts-1) ; 
-
-    //Fill new grid XNEW[nPts],duplicate from PREMIX REGRID SUBROUTINE
-    for(size_t j=2;j<=nPts-1;j++){
-        ETAJ= (j-1)*DETA; 
-
-        for(size_t i=ISTART;i<=nPts;i++){
-            if(ETAJ <= WORK(i)){
-                DEL = (ETAJ-WORK(i-1))/(WORK(i)-WORK(i-1)) ; 
-                XNEW(j)=R(i-1)+(R(i)-R(i-1))*DEL;
-                break;
-            }else{
-                ISTART =i;
-            }
-
-        }
-    }
-
-    //Interpolate solution based on XNEW[]&XOLD[]
-    for(size_t i=1;i<=nPts;i++){
-        XOLD[i-1]=R(i);
-    }
-
-    INTERPO(ydata,ydotdata,nvar,nPts,XNEW,XOLD);
-}
-
-
-void INTERPO(double* y,double* ydot,const size_t nvar,size_t nPts,const double XNEW[], const double XOLD[]){
-    double ytemp[nPts],ydottemp[nPts] ; 
-    
-    gsl_interp_accel* acc; 
-    gsl_spline* spline; 
-    acc = gsl_interp_accel_alloc();
-    spline = gsl_spline_alloc(gsl_interp_steffen,nPts);
-    
-    gsl_interp_accel* accdot; 
-    gsl_spline* splinedot; 
-    accdot = gsl_interp_accel_alloc();
-    splinedot = gsl_spline_alloc(gsl_interp_steffen,nPts);
-
-    for(size_t j=0;j<nvar;j++){
-        
-        for(size_t i=0;i<nPts;i++){
-            ytemp[i]=y[j+i*nvar];
-            ydottemp[i]=y[j+i*nvar];
-        }
-
-        gsl_spline_init(spline,XOLD,ytemp,nPts);
-        gsl_spline_init(splinedot,XOLD,ydottemp,nPts);
-        
-        for(size_t i=0;i<nPts;i++){
-            y[j+i*nvar]=gsl_spline_eval(spline,XNEW[i],acc);
-            ydot[j+i*nvar]=gsl_spline_eval(splinedot,XNEW[i],accdot);
-        }
-
-    }
-
-    gsl_interp_accel_free(acc);
-    gsl_spline_free(spline);
-
-    gsl_interp_accel_free(accdot);
-    gsl_spline_free(splinedot);
-
-}
-
-double maxTemperaturePosition(const double* y,const size_t nt,const size_t nvar,const double *x ,size_t nPts){
-    double maxT = 0.0e0;
-    double TempT = 0.0e0;
-    double pos = 0.0e0;
-    for (size_t i=1;i<=nPts;i++){
-        TempT = y[(i-1)*nvar+nt] ; 
-        if(TempT > maxT){
-            maxT = TempT ; 
-            pos = x[i-1];
-        }
-    }
-    return(pos); 
-}
-
-double maxTemperature(const double* y,const size_t nt,const size_t nvar ,size_t nPts){
-    double maxT = 0.0e0;
-    double TempT = 0.0e0;
-    //int index = 0 ; 
-    for (size_t i=1;i<=nPts;i++){
-        TempT = y[(i-1)*nvar+nt] ; 
-        if(TempT > maxT){
-            maxT = TempT ; 
-        }
-    }
-    return(maxT); 
-}
-//Index here is 1-based
-int maxTemperatureIndex(const double* y,const size_t nt,const size_t nvar ,size_t nPts){
-    double maxT = 0.0e0;
-    double TempT = 0.0e0;
-    int index = 0 ; 
-    for (size_t i=1;i<=nPts;i++){
-        TempT = y[(i-1)*nvar+nt] ; 
-        if(TempT > maxT){
-            maxT = TempT ; 
-            index = i; 
-        }
-    }
-    return(index); 
-}
-
-double maxCurvPositionR(const double* y, const size_t nt, 
-	               const size_t nvar, const size_t nr, size_t nPts){
-	double maxCurvT=0.0e0;
-	double gradTp=0.0e0;
-	double gradTm=0.0e0;
-	double curvT=0.0e0;
-	double dx=0.0e0;
-    double dr=0.0e0;
-	double pos=0.0e0;
-	size_t j,jm,jp;
-    size_t r,rp,rm;
-	for (size_t i = 1; i <nPts-1; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		jp=(i+1)*nvar+nt;
-        r = i*nvar+nr;
-        rm = (i-1)*nvar+nr;
-        rp = (i+1)*nvar+nr; 
-		//gradTp=fabs((y[jp]-y[j])/(x[i+1]-x[i]));
-		//gradTm=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		//dx=0.5e0*((x[i]+x[i+1])-(x[i-1]+x[i]));
-		//curvT=(gradTp-gradTm)/dx;
-        gradTp = fabs((y[jp]-y[j])/(y[rp]-y[r]));
-        gradTp = fabs((y[j]-y[jm])/(y[r]-y[rm]));
-		dr = 0.5e0*(y[rp]-y[rm]);
-        curvT=(gradTp-gradTm)/dr; 
-        if (curvT>=maxCurvT) {
-			maxCurvT=curvT;
-			pos=y[r];
-		}
-	}
-	return(pos);
-}
-
-int maxCurvIndexR(const double* y, const size_t nt, 
-	               const size_t nvar, const size_t nr, size_t nPts){
-	double maxCurvT=0.0e0;
-	double gradTp=0.0e0;
-	double gradTm=0.0e0;
-	double curvT=0.0e0;
-	double dx=0.0e0;
-    double dr=0.0e0;
-	int pos=0;
-	size_t j,jm,jp;
-    size_t r,rm,rp;
-	for (size_t i = 1; i <nPts-1; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		jp=(i+1)*nvar+nt;
-        r = i*nvar+nr;
-        rm = (i-1)*nvar+nr;
-        rp = (i+1)*nvar+nr; 
-		//gradTp=fabs((y[jp]-y[j])/(x[i+1]-x[i]));
-		//gradTm=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		//dx=0.5e0*((x[i]+x[i+1])-(x[i-1]+x[i]));
-		//curvT=(gradTp-gradTm)/dx;
-        gradTp = fabs((y[jp]-y[j])/(y[rp]-y[r]));
-        gradTp = fabs((y[j]-y[jm])/(y[r]-y[rm]));
-		dr = 0.5e0*(y[rp]-y[rm]);
-        curvT=(gradTp-gradTm)/dr; 
-        if (curvT>=maxCurvT) {
-			maxCurvT=curvT;
-			pos=i;
-		}
-	}
-	return(pos);
-}
-
-double maxGradPosition(const double* y, const size_t nt, 
-	               const size_t nvar, const double* x, size_t nPts){
-	double maxGradT=0.0e0;
-	double gradT=0.0e0;
-	double pos=0.0e0;
-	size_t j,jm;
-	for (size_t i = 1; i <nPts; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		gradT=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		if (gradT>=maxGradT) {
-			maxGradT=gradT;
-			pos=x[i];
-		}
-	}
-	return(pos);
-}
-
-int maxGradIndex(const double* y, const size_t nt, 
-	         const size_t nvar, const double* x, size_t nPts){
-	double maxGradT=0.0e0;
-	double gradT=0.0e0;
-	int pos=0;
-	size_t j,jm;
-	for (size_t i = 1; i <nPts; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		gradT=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		if (gradT>=maxGradT) {
-			maxGradT=gradT;
-			pos=i;
-		}
-	}
-	return(pos);
-}
-
-double maxCurvPosition(const double* y, const size_t nt, 
-	               const size_t nvar, const double* x, size_t nPts){
-	double maxCurvT=0.0e0;
-	double gradTp=0.0e0;
-	double gradTm=0.0e0;
-	double curvT=0.0e0;
-	double dx=0.0e0;
-	double pos=0.0e0;
-	size_t j,jm,jp;
-	for (size_t i = 1; i <nPts-1; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		jp=(i+1)*nvar+nt;
-		gradTp=fabs((y[jp]-y[j])/(x[i+1]-x[i]));
-		gradTm=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		dx=0.5e0*((x[i]+x[i+1])-(x[i-1]+x[i]));
-		curvT=(gradTp-gradTm)/dx;
-		if (curvT>=maxCurvT) {
-			maxCurvT=curvT;
-			pos=x[i];
-		}
-	}
-	return(pos);
-}
-
-int maxCurvIndex(const double* y, const size_t nt, 
-	               const size_t nvar, const double* x, size_t nPts){
-	double maxCurvT=0.0e0;
-	double gradTp=0.0e0;
-	double gradTm=0.0e0;
-	double curvT=0.0e0;
-	double dx=0.0e0;
-	int pos=0;
-	size_t j,jm,jp;
-	for (size_t i = 1; i <nPts-1; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		jp=(i+1)*nvar+nt;
-		gradTp=fabs((y[jp]-y[j])/(x[i+1]-x[i]));
-		gradTm=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		dx=0.5e0*((x[i]+x[i+1])-(x[i-1]+x[i]));
-		curvT=(gradTp-gradTm)/dx;
-		if (curvT>=maxCurvT) {
-			maxCurvT=curvT;
-			pos=i;
-		}
-	}
-	return(pos);
-}
-
-//double isothermPosition(const double* y, const double T, const size_t nt, 
-//	                const size_t nvar, const double* x, const size_t nPts){
-//	double pos=x[nPts-1];
-//	size_t j;
-//	for (size_t i = 1; i <nPts; i++) {
-//		j=i*nvar+nt;
-//		if (y[j]<=T) {
-//			pos=x[i];
-//			break;
-//		}
-//	}
-//	return(pos);
-//}
-
-//******************* scan the temperature from left to right ******************//
-double isothermPosition(const double* y, const double T, const size_t nt, 
-	                const size_t nvar, const double* x, const size_t nPts){
-	double pos=x[0];
-	size_t j;
-	for (size_t i = 0; i <nPts; i++) {
-		j=i*nvar+nt;
-		if (y[j]>=T) {
-			pos=x[i];
-			break;
-		}
-	}
-	return(pos);
-}
-
-void updateSolution(double* y, double* ydot, const size_t nvar,
-		    const double xOld[],const double xNew[],const size_t nPts){
-
-	double ytemp[nPts],ydottemp[nPts];
-
-	gsl_interp_accel* acc;
-	gsl_spline* spline;
-	acc = gsl_interp_accel_alloc();
-	spline = gsl_spline_alloc(gsl_interp_steffen, nPts);
-
-	gsl_interp_accel* accdot;
-	gsl_spline* splinedot;
-	accdot    = gsl_interp_accel_alloc();
-	splinedot = gsl_spline_alloc(gsl_interp_steffen, nPts);
-
-	for (size_t j = 0; j < nvar; j++) {
-
-		for (size_t i = 0; i < nPts; i++) {
-			ytemp[i]=y[j+i*nvar];
-			ydottemp[i]=ydot[j+i*nvar];
-		}
-
-		gsl_spline_init(spline,xOld,ytemp,nPts);
-		gsl_spline_init(splinedot,xOld,ydottemp,nPts);
-
-		for (size_t i = 0; i < nPts; i++) {
-
-		      	y[j+i*nvar]=gsl_spline_eval(spline,xNew[i],acc);
-		      	ydot[j+i*nvar]=gsl_spline_eval(splinedot,xNew[i],accdot);
-		}
-	}
-
-	//Exploring "fixing" boundary conditions:
-	//for (size_t j = 1; j < nvar; j++) {
-	//	//printf("%15.6e\t%15.6e\n", y[j],y[j+nvar]);
-	//	y[j]=y[j+nvar];
-	//	//y[j+(nPts-1)*nvar]=y[j+(nPts-2)*nvar];
-	//	//ydot[j+nvar]=ydot[j];
-	//}
-	//y[0]=0.0e0;
-	
-	gsl_interp_accel_free(acc);
-	gsl_spline_free(spline);
-
-	gsl_interp_accel_free(accdot);
-	gsl_spline_free(splinedot);
-}
-
-//Locate bath gas:
-size_t BathGasIndex(UserData data){
-	size_t index=0;
-	double max1;
-	double max=data->gas->massFraction(0);
-	for(size_t k=1;k<data->nsp;k++){
-		max1=data->gas->massFraction(k);
-		if(max1>=max){
-			max=max1;
-			index=k;
-		}
-	}
-	return(index+1);
-}
-
-//Locate Oxidizer:
-size_t oxidizerIndex(UserData data){
-	size_t index=0;
-	for(size_t k=1;k<data->nsp;k++){
-		if(data->gas->speciesName(k-1)=="O2"){
-			index=k;
-		}
-	}
-	return(index);
-}
-
-//Locate OH:
-size_t OHIndex(UserData data){
-	size_t index=0;
-	for(size_t k=1;k<data->nsp;k++){
-		if(data->gas->speciesName(k-1)=="OH"){
-			index=k;
-		}
-	}
-	return(index);
-}
-
-//Locate HO2:
-size_t HO2Index(UserData data){
-	size_t index=0;
-	for(size_t k=1;k<data->nsp;k++){
-		if(data->gas->speciesName(k-1)=="HO2"){
-			index=k;
-		}
-	}
-	return(index);
-}
-
-//Locate species index:
-size_t specIndex(UserData data,char *specName){
-	size_t index=0;
-	for(size_t k=1;k<data->nsp;k++){
-		if(data->gas->speciesName(k-1)==specName){
-			index=k;
-		}
-	}
-	return(index);
-}
-
-int setAlgebraicVariables(N_Vector* id, UserData data){
-	double *iddata;
-    char* specPtr[2]; 
-
-  	N_VConst(ONE, *id);
-  	iddata   = N_VGetArrayPointer_OpenMP(*id);
-	data->k_bath=BathGasIndex(data);
-	data->k_oxidizer=oxidizerIndex(data);
-	data->k_OH=OHIndex(data);
-	data->k_HO2=HO2Index(data);
-    //use char* pointer to get the address
-    for(int i=0;i<2;i++){
-        specPtr[i] = data->dropSpec[i];
-    }
-	data->k_drop[0]=specIndex(data,specPtr[0]);
-    data->k_drop[1]=specIndex(data,specPtr[1]);
-
-	printf("Oxidizer index: %lu\n",data->k_oxidizer);
-	printf("Bath gas index:%lu\n",data->k_bath);
-	printf("Droplet species index:%lu,%lu\n",data->k_drop[0],data->k_drop[1]);
-	for (size_t i = 1; i <=data->npts; i++) {
-		/*Algebraic variables: indicated by ZERO.*/
-		Rid(i)=ZERO;
-		Pid(i)=ZERO;
-		Yid(i,data->k_bath)=ZERO;
-		Mdotid(i)=ZERO;
-	}	
-	Mdotid(1)=ZERO;
-	Rid(1)=ONE;
-	Yid(1,data->k_drop[0])=ZERO;
-    Yid(1,data->k_drop[1])=ZERO;
-	Tid(data->npts)=ZERO;
-	if(data->constantPressure){
-		Pid(data->npts)=ONE;
-	}else{
-		Pid(data->npts)=ZERO;
-		Rid(data->npts)=ONE;
-	}
-	if(data->dirichletInner){
-		Tid(1)=ZERO; 
-	}else{
-		Tid(1)=ONE;
-	}
-	if(data->dirichletOuter){
-		for (size_t k = 1; k <=data->nsp; k++) {
-			if(k!=data->k_bath){
-				Yid(data->npts,k)=ONE;
-			}
-			Yid(1,k)=ZERO;
-			Tid(data->npts)=ONE;
-		}
-	}else{
-		for (size_t k = 1; k <=data->nsp; k++){
-			Yid(1,k)=ZERO;
-			Yid(data->npts,k)=ZERO;
-			Tid(data->npts)=ZERO;
-		}
-	}
-	return(0);
-}
-
-inline double calc_area(double x,int* i){
-	switch (*i) {
-		case 0:
-			return(ONE);
-		case 1:
-			return(x);
-		case 2:
-			return(x*x);
-		default:
-			return(ONE);
-	}
-}
-
-void readInitialCondition(FILE* input, double* ydata, const size_t nvar, const size_t nr, const size_t nPts, double Rg){
-
-	FILE* output;output=fopen("test.dat","w");
-
-	size_t bufLen=10000;
-	size_t nRows=0;
-	size_t nColumns=nvar;
-
-	char buf[bufLen];
-	char buf1[bufLen];
-	char comment[1];
-	char *ret;
-
-	while (fgets(buf,bufLen, input)!=NULL){
-		comment[0]=buf[0];
-		if(strncmp(comment,"#",1)!=0){
-			nRows++;
-		}
-	}
-	rewind(input);
-
-	printf("nRows: %ld\n", nRows);
-	double y[nRows*nColumns];
-
-	size_t i=0;
-	while (fgets(buf,bufLen, input)!=NULL){
-		comment[0]=buf[0];
-		if(strncmp(comment,"#",1)==0){
-		}
-		else{
-			ret=strtok(buf,"\t");
-			size_t j=0;
-			y[i*nColumns+j]=(double)(atof(ret));
-			j++;
-			while(ret!=NULL){
-				ret=strtok(NULL,"\t");
-				if(j<nColumns){
-					y[i*nColumns+j]=(double)(atof(ret));
-				}
-				j++;
-			}
-			i++;
-		}
-	}
-
-	for (i = 0; i < nRows; i++) {
-		for (size_t j = 0; j < nColumns; j++) {
-			fprintf(output, "%15.6e\t",y[i*nColumns+j]);
-		}
-		fprintf(output, "\n");
-	}
-	fclose(output);
-
-	//double xOld[nRows],xNew[nPts],ytemp[nPts];
-	double xOld[nRows],xNew[nPts],ytemp[nRows];
-
-	for (size_t j = 0; j < nRows; j++) {
-		xOld[j]=y[j*nColumns+nr];
-	}
-
-	//double dx=(xOld[nRows-1] - xOld[0])/((double)(nPts)-1.0e0);
-	//for (size_t j = 0; j < nPts-1; j++) {
-	//	xNew[j]=(double)j*dx + xOld[0];
-	//}
-	//xNew[nPts-1]=xOld[nRows-1];
-	double dX0;
-	int NN = nPts-2;
-	
-	dX0 = (xOld[nRows-1]-xOld[0])*(pow(Rg,1.0/NN) - 1.0)/(pow(Rg,(NN+1.0)/NN) - 1.0);
-	xNew[0] = xOld[0];
-	for (size_t i = 1; i < nPts-1; i++) {
-		xNew[i]=xNew[i-1]+dX0*pow(Rg,(i-1.0)/NN);
-	}
-	xNew[nPts-1] = xOld[nRows-1];
-
-	gsl_interp_accel* acc;
-	gsl_spline* spline;
-	acc = gsl_interp_accel_alloc();
-	spline = gsl_spline_alloc(gsl_interp_steffen, nRows);
-
-	for (size_t j = 0; j < nColumns; j++) {
-
-		for (size_t k = 0; k < nRows; k++) {
-			ytemp[k]=y[j+k*nColumns];
-		}
-
-		gsl_spline_init(spline,xOld,ytemp,nRows);
-
-		for (size_t k = 0; k < nPts; k++) {
-		      	ydata[j+k*nColumns]=gsl_spline_eval(spline,xNew[k],acc);
-		}
-	}
-	
-	gsl_interp_accel_free(acc);
-	gsl_spline_free(spline);
-
-}
-
-double systemMass(double* ydata,UserData data){
-	double mass=0.0e0;
-	double rho;
-	for (size_t i = 2; i <=data->npts; i++) {
-  		data->gas->setState_TPY(T(i), P(i), &Y(i,1));   
-		rho=data->gas->density();                                           
-		//psi(i)=psi(i-1)+rho*(R(i)-R(i-1))*calc_area(HALF*(R(i)+R(i-1)),&m);
-		mass+=rho*(R(i)-R(i-1))*calc_area(R(i),&data->metric);
-	}
-	return(mass);
-}
-
-
-int initializePsiGrid(double* ydata, double* psidata, UserData data){
-
-	double rho,rhom;
-	/*Create a psi grid that corresponds CONSISTENTLY to the spatial grid
-	 * "R" created above. Note that the Lagrangian variable psi has  units
-	 * of kg. */
-	psi(1)=ZERO;
-	for (size_t i = 2; i <=data->npts; i++) {
-  		data->gas->setState_TPY(T(i), P(i), &Y(i,1));   
-		rho=data->gas->density();                                           
-  		data->gas->setState_TPY(T(i-1), P(i-1), &Y(i-1,1));   
-		rhom=data->gas->density();                                           
-		//psi(i)=psi(i-1)+rho*(R(i)-R(i-1))*calc_area(HALF*(R(i)+R(i-1)),&data->metric);
-		//psi(i)=psi(i-1)+rho*(R(i)-R(i-1))*calc_area(R(i),&data->metric);
-		psi(i)=psi(i-1)+(R(i)-R(i-1))*(rho*calc_area(R(i),&data->metric)+rhom*calc_area(R(i-1),&data->metric))/TWO;
-	}
-
-	/*The mass of the entire system is the value of psi at the last grid
-	 * point. Normalize psi by this mass so that it varies from zero to
-	 * one. This makes psi dimensionless. So the mass needs to be
-	 * multiplied back in the approporiate places in the governing
-	 * equations so that units match.*/
-	data->mass=psi(data->npts);
-	for (size_t i = 1; i <=data->npts; i++) {
-		psi(i)=psi(i)/data->mass;
-	}
-	return(0);
-}
-
-
-int setInitialCondition(N_Vector* y, 
-	    		N_Vector* ydot, 
-            		UserData data){
-	double* ydata;
-	double* ydotdata;
-	double* psidata;
-	double* innerMassFractionsData, Rd, massDrop;
-	double rhomhalf, lambdamhalf, YVmhalf[data->nsp];
-	double f=ZERO;
-	double g=ZERO;
-
-	double perturb,rho;
-	double epsilon=ZERO;
-	int m,ier;
-  	ydata    = N_VGetArrayPointer_OpenMP(*y);
-  	ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
-	innerMassFractionsData =  data->innerMassFractions;
-	Rd = data->Rd;
-	massDrop = data->massDrop;
-
-	//Mass of droplet
-	//massDrop=1.0/3.0*Rd*Rd*Rd*997.0; //TODO: The density of the droplet should be a user input
-    //massDrop=1.0/3.0*Rd*Rd*Rd*684.0; //TODO:The density of the droplet(n-heptane) should be a user input 
-	massDrop = 1.0/3.0*Rd*Rd*Rd*data->dropRho;
-    if(data->adaptiveGrid){
-  		psidata  = data->grid->xOld;
-	}
-	else{
-  		psidata  = data->uniformGrid;
-	}
-
-	m=data->metric;
-
-	data->innerTemperature=data->initialTemperature;
-	for (size_t k = 1; k <=data->nsp; k++) {
-  		innerMassFractionsData[k-1]=data->gas->massFraction(k-1);
-	}
-
-	//Define Grid:
-	double dR=(data->domainLength)/((double)(data->npts)-1.0e0);
-	double dv=(pow(data->domainLength,1+data->metric)-pow(data->firstRadius*data->domainLength,1+data->metric))/((double)(data->npts)-1.0e0);
-	
-    //Initialize the R(i),T(i)(data->initialTemperature),Y(i,k),P(i)
-    for (size_t i = 1; i <=data->npts; i++) {
-		if(data->metric==0){
-			R(i)=Rd+(double)((i-1)*dR);
-		}else{
-			if(i==1){
-				R(i)=ZERO;
-			}else if(i==2){
-				R(i)=data->firstRadius*data->domainLength;
-			}else{
-				R(i)=pow(pow(R(i-1),1+data->metric)+dv,1.0/((double)(1+data->metric)));
-			}
-		}
-		T(i)=data->initialTemperature;
-		for (size_t k = 1; k <=data->nsp; k++) {
-  	        	Y(i,k)=data->gas->massFraction(k-1);	//Indexing different in Cantera
-		}
-  	        P(i)=data->initialPressure*Cantera::OneAtm;
-	}	
-	R(data->npts)=data->domainLength+data->Rd;
-    
-//    /********** test R(i) and the volumn between grids *****************/
-//    printf("Print the first 4 R(i)s and volumn between them: \n") ; 
-//    printf("Grids: 1st:%2.6e,2nd:%2.6e,3rd:%2.6e,4th:%2.6e \n",R(1),R(2),R(3),R(4));
-//    double v1,v2,v3,v4,v5; 
-//    v1 =pow(R(2),1+data->metric) - pow(R(1),1+data->metric);
-//    v2 =pow(R(3),1+data->metric) - pow(R(2),1+data->metric);
-//    v3 =pow(R(4),1+data->metric) - pow(R(3),1+data->metric);
-//    v4 =pow(R(5),1+data->metric) - pow(R(4),1+data->metric); 
-//    v5 =pow(R(6),1+data->metric) - pow(R(5),1+data->metric);
-//    printf("Volumn: 1st:%2.6e,2nd:%2.6e,3rd:%2.6e,4th:%2.6e,5th:%2.6e\n",v1,v2,v3,v4,v5) ; 
-
-
-	double Tmax;
-	double Tmin=data->initialTemperature;
-	double w=data->mixingWidth;
-	double YN2=ZERO;
-	double YO2=ZERO;
-	double YFuel,YOxidizer,sum;
-
-	//if(data->problemType==0){
-	//	data->gas->equilibrate("HP");
-	//	data->maxTemperature=data->gas->temperature();
-	//}
-	//else if(data->problemType==1){
-	//	/*Premixed Combustion: Equilibrium products comprise ignition
-	//	 * kernel at t=0. The width of the kernel is "mixingWidth"
-	//	 * shifted by "shift" from the center.*/
-	//	data->gas->equilibrate("HP");
-	//	Tmax=data->gas->temperature();
-	//	for (size_t i = 1; i <=data->npts; i++) {
-	//		g=HALF*(tanh((R(i)-data->shift)/w)+ONE);	//increasing function of x
-	//		f=ONE-g;					//decreasing function of x
-	//		T(i)=(Tmax-Tmin)*f+Tmin;
-	//		for (size_t k = 1; k <=data->nsp; k++) {
-	//			Y(i,k)=(data->gas->massFraction(k-1)-Y(i,k))*f+Y(i,k);
-	//		}
-	//	}
-	//	if(data->dirichletOuter){
-	//		T(data->npts)=data->wallTemperature;
-	//	}
-	//}
-	//else if(data->problemType==2){
-	//	FILE* input;
-	//	if(input=fopen("initialCondition.dat","r")){
-	//		readInitialCondition(input, ydata, data->nvar, data->nr, data->npts);
-	//		fclose(input);
-	//	}
-	//	else{
-	//		printf("file initialCondition.dat not found!\n");
-	//		return(-1);
-	//	}
-	//}
-
-	initializePsiGrid(ydata,psidata,data);
-
-	if(data->adaptiveGrid){
-	//	if(data->problemType!=0){
-	//		data->grid->position=maxGradPosition(ydata, data->nt, data->nvar,
-	//						 data->grid->xOld, data->npts);
-	//		//data->grid->position=maxCurvPosition(ydata, data->nt, data->nvar,
-	//		//				 data->grid->xOld, data->npts);
-	//	}
-	//	else{
-	//	}
-		if(data->problemType!=3){
-			data->grid->position=0.0e0;
-			double x=data->grid->position+data->gridOffset*data->grid->leastMove;
-			printf("New grid center:%15.6e\n",x);
-
-//            /**************** TEST THE data->grid->xOld *******************/
-//            double* ptr3 = data->grid->xOld ; 
-//            printf("SetInitialCondition function is called,before reGrid,Start print the first 5 elements of the xOld array : \n");
-//            printf("1st:%.6f, 2nd:%.6f, 3rd:%.6f, 4th:%.6f, 5th:%.6f.\n",ptr3[0],ptr3[1],ptr3[2],ptr3[3],ptr3[4]);
-			
-            ier=reGrid(data->grid, x);
-			if(ier==-1)return(-1);
-
-//            /**************** TEST THE data->grid->xOld *******************/
-//            double* ptr = data->grid->xOld ; 
-//            printf("SetInitialCondition function is called,after reGrid,Start print the first 5 elements of the xOld array : \n");
-//            printf("1st:%.6f, 2nd:%.6f, 3rd:%.6f, 4th:%.6f, 5th:%.6f.\n",ptr[0],ptr[1],ptr[2],ptr[3],ptr[4]);
-
-
-			updateSolution(ydata, ydotdata, data->nvar,
-			               data->grid->xOld,data->grid->x,data->npts);
-			storeGrid(data->grid->x,data->grid->xOld,data->npts);
-		}
-	}
-	else{
-		double Rg = data->Rg, dpsi0;
-		int NN = data->npts-2;
-		double psiNew[data->npts];
-		
-		dpsi0 = (pow(Rg,1.0/NN) - 1.0)/(pow(Rg,(NN+1.0)/NN) - 1.0);
-		psiNew[0] = 0;
-		for (size_t i = 1; i < data->npts-1; i++) {
-			psiNew[i]=psiNew[i-1]+dpsi0*pow(Rg,(i-1.0)/NN);
-		}
-		psiNew[data->npts-1] = 1.0;
-		printf("Last point:%15.6e\n",psiNew[data->npts-1]);
-		updateSolution(ydata, ydotdata, data->nvar,
-		               data->uniformGrid,psiNew,data->npts);
-		storeGrid(psiNew,data->uniformGrid,data->npts);
-
-		//double psiNew[data->npts];
-		//double dpsi=1.0e0/((double)(data->npts)-1.0e0);
-		//for (size_t i = 0; i < data->npts; i++) {
-		//	psiNew[i]=(double)(i)*dpsi;
-		//}
-		//printf("Last point:%15.6e\n",psiNew[data->npts-1]);
-		//updateSolution(ydata, ydotdata, data->nvar,
-		//               data->uniformGrid,psiNew,data->npts);
-		//storeGrid(psiNew,data->uniformGrid,data->npts);
-	}
-
-	if(data->problemType==0){
-		data->gas->equilibrate("HP");
-		data->maxTemperature=data->gas->temperature();
-	}
-	else if(data->problemType==1){
-		/*Premixed Combustion: Equilibrium products comprise ignition
-		 * kernel at t=0. The width of the kernel is "mixingWidth"
-		 * shifted by "shift" from the center.*/
-		data->gas->equilibrate("HP");
-		Tmax=data->gas->temperature();
-		for (size_t i = 1; i <=data->npts; i++) {
-			g=HALF*(tanh((R(i)-data->shift)/w)+ONE);	//increasing function of x
-			f=ONE-g;					//decreasing function of x
-			T(i)=(Tmax-Tmin)*f+Tmin;
-			for (size_t k = 1; k <=data->nsp; k++) {
-				Y(i,k)=(data->gas->massFraction(k-1)-Y(i,k))*f+Y(i,k);
-			}
-		}
-		if(data->dirichletOuter){
-			T(data->npts)=data->wallTemperature;
-		}
-	}
-	else if(data->problemType==2){
-		FILE* input;
-		if(input=fopen("initialCondition.dat","r")){
-			readInitialCondition(input, ydata, data->nvar, data->nr, data->npts, data->Rg);
-			fclose(input);
-		}
-		else{
-			printf("file initialCondition.dat not found!\n");
-			return(-1);
-		}
-		initializePsiGrid(ydata,psidata,data);
-	}
-	else if(data->problemType==3){
-		FILE* input;
-		if(input=fopen("restart.bin","r")){
-			readRestart(y, ydot, input, data);
-			fclose(input);
-			printf("Restart solution loaded!\n");
-			printf("Problem starting at t=%15.6e\n",data->tNow);
-			return(0);
-		}
-		else{
-			printf("file restart.bin not found!\n");
-			return(-1);
-		}
-	}
-
-	if(data->reflectProblem){
-		double temp;
-		int j=1;
-		while (data->npts+1-2*j>=0) {
-			temp=T(j);
-			T(j)=T(data->npts+1-j);
-			T(data->npts+1-j)=temp;
-			for (size_t k = 1; k <=data->nsp; k++) {
-				temp=Y(j,k);
-				Y(j,k)=Y(data->npts+1-j,k);
-				Y(data->npts+1-j,k)=temp;
-			}
-			j=j+1;
-		}
-	}
-
-	/*Floor small values to zero*/
-	for (size_t i = 1; i <=data->npts; i++) {
-		for (size_t k = 1; k <=data->nsp; k++) {
-			if(fabs(Y(i,k))<=data->massFractionTolerance){
-				Y(i,k)=0.0e0;
-			}
-		}
-	}
-
-	//Set grid to location of maximum curvature calculated by r instead of x:
-	if(data->adaptiveGrid){
-		//data->grid->position=maxCurvPosition(ydata, data->nt, data->nvar,
-		//		  		data->grid->x, data->npts);
-        int maxCurvII = 0; 
-        maxCurvII = maxCurvIndexR(ydata,data->nt,data->nvar,data->nr,data->npts);
-        
-        data->grid->position = data->grid->x[maxCurvII];
-		ier=reGrid(data->grid, data->grid->position);
-		updateSolution(ydata, ydotdata, data->nvar,
-		               data->grid->xOld,data->grid->x,data->npts);
-		storeGrid(data->grid->x,data->grid->xOld,data->npts);
-        
-        /******** Test the maxCurvPosition and related variables *******/
-        printf("The maxCurvPositition(based on r) is : %.6f,Temperature is : %.3f \n",data->grid->position,T(maxCurvII+1));
-	}
-
-
-	/*Ensure consistent boundary conditions*/	
-	//T(1)=T(2);
-	//for (size_t k = 1; k <=data->nsp; k++) {
-	//	Y(1,k)=Y(2,k);
-	//	Y(data->npts,k)=Y(data->npts-1,k);
-	//}
-
-	return(0);
-}
-
-inline double Qdot(double* t, 
-	    	   double* x, 
-	    	   double* ignTime, 
-	    	   double* kernelSize, 
-	    	   double* maxQdot){
-	double qdot;
-	if(*x<=*kernelSize){
-		if((*t)<=(*ignTime)){
-			qdot=(*maxQdot);
-		}
-		else{
-			qdot=0.0e0;
-		}
-	}else{
-		qdot=0.0e0;
-	}
-	return(qdot);
-}
-
-inline void setGas(UserData data, 
-	    double *ydata, 
-	    size_t gridPoint){
-  	data->gas->setTemperature(T(gridPoint)); 	        
-  	data->gas->setMassFractions_NoNorm(&Y(gridPoint,1)); 	
-  	data->gas->setPressure(P(gridPoint));
-}
-
-void getTransport(UserData data, 
-		  double *ydata, 
-		  size_t gridPoint,
-		  double *rho,
-		  double *lambda,
-		  double YV[]){
-
-	double YAvg[data->nsp],
-		 XLeft[data->nsp],
-		 XRight[data->nsp],
-		 gradX[data->nsp];
-
-	setGas(data,ydata,gridPoint);
-	data->gas->getMoleFractions(XLeft);                                     
-	setGas(data,ydata,gridPoint+1);
-	data->gas->getMoleFractions(XRight);                                     
-                                                                             
-	for (size_t k = 1; k <=data->nsp; k++) {                                          
-		YAvg(k)=HALF*(Y(gridPoint,k)+
-			      Y(gridPoint+1,k));                                 
-		gradX(k)=(XRight(k)-XLeft(k))/
-			 (R(gridPoint+1)-R(gridPoint));                       
-	}                                                                    
-	double TAvg = HALF*(T(gridPoint)+T(gridPoint+1));
-	double gradT=(T(gridPoint+1)-T(gridPoint))/
-		       (R(gridPoint+1)-R(gridPoint));                                  
-
-
-  	data->gas->setTemperature(TAvg); 	        
-  	data->gas->setMassFractions_NoNorm(YAvg); 	
-  	data->gas->setPressure(P(gridPoint));
-
-	*rho=data->gas->density();                                       
-	*lambda=data->trmix->thermalConductivity();                      
-	data->trmix->getSpeciesFluxes(1,&gradT,data->nsp,                     
-				      gradX,data->nsp,YV);                
-	//setGas(data,ydata,gridPoint);
-}
-
-int residue(double t, N_Vector y, N_Vector ydot, N_Vector res, void *user_data){
-
-	/*Declare and fetch nvectors and user data:*/
-
-  	double *ydata, *ydotdata, *resdata, *psidata, *innerMassFractionsData;
-  	
-	UserData data;
-	data = (UserData)user_data;
-	size_t npts=data->npts;
-	size_t nsp=data->nsp;
-	size_t k_bath = data->k_bath;
-	size_t k_drop[2] = {data->k_drop[0],data->k_drop[1]};
-
-	ydata 	= N_VGetArrayPointer_OpenMP(y); 
-	ydotdata= N_VGetArrayPointer_OpenMP(ydot); 
-	resdata = N_VGetArrayPointer_OpenMP(res);
-	if(data->adaptiveGrid==1){
-		psidata = data->grid->x;
-	}else{
-		psidata = data->uniformGrid;
-	}
-
-	innerMassFractionsData =  data->innerMassFractions;
-
-	/* Grid stencil:*/
-
-	/*-------|---------*---------|---------*---------|-------*/
-	/*-------|---------*---------|---------*---------|-------*/
-	/*-------|---------*---------|---------*---------|-------*/
-	/*-------m-------mhalf-------j-------phalf-------p-------*/
-	/*-------|---------*---------|---------*---------|-------*/
-	/*-------|---------*---------|---------*---------|-------*/
-	/*-------|<=======dxm=======>|<=======dxp=======>|-------*/
-	/*-------|---------*<======dxav=======>*---------|-------*/
-	/*-------|<================dxpm=================>|-------*/
-
-	/* Various variables defined for book-keeping and storing previously
-	 * calculated values:
-	 * rho		: densities at points  m, mhalf, j, p, and phalf.
-	 * area		: the matric at points m, mhalf, j, p, and phalf.
-	 * m 		: exponent that determines geometry;
-	 * lambda	: thermal conductivities at mhalf and phalf.
-	 * mdot		: mass flow rate at m, j, and p.
-	 * X		: mole fractions at j and p.
-	 * YV		: diffusion fluxes at mhalf and phalf.
-	 * Tgrad	: temperature gradient at mhalf and phalf.
-	 * Tav		: average temperature between two points.
-	 * Pav		: average pressure between two points.
-	 * Yav		: average mass fractions between two points.
-	 * Xgradhalf	: mole fraction gradient at j.
-	 * Cpb		: mass based bulk specific heat.
-	 * tranTerm	: transient terms.
-	 * advTerm	: advection terms.
-	 * diffTerm	: diffusion terms.
-	 * srcTerm	: source terms.
-	 */
-
-	double rhomhalf,  rhom, lambdamhalf, YVmhalf[nsp], 
-		 rho, 
-		 rhophalf, lambdaphalf, YVphalf[nsp],
-		 Cpb, Cvb,  Cp[nsp], Cpl[2], dHvl[2], rhol,  wdot[nsp],   enthalpy[nsp], energy[nsp],
-		 tranTerm, diffTerm,    srcTerm, advTerm,
-		 area,areamhalf,areaphalf,aream,areamhalfsq,areaphalfsq;
-	
-	/*Aliases for difference coefficients:*/
-	double cendfm, cendfc, cendfp;
-	/*Aliases for various grid spacings:*/
-	double dpsip, dpsiav, dpsipm, dpsim, dpsimm;
-	dpsip=dpsiav=dpsipm=dpsim=dpsimm=ONE;
-	//double mass, mdotIn;
-	double mass, massDrop;
-	double sum, sum1, sum2, sum3;
-
-	size_t j,k;
-	int m;
-	m=data->metric;					//Unitless
-	mass=data->mass;				//Units: kg
-	//massDrop=data->massDrop;		//Units: kg
-	//mdotIn=data->mdot*calc_area(R(npts),&m);	//Units: kg/s
-
-//	/*evaluate properties at j=1*************************/
-	setGas(data,ydata,1);
-	rhom=data->gas->density();                                       
-    Cpb=data->gas->cp_mass();       	//J/kg/K
-    Cvb=data->gas->cv_mass();       	//J/kg/K
-	//TODO: Create user input model for these. They should not be constant
-	//Cpl=4.182e03;						//J/kg/K for liquid water
-	//Cpl=  5.67508633e-07*pow(T(1),4) - 7.78060597e-04*pow(T(1),3) + 4.08310544e-01*pow(T(1),2)  //J/kg/K for liquid water  
-    //     - 9.62429538e+01*T(1)        + 1.27131046e+04;
-    
-    /*Update specific heat:Cpl for liquid proprane&n-heptane&dodecane*/
-   /*Based on the existiong data,a linear expression is used*/
-   // Cpl= 12.10476*T(1) - 746.60143; // Unit:J/(kg*K), Need to be improved later
-    //Cpl[0] = 2.423*T(1)+1661.074; //Unit:J/(kg*K),range:1atm,propane 
-    Cpl[0] = 3.336*T(1)+1289.5; //Unit:J/(kg*K),range:1atm,n-Heptane
-    Cpl[1] = 3.815*T(1)+1081.8; //Unit:J/(kg*K),range:1atm,n-Dodecane
-    double Cp_l = 0.0; 
-    for(size_t i=0;i<=1;i++){
-        Cp_l=Cp_l+Cpl[i]*data->dropMassFrac[i];
-    }
-
-	//dHvl=2.260e6;						//J/kg	heat of vaporization of water
-	//double Tr = T(1)/647.1;				//Reduced Temperature: Droplet Temperature divided by critical temperature of water
-	//dHvl= 5.2053e07*pow(1-Tr,0.3199 - 0.212*Tr + 0.25795*Tr*Tr)/18.01;	//J/kg	latent heat of vaporization of water
-    
-    double Tr1 = T(1)/369.8;            //Reduced Temperature;
-    dHvl[0] = 6.32716e5*exp(-0.0208*Tr1)*pow((1-Tr1),0.3766);    //Unit:J/kg,Latent Heat of Vaporizaiton of Liquid n-propane,NIST
-
-    double Tr2 = T(1)/540.2;            //Reduced Temperature:Droplet Temperature divided by critical temperature of liquid n-heptane, Source:NIST
-    dHvl[1] = 5.366e5*exp(-0.2831*Tr2) * pow((1-Tr2),0.2831);    //Unit:J/kg, latent heat of vaporization of liquid n-heptane, Source: NIST
-    
-    double dHv_l = 0.0; 
-    for(size_t i=0;i<=1;i++){
-        dHv_l=dHv_l+dHvl[i]*data->dropMassFrac[i];
-    }
-
-    /*Following section is related to the property of water*/
-    //rhol = 997.0;	
-	//massDrop=1.0/3.0*R(1)*R(1)*R(1)*997.0; //TODO: The density of the droplet should be a user input
-    
-    /*Following section is related to the property of liquid n-heptane and n-dodecane (mainly density rho)*/
-    /*Density of these two species should be temperature dependent*/
-    //data->dropDens[0] = -1.046*T(1)+823.794;       //Unit:kg/m^3,density of propane @1atm
-    data->dropDens[0] = -0.858*T(1)+933.854;       //Unit:kg/m^3,density of n-Heptane @1atm
-    data->dropDens[1] = -0.782*T(1)+979.643;       //Unit:kg/m^3,density of n-Dodecane @1atm
-    //rhol = data->dropRho;                          //Unit:kg/m^3
-    rhol = 0.0; 
-    for(size_t i=0;i<=1;i++){
-       rhol = rhol + data->dropMassFrac[i]*data->dropDens[i];
-    }
-    massDrop = 1.0/3.0*R(1)*R(1)*R(1)*rhol;  //Unit:kg, this is the mass of liquid droplet  
-
-    aream= calc_area(R(1),&m);	    
-    
- 
-	/*******************************************************************/
-	/*Calculate values at j=2's m and mhalf*****************************/
-
-	getTransport(data, ydata, 1, &rhomhalf,&lambdamhalf,YVmhalf);
-	areamhalf= calc_area(HALF*(R(1)+R(2)),&m);                                 
-	aream = calc_area(R(1),&m);                                 
-	areamhalfsq= areamhalf*areamhalf;                                   
-                                                                             
-	/*******************************************************************/
-
-	/*Fill up res with left side (center) boundary conditions:**********/
-	/*We impose zero fluxes at the center:*/                        
-
-
-	/*Mass:*/                                                            
-	if(data->quasiSteady){
-		Rres(1)=Rdot(1); // Should remain satisfied for quasi-steady droplet
-	}else{
-		Rres(1)=Rdot(1) + Mdot(1)/rhol/aream; 
-	}
-                                                                        
-	/*Species:*/                                                    
-	sum=ZERO;
-	
-	//TODO: Antoine Parameters should be part of user input, not hardcoded
-	//Yres(1,k_drop)=Y(1,k_drop) - 1.0e5*pow(10,4.6543-(1435.264/(T(1)-64.848)))*data->gas->molecularWeight(k_drop-1) 
-	//			    / P(1) / data->gas->meanMolecularWeight();
-	//Yres(1,k_drop)=Y(1,k_drop) - 1.0e3*pow(2.71828,16.7-(4060.0/(T(1)-37.0)))*data->gas->molecularWeight(k_drop-1) 
-	//			    / P(1) / data->gas->meanMolecularWeight();
-	//Yres(1,k_drop)=Y(1,k_drop)-2.566785e-02;
-	
-    /*Following using the Antoine Parameters to calculate the pressure of volatile component(n-heptane)*/
-    //Antoine parameter from NIST website
-    double p_i[2]={0.0,0.0} ; 
-    
-    p_i[0] = 1.0e5*pow(10,4.53678-(1149.36/(T(1)+24.906)))*data->dropMassFrac[0] ;    //unit:Pa,For N-PROPANE
-    p_i[1] = 1.0e5*pow(10,4.02832-(1268.636/(T(1)-56.199)))*data->dropMassFrac[1] ;    //unit:Pa,FOR N-HEPTANE 
-    //p_i = 1.0e3*pow(2.71828,16.7-(4060.0/(T(1)-37.0)));     //Unit:Pa,FOR WATER
-    //Yres(1,k_drop)=Y(1,k_drop) - p_i * data->gas->molecularWeight(k_drop-1) 
-	//			    / P(1) / data->gas->meanMolecularWeight();
-    for(size_t i=0;i<=1;i++){
-        Yres(1,k_drop[i])=Y(1,k_drop[i])-p_i[i]*data->gas->molecularWeight(k_drop[i]-1)/(P(1)*data->gas->meanMolecularWeight());           
-    }
-
-	
-    sum=sum+Y(1,k_drop[0])+Y(1,k_drop[1]);
-
-	//Mdotres(1)=Mdot(1) - (YVmhalf(k_drop)*areamhalf) / (1-Y(1,k_drop)); //Evaporating mass
-    Mdotres(1)= Mdot(1) - ((YVmhalf(k_drop[0])+YVmhalf(k_drop[1])) *areamhalf) / (1-Y(1,k_drop[0])-Y(1,k_drop[1]) ); //Evaporating mass
-	for (k = 1; k <=nsp; k++) {                                        
-		if(k!=k_bath && k!=k_drop[0] && k!=k_drop[1]){
-			//TODO: May need to include chemical source term
-			Yres(1,k)=Y(1,k)*Mdot(1) + YVmhalf(k)*areamhalf;
-			//Yres(1,k)=YVmhalf(k)*areamhalf;
-		    sum=sum+Y(1,k);
-			//if(fabs(Mdot(1))>1e-14){
-		      		///Yres(1,k)=innerMassFractionsData[k-1]-
-					///  Y(1,k)-
-					///  (YVmhalf(k)*areamhalf)/Mdot(1);
-					
-			//}
-			//else{
-		    //  		//Yres(1,k)=Y(1,k)-innerMassFractionsData[k-1];
-		    //  		Yres(1,k)=Y(2,k)-Y(1,k);
-			//	/*The below flux boundary condition makes the
-			//	 * problem more prone to diverge. How does one
-			//	 * fix this?*/
-		    //  		//Yres(1,k)=YVmhalf(k);
-			//}
-		}
-	}                                                                 
-	Yres(1,k_bath)=ONE-sum-Y(1,k_bath);                                     
-	
-	/*Energy:*/                                                     
-	if(data->dirichletInner){
-		//Tres(1)=Tdot(1);
-		//Tres(1)=T(1)-data->innerTemperature;
-        /*Following code should be revised in the future*/
-		//Tres(1)=lambdamhalf*rhomhalf*areamhalfsq*(T(2)-T(1))/((psi(2)-psi(1))*mass)/dHv_l - YVmhalf(k_drop)*areamhalf/(1-Y(1,k_drop));
-	}else{
-		//Tres(1)=Tdot(1) - 
-		//	(rhomhalf*areamhalfsq*lambdamhalf*(T(2)-T(1))/((psi(2)-psi(1))*mass) - Mdot(1)*dHvl)
-		//	/ (massDrop * Cpl);
-		
-        //Tres(1)=Tdot(1) - 
-		//	(areamhalf*lambdamhalf*(T(2)-T(1))/(R(2)-R(1)) - Mdot(1)*dHvl)
-		//	/ (massDrop * Cpl);
-		Tres(1)=Tdot(1) - 
-			(areamhalf*lambdamhalf*(T(2)-T(1))/(R(2)-R(1)) - Mdot(1)*dHv_l)
-			/ (massDrop * Cp_l);
-
-
-
-		//Tres(1)=T(2)-T(1);
-		//Tres(1)=Tdot(1) - (Pdot(1)/(rhom*Cpb))
-		//	+(double)(data->metric+1)*(rhomhalf*lambdamhalf*areamhalfsq*(T(2)-T(1))/psi(2)-psi(1));
-	}
-
-	/*Pressure:*/                                                        
-	Pres(1)=P(2)-P(1);
-	/*Fill up res with governing equations at inner points:*************/
-	for (j = 2; j < npts; j++) {                                         
-                                                                             
-		/*evaluate various mesh differences*///                      
-        	dpsip =        (psi(j+1) - psi(j)  )*mass;                            
-        	dpsim =        (psi(j)   - psi(j-1))*mass;                            
-        	dpsiav =  HALF*(psi(j+1) - psi(j-1))*mass;                            
-        	dpsipm =       (psi(j+1) - psi(j-1))*mass;                            
-		/***********************************///                      
-                                                                             
-		/*evaluate various central difference coefficients*/       
-        	cendfm = - dpsip / (dpsim*dpsipm);                               
-        	cendfc =   (dpsip-dpsim) / (dpsip*dpsim);                         
-        	cendfp =   dpsim / (dpsip*dpsipm);                               
-		/**************************************************/
-                                                                   
-                                                                  
-		/*evaluate properties at j*************************/
-		setGas(data,ydata,j);
-		rho=data->gas->density();		//kg/m^3
-        	Cpb=data->gas->cp_mass();       	//J/kg/K
-        	Cvb=data->gas->cv_mass();       	//J/kg/K
-		data->gas->getNetProductionRates(wdot); //kmol/m^3
-		data->gas->getEnthalpy_RT(enthalpy);	//unitless
-		data->gas->getCp_R(Cp);			//unitless
-		area = calc_area(R(j),&m);	        //m^2
-                                                                           
-		/*evaluate properties at p*************************/
-		getTransport(data, ydata, j, &rhophalf,&lambdaphalf,YVphalf);
-		areaphalf= calc_area(HALF*(R(j)+R(j+1)),&m);	    
-		areaphalfsq= areaphalf*areaphalf;		    
-		/**************************************************///     
-
-		/*Evaporating Mass*/
-		Mdotres(j)=Mdot(j) - Mdot(j-1); 
-
-		/*Mass:*/
-		/* ∂r/∂ψ = 1/ρA */
-		Rres(j)=((R(j)-R(j-1))/dpsim)-(TWO/(rhom*aream+rho*area));
-
-		/*Energy:*/
-		/* ∂T/∂t = - ṁ(∂T/∂ψ) 
-		 * 	   + (∂/∂ψ)(λρA²∂T/∂ψ) 
-		 * 	   - (A/cₚ) ∑ YᵢVᵢcₚᵢ(∂T/∂ψ) 
-		 * 	   - (1/ρcₚ)∑ ώᵢhᵢ 
-		 * 	   + (1/ρcₚ)(∂P/∂t) */
-		/*Notes: 
-		 * λ has units J/m/s/K.
-		 * YᵢVᵢ has units kg/m^2/s.
-		 * hᵢ has units J/kmol, so we must multiply the enthalpy
-		 * defined above (getEnthalpy_RT) by T (K) and the gas constant
-		 * (J/kmol/K) to get the right units.
-		 * cₚᵢ has units J/kg/K, so we must multiply the specific heat
-		 * defined above (getCp_R) by the gas constant (J/kmol/K) and
-		 * divide by the molecular weight (kg/kmol) to get the right
-		 * units.
-		 * */
-
-		//enthalpy formulation:
-		//tranTerm = Tdot(j) - (Pdot(j)/(rho*Cpb));
-		tranTerm = Tdot(j);
-		sum=ZERO;
-		sum1=ZERO;
-		for (k = 1; k <=nsp; k++) {
-			sum=sum+wdot(k)*enthalpy(k);
-			sum1=sum1+(Cp(k)/data->gas->molecularWeight(k-1))*rho
-			     *HALF*(YVmhalf(k)+YVphalf(k));
-		}
-		sum=sum*Cantera::GasConstant*T(j);
-		sum1=sum1*Cantera::GasConstant;
-		diffTerm  =(( (rhophalf*areaphalfsq*lambdaphalf*(T(j+1)-T(j))/dpsip)
-			      -(rhomhalf*areamhalfsq*lambdamhalf*(T(j)-T(j-1))/dpsim) )
-			     /(dpsiav*Cpb) )
-			  -(sum1*area*(cendfp*T(j+1)
-			              +cendfc*T(j)
-			              +cendfm*T(j-1))/Cpb);
-		srcTerm   = (sum-Qdot(&t,&R(j),&data->ignTime,&data->kernelSize,&data->maxQDot))/(rho*Cpb); // Qdot is forced heating to cause ignition, sum is the conversion of chemical enthalpy to sensible enthalpy
-		advTerm   = (Mdot(j)*(T(j)-T(j-1))/dpsim);
-		Tres(j)= tranTerm - (Pdot(j)/(rho*Cpb))
-			+advTerm 
-			-diffTerm
-			+srcTerm;
-
-	//	//energy formulation:
-	//	tranTerm = Tdot(j);
-	//	sum=ZERO;
-	//	sum1=ZERO;
-	//	sum2=ZERO;
-	//	sum3=ZERO;
-	//	for (k = 1; k <=nsp; k++) {
-	//		energy(k)=enthalpy(k)-ONE;
-	//		sum=sum+wdot(k)*energy(k);
-	//		sum1=sum1+(Cp(k)/data->gas->molecularWeight(k-1))*rho
-	//		     *HALF*(YVmhalf(k)+YVphalf(k));
-	//		sum2=sum2+(YVmhalf(k)/data->gas->molecularWeight(k-1));
-	//		sum3=sum3+(YVphalf(k)/data->gas->molecularWeight(k-1));
-	//	}
-	//	sum=sum*Cantera::GasConstant*T(j);
-	//	sum1=sum1*Cantera::GasConstant;
-	//	diffTerm  =(( (rhophalf*areaphalfsq*lambdaphalf*(T(j+1)-T(j))/dpsip)
-	//		      -(rhomhalf*areamhalfsq*lambdamhalf*(T(j)-T(j-1))/dpsim) )
-	//		     /(dpsiav*Cvb) )
-	//		  -(sum1*area*(cendfp*T(j+1)
-	//		              +cendfc*T(j)
-	//		              +cendfm*T(j-1))/Cvb);
-	//	srcTerm   = (sum-Qdot(&t,&R(j),&data->ignTime,&data->kernelSize,&data->maxQDot))/(rho*Cvb);
-	//	advTerm   = (mdotIn*(T(j)-T(j-1))/dpsim);
-	//	advTerm = advTerm + (Cantera::GasConstant*T(j)*area/Cvb)*((sum3-sum2)/dpsiav);
-	//	Tres(j)= tranTerm
-	//		+advTerm 
-	//		-diffTerm
-	//		+srcTerm;
-
-		/*Species:*/
-		/* ∂Yᵢ/∂t = - ṁ(∂Yᵢ/∂ψ) 
-		 * 	    - (∂/∂ψ)(AYᵢVᵢ) 
-		 * 	    + (ώᵢWᵢ/ρ)  */
-
-		sum=ZERO;
-		for (k = 1; k <=nsp; k++) {
-			if(k!=k_bath){
-				tranTerm  = Ydot(j,k);
-				diffTerm  = (YVphalf(k)*areaphalf
-					    -YVmhalf(k)*areamhalf)/dpsiav;
-				srcTerm   = wdot(k)
-			     		    *(data->gas->molecularWeight(k-1))/rho;
-				advTerm   = (Mdot(j)*(Y(j,k)-Y(j-1,k))/dpsim);
-
-				Yres(j,k)= tranTerm 
-					  +advTerm
-					  +diffTerm
-					  -srcTerm;
-
-		      		sum=sum+Y(j,k);
-			}
-		}
-		Yres(j,k_bath)=ONE-sum-Y(j,k_bath);
-
-		/*Pressure:*/
-		Pres(j) = P(j+1)-P(j);
-
-		/*Assign values evaluated at p and phalf to m       
-		 * and mhalf to save some cpu cost:****************/
-		areamhalf=areaphalf;                                
-		areamhalfsq=areaphalfsq;                            
-		aream=area;
-		rhom=rho;
-		rhomhalf=rhophalf;                                  
-		lambdamhalf=lambdaphalf;                            
-		for (k = 1; k <=nsp; k++) {                         
-			YVmhalf(k)=YVphalf(k);                      
-		}                                                   
-		/**************************************************/
-		                                                    
-	}                                                           
-	/*******************************************************************///
-
-
-	/*Fill up res with right side (wall) boundary conditions:***********/
-	/*We impose zero fluxes at the wall:*/                               
-	setGas(data,ydata,npts);
-	rho=data->gas->density();                               
-	area = calc_area(R(npts),&m);				   
-
-	/*Mass:*/                                                          
-	dpsim=(psi(npts)-psi(npts-1))*mass;
-	Rres(npts)=((R(npts)-R(npts-1))/dpsim)-(TWO/(rhom*aream+rho*area));
-
-	/*Energy:*/                                             
-	if(data->dirichletOuter){
-		//Tres(npts)=T(npts)-data->wallTemperature;
-		Tres(npts)=Tdot(npts);
-	}
-	else{
-		Tres(npts)=T(npts)-T(npts-1);
-	}
-                                                                
-	/*Species:*/                                            
-	sum=ZERO;
-	if(data->dirichletOuter){
-		for (k = 1; k <=nsp; k++) {                             
-			if(k!=k_bath){
-			    	Yres(npts,k)=Ydot(npts,k);
-			    	sum=sum+Y(npts,k);
-			}
-		}                                                       
-	}
-	else{
-		for (k = 1; k <=nsp; k++) {                             
-			if(k!=k_bath){
-			    	Yres(npts,k)=Y(npts,k)-Y(npts-1,k);
-			    	//Yres(npts,k)=YVmhalf(k);         
-			    	sum=sum+Y(npts,k);
-			}
-		}                                                       
-	}
-	Yres(npts,k_bath)=ONE-sum-Y(npts,k_bath);             
-                                                                
-	
-	/*Pressure:*/                                                      
-	if(data->constantPressure){
-		Pres(npts)=Pdot(npts)-data->dPdt;                                     
-	}
-	else{
-		Pres(npts)=R(npts)-data->domainLength;                     
-		//Pres(npts)=Rdot(npts);                     
-	}
-
-	/*Evaporating Mass*/
-	Mdotres(npts)=Mdot(npts) - Mdot(npts-1); 
-
-	//for (j = 1; j <=npts; j++) {
-	//	//for (k = 1; k <=nsp; k++) {
-	//	//	Yres(j,k)=Ydot(j,k);
-	//	//}
-	//	//Tres(j)=Tdot(j);
-	//}
-
-	return(0);
-
-}
-
-void printSpaceTimeHeader(UserData data)
-{
-	fprintf((data->output), "%15s\t","#1");
-	for (size_t k = 1; k <=data->nvar+1; k++) {
-		fprintf((data->output), "%15lu\t",k+1);
-	}
-	fprintf((data->output), "%15lu\n",data->nvar+3);
-
-	fprintf((data->output), "%15s\t%15s\t%15s\t","#psi","time(s)","dpsi");
-	fprintf((data->output), "%15s\t%15s\t","radius(m)","Temp(K)");
-	for (size_t k = 1; k <=data->nsp; k++) {
-		fprintf((data->output), "%15s\t",data->gas->speciesName(k-1).c_str());
-	}
-	fprintf((data->output), "%15s\t","Pressure(Pa)");
-	fprintf((data->output), "%15s\n","Mdot (kg/s)");
-}
-
-void printSpaceTimeOutput(double t, N_Vector* y, FILE* output, UserData data)
-{
-	double *ydata,*psidata;
-  	ydata    = N_VGetArrayPointer_OpenMP(*y);
-
-	if(data->adaptiveGrid){
-  		psidata  = data->grid->x;
-	}else{
-  		psidata  = data->uniformGrid;
-	}
-
-	for (size_t i = 0; i < data->npts; i++) {
-		fprintf(output, "%15.9e\t%15.9e\t",psi(i+1),t);
-		if(i==0){
-			fprintf(output, "%15.9e\t",psi(2)-psi(1));
-		}
-		else{
-			fprintf(output, "%15.6e\t",psi(i+1)-psi(i));
-		}
-		for (size_t j = 0; j < data->nvar; j++) {
-			if(j!=data->nvar-1){
-				fprintf(output, "%15.9e\t",ydata[j+i*data->nvar]);
-			}else{
-				fprintf(output, "%15.9e",ydata[j+i*data->nvar]);
-			}
-		}
-		fprintf(output, "\n");
-	}
-	fprintf(output, "\n");
-}
-
-void writeRestart(double t, N_Vector* y, N_Vector* ydot, FILE* output, UserData data){
-	double *ydata,*psidata, *ydotdata;
-	ydata = N_VGetArrayPointer_OpenMP(*y);
-	ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
-	if(data->adaptiveGrid){
-  		psidata  = data->grid->x;
-	}else{
-  		psidata  = data->uniformGrid;
-	}
- 	fwrite(&t, sizeof(t), 1, output);		//write time
- 	fwrite(psidata, data->npts*sizeof(psidata), 1, output);	//write grid
- 	fwrite(ydata, data->neq*sizeof(ydata), 1, output);	//write solution
- 	fwrite(ydotdata, data->neq*sizeof(ydotdata), 1, output);	//write solutiondot
-}
-
-void readRestart(N_Vector* y, N_Vector* ydot, FILE* input, UserData data){
-	double *ydata,*psidata, *ydotdata;
-	double t;
-	if(data->adaptiveGrid){
-  		psidata  = data->grid->x;
-	}else{
-  		psidata  = data->uniformGrid;
-	}
-	ydata = N_VGetArrayPointer_OpenMP(*y);
-	ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
- 	fread(&t, sizeof(t), 1, input);
-	data->tNow=t;
- 	fread(psidata, data->npts*sizeof(psidata), 1, input);
- 	fread(ydata, data->neq*sizeof(ydata), 1, input);
- 	fread(ydotdata, data->neq*sizeof(ydotdata), 1, input);
-	if(data->adaptiveGrid){
-		storeGrid(data->grid->x,data->grid->xOld,data->npts);
-	}
-}
-
-void printGlobalHeader(UserData data)
-{
-	fprintf((data->globalOutput), "%8s\t","#Time(s)");
-	//fprintf((data->globalOutput), "%15s","S_u(exp*)(m/s)");
-	fprintf((data->globalOutput), "%15s","bFlux(kg/m^2/s)");
-	fprintf((data->globalOutput), "%16s","  IsothermPos(m)");
-	fprintf((data->globalOutput), "%15s\t","Pressure(Pa)");
-	fprintf((data->globalOutput), "%15s\t","Pdot(Pa/s)");
-	fprintf((data->globalOutput), "%15s\t","gamma");
-	fprintf((data->globalOutput), "%15s\t","S_u(m/s)");
-	fprintf((data->globalOutput), "%15s\t","Tu(K)");
-	fprintf((data->globalOutput), "\n");
-}
-//
-//void printSpaceTimeRates(double t, N_Vector ydot, UserData data)
-//{
-//	double *ydotdata,*psidata;
-//  	ydotdata    = N_VGetArrayPointer_OpenMP(ydot);
-//  	psidata    = N_VGetArrayPointer_OpenMP(data->grid);
-//	for (int i = 0; i < data->npts; i++) {
-//		fprintf((data->ratesOutput), "%15.6e\t%15.6e\t",psi(i+1),t);
-//		for (int j = 0; j < data->nvar; j++) {
-//			fprintf((data->ratesOutput), "%15.6e\t",ydotdata[j+i*data->nvar]);
-//		}
-//		fprintf((data->ratesOutput), "\n");
-//	}
-//	fprintf((data->ratesOutput), "\n\n");
-//}
-//
-void printGlobalVariables(double t, N_Vector* y, N_Vector* ydot, UserData data)
-{
-	double *ydata,*ydotdata, *innerMassFractionsData, *psidata;
-	innerMassFractionsData =  data->innerMassFractions;
-
-	if(data->adaptiveGrid){
-  		psidata  = data->grid->x;
-	}else{
-  		psidata  = data->uniformGrid;
-	}
-
-	double TAvg, RAvg, YAvg, psiAvg;
-  	ydata    = N_VGetArrayPointer_OpenMP(*y);
-  	ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
-	TAvg=data->isotherm;
-	double sum=ZERO;
-	double dpsim,area,aream,drdt;
-	double Cpb,Cvb,gamma,rho,flameArea,Tu;
-
-
-	/*Find the isotherm chosen by the user*/
-	size_t j=1;
-	size_t jj=1;
-	size_t jjj=1;
-	double wdot[data->nsp];
-	double wdotMax=0.0e0;
-	double advTerm=0.0e0;
-	psiAvg=0.0e0;
-	if(T(data->npts)>T(1)){
-		while (T(j)<TAvg) {
-			j=j+1;
-		}
-		YAvg=innerMassFractionsData[data->k_oxidizer-1]-Y(data->npts,data->k_oxidizer);
-		while (fabs((T(jj+1)-T(jj))/T(jj))>1e-08) {
-			jj=jj+1;
-		}
-
-		setGas(data,ydata,jj);
-		Tu=T(jj);
-		rho=data->gas->density();
-        	Cpb=data->gas->cp_mass();       	//J/kg/K
-        	Cvb=data->gas->cv_mass();       	//J/kg/K
-		gamma=Cpb/Cvb;
-		
-	}
-	else{
-		while (T(j)>TAvg) {
-			j=j+1;
-		}
-		YAvg=innerMassFractionsData[data->k_oxidizer-1]-Y(1,data->k_oxidizer);
-		while (fabs((T(data->npts-jj-1)-T(data->npts-jj))/T(data->npts-jj))>1e-08) {
-			jj=jj+1;
-		}
-
-		setGas(data,ydata,data->npts-jj);
-		Tu=T(data->npts-jj);
-		rho=data->gas->density();
-        	Cpb=data->gas->cp_mass();       	//J/kg/K
-        	Cvb=data->gas->cv_mass();       	//J/kg/K
-		gamma=Cpb/Cvb;
-	}
-	if(T(j)<TAvg){
-		RAvg=((R(j+1)-R(j))/(T(j+1)-T(j)))*(TAvg-T(j))+R(j);
-	}
-	else{
-		RAvg=((R(j)-R(j-1))/(T(j)-T(j-1)))*(TAvg-T(j-1))+R(j-1);
-	}
-
-	////Experimental burning speed calculation:	
-	//int nMax=0;
-	////nMax=maxCurvIndex(ydata, data->nt, data->nvar,
-	////     	data->grid->x, data->npts);
-	//nMax=maxGradIndex(ydata, data->nt, data->nvar,
-	//     	data->grid->x, data->npts);
-	//advTerm=(T(nMax)-T(nMax-1))/(data->mass*(psi(nMax)-psi(nMax-1)));
-	//aream=calc_area(R(nMax),&data->metric);	    
-	////setGas(data,ydata,nMax);
-	////rho=data->gas->density();
-	//psiAvg=-Tdot(nMax)/(rho*aream*advTerm);
-	////if(t>data->ignTime){
-	////	for(size_t n=2;n<data->npts;n++){
-	////		setGas(data,ydata,n);
-	////		data->gas->getNetProductionRates(wdot); //kmol/m^3
-	////		advTerm=(T(n)-T(n-1))/(data->mass*(psi(n)-psi(n-1)));
-	////		if(fabs(wdot[data->k_oxidizer-1])>=wdotMax){
-	////			aream=calc_area(R(n),&data->metric);	    
-	////			psiAvg=-Tdot(n)/(rho*aream*advTerm);
-	////			wdotMax=fabs(wdot[data->k_oxidizer-1]);
-	////		}
-	////	}
-	////}
-	////else{
-	////	psiAvg=0.0e0;
-	////}
-
-
-	//drdt=(RAvg-data->flamePosition[1])/(t-data->flameTime[1]);
-	//data->flamePosition[0]=data->flamePosition[1];
-	//data->flamePosition[1]=RAvg;
-	//data->flameTime[0]=data->flameTime[1];
-	//data->flameTime[1]=t;
-	//flameArea=calc_area(RAvg,&data->metric);
-
-	/*Use the Trapezoidal rule to calculate the mass burning rate based on
-	 * the consumption of O2*/
-	aream= calc_area(R(1)+1e-03*data->domainLength,&data->metric);	    
-	for (j = 2; j <data->npts; j++) {
-        	dpsim=(psi(j)-psi(j-1))*data->mass;                            
-		area= calc_area(R(j),&data->metric);	    
-		sum=sum+HALF*dpsim*((Ydot(j-1,data->k_oxidizer)/aream)
-				   +(Ydot(j,data->k_oxidizer)/area));
-		aream=area;
-	}
-
-	//double maxOH,maxHO2;
-	//maxOH=0.0e0;
-	//maxHO2=0.0e0;
-	//for(j=1;j<data->npts;j++){
-	//	if(Y(j,data->k_OH)>maxOH){
-	//		maxOH=Y(j,data->k_OH);
-	//	}
-	//}
-	//for(j=1;j<data->npts;j++){
-	//	if(Y(j,data->k_HO2)>maxHO2){
-	//		maxHO2=Y(j,data->k_HO2);
-	//	}
-	//}
-
-	fprintf((data->globalOutput), "%15.6e\t",t);
-	//fprintf((data->globalOutput), "%15.6e\t",psiAvg);
-	fprintf((data->globalOutput), "%15.6e\t",fabs(sum)/YAvg);
-	fprintf((data->globalOutput), "%15.6e\t",RAvg);
-	fprintf((data->globalOutput), "%15.6e\t",P(data->npts));
-	fprintf((data->globalOutput), "%15.6e\t",Pdot(data->npts));
-	fprintf((data->globalOutput), "%15.6e\t",gamma);
-	fprintf((data->globalOutput), "%15.6e\t",fabs(sum)/(YAvg*rho));
-	fprintf((data->globalOutput), "%15.6e\t",Tu);
-	fprintf((data->globalOutput), "\n");
-}
-
-//
-//void printSpaceTimeOutputInterpolated(double t, N_Vector y, UserData data)
-//{
-//	double *ydata,*psidata;
-//  	ydata    = N_VGetArrayPointer_OpenMP(y);
-//  	psidata    = N_VGetArrayPointer_OpenMP(data->grid);
-//	for (int i = 0; i < data->npts; i++) {
-//		fprintf((data->gridOutput), "%15.6e\t%15.6e\t",psi(i+1),t);
-//		for (int j = 0; j < data->nvar; j++) {
-//			fprintf((data->gridOutput), "%15.6e\t",ydata[j+i*data->nvar]);
-//		}
-//		fprintf((data->gridOutput), "\n");
-//	}
-//	fprintf((data->gridOutput), "\n\n");
-//}
-//
-//
-////void repairSolution(N_Vector y, N_Vector ydot, UserData data){
-////	int npts=data->npts;
-////  	double *ydata;
-////  	double *ydotdata;
-////	ydata    = N_VGetArrayPointer_OpenMP(y); 
-////	ydotdata    = N_VGetArrayPointer_OpenMP(ydot); 
-////
-////	T(2)=T(1);
-////	T(npts-1)=T(npts);
-////	Tdot(2)=Tdot(1);
-////	Tdot(npts-1)=Tdot(npts);
-////	for (int k = 1; k <=data->nsp; k++) {
-////		    Y(2,k)=Y(1,k);
-////		    Y(npts-1,k)=Y(npts,k);
-////
-////		    Ydot(2,k)=Ydot(1,k);
-////		    Ydot(npts-1,k)=Ydot(npts,k);
-////	}
-////}
-
-
-/*Following functions are added to derive the characteristic time scale of species*/
-void getTimescale(UserData data, N_Vector* y){
-	size_t i, k, nsp,npts ; 
-	nsp = data->nsp ; 
-	npts = data->npts ; 
-	double rho, wdot_mole[nsp], wdot_mass[nsp],MW[nsp],concentra[nsp]; 
-	//double time_scale[npts*nsp] ;   
-
-	double* ydata ; 
-	ydata = N_VGetArrayPointer_OpenMP(*y); //access the data stored in N_Vector* y 
-	
-	for(i=1; i<= npts;i++){
-		setGas(data,ydata,i); //set the gas state at each grid point
-		rho = data->gas->density(); //get the averaged density at each grid point, Unit:kg/m^3
-		data->gas->getNetProductionRates(wdot_mole) ; //Unit:kmol/(m^3 * s)
-		
-		for(k=1; k<= nsp; k++){
-			MW(k) = data->gas->molecularWeight(k-1) ; //Unit:kg/kmol
-		}
-
-		for(k=1; k<= nsp; k++){
-			wdot_mass(k) = wdot_mole(k) * MW(k) ; //Unit:kg/(m^3 * s)
-		}
-
-		for(k=1; k<= nsp; k++){
-			concentra(k) = Y(i,k) * rho ;  //Unit:kg/m^3
-		}
-
-		for(k=1;k<= nsp;k++){
-			data->time_scale(i,k) = concentra(k)/(wdot_mass(k)+ 1.00e-16) ; 
-		}
-
-	}
-}
-
-
-void printTimescaleHeader(UserData data)
-{
-	fprintf((data->timescaleOutput), "%15s\t","#1");
-	for (size_t k = 1; k <=data->nsp+1; k++) {
-		fprintf((data->timescaleOutput), "%15lu\t",k+1);
-	}
-	fprintf((data->timescaleOutput), "%15lu\n",data->nsp+3);
-
-
-	fprintf((data->timescaleOutput), "%15s\t%15s\t%15s\t","#time","radius","Temp(K)");
-	//fprintf((data->output), "%15s\t%15s\t","radius(m)","Temp(K)");
-	for (size_t k = 1; k <=(data->nsp); k++) {
-		fprintf((data->timescaleOutput), "%15s\t",data->gas->speciesName(k-1).c_str());
-	}
-	//fprintf((data->output), "%15s\t","Pressure(Pa)");
-	//fprintf((data->timescaleOutput), "%15s\n",data->gas->speciesName(data->nsp-1).c_str());
-	//fprintf((data->output), "%15s\n","Mdot (kg/s)");
-	fprintf((data->timescaleOutput), "\n");
-}
-
-void printTimescaleOutput(double t,N_Vector* y,FILE* output,UserData data)
-{
-	double* ydata; 
-	ydata = N_VGetArrayPointer_OpenMP(*y); 
-
-	for(size_t i=1 ; i<= data->npts; i++){
-		fprintf(output, "%15.9e\t%15.9e\t",t,R(i));
-		fprintf(output, "%15.9e\t",T(i));
-        
-		for(size_t k=1; k<=data->nsp;k++){
-			fprintf(output, "%15.9e\t",data->time_scale(i,k));
-		}
-		fprintf(output, "\n");
-	}
-	fprintf(output, "\n");
-}
-
-void floorSmallValue(UserData data, N_Vector* y)
-{
-    double* ydata;
-    ydata = N_VGetArrayPointer_OpenMP(*y);
-    //double sum = 0.00; 
-    size_t k_bath = data->k_bath;
-   
-	/*Floor small values to zero*/
-	for (size_t i = 1; i <=data->npts; i++) {
-		for (size_t k = 1; k <=data->nsp; k++) {
-			if(fabs(Y(i,k))<=data->massFractionTolerance){
-				Y(i,k)=0.0e0;
-			}
-		}
-	}
-    
-    /*Dump the error to the bath gas*/
-	for (size_t i = 1; i <=data->npts; i++) {
-        double sum = 0.00;
-		for (size_t k = 1; k <=data->nsp; k++) {
-			if(k!=k_bath){
-				sum = sum + Y(i,k);
-			}
-		}
-        Y(i,k_bath) = ONE-sum;
-	}
-    
-
-}
-
-void resetTolerance(UserData data, N_Vector* y,N_Vector* atolv)
-{
-    double* ydata;
-    realtype* atolvdata; 
-    ydata = N_VGetArrayPointer_OpenMP(*y);
-    atolvdata = N_VGetArrayPointer_OpenMP(*atolv);
-    double relTol,radTol,tempTol,presTol,massFracTol,bathGasTol,mdotTol;
-    double maxT=0.00, deltaT=400.0;
-    relTol = 1.0e-03 ; 
-    radTol = 1.0e-05 ; 
-    tempTol = 1.0e-03 ; 
-    presTol = 1.0e-3 ; 
-    massFracTol = 1.0e-06; 
-    bathGasTol = 1.0e-05 ; 
-    mdotTol = 1.0e-10 ; 
-
-
-    /*Get the maximum Temperature*/
-    for (size_t i =1;i <= data->npts;i++){
-        if(T(i) > maxT){
-            maxT = T(i);
-        }
-    }
-
-    /*reset the tolerance when maxT > initialTemperature +deltaT*/
-    if(maxT >= (data->initialTemperature + deltaT)){
-        data->relativeTolerance = relTol;
-
-        for(size_t i =1; i<=data->npts; i++){
-            atolT(i) = tempTol; 
-            atolR(i) = radTol ; 
-            atolP(i) = presTol ;
-            atolMdot(i) = mdotTol ; 
-            
-            for(size_t k =1; k<= data->nsp; k++){
-                if(k!=data->k_bath){
-                    atolY(i,k) = massFracTol;
-                }else{
-                    atolY(i,k) = bathGasTol;
-                }
-            }
-        }
-    }
-
-}
-
-void getReactions(UserData data,N_Vector* y,FILE* output){
-    double Tmax;
-    double* ydata; 
-    //double deltaT = 400.0;
-    //int i = 0;
-    size_t nRxns;
-    int index;
-    nRxns = data->gas->nReactions();
-    //DEBUG
-    printf("Total Number of Rxns:%zu \n",nRxns);
-    double fwdROP[nRxns],revROP[nRxns],netROP[nRxns];
-    std::string* rxnArr = new std::string[nRxns];
-    /*DEBUG*/
-  	printf("Memory Allocation for Rxns Array Succeed!\n");
-    ydata = N_VGetArrayPointer_OpenMP(*y);
-    Tmax = maxTemperature(ydata,data->nt,data->nvar,data->npts);
-    //get the rxns' equation array
-    for(size_t ii=0;ii<nRxns;ii++){
-        rxnArr[ii]= data->gas->reactionString(ii);
-    }
-    if(Tmax>=(data->initialTemperature+data->deltaT)){
-        index = maxTemperatureIndex(ydata,data->nt,data->nvar,data->npts); 
-        setGas(data,ydata,index);
-        /*Get forward/reverse/net rate of progress of rxns*/
-        data->gas->getRevRatesOfProgress(revROP);
-        data->gas->getFwdRatesOfProgress(fwdROP);
-        data->gas->getNetRatesOfProgress(netROP);
-	    for(size_t j=0 ; j<nRxns; j++){
-            fprintf(output,"%30s\t",rxnArr[j]);
-            fprintf(output,"%15.9e\t%15.9e\t%15.9e\t\n",fwdROP[j],revROP[j],netROP[j]);
-	    }
-	    fprintf(output, "\n");
-        fclose(output);
-     }
-     delete[] rxnArr;
-}
-
-void getSpecies(UserData data,N_Vector* y,FILE* output){
-    double Tmax;
-    double* ydata; 
-    //double deltaT = 400.0;
-    //int i = 0;
-    int index;
-    double fwdROP[data->nsp],revROP[data->nsp],netROP[data->nsp];
-    std::string* spArr = new std::string[data->nsp];
-    /*DEBUG*/
-  	printf("Memory Allocation for Species Array Succeed!\n");
-    ydata = N_VGetArrayPointer_OpenMP(*y);
-    Tmax = maxTemperature(ydata,data->nt,data->nvar,data->npts);
-    //get the species name array
-    for(size_t ii=0;ii<data->nsp;ii++){
-        spArr[ii]= data->gas->speciesName(ii);
-    }
-   
-    if(Tmax>=(data->initialTemperature+data->deltaT)){
-        //i = i + 1 ;
-        index = maxTemperatureIndex(ydata,data->nt,data->nvar,data->npts); 
-        setGas(data,ydata,index);
-        /*Get forward/reverse/net rate of progress of rxns*/
-        data->gas->getDestructionRates(revROP);
-        data->gas->getCreationRates(fwdROP);
-        data->gas->getNetProductionRates(netROP);
-        /*Print data to the pertinent output file*/
-	    for(size_t j=0 ; j<data->nsp; j++){
-            fprintf(output,"%15s\t",spArr[j]);
-            fprintf(output,"%15.9e\t%15.9e\t%15.9e\t\n",fwdROP[j],revROP[j],netROP[j]);
-	    }
-	    fprintf(output, "\n");
-        fclose(output);
-    }
-    delete[] spArr;
-}
diff --git a/residue.d b/residue.d
deleted file mode 100644
index d15b94b..0000000
--- a/residue.d
+++ /dev/null
@@ -1,67 +0,0 @@
-residue.o: residue.cpp residue.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_types.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_config.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/nvector/nvector_openmp.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_nvector.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/IdealGasMix.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/IdealGasPhase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/ThermoPhase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/Phase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ctexceptions.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/fmt.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ct_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/config.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/format.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/core.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/format-inl.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/format.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/printf.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/ostream.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/ext/fmt/ostream.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/Elements.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ct_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/Species.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/AnyMap.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/global.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/AnyMap.inl.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ValueCache.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/MultiSpeciesThermo.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/SpeciesThermoInterpType.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/speciesThermoTypes.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/GasKinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/BulkKinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Kinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/thermo/ThermoPhase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/StoichManager.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/stringUtils.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Reaction.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/utilities.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/global.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/RxnRates.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/reaction_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Falloff.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/RateCoeffMgr.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/RxnRates.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/ThirdBodyCalc.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/FalloffMgr.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/reaction_defs.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/FalloffFactory.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/FactoryBase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/Reaction.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/kinetics/importKinetics.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/stringUtils.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportFactory.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportBase.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LiquidTransportParams.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportParams.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/numerics/DenseMatrix.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/Array.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/utilities.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LiquidTranInteraction.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LiquidTransportData.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/LTPspecies.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/transport/TransportData.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/xml.h \
- /opt/scientific/cantera-2.4_gnu_blas/include/cantera/base/ctexceptions.h \
- UserData.h gridRoutines.h parse.h parse.hpp macros.h timing.hpp
diff --git a/residue.h b/residue.h
deleted file mode 100644
index eb29392..0000000
--- a/residue.h
+++ /dev/null
@@ -1,116 +0,0 @@
-#ifndef SUNDIALS_DEF
-#define SUNDIALS_DEF
-#include <sundials/sundials_types.h>
-#include <nvector/nvector_openmp.h>
-#endif
-
-#ifndef PRINT_DEF
-#define PRINT_DEF
-#include <string.h>	//for strings
-#include <string>
-#include <cstring>
-#include <stdio.h>	//for printf,scanf
-#include <stdlib.h>	//for atoi, atof
-#endif
-
-#ifndef CANTERA_DEF
-#define CANTERA_DEF
-#include <cantera/IdealGasMix.h>
-#include <cantera/transport.h>
-#endif
-
-#include "UserData.h"
-
-void REGRID(double* ydata,double* ydotdata,UserData data);
-
-void INTERPO(double* y,double* ydot,const size_t nvar,size_t nPts,const double XNEW[], const double XOLD[]);
-
-double maxTemperaturePosition(const double* y,const size_t nt,const size_t nvar,const double* x ,size_t nPts);
-
-double maxTemperature(const double* y,const size_t nt, const size_t nvar, size_t nPts); 
-
-int maxTemperatureIndex(const double* y,const size_t nt,const size_t nvar ,size_t nPts);
-
-double maxCurvPositionR(const double* y, const size_t nt, 
-	               const size_t nvar, const size_t nr, size_t nPts);
-
-int maxCurvIndexR(const double* y, const size_t nt, 
-	               const size_t nvar, const size_t nr, size_t nPts);
-
-double maxGradPosition(const double* y, const size_t nt, 
-	               const size_t nvar, const double* x, size_t nPts);
-
-int maxGradIndex(const double* y, const size_t nt, 
-	         const size_t nvar, const double* x, size_t nPts);
-
-double maxCurvPosition(const double* y, const size_t nt, 
-	               const size_t nvar, const double* x, size_t nPts);
-
-int maxCurvIndex(const double* y, const size_t nt, 
-	               const size_t nvar, const double* x, size_t nPts);
-
-double isothermPosition(const double* y, const double T, const size_t nt, 
-	                const size_t nvar, const double* x, const size_t nPts);
-
-int setAlgebraicVariables(N_Vector *id,UserData data);
-
-inline double calc_area(double x,int* i);
-
-void updateSolution(double* y, double* ydot, const size_t nvar,
-		    const double xOld[],const double xNew[],const size_t npts);
-
-void readInitialCondition(FILE* input, double* ydata, const size_t nvar, const size_t nr, const size_t nPts);
-
-double systemMass(double* ydata, UserData data);
-
-int initializePsiGrid(double* ydata, double* psidata, UserData data);
-
-int setInitialCondition(N_Vector* y, 
-	    		N_Vector* ydot, 
-            		UserData data);
-
-
-inline void setGas(UserData data, double *ydata, size_t gridPoint);
-
-void getTransport(UserData data, 
-		  double *ydata, 
-		  size_t gridPoint,
-		  double *rho,
-		  double *lambda,
-		  double *YV);
-
-int residue(double t, 
-	    N_Vector y, 
-	    N_Vector ydot, 
-	    N_Vector res, 
-            void *user_data);
-
-void trackFlameOH(N_Vector y,UserData data);
-void trackFlame(N_Vector y,UserData data);
-size_t BathGasIndex(UserData data);
-size_t oxidizerIndex(UserData data);
-
-inline double Qdot(double* t, 
-	           double* x, 
-	           double* ignTime, 
-	           double* kernelSize, 
-	           double* maxQdot);
-
-void printSpaceTimeHeader(UserData data);
-void printSpaceTimeOutput(double t, N_Vector* y, FILE* output, UserData data);
-void printSpaceTimeRates(double t, N_Vector ydot, UserData data);
-void printGlobalHeader(UserData data);
-void printGlobalVariables(double t, N_Vector* y, N_Vector* ydot, UserData data);
-void printSpaceTimeOutputInterpolated(double t, N_Vector y, UserData data);
-
-void writeRestart(double t, N_Vector* y, N_Vector* ydot, FILE* output, UserData data);
-void readRestart(N_Vector* y, N_Vector* ydot, FILE* input, UserData data);
-
-void getTimescale(UserData data, N_Vector* y);
-void printTimescaleHeader(UserData data);
-void printTimescaleOutput(double t,N_Vector* y,FILE* output,UserData data);
-void floorSmallValue(UserData data, N_Vector* y);
-void resetTolerance(UserData data, N_Vector* y,N_Vector* atolv);
-
-void getReactions(UserData data,N_Vector* y,FILE* output);
-void getSpecies(UserData data,N_Vector* y,FILE* output);
diff --git a/residue.o b/residue.o
deleted file mode 100644
index 37cdc94..0000000
Binary files a/residue.o and /dev/null differ
diff --git a/solution.cpp b/solution.cpp
deleted file mode 100644
index 9e13b06..0000000
--- a/solution.cpp
+++ /dev/null
@@ -1,90 +0,0 @@
-#include "solution.h"
-int allocateSolution(size_t neq, 
-		     int nThreads,
-		     N_Vector *y, 
-		     N_Vector *ydot, 
-		     N_Vector *res, 
-		     N_Vector *id, 
-		     N_Vector *atolv,
-		     N_Vector *constraints){
-
-
-  	*y = N_VNew_OpenMP(neq,nThreads);
-  	if(*y==NULL){
-		printf("Allocation Failed!\n");
-		return(1);
-	}
-  	N_VConst((realtype)(0.0e0), *y);
-
-  	*ydot = N_VNew_OpenMP(neq,nThreads);
-  	if(*ydot==NULL){
-		printf("Allocation Failed!\n");
-		return(1);
-	}
-  	N_VConst((realtype)(0.0e0), *ydot);
-
-  	*res = N_VNew_OpenMP(neq,nThreads);
-  	if(*res==NULL){
-		printf("Allocation Failed!\n");
-		return(1);
-	}
-  	N_VConst((realtype)(0.0e0), *res);
-
-  	*id = N_VNew_OpenMP(neq,nThreads);
-  	if(*id==NULL){
-		printf("Allocation Failed!\n");
-		return(1);
-	}
-  	N_VConst((realtype)(1.0e0), *id);
-
-  	*atolv = N_VNew_OpenMP(neq,nThreads);
-  	if(*atolv==NULL){
-		printf("Allocation Failed!\n");
-		return(1);
-	}
-  	N_VConst((realtype)(0.0e0), *atolv);
-
-  	*constraints = N_VNew_OpenMP(neq,nThreads);
-  	if(*constraints==NULL){
-		printf("Allocation Failed!\n");
-		return(1);
-	}
-  	N_VConst((realtype)(0.0e0), *constraints);
-
-	return(0);
-}
-
-void freeSolution(N_Vector *y, 
-		  N_Vector *ydot, 
-		  N_Vector *res, 
-		  N_Vector *id, 
-		  N_Vector *atolv,
-		  N_Vector *constraints){
-
-  	if(*y!=NULL){
-		N_VDestroy_OpenMP(*y);
-		printf("y Destroyed!\n");
-	}
-	if(*ydot!=NULL){
-  		N_VDestroy_OpenMP(*ydot);
-		printf("ydot Destroyed!\n");
-	}
-	if(*res!=NULL){
-  		N_VDestroy_OpenMP(*res);
-		printf("res Destroyed!\n");
-	}
-	if(*id!=NULL){
-  		N_VDestroy_OpenMP(*id);
-		printf("id Destroyed!\n");
-	}
-	if(*atolv!=NULL){
-  		N_VDestroy_OpenMP(*atolv);
-		printf("atolv Destroyed!\n");
-	}
-
-	if(*constraints!=NULL){
-  		N_VDestroy_OpenMP(*constraints);
-		printf("constraints Destroyed!\n");
-	}
-	printf("\n\n");
-}
diff --git a/solution.d b/solution.d
deleted file mode 100644
index c73e56c..0000000
--- a/solution.d
+++ /dev/null
@@ -1,5 +0,0 @@
-solution.o: solution.cpp solution.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_types.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_config.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/nvector/nvector_openmp.h \
- /opt/scientific/sundials-3.1.1_intel_mkl/include/sundials/sundials_nvector.h
diff --git a/solution.h b/solution.h
deleted file mode 100644
index 7f220c3..0000000
--- a/solution.h
+++ /dev/null
@@ -1,15 +0,0 @@
-#ifndef PRINT_DEF
-#define PRINT_DEF
-#include <string.h>	//for strings
-#include <stdio.h>	//for printf,scanf
-#include <stdlib.h>	//for atoi, atof
-#endif
-
-#ifndef SUNDIALS_DEF
-#define SUNDIALS_DEF
-#include <sundials/sundials_types.h>
-#include <nvector/nvector_openmp.h>
-#endif
-
-int allocateSolution(size_t neq, int nThreads, N_Vector *y, N_Vector *ydot, N_Vector *res, N_Vector *id, N_Vector *atolv, N_Vector *constraints);
-void freeSolution(N_Vector *y, N_Vector *ydot, N_Vector *res, N_Vector *id, N_Vector *atolv, N_Vector *constraints);
diff --git a/solution.o b/solution.o
deleted file mode 100644
index f6e84ed..0000000
Binary files a/solution.o and /dev/null differ
diff --git a/src/UserData.cpp b/src/UserData.cpp
index 995d1f1..d43b70c 100644
--- a/src/UserData.cpp
+++ b/src/UserData.cpp
@@ -2,7 +2,18 @@
 #include "parse.h"
 
 void freeUserData(UserData data){
+
 	if(data!=NULL){
+        /*destructor for C++ vector*/
+        using Td = std::vector<double>;
+        using Ts = std::vector<std::string>;
+        using Tt = std::vector<size_t>;
+        data->dropMole.~Td();
+        data->dropSpec.~Ts();
+        data->gamma.~Td();
+        data->MW.~Td();
+        data->k_drop.~Tt();
+
 		if(data->trmix!=NULL){
 			delete data->trmix;
 			printf("Transport Deleted!\n");
@@ -53,10 +64,10 @@ void freeUserData(UserData data){
   			fclose(data->globalOutput);
 			printf("Global Output File Cleared from Memory!\n");
 		}
-		if(data->timescaleOutput!=NULL){
-  			fclose(data->timescaleOutput);
-			printf("Characteristic Timescale Output File Cleared from Memory!\n");
-		}
+		// if(data->timescaleOutput!=NULL){
+  		// 	fclose(data->timescaleOutput);
+		// 	printf("Characteristic Timescale Output File Cleared from Memory!\n");
+		// }
 		//if(data->rxnROPOutput!=NULL){
   		//	fclose(data->rxnROPOutput);
 		//	printf("Reactions Rate of Progress Output File Cleared from Memory!\n");
@@ -74,6 +85,11 @@ UserData allocateUserData(FILE *input){
 
 	UserData data;
   	data = (UserData) malloc(sizeof *data);
+    new(&(data->dropMole)) std::vector<double>;
+    new(&(data->dropSpec)) std::vector<std::string>;
+    new(&(data->gamma))   std::vector<double>;
+    new(&(data->MW))   std::vector<double>;
+    new(&(data->k_drop))   std::vector<size_t>;
 
 	if(!data){
 		printf("Allocation Failed!\n");
@@ -83,9 +99,14 @@ UserData allocateUserData(FILE *input){
 
 	int ier;
 
-	ier=parseNumber<size_t>(input, "basePts"	, MAXBUFLEN, &data->npts);
-	if(ier==-1 || data->npts<=0){
-		printf("Enter non-zero basePts!\n");
+	ier=parseNumber<size_t>(input, "liquidBasePts"	, MAXBUFLEN, &data->l_npts);
+	if(ier==-1 || data->l_npts<=0){
+		printf("Enter non-zero liquidbasePts!\n");
+		return(NULL);
+	}
+	ier=parseNumber<size_t>(input, "gasBasePts"	, MAXBUFLEN, &data->g_npts);
+	if(ier==-1 || data->g_npts<=0){
+		printf("Enter non-zero gasBasePts!\n");
 		return(NULL);
 	}
 
@@ -120,16 +141,16 @@ UserData allocateUserData(FILE *input){
 		return(NULL);
 	}
 
-	ier=parseNumber<int>(input,"dropType",MAXBUFLEN,&data->dropType);
+	ier=parseNumber<int>(input,"dropletType",MAXBUFLEN,&data->dropType);
 	if(ier==-1 || (data->dropType!=0 
 		       && data->dropType!=1)){
 		printf("include valid dropletType!\n");
 		printf("0: single component droplet\n");
-		printf("1: multi-component droplet\n");
+		printf("1: bi-component droplet\n");
 		return(NULL);
 	}
 
-	ier=parseDropSpec<double>(input,"dropletMole",MAXBUFLEN,&data->dropType,dropMole);
+	ier=parseDropSpec<double>(input,"dropletMole",MAXBUFLEN,&data->dropType,data->dropMole);
 	if(ier== -1){
 		printf("include correct format for droplet mole fraction!\n");
 		printf("single composition droplet: dropletMole:1.00\n");
@@ -137,7 +158,7 @@ UserData allocateUserData(FILE *input){
 		return(NULL);
 	}
 
-	ier=parseDropSpec<std::string>(input,"dropletComposition",MAXBUFLEN,&data->dropType,dropSpec);
+	ier=parseDropSpec<std::string>(input,"dropletComposition",MAXBUFLEN,&data->dropType,data->dropSpec);
 	if(ier== -1){
 		printf("include correct format for droplet composition!\n");
 		printf("single composition droplet: dropletComposition:n-heptane\n");
@@ -146,14 +167,14 @@ UserData allocateUserData(FILE *input){
 	}
 	
 	
-	//ier=parseNumber<int>(input, "quasiSteady"	, MAXBUFLEN, &data->quasiSteady);
-	//if(ier==-1 || (data->quasiSteady!=0 
-	//	       && data->quasiSteady!=1)){
-	//	printf("include valid quasiSteady!\n");
-	//	printf("0: The droplet surface recedes and the droplet losses mass\n");
-	//	printf("1: The droplet surface does not move and the droplet mass is constant\n");
-	//	return(NULL);
-	//}
+	ier=parseNumber<int>(input, "quasiSteady"	, MAXBUFLEN, &data->quasiSteady);
+	if(ier==-1 || (data->quasiSteady!=0 
+		       && data->quasiSteady!=1)){
+		printf("include valid quasiSteady!\n");
+		printf("0: The droplet surface recedes and the droplet losses mass\n");
+		printf("1: The droplet surface does not move and the droplet mass is constant\n");
+		return(NULL);
+	}
 
 	ier=parseNumber<double>(input, "dPdt", MAXBUFLEN, &data->dPdt);
 
@@ -340,6 +361,13 @@ UserData allocateUserData(FILE *input){
     		}
 	}
 
+//	/*No. of liquid phase species is determined by droplet type, either 1 or 2*/
+//	if(data->dropType==0){
+//		data->l_nsp=1;
+//	}else{
+//		data->l_nsp=2;
+//	}
+
 	ier=parseNumber<char>(input, "transportModel", MAXBUFLEN, tran);
 	if(ier==-1){
 		printf("Enter transportModel!\n");
@@ -371,7 +399,7 @@ UserData allocateUserData(FILE *input){
     			}
 		}
 	}
-
+	
 	//ier=parseNumber<char>(input, "dropletComposition", MAXBUFLEN, data->dropSpec);
 	//if(ier==-1){
 	//	printf("Enter composition of droplet!\n");
@@ -390,43 +418,62 @@ UserData allocateUserData(FILE *input){
     
 
 	ier=parseNumber<double>(input, "PCAD", MAXBUFLEN, &data->PCAD);
-	if(ier==-1){
-		printf("Enter PCAD value!\n");
-		return(NULL);
-	}
+	// if(ier==-1){
+	// 	printf("Enter PCAD value!\n");
+	// 	return(NULL);
+	// }
     ier=parseNumber<double>(input,"RGTC", MAXBUFLEN, &data->RGTC);
-	if(ier==-1){
-		printf("Enter PGTC value!\n");
-		return(NULL);
-	}
+	// if(ier==-1){
+	// 	printf("Enter PGTC value!\n");
+	// 	return(NULL);
+	// }
     ier=parseNumber<int>(input,"JJRG", MAXBUFLEN, &data->JJRG);
-	if(ier==-1){
-		printf("Enter JJRG value!\n");
-		return(NULL);
-	}
+	// if(ier==-1){
+	// 	printf("Enter JJRG value!\n");
+	// 	return(NULL);
+	// }
     ier=parseNumber<double>(input,"deltaT", MAXBUFLEN, &data->deltaT);
-	if(ier==-1){
-		printf("Enter deltaT value!\n");
-		return(NULL);
-	}
+	// if(ier==-1){
+	// 	printf("Enter deltaT value!\n");
+	// 	return(NULL);
+	// }
 	
     data->nr=0;
 	//data->np=data->nr+1;
 	data->nt=data->nr+1;
 	data->ny=data->nt+1;
 	data->np=data->ny+data->nsp;
-	data->nm=data->np+1;
-				
+	data->nm=data->np+1;			
 	data->nvar=data->nsp+4;		 //assign no: of variables (R,T,P,Mdot,nsp species)
 
-
-    double MW[2]; 
-    for(int i=0;i<=1;i++){
-        int speciesIndex = data->gas->speciesIndex(data->dropSpec[i]);
-        double weight = data->gas->molecularWeight(speciesIndex);
-        MW[i]= weight;
+	// data->l_nr=0;
+	// data->np=data->nr+1;
+	// data->l_nt=data->l_nr+1;
+	// data->l_ny=data->l_nt+1;
+	// data->l_np=data->l_ny+data->l_nsp; //l_nsp is either 1 or 2
+	// data->l_nm=data->l_np+1;			
+	// data->l_nvar=data->l_nsp+4;
+
+	data->npts = data->l_npts+data->g_npts;
+    //std::vector<double> MW(data->dropMole.size());
+    for(size_t ii=0;ii< data->dropMole.size();ii++){
+//        printf("Print inside the loop.\n" ) ;
+//        printf("Print dropSpec component :%s! \n",data->dropSpec[0].c_str());
+//        size_t index = 0;
+        for(size_t k = 1; k <= data->nsp; k++) {
+            printf("spcies name :%s! \t",data->gas->speciesName(k-1).c_str());
+            if(data->gas->speciesName(k - 1)==data->dropSpec[ii] ) {
+//                index = k;
+                double weight = data->gas->molecularWeight(k-1);
+                printf("Molecular weight is: %.3f. \n",weight) ;
+                data->MW.push_back(weight);
+            }
+        }
+    }
+//    printf("MW array size: %zu\n",data->MW.size());
+    for(auto & arg :data->MW){
+        printf("Molecular weight : %.3f. \n",arg) ;
     }
-
     // double massSum = 0.0; 
     // for(int i=0;i<=1;i++){
     //     massSum = massSum + data->dropMole[i] * MW[i];
@@ -437,19 +484,29 @@ UserData allocateUserData(FILE *input){
     //     data->dropRho = data->dropRho + data->dropMassFrac[i]*data->dropDens[i];
     // }
 	
-    printf("Density of droplet is: %.3f [kg/m^3]\n",data->dropRho);
-	//Mass of droplet
+    // printf("Density of droplet is: %.3f [kg/m^3]\n",data->dropRho);
+	// Mass of droplet
 	//data->massDrop=1.0/3.0*pow(data->Rd,3)*997.0; //TODO: The density of the droplet should be a user input
     //data->massDrop=1.0/3.0*pow(data->Rd,3)*684.00; //TODO: The density of the droplet(n-heptane) should be a user input
-    data->massDrop=1.0/3.0*pow(data->Rd,3)*data->dropRho;
+    // data->massDrop=1.0/3.0*pow(data->Rd,3)*data->dropRho;
 
 	/* Update the gamma using UNIFAC method for propane and n-heptane */
-	getGamma(data->dropMole,data->gamma) ; 
-	printf("Gamma of Propane and n-heptane are %.3f and %.3f .\n",data->gamma[0],data->gamma[1]) ;
+	/*Note: gamma only need to be calculated when droplet type = 1, i.e. bi-component*/
+	getGamma(data->dropMole,data->gamma); 
+//	printf("Gamma of Propane and n-heptane are %.3f and %.3f .\n",data->gamma[0],data->gamma[1]) ;
+    if(data->dropType == 0){
+        printf("Single component droplet problem, activity coeffcient is 1. \n");
+    }else{
+        for(auto & arg : data->gamma) {
+            printf("Initial activity coeffcient %.3f .\n",arg);
+        }
+    }
 
 	if(!data->adaptiveGrid){
 		data->uniformGrid = new double [data->npts];
-		data->neq=data->nvar*data->npts;
+		// data->g_neq=data->g_nvar*data->g_npts; 
+		// data->l_neq=data->l_nvar*data->l_npts;
+		data->neq=data->npts*data->nvar;
 	}
 	else{
 		data->grid=(UserGrid) malloc(sizeof *data->grid);
@@ -469,9 +526,9 @@ UserData allocateUserData(FILE *input){
 	data->output=fopen("output.dat","w");
 	data->globalOutput=fopen("globalOutput.dat","w");
 	data->gridOutput=fopen("grid.dat","w");
-	data->timescaleOutput=fopen("timeScale.dat","w") ;
-    data->rxnROPOutput=fopen("rxnROP.dat","w");
-    data->spROPOutput=fopen("spROP.dat","w");
+	// data->timescaleOutput=fopen("timeScale.dat","w") ;
+    // data->rxnROPOutput=fopen("rxnROP.dat","w");
+    // data->spROPOutput=fopen("spROP.dat","w");
 	//data->ratesOutput=fopen("rates.dat","w");
 	
 	data->innerMassFractions = new double [data->nsp];
@@ -518,6 +575,7 @@ void setSaneDefaults(UserData data){
 	data->pressureTolerance=1e-06;
 	data->massFractionTolerance=1e-09;
 	data->bathGasTolerance=1e-06;
+	data->MdotTolerance=1e-09;
 	data->finalTime=1e-02;
 	data->tNow=0.0e0;
 	data->setConstraints=0;
@@ -571,5 +629,46 @@ void getGamma(const double mole[],double gamma[]){
     for(int i=0; i<v_.size(); i++){
         gamma[i] = gammaC_[i] ;
     }
+}
+
+
+void getGamma(const std::vector<double>& mole,std::vector<double>& gamma){
+	size_t sz = mole.size();
+	if (sz == 1){
+		gamma.push_back(1); 
+	}else{
+        gamma.reserve(mole.size());
+		/* define relevant matrix */
+		Eigen::Matrix2d nu_ ;
+		nu_ << 2,1,2,5;
+		/* define relevant vectors */
+		Eigen::Vector2d R_(0.9011,0.6744),Q_(0.8480,0.5400);
+		Eigen::Vector2d r_,q_,x_,l_,ones_(1.0,1.0),v_,ksi_,gammaC_;
+		double sum_q, sum_r,sum_l;
+
+		r_ = nu_ * R_ ;
+		q_ = nu_ * Q_ ;
+		x_ << mole[0], mole[1] ;
+
+		sum_q = x_.dot(q_) ;
+		sum_r = x_.dot(r_) ;
+
+		for(size_t i=0; i<v_.size() ; i++){
+			v_[i] = q_[i] * x_[i] / sum_q;
+			ksi_[i] = r_[i] * x_[i] / sum_r ;
+		}
 
+		l_ = 5 * (r_ - q_) - (r_ - ones_) ;
+		sum_l = l_.dot(x_) ;
+		/* calculate the gamma_c  */
+		for(size_t i=0; i<v_.size() ; i++){
+			gammaC_[i] =std::exp( std::log(ksi_[i]/x_[i]) + 5*q_[i]*std::log(v_[i]/ksi_[i]) + l_[i] - ksi_[i]/x_[i]*sum_l );
+		}
+		/******* gamma_R for both propane and n-heptane are 0 **********/
+		/* return the gamma */
+		for(size_t i=0; i<v_.size(); i++){
+			gamma.push_back(gammaC_[i]);
+		}
+	}
+	
 }
\ No newline at end of file
diff --git a/src/main.cpp b/src/main.cpp
index b5568c9..2b7da4e 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -33,11 +33,10 @@ void freeAtLast(void* mem, N_Vector *y,
 int main(){
 
 	// Read input file specifying the details of the case and store them
-  	FILE *input;input=fopen("input.dat","r");
-  	UserData data;data=NULL;data=allocateUserData(input);
+  	FILE *input =fopen("input.dat","r");
+  	UserData data=allocateUserData(input);
 	fclose(input);
-	data->clockStart=get_wall_time();
-
+    data->clockStart=get_wall_time();
 
 //     /**************** TEST THE xOld *******************/
 //     double* ptr1 = data->grid->xOld ; 
@@ -118,7 +117,7 @@ int main(){
 	ier=IDADlsSetLinearSolver(mem,LS,A);
   	//ier = IDABand(mem, data->neq, mu, ml);
 
-        constraintsdata = N_VGetArrayPointer_OpenMP(constraints);
+    constraintsdata = N_VGetArrayPointer_OpenMP(constraints);
 	if(data->setConstraints){
 		for (size_t i = 1; i <=data->npts; i++) {
              		for (size_t k = 1; k <=data->nsp; k++) {
@@ -137,9 +136,11 @@ int main(){
   	if(check_flag(&ier, "IDASetSuppressAlg", 1)) return(1);
 
 	//ier= IDASetMaxNumStepsIC(mem, 1);
-	//ier= IDASetMaxNumJacsIC(mem,8);
-	//ier= IDASetMaxNumItersIC(mem,100);
-	//ier= IDASetMaxBacksIC(mem,2000);
+//    ier= IDASetMaxNumStepsIC(mem, 8);
+    //ier= IDASetMaxNumJacsIC(mem,8);
+//	ier= IDASetMaxNumItersIC(mem,100);
+//	ier= IDASetMaxBacksIC(mem,2000);
+//	ier= IDASetMaxBacksIC(mem,1000);
 	//ier = IDASetLineSearchOffIC(mem,SUNTRUE);
 
 	//////// DEBUG ///////////
@@ -169,7 +170,8 @@ int main(){
 		printf("Calculating Initial Conditions:\n");
 		printf("Cross your fingers...\n");
 
-  		ier = IDACalcIC(mem, IDA_YA_YDP_INIT, 1e-5*finalTime);
+//  		ier = IDACalcIC(mem, IDA_YA_YDP_INIT, 1e-5*finalTime);
+  		ier = IDACalcIC(mem, IDA_YA_YDP_INIT, 1e-7*finalTime);
 
 		//If at first IDACalcIC doesn't succeed, try, try, try again:
 		for (int i = 0; i < 10; i++) {
@@ -195,7 +197,7 @@ int main(){
 
 	printSpaceTimeHeader(data);
 	printGlobalHeader(data);
-	printTimescaleHeader(data);
+	//printTimescaleHeader(data);
 	printSpaceTimeOutput(tNow, &y, data->output, data);
 	printSpaceTimeOutput(tNow, &y, data->gridOutput, data);
 
@@ -223,11 +225,11 @@ int main(){
 			//xOld=isothermPosition(ydata, data->isotherm, data->nt, 
 	        //        		   data->nvar, data->grid->x, data->npts);
 		}
-		while (tNow<=finalTime && R(1)>100e-9) {
+		while (tNow<=finalTime && R(data->l_npts)>100e-9) {
 			t1=tNow;
             
             /*Floor small value to zero*/
-            floorSmallValue(data, &y);
+            // floorSmallValue(data, &y);
             
 
 			if(data->quasiSteady){
@@ -249,9 +251,9 @@ int main(){
   			ier = IDAGetCurrentOrder(mem, &kcur);
 
             /******** Print the max Temperature *********/
-            double maxT = 0.00; 
-            maxT = maxTemperature(ydata,data->nt,data->nvar,data->npts);
-            printf("Maximum temperature is : %.3f[K] \n",maxT);
+            // double maxT = 0.00; 
+            // maxT = maxTemperature(ydata,data->nt,data->nvar,data->npts);
+            // printf("Maximum temperature is : %.3f[K] \n",maxT);
 
 			if(data->adaptiveGrid==1 && data->moveGrid==1){
 				x=maxCurvPosition(ydata, data->nt, data->nvar,
@@ -337,65 +339,64 @@ int main(){
 			}
             
 			/*Print Liquid Thermodynamic data*/
-			double rho = getLiquidRho(data->dropMole,T(1),P(1));
-			double Cp = getLiquidCp(data->dropMole,T(1),P(1)); 
-			double deltaH = getLiquidHv(data->dropMole,T(1),P(1));
-			double boil_T = getLiquidMaxT(data->dropMole,P(1));
-			printf("The Mean Density of Liquid Phase:%6.3e [kg/m^3]\n",rho);
-			printf("The Mean Specific Heat Capacity of Liquid Phase:%6.3e  [J/(kg*K)]\n",Cp);
-			printf("The Mean Heat of Evaporation of Liquid Phase:%6.3e  [J/kg]\n",deltaH);
-			printf("The Boiling Point of More Volitile Component (Propane):%6.3e [K]\n",boil_T);
-            printf("Temperature at the liquid/gas phase interface:%6.3e [K]\n\n",T(1));
+			// double rho = getLiquidRho(data->dropMole,T(1),P(1));
+			// double Cp = getLiquidCp(data->dropMole,T(1),P(1)); 
+			// double deltaH = getLiquidHv(data->dropMole,T(1),P(1));
+			// double boil_T = getLiquidMaxT(data->dropMole,P(1));
+			// printf("The Mean Density of Liquid Phase:%6.3e [kg/m^3]\n",rho);
+			// printf("The Mean Specific Heat Capacity of Liquid Phase:%6.3e  [J/(kg*K)]\n",Cp);
+			// printf("The Mean Heat of Evaporation of Liquid Phase:%6.3e  [J/kg]\n",deltaH);
+			// printf("The Boiling Point of More Volitile Component (Propane):%6.3e [K]\n",boil_T);
+            // printf("Temperature at the liquid/gas phase interface:%6.3e [K]\n\n",T(1));
 
             /*reset the tolerance after ignition*/
             //resetTolerance(data,&y,&atolv);
             
             /*regrid and update the solution based on R,re-initialize the problem*/
             /*For the time being,we only allow TORC to REGRID once for each run*/
-            
-            if(data->JJRG ==1 && (maxT >= data->initialTemperature+data->deltaT)){
-               if(RGCOUNT<1){
-                RGCOUNT = RGCOUNT +1;
-                REGRID(ydata,ydotdata,data);
-                initializePsiGrid(ydata,data->uniformGrid,data);
-                printf("REGRID Complete!Restarting Problem at %15.6e s\n",tNow);
-                ier = IDAReInit(mem,tNow,y,ydot);
-                
-                if(check_flag(&ier,"IDAReInit",1)){
-                    freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
-                    return(-1);
-                }
-
-                ier= IDASetInitStep(mem,1e-01*dt);
-                //ier= IDASetInitStep(mem,0.0);
-                printf("Reinitialized!Calculating Initial Conditions:\n");
-                printf("Cross your fingers...\n");
-  			    ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+1e-01*dt);
-  			    if(check_flag(&ier, "IDACalcIC", 1)){
-  			    	ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+1e+01*dt);
-			    }
-			    //Every once in a while, for reasons
-			    //that befuddle this mathematically
-			    //lesser author, IDACalcIC fails. Here,
-			    //I desperately try to make it converge
-			    //again by sampling increasingly larger
-			    //time-steps:
-			    for (int i = 0; i < 10; i++) {
-  			    	ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+(1e-01+pow(10,i)*dt));
-			    	if(ier==0){
-			    		break;
-			    	}
-			    }
-			    //Failure :( Back to the drawing board:
-  			    if(check_flag(&ier, "IDACalcIC", 1)){
-			    	freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
-		        		return(-1);
-			    }
-			    printf("Initial (Consistent) Conditions Calculated!\n");
-			    printf("------------------------------------------\n\n");
-
-                }
-            }
+//            if(data->JJRG ==1 && (maxT >= data->initialTemperature+data->deltaT)){
+//               if(RGCOUNT<1){
+//                RGCOUNT = RGCOUNT +1;
+//                REGRID(ydata,ydotdata,data);
+//                initializePsiGrid(ydata,data->uniformGrid,data);
+//                printf("REGRID Complete!Restarting Problem at %15.6e s\n",tNow);
+//                ier = IDAReInit(mem,tNow,y,ydot);
+//
+//                if(check_flag(&ier,"IDAReInit",1)){
+//                    freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
+//                    return(-1);
+//                }
+//
+//                ier= IDASetInitStep(mem,1e-01*dt);
+//                //ier= IDASetInitStep(mem,0.0);
+//                printf("Reinitialized!Calculating Initial Conditions:\n");
+//                printf("Cross your fingers...\n");
+//  			    ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+1e-01*dt);
+//  			    if(check_flag(&ier, "IDACalcIC", 1)){
+//  			    	ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+1e+01*dt);
+//			    }
+//			    //Every once in a while, for reasons
+//			    //that befuddle this mathematically
+//			    //lesser author, IDACalcIC fails. Here,
+//			    //I desperately try to make it converge
+//			    //again by sampling increasingly larger
+//			    //time-steps:
+//			    for (int i = 0; i < 10; i++) {
+//  			    	ier = IDACalcIC(mem, IDA_YA_YDP_INIT, tNow+(1e-01+pow(10,i)*dt));
+//			    	if(ier==0){
+//			    		break;
+//			    	}
+//			    }
+//			    //Failure :( Back to the drawing board:
+//  			    if(check_flag(&ier, "IDACalcIC", 1)){
+//			    	freeAtLast(mem,&y,&ydot,&res,&id,&atolv,&constraints,data);
+//		        		return(-1);
+//			    }
+//			    printf("Initial (Consistent) Conditions Calculated!\n");
+//			    printf("------------------------------------------\n\n");
+//
+//                }
+//            }
 
             /*Floor small value to zero*/
             //floorSmallValue(data, &y);
@@ -409,11 +410,11 @@ int main(){
            
            /*Get and Print Rxns Rate of Progress and Specie Rate of Production data*/ 
            /*Following code snippet will be executed only once*/
-           if(ii==0 && maxT >=(data->initialTemperature+data->deltaT)){
-                getReactions(data,&y,data->rxnROPOutput);
-                getSpecies(data,&y,data->spROPOutput);
-                ii++; 
-           }
+        //    if(ii==0 && maxT >=(data->initialTemperature+data->deltaT)){
+        //         getReactions(data,&y,data->rxnROPOutput);
+        //         getSpecies(data,&y,data->spROPOutput);
+        //         ii++; 
+        //    }
 //            getTimescale(data,&y);
 //			if(count%data->nSaves==0){
 //				printTimescaleOutput(tNow,&y, data->timescaleOutput,data);
diff --git a/src/parse.cpp b/src/parse.cpp
index a4060ce..4e31908 100644
--- a/src/parse.cpp
+++ b/src/parse.cpp
@@ -85,46 +85,48 @@ int parseDrop(FILE* input, const char* keyword,char dropSpec[][10],double dropMo
 	return(-1);
 }
 
-/* Specialization for string */
-template<>
-int parseDropSpec<std::string>(FILE* input, const char* keyword, const size_t bufLen,const int* dropType, std::vector<std::string>& dropPara){
-    char buf[bufLen];
-    char buf1[bufLen];
-    char comment[1];
-    char *ret;
 
-    while (fgets(buf,bufLen, input)!=NULL){
-        comment[0]=buf[0];
-        if(strncmp(comment,"#",1)==0){
-            //printf("Comment!:%s\n",buf);
-        }
-        else{
-            ret=strtok(buf,"=");
-            if(strcmp(ret,keyword)==0){
-                /*offset buf by keyword size + 1 for the "="*/
-                /* Second argument in the strncpy function is the address !!! */
-                /* Note: current version of code can only take dropType =0 or 1 */
-                strncpy(buf1, buf+strlen(keyword)+1, bufLen);
-                printf("%10s: ",keyword);
-                if(*dropType ==0){
-                    /* Convert from char* to string */
-                    std::string str(buf1);
-                    dropPara.push_back(str);
-                    printf("%s\n",dropPara[0].c_str());
-                }else{
-                    std::istringstream iss(buf1) ;
-                    std::string token;
-                    while(std::getline(iss,token,',')){
-                        //std::stod(token);
-                        dropPara.push_back(token);
-                    }
-                    printf("%s,%s\n",dropPara[0].c_str(),dropPara[1].c_str());
-                }
-                rewind(input);
-                return(0);
-            }
-        }
-    }
-    rewind(input);
-    return(-1);
-}
\ No newline at end of file
+
+///* Specialization for string */
+//template<>
+//int parseDropSpec<std::string>(FILE* input, const char* keyword, const size_t bufLen,const int* dropType, std::vector<std::string>& dropPara){
+//    char buf[bufLen];
+//    char buf1[bufLen];
+//    char comment[1];
+//    char *ret;
+//
+//    while (fgets(buf,bufLen, input)!=NULL){
+//        comment[0]=buf[0];
+//        if(strncmp(comment,"#",1)==0){
+//            //printf("Comment!:%s\n",buf);
+//        }
+//        else{
+//            ret=strtok(buf,"=");
+//            if(strcmp(ret,keyword)==0){
+//                /*offset buf by keyword size + 1 for the "="*/
+//                /* Second argument in the strncpy function is the address !!! */
+//                /* Note: current version of code can only take dropType =0 or 1 */
+//                strncpy(buf1, buf+strlen(keyword)+1, bufLen);
+//                printf("%10s: ",keyword);
+//                if(*dropType ==0){
+//                    /* Convert from char* to string */
+//                    std::string str(buf1);
+//                    dropPara.push_back(str);
+//                    printf("%s\n",dropPara[0].c_str());
+//                }else{
+//                    std::istringstream iss(buf1) ;
+//                    std::string token;
+//                    while(std::getline(iss,token,',')){
+//                        //std::stod(token);
+//                        dropPara.push_back(token);
+//                    }
+//                    printf("%s,%s\n",dropPara[0].c_str(),dropPara[1].c_str());
+//                }
+//                rewind(input);
+//                return(0);
+//            }
+//        }
+//    }
+//    rewind(input);
+//    return(-1);
+//}
\ No newline at end of file
diff --git a/src/residue.cpp b/src/residue.cpp
index 4c92286..de2a133 100644
--- a/src/residue.cpp
+++ b/src/residue.cpp
@@ -1,114 +1,118 @@
 #ifndef GSL_DEF
 #define GSL_DEF
+
 #include <gsl/gsl_math.h>
 #include <gsl/gsl_spline.h>
+
 #endif
+
 #include "residue.h"
 #include "macros.h"
 #include <cmath>
 #include <stdio.h>
 #include "timing.hpp"
 
-void REGRID(double* ydata,double* ydotdata,UserData data){
+void REGRID(double *ydata, double *ydotdata, UserData data) {
     size_t nPts = data->npts;
     size_t nvar = data->nvar;
-    double WORK[nPts],XNEW[nPts],XOLD[nPts]; 
-    double P,R,R0,R1,R2,TV1,TV2,XLEN,B1,B2;
-    double DX,DDX;
-    double DETA,ETAJ,DEL;
-    size_t ISTART; 
+    double WORK[nPts], XNEW[nPts], XOLD[nPts];
+    double P, R, R0, R1, R2, TV1, TV2, XLEN, B1, B2;
+    double DX, DDX;
+    double DETA, ETAJ, DEL;
+    size_t ISTART;
     P = data->PCAD;
     R = data->RGTC;
-    R0 =1.0 - P;
-    R1 =P*R/(R+1.0);
-    R2 =P - R1 ; 
-    TV1 = 0.0; 
+    R0 = 1.0 - P;
+    R1 = P * R / (R + 1.0);
+    R2 = P - R1;
+    TV1 = 0.0;
     TV2 = 0.0;
 
-    for(size_t i=2;i<=nPts;i++){
-        TV1 = TV1 + fabs(T(i)-T(i-1));
+    for (size_t i = 2; i <= nPts; i++) {
+        TV1 = TV1 + fabs(T(i) - T(i - 1));
     }
-    
-    for(size_t i=2;i<=nPts-1;i++){
-        TV2 = TV2 +  fabs( (T(i+1)-T(i))/(R(i+1)-R(i)) - (T(i)-T(i-1))/(R(i)-R(i-1)) );
+
+    for (size_t i = 2; i <= nPts - 1; i++) {
+        TV2 = TV2 + fabs((T(i + 1) - T(i)) / (R(i + 1) - R(i)) - (T(i) - T(i - 1)) / (R(i) - R(i - 1)));
     }
-    
-    XLEN = R(nPts) - R(1); 
-    B1 = R1* XLEN/ ( (1.0-P)*TV1);
-    B2 = R2* XLEN/ ( (1.0-P)*TV2);
+
+    XLEN = R(nPts) - R(1);
+    B1 = R1 * XLEN / ((1.0 - P) * TV1);
+    B2 = R2 * XLEN / ((1.0 - P) * TV2);
 
     //Compute partial sum of weight function
-    WORK(1) =0.0;
+    WORK(1) = 0.0;
     DX = 0.0;
-    for(size_t i=2;i<=nPts-1;i++){
-        DX = R(i) - R(i-1) ; 
-        WORK(i) = DX + B1*fabs(T(i)-T(i-1)) + WORK(i-1)+B2*fabs( (T(i+1)-T(i))/(R(i+1)-R(i)) - (T(i)-T(i-1))/(R(i)-R(i-1)) );
+    for (size_t i = 2; i <= nPts - 1; i++) {
+        DX = R(i) - R(i - 1);
+        WORK(i) = DX + B1 * fabs(T(i) - T(i - 1)) + WORK(i - 1) +
+                  B2 * fabs((T(i + 1) - T(i)) / (R(i + 1) - R(i)) - (T(i) - T(i - 1)) / (R(i) - R(i - 1)));
     }
-    
-    DDX = R(nPts) - R(nPts-1); 
-    WORK(nPts) = WORK(nPts-1) +DDX ; 
-    
-    for(size_t i=2;i<=nPts;i++){
-        WORK(i) = WORK(i)/WORK(nPts); 
+
+    DDX = R(nPts) - R(nPts - 1);
+    WORK(nPts) = WORK(nPts - 1) + DDX;
+
+    for (size_t i = 2; i <= nPts; i++) {
+        WORK(i) = WORK(i) / WORK(nPts);
     }
-        
-    XNEW(1)=R(1); 
-    XNEW(nPts)=R(nPts); 
-    ISTART =2;
+
+    XNEW(1) = R(1);
+    XNEW(nPts) = R(nPts);
+    ISTART = 2;
     //double DETA;
-    DETA = 1.0/(nPts-1) ; 
+    DETA = 1.0 / (nPts - 1);
 
     //Fill new grid XNEW[nPts],duplicate from PREMIX REGRID SUBROUTINE
-    for(size_t j=2;j<=nPts-1;j++){
-        ETAJ= (j-1)*DETA; 
+    for (size_t j = 2; j <= nPts - 1; j++) {
+        ETAJ = (j - 1) * DETA;
 
-        for(size_t i=ISTART;i<=nPts;i++){
-            if(ETAJ <= WORK(i)){
-                DEL = (ETAJ-WORK(i-1))/(WORK(i)-WORK(i-1)) ; 
-                XNEW(j)=R(i-1)+(R(i)-R(i-1))*DEL;
+        for (size_t i = ISTART; i <= nPts; i++) {
+            if (ETAJ <= WORK(i)) {
+                DEL = (ETAJ - WORK(i - 1)) / (WORK(i) - WORK(i - 1));
+                XNEW(j) = R(i - 1) + (R(i) - R(i - 1)) * DEL;
                 break;
-            }else{
-                ISTART =i;
+            } else {
+                ISTART = i;
             }
 
         }
     }
 
     //Interpolate solution based on XNEW[]&XOLD[]
-    for(size_t i=1;i<=nPts;i++){
-        XOLD[i-1]=R(i);
+    for (size_t i = 1; i <= nPts; i++) {
+        XOLD[i - 1] = R(i);
     }
 
-    INTERPO(ydata,ydotdata,nvar,nPts,XNEW,XOLD);
+    INTERPO(ydata, ydotdata, nvar, nPts, XNEW, XOLD);
 }
 
 
-void INTERPO(double* y,double* ydot,const size_t nvar,size_t nPts,const double XNEW[], const double XOLD[]){
-    double ytemp[nPts],ydottemp[nPts] ; 
-    
-    gsl_interp_accel* acc; 
-    gsl_spline* spline; 
+void INTERPO(double *y, double *ydot, const size_t nvar, size_t nPts, const double XNEW[], const double XOLD[]) {
+    double ytemp[nPts], ydottemp[nPts];
+
+    gsl_interp_accel *acc;
+    gsl_spline *spline;
     acc = gsl_interp_accel_alloc();
-    spline = gsl_spline_alloc(gsl_interp_steffen,nPts);
-    
-    gsl_interp_accel* accdot; 
-    gsl_spline* splinedot; 
+    spline = gsl_spline_alloc(gsl_interp_steffen, nPts);
+
+    gsl_interp_accel *accdot;
+    gsl_spline *splinedot;
     accdot = gsl_interp_accel_alloc();
-    splinedot = gsl_spline_alloc(gsl_interp_steffen,nPts);
+    splinedot = gsl_spline_alloc(gsl_interp_steffen, nPts);
 
-    for(size_t j=0;j<nvar;j++){
-        
-        for(size_t i=0;i<nPts;i++){
-            ytemp[i]=y[j+i*nvar];
-            ydottemp[i]=y[j+i*nvar];
+    for (size_t j = 0; j < nvar; j++) {
+
+        for (size_t i = 0; i < nPts; i++) {
+            ytemp[i] = y[j + i * nvar];
+            ydottemp[i] = y[j + i * nvar];
         }
 
-        gsl_spline_init(spline,XOLD,ytemp,nPts);
-        gsl_spline_init(splinedot,XOLD,ydottemp,nPts);
-        
-        for(size_t i=0;i<nPts;i++){
-            y[j+i*nvar]=gsl_spline_eval(spline,XNEW[i],acc);
-            ydot[j+i*nvar]=gsl_spline_eval(splinedot,XNEW[i],accdot);
+        gsl_spline_init(spline, XOLD, ytemp, nPts);
+        gsl_spline_init(splinedot, XOLD, ydottemp, nPts);
+
+        for (size_t i = 0; i < nPts; i++) {
+            y[j + i * nvar] = gsl_spline_eval(spline, XNEW[i], acc);
+            ydot[j + i * nvar] = gsl_spline_eval(splinedot, XNEW[i], accdot);
         }
 
     }
@@ -121,202 +125,203 @@ void INTERPO(double* y,double* ydot,const size_t nvar,size_t nPts,const double X
 
 }
 
-double maxTemperaturePosition(const double* y,const size_t nt,const size_t nvar,const double *x ,size_t nPts){
+double maxTemperaturePosition(const double *y, const size_t nt, const size_t nvar, const double *x, size_t nPts) {
     double maxT = 0.0e0;
     double TempT = 0.0e0;
     double pos = 0.0e0;
-    for (size_t i=1;i<=nPts;i++){
-        TempT = y[(i-1)*nvar+nt] ; 
-        if(TempT > maxT){
-            maxT = TempT ; 
-            pos = x[i-1];
+    for (size_t i = 1; i <= nPts; i++) {
+        TempT = y[(i - 1) * nvar + nt];
+        if (TempT > maxT) {
+            maxT = TempT;
+            pos = x[i - 1];
         }
     }
-    return(pos); 
+    return (pos);
 }
 
-double maxTemperature(const double* y,const size_t nt,const size_t nvar ,size_t nPts){
+double maxTemperature(const double *y, const size_t nt, const size_t nvar, size_t nPts) {
     double maxT = 0.0e0;
     double TempT = 0.0e0;
-    //int index = 0 ; 
-    for (size_t i=1;i<=nPts;i++){
-        TempT = y[(i-1)*nvar+nt] ; 
-        if(TempT > maxT){
-            maxT = TempT ; 
+    //int index = 0 ;
+    for (size_t i = 1; i <= nPts; i++) {
+        TempT = y[(i - 1) * nvar + nt];
+        if (TempT > maxT) {
+            maxT = TempT;
         }
     }
-    return(maxT); 
+    return (maxT);
 }
+
 //Index here is 1-based
-int maxTemperatureIndex(const double* y,const size_t nt,const size_t nvar ,size_t nPts){
+int maxTemperatureIndex(const double *y, const size_t nt, const size_t nvar, size_t nPts) {
     double maxT = 0.0e0;
     double TempT = 0.0e0;
-    int index = 0 ; 
-    for (size_t i=1;i<=nPts;i++){
-        TempT = y[(i-1)*nvar+nt] ; 
-        if(TempT > maxT){
-            maxT = TempT ; 
-            index = i; 
+    int index = 0;
+    for (size_t i = 1; i <= nPts; i++) {
+        TempT = y[(i - 1) * nvar + nt];
+        if (TempT > maxT) {
+            maxT = TempT;
+            index = i;
         }
     }
-    return(index); 
+    return (index);
 }
 
-double maxCurvPositionR(const double* y, const size_t nt, 
-	               const size_t nvar, const size_t nr, size_t nPts){
-	double maxCurvT=0.0e0;
-	double gradTp=0.0e0;
-	double gradTm=0.0e0;
-	double curvT=0.0e0;
-	double dx=0.0e0;
-    double dr=0.0e0;
-	double pos=0.0e0;
-	size_t j,jm,jp;
-    size_t r,rp,rm;
-	for (size_t i = 1; i <nPts-1; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		jp=(i+1)*nvar+nt;
-        r = i*nvar+nr;
-        rm = (i-1)*nvar+nr;
-        rp = (i+1)*nvar+nr; 
-		//gradTp=fabs((y[jp]-y[j])/(x[i+1]-x[i]));
-		//gradTm=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		//dx=0.5e0*((x[i]+x[i+1])-(x[i-1]+x[i]));
-		//curvT=(gradTp-gradTm)/dx;
-        gradTp = fabs((y[jp]-y[j])/(y[rp]-y[r]));
-        gradTp = fabs((y[j]-y[jm])/(y[r]-y[rm]));
-		dr = 0.5e0*(y[rp]-y[rm]);
-        curvT=(gradTp-gradTm)/dr; 
-        if (curvT>=maxCurvT) {
-			maxCurvT=curvT;
-			pos=y[r];
-		}
-	}
-	return(pos);
+double maxCurvPositionR(const double *y, const size_t nt,
+                        const size_t nvar, const size_t nr, size_t nPts) {
+    double maxCurvT = 0.0e0;
+    double gradTp = 0.0e0;
+    double gradTm = 0.0e0;
+    double curvT = 0.0e0;
+    double dx = 0.0e0;
+    double dr = 0.0e0;
+    double pos = 0.0e0;
+    size_t j, jm, jp;
+    size_t r, rp, rm;
+    for (size_t i = 1; i < nPts - 1; i++) {
+        j = i * nvar + nt;
+        jm = (i - 1) * nvar + nt;
+        jp = (i + 1) * nvar + nt;
+        r = i * nvar + nr;
+        rm = (i - 1) * nvar + nr;
+        rp = (i + 1) * nvar + nr;
+        //gradTp=fabs((y[jp]-y[j])/(x[i+1]-x[i]));
+        //gradTm=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
+        //dx=0.5e0*((x[i]+x[i+1])-(x[i-1]+x[i]));
+        //curvT=(gradTp-gradTm)/dx;
+        gradTp = fabs((y[jp] - y[j]) / (y[rp] - y[r]));
+        gradTp = fabs((y[j] - y[jm]) / (y[r] - y[rm]));
+        dr = 0.5e0 * (y[rp] - y[rm]);
+        curvT = (gradTp - gradTm) / dr;
+        if (curvT >= maxCurvT) {
+            maxCurvT = curvT;
+            pos = y[r];
+        }
+    }
+    return (pos);
 }
 
-int maxCurvIndexR(const double* y, const size_t nt, 
-	               const size_t nvar, const size_t nr, size_t nPts){
-	double maxCurvT=0.0e0;
-	double gradTp=0.0e0;
-	double gradTm=0.0e0;
-	double curvT=0.0e0;
-	double dx=0.0e0;
-    double dr=0.0e0;
-	int pos=0;
-	size_t j,jm,jp;
-    size_t r,rm,rp;
-	for (size_t i = 1; i <nPts-1; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		jp=(i+1)*nvar+nt;
-        r = i*nvar+nr;
-        rm = (i-1)*nvar+nr;
-        rp = (i+1)*nvar+nr; 
-		//gradTp=fabs((y[jp]-y[j])/(x[i+1]-x[i]));
-		//gradTm=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		//dx=0.5e0*((x[i]+x[i+1])-(x[i-1]+x[i]));
-		//curvT=(gradTp-gradTm)/dx;
-        gradTp = fabs((y[jp]-y[j])/(y[rp]-y[r]));
-        gradTp = fabs((y[j]-y[jm])/(y[r]-y[rm]));
-		dr = 0.5e0*(y[rp]-y[rm]);
-        curvT=(gradTp-gradTm)/dr; 
-        if (curvT>=maxCurvT) {
-			maxCurvT=curvT;
-			pos=i;
-		}
-	}
-	return(pos);
+int maxCurvIndexR(const double *y, const size_t nt,
+                  const size_t nvar, const size_t nr, size_t nPts) {
+    double maxCurvT = 0.0e0;
+    double gradTp = 0.0e0;
+    double gradTm = 0.0e0;
+    double curvT = 0.0e0;
+    double dx = 0.0e0;
+    double dr = 0.0e0;
+    int pos = 0;
+    size_t j, jm, jp;
+    size_t r, rm, rp;
+    for (size_t i = 1; i < nPts - 1; i++) {
+        j = i * nvar + nt;
+        jm = (i - 1) * nvar + nt;
+        jp = (i + 1) * nvar + nt;
+        r = i * nvar + nr;
+        rm = (i - 1) * nvar + nr;
+        rp = (i + 1) * nvar + nr;
+        //gradTp=fabs((y[jp]-y[j])/(x[i+1]-x[i]));
+        //gradTm=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
+        //dx=0.5e0*((x[i]+x[i+1])-(x[i-1]+x[i]));
+        //curvT=(gradTp-gradTm)/dx;
+        gradTp = fabs((y[jp] - y[j]) / (y[rp] - y[r]));
+        gradTp = fabs((y[j] - y[jm]) / (y[r] - y[rm]));
+        dr = 0.5e0 * (y[rp] - y[rm]);
+        curvT = (gradTp - gradTm) / dr;
+        if (curvT >= maxCurvT) {
+            maxCurvT = curvT;
+            pos = i;
+        }
+    }
+    return (pos);
 }
 
-double maxGradPosition(const double* y, const size_t nt, 
-	               const size_t nvar, const double* x, size_t nPts){
-	double maxGradT=0.0e0;
-	double gradT=0.0e0;
-	double pos=0.0e0;
-	size_t j,jm;
-	for (size_t i = 1; i <nPts; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		gradT=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		if (gradT>=maxGradT) {
-			maxGradT=gradT;
-			pos=x[i];
-		}
-	}
-	return(pos);
+double maxGradPosition(const double *y, const size_t nt,
+                       const size_t nvar, const double *x, size_t nPts) {
+    double maxGradT = 0.0e0;
+    double gradT = 0.0e0;
+    double pos = 0.0e0;
+    size_t j, jm;
+    for (size_t i = 1; i < nPts; i++) {
+        j = i * nvar + nt;
+        jm = (i - 1) * nvar + nt;
+        gradT = fabs((y[j] - y[jm]) / (x[i] - x[i - 1]));
+        if (gradT >= maxGradT) {
+            maxGradT = gradT;
+            pos = x[i];
+        }
+    }
+    return (pos);
 }
 
-int maxGradIndex(const double* y, const size_t nt, 
-	         const size_t nvar, const double* x, size_t nPts){
-	double maxGradT=0.0e0;
-	double gradT=0.0e0;
-	int pos=0;
-	size_t j,jm;
-	for (size_t i = 1; i <nPts; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		gradT=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		if (gradT>=maxGradT) {
-			maxGradT=gradT;
-			pos=i;
-		}
-	}
-	return(pos);
+int maxGradIndex(const double *y, const size_t nt,
+                 const size_t nvar, const double *x, size_t nPts) {
+    double maxGradT = 0.0e0;
+    double gradT = 0.0e0;
+    int pos = 0;
+    size_t j, jm;
+    for (size_t i = 1; i < nPts; i++) {
+        j = i * nvar + nt;
+        jm = (i - 1) * nvar + nt;
+        gradT = fabs((y[j] - y[jm]) / (x[i] - x[i - 1]));
+        if (gradT >= maxGradT) {
+            maxGradT = gradT;
+            pos = i;
+        }
+    }
+    return (pos);
 }
 
-double maxCurvPosition(const double* y, const size_t nt, 
-	               const size_t nvar, const double* x, size_t nPts){
-	double maxCurvT=0.0e0;
-	double gradTp=0.0e0;
-	double gradTm=0.0e0;
-	double curvT=0.0e0;
-	double dx=0.0e0;
-	double pos=0.0e0;
-	size_t j,jm,jp;
-	for (size_t i = 1; i <nPts-1; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		jp=(i+1)*nvar+nt;
-		gradTp=fabs((y[jp]-y[j])/(x[i+1]-x[i]));
-		gradTm=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		dx=0.5e0*((x[i]+x[i+1])-(x[i-1]+x[i]));
-		curvT=(gradTp-gradTm)/dx;
-		if (curvT>=maxCurvT) {
-			maxCurvT=curvT;
-			pos=x[i];
-		}
-	}
-	return(pos);
+double maxCurvPosition(const double *y, const size_t nt,
+                       const size_t nvar, const double *x, size_t nPts) {
+    double maxCurvT = 0.0e0;
+    double gradTp = 0.0e0;
+    double gradTm = 0.0e0;
+    double curvT = 0.0e0;
+    double dx = 0.0e0;
+    double pos = 0.0e0;
+    size_t j, jm, jp;
+    for (size_t i = 1; i < nPts - 1; i++) {
+        j = i * nvar + nt;
+        jm = (i - 1) * nvar + nt;
+        jp = (i + 1) * nvar + nt;
+        gradTp = fabs((y[jp] - y[j]) / (x[i + 1] - x[i]));
+        gradTm = fabs((y[j] - y[jm]) / (x[i] - x[i - 1]));
+        dx = 0.5e0 * ((x[i] + x[i + 1]) - (x[i - 1] + x[i]));
+        curvT = (gradTp - gradTm) / dx;
+        if (curvT >= maxCurvT) {
+            maxCurvT = curvT;
+            pos = x[i];
+        }
+    }
+    return (pos);
 }
 
-int maxCurvIndex(const double* y, const size_t nt, 
-	               const size_t nvar, const double* x, size_t nPts){
-	double maxCurvT=0.0e0;
-	double gradTp=0.0e0;
-	double gradTm=0.0e0;
-	double curvT=0.0e0;
-	double dx=0.0e0;
-	int pos=0;
-	size_t j,jm,jp;
-	for (size_t i = 1; i <nPts-1; i++) {
-		j=i*nvar+nt;
-		jm=(i-1)*nvar+nt;
-		jp=(i+1)*nvar+nt;
-		gradTp=fabs((y[jp]-y[j])/(x[i+1]-x[i]));
-		gradTm=fabs((y[j]-y[jm])/(x[i]-x[i-1]));
-		dx=0.5e0*((x[i]+x[i+1])-(x[i-1]+x[i]));
-		curvT=(gradTp-gradTm)/dx;
-		if (curvT>=maxCurvT) {
-			maxCurvT=curvT;
-			pos=i;
-		}
-	}
-	return(pos);
+int maxCurvIndex(const double *y, const size_t nt,
+                 const size_t nvar, const double *x, size_t nPts) {
+    double maxCurvT = 0.0e0;
+    double gradTp = 0.0e0;
+    double gradTm = 0.0e0;
+    double curvT = 0.0e0;
+    double dx = 0.0e0;
+    int pos = 0;
+    size_t j, jm, jp;
+    for (size_t i = 1; i < nPts - 1; i++) {
+        j = i * nvar + nt;
+        jm = (i - 1) * nvar + nt;
+        jp = (i + 1) * nvar + nt;
+        gradTp = fabs((y[jp] - y[j]) / (x[i + 1] - x[i]));
+        gradTm = fabs((y[j] - y[jm]) / (x[i] - x[i - 1]));
+        dx = 0.5e0 * ((x[i] + x[i + 1]) - (x[i - 1] + x[i]));
+        curvT = (gradTp - gradTm) / dx;
+        if (curvT >= maxCurvT) {
+            maxCurvT = curvT;
+            pos = i;
+        }
+    }
+    return (pos);
 }
 
-//double isothermPosition(const double* y, const double T, const size_t nt, 
+//double isothermPosition(const double* y, const double T, const size_t nt,
 //	                const size_t nvar, const double* x, const size_t nPts){
 //	double pos=x[nPts-1];
 //	size_t j;
@@ -331,731 +336,1417 @@ int maxCurvIndex(const double* y, const size_t nt,
 //}
 
 //******************* scan the temperature from left to right ******************//
-double isothermPosition(const double* y, const double T, const size_t nt, 
-	                const size_t nvar, const double* x, const size_t nPts){
-	double pos=x[0];
-	size_t j;
-	for (size_t i = 0; i <nPts; i++) {
-		j=i*nvar+nt;
-		if (y[j]>=T) {
-			pos=x[i];
-			break;
-		}
-	}
-	return(pos);
+double isothermPosition(const double *y, const double T, const size_t nt,
+                        const size_t nvar, const double *x, const size_t nPts) {
+    double pos = x[0];
+    size_t j;
+    for (size_t i = 0; i < nPts; i++) {
+        j = i * nvar + nt;
+        if (y[j] >= T) {
+            pos = x[i];
+            break;
+        }
+    }
+    return (pos);
 }
 
-void updateSolution(double* y, double* ydot, const size_t nvar,
-		    const double xOld[],const double xNew[],const size_t nPts){
+void updateSolution(double *y, double *ydot, const size_t nvar,
+                    const double xOld[], const double xNew[], const size_t nPts) {
+
+    double ytemp[nPts], ydottemp[nPts];
 
-	double ytemp[nPts],ydottemp[nPts];
+    gsl_interp_accel *acc;
+    gsl_spline *spline;
+    acc = gsl_interp_accel_alloc();
+    spline = gsl_spline_alloc(gsl_interp_steffen, nPts);
 
-	gsl_interp_accel* acc;
-	gsl_spline* spline;
-	acc = gsl_interp_accel_alloc();
-	spline = gsl_spline_alloc(gsl_interp_steffen, nPts);
+    gsl_interp_accel *accdot;
+    gsl_spline *splinedot;
+    accdot = gsl_interp_accel_alloc();
+    splinedot = gsl_spline_alloc(gsl_interp_steffen, nPts);
 
-	gsl_interp_accel* accdot;
-	gsl_spline* splinedot;
-	accdot    = gsl_interp_accel_alloc();
-	splinedot = gsl_spline_alloc(gsl_interp_steffen, nPts);
+    for (size_t j = 0; j < nvar; j++) {
 
-	for (size_t j = 0; j < nvar; j++) {
+        for (size_t i = 0; i < nPts; i++) {
+            ytemp[i] = y[j + i * nvar];
+            ydottemp[i] = ydot[j + i * nvar];
+        }
 
-		for (size_t i = 0; i < nPts; i++) {
-			ytemp[i]=y[j+i*nvar];
-			ydottemp[i]=ydot[j+i*nvar];
-		}
+        gsl_spline_init(spline, xOld, ytemp, nPts);
+        gsl_spline_init(splinedot, xOld, ydottemp, nPts);
 
-		gsl_spline_init(spline,xOld,ytemp,nPts);
-		gsl_spline_init(splinedot,xOld,ydottemp,nPts);
+        for (size_t i = 0; i < nPts; i++) {
 
-		for (size_t i = 0; i < nPts; i++) {
+            y[j + i * nvar] = gsl_spline_eval(spline, xNew[i], acc);
+            ydot[j + i * nvar] = gsl_spline_eval(splinedot, xNew[i], accdot);
+        }
+    }
 
-		      	y[j+i*nvar]=gsl_spline_eval(spline,xNew[i],acc);
-		      	ydot[j+i*nvar]=gsl_spline_eval(splinedot,xNew[i],accdot);
-		}
-	}
+    //Exploring "fixing" boundary conditions:
+    //for (size_t j = 1; j < nvar; j++) {
+    //	//printf("%15.6e\t%15.6e\n", y[j],y[j+nvar]);
+    //	y[j]=y[j+nvar];
+    //	//y[j+(nPts-1)*nvar]=y[j+(nPts-2)*nvar];
+    //	//ydot[j+nvar]=ydot[j];
+    //}
+    //y[0]=0.0e0;
 
-	//Exploring "fixing" boundary conditions:
-	//for (size_t j = 1; j < nvar; j++) {
-	//	//printf("%15.6e\t%15.6e\n", y[j],y[j+nvar]);
-	//	y[j]=y[j+nvar];
-	//	//y[j+(nPts-1)*nvar]=y[j+(nPts-2)*nvar];
-	//	//ydot[j+nvar]=ydot[j];
-	//}
-	//y[0]=0.0e0;
-	
-	gsl_interp_accel_free(acc);
-	gsl_spline_free(spline);
+    gsl_interp_accel_free(acc);
+    gsl_spline_free(spline);
 
-	gsl_interp_accel_free(accdot);
-	gsl_spline_free(splinedot);
+    gsl_interp_accel_free(accdot);
+    gsl_spline_free(splinedot);
 }
 
 //Locate bath gas:
-size_t BathGasIndex(UserData data){
-	size_t index=0;
-	double max1;
-	double max=data->gas->massFraction(0);
-	for(size_t k=1;k<data->nsp;k++){
-		max1=data->gas->massFraction(k);
-		if(max1>=max){
-			max=max1;
-			index=k;
-		}
-	}
-	return(index+1);
+size_t BathGasIndex(UserData data) {
+    size_t index = 0;
+    double max1;
+    double max = data->gas->massFraction(0);
+    for (size_t k = 1; k < data->nsp; k++) {
+        max1 = data->gas->massFraction(k);
+        if (max1 >= max) {
+            max = max1;
+            index = k;
+        }
+    }
+    return (index + 1);
 }
 
 //Locate Oxidizer:
-size_t oxidizerIndex(UserData data){
-	size_t index=0;
-	for(size_t k=1;k<data->nsp;k++){
-		if(data->gas->speciesName(k-1)=="O2"){
-			index=k;
-		}
-	}
-	return(index);
+size_t oxidizerIndex(UserData data) {
+    size_t index = 0;
+    for (size_t k = 1; k < data->nsp; k++) {
+        if (data->gas->speciesName(k - 1) == "O2") {
+            index = k;
+        }
+    }
+    return (index);
 }
 
 //Locate OH:
-size_t OHIndex(UserData data){
-	size_t index=0;
-	for(size_t k=1;k<data->nsp;k++){
-		if(data->gas->speciesName(k-1)=="OH"){
-			index=k;
-		}
-	}
-	return(index);
+size_t OHIndex(UserData data) {
+    size_t index = 0;
+    for (size_t k = 1; k < data->nsp; k++) {
+        if (data->gas->speciesName(k - 1) == "OH") {
+            index = k;
+        }
+    }
+    return (index);
 }
 
 //Locate HO2:
-size_t HO2Index(UserData data){
-	size_t index=0;
-	for(size_t k=1;k<data->nsp;k++){
-		if(data->gas->speciesName(k-1)=="HO2"){
-			index=k;
-		}
-	}
-	return(index);
+size_t HO2Index(UserData data) {
+    size_t index = 0;
+    for (size_t k = 1; k < data->nsp; k++) {
+        if (data->gas->speciesName(k - 1) == "HO2") {
+            index = k;
+        }
+    }
+    return (index);
 }
 
 //Locate species index:
-size_t specIndex(UserData data,char *specName){
-	size_t index=0;
-	for(size_t k=1;k<data->nsp;k++){
-		if(data->gas->speciesName(k-1)==specName){
-			index=k;
-		}
-	}
-	return(index);
+/*1-based index*/
+size_t specIndex(UserData data, const char *specName) {
+    size_t index = 0;
+    for (size_t k = 1; k <= data->nsp; k++) {
+        if (data->gas->speciesName(k - 1) == specName) {
+            index = k;
+        }
+    }
+    return (index);
 }
 
-int setAlgebraicVariables(N_Vector* id, UserData data,const double* ydata){
-	double *iddata;
-    char* specPtr[2]; 
-
-  	N_VConst(ONE, *id);
-  	iddata   = N_VGetArrayPointer_OpenMP(*id);
-	data->k_bath=BathGasIndex(data);
-	data->k_oxidizer=oxidizerIndex(data);
-	data->k_OH=OHIndex(data);
-	data->k_HO2=HO2Index(data);
-    //use char* pointer to get the address
-    for(int i=0;i<2;i++){
-        specPtr[i] = data->dropSpec[i];
-    }
-	data->k_drop[0]=specIndex(data,specPtr[0]);
-    data->k_drop[1]=specIndex(data,specPtr[1]);
-
-	printf("Oxidizer index: %lu\n",data->k_oxidizer);
-	printf("Bath gas index:%lu\n",data->k_bath);
-	printf("Droplet species index:%lu,%lu\n",data->k_drop[0],data->k_drop[1]);
-	for (size_t i = 1; i <=data->npts; i++) {
-		/*Algebraic variables: indicated by ZERO.*/
-		Rid(i)=ZERO;
-		Pid(i)=ZERO;
-		Yid(i,data->k_bath)=ZERO;
-		Mdotid(i)=ZERO;
-	}	
-	Mdotid(1)=ZERO;
-	Rid(1)=ONE;
-	Yid(1,data->k_drop[0])=ZERO;
-    Yid(1,data->k_drop[1])=ZERO;
-	Tid(data->npts)=ZERO;
-	if(data->constantPressure){
-		Pid(data->npts)=ONE;
-	}else{
-		Pid(data->npts)=ZERO;
-		Rid(data->npts)=ONE;
-	}
-	if(data->dirichletInner){
-		Tid(1)=ZERO; 
-	}else{
-		//double T_boil = getLiquidMaxT(data->dropMole,P(1));
-		//if(T(1) <= T_boil){
-		//	Tid(1)=ONE;
-		//}else{
-		//	Tid(1)=ZERO;	
-		//}
-		Tid(1)=ONE;
-	}
-	if(data->dirichletOuter){
-		for (size_t k = 1; k <=data->nsp; k++) {
-			if(k!=data->k_bath){
-				Yid(data->npts,k)=ONE;
-			}
-			Yid(1,k)=ZERO;
-			Tid(data->npts)=ONE;
-		}
-	}else{
-		for (size_t k = 1; k <=data->nsp; k++){
-			Yid(1,k)=ZERO;
-			Yid(data->npts,k)=ZERO;
-			Tid(data->npts)=ZERO;
-		}
-	}
-	return(0);
+/*a similar function will be used*/
+/*therefore the original function will be commented out*/
+// int setAlgebraicVariables(N_Vector* id, UserData data,const double* ydata){
+// 	double *iddata;
+//     //char* specPtr[2];
+
+//   	N_VConst(ONE, *id);
+//   	iddata   = N_VGetArrayPointer_OpenMP(*id);
+// 	data->k_bath=BathGasIndex(data);
+// 	data->k_oxidizer=oxidizerIndex(data);
+// 	data->k_OH=OHIndex(data);
+// 	data->k_HO2=HO2Index(data);
+//     /*use char* pointer to get the address*/
+//     // for(int i=0;i<2;i++){
+//     //     specPtr[i] = data->dropSpec[i];
+//     // }
+// 	// data->k_drop[0]=specIndex(data,specPtr[0]);
+//     // data->k_drop[1]=specIndex(data,specPtr[1]);
+
+// 	for (size_t i = 0; i < data->dropMole.size(); i++){
+// 		size_t index = specIndex(data,data->dropSpec[i]);
+// 		data->k_drop.push_back(index);
+// 	}
+
+// 	printf("Oxidizer index: %lu\n",data->k_oxidizer);
+// 	printf("Bath gas index:%lu\n",data->k_bath);
+// 	printf("Droplet species index: ");
+// 	for (size_t i = 0; i < data->dropMole.size(); i++)
+// 	{
+// 		printf("%lu\t",data->k_drop[i]);
+// 	}
+// 	printf("\n");
+
+// 	/*set governing equations' id*/
+// 	for (size_t i = 1; i <=data->npts; i++) {
+// 		/*Algebraic variables: indicated by ZERO.*/
+// 		Rid(i)=ZERO;
+// 		Pid(i)=ZERO;
+// 		Yid(i,data->k_bath)=ZERO;
+// 		Mdotid(i)=ZERO;
+// 	}
+// 	Mdotid(1)=ZERO;
+// 	Rid(1)=ONE;
+// 	Yid(1,data->k_drop[0])=ZERO;
+//     Yid(1,data->k_drop[1])=ZERO;
+// 	Tid(data->npts)=ZERO;
+// 	if(data->constantPressure){
+// 		Pid(data->npts)=ONE;
+// 	}else{
+// 		Pid(data->npts)=ZERO;
+// 		Rid(data->npts)=ONE;
+// 	}
+// 	if(data->dirichletInner){
+// 		Tid(1)=ZERO;
+// 	}else{
+// 		//double T_boil = getLiquidMaxT(data->dropMole,P(1));
+// 		//if(T(1) <= T_boil){
+// 		//	Tid(1)=ONE;
+// 		//}else{
+// 		//	Tid(1)=ZERO;
+// 		//}
+// 		Tid(1)=ONE;
+// 	}
+// 	if(data->dirichletOuter){
+// 		for (size_t k = 1; k <=data->nsp; k++) {
+// 			if(k!=data->k_bath){
+// 				Yid(data->npts,k)=ONE;
+// 			}
+// 			Yid(1,k)=ZERO;
+// 			Tid(data->npts)=ONE;
+// 		}
+// 	}else{
+// 		for (size_t k = 1; k <=data->nsp; k++){
+// 			Yid(1,k)=ZERO;
+// 			Yid(data->npts,k)=ZERO;
+// 			Tid(data->npts)=ZERO;
+// 		}
+// 	}
+// 	return(0);
+// }
+
+int setAlgebraicVariables(N_Vector *id, UserData data, const double *ydata) {
+    double *iddata;
+    //char* specPtr[2];
+
+    N_VConst(ONE, *id);
+    iddata = N_VGetArrayPointer_OpenMP(*id);
+    data->k_bath = BathGasIndex(data);
+    data->k_oxidizer = oxidizerIndex(data);
+    data->k_OH = OHIndex(data);
+    data->k_HO2 = HO2Index(data);
+    /*use char* pointer to get the address*/
+    // for(int i=0;i<2;i++){
+    //     specPtr[i] = data->dropSpec[i];
+    // }
+    // data->k_drop[0]=specIndex(data,specPtr[0]);
+    // data->k_drop[1]=specIndex(data,specPtr[1]);
+
+    for (size_t i = 0; i < data->dropMole.size(); i++) {
+        size_t index = 0;
+        for (size_t k = 1; k <= data->nsp; k++) {
+            if (data->gas->speciesName(k - 1) == data->dropSpec[i]) {
+                index = k;
+            }
+        }
+//        size_t index = specIndex(data, data->dropSpec[i].c_str());
+        data->k_drop.push_back(index);
+    }
+
+    printf("Oxidizer index: %lu\n", data->k_oxidizer);
+    printf("Bath gas index:%lu\n", data->k_bath);
+    printf("Droplet species index: ");
+
+    for(auto & arg : data->k_drop){
+        printf("%lu,\t",arg) ;
+    }
+    printf("\n");
+
+    /*set governing equations' id*/
+    for (size_t i = 1; i <= data->npts; i++) {
+        /*Algebraic variables: indicated by ZERO.*/
+        Rid(i) = ZERO;
+        Pid(i) = ZERO;
+        Yid(i, data->k_bath) = ZERO;
+        Mdotid(i) = ZERO;
+        Tid(i) = ONE;
+    }
+    Mdotid(1) = ZERO;
+
+    /*set radius ids*/
+    Rid(1) = ONE;
+    Rid(data->l_npts) = ONE;
+
+    /*set temperature ids*/
+    Tid(1) = ZERO;
+    Tid(data->l_npts) = ZERO;
+    Tid(data->l_npts + 1) = ZERO;
+
+    /*set liquid phase mass fraction (y) ids*/
+    if (data->dropType == 0) {
+        for (size_t k = 1; k <= data->nsp; k++) {
+            for (size_t i = 1; i <= data->l_npts; i++) {
+                if (i == 1) {
+                    Yid(i, k) = ONE;
+                } else {
+                    Yid(i, k) = ZERO;
+                }
+            }
+        }
+    } else {
+        for (size_t i = 1; i <= data->l_npts; i++) {
+            for (size_t k = 1; k <= data->nsp; k++) {
+                if (i == 1) {
+                    if (k == data->k_drop[0] || k == data->k_drop[1]) {
+                        Yid(i, k) = ZERO;
+                    } else {
+                        Yid(i, k) = ONE;
+                    }
+                } else if (i == data->l_npts) {
+                    Yid(i, k) = ZERO;
+                } else {
+                    if (k == data->k_drop[0]) {
+                        Yid(i, k) = ONE;
+                    } else {
+                        Yid(i, k) = ZERO;
+                    }
+                }
+            }
+        }
+
+    }
+
+//    for (size_t k = 1; k <= data->nsp; k++) {
+//        Yid(data->l_npts + 1, k) = ZERO;
+//    }
+
+    /*set gas phase mass fraction (y) ids*/
+    for (size_t i = (data->l_npts + 1); i <= (data->npts - 1); i++) {
+        for (size_t k = 1; k <= data->nsp; k++) {
+            if (i == (data->l_npts + 1)) {
+                Yid(i, k) = ZERO;
+            } else {
+                if (k == data->k_bath) {
+                    Yid(i, k) = ZERO;
+                } else {
+                    Yid(i, k) = ONE;
+                }
+            }
+        }
+    }
+
+    //Yid(1,data->k_drop[0])=ZERO;
+    //Yid(1,data->k_drop[1])=ZERO;
+    //Tid(data->npts)=ZERO;
+
+    // if(data->dirichletInner){
+    // 	Tid(1)=ZERO;
+    // }else{
+    // 	//double T_boil = getLiquidMaxT(data->dropMole,P(1));
+    // 	//if(T(1) <= T_boil){
+    // 	//	Tid(1)=ONE;
+    // 	//}else{
+    // 	//	Tid(1)=ZERO;
+    // 	//}
+    // 	Tid(1)=ONE;
+    // }
+    if (data->constantPressure) {
+        Pid(data->npts) = ONE;
+    } else {
+        Pid(data->npts) = ZERO;
+        /*Rres(npts) seems to be algebric all the time?*/
+        Rid(data->npts) = ONE;
+    }
+    if (data->dirichletOuter) {
+        for (size_t k = 1; k <= data->nsp; k++) {
+            if (k != data->k_bath) {
+                Yid(data->npts, k) = ONE;
+            }
+            //Yid(1,k)=ZERO;
+            Tid(data->npts) = ONE;
+        }
+    } else {
+        for (size_t k = 1; k <= data->nsp; k++) {
+            //Yid(1,k)=ZERO;
+            Yid(data->npts, k) = ZERO;
+            Tid(data->npts) = ZERO;
+        }
+    }
+
+    printIddata(data,iddata);
+    return (0);
 }
 
-inline double calc_area(double x,int* i){
-	switch (*i) {
-		case 0:
-			return(ONE);
-		case 1:
-			return(x);
-		case 2:
-			return(x*x);
-		default:
-			return(ONE);
-	}
+inline double calc_area(double x, int *i) {
+    switch (*i) {
+        case 0:
+            return (ONE);
+        case 1:
+            return (x);
+        case 2:
+            return (x * x);
+        default:
+            return (ONE);
+    }
 }
+/*Similar to function:"setInitialCondition"*/
+/*"readInitialCondition" will also be revised here for two-phase LTORC*/
+// void readInitialCondition(FILE* input, double* ydata, const size_t nvar, const size_t nr, const size_t nPts, double Rg){
+
+// 	FILE* output;output=fopen("test.dat","w");
+
+// 	size_t bufLen=10000;
+// 	size_t nRows=0;
+// 	size_t nColumns=nvar;
+
+// 	char buf[bufLen];
+// 	char buf1[bufLen];
+// 	char comment[1];
+// 	char *ret;
+
+// 	while (fgets(buf,bufLen, input)!=NULL){
+// 		comment[0]=buf[0];
+// 		if(strncmp(comment,"#",1)!=0){
+// 			nRows++;
+// 		}
+// 	}
+// 	rewind(input);
+
+// 	printf("nRows: %ld\n", nRows);
+// 	double y[nRows*nColumns];
+
+// 	size_t i=0;
+// 	while (fgets(buf,bufLen, input)!=NULL){
+// 		comment[0]=buf[0];
+// 		if(strncmp(comment,"#",1)==0){
+// 		}
+// 		else{
+// 			ret=strtok(buf,"\t");
+// 			size_t j=0;
+// 			y[i*nColumns+j]=(double)(atof(ret));
+// 			j++;
+// 			while(ret!=NULL){
+// 				ret=strtok(NULL,"\t");
+// 				if(j<nColumns){
+// 					y[i*nColumns+j]=(double)(atof(ret));
+// 				}
+// 				j++;
+// 			}
+// 			i++;
+// 		}
+// 	}
+
+// 	for (i = 0; i < nRows; i++) {
+// 		for (size_t j = 0; j < nColumns; j++) {
+// 			fprintf(output, "%15.6e\t",y[i*nColumns+j]);
+// 		}
+// 		fprintf(output, "\n");
+// 	}
+// 	fclose(output);
+
+// 	//double xOld[nRows],xNew[nPts],ytemp[nPts];
+// 	double xOld[nRows],xNew[nPts],ytemp[nRows];
+
+// 	for (size_t j = 0; j < nRows; j++) {
+// 		xOld[j]=y[j*nColumns+nr];
+// 	}
+
+// 	//double dx=(xOld[nRows-1] - xOld[0])/((double)(nPts)-1.0e0);
+// 	//for (size_t j = 0; j < nPts-1; j++) {
+// 	//	xNew[j]=(double)j*dx + xOld[0];
+// 	//}
+// 	//xNew[nPts-1]=xOld[nRows-1];
+// 	double dX0;
+// 	int NN = nPts-2;
+
+// 	dX0 = (xOld[nRows-1]-xOld[0])*(pow(Rg,1.0/NN) - 1.0)/(pow(Rg,(NN+1.0)/NN) - 1.0);
+// 	xNew[0] = xOld[0];
+// 	for (size_t i = 1; i < nPts-1; i++) {
+// 		xNew[i]=xNew[i-1]+dX0*pow(Rg,(i-1.0)/NN);
+// 	}
+// 	xNew[nPts-1] = xOld[nRows-1];
+
+// 	gsl_interp_accel* acc;
+// 	gsl_spline* spline;
+// 	acc = gsl_interp_accel_alloc();
+// 	spline = gsl_spline_alloc(gsl_interp_steffen, nRows);
+
+// 	for (size_t j = 0; j < nColumns; j++) {
+
+// 		for (size_t k = 0; k < nRows; k++) {
+// 			ytemp[k]=y[j+k*nColumns];
+// 		}
+
+// 		gsl_spline_init(spline,xOld,ytemp,nRows);
+
+// 		for (size_t k = 0; k < nPts; k++) {
+// 		      	ydata[j+k*nColumns]=gsl_spline_eval(spline,xNew[k],acc);
+// 		}
+// 	}
+
+// 	gsl_interp_accel_free(acc);
+// 	gsl_spline_free(spline);
+
+// }
+
+void readInitialCondition(FILE *input, double *ydata, const size_t nvar, const size_t nr, const size_t nPts,
+                          const size_t l_nPts, double Rg) {
+
+    FILE *output;
+    output = fopen("test.dat", "w");
+
+    size_t bufLen = 10000;
+    size_t nRows = 0;
+    size_t nColumns = nvar;
+
+    char buf[bufLen];
+    char buf1[bufLen];
+    char comment[1];
+    char *ret;
+
+    //get the # of rows in the input file:"initialCondition.dat, which equals to # of grid points"
+    while (fgets(buf, bufLen, input) != NULL) {
+        comment[0] = buf[0];
+        if (strncmp(comment, "#", 1) != 0) {
+            nRows++;
+        }
+    }
+    rewind(input);
+
+    printf("nRows: %ld\n", nRows);
+    double y[nRows * nColumns];
+
+    /*extract the initial data from file to y[] array*/
+    size_t i = 0;
+    while (fgets(buf, bufLen, input) != NULL) {
+        comment[0] = buf[0];
+        if (strncmp(comment, "#", 1) == 0) {
+        } else {
+            ret = strtok(buf, "\t");
+            size_t j = 0;
+            y[i * nColumns + j] = (double) (atof(ret));
+            j++;
+            while (ret != NULL) {
+                ret = strtok(NULL, "\t");
+                if (j < nColumns) {
+                    y[i * nColumns + j] = (double) (atof(ret));
+                }
+                j++;
+            }
+            i++;
+        }
+    }
+
+    /*print out y[] array to test file*/
+    for (i = 0; i < nRows; i++) {
+        for (size_t j = 0; j < nColumns; j++) {
+            fprintf(output, "%15.6e\t", y[i * nColumns + j]);
+        }
+        fprintf(output, "\n");
+    }
+    fclose(output);
 
-void readInitialCondition(FILE* input, double* ydata, const size_t nvar, const size_t nr, const size_t nPts, double Rg){
-
-	FILE* output;output=fopen("test.dat","w");
-
-	size_t bufLen=10000;
-	size_t nRows=0;
-	size_t nColumns=nvar;
-
-	char buf[bufLen];
-	char buf1[bufLen];
-	char comment[1];
-	char *ret;
-
-	while (fgets(buf,bufLen, input)!=NULL){
-		comment[0]=buf[0];
-		if(strncmp(comment,"#",1)!=0){
-			nRows++;
-		}
-	}
-	rewind(input);
-
-	printf("nRows: %ld\n", nRows);
-	double y[nRows*nColumns];
-
-	size_t i=0;
-	while (fgets(buf,bufLen, input)!=NULL){
-		comment[0]=buf[0];
-		if(strncmp(comment,"#",1)==0){
-		}
-		else{
-			ret=strtok(buf,"\t");
-			size_t j=0;
-			y[i*nColumns+j]=(double)(atof(ret));
-			j++;
-			while(ret!=NULL){
-				ret=strtok(NULL,"\t");
-				if(j<nColumns){
-					y[i*nColumns+j]=(double)(atof(ret));
-				}
-				j++;
-			}
-			i++;
-		}
-	}
-
-	for (i = 0; i < nRows; i++) {
-		for (size_t j = 0; j < nColumns; j++) {
-			fprintf(output, "%15.6e\t",y[i*nColumns+j]);
-		}
-		fprintf(output, "\n");
-	}
-	fclose(output);
-
-	//double xOld[nRows],xNew[nPts],ytemp[nPts];
-	double xOld[nRows],xNew[nPts],ytemp[nRows];
-
-	for (size_t j = 0; j < nRows; j++) {
-		xOld[j]=y[j*nColumns+nr];
-	}
-
-	//double dx=(xOld[nRows-1] - xOld[0])/((double)(nPts)-1.0e0);
-	//for (size_t j = 0; j < nPts-1; j++) {
-	//	xNew[j]=(double)j*dx + xOld[0];
-	//}
-	//xNew[nPts-1]=xOld[nRows-1];
-	double dX0;
-	int NN = nPts-2;
-	
-	dX0 = (xOld[nRows-1]-xOld[0])*(pow(Rg,1.0/NN) - 1.0)/(pow(Rg,(NN+1.0)/NN) - 1.0);
-	xNew[0] = xOld[0];
-	for (size_t i = 1; i < nPts-1; i++) {
-		xNew[i]=xNew[i-1]+dX0*pow(Rg,(i-1.0)/NN);
-	}
-	xNew[nPts-1] = xOld[nRows-1];
-
-	gsl_interp_accel* acc;
-	gsl_spline* spline;
-	acc = gsl_interp_accel_alloc();
-	spline = gsl_spline_alloc(gsl_interp_steffen, nRows);
-
-	for (size_t j = 0; j < nColumns; j++) {
-
-		for (size_t k = 0; k < nRows; k++) {
-			ytemp[k]=y[j+k*nColumns];
-		}
-
-		gsl_spline_init(spline,xOld,ytemp,nRows);
-
-		for (size_t k = 0; k < nPts; k++) {
-		      	ydata[j+k*nColumns]=gsl_spline_eval(spline,xNew[k],acc);
-		}
-	}
-	
-	gsl_interp_accel_free(acc);
-	gsl_spline_free(spline);
+    //double xOld[nRows],xNew[nPts],ytemp[nPts];
+    //double xOld[nRows],xNew[nPts],ytemp[nRows];
+    double xOld[nRows], xNew[nPts];
 
-}
+    /*get the x(radial) coordinate from y[] array*/
+    for (size_t j = 0; j < nRows; j++) {
+        xOld[j] = y[j * nColumns + nr];
+    }
+
+    /*get the first index of droplet interface:adjacent r equals*/
+    size_t interII;
+    for (size_t i = 0; i < nRows; i++) {
+        interII = i;
+        if (xOld[i] == xOld[i + 1]) {
+            break;
+        }
+    }
+
+    //double dx=(xOld[nRows-1] - xOld[0])/((double)(nPts)-1.0e0);
+    //for (size_t j = 0; j < nPts-1; j++) {
+    //	xNew[j]=(double)j*dx + xOld[0];
+    //}
+    //xNew[nPts-1]=xOld[nRows-1];
+
+    double dX0, dXL;
+    int NN = nPts - l_nPts - 2;
+
+    /*re-calculate the spatial coordinate: uniform grid in liquid phase and non-uniform for gas(fixed ratio)*/
+    dXL = (xOld[interII] - xOld[0]) / (l_nPts - 1);
+    // dX0 = (xOld[nRows-1]-xOld[0])*(pow(Rg,1.0/NN) - 1.0)/(pow(Rg,(NN+1.0)/NN) - 1.0);
+    xNew[0] = xOld[0];
+    for (size_t i = 1; i < l_nPts; i++) {
+        xNew[i] = xNew[i - 1] + dXL;
+    }
+    xNew[l_nPts - 1] = xOld[interII];
+    xNew[l_nPts] = xNew[l_nPts-1];
+
+    dX0 = (xOld[nRows - 1]- xOld[interII] ) * (pow(Rg, 1.0 / NN) - 1.0) / (pow(Rg, (NN + 1.0) / NN) - 1.0);
 
-double systemMass(double* ydata,UserData data){
-	double mass=0.0e0;
-	double rho;
-	for (size_t i = 2; i <=data->npts; i++) {
-  		data->gas->setState_TPY(T(i), P(i), &Y(i,1));   
-		rho=data->gas->density();                                           
-		//psi(i)=psi(i-1)+rho*(R(i)-R(i-1))*calc_area(HALF*(R(i)+R(i-1)),&m);
-		mass+=rho*(R(i)-R(i-1))*calc_area(R(i),&data->metric);
-	}
-	return(mass);
+    double ratio = pow(Rg,1.0/NN);
+    for (size_t ii = (l_nPts + 1); ii <= (nPts - 2); ii++) {
+        xNew[ii] = xNew[ii - 1] + dX0 * pow(ratio,(ii-l_nPts-1)) ;
+    }
+    xNew[nPts - 1] = xOld[nRows - 1];
+
+    /*pass variable data from ytemp[] to ydata[] array using spline interpolation*/
+    /*interpolate the liquid phase state variables with old array of size (interII+1)*/
+    double ytemp0[interII + 1];
+    double xOld0[interII + 1];
+    std::copy(xOld, xOld + interII + 1, xOld0);
+    gsl_interp_accel *acc;
+    gsl_spline *spline;
+    acc = gsl_interp_accel_alloc();
+    spline = gsl_spline_alloc(gsl_interp_steffen, interII + 1);
+    for (size_t j = 0; j < nColumns; j++) {
+        for (size_t k = 0; k < (interII + 1); k++) {
+            ytemp0[k] = y[j + k * nColumns];
+        }
+        gsl_spline_init(spline, xOld0, ytemp0, interII + 1);
+
+        for (size_t k = 0; k < l_nPts; k++) {
+            ydata[j + k * nColumns] = gsl_spline_eval(spline, xNew[k], acc);
+        }
+    }
+    gsl_interp_accel_free(acc);
+    gsl_spline_free(spline);
+
+    /*interpolate the gas phase state variables with old array of size (nRows-interII-1)*/
+    double ytemp1[nRows - interII - 1];
+    double xOld1[nRows - interII - 1];
+    std::copy(xOld + interII + 1, xOld + nRows, xOld1);
+    gsl_interp_accel *acc1;
+    gsl_spline *spline1;
+    acc1 = gsl_interp_accel_alloc();
+    spline1 = gsl_spline_alloc(gsl_interp_steffen, nRows - interII - 1);
+    for (size_t j = 0; j < nColumns; j++) {
+
+        for (size_t k = (interII + 1); k < nRows; k++) {
+            // ytemp[k]=y[j+k*nColumns];
+            ytemp1[k - interII - 1] = y[j + k * nColumns];
+        }
+
+        gsl_spline_init(spline1, xOld1, ytemp1, nRows - interII - 1);
+
+        for (size_t k = l_nPts; k < nPts; k++) {
+            ydata[j + k * nColumns] = gsl_spline_eval(spline1, xNew[k], acc);
+        }
+    }
+    gsl_interp_accel_free(acc1);
+    gsl_spline_free(spline1);
 }
 
+double systemMass(double *ydata, UserData data) {
+    double mass = 0.0e0;
+    double rho;
+    for (size_t i = 2; i <= data->npts; i++) {
+        data->gas->setState_TPY(T(i), P(i), &Y(i, 1));
+        rho = data->gas->density();
+        //psi(i)=psi(i-1)+rho*(R(i)-R(i-1))*calc_area(HALF*(R(i)+R(i-1)),&m);
+        mass += rho * (R(i) - R(i - 1)) * calc_area(R(i), &data->metric);
+    }
+    return (mass);
+}
 
-int initializePsiGrid(double* ydata, double* psidata, UserData data){
+/*a different function:initializePsiEtaGrid is implement*/
+/*similar to the following function, it create a psi grid in the gas phase*/
+/*and a eta grid in the liquid phase*/
+int initializePsiGrid(double *ydata, double *psidata, UserData data) {
 
-	double rho,rhom;
-	/*Create a psi grid that corresponds CONSISTENTLY to the spatial grid
+    double rho, rhom;
+    /*Create a psi grid that corresponds CONSISTENTLY to the spatial grid
 	 * "R" created above. Note that the Lagrangian variable psi has  units
 	 * of kg. */
-	psi(1)=ZERO;
-	for (size_t i = 2; i <=data->npts; i++) {
-  		data->gas->setState_TPY(T(i), P(i), &Y(i,1));   
-		rho=data->gas->density();                                           
-  		data->gas->setState_TPY(T(i-1), P(i-1), &Y(i-1,1));   
-		rhom=data->gas->density();                                           
-		//psi(i)=psi(i-1)+rho*(R(i)-R(i-1))*calc_area(HALF*(R(i)+R(i-1)),&data->metric);
-		//psi(i)=psi(i-1)+rho*(R(i)-R(i-1))*calc_area(R(i),&data->metric);
-		psi(i)=psi(i-1)+(R(i)-R(i-1))*(rho*calc_area(R(i),&data->metric)+rhom*calc_area(R(i-1),&data->metric))/TWO;
-	}
-
-	/*The mass of the entire system is the value of psi at the last grid
+    psi(1) = ZERO;
+    for (size_t i = 2; i <= data->npts; i++) {
+        data->gas->setState_TPY(T(i), P(i), &Y(i, 1));
+        rho = data->gas->density();
+        data->gas->setState_TPY(T(i - 1), P(i - 1), &Y(i - 1, 1));
+        rhom = data->gas->density();
+        //psi(i)=psi(i-1)+rho*(R(i)-R(i-1))*calc_area(HALF*(R(i)+R(i-1)),&data->metric);
+        //psi(i)=psi(i-1)+rho*(R(i)-R(i-1))*calc_area(R(i),&data->metric);
+        psi(i) = psi(i - 1) + (R(i) - R(i - 1)) *
+                              (rho * calc_area(R(i), &data->metric) + rhom * calc_area(R(i - 1), &data->metric)) / TWO;
+    }
+
+    /*The mass of the entire system is the value of psi at the last grid
 	 * point. Normalize psi by this mass so that it varies from zero to
 	 * one. This makes psi dimensionless. So the mass needs to be
 	 * multiplied back in the approporiate places in the governing
 	 * equations so that units match.*/
-	data->mass=psi(data->npts);
-	for (size_t i = 1; i <=data->npts; i++) {
-		psi(i)=psi(i)/data->mass;
-	}
-	return(0);
+    data->mass = psi(data->npts);
+    for (size_t i = 1; i <= data->npts; i++) {
+        psi(i) = psi(i) / data->mass;
+    }
+    return (0);
 }
 
+/*create the psi grid in the gas phase and eta grid in the liquid phase*/
+/*note: psi has units of kg. while eta is dimensionless*/
+int initializePsiEtaGrid(double *ydata, double *psidata, UserData data) {
+    double rho, rhom, rhop;
+    /*Create a psi grid that corresponds CONSISTENTLY to the spatial grid
+	 * "R" created above. Note that the Lagrangian variable psi has  units
+	 * of kg. */
+    /*create the psi grid in gas phase*/
+    psi(data->l_npts + 1) = ZERO;
+    for (size_t i = data->l_npts + 2; i <= data->npts; i++) {
+        data->gas->setState_TPY(T(i), P(i), &Y(i, 1));
+        rho = data->gas->density();
+        data->gas->setState_TPY(T(i - 1), P(i - 1), &Y(i - 1, 1));
+        rhom = data->gas->density();
+        //psi(i)=psi(i-1)+rho*(R(i)-R(i-1))*calc_area(HALF*(R(i)+R(i-1)),&data->metric);
+        //psi(i)=psi(i-1)+rho*(R(i)-R(i-1))*calc_area(R(i),&data->metric);
+        psi(i) = psi(i - 1) + (R(i) - R(i - 1)) *
+                              (rho * calc_area(R(i), &data->metric) + rhom * calc_area(R(i - 1), &data->metric)) / TWO;
+    }
+
+    /*create the \eta grid for liquid phase*/
+    /*for the time being, liquid phase species are hard coded*/
+    std::vector<std::string> composition = components(data->dropType);
+    psi(data->l_npts) = ZERO;
+    if (data->dropType == 0) {
+        for (size_t i = data->l_npts - 1; i >= 1; i--) {
+            rho = getLiquidDensity(T(i), P(i), composition);
+            rhop = getLiquidDensity(T(i + 1), P(i + 1), composition);
+            psi(i) = psi(i + 1) + (R(i + 1) - R(i)) *
+                                  (rho * calc_area(R(i), &data->metric) + rhop * calc_area(R(i + 1), &data->metric)) /
+                                  TWO;
+        }
+    } else if (data->dropType == 1) {
+        for (size_t i = data->l_npts - 1; i >= 1; i--) {
+            std::vector<double> moleFrac, moleFracp;
+            moleFrac = getLiquidmolevec(data, ydata, i);
+            moleFracp = getLiquidmolevec(data, ydata, i + 1);
+            rho = getLiquidDensity(T(i), P(i), composition, moleFrac);
+            rhop = getLiquidDensity(T(i + 1), P(i + 1), composition, moleFracp);
+            psi(i) = psi(i + 1) + (R(i + 1) - R(i)) *
+                                  (rho * calc_area(R(i), &data->metric) + rhop * calc_area(R(i + 1), &data->metric)) /
+                                  TWO;
+        }
+    }
+    /*according to the mehtod described by Stauch et al.*/
+    /*eta should be dimensionless, so we normalize the eta with total mass of droplet*/
+    double dropmass = psi(1);
+    for (size_t i = data->l_npts; i >= 1; i--) {
+        psi(i) = psi(i) / dropmass;
+    }
+
+    /*The mass of the entire system is the value of psi at the last grid
+	 * point. Normalize psi by this mass so that it varies from zero to
+	 * one. This makes psi dimensionless. So the mass needs to be
+	 * multiplied back in the approporiate places in the governing
+	 * equations so that units match.*/
+
+    // data->mass=psi(data->npts);
+    // for (size_t i = 1; i <=data->npts; i++) {
+    // 	psi(i)=psi(i)/data->mass;
+    // }
+
 
-int setInitialCondition(N_Vector* y, 
-	    		N_Vector* ydot, 
-            		UserData data){
-	double* ydata;
-	double* ydotdata;
-	double* psidata;
-	double* innerMassFractionsData, Rd, massDrop;
-	double rhomhalf, lambdamhalf, YVmhalf[data->nsp];
-	double f=ZERO;
-	double g=ZERO;
-
-	double perturb,rho;
-	double epsilon=ZERO;
-	int m,ier;
-  	ydata    = N_VGetArrayPointer_OpenMP(*y);
-  	ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
-	innerMassFractionsData =  data->innerMassFractions;
-	Rd = data->Rd;
-	massDrop = data->massDrop;
-
-	//Mass of droplet
-	//massDrop=1.0/3.0*Rd*Rd*Rd*997.0; //TODO: The density of the droplet should be a user input
-    //massDrop=1.0/3.0*Rd*Rd*Rd*684.0; //TODO:The density of the droplet(n-heptane) should be a user input 
-	massDrop = 1.0/3.0*Rd*Rd*Rd*data->dropRho;
-    if(data->adaptiveGrid){
-  		psidata  = data->grid->xOld;
-	}
-	else{
-  		psidata  = data->uniformGrid;
-	}
-
-	m=data->metric;
-
-	data->innerTemperature=data->initialTemperature;
-	for (size_t k = 1; k <=data->nsp; k++) {
-  		innerMassFractionsData[k-1]=data->gas->massFraction(k-1);
-	}
-
-	//Define Grid:
-	double dR=(data->domainLength)/((double)(data->npts)-1.0e0);
-	double dv=(pow(data->domainLength,1+data->metric)-pow(data->firstRadius*data->domainLength,1+data->metric))/((double)(data->npts)-1.0e0);
-	
-    //Initialize the R(i),T(i)(data->initialTemperature),Y(i,k),P(i)
-    for (size_t i = 1; i <=data->npts; i++) {
-		if(data->metric==0){
-			R(i)=Rd+(double)((i-1)*dR);
-		}else{
-			if(i==1){
-				R(i)=ZERO;
-			}else if(i==2){
-				R(i)=data->firstRadius*data->domainLength;
-			}else{
-				R(i)=pow(pow(R(i-1),1+data->metric)+dv,1.0/((double)(1+data->metric)));
-			}
-		}
-		T(i)=data->initialTemperature;
-		for (size_t k = 1; k <=data->nsp; k++) {
-  	        	Y(i,k)=data->gas->massFraction(k-1);	//Indexing different in Cantera
-		}
-  	        P(i)=data->initialPressure*Cantera::OneAtm;
-	}	
-	R(data->npts)=data->domainLength+data->Rd;
     
+    return (0);
+}
+
+/*A different setInitialCondition is implemented based on the problemType =2 */
+/*As such, the following function is commented*/
+// int setInitialCondition(N_Vector* y,
+// 	    		N_Vector* ydot,
+//             		UserData data){
+// 	double* ydata;
+// 	double* ydotdata;
+// 	double* psidata;
+// 	double* innerMassFractionsData, Rd, massDrop;
+// 	double rhomhalf, lambdamhalf, YVmhalf[data->nsp];
+// 	double f=ZERO;
+// 	double g=ZERO;
+
+// 	double perturb,rho;
+// 	double epsilon=ZERO;
+// 	int m,ier;
+//   	ydata    = N_VGetArrayPointer_OpenMP(*y);
+//   	ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
+// 	innerMassFractionsData =  data->innerMassFractions;
+// 	Rd = data->Rd;
+// 	// massDrop = data->massDrop;
+
+// 	//Mass of droplet
+// 	//massDrop=1.0/3.0*Rd*Rd*Rd*997.0; //TODO: The density of the droplet should be a user input
+//     // massDrop=1.0/3.0*Rd*Rd*Rd*684.0; //TODO:The density of the droplet(n-heptane) should be a user input
+// 	// massDrop = 1.0/3.0*Rd*Rd*Rd*data->dropRho;
+//     if(data->adaptiveGrid){
+//   		psidata  = data->grid->xOld;
+// 	}
+// 	else{
+//   		psidata  = data->uniformGrid;
+// 	}
+
+// 	m=data->metric;
+
+// 	data->innerTemperature=data->initialTemperature;
+// 	for (size_t k = 1; k <=data->nsp; k++) {
+//   		innerMassFractionsData[k-1]=data->gas->massFraction(k-1);
+// 	}
+
+// 	//Define Grid:
+// 	double dR=(data->domainLength)/((double)(data->npts)-1.0e0);
+// 	double dv=(pow(data->domainLength,1+data->metric)-pow(data->firstRadius*data->domainLength,1+data->metric))/((double)(data->npts)-1.0e0);
+
+//     //Initialize the R(i),T(i)(data->initialTemperature),Y(i,k),P(i)
+//     for (size_t i = 1; i <=data->npts; i++) {
+// 		if(data->metric==0){
+// 			R(i)=Rd+(double)((i-1)*dR);
+// 		}else{
+// 			if(i==1){
+// 				R(i)=ZERO;
+// 			}else if(i==2){
+// 				R(i)=data->firstRadius*data->domainLength;
+// 			}else{
+// 				R(i)=pow(pow(R(i-1),1+data->metric)+dv,1.0/((double)(1+data->metric)));
+// 			}
+// 		}
+// 		T(i)=data->initialTemperature;
+// 		for (size_t k = 1; k <=data->nsp; k++) {
+//   	        	Y(i,k)=data->gas->massFraction(k-1);	//Indexing different in Cantera
+// 		}
+//   	        P(i)=data->initialPressure*Cantera::OneAtm;
+// 	}
+// 	R(data->npts)=data->domainLength+data->Rd;
+
+// //    /********** test R(i) and the volumn between grids *****************/
+// //    printf("Print the first 4 R(i)s and volumn between them: \n") ;
+// //    printf("Grids: 1st:%2.6e,2nd:%2.6e,3rd:%2.6e,4th:%2.6e \n",R(1),R(2),R(3),R(4));
+// //    double v1,v2,v3,v4,v5;
+// //    v1 =pow(R(2),1+data->metric) - pow(R(1),1+data->metric);
+// //    v2 =pow(R(3),1+data->metric) - pow(R(2),1+data->metric);
+// //    v3 =pow(R(4),1+data->metric) - pow(R(3),1+data->metric);
+// //    v4 =pow(R(5),1+data->metric) - pow(R(4),1+data->metric);
+// //    v5 =pow(R(6),1+data->metric) - pow(R(5),1+data->metric);
+// //    printf("Volumn: 1st:%2.6e,2nd:%2.6e,3rd:%2.6e,4th:%2.6e,5th:%2.6e\n",v1,v2,v3,v4,v5) ;
+
+
+// 	double Tmax;
+// 	double Tmin=data->initialTemperature;
+// 	double w=data->mixingWidth;
+// 	double YN2=ZERO;
+// 	double YO2=ZERO;
+// 	double YFuel,YOxidizer,sum;
+
+// 	//if(data->problemType==0){
+// 	//	data->gas->equilibrate("HP");
+// 	//	data->maxTemperature=data->gas->temperature();
+// 	//}
+// 	//else if(data->problemType==1){
+// 	//	/*Premixed Combustion: Equilibrium products comprise ignition
+// 	//	 * kernel at t=0. The width of the kernel is "mixingWidth"
+// 	//	 * shifted by "shift" from the center.*/
+// 	//	data->gas->equilibrate("HP");
+// 	//	Tmax=data->gas->temperature();
+// 	//	for (size_t i = 1; i <=data->npts; i++) {
+// 	//		g=HALF*(tanh((R(i)-data->shift)/w)+ONE);	//increasing function of x
+// 	//		f=ONE-g;					//decreasing function of x
+// 	//		T(i)=(Tmax-Tmin)*f+Tmin;
+// 	//		for (size_t k = 1; k <=data->nsp; k++) {
+// 	//			Y(i,k)=(data->gas->massFraction(k-1)-Y(i,k))*f+Y(i,k);
+// 	//		}
+// 	//	}
+// 	//	if(data->dirichletOuter){
+// 	//		T(data->npts)=data->wallTemperature;
+// 	//	}
+// 	//}
+// 	//else if(data->problemType==2){
+// 	//	FILE* input;
+// 	//	if(input=fopen("initialCondition.dat","r")){
+// 	//		readInitialCondition(input, ydata, data->nvar, data->nr, data->npts);
+// 	//		fclose(input);
+// 	//	}
+// 	//	else{
+// 	//		printf("file initialCondition.dat not found!\n");
+// 	//		return(-1);
+// 	//	}
+// 	//}
+
+// 	initializePsiGrid(ydata,psidata,data);
+
+// 	if(data->adaptiveGrid){
+// 	//	if(data->problemType!=0){
+// 	//		data->grid->position=maxGradPosition(ydata, data->nt, data->nvar,
+// 	//						 data->grid->xOld, data->npts);
+// 	//		//data->grid->position=maxCurvPosition(ydata, data->nt, data->nvar,
+// 	//		//				 data->grid->xOld, data->npts);
+// 	//	}
+// 	//	else{
+// 	//	}
+// 		if(data->problemType!=3){
+// 			data->grid->position=0.0e0;
+// 			double x=data->grid->position+data->gridOffset*data->grid->leastMove;
+// 			printf("New grid center:%15.6e\n",x);
+
+//             ier=reGrid(data->grid, x);
+// 			if(ier==-1)return(-1);
+
+// 			updateSolution(ydata, ydotdata, data->nvar,
+// 			               data->grid->xOld,data->grid->x,data->npts);
+// 			storeGrid(data->grid->x,data->grid->xOld,data->npts);
+// 		}
+// 	}
+// 	else{
+// 		double Rg = data->Rg, dpsi0;
+// 		int NN = data->npts-2;
+// 		double psiNew[data->npts];
+
+// 		dpsi0 = (pow(Rg,1.0/NN) - 1.0)/(pow(Rg,(NN+1.0)/NN) - 1.0);
+// 		psiNew[0] = 0;
+// 		for (size_t i = 1; i < data->npts-1; i++) {
+// 			psiNew[i]=psiNew[i-1]+dpsi0*pow(Rg,(i-1.0)/NN);
+// 		}
+// 		psiNew[data->npts-1] = 1.0;
+// 		printf("Last point:%15.6e\n",psiNew[data->npts-1]);
+// 		updateSolution(ydata, ydotdata, data->nvar,
+// 		               data->uniformGrid,psiNew,data->npts);
+// 		storeGrid(psiNew,data->uniformGrid,data->npts);
+
+// 		//double psiNew[data->npts];
+// 		//double dpsi=1.0e0/((double)(data->npts)-1.0e0);
+// 		//for (size_t i = 0; i < data->npts; i++) {
+// 		//	psiNew[i]=(double)(i)*dpsi;
+// 		//}
+// 		//printf("Last point:%15.6e\n",psiNew[data->npts-1]);
+// 		//updateSolution(ydata, ydotdata, data->nvar,
+// 		//               data->uniformGrid,psiNew,data->npts);
+// 		//storeGrid(psiNew,data->uniformGrid,data->npts);
+// 	}
+
+// 	if(data->problemType==0){
+// 		data->gas->equilibrate("HP");
+// 		data->maxTemperature=data->gas->temperature();
+// 	}
+// 	else if(data->problemType==1){
+// 		/*Premixed Combustion: Equilibrium products comprise ignition
+// 		 * kernel at t=0. The width of the kernel is "mixingWidth"
+// 		 * shifted by "shift" from the center.*/
+// 		data->gas->equilibrate("HP");
+// 		Tmax=data->gas->temperature();
+// 		for (size_t i = 1; i <=data->npts; i++) {
+// 			g=HALF*(tanh((R(i)-data->shift)/w)+ONE);	//increasing function of x
+// 			f=ONE-g;					//decreasing function of x
+// 			T(i)=(Tmax-Tmin)*f+Tmin;
+// 			for (size_t k = 1; k <=data->nsp; k++) {
+// 				Y(i,k)=(data->gas->massFraction(k-1)-Y(i,k))*f+Y(i,k);
+// 			}
+// 		}
+// 		if(data->dirichletOuter){
+// 			T(data->npts)=data->wallTemperature;
+// 		}
+// 	}
+// 	else if(data->problemType==2){
+// 		FILE* input;
+// 		if(input=fopen("initialCondition.dat","r")){
+// 			readInitialCondition(input, ydata, data->nvar, data->nr, data->npts, data->Rg);
+// 			fclose(input);
+// 		}
+// 		else{
+// 			printf("file initialCondition.dat not found!\n");
+// 			return(-1);
+// 		}
+// 		initializePsiGrid(ydata,psidata,data);
+// 	}
+// 	else if(data->problemType==3){
+// 		FILE* input;
+// 		if(input=fopen("restart.bin","r")){
+// 			readRestart(y, ydot, input, data);
+// 			fclose(input);
+// 			printf("Restart solution loaded!\n");
+// 			printf("Problem starting at t=%15.6e\n",data->tNow);
+// 			return(0);
+// 		}
+// 		else{
+// 			printf("file restart.bin not found!\n");
+// 			return(-1);
+// 		}
+// 	}
+
+// 	if(data->reflectProblem){
+// 		double temp;
+// 		int j=1;
+// 		while (data->npts+1-2*j>=0) {
+// 			temp=T(j);
+// 			T(j)=T(data->npts+1-j);
+// 			T(data->npts+1-j)=temp;
+// 			for (size_t k = 1; k <=data->nsp; k++) {
+// 				temp=Y(j,k);
+// 				Y(j,k)=Y(data->npts+1-j,k);
+// 				Y(data->npts+1-j,k)=temp;
+// 			}
+// 			j=j+1;
+// 		}
+// 	}
+
+// 	/*Floor small values to zero*/
+// 	for (size_t i = 1; i <=data->npts; i++) {
+// 		for (size_t k = 1; k <=data->nsp; k++) {
+// 			if(fabs(Y(i,k))<=data->massFractionTolerance){
+// 				Y(i,k)=0.0e0;
+// 			}
+// 		}
+// 	}
+
+// 	//Set grid to location of maximum curvature calculated by r instead of x:
+// 	if(data->adaptiveGrid){
+// 		//data->grid->position=maxCurvPosition(ydata, data->nt, data->nvar,
+// 		//		  		data->grid->x, data->npts);
+//         int maxCurvII = 0;
+//         maxCurvII = maxCurvIndexR(ydata,data->nt,data->nvar,data->nr,data->npts);
+
+//         data->grid->position = data->grid->x[maxCurvII];
+// 		ier=reGrid(data->grid, data->grid->position);
+// 		updateSolution(ydata, ydotdata, data->nvar,
+// 		               data->grid->xOld,data->grid->x,data->npts);
+// 		storeGrid(data->grid->x,data->grid->xOld,data->npts);
+
+//         /******** Test the maxCurvPosition and related variables *******/
+//         printf("The maxCurvPositition(based on r) is : %.6f,Temperature is : %.3f \n",data->grid->position,T(maxCurvII+1));
+// 	}
+
+
+// 	/*Ensure consistent boundary conditions*/
+// 	//T(1)=T(2);
+// 	//for (size_t k = 1; k <=data->nsp; k++) {
+// 	//	Y(1,k)=Y(2,k);
+// 	//	Y(data->npts,k)=Y(data->npts-1,k);
+// 	//}
+
+// 	return(0);
+// }
+
+/*Revise the setInitialCondition function to be suitable for two-phase TORC*/
+int setInitialCondition(N_Vector *y,
+                        N_Vector *ydot,
+                        UserData data) {
+    double *ydata;
+    double *ydotdata;
+    double *psidata;
+    double *innerMassFractionsData, Rd, massDrop;
+    double rhomhalf, lambdamhalf, YVmhalf[data->nsp];
+    double f = ZERO;
+    double g = ZERO;
+
+    double perturb, rho;
+    double epsilon = ZERO;
+    int m, ier;
+    ydata = N_VGetArrayPointer_OpenMP(*y);
+    ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
+    innerMassFractionsData = data->innerMassFractions;
+    Rd = data->Rd;
+    // massDrop = data->massDrop;
+
+    //Mass of droplet
+    // massDrop=1.0/3.0*Rd*Rd*Rd*997.0; //TODO: The density of the droplet should be a user input
+    // massDrop=1.0/3.0*Rd*Rd*Rd*684.0; //TODO:The density of the droplet(n-heptane) should be a user input
+    // massDrop = 1.0/3.0*Rd*Rd*Rd*data->dropRho;
+    if (data->adaptiveGrid) {
+        psidata = data->grid->xOld;
+    } else {
+        psidata = data->uniformGrid;
+    }
+
+    m = data->metric;
+
+    data->innerTemperature = data->initialTemperature;
+    for (size_t k = 1; k <= data->nsp; k++) {
+        innerMassFractionsData[k - 1] = data->gas->massFraction(k - 1);
+    }
+
+    //Define Grid:
+    double dR = (data->domainLength) / ((double) (data->g_npts) - 1.0e0);
+    double dv = (pow(data->domainLength, 1 + data->metric) -
+                 pow(data->firstRadius * data->domainLength, 1 + data->metric)) / ((double) (data->g_npts) - 1.0e0);
+
+
+    // //Initialize the R(i),T(i)(data->initialTemperature),Y(i,k),P(i)
+    // for (size_t i = 1; i <=data->npts; i++) {
+    // 	if(data->metric==0){
+    // 		R(i)=Rd+(double)((i-1)*dR);
+    // 	}else{
+    // 		if(i==1){
+    // 			R(i)=ZERO;
+    // 		}else if(i==2){
+    // 			R(i)=data->firstRadius*data->domainLength;
+    // 		}else{
+    // 			R(i)=pow(pow(R(i-1),1+data->metric)+dv,1.0/((double)(1+data->metric)));
+    // 		}
+    // 	}
+    // 	T(i)=data->initialTemperature;
+    // 	for (size_t k = 1; k <=data->nsp; k++) {
+    //         	Y(i,k)=data->gas->massFraction(k-1);	//Indexing different in Cantera
+    // 	}
+    //         P(i)=data->initialPressure*Cantera::OneAtm;
+    // }
+    // R(data->npts)=data->domainLength+data->Rd;
+
+
 //    /********** test R(i) and the volumn between grids *****************/
-//    printf("Print the first 4 R(i)s and volumn between them: \n") ; 
+//    printf("Print the first 4 R(i)s and volumn between them: \n") ;
 //    printf("Grids: 1st:%2.6e,2nd:%2.6e,3rd:%2.6e,4th:%2.6e \n",R(1),R(2),R(3),R(4));
-//    double v1,v2,v3,v4,v5; 
+//    double v1,v2,v3,v4,v5;
 //    v1 =pow(R(2),1+data->metric) - pow(R(1),1+data->metric);
 //    v2 =pow(R(3),1+data->metric) - pow(R(2),1+data->metric);
 //    v3 =pow(R(4),1+data->metric) - pow(R(3),1+data->metric);
-//    v4 =pow(R(5),1+data->metric) - pow(R(4),1+data->metric); 
+//    v4 =pow(R(5),1+data->metric) - pow(R(4),1+data->metric);
 //    v5 =pow(R(6),1+data->metric) - pow(R(5),1+data->metric);
-//    printf("Volumn: 1st:%2.6e,2nd:%2.6e,3rd:%2.6e,4th:%2.6e,5th:%2.6e\n",v1,v2,v3,v4,v5) ; 
-
-
-	double Tmax;
-	double Tmin=data->initialTemperature;
-	double w=data->mixingWidth;
-	double YN2=ZERO;
-	double YO2=ZERO;
-	double YFuel,YOxidizer,sum;
-
-	//if(data->problemType==0){
-	//	data->gas->equilibrate("HP");
-	//	data->maxTemperature=data->gas->temperature();
-	//}
-	//else if(data->problemType==1){
-	//	/*Premixed Combustion: Equilibrium products comprise ignition
-	//	 * kernel at t=0. The width of the kernel is "mixingWidth"
-	//	 * shifted by "shift" from the center.*/
-	//	data->gas->equilibrate("HP");
-	//	Tmax=data->gas->temperature();
-	//	for (size_t i = 1; i <=data->npts; i++) {
-	//		g=HALF*(tanh((R(i)-data->shift)/w)+ONE);	//increasing function of x
-	//		f=ONE-g;					//decreasing function of x
-	//		T(i)=(Tmax-Tmin)*f+Tmin;
-	//		for (size_t k = 1; k <=data->nsp; k++) {
-	//			Y(i,k)=(data->gas->massFraction(k-1)-Y(i,k))*f+Y(i,k);
-	//		}
-	//	}
-	//	if(data->dirichletOuter){
-	//		T(data->npts)=data->wallTemperature;
-	//	}
-	//}
-	//else if(data->problemType==2){
-	//	FILE* input;
-	//	if(input=fopen("initialCondition.dat","r")){
-	//		readInitialCondition(input, ydata, data->nvar, data->nr, data->npts);
-	//		fclose(input);
-	//	}
-	//	else{
-	//		printf("file initialCondition.dat not found!\n");
-	//		return(-1);
-	//	}
-	//}
-
-	initializePsiGrid(ydata,psidata,data);
-
-	if(data->adaptiveGrid){
-	//	if(data->problemType!=0){
-	//		data->grid->position=maxGradPosition(ydata, data->nt, data->nvar,
-	//						 data->grid->xOld, data->npts);
-	//		//data->grid->position=maxCurvPosition(ydata, data->nt, data->nvar,
-	//		//				 data->grid->xOld, data->npts);
-	//	}
-	//	else{
-	//	}
-		if(data->problemType!=3){
-			data->grid->position=0.0e0;
-			double x=data->grid->position+data->gridOffset*data->grid->leastMove;
-			printf("New grid center:%15.6e\n",x);
-
-//            /**************** TEST THE data->grid->xOld *******************/
-//            double* ptr3 = data->grid->xOld ; 
-//            printf("SetInitialCondition function is called,before reGrid,Start print the first 5 elements of the xOld array : \n");
-//            printf("1st:%.6f, 2nd:%.6f, 3rd:%.6f, 4th:%.6f, 5th:%.6f.\n",ptr3[0],ptr3[1],ptr3[2],ptr3[3],ptr3[4]);
-			
-            ier=reGrid(data->grid, x);
-			if(ier==-1)return(-1);
-
-//            /**************** TEST THE data->grid->xOld *******************/
-//            double* ptr = data->grid->xOld ; 
-//            printf("SetInitialCondition function is called,after reGrid,Start print the first 5 elements of the xOld array : \n");
-//            printf("1st:%.6f, 2nd:%.6f, 3rd:%.6f, 4th:%.6f, 5th:%.6f.\n",ptr[0],ptr[1],ptr[2],ptr[3],ptr[4]);
-
-
-			updateSolution(ydata, ydotdata, data->nvar,
-			               data->grid->xOld,data->grid->x,data->npts);
-			storeGrid(data->grid->x,data->grid->xOld,data->npts);
-		}
-	}
-	else{
-		double Rg = data->Rg, dpsi0;
-		int NN = data->npts-2;
-		double psiNew[data->npts];
-		
-		dpsi0 = (pow(Rg,1.0/NN) - 1.0)/(pow(Rg,(NN+1.0)/NN) - 1.0);
-		psiNew[0] = 0;
-		for (size_t i = 1; i < data->npts-1; i++) {
-			psiNew[i]=psiNew[i-1]+dpsi0*pow(Rg,(i-1.0)/NN);
-		}
-		psiNew[data->npts-1] = 1.0;
-		printf("Last point:%15.6e\n",psiNew[data->npts-1]);
-		updateSolution(ydata, ydotdata, data->nvar,
-		               data->uniformGrid,psiNew,data->npts);
-		storeGrid(psiNew,data->uniformGrid,data->npts);
-
-		//double psiNew[data->npts];
-		//double dpsi=1.0e0/((double)(data->npts)-1.0e0);
-		//for (size_t i = 0; i < data->npts; i++) {
-		//	psiNew[i]=(double)(i)*dpsi;
-		//}
-		//printf("Last point:%15.6e\n",psiNew[data->npts-1]);
-		//updateSolution(ydata, ydotdata, data->nvar,
-		//               data->uniformGrid,psiNew,data->npts);
-		//storeGrid(psiNew,data->uniformGrid,data->npts);
-	}
-
-	if(data->problemType==0){
-		data->gas->equilibrate("HP");
-		data->maxTemperature=data->gas->temperature();
-	}
-	else if(data->problemType==1){
-		/*Premixed Combustion: Equilibrium products comprise ignition
+//    printf("Volumn: 1st:%2.6e,2nd:%2.6e,3rd:%2.6e,4th:%2.6e,5th:%2.6e\n",v1,v2,v3,v4,v5) ;
+
+    double Tmax;
+    double Tmin = data->initialTemperature;
+    double w = data->mixingWidth;
+    double YN2 = ZERO;
+    double YO2 = ZERO;
+    double YFuel, YOxidizer, sum;
+
+    //if(data->problemType==0){
+    //	data->gas->equilibrate("HP");
+    //	data->maxTemperature=data->gas->temperature();
+    //}
+    //else if(data->problemType==1){
+    //	/*Premixed Combustion: Equilibrium products comprise ignition
+    //	 * kernel at t=0. The width of the kernel is "mixingWidth"
+    //	 * shifted by "shift" from the center.*/
+    //	data->gas->equilibrate("HP");
+    //	Tmax=data->gas->temperature();
+    //	for (size_t i = 1; i <=data->npts; i++) {
+    //		g=HALF*(tanh((R(i)-data->shift)/w)+ONE);	//increasing function of x
+    //		f=ONE-g;					//decreasing function of x
+    //		T(i)=(Tmax-Tmin)*f+Tmin;
+    //		for (size_t k = 1; k <=data->nsp; k++) {
+    //			Y(i,k)=(data->gas->massFraction(k-1)-Y(i,k))*f+Y(i,k);
+    //		}
+    //	}
+    //	if(data->dirichletOuter){
+    //		T(data->npts)=data->wallTemperature;
+    //	}
+    //}
+    //else if(data->problemType==2){
+    //	FILE* input;
+    //	if(input=fopen("initialCondition.dat","r")){
+    //		readInitialCondition(input, ydata, data->nvar, data->nr, data->npts);
+    //		fclose(input);
+    //	}
+    //	else{
+    //		printf("file initialCondition.dat not found!\n");
+    //		return(-1);
+    //	}
+    //}
+
+    // initializePsiGrid(ydata,psidata,data);
+
+
+    // if(data->adaptiveGrid){
+    // //	if(data->problemType!=0){
+    // //		data->grid->position=maxGradPosition(ydata, data->nt, data->nvar,
+    // //						 data->grid->xOld, data->npts);
+    // //		//data->grid->position=maxCurvPosition(ydata, data->nt, data->nvar,
+    // //		//				 data->grid->xOld, data->npts);
+    // //	}
+    // //	else{
+    // //	}
+    // 	if(data->problemType!=3){
+    // 		data->grid->position=0.0e0;
+    // 		double x=data->grid->position+data->gridOffset*data->grid->leastMove;
+    // 		printf("New grid center:%15.6e\n",x);
+
+    //         ier=reGrid(data->grid, x);
+    // 		if(ier==-1)return(-1);
+
+    // 		updateSolution(ydata, ydotdata, data->nvar,
+    // 		               data->grid->xOld,data->grid->x,data->npts);
+    // 		storeGrid(data->grid->x,data->grid->xOld,data->npts);
+    // 	}
+    // }
+    // else{
+    // 	double Rg = data->Rg, dpsi0;
+    // 	int NN = data->npts-2;
+    // 	double psiNew[data->npts];
+
+    // 	dpsi0 = (pow(Rg,1.0/NN) - 1.0)/(pow(Rg,(NN+1.0)/NN) - 1.0);
+    // 	psiNew[0] = 0;
+    // 	for (size_t i = 1; i < data->npts-1; i++) {
+    // 		psiNew[i]=psiNew[i-1]+dpsi0*pow(Rg,(i-1.0)/NN);
+    // 	}
+    // 	psiNew[data->npts-1] = 1.0;
+    // 	printf("Last point:%15.6e\n",psiNew[data->npts-1]);
+    // 	updateSolution(ydata, ydotdata, data->nvar,
+    // 	               data->uniformGrid,psiNew,data->npts);
+    // 	storeGrid(psiNew,data->uniformGrid,data->npts);
+
+    // 	//double psiNew[data->npts];
+    // 	//double dpsi=1.0e0/((double)(data->npts)-1.0e0);
+    // 	//for (size_t i = 0; i < data->npts; i++) {
+    // 	//	psiNew[i]=(double)(i)*dpsi;
+    // 	//}
+    // 	//printf("Last point:%15.6e\n",psiNew[data->npts-1]);
+    // 	//updateSolution(ydata, ydotdata, data->nvar,
+    // 	//               data->uniformGrid,psiNew,data->npts);
+    // 	//storeGrid(psiNew,data->uniformGrid,data->npts);
+    // }
+
+    if (data->problemType == 0) {
+        data->gas->equilibrate("HP");
+        data->maxTemperature = data->gas->temperature();
+    } else if (data->problemType == 1) {
+        /*Premixed Combustion: Equilibrium products comprise ignition
 		 * kernel at t=0. The width of the kernel is "mixingWidth"
 		 * shifted by "shift" from the center.*/
-		data->gas->equilibrate("HP");
-		Tmax=data->gas->temperature();
-		for (size_t i = 1; i <=data->npts; i++) {
-			g=HALF*(tanh((R(i)-data->shift)/w)+ONE);	//increasing function of x
-			f=ONE-g;					//decreasing function of x
-			T(i)=(Tmax-Tmin)*f+Tmin;
-			for (size_t k = 1; k <=data->nsp; k++) {
-				Y(i,k)=(data->gas->massFraction(k-1)-Y(i,k))*f+Y(i,k);
-			}
-		}
-		if(data->dirichletOuter){
-			T(data->npts)=data->wallTemperature;
-		}
-	}
-	else if(data->problemType==2){
-		FILE* input;
-		if(input=fopen("initialCondition.dat","r")){
-			readInitialCondition(input, ydata, data->nvar, data->nr, data->npts, data->Rg);
-			fclose(input);
-		}
-		else{
-			printf("file initialCondition.dat not found!\n");
-			return(-1);
-		}
-		initializePsiGrid(ydata,psidata,data);
-	}
-	else if(data->problemType==3){
-		FILE* input;
-		if(input=fopen("restart.bin","r")){
-			readRestart(y, ydot, input, data);
-			fclose(input);
-			printf("Restart solution loaded!\n");
-			printf("Problem starting at t=%15.6e\n",data->tNow);
-			return(0);
-		}
-		else{
-			printf("file restart.bin not found!\n");
-			return(-1);
-		}
-	}
-
-	if(data->reflectProblem){
-		double temp;
-		int j=1;
-		while (data->npts+1-2*j>=0) {
-			temp=T(j);
-			T(j)=T(data->npts+1-j);
-			T(data->npts+1-j)=temp;
-			for (size_t k = 1; k <=data->nsp; k++) {
-				temp=Y(j,k);
-				Y(j,k)=Y(data->npts+1-j,k);
-				Y(data->npts+1-j,k)=temp;
-			}
-			j=j+1;
-		}
-	}
-
-	/*Floor small values to zero*/
-	for (size_t i = 1; i <=data->npts; i++) {
-		for (size_t k = 1; k <=data->nsp; k++) {
-			if(fabs(Y(i,k))<=data->massFractionTolerance){
-				Y(i,k)=0.0e0;
-			}
-		}
-	}
-
-	//Set grid to location of maximum curvature calculated by r instead of x:
-	if(data->adaptiveGrid){
-		//data->grid->position=maxCurvPosition(ydata, data->nt, data->nvar,
-		//		  		data->grid->x, data->npts);
-        int maxCurvII = 0; 
-        maxCurvII = maxCurvIndexR(ydata,data->nt,data->nvar,data->nr,data->npts);
-        
+        data->gas->equilibrate("HP");
+        Tmax = data->gas->temperature();
+        for (size_t i = 1; i <= data->npts; i++) {
+            g = HALF * (tanh((R(i) - data->shift) / w) + ONE);    //increasing function of x
+            f = ONE - g;                    //decreasing function of x
+            T(i) = (Tmax - Tmin) * f + Tmin;
+            for (size_t k = 1; k <= data->nsp; k++) {
+                Y(i, k) = (data->gas->massFraction(k - 1) - Y(i, k)) * f + Y(i, k);
+            }
+        }
+        if (data->dirichletOuter) {
+            T(data->npts) = data->wallTemperature;
+        }
+    } else if (data->problemType == 2) {
+        FILE *input;
+        if (input = fopen("initialCondition.dat", "r")) {
+            readInitialCondition(input, ydata, data->nvar, data->nr, data->npts, data->l_npts, data->Rg);
+            fclose(input);
+        } else {
+            printf("file initialCondition.dat not found!\n");
+            return (-1);
+        }
+        // initializePsiGrid(ydata,psidata,data);
+        initializePsiEtaGrid(ydata, psidata, data);
+    } else if (data->problemType == 3) {
+        FILE *input;
+        if (input = fopen("restart.bin", "r")) {
+            readRestart(y, ydot, input, data);
+            fclose(input);
+            printf("Restart solution loaded!\n");
+            printf("Problem starting at t=%15.6e\n", data->tNow);
+            return (0);
+        } else {
+            printf("file restart.bin not found!\n");
+            return (-1);
+        }
+    }
+
+    if (data->reflectProblem) {
+        double temp;
+        int j = 1;
+        while (data->npts + 1 - 2 * j >= 0) {
+            temp = T(j);
+            T(j) = T(data->npts + 1 - j);
+            T(data->npts + 1 - j) = temp;
+            for (size_t k = 1; k <= data->nsp; k++) {
+                temp = Y(j, k);
+                Y(j, k) = Y(data->npts + 1 - j, k);
+                Y(data->npts + 1 - j, k) = temp;
+            }
+            j = j + 1;
+        }
+    }
+
+    /*Floor small values to zero*/
+    for (size_t i = 1; i <= data->npts; i++) {
+        for (size_t k = 1; k <= data->nsp; k++) {
+            if (fabs(Y(i, k)) <= data->massFractionTolerance) {
+                Y(i, k) = 0.0e0;
+            }
+        }
+    }
+
+    //Set grid to location of maximum curvature calculated by r instead of x:
+    if (data->adaptiveGrid) {
+        //data->grid->position=maxCurvPosition(ydata, data->nt, data->nvar,
+        //		  		data->grid->x, data->npts);
+        int maxCurvII = 0;
+        maxCurvII = maxCurvIndexR(ydata, data->nt, data->nvar, data->nr, data->npts);
+
         data->grid->position = data->grid->x[maxCurvII];
-		ier=reGrid(data->grid, data->grid->position);
-		updateSolution(ydata, ydotdata, data->nvar,
-		               data->grid->xOld,data->grid->x,data->npts);
-		storeGrid(data->grid->x,data->grid->xOld,data->npts);
-        
+        ier = reGrid(data->grid, data->grid->position);
+        updateSolution(ydata, ydotdata, data->nvar,
+                       data->grid->xOld, data->grid->x, data->npts);
+        storeGrid(data->grid->x, data->grid->xOld, data->npts);
+
         /******** Test the maxCurvPosition and related variables *******/
-        printf("The maxCurvPositition(based on r) is : %.6f,Temperature is : %.3f \n",data->grid->position,T(maxCurvII+1));
-	}
+        printf("The maxCurvPositition(based on r) is : %.6f,Temperature is : %.3f \n", data->grid->position,
+               T(maxCurvII + 1));
+    }
 
 
-	/*Ensure consistent boundary conditions*/	
-	//T(1)=T(2);
-	//for (size_t k = 1; k <=data->nsp; k++) {
-	//	Y(1,k)=Y(2,k);
-	//	Y(data->npts,k)=Y(data->npts-1,k);
-	//}
+    /*Ensure consistent boundary conditions*/
+    //T(1)=T(2);
+    //for (size_t k = 1; k <=data->nsp; k++) {
+    //	Y(1,k)=Y(2,k);
+    //	Y(data->npts,k)=Y(data->npts-1,k);
+    //}
+    printPsidata(data,psidata);
 
-	return(0);
+    return (0);
 }
 
-inline double Qdot(double* t, 
-	    	   double* x, 
-	    	   double* ignTime, 
-	    	   double* kernelSize, 
-	    	   double* maxQdot){
-	double qdot;
-	if(*x<=*kernelSize){
-		if((*t)<=(*ignTime)){
-			qdot=(*maxQdot);
-		}
-		else{
-			qdot=0.0e0;
-		}
-	}else{
-		qdot=0.0e0;
-	}
-	return(qdot);
+inline double Qdot(double *t,
+                   double *x,
+                   double *ignTime,
+                   double *kernelSize,
+                   double *maxQdot) {
+    double qdot;
+    if (*x <= *kernelSize) {
+        if ((*t) <= (*ignTime)) {
+            qdot = (*maxQdot);
+        } else {
+            qdot = 0.0e0;
+        }
+    } else {
+        qdot = 0.0e0;
+    }
+    return (qdot);
 }
 
-inline void setGas(UserData data, 
-	    double *ydata, 
-	    size_t gridPoint){
-  	data->gas->setTemperature(T(gridPoint)); 	        
-  	data->gas->setMassFractions_NoNorm(&Y(gridPoint,1)); 	
-  	data->gas->setPressure(P(gridPoint));
+inline void setGas(UserData data,
+                   double *ydata,
+                   size_t gridPoint) {
+    data->gas->setTemperature(T(gridPoint));
+    data->gas->setMassFractions_NoNorm(&Y(gridPoint, 1));
+    data->gas->setPressure(P(gridPoint));
 }
 
-void getTransport(UserData data, 
-		  double *ydata, 
-		  size_t gridPoint,
-		  double *rho,
-		  double *lambda,
-		  double YV[]){
-
-	double YAvg[data->nsp],
-		 XLeft[data->nsp],
-		 XRight[data->nsp],
-		 gradX[data->nsp];
-
-	setGas(data,ydata,gridPoint);
-	data->gas->getMoleFractions(XLeft);                                     
-	setGas(data,ydata,gridPoint+1);
-	data->gas->getMoleFractions(XRight);                                     
-                                                                             
-	for (size_t k = 1; k <=data->nsp; k++) {                                          
-		YAvg(k)=HALF*(Y(gridPoint,k)+
-			      Y(gridPoint+1,k));                                 
-		gradX(k)=(XRight(k)-XLeft(k))/
-			 (R(gridPoint+1)-R(gridPoint));                       
-	}                                                                    
-	double TAvg = HALF*(T(gridPoint)+T(gridPoint+1));
-	double gradT=(T(gridPoint+1)-T(gridPoint))/
-		       (R(gridPoint+1)-R(gridPoint));                                  
-
-
-  	data->gas->setTemperature(TAvg); 	        
-  	data->gas->setMassFractions_NoNorm(YAvg); 	
-  	data->gas->setPressure(P(gridPoint));
-
-	*rho=data->gas->density();                                       
-	*lambda=data->trmix->thermalConductivity();                      
-	data->trmix->getSpeciesFluxes(1,&gradT,data->nsp,                     
-				      gradX,data->nsp,YV);                
-	//setGas(data,ydata,gridPoint);
+void getTransport(UserData data,
+                  double *ydata,
+                  size_t gridPoint,
+                  double *rho,
+                  double *lambda,
+                  double YV[]) {
+
+    double YAvg[data->nsp],
+            XLeft[data->nsp],
+            XRight[data->nsp],
+            gradX[data->nsp];
+
+    setGas(data, ydata, gridPoint);
+    data->gas->getMoleFractions(XLeft);
+    setGas(data, ydata, gridPoint + 1);
+    data->gas->getMoleFractions(XRight);
+
+    for (size_t k = 1; k <= data->nsp; k++) {
+        YAvg(k) = HALF * (Y(gridPoint, k) +
+                          Y(gridPoint + 1, k));
+        gradX(k) = (XRight(k) - XLeft(k)) /
+                   (R(gridPoint + 1) - R(gridPoint));
+    }
+    double TAvg = HALF * (T(gridPoint) + T(gridPoint + 1));
+    double gradT = (T(gridPoint + 1) - T(gridPoint)) /
+                   (R(gridPoint + 1) - R(gridPoint));
+
+
+    data->gas->setTemperature(TAvg);
+    data->gas->setMassFractions_NoNorm(YAvg);
+    data->gas->setPressure(P(gridPoint));
+
+    *rho = data->gas->density();
+    *lambda = data->trmix->thermalConductivity();
+    data->trmix->getSpeciesFluxes(1, &gradT, data->nsp,
+                                  gradX, data->nsp, YV);
+    //setGas(data,ydata,gridPoint);
+}
+
+void getGasMassFlux(UserData data,
+                  double *ydata,
+                  size_t gridPoint,
+                  double YV[]) {
+
+    double YAvg[data->nsp],
+            XLeft[data->nsp],
+            XRight[data->nsp],
+            gradX[data->nsp];
+
+    setGas(data, ydata, gridPoint);
+    data->gas->getMoleFractions(XLeft);
+    setGas(data, ydata, gridPoint + 1);
+    data->gas->getMoleFractions(XRight);
+
+    for (size_t k = 1; k <= data->nsp; k++) {
+        YAvg(k) = HALF * (Y(gridPoint, k) +
+                          Y(gridPoint + 1, k));
+        gradX(k) = (XRight(k) - XLeft(k)) /
+                   (R(gridPoint + 1) - R(gridPoint));
+    }
+    double TAvg = HALF * (T(gridPoint) + T(gridPoint + 1));
+    double gradT = (T(gridPoint + 1) - T(gridPoint)) /
+                   (R(gridPoint + 1) - R(gridPoint));
+
+
+    data->gas->setTemperature(TAvg);
+    data->gas->setMassFractions_NoNorm(YAvg);
+    data->gas->setPressure(P(gridPoint));
+
+    data->trmix->getSpeciesFluxes(1, &gradT, data->nsp,
+                                  gradX, data->nsp, YV);
+    //setGas(data,ydata,gridPoint);
 }
 
-int residue(double t, N_Vector y, N_Vector ydot, N_Vector res, void *user_data){
-
-	/*Declare and fetch nvectors and user data:*/
-
-  	double *ydata, *ydotdata, *resdata, *psidata, *innerMassFractionsData;
-  	
-	UserData data;
-	data = (UserData)user_data;
-	size_t npts=data->npts;
-	size_t nsp=data->nsp;
-	size_t k_bath = data->k_bath;
-	size_t k_drop[2] = {data->k_drop[0],data->k_drop[1]};
-
-	ydata 	= N_VGetArrayPointer_OpenMP(y); 
-	ydotdata= N_VGetArrayPointer_OpenMP(ydot); 
-	resdata = N_VGetArrayPointer_OpenMP(res);
-	if(data->adaptiveGrid==1){
-		psidata = data->grid->x;
-	}else{
-		psidata = data->uniformGrid;
-	}
-
-	innerMassFractionsData =  data->innerMassFractions;
-
-	/* Grid stencil:*/
-
-	/*-------|---------*---------|---------*---------|-------*/
-	/*-------|---------*---------|---------*---------|-------*/
-	/*-------|---------*---------|---------*---------|-------*/
-	/*-------m-------mhalf-------j-------phalf-------p-------*/
-	/*-------|---------*---------|---------*---------|-------*/
-	/*-------|---------*---------|---------*---------|-------*/
-	/*-------|<=======dxm=======>|<=======dxp=======>|-------*/
-	/*-------|---------*<======dxav=======>*---------|-------*/
-	/*-------|<================dxpm=================>|-------*/
-
-	/* Various variables defined for book-keeping and storing previously
+int residue(double t, N_Vector y, N_Vector ydot, N_Vector res, void *user_data) {
+
+    /*Declare and fetch nvectors and user data:*/
+    double *ydata, *ydotdata, *resdata, *psidata, *innerMassFractionsData;
+
+    UserData data;
+    data = (UserData) user_data;
+    size_t npts = data->npts;
+    size_t nsp = data->nsp;
+    size_t k_bath = data->k_bath;
+    size_t l_npts = data->l_npts;
+    int dropType = data->dropType;
+
+    std::vector<size_t> k_drop = data->k_drop;
+    std::vector<std::string> dropSpec = data->dropSpec;
+    std::vector<std::string> composition = components(data->dropType);
+    std::vector<double> dropMole = data->dropMole;
+
+    ydata = N_VGetArrayPointer_OpenMP(y);
+    ydotdata = N_VGetArrayPointer_OpenMP(ydot);
+    resdata = N_VGetArrayPointer_OpenMP(res);
+    if (data->adaptiveGrid == 1) {
+        psidata = data->grid->x;
+    } else {
+        psidata = data->uniformGrid;
+    }
+
+    innerMassFractionsData = data->innerMassFractions;
+
+    /* Grid stencil:*/
+
+    /*-------|---------*---------|---------*---------|-------*/
+    /*-------|---------*---------|---------*---------|-------*/
+    /*-------|---------*---------|---------*---------|-------*/
+    /*-------m-------mhalf-------j-------phalf-------p-------*/
+    /*-------|---------*---------|---------*---------|-------*/
+    /*-------|---------*---------|---------*---------|-------*/
+    /*-------|<=======dxm=======>|<=======dxp=======>|-------*/
+    /*-------|---------*<======dxav=======>*---------|-------*/
+    /*-------|<================dxpm=================>|-------*/
+
+    /* Various variables defined for book-keeping and storing previously
 	 * calculated values:
 	 * rho		: densities at points  m, mhalf, j, p, and phalf.
 	 * area		: the matric at points m, mhalf, j, p, and phalf.
@@ -1076,55 +1767,248 @@ int residue(double t, N_Vector y, N_Vector ydot, N_Vector res, void *user_data){
 	 * srcTerm	: source terms.
 	 */
 
-	double rhomhalf,  rhom, lambdamhalf, YVmhalf[nsp], 
-		 rho, 
-		 rhophalf, lambdaphalf, YVphalf[nsp],
-		 Cpb, Cvb,  Cp[nsp], Cpl[2], dHvl[2], rhol,  wdot[nsp],   enthalpy[nsp], energy[nsp],T_boil,
-		 tranTerm, diffTerm,    srcTerm, advTerm,
-		 area,areamhalf,areaphalf,aream,areamhalfsq,areaphalfsq;
-	
-	/*Aliases for difference coefficients:*/
-	double cendfm, cendfc, cendfp;
-	/*Aliases for various grid spacings:*/
-	double dpsip, dpsiav, dpsipm, dpsim, dpsimm;
-	dpsip=dpsiav=dpsipm=dpsim=dpsimm=ONE;
-	//double mass, mdotIn;
-	double mass, massDrop;
-	double sum, sum1, sum2, sum3;
-
-	size_t j,k;
-	int m;
-	m=data->metric;					//Unitless
-	mass=data->mass;				//Units: kg
-	//massDrop=data->massDrop;		//Units: kg
-	//mdotIn=data->mdot*calc_area(R(npts),&m);	//Units: kg/s
-
-//	/*evaluate properties at j=1*************************/
-	setGas(data,ydata,1);
-	rhom=data->gas->density();                                       
-    Cpb=data->gas->cp_mass();       	//J/kg/K
-    Cvb=data->gas->cv_mass();       	//J/kg/K
-	//TODO: Create user input model for these. They should not be constant
-	//Cpl=4.182e03;						//J/kg/K for liquid water
-	//Cpl=  5.67508633e-07*pow(T(1),4) - 7.78060597e-04*pow(T(1),3) + 4.08310544e-01*pow(T(1),2)  //J/kg/K for liquid water  
+    double rhomhalf, rhom, lambdamhalf, YVmhalf[nsp],
+            rho, Diffcoeffphalf, Diffcoeffmhalf,propYVmhalf,propYVphalf,
+            rhophalf, lambdaphalf, YVphalf[nsp],
+            Cpb, Cvb, Cp[nsp], Cpl[2], dHvl[2], rhol, wdot[nsp], enthalpy[nsp], energy[nsp], T_boil,
+            tranTerm, diffTerm, srcTerm, advTerm,
+            area, areamhalf, areaphalf, aream, areamhalfsq, areaphalfsq;
+
+    /*Aliases for difference coefficients:*/
+    double cendfm, cendfc, cendfp;
+    /*Aliases for various grid spacings:*/
+    double dpsip, dpsiav, dpsipm, dpsim, dpsimm;
+    dpsip = dpsiav = dpsipm = dpsim = dpsimm = ONE;
+    //double mass, mdotIn;
+    double mass, massDrop;
+    double sum, sum1, sum2, sum3;
+
+    std::vector<double> vapheat, mole_,liquidCp,vapPres;
+
+//    size_t j, k;
+    int m;
+    m = data->metric;                    //Unitless
+    mass = data->mass;                //Units: kg
+
+    /*evaluate and implement the governing equations in the liquid phase*/
+
+    /*implement res @ left boundary i.e., first grid point*/
+    Rres(1) = Rdot(1);
+    if (dropType == 0) {
+        // Yres(1,data->k_drop[0]) = Ydot(1,data->k_drop[0]);
+        for (size_t k = 1; k <= nsp; k++) {
+            Yres(1, k) = Ydot(1, k);
+        }
+    } else {
+        for (size_t k = 1; k <= nsp; k++) {
+            if (k == k_drop[0]) {
+                Yres(1, k) = Y(2, k) - Y(1, k);
+            } else if (k == k_drop[1]) {
+                Yres(1, k) = ONE - Y(1, k_drop[0]) - Y(1, k);
+            } else {
+                Yres(1, k) = Ydot(1, k);
+            }
+        }
+    }
+    Pres(1) = P(2) - P(1);
+    Mdotres(1) = Mdot(2) - Mdot(1);
+    Tres(1) = T(2) - T(1);
+
+    /*set governing equations at intermediate grid points */
+    massDrop = dropletmass(data, ydata);
+    if (dropType == 0) {
+        for (size_t j = 2; j <= l_npts - 1; j++) {
+            /*Mass:*/
+            /* ∂r/∂ψ = 1/ρA */
+            dpsim = - (psi(j) - psi(j - 1));
+            dpsip = - (psi(j + 1) - psi(j));
+            dpsiav = - (HALF * (psi(j + 1) - psi(j - 1)));
+            rho = getLiquidDensity(T(j), P(j), composition);
+            rhom = getLiquidDensity(T(j - 1), P(j - 1), composition);
+            rhophalf = getLiquidDensity(HALF * (T(j) + T(j + 1)), HALF * (P(j) + P(j + 1)), composition);
+            rhomhalf = getLiquidDensity(HALF * (T(j) + T(j - 1)), HALF * (P(j) + P(j - 1)), composition);
+
+            Cpb = getLiquidCpb(T(j), P(j), composition);
+            lambdaphalf = getLiquidCond(HALF * (T(j) + T(j + 1)), HALF * (P(j) + P(j + 1)), composition);
+            lambdamhalf = getLiquidCond(HALF * (T(j) + T(j - 1)), HALF * (P(j) + P(j - 1)), composition);
+
+            aream = calc_area(R(j - 1), &m);
+            areamhalf = calc_area(HALF * (R(j) + R(j - 1)), &m);
+            areaphalf = calc_area(HALF * (R(j + 1) + R(j)), &m);
+            areamhalfsq = areamhalf * areamhalf;
+            areaphalfsq = areaphalf * areaphalf;
+            area = calc_area(R(j), &m);
+
+            Rres(j) = ((R(j) - R(j - 1)) / dpsim) - massDrop * (TWO / (rhom * aream + rho * area));
+            Mdotres(j) = Mdot(j + 1) - Mdot(j);
+            Pres(j) = P(j + 1) - P(j);
+            for (size_t k = 1; k <= nsp; k++) {
+                Yres(j, k) = Y(j, k) - Y(j - 1, k);
+            }
+
+            tranTerm = Tdot(j);
+            advTerm = psi(j) * (-Mdot(j)) / massDrop * (T(j) - T(j - 1)) / dpsim ;
+            diffTerm = 1 / (Cpb * massDrop * massDrop) *
+                       (rhophalf * areaphalfsq * lambdaphalf * (T(j + 1) - T(j)) / dpsip -
+                        rhomhalf * areamhalfsq * lambdamhalf * (T(j) - T(j - 1)) / dpsim) / dpsiav;
+            Tres(j) = tranTerm - advTerm - diffTerm;
+        }
+
+        /*Fill up the res at l_npts*/
+        rho = getLiquidDensity(T(l_npts), P(l_npts), composition);
+        area = calc_area(R(l_npts), &m);
+        lambdamhalf = getLiquidCond(T(l_npts), P(l_npts), composition);
+        lambdaphalf = getGasCond(data, ydata, l_npts+1);
+        vapheat = getLiquidVH(P(l_npts+1), data->dropType);
+
+        Rres(l_npts) = Mdot(l_npts) + rho * Rdot(l_npts) * area;
+        Mdotres(l_npts) = Mdot(l_npts + 1) - Mdot(l_npts);
+        Pres(l_npts) = P(l_npts + 1) - P(l_npts);
+        for (size_t k = 1; k <= nsp; k++) {
+            Yres(l_npts, k) = Y(l_npts, k) - Y(l_npts - 1, k);
+        }
+        Tres(l_npts) = lambdamhalf * (T(l_npts) - T(l_npts - 1)) / (R(l_npts) - R(l_npts - 1)) * area +
+                       Mdot(l_npts) * vapheat[0] -
+                       lambdaphalf * (T(l_npts + 2) - T(l_npts + 1)) / (R(l_npts + 2) - R(l_npts + 1)) * area;
+    } else {
+        /*binary component case*/
+        /*implementation of liquid phase inner grid points*/
+        for (size_t j = 2; j <= l_npts - 1; j++) {
+            mole_ = getLiquidmolevec(data, ydata, j);
+
+            dpsim = - (psi(j) - psi(j - 1));
+            dpsip = - (psi(j + 1) - psi(j));
+            dpsiav = - (HALF * (psi(j + 1) - psi(j - 1)));
+
+            /*evaluate various central difference coefficients*/
+            cendfm = -dpsip / (dpsim * dpsipm);
+            cendfc = (dpsip - dpsim) / (dpsip * dpsim);
+            cendfp = dpsim / (dpsip * dpsipm);
+            /**************************************************/
+
+            rho = getLiquidDensity(T(j), P(j), composition, mole_);
+            rhom = getLiquidDensity(T(j - 1), P(j - 1), composition, mole_);
+            rhophalf = getLiquidDensity(HALF * (T(j) + T(j + 1)), HALF * (P(j) + P(j + 1)), composition, mole_);
+            rhomhalf = getLiquidDensity(HALF * (T(j) + T(j - 1)), HALF * (P(j) + P(j - 1)), composition, mole_);
+
+            Cpb = getLiquidCpb(T(j), P(j), composition, mole_);
+            liquidCp = getLiquidCp(T(j),P(j),composition);
+
+            lambdaphalf = getLiquidCond(HALF * (T(j) + T(j + 1)), HALF * (P(j) + P(j + 1)), composition, mole_);
+            lambdamhalf = getLiquidCond(HALF * (T(j) + T(j - 1)), HALF * (P(j) + P(j - 1)), composition, mole_);
+
+            aream = calc_area(R(j - 1), &m);
+            areamhalf = calc_area(HALF * (R(j) + R(j - 1)), &m);
+            areaphalf = calc_area(HALF * (R(j + 1) + R(j)), &m);
+            areamhalfsq = areamhalf * areamhalf;
+            areaphalfsq = areaphalf * areaphalf;
+            area = calc_area(R(j), &m);
+
+            Diffcoeffphalf = getLiquidmassdiff(data, ydata, j, HALF * (T(j) + T(j + 1)));
+            Diffcoeffmhalf = getLiquidmassdiff(data, ydata, j, HALF * (T(j) + T(j - 1)));
+
+            Rres(j) = ((R(j) - R(j - 1)) / dpsim) - massDrop * (TWO / (rhom * aream + rho * area));
+            Mdotres(j) = Mdot(j + 1) - Mdot(j);
+            Pres(j) = P(j + 1) - P(j);
+
+             propYVphalf = (-Diffcoeffphalf * (Y(j + 1, k_drop[0]) - Y(j, k_drop[0])) / (R(j + 1) - R(j)));
+             propYVmhalf = (-Diffcoeffmhalf * (Y(j, k_drop[0]) - Y(j - 1, k_drop[0])) / (R(j) - R(j - 1)));
+
+            liquidCp = getLiquidCp(T(j),P(j),composition);
+            /*species equation*/
+            for (size_t k = 1; k <= nsp; k++) {
+                if (k != k_drop[0] && k != k_drop[1]) {
+                    Yres(j, k) = Y(j, k) - Y(j - 1, k);
+                } else if (k == k_drop[0]) {
+                    tranTerm = Ydot(j, k);
+                    advTerm = 1 / massDrop * (psi(j) * (-Mdot(j))) * (Y(j, k) - Y(j - 1, k)) / dpsim;
+                    diffTerm = 1 / massDrop *
+                               (areaphalf * rhophalf * propYVphalf
+                                - areamhalf * rhomhalf * propYVmhalf )
+                                / dpsiav;
+                    Yres(j, k) = tranTerm - advTerm + diffTerm;
+                } else{
+                    Yres(j,k) = ONE - Y(j,k_drop[0]);
+                }
+            }
+            /*energy equation*/
+            tranTerm  = Tdot(j);
+            advTerm = 1/massDrop *(psi(j)*(-Mdot(j)))* (T(j)-T(j-1))/(psi(j)-psi(j-1));
+            double diffTerm1 = 1/(Cpb*massDrop*massDrop) * ( (rhophalf*areaphalfsq*lambdaphalf*(T(j+1)-T(j))/(psi(j+1)-psi(j)) )
+                    - (rhomhalf*areamhalfsq*lambdamhalf*(T(j)-T(j-1))/(psi(j)-psi(j-1)) ) ) /dpsiav;
+            double diffTerm2 = area/(Cpb*massDrop)*rho*(cendfp*T(j+1)+cendfc*T(j)+cendfm*T(j-1)) *
+                    (HALF*((propYVphalf+propYVmhalf)*liquidCp[0]+(-propYVphalf-propYVmhalf)*liquidCp[1])) ;
+            diffTerm = diffTerm1 - diffTerm2 ;
+            Tres(j) = tranTerm - advTerm - diffTerm ;
+        }
+
+        /*implementation of right boundary of liquid phase*/
+        mole_ = getLiquidmolevec(data,ydata,l_npts);
+        rho = getLiquidDensity(T(l_npts), P(l_npts), composition,mole_);
+        area = calc_area(R(l_npts), &m);
+        lambdamhalf = getLiquidCond(T(l_npts), P(l_npts), composition,mole_);
+        lambdaphalf = getGasCond(data, ydata, l_npts+1);
+
+        propYVmhalf = (-Diffcoeffmhalf * (Y(l_npts, k_drop[0]) - Y(l_npts - 1, k_drop[0])) / (R(l_npts) - R(l_npts - 1)));
+        getGasMassFlux(data,ydata,l_npts+1,YVphalf);
+
+        Diffcoeffmhalf = getLiquidmassdiff(data, ydata, l_npts, HALF * (T(l_npts) + T(l_npts - 1)));
+        vapheat = getLiquidVH(P(l_npts), data->dropType);
+
+        Rres(l_npts) = Mdot(l_npts) + rho * Rdot(l_npts) * area;
+        Mdotres(l_npts) = Mdot(l_npts + 1) - Mdot(l_npts);
+        Pres(l_npts) = P(l_npts + 1) - P(l_npts);
+
+        /*species formualtion*/
+        for (size_t k = 1; k <= nsp; k++) {
+            if (k == k_drop[0]) {
+                Yres(l_npts, k) = Mdot(l_npts) * Y(l_npts, k) + area * rho *
+                                                                (-Diffcoeffmhalf * (Y(l_npts, k) - Y(l_npts - 1, k)) /
+                                                                 (R(l_npts) - R(l_npts - 1)))
+                                  - Mdot(l_npts) * Y(l_npts + 1, k) - area * YVphalf[k_drop[0] - 1];
+            } else if (k == k_drop[1]) {
+                Yres(l_npts, k) = ONE - Y(l_npts, k_drop[0]) - Y(l_npts, k);
+            } else {
+                Yres(l_npts, k) = Y(l_npts, k) - Y(l_npts - 1, k);
+            }
+        }
+
+        /*temperature formulation*/
+        double epsilon = Y(l_npts + 1, k_drop[0]) + YVphalf[k_drop[0] - 1] * area / Mdot(l_npts);
+        Tres(l_npts) = lambdamhalf * (T(l_npts) - T(l_npts - 1)) / (R(l_npts) - R(l_npts - 1)) * area
+                       + Mdot(l_npts) * (epsilon * vapheat[0] + (1 - epsilon) * vapheat[1])
+                       - lambdaphalf * (T(l_npts + 2) - T(l_npts + 1)) / (R(l_npts + 2) - R(l_npts + 1)) * area;
+    }
+
+    //massDrop=data->massDrop;		//Units: kg
+    //mdotIn=data->mdot*calc_area(R(npts),&m);	//Units: kg/s
+
+//	/*evaluate properties at j=l_npts+1 *************************/
+    setGas(data, ydata, l_npts+1);
+    rhom = data->gas->density();
+    Cpb = data->gas->cp_mass();        //J/kg/K
+    Cvb = data->gas->cv_mass();        //J/kg/K
+    //TODO: Create user input model for these. They should not be constant
+    //Cpl=4.182e03;						//J/kg/K for liquid water
+    //Cpl=  5.67508633e-07*pow(T(1),4) - 7.78060597e-04*pow(T(1),3) + 4.08310544e-01*pow(T(1),2)  //J/kg/K for liquid water
     //     - 9.62429538e+01*T(1)        + 1.27131046e+04;
-    
+
     /*Update specific heat:Cpl for liquid proprane&n-heptane&dodecane*/
-   /*Based on the existiong data,a linear expression is used*/
-   // Cpl= 12.10476*T(1) - 746.60143; // Unit:J/(kg*K), Need to be improved later
-    //Cpl[0] = 2.423*T(1)+1661.074; //Unit:J/(kg*K),range:1atm,propane 
+    /*Based on the existiong data,a linear expression is used*/
+    // Cpl= 12.10476*T(1) - 746.60143; // Unit:J/(kg*K), Need to be improved later
+    //Cpl[0] = 2.423*T(1)+1661.074; //Unit:J/(kg*K),range:1atm,propane
     //Cpl[0] = 3.336*T(1)+1289.5; //Unit:J/(kg*K),range:1atm,n-Heptane
     //Cpl[1] = 3.815*T(1)+1081.8; //Unit:J/(kg*K),range:1atm,n-Dodecane
-    double Cp_l = 0.0; 
-    Cp_l = getLiquidCp(data->dropMole,T(1),P(1));
+//    double Cp_l = 0.0;
+//    Cp_l = getLiquidCp(data->dropMole,T(1),P(1));
     //for(size_t i=0;i<=1;i++){
     //    Cp_l=Cp_l+Cpl[i]*data->dropMassFrac[i];
     //}
 
-	//dHvl=2.260e6;						//J/kg	heat of vaporization of water
-	//double Tr = T(1)/647.1;				//Reduced Temperature: Droplet Temperature divided by critical temperature of water
-	//dHvl= 5.2053e07*pow(1-Tr,0.3199 - 0.212*Tr + 0.25795*Tr*Tr)/18.01;	//J/kg	latent heat of vaporization of water
-    
+    //dHvl=2.260e6;						//J/kg	heat of vaporization of water
+    //double Tr = T(1)/647.1;				//Reduced Temperature: Droplet Temperature divided by critical temperature of water
+    //dHvl= 5.2053e07*pow(1-Tr,0.3199 - 0.212*Tr + 0.25795*Tr*Tr)/18.01;	//J/kg	latent heat of vaporization of water
+
     //double Tr1 = T(1)/369.8;            //Reduced Temperature;
     //dHvl[0] = 6.32716e5*exp(-0.0208*Tr1)*pow((1-Tr1),0.3766);    //Unit:J/kg,Latent Heat of Vaporizaiton of Liquid n-propane,NIST
 
@@ -1132,191 +2016,234 @@ int residue(double t, N_Vector y, N_Vector ydot, N_Vector res, void *user_data){
     //dHvl[0] = 5.366e5*exp(-0.2831*Tr2) * pow((1-Tr2),0.2831);    //Unit:J/kg, latent heat of vaporization of liquid n-heptane, Source: NIST
 
     //dHvl[1] = 358.118e3;  //Unit:J/kg,latent heat of vaporization of n-dodecane,Source:NIST
-    
-    double dHv_l = 0.0; 
-    dHv_l = getLiquidHv(data->dropMole,T(1),P(1));
+
+//    double dHv_l = 0.0;
+//    dHv_l = getLiquidHv(data->dropMole,T(1),P(1));
     //for(size_t i=0;i<=1;i++){
     //    dHv_l=dHv_l+dHvl[i]*data->dropMassFrac[i];
     //}
 
     /*Following section is related to the property of water*/
-    //rhol = 997.0;	
-	//massDrop=1.0/3.0*R(1)*R(1)*R(1)*997.0; //TODO: The density of the droplet should be a user input
-    
+    //rhol = 997.0;
+    //massDrop=1.0/3.0*R(1)*R(1)*R(1)*997.0; //TODO: The density of the droplet should be a user input
+
     /*Following section is related to the property of liquid n-heptane and n-dodecane (mainly density rho)*/
     /*Density of these two species should be temperature dependent*/
     //data->dropDens[0] = -1.046*T(1)+823.794;       //Unit:kg/m^3,density of propane @1atm
     //data->dropDens[0] = -0.858*T(1)+933.854;       //Unit:kg/m^3,density of n-Heptane @1atm
     //data->dropDens[1] = -0.782*T(1)+979.643;       //Unit:kg/m^3,density of n-Dodecane @1atm
     //rhol = data->dropRho;                          //Unit:kg/m^3
-    rhol = 0.0; 
-    rhol = getLiquidRho(data->dropMole,T(1),P(1));
+//    rhol = 0.0;
+//    rhol = getLiquidRho(data->dropMole,T(1),P(1));
     //for(size_t i=0;i<=1;i++){
     //   rhol = rhol + data->dropMassFrac[i]*data->dropDens[i];
     //}
-    massDrop = 1.0/3.0*R(1)*R(1)*R(1)*rhol;  //Unit:kg, this is the mass of liquid droplet  
+//    massDrop = 1.0/3.0*R(1)*R(1)*R(1)*rhol;  //Unit:kg, this is the mass of liquid droplet
+
+//    aream = calc_area(R(1), &m);
+
+
+    /*******************************************************************/
+    /*Calculate values at j=l_npts+2 's m and mhalf*****************************/
+//    getTransport(data, ydata, 1, &rhomhalf, &lambdamhalf, YVmhalf);
+//    areamhalf = calc_area(HALF * (R(1) + R(2)), &m);
+//    aream = calc_area(R(1), &m);
+//    areamhalfsq = areamhalf * areamhalf;
+
+    getTransport(data, ydata, l_npts+1, &rhomhalf, &lambdamhalf, YVmhalf);
+    areamhalf = calc_area(HALF * (R(l_npts+1) + R(l_npts+2)), &m);
+    aream = calc_area(R(l_npts+1), &m);
+    areamhalfsq = areamhalf * areamhalf;
+
+    /*******************************************************************/
+
+    /*Fill up res with left side (center) boundary conditions:**********/
+    /*We impose zero fluxes at the center:*/
+
+
+    /*Mass:*/
+    if (data->quasiSteady) {
+//        Rres(1) = Rdot(1); // Should remain satisfied for quasi-steady droplet
+        Rres(l_npts+1) = Rdot(l_npts) ;
+    } else {
+        Rres(l_npts+1) = R(l_npts+1) - R(l_npts) ;
+//        Rres(1) = Rdot(1) + Mdot(1) / rhol / aream;
+    }
+
+    //TODO: Antoine Parameters should be part of user input, not hardcoded
+    //Yres(1,k_drop)=Y(1,k_drop) - 1.0e5*pow(10,4.6543-(1435.264/(T(1)-64.848)))*data->gas->molecularWeight(k_drop-1)
+    //			    / P(1) / data->gas->meanMolecularWeight();
+    //Yres(1,k_drop)=Y(1,k_drop) - 1.0e3*pow(2.71828,16.7-(4060.0/(T(1)-37.0)))*data->gas->molecularWeight(k_drop-1)
+    //			    / P(1) / data->gas->meanMolecularWeight();
+    //Yres(1,k_drop)=Y(1,k_drop)-2.566785e-02;
 
-    aream= calc_area(R(1),&m);	    
-    
- 
-	/*******************************************************************/
-	/*Calculate values at j=2's m and mhalf*****************************/
-
-	getTransport(data, ydata, 1, &rhomhalf,&lambdamhalf,YVmhalf);
-	areamhalf= calc_area(HALF*(R(1)+R(2)),&m);                                 
-	aream = calc_area(R(1),&m);                                 
-	areamhalfsq= areamhalf*areamhalf;                                   
-                                                                             
-	/*******************************************************************/
-
-	/*Fill up res with left side (center) boundary conditions:**********/
-	/*We impose zero fluxes at the center:*/                        
-
-
-	/*Mass:*/                                                            
-	if(data->quasiSteady){
-		Rres(1)=Rdot(1); // Should remain satisfied for quasi-steady droplet
-	}else{
-		Rres(1)=Rdot(1) + Mdot(1)/rhol/aream; 
-	}
-                                                                        
-	/*Species:*/                                                    
-	sum=ZERO;
-	
-	//TODO: Antoine Parameters should be part of user input, not hardcoded
-	//Yres(1,k_drop)=Y(1,k_drop) - 1.0e5*pow(10,4.6543-(1435.264/(T(1)-64.848)))*data->gas->molecularWeight(k_drop-1) 
-	//			    / P(1) / data->gas->meanMolecularWeight();
-	//Yres(1,k_drop)=Y(1,k_drop) - 1.0e3*pow(2.71828,16.7-(4060.0/(T(1)-37.0)))*data->gas->molecularWeight(k_drop-1) 
-	//			    / P(1) / data->gas->meanMolecularWeight();
-	//Yres(1,k_drop)=Y(1,k_drop)-2.566785e-02;
-	
     /*Following using the Antoine Parameters to calculate the pressure of volatile component(n-heptane)*/
     /*Antoine parameter from NIST website*/
     /*Raoult's Law is applied to calculate the partial vapor pressure*/
-    double p_i[2]={0.0,0.0} ; 
-    p_i[0] = 1.0e5*pow(10,4.53678-(1149.36/(T(1)+24.906)))*data->dropMole[0]*data->gamma[0] ;    //unit:Pa,Helgeson and Sage,1967,Propane
-    //p_i[0] = 1.0e5*pow(10,4.02832-(1268.636/(T(1)-56.199)))*data->dropMole[0] ;
-	p_i[1] = 1.0e5*pow(10,4.02832-(1268.636/(T(1)-56.199)))*data->dropMole[1]*data->gamma[1] ;    //unit:Pa,n-Heptane
+//    double p_i[2] = {0.0, 0.0};
+//    p_i[0] = 1.0e5 * pow(10, 4.53678 - (1149.36 / (T(1) + 24.906))) * data->dropMole[0] *
+//             data->gamma[0];    //unit:Pa,Helgeson and Sage,1967,Propane
+//    //p_i[0] = 1.0e5*pow(10,4.02832-(1268.636/(T(1)-56.199)))*data->dropMole[0] ;
+//    p_i[1] = 1.0e5 * pow(10, 4.02832 - (1268.636 / (T(1) - 56.199))) * data->dropMole[1] *
+//             data->gamma[1];    //unit:Pa,n-Heptane
     //p_i[1] = 1.0e5*pow(10,4.10549-(1625.928/(T(1)-92.839)))*data->dropMole[1] ;    //Unit:Pa.Williamham and Taylor,n-dodecane
 
+    /*for both dropletTypes(0,1),implementations of Rres,Tres,Pres are the same
+     * only Yres and Mdotres are different */
+    /*Species:*/
+    sum = ZERO;
+    /*single component case*/
+    if (dropType == 0) {
+        double hepPres = 1.0e5 * pow(10, 4.02832 - (1268.636 / (T(l_npts+1) - 56.199)));
+        Yres(l_npts + 1, k_drop[0]) = Y(l_npts + 1, k_drop[0]) - hepPres * data->gas->molecularWeight(k_drop[0] - 1) /
+                                                                 (P(l_npts + 1) * data->gas->meanMolecularWeight());
+        sum = sum + Y(l_npts + 1, k_drop[0]);
+        Mdotres(l_npts + 1) = Mdot(l_npts + 1) - (YVmhalf(k_drop[0]) * areamhalf) / (1 - Y(l_npts + 1, k_drop[0]));
+        for (size_t k = 1; k <= nsp; k++) {
+            if (k != k_bath && k != k_drop[0]) {
+                Yres(l_npts + 1, k) = Y(l_npts + 1, k) * Mdot(l_npts + 1) + YVmhalf(k) * areamhalf;
+                sum = sum + Y(l_npts + 1, k);
+            }
+        }
+        Yres(l_npts + 1, k_bath) = ONE - sum - Y(l_npts + 1, k_bath);
+    }
+
+    /*binary componet case for gas phase LHS boundary*/
+    if(dropType == 1){
+        mole_ = getLiquidmolevec(data,ydata,l_npts);
+        vapPres = getVapPressure(data,ydata,l_npts+1,mole_);
+
+        for (size_t i = 0; i < k_drop.size(); i++) {
+            Yres(l_npts+1, k_drop[i]) = Y(l_npts+1, k_drop[i]) - vapPres[i] * data->gas->molecularWeight(k_drop[i] - 1) /
+                                                                 (P(l_npts+1) * data->gas->meanMolecularWeight());
+            sum = sum + Y(l_npts+1, k_drop[i]);
+        }
+        Mdotres(l_npts+1) = Mdot(l_npts+1) - ((YVmhalf(k_drop[0]) + YVmhalf(k_drop[1])) * areamhalf) /
+                (1 - Y(l_npts+1, k_drop[0]) - Y(l_npts+1, k_drop[1]));
+        for (size_t k = 1; k <= nsp; k++) {
+            if (k != k_bath && k != k_drop[0] && k != k_drop[1]) {
+                //TODO: May need to include chemical source term
+                Yres(l_npts+1, k) = Y(l_npts+1, k) * Mdot(l_npts+1) + YVmhalf(k) * areamhalf;
+                //Yres(1,k)=YVmhalf(k)*areamhalf;
+                sum = sum + Y(l_npts+1, k);
+                //if(fabs(Mdot(1))>1e-14){
+                ///Yres(1,k)=innerMassFractionsData[k-1]-
+                ///  Y(1,k)-
+                ///  (YVmhalf(k)*areamhalf)/Mdot(1);
+
+                //}
+                //else{
+                //  		//Yres(1,k)=Y(1,k)-innerMassFractionsData[k-1];
+                //  		Yres(1,k)=Y(2,k)-Y(1,k);
+                //	/*The below flux boundary condition makes the
+                //	 * problem more prone to diverge. How does one
+                //	 * fix this?*/
+                //  		//Yres(1,k)=YVmhalf(k);
+                //}
+            }
+        }
+        Yres(l_npts+1, k_bath) = ONE - sum - Y(l_npts+1, k_bath);
+    }
+
+
 
     //p_i = 1.0e3*pow(2.71828,16.7-(4060.0/(T(1)-37.0)));     //Unit:Pa,FOR WATER
-    //Yres(1,k_drop)=Y(1,k_drop) - p_i * data->gas->molecularWeight(k_drop-1) 
-	//			    / P(1) / data->gas->meanMolecularWeight();
-    for(size_t i=0;i<=1;i++){
-        Yres(1,k_drop[i])=Y(1,k_drop[i])-p_i[i]*data->gas->molecularWeight(k_drop[i]-1)/(P(1)*data->gas->meanMolecularWeight());           
-    }
-	
-    sum=sum+Y(1,k_drop[0])+Y(1,k_drop[1]);
-
-	//Mdotres(1)=Mdot(1) - (YVmhalf(k_drop)*areamhalf) / (1-Y(1,k_drop)); //Evaporating mass
-    Mdotres(1)= Mdot(1) - ((YVmhalf(k_drop[0])+YVmhalf(k_drop[1])) *areamhalf) / (1-Y(1,k_drop[0])-Y(1,k_drop[1]) ); //Evaporating mass
-	for (k = 1; k <=nsp; k++) {                                        
-		if(k!=k_bath && k!=k_drop[0] && k!=k_drop[1]){
-			//TODO: May need to include chemical source term
-			Yres(1,k)=Y(1,k)*Mdot(1) + YVmhalf(k)*areamhalf;
-			//Yres(1,k)=YVmhalf(k)*areamhalf;
-		    sum=sum+Y(1,k);
-			//if(fabs(Mdot(1))>1e-14){
-		      		///Yres(1,k)=innerMassFractionsData[k-1]-
-					///  Y(1,k)-
-					///  (YVmhalf(k)*areamhalf)/Mdot(1);
-					
-			//}
-			//else{
-		    //  		//Yres(1,k)=Y(1,k)-innerMassFractionsData[k-1];
-		    //  		Yres(1,k)=Y(2,k)-Y(1,k);
-			//	/*The below flux boundary condition makes the
-			//	 * problem more prone to diverge. How does one
-			//	 * fix this?*/
-		    //  		//Yres(1,k)=YVmhalf(k);
-			//}
-		}
-	}                                                                 
-	Yres(1,k_bath)=ONE-sum-Y(1,k_bath);                                     
-	
-	/*Energy:*/                                                     
-	if(data->dirichletInner){
-		//Tres(1)=Tdot(1);
-		//Tres(1)=T(1)-data->innerTemperature;
+    //Yres(1,k_drop)=Y(1,k_drop) - p_i * data->gas->molecularWeight(k_drop-1)
+    //			    / P(1) / data->gas->meanMolecularWeight();
+
+
+
+
+    //Mdotres(1)=Mdot(1) - (YVmhalf(k_drop)*areamhalf) / (1-Y(1,k_drop)); //Evaporating mass
+
+
+
+    /*Energy:*/
+    if (data->dirichletInner) {
+        //Tres(1)=Tdot(1);
+        //Tres(1)=T(1)-data->innerTemperature;
         /*Following code should be revised in the future*/
-		//Tres(1)=lambdamhalf*rhomhalf*areamhalfsq*(T(2)-T(1))/((psi(2)-psi(1))*mass)/dHv_l - YVmhalf(k_drop)*areamhalf/(1-Y(1,k_drop));
-	}else{
-		//Tres(1)=Tdot(1) - 
-		//	(rhomhalf*areamhalfsq*lambdamhalf*(T(2)-T(1))/((psi(2)-psi(1))*mass) - Mdot(1)*dHvl)
-		//	/ (massDrop * Cpl);
-		
-        //Tres(1)=Tdot(1) - 
-		//	(areamhalf*lambdamhalf*(T(2)-T(1))/(R(2)-R(1)) - Mdot(1)*dHvl)
-		//	/ (massDrop * Cpl);
-
-		/**** Boundary Condition for Temperature @ 1st grid point,
-		 * Temperature should not exceed boiling temperature of each liquid component *****/
-		T_boil = getLiquidMaxT(data->dropMole,P(1));
-		if(T(1) <= T_boil)
-		{
-			Tres(1)=Tdot(1) - 
-			(areamhalf*lambdamhalf*(T(2)-T(1))/(R(2)-R(1)) - Mdot(1)*dHv_l)
-			/ (massDrop * Cp_l);
-		}else{
-			//Tres(1)=T(1)-T_boil;
-			Tres(1)=Tdot(1); 
-		}
-		
-		//Tres(1)=T(2)-T(1);
-		//Tres(1)=Tdot(1) - (Pdot(1)/(rhom*Cpb))
-		//	+(double)(data->metric+1)*(rhomhalf*lambdamhalf*areamhalfsq*(T(2)-T(1))/psi(2)-psi(1));
-	}
-
-	/*Pressure:*/                                                        
-	Pres(1)=P(2)-P(1);
-	/*Fill up res with governing equations at inner points:*************/
-	for (j = 2; j < npts; j++) {                                         
-                                                                             
-		/*evaluate various mesh differences*///                      
-        	dpsip =        (psi(j+1) - psi(j)  )*mass;                            
-        	dpsim =        (psi(j)   - psi(j-1))*mass;                            
-        	dpsiav =  HALF*(psi(j+1) - psi(j-1))*mass;                            
-        	dpsipm =       (psi(j+1) - psi(j-1))*mass;                            
-		/***********************************///                      
-                                                                             
-		/*evaluate various central difference coefficients*/       
-        	cendfm = - dpsip / (dpsim*dpsipm);                               
-        	cendfc =   (dpsip-dpsim) / (dpsip*dpsim);                         
-        	cendfp =   dpsim / (dpsip*dpsipm);                               
-		/**************************************************/
-                                                                   
-                                                                  
-		/*evaluate properties at j*************************/
-		setGas(data,ydata,j);
-		rho=data->gas->density();		//kg/m^3
-        	Cpb=data->gas->cp_mass();       	//J/kg/K
-        	Cvb=data->gas->cv_mass();       	//J/kg/K
-		data->gas->getNetProductionRates(wdot); //kmol/m^3
-		data->gas->getEnthalpy_RT(enthalpy);	//unitless
-		data->gas->getCp_R(Cp);			//unitless
-		area = calc_area(R(j),&m);	        //m^2
-                                                                           
-		/*evaluate properties at p*************************/
-		getTransport(data, ydata, j, &rhophalf,&lambdaphalf,YVphalf);
-		areaphalf= calc_area(HALF*(R(j)+R(j+1)),&m);	    
-		areaphalfsq= areaphalf*areaphalf;		    
-		/**************************************************///     
-
-		/*Evaporating Mass*/
-		Mdotres(j)=Mdot(j) - Mdot(j-1); 
-
-		/*Mass:*/
-		/* ∂r/∂ψ = 1/ρA */
-		Rres(j)=((R(j)-R(j-1))/dpsim)-(TWO/(rhom*aream+rho*area));
-
-		/*Energy:*/
-		/* ∂T/∂t = - ṁ(∂T/∂ψ) 
-		 * 	   + (∂/∂ψ)(λρA²∂T/∂ψ) 
-		 * 	   - (A/cₚ) ∑ YᵢVᵢcₚᵢ(∂T/∂ψ) 
-		 * 	   - (1/ρcₚ)∑ ώᵢhᵢ 
+        //Tres(1)=lambdamhalf*rhomhalf*areamhalfsq*(T(2)-T(1))/((psi(2)-psi(1))*mass)/dHv_l - YVmhalf(k_drop)*areamhalf/(1-Y(1,k_drop));
+    } else {
+        //Tres(1)=Tdot(1) -
+        //	(rhomhalf*areamhalfsq*lambdamhalf*(T(2)-T(1))/((psi(2)-psi(1))*mass) - Mdot(1)*dHvl)
+        //	/ (massDrop * Cpl);
+
+        //Tres(1)=Tdot(1) -
+        //	(areamhalf*lambdamhalf*(T(2)-T(1))/(R(2)-R(1)) - Mdot(1)*dHvl)
+        //	/ (massDrop * Cpl);
+
+        /**** Boundary Condition for Temperature @ 1st grid point,
+		 *** Temperature should not exceed boiling temperature of each liquid component *****/
+//        T_boil = getLiquidMaxT(data->dropMole, P(1));
+//        if (T(1) <= T_boil) {
+//            Tres(1) = Tdot(1) -
+//                      (areamhalf * lambdamhalf * (T(2) - T(1)) / (R(2) - R(1)) - Mdot(1) * dHv_l)
+//                      / (massDrop * Cp_l);
+//        } else {
+//            //Tres(1)=T(1)-T_boil;
+//            Tres(1) = Tdot(1);
+//        }
+        Tres(l_npts+1) = T(l_npts+1) - T(l_npts) ;
+
+        //Tres(1)=T(2)-T(1);
+        //Tres(1)=Tdot(1) - (Pdot(1)/(rhom*Cpb))
+        //	+(double)(data->metric+1)*(rhomhalf*lambdamhalf*areamhalfsq*(T(2)-T(1))/psi(2)-psi(1));
+    }
+
+    /*Pressure:*/
+    Pres(l_npts+1) = P(l_npts+2) - P(l_npts+1);
+    /*Fill up res with governing equations at inner points:*************/
+    for (size_t j = l_npts+2 ; j < npts; j++) {
+
+        /*evaluate various mesh differences*///
+//        dpsip = (psi(j + 1) - psi(j)) * mass;
+//        dpsim = (psi(j) - psi(j - 1)) * mass;
+//        dpsiav = HALF * (psi(j + 1) - psi(j - 1)) * mass;
+//        dpsipm = (psi(j + 1) - psi(j - 1)) * mass;
+        dpsip = (psi(j + 1) - psi(j)) ;
+        dpsim = (psi(j) - psi(j - 1)) ;
+        dpsiav = HALF * (psi(j + 1) - psi(j - 1)) ;
+        dpsipm = (psi(j + 1) - psi(j - 1)) ;
+        /***********************************///
+
+        /*evaluate various central difference coefficients*/
+        cendfm = -dpsip / (dpsim * dpsipm);
+        cendfc = (dpsip - dpsim) / (dpsip * dpsim);
+        cendfp = dpsim / (dpsip * dpsipm);
+        /**************************************************/
+
+
+        /*evaluate properties at j*************************/
+        setGas(data, ydata, j);
+        rho = data->gas->density();        //kg/m^3
+        Cpb = data->gas->cp_mass();        //J/kg/K
+        Cvb = data->gas->cv_mass();        //J/kg/K
+        data->gas->getNetProductionRates(wdot); //kmol/m^3
+        data->gas->getEnthalpy_RT(enthalpy);    //unitless
+        data->gas->getCp_R(Cp);            //unitless
+        area = calc_area(R(j), &m);            //m^2
+
+        /*evaluate properties at p*************************/
+        getTransport(data, ydata, j, &rhophalf, &lambdaphalf, YVphalf);
+        areaphalf = calc_area(HALF * (R(j) + R(j + 1)), &m);
+        areaphalfsq = areaphalf * areaphalf;
+        /**************************************************///
+
+        /*Evaporating Mass*/
+        Mdotres(j) = Mdot(j) - Mdot(j - 1);
+
+        /*Mass:*/
+        /* ∂r/∂ψ = 1/ρA */
+        Rres(j) = ((R(j) - R(j - 1)) / dpsim) - (TWO / (rhom * aream + rho * area));
+
+        /*Energy:*/
+        /* ∂T/∂t = - ṁ(∂T/∂ψ)
+		 * 	   + (∂/∂ψ)(λρA²∂T/∂ψ)
+		 * 	   - (A/cₚ) ∑ YᵢVᵢcₚᵢ(∂T/∂ψ)
+		 * 	   - (1/ρcₚ)∑ ώᵢhᵢ
 		 * 	   + (1/ρcₚ)(∂P/∂t) */
-		/*Notes: 
+        /*Notes:
 		 * λ has units J/m/s/K.
 		 * YᵢVᵢ has units kg/m^2/s.
 		 * hᵢ has units J/kmol, so we must multiply the enthalpy
@@ -1328,266 +2255,261 @@ int residue(double t, N_Vector y, N_Vector ydot, N_Vector res, void *user_data){
 		 * units.
 		 * */
 
-		//enthalpy formulation:
-		//tranTerm = Tdot(j) - (Pdot(j)/(rho*Cpb));
-		tranTerm = Tdot(j);
-		sum=ZERO;
-		sum1=ZERO;
-		for (k = 1; k <=nsp; k++) {
-			sum=sum+wdot(k)*enthalpy(k);
-			sum1=sum1+(Cp(k)/data->gas->molecularWeight(k-1))*rho
-			     *HALF*(YVmhalf(k)+YVphalf(k));
-		}
-		sum=sum*Cantera::GasConstant*T(j);
-		sum1=sum1*Cantera::GasConstant;
-		diffTerm  =(( (rhophalf*areaphalfsq*lambdaphalf*(T(j+1)-T(j))/dpsip)
-			      -(rhomhalf*areamhalfsq*lambdamhalf*(T(j)-T(j-1))/dpsim) )
-			     /(dpsiav*Cpb) )
-			  -(sum1*area*(cendfp*T(j+1)
-			              +cendfc*T(j)
-			              +cendfm*T(j-1))/Cpb);
-		srcTerm   = (sum-Qdot(&t,&R(j),&data->ignTime,&data->kernelSize,&data->maxQDot))/(rho*Cpb); // Qdot is forced heating to cause ignition, sum is the conversion of chemical enthalpy to sensible enthalpy
-		advTerm   = (Mdot(j)*(T(j)-T(j-1))/dpsim);
-		Tres(j)= tranTerm - (Pdot(j)/(rho*Cpb))
-			+advTerm 
-			-diffTerm
-			+srcTerm;
-
-	//	//energy formulation:
-	//	tranTerm = Tdot(j);
-	//	sum=ZERO;
-	//	sum1=ZERO;
-	//	sum2=ZERO;
-	//	sum3=ZERO;
-	//	for (k = 1; k <=nsp; k++) {
-	//		energy(k)=enthalpy(k)-ONE;
-	//		sum=sum+wdot(k)*energy(k);
-	//		sum1=sum1+(Cp(k)/data->gas->molecularWeight(k-1))*rho
-	//		     *HALF*(YVmhalf(k)+YVphalf(k));
-	//		sum2=sum2+(YVmhalf(k)/data->gas->molecularWeight(k-1));
-	//		sum3=sum3+(YVphalf(k)/data->gas->molecularWeight(k-1));
-	//	}
-	//	sum=sum*Cantera::GasConstant*T(j);
-	//	sum1=sum1*Cantera::GasConstant;
-	//	diffTerm  =(( (rhophalf*areaphalfsq*lambdaphalf*(T(j+1)-T(j))/dpsip)
-	//		      -(rhomhalf*areamhalfsq*lambdamhalf*(T(j)-T(j-1))/dpsim) )
-	//		     /(dpsiav*Cvb) )
-	//		  -(sum1*area*(cendfp*T(j+1)
-	//		              +cendfc*T(j)
-	//		              +cendfm*T(j-1))/Cvb);
-	//	srcTerm   = (sum-Qdot(&t,&R(j),&data->ignTime,&data->kernelSize,&data->maxQDot))/(rho*Cvb);
-	//	advTerm   = (mdotIn*(T(j)-T(j-1))/dpsim);
-	//	advTerm = advTerm + (Cantera::GasConstant*T(j)*area/Cvb)*((sum3-sum2)/dpsiav);
-	//	Tres(j)= tranTerm
-	//		+advTerm 
-	//		-diffTerm
-	//		+srcTerm;
-
-		/*Species:*/
-		/* ∂Yᵢ/∂t = - ṁ(∂Yᵢ/∂ψ) 
-		 * 	    - (∂/∂ψ)(AYᵢVᵢ) 
+        //enthalpy formulation:
+        //tranTerm = Tdot(j) - (Pdot(j)/(rho*Cpb));
+        tranTerm = Tdot(j);
+        sum = ZERO;
+        sum1 = ZERO;
+        for (size_t k = 1; k <= nsp; k++) {
+            sum = sum + wdot(k) * enthalpy(k);
+            sum1 = sum1 + (Cp(k) / data->gas->molecularWeight(k - 1)) * HALF * (YVmhalf(k) + YVphalf(k));
+        }
+        sum = sum * Cantera::GasConstant * T(j);
+        sum1 = sum1 * Cantera::GasConstant;
+        diffTerm = (((rhophalf * areaphalfsq * lambdaphalf * (T(j + 1) - T(j)) / dpsip)
+                     - (rhomhalf * areamhalfsq * lambdamhalf * (T(j) - T(j - 1)) / dpsim))
+                    / (dpsiav * Cpb))
+                   - (sum1 * area * (cendfp * T(j + 1)
+                                     + cendfc * T(j)
+                                     + cendfm * T(j - 1)) / Cpb);
+        srcTerm = (sum - Qdot(&t, &R(j), &data->ignTime, &data->kernelSize, &data->maxQDot)) / (rho *
+                                                                                                Cpb); // Qdot is forced heating to cause ignition, sum is the conversion of chemical enthalpy to sensible enthalpy
+        advTerm = (Mdot(j) * (T(j) - T(j - 1)) / dpsim);
+        Tres(j) = tranTerm - (Pdot(j) / (rho * Cpb))
+                  + advTerm
+                  - diffTerm
+                  + srcTerm;
+
+        //	//energy formulation:
+        //	tranTerm = Tdot(j);
+        //	sum=ZERO;
+        //	sum1=ZERO;
+        //	sum2=ZERO;
+        //	sum3=ZERO;
+        //	for (k = 1; k <=nsp; k++) {
+        //		energy(k)=enthalpy(k)-ONE;
+        //		sum=sum+wdot(k)*energy(k);
+        //		sum1=sum1+(Cp(k)/data->gas->molecularWeight(k-1))*rho
+        //		     *HALF*(YVmhalf(k)+YVphalf(k));
+        //		sum2=sum2+(YVmhalf(k)/data->gas->molecularWeight(k-1));
+        //		sum3=sum3+(YVphalf(k)/data->gas->molecularWeight(k-1));
+        //	}
+        //	sum=sum*Cantera::GasConstant*T(j);
+        //	sum1=sum1*Cantera::GasConstant;
+        //	diffTerm  =(( (rhophalf*areaphalfsq*lambdaphalf*(T(j+1)-T(j))/dpsip)
+        //		      -(rhomhalf*areamhalfsq*lambdamhalf*(T(j)-T(j-1))/dpsim) )
+        //		     /(dpsiav*Cvb) )
+        //		  -(sum1*area*(cendfp*T(j+1)
+        //		              +cendfc*T(j)
+        //		              +cendfm*T(j-1))/Cvb);
+        //	srcTerm   = (sum-Qdot(&t,&R(j),&data->ignTime,&data->kernelSize,&data->maxQDot))/(rho*Cvb);
+        //	advTerm   = (mdotIn*(T(j)-T(j-1))/dpsim);
+        //	advTerm = advTerm + (Cantera::GasConstant*T(j)*area/Cvb)*((sum3-sum2)/dpsiav);
+        //	Tres(j)= tranTerm
+        //		+advTerm
+        //		-diffTerm
+        //		+srcTerm;
+
+        /*Species:*/
+        /* ∂Yᵢ/∂t = - ṁ(∂Yᵢ/∂ψ)
+		 * 	    - (∂/∂ψ)(AYᵢVᵢ)
 		 * 	    + (ώᵢWᵢ/ρ)  */
 
-		sum=ZERO;
-		for (k = 1; k <=nsp; k++) {
-			if(k!=k_bath){
-				tranTerm  = Ydot(j,k);
-				diffTerm  = (YVphalf(k)*areaphalf
-					    -YVmhalf(k)*areamhalf)/dpsiav;
-				srcTerm   = wdot(k)
-			     		    *(data->gas->molecularWeight(k-1))/rho;
-				advTerm   = (Mdot(j)*(Y(j,k)-Y(j-1,k))/dpsim);
-
-				Yres(j,k)= tranTerm 
-					  +advTerm
-					  +diffTerm
-					  -srcTerm;
-
-		      		sum=sum+Y(j,k);
-			}
-		}
-		Yres(j,k_bath)=ONE-sum-Y(j,k_bath);
-
-		/*Pressure:*/
-		Pres(j) = P(j+1)-P(j);
-
-		/*Assign values evaluated at p and phalf to m       
+        sum = ZERO;
+        for (size_t k = 1; k <= nsp; k++) {
+            if (k != k_bath) {
+                tranTerm = Ydot(j, k);
+                diffTerm = (YVphalf(k) * areaphalf
+                            - YVmhalf(k) * areamhalf) / dpsiav;
+                srcTerm = wdot(k)
+                          * (data->gas->molecularWeight(k - 1)) / rho;
+                advTerm = (Mdot(j) * (Y(j, k) - Y(j - 1, k)) / dpsim);
+
+                Yres(j, k) = tranTerm
+                             + advTerm
+                             + diffTerm
+                             - srcTerm;
+
+                sum = sum + Y(j, k);
+            }
+        }
+        Yres(j, k_bath) = ONE - sum - Y(j, k_bath);
+
+        /*Pressure:*/
+        Pres(j) = P(j + 1) - P(j);
+
+        /*Assign values evaluated at p and phalf to m
 		 * and mhalf to save some cpu cost:****************/
-		areamhalf=areaphalf;                                
-		areamhalfsq=areaphalfsq;                            
-		aream=area;
-		rhom=rho;
-		rhomhalf=rhophalf;                                  
-		lambdamhalf=lambdaphalf;                            
-		for (k = 1; k <=nsp; k++) {                         
-			YVmhalf(k)=YVphalf(k);                      
-		}                                                   
-		/**************************************************/
-		                                                    
-	}                                                           
-	/*******************************************************************///
-
-
-	/*Fill up res with right side (wall) boundary conditions:***********/
-	/*We impose zero fluxes at the wall:*/                               
-	setGas(data,ydata,npts);
-	rho=data->gas->density();                               
-	area = calc_area(R(npts),&m);				   
-
-	/*Mass:*/                                                          
-	dpsim=(psi(npts)-psi(npts-1))*mass;
-	Rres(npts)=((R(npts)-R(npts-1))/dpsim)-(TWO/(rhom*aream+rho*area));
-
-	/*Energy:*/                                             
-	if(data->dirichletOuter){
-		//Tres(npts)=T(npts)-data->wallTemperature;
-		Tres(npts)=Tdot(npts);
-	}
-	else{
-		Tres(npts)=T(npts)-T(npts-1);
-	}
-                                                                
-	/*Species:*/                                            
-	sum=ZERO;
-	if(data->dirichletOuter){
-		for (k = 1; k <=nsp; k++) {                             
-			if(k!=k_bath){
-			    	Yres(npts,k)=Ydot(npts,k);
-			    	sum=sum+Y(npts,k);
-			}
-		}                                                       
-	}
-	else{
-		for (k = 1; k <=nsp; k++) {                             
-			if(k!=k_bath){
-			    	Yres(npts,k)=Y(npts,k)-Y(npts-1,k);
-			    	//Yres(npts,k)=YVmhalf(k);         
-			    	sum=sum+Y(npts,k);
-			}
-		}                                                       
-	}
-	Yres(npts,k_bath)=ONE-sum-Y(npts,k_bath);             
-                                                                
-	
-	/*Pressure:*/                                                      
-	if(data->constantPressure){
-		Pres(npts)=Pdot(npts)-data->dPdt;                                     
-	}
-	else{
-		Pres(npts)=R(npts)-data->domainLength;                     
-		//Pres(npts)=Rdot(npts);                     
-	}
-
-	/*Evaporating Mass*/
-	Mdotres(npts)=Mdot(npts) - Mdot(npts-1); 
-
-	//for (j = 1; j <=npts; j++) {
-	//	//for (k = 1; k <=nsp; k++) {
-	//	//	Yres(j,k)=Ydot(j,k);
-	//	//}
-	//	//Tres(j)=Tdot(j);
-	//}
-
-	return(0);
+        areamhalf = areaphalf;
+        areamhalfsq = areaphalfsq;
+        aream = area;
+        rhom = rho;
+        rhomhalf = rhophalf;
+        lambdamhalf = lambdaphalf;
+        for (size_t k = 1; k <= nsp; k++) {
+            YVmhalf(k) = YVphalf(k);
+        }
+        /**************************************************/
+
+    }
+    /*******************************************************************///
+
+
+    /*Fill up res with right side (wall) boundary conditions:***********/
+    /*We impose zero fluxes at the wall:*/
+    setGas(data, ydata, npts);
+    rho = data->gas->density();
+    area = calc_area(R(npts), &m);
+
+    /*Mass:*/
+//    dpsim = (psi(npts) - psi(npts - 1)) * mass;
+    dpsim = (psi(npts) - psi(npts - 1)) ;
+    Rres(npts) = ((R(npts) - R(npts - 1)) / dpsim) - (TWO / (rhom * aream + rho * area));
+
+    /*Energy:*/
+    if (data->dirichletOuter) {
+        //Tres(npts)=T(npts)-data->wallTemperature;
+        Tres(npts) = Tdot(npts);
+    } else {
+        Tres(npts) = T(npts) - T(npts - 1);
+    }
+
+    /*Species:*/
+    sum = ZERO;
+    if (data->dirichletOuter) {
+        for (size_t k = 1; k <= nsp; k++) {
+            if (k != k_bath) {
+                Yres(npts, k) = Ydot(npts, k);
+                sum = sum + Y(npts, k);
+            }
+        }
+    } else {
+        for (size_t k = 1; k <= nsp; k++) {
+            if (k != k_bath) {
+                Yres(npts, k) = Y(npts, k) - Y(npts - 1, k);
+                //Yres(npts,k)=YVmhalf(k);
+                sum = sum + Y(npts, k);
+            }
+        }
+    }
+    Yres(npts, k_bath) = ONE - sum - Y(npts, k_bath);
+
+
+    /*Pressure:*/
+    if (data->constantPressure) {
+        Pres(npts) = Pdot(npts) - data->dPdt;
+    } else {
+        Pres(npts) = R(npts) - data->domainLength;
+        //Pres(npts)=Rdot(npts);
+    }
+
+    /*Evaporating Mass*/
+    Mdotres(npts) = Mdot(npts) - Mdot(npts - 1);
+
+    //for (j = 1; j <=npts; j++) {
+    //	//for (k = 1; k <=nsp; k++) {
+    //	//	Yres(j,k)=Ydot(j,k);
+    //	//}
+    //	//Tres(j)=Tdot(j);
+    //}
+
+    return (0);
 
 }
 
-void printSpaceTimeHeader(UserData data)
-{
-	fprintf((data->output), "%15s\t","#1");
-	for (size_t k = 1; k <=data->nvar+1; k++) {
-		fprintf((data->output), "%15lu\t",k+1);
-	}
-	fprintf((data->output), "%15lu\n",data->nvar+3);
-
-	fprintf((data->output), "%15s\t%15s\t%15s\t","#psi","time(s)","dpsi");
-	fprintf((data->output), "%15s\t%15s\t","radius(m)","Temp(K)");
-	for (size_t k = 1; k <=data->nsp; k++) {
-		fprintf((data->output), "%15s\t",data->gas->speciesName(k-1).c_str());
-	}
-	fprintf((data->output), "%15s\t","Pressure(Pa)");
-	fprintf((data->output), "%15s\n","Mdot (kg/s)");
+void printSpaceTimeHeader(UserData data) {
+    fprintf((data->output), "%15s\t", "#1");
+    for (size_t k = 1; k <= data->nvar + 1; k++) {
+        fprintf((data->output), "%15lu\t", k + 1);
+    }
+    fprintf((data->output), "%15lu\n", data->nvar + 3);
+
+    fprintf((data->output), "%15s\t%15s\t%15s\t", "#psi", "time(s)", "dpsi");
+    fprintf((data->output), "%15s\t%15s\t", "radius(m)", "Temp(K)");
+    for (size_t k = 1; k <= data->nsp; k++) {
+        fprintf((data->output), "%15s\t", data->gas->speciesName(k - 1).c_str());
+    }
+    fprintf((data->output), "%15s\t", "Pressure(Pa)");
+    fprintf((data->output), "%15s\n", "Mdot (kg/s)");
 }
 
-void printSpaceTimeOutput(double t, N_Vector* y, FILE* output, UserData data)
-{
-	double *ydata,*psidata;
-  	ydata    = N_VGetArrayPointer_OpenMP(*y);
-
-	if(data->adaptiveGrid){
-  		psidata  = data->grid->x;
-	}else{
-  		psidata  = data->uniformGrid;
-	}
-
-	for (size_t i = 0; i < data->npts; i++) {
-		fprintf(output, "%15.9e\t%15.9e\t",psi(i+1),t);
-		if(i==0){
-			fprintf(output, "%15.9e\t",psi(2)-psi(1));
-		}
-		else{
-			fprintf(output, "%15.6e\t",psi(i+1)-psi(i));
-		}
-		for (size_t j = 0; j < data->nvar; j++) {
-			if(j!=data->nvar-1){
-				fprintf(output, "%15.9e\t",ydata[j+i*data->nvar]);
-			}else{
-				fprintf(output, "%15.9e",ydata[j+i*data->nvar]);
-			}
-		}
-		fprintf(output, "\n");
-	}
-	fprintf(output, "\n");
+void printSpaceTimeOutput(double t, N_Vector *y, FILE *output, UserData data) {
+    double *ydata, *psidata;
+    ydata = N_VGetArrayPointer_OpenMP(*y);
+
+    if (data->adaptiveGrid) {
+        psidata = data->grid->x;
+    } else {
+        psidata = data->uniformGrid;
+    }
+
+    for (size_t i = 0; i < data->npts; i++) {
+        fprintf(output, "%15.9e\t%15.9e\t", psi(i + 1), t);
+        if (i == 0) {
+            fprintf(output, "%15.9e\t", psi(2) - psi(1));
+        } else {
+            fprintf(output, "%15.6e\t", psi(i + 1) - psi(i));
+        }
+        for (size_t j = 0; j < data->nvar; j++) {
+            if (j != data->nvar - 1) {
+                fprintf(output, "%15.9e\t", ydata[j + i * data->nvar]);
+            } else {
+                fprintf(output, "%15.9e", ydata[j + i * data->nvar]);
+            }
+        }
+        fprintf(output, "\n");
+    }
+    fprintf(output, "\n");
 }
 
-void writeRestart(double t, N_Vector* y, N_Vector* ydot, FILE* output, UserData data){
-	double *ydata,*psidata, *ydotdata;
-	ydata = N_VGetArrayPointer_OpenMP(*y);
-	ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
-	if(data->adaptiveGrid){
-  		psidata  = data->grid->x;
-	}else{
-  		psidata  = data->uniformGrid;
-	}
- 	fwrite(&t, sizeof(t), 1, output);		//write time
- 	fwrite(psidata, data->npts*sizeof(psidata), 1, output);	//write grid
- 	fwrite(ydata, data->neq*sizeof(ydata), 1, output);	//write solution
- 	fwrite(ydotdata, data->neq*sizeof(ydotdata), 1, output);	//write solutiondot
+void writeRestart(double t, N_Vector *y, N_Vector *ydot, FILE *output, UserData data) {
+    double *ydata, *psidata, *ydotdata;
+    ydata = N_VGetArrayPointer_OpenMP(*y);
+    ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
+    if (data->adaptiveGrid) {
+        psidata = data->grid->x;
+    } else {
+        psidata = data->uniformGrid;
+    }
+    fwrite(&t, sizeof(t), 1, output);        //write time
+    fwrite(psidata, data->npts * sizeof(psidata), 1, output);    //write grid
+    fwrite(ydata, data->neq * sizeof(ydata), 1, output);    //write solution
+    fwrite(ydotdata, data->neq * sizeof(ydotdata), 1, output);    //write solutiondot
 }
 
-void readRestart(N_Vector* y, N_Vector* ydot, FILE* input, UserData data){
-	double *ydata,*psidata, *ydotdata;
-	double t;
-	if(data->adaptiveGrid){
-  		psidata  = data->grid->x;
-	}else{
-  		psidata  = data->uniformGrid;
-	}
-	ydata = N_VGetArrayPointer_OpenMP(*y);
-	ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
- 	fread(&t, sizeof(t), 1, input);
-	data->tNow=t;
- 	fread(psidata, data->npts*sizeof(psidata), 1, input);
- 	fread(ydata, data->neq*sizeof(ydata), 1, input);
- 	fread(ydotdata, data->neq*sizeof(ydotdata), 1, input);
-	if(data->adaptiveGrid){
-		storeGrid(data->grid->x,data->grid->xOld,data->npts);
-	}
+void readRestart(N_Vector *y, N_Vector *ydot, FILE *input, UserData data) {
+    double *ydata, *psidata, *ydotdata;
+    double t;
+    if (data->adaptiveGrid) {
+        psidata = data->grid->x;
+    } else {
+        psidata = data->uniformGrid;
+    }
+    ydata = N_VGetArrayPointer_OpenMP(*y);
+    ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
+    fread(&t, sizeof(t), 1, input);
+    data->tNow = t;
+    fread(psidata, data->npts * sizeof(psidata), 1, input);
+    fread(ydata, data->neq * sizeof(ydata), 1, input);
+    fread(ydotdata, data->neq * sizeof(ydotdata), 1, input);
+    if (data->adaptiveGrid) {
+        storeGrid(data->grid->x, data->grid->xOld, data->npts);
+    }
 }
 
-void printGlobalHeader(UserData data)
-{
-	fprintf((data->globalOutput), "%8s\t","#Time(s)");
-	//fprintf((data->globalOutput), "%15s","S_u(exp*)(m/s)");
-	fprintf((data->globalOutput), "%15s","bFlux(kg/m^2/s)");
-	fprintf((data->globalOutput), "%16s","  IsothermPos(m)");
-	fprintf((data->globalOutput), "%15s\t","Pressure(Pa)");
-	fprintf((data->globalOutput), "%15s\t","Pdot(Pa/s)");
-	fprintf((data->globalOutput), "%15s\t","gamma");
-	fprintf((data->globalOutput), "%15s\t","S_u(m/s)");
-	fprintf((data->globalOutput), "%15s\t","Tu(K)");
-	fprintf((data->globalOutput), "\n");
+void printGlobalHeader(UserData data) {
+    fprintf((data->globalOutput), "%8s\t", "#Time(s)");
+    //fprintf((data->globalOutput), "%15s","S_u(exp*)(m/s)");
+    fprintf((data->globalOutput), "%15s", "bFlux(kg/m^2/s)");
+    fprintf((data->globalOutput), "%16s", "  IsothermPos(m)");
+    fprintf((data->globalOutput), "%15s\t", "Pressure(Pa)");
+    fprintf((data->globalOutput), "%15s\t", "Pdot(Pa/s)");
+    fprintf((data->globalOutput), "%15s\t", "gamma");
+    fprintf((data->globalOutput), "%15s\t", "S_u(m/s)");
+    fprintf((data->globalOutput), "%15s\t", "Tu(K)");
+    fprintf((data->globalOutput), "\n");
 }
+
 //
 //void printSpaceTimeRates(double t, N_Vector ydot, UserData data)
 //{
@@ -1604,144 +2526,141 @@ void printGlobalHeader(UserData data)
 //	fprintf((data->ratesOutput), "\n\n");
 //}
 //
-void printGlobalVariables(double t, N_Vector* y, N_Vector* ydot, UserData data)
-{
-	double *ydata,*ydotdata, *innerMassFractionsData, *psidata;
-	innerMassFractionsData =  data->innerMassFractions;
-
-	if(data->adaptiveGrid){
-  		psidata  = data->grid->x;
-	}else{
-  		psidata  = data->uniformGrid;
-	}
-
-	double TAvg, RAvg, YAvg, psiAvg;
-  	ydata    = N_VGetArrayPointer_OpenMP(*y);
-  	ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
-	TAvg=data->isotherm;
-	double sum=ZERO;
-	double dpsim,area,aream,drdt;
-	double Cpb,Cvb,gamma,rho,flameArea,Tu;
-
-
-	/*Find the isotherm chosen by the user*/
-	size_t j=1;
-	size_t jj=1;
-	size_t jjj=1;
-	double wdot[data->nsp];
-	double wdotMax=0.0e0;
-	double advTerm=0.0e0;
-	psiAvg=0.0e0;
-	if(T(data->npts)>T(1)){
-		while (T(j)<TAvg) {
-			j=j+1;
-		}
-		YAvg=innerMassFractionsData[data->k_oxidizer-1]-Y(data->npts,data->k_oxidizer);
-		while (fabs((T(jj+1)-T(jj))/T(jj))>1e-08) {
-			jj=jj+1;
-		}
-
-		setGas(data,ydata,jj);
-		Tu=T(jj);
-		rho=data->gas->density();
-        	Cpb=data->gas->cp_mass();       	//J/kg/K
-        	Cvb=data->gas->cv_mass();       	//J/kg/K
-		gamma=Cpb/Cvb;
-		
-	}
-	else{
-		while (T(j)>TAvg) {
-			j=j+1;
-		}
-		YAvg=innerMassFractionsData[data->k_oxidizer-1]-Y(1,data->k_oxidizer);
-		while (fabs((T(data->npts-jj-1)-T(data->npts-jj))/T(data->npts-jj))>1e-08) {
-			jj=jj+1;
-		}
-
-		setGas(data,ydata,data->npts-jj);
-		Tu=T(data->npts-jj);
-		rho=data->gas->density();
-        	Cpb=data->gas->cp_mass();       	//J/kg/K
-        	Cvb=data->gas->cv_mass();       	//J/kg/K
-		gamma=Cpb/Cvb;
-	}
-	if(T(j)<TAvg){
-		RAvg=((R(j+1)-R(j))/(T(j+1)-T(j)))*(TAvg-T(j))+R(j);
-	}
-	else{
-		RAvg=((R(j)-R(j-1))/(T(j)-T(j-1)))*(TAvg-T(j-1))+R(j-1);
-	}
-
-	////Experimental burning speed calculation:	
-	//int nMax=0;
-	////nMax=maxCurvIndex(ydata, data->nt, data->nvar,
-	////     	data->grid->x, data->npts);
-	//nMax=maxGradIndex(ydata, data->nt, data->nvar,
-	//     	data->grid->x, data->npts);
-	//advTerm=(T(nMax)-T(nMax-1))/(data->mass*(psi(nMax)-psi(nMax-1)));
-	//aream=calc_area(R(nMax),&data->metric);	    
-	////setGas(data,ydata,nMax);
-	////rho=data->gas->density();
-	//psiAvg=-Tdot(nMax)/(rho*aream*advTerm);
-	////if(t>data->ignTime){
-	////	for(size_t n=2;n<data->npts;n++){
-	////		setGas(data,ydata,n);
-	////		data->gas->getNetProductionRates(wdot); //kmol/m^3
-	////		advTerm=(T(n)-T(n-1))/(data->mass*(psi(n)-psi(n-1)));
-	////		if(fabs(wdot[data->k_oxidizer-1])>=wdotMax){
-	////			aream=calc_area(R(n),&data->metric);	    
-	////			psiAvg=-Tdot(n)/(rho*aream*advTerm);
-	////			wdotMax=fabs(wdot[data->k_oxidizer-1]);
-	////		}
-	////	}
-	////}
-	////else{
-	////	psiAvg=0.0e0;
-	////}
-
-
-	//drdt=(RAvg-data->flamePosition[1])/(t-data->flameTime[1]);
-	//data->flamePosition[0]=data->flamePosition[1];
-	//data->flamePosition[1]=RAvg;
-	//data->flameTime[0]=data->flameTime[1];
-	//data->flameTime[1]=t;
-	//flameArea=calc_area(RAvg,&data->metric);
-
-	/*Use the Trapezoidal rule to calculate the mass burning rate based on
+void printGlobalVariables(double t, N_Vector *y, N_Vector *ydot, UserData data) {
+    double *ydata, *ydotdata, *innerMassFractionsData, *psidata;
+    innerMassFractionsData = data->innerMassFractions;
+
+    if (data->adaptiveGrid) {
+        psidata = data->grid->x;
+    } else {
+        psidata = data->uniformGrid;
+    }
+
+    double TAvg, RAvg, YAvg, psiAvg;
+    ydata = N_VGetArrayPointer_OpenMP(*y);
+    ydotdata = N_VGetArrayPointer_OpenMP(*ydot);
+    TAvg = data->isotherm;
+    double sum = ZERO;
+    double dpsim, area, aream, drdt;
+    double Cpb, Cvb, gamma, rho, flameArea, Tu;
+
+
+    /*Find the isotherm chosen by the user*/
+    size_t j = 1;
+    size_t jj = 1;
+    size_t jjj = 1;
+    double wdot[data->nsp];
+    double wdotMax = 0.0e0;
+    double advTerm = 0.0e0;
+    psiAvg = 0.0e0;
+    if (T(data->npts) > T(1)) {
+        while (T(j) < TAvg) {
+            j = j + 1;
+        }
+        YAvg = innerMassFractionsData[data->k_oxidizer - 1] - Y(data->npts, data->k_oxidizer);
+        while (fabs((T(jj + 1) - T(jj)) / T(jj)) > 1e-08) {
+            jj = jj + 1;
+        }
+
+        setGas(data, ydata, jj);
+        Tu = T(jj);
+        rho = data->gas->density();
+        Cpb = data->gas->cp_mass();        //J/kg/K
+        Cvb = data->gas->cv_mass();        //J/kg/K
+        gamma = Cpb / Cvb;
+
+    } else {
+        while (T(j) > TAvg) {
+            j = j + 1;
+        }
+        YAvg = innerMassFractionsData[data->k_oxidizer - 1] - Y(1, data->k_oxidizer);
+        while (fabs((T(data->npts - jj - 1) - T(data->npts - jj)) / T(data->npts - jj)) > 1e-08) {
+            jj = jj + 1;
+        }
+
+        setGas(data, ydata, data->npts - jj);
+        Tu = T(data->npts - jj);
+        rho = data->gas->density();
+        Cpb = data->gas->cp_mass();        //J/kg/K
+        Cvb = data->gas->cv_mass();        //J/kg/K
+        gamma = Cpb / Cvb;
+    }
+    if (T(j) < TAvg) {
+        RAvg = ((R(j + 1) - R(j)) / (T(j + 1) - T(j))) * (TAvg - T(j)) + R(j);
+    } else {
+        RAvg = ((R(j) - R(j - 1)) / (T(j) - T(j - 1))) * (TAvg - T(j - 1)) + R(j - 1);
+    }
+
+    ////Experimental burning speed calculation:
+    //int nMax=0;
+    ////nMax=maxCurvIndex(ydata, data->nt, data->nvar,
+    ////     	data->grid->x, data->npts);
+    //nMax=maxGradIndex(ydata, data->nt, data->nvar,
+    //     	data->grid->x, data->npts);
+    //advTerm=(T(nMax)-T(nMax-1))/(data->mass*(psi(nMax)-psi(nMax-1)));
+    //aream=calc_area(R(nMax),&data->metric);
+    ////setGas(data,ydata,nMax);
+    ////rho=data->gas->density();
+    //psiAvg=-Tdot(nMax)/(rho*aream*advTerm);
+    ////if(t>data->ignTime){
+    ////	for(size_t n=2;n<data->npts;n++){
+    ////		setGas(data,ydata,n);
+    ////		data->gas->getNetProductionRates(wdot); //kmol/m^3
+    ////		advTerm=(T(n)-T(n-1))/(data->mass*(psi(n)-psi(n-1)));
+    ////		if(fabs(wdot[data->k_oxidizer-1])>=wdotMax){
+    ////			aream=calc_area(R(n),&data->metric);
+    ////			psiAvg=-Tdot(n)/(rho*aream*advTerm);
+    ////			wdotMax=fabs(wdot[data->k_oxidizer-1]);
+    ////		}
+    ////	}
+    ////}
+    ////else{
+    ////	psiAvg=0.0e0;
+    ////}
+
+
+    //drdt=(RAvg-data->flamePosition[1])/(t-data->flameTime[1]);
+    //data->flamePosition[0]=data->flamePosition[1];
+    //data->flamePosition[1]=RAvg;
+    //data->flameTime[0]=data->flameTime[1];
+    //data->flameTime[1]=t;
+    //flameArea=calc_area(RAvg,&data->metric);
+
+    /*Use the Trapezoidal rule to calculate the mass burning rate based on
 	 * the consumption of O2*/
-	aream= calc_area(R(1)+1e-03*data->domainLength,&data->metric);	    
-	for (j = 2; j <data->npts; j++) {
-        	dpsim=(psi(j)-psi(j-1))*data->mass;                            
-		area= calc_area(R(j),&data->metric);	    
-		sum=sum+HALF*dpsim*((Ydot(j-1,data->k_oxidizer)/aream)
-				   +(Ydot(j,data->k_oxidizer)/area));
-		aream=area;
-	}
-
-	//double maxOH,maxHO2;
-	//maxOH=0.0e0;
-	//maxHO2=0.0e0;
-	//for(j=1;j<data->npts;j++){
-	//	if(Y(j,data->k_OH)>maxOH){
-	//		maxOH=Y(j,data->k_OH);
-	//	}
-	//}
-	//for(j=1;j<data->npts;j++){
-	//	if(Y(j,data->k_HO2)>maxHO2){
-	//		maxHO2=Y(j,data->k_HO2);
-	//	}
-	//}
-
-	fprintf((data->globalOutput), "%15.6e\t",t);
-	//fprintf((data->globalOutput), "%15.6e\t",psiAvg);
-	fprintf((data->globalOutput), "%15.6e\t",fabs(sum)/YAvg);
-	fprintf((data->globalOutput), "%15.6e\t",RAvg);
-	fprintf((data->globalOutput), "%15.6e\t",P(data->npts));
-	fprintf((data->globalOutput), "%15.6e\t",Pdot(data->npts));
-	fprintf((data->globalOutput), "%15.6e\t",gamma);
-	fprintf((data->globalOutput), "%15.6e\t",fabs(sum)/(YAvg*rho));
-	fprintf((data->globalOutput), "%15.6e\t",Tu);
-	fprintf((data->globalOutput), "\n");
+    aream = calc_area(R(1) + 1e-03 * data->domainLength, &data->metric);
+    for (j = 2; j < data->npts; j++) {
+        dpsim = (psi(j) - psi(j - 1)) * data->mass;
+        area = calc_area(R(j), &data->metric);
+        sum = sum + HALF * dpsim * ((Ydot(j - 1, data->k_oxidizer) / aream)
+                                    + (Ydot(j, data->k_oxidizer) / area));
+        aream = area;
+    }
+
+    //double maxOH,maxHO2;
+    //maxOH=0.0e0;
+    //maxHO2=0.0e0;
+    //for(j=1;j<data->npts;j++){
+    //	if(Y(j,data->k_OH)>maxOH){
+    //		maxOH=Y(j,data->k_OH);
+    //	}
+    //}
+    //for(j=1;j<data->npts;j++){
+    //	if(Y(j,data->k_HO2)>maxHO2){
+    //		maxHO2=Y(j,data->k_HO2);
+    //	}
+    //}
+
+    fprintf((data->globalOutput), "%15.6e\t", t);
+    //fprintf((data->globalOutput), "%15.6e\t",psiAvg);
+    fprintf((data->globalOutput), "%15.6e\t", fabs(sum) / YAvg);
+    fprintf((data->globalOutput), "%15.6e\t", RAvg);
+    fprintf((data->globalOutput), "%15.6e\t", P(data->npts));
+    fprintf((data->globalOutput), "%15.6e\t", Pdot(data->npts));
+    fprintf((data->globalOutput), "%15.6e\t", gamma);
+    fprintf((data->globalOutput), "%15.6e\t", fabs(sum) / (YAvg * rho));
+    fprintf((data->globalOutput), "%15.6e\t", Tu);
+    fprintf((data->globalOutput), "\n");
 }
 
 //
@@ -1765,8 +2684,8 @@ void printGlobalVariables(double t, N_Vector* y, N_Vector* ydot, UserData data)
 ////	int npts=data->npts;
 ////  	double *ydata;
 ////  	double *ydotdata;
-////	ydata    = N_VGetArrayPointer_OpenMP(y); 
-////	ydotdata    = N_VGetArrayPointer_OpenMP(ydot); 
+////	ydata    = N_VGetArrayPointer_OpenMP(y);
+////	ydotdata    = N_VGetArrayPointer_OpenMP(ydot);
 ////
 ////	T(2)=T(1);
 ////	T(npts-1)=T(npts);
@@ -1783,147 +2702,143 @@ void printGlobalVariables(double t, N_Vector* y, N_Vector* ydot, UserData data)
 
 
 /*Following functions are added to derive the characteristic time scale of species*/
-void getTimescale(UserData data, N_Vector* y){
-	size_t i, k, nsp,npts ; 
-	nsp = data->nsp ; 
-	npts = data->npts ; 
-	double rho, wdot_mole[nsp], wdot_mass[nsp],MW[nsp],concentra[nsp]; 
-	//double time_scale[npts*nsp] ;   
-
-	double* ydata ; 
-	ydata = N_VGetArrayPointer_OpenMP(*y); //access the data stored in N_Vector* y 
-	
-	for(i=1; i<= npts;i++){
-		setGas(data,ydata,i); //set the gas state at each grid point
-		rho = data->gas->density(); //get the averaged density at each grid point, Unit:kg/m^3
-		data->gas->getNetProductionRates(wdot_mole) ; //Unit:kmol/(m^3 * s)
-		
-		for(k=1; k<= nsp; k++){
-			MW(k) = data->gas->molecularWeight(k-1) ; //Unit:kg/kmol
-		}
-
-		for(k=1; k<= nsp; k++){
-			wdot_mass(k) = wdot_mole(k) * MW(k) ; //Unit:kg/(m^3 * s)
-		}
-
-		for(k=1; k<= nsp; k++){
-			concentra(k) = Y(i,k) * rho ;  //Unit:kg/m^3
-		}
-
-		for(k=1;k<= nsp;k++){
-			data->time_scale(i,k) = concentra(k)/(wdot_mass(k)+ 1.00e-16) ; 
-		}
-
-	}
+void getTimescale(UserData data, N_Vector *y) {
+    size_t i, k, nsp, npts;
+    nsp = data->nsp;
+    npts = data->npts;
+    double rho, wdot_mole[nsp], wdot_mass[nsp], MW[nsp], concentra[nsp];
+    //double time_scale[npts*nsp] ;
+
+    double *ydata;
+    ydata = N_VGetArrayPointer_OpenMP(*y); //access the data stored in N_Vector* y
+
+    for (i = 1; i <= npts; i++) {
+        setGas(data, ydata, i); //set the gas state at each grid point
+        rho = data->gas->density(); //get the averaged density at each grid point, Unit:kg/m^3
+        data->gas->getNetProductionRates(wdot_mole); //Unit:kmol/(m^3 * s)
+
+        for (k = 1; k <= nsp; k++) {
+            MW(k) = data->gas->molecularWeight(k - 1); //Unit:kg/kmol
+        }
+
+        for (k = 1; k <= nsp; k++) {
+            wdot_mass(k) = wdot_mole(k) * MW(k); //Unit:kg/(m^3 * s)
+        }
+
+        for (k = 1; k <= nsp; k++) {
+            concentra(k) = Y(i, k) * rho;  //Unit:kg/m^3
+        }
+
+        for (k = 1; k <= nsp; k++) {
+            data->time_scale(i, k) = concentra(k) / (wdot_mass(k) + 1.00e-16);
+        }
+
+    }
 }
 
 
-void printTimescaleHeader(UserData data)
-{
-	fprintf((data->timescaleOutput), "%15s\t","#1");
-	for (size_t k = 1; k <=data->nsp+1; k++) {
-		fprintf((data->timescaleOutput), "%15lu\t",k+1);
-	}
-	fprintf((data->timescaleOutput), "%15lu\n",data->nsp+3);
-
-
-	fprintf((data->timescaleOutput), "%15s\t%15s\t%15s\t","#time","radius","Temp(K)");
-	//fprintf((data->output), "%15s\t%15s\t","radius(m)","Temp(K)");
-	for (size_t k = 1; k <=(data->nsp); k++) {
-		fprintf((data->timescaleOutput), "%15s\t",data->gas->speciesName(k-1).c_str());
-	}
-	//fprintf((data->output), "%15s\t","Pressure(Pa)");
-	//fprintf((data->timescaleOutput), "%15s\n",data->gas->speciesName(data->nsp-1).c_str());
-	//fprintf((data->output), "%15s\n","Mdot (kg/s)");
-	fprintf((data->timescaleOutput), "\n");
+void printTimescaleHeader(UserData data) {
+    fprintf((data->timescaleOutput), "%15s\t", "#1");
+    for (size_t k = 1; k <= data->nsp + 1; k++) {
+        fprintf((data->timescaleOutput), "%15lu\t", k + 1);
+    }
+    fprintf((data->timescaleOutput), "%15lu\n", data->nsp + 3);
+
+
+    fprintf((data->timescaleOutput), "%15s\t%15s\t%15s\t", "#time", "radius", "Temp(K)");
+    //fprintf((data->output), "%15s\t%15s\t","radius(m)","Temp(K)");
+    for (size_t k = 1; k <= (data->nsp); k++) {
+        fprintf((data->timescaleOutput), "%15s\t", data->gas->speciesName(k - 1).c_str());
+    }
+    //fprintf((data->output), "%15s\t","Pressure(Pa)");
+    //fprintf((data->timescaleOutput), "%15s\n",data->gas->speciesName(data->nsp-1).c_str());
+    //fprintf((data->output), "%15s\n","Mdot (kg/s)");
+    fprintf((data->timescaleOutput), "\n");
 }
 
-void printTimescaleOutput(double t,N_Vector* y,FILE* output,UserData data)
-{
-	double* ydata; 
-	ydata = N_VGetArrayPointer_OpenMP(*y); 
-
-	for(size_t i=1 ; i<= data->npts; i++){
-		fprintf(output, "%15.9e\t%15.9e\t",t,R(i));
-		fprintf(output, "%15.9e\t",T(i));
-        
-		for(size_t k=1; k<=data->nsp;k++){
-			fprintf(output, "%15.9e\t",data->time_scale(i,k));
-		}
-		fprintf(output, "\n");
-	}
-	fprintf(output, "\n");
+void printTimescaleOutput(double t, N_Vector *y, FILE *output, UserData data) {
+    double *ydata;
+    ydata = N_VGetArrayPointer_OpenMP(*y);
+
+    for (size_t i = 1; i <= data->npts; i++) {
+        fprintf(output, "%15.9e\t%15.9e\t", t, R(i));
+        fprintf(output, "%15.9e\t", T(i));
+
+        for (size_t k = 1; k <= data->nsp; k++) {
+            fprintf(output, "%15.9e\t", data->time_scale(i, k));
+        }
+        fprintf(output, "\n");
+    }
+    fprintf(output, "\n");
 }
 
-void floorSmallValue(UserData data, N_Vector* y)
-{
-    double* ydata;
+void floorSmallValue(UserData data, N_Vector *y) {
+    double *ydata;
     ydata = N_VGetArrayPointer_OpenMP(*y);
-    //double sum = 0.00; 
+    //double sum = 0.00;
     size_t k_bath = data->k_bath;
-   
-	/*Floor small values to zero*/
-	for (size_t i = 1; i <=data->npts; i++) {
-		for (size_t k = 1; k <=data->nsp; k++) {
-			if(fabs(Y(i,k))<=data->massFractionTolerance){
-				Y(i,k)=0.0e0;
-			}
-		}
-	}
-    
+
+    /*Floor small values to zero*/
+    for (size_t i = 1; i <= data->npts; i++) {
+        for (size_t k = 1; k <= data->nsp; k++) {
+            if (fabs(Y(i, k)) <= data->massFractionTolerance) {
+                Y(i, k) = 0.0e0;
+            }
+        }
+    }
+
     /*Dump the error to the bath gas*/
-	for (size_t i = 1; i <=data->npts; i++) {
+    for (size_t i = 1; i <= data->npts; i++) {
         double sum = 0.00;
-		for (size_t k = 1; k <=data->nsp; k++) {
-			if(k!=k_bath){
-				sum = sum + Y(i,k);
-			}
-		}
-        Y(i,k_bath) = ONE-sum;
-	}
-    
+        for (size_t k = 1; k <= data->nsp; k++) {
+            if (k != k_bath) {
+                sum = sum + Y(i, k);
+            }
+        }
+        Y(i, k_bath) = ONE - sum;
+    }
+
 
 }
 
-void resetTolerance(UserData data, N_Vector* y,N_Vector* atolv)
-{
-    double* ydata;
-    realtype* atolvdata; 
+void resetTolerance(UserData data, N_Vector *y, N_Vector *atolv) {
+    double *ydata;
+    realtype *atolvdata;
     ydata = N_VGetArrayPointer_OpenMP(*y);
     atolvdata = N_VGetArrayPointer_OpenMP(*atolv);
-    double relTol,radTol,tempTol,presTol,massFracTol,bathGasTol,mdotTol;
-    double maxT=0.00, deltaT=400.0;
-    relTol = 1.0e-03 ; 
-    radTol = 1.0e-05 ; 
-    tempTol = 1.0e-03 ; 
-    presTol = 1.0e-3 ; 
-    massFracTol = 1.0e-06; 
-    bathGasTol = 1.0e-05 ; 
-    mdotTol = 1.0e-10 ; 
+    double relTol, radTol, tempTol, presTol, massFracTol, bathGasTol, mdotTol;
+    double maxT = 0.00, deltaT = 400.0;
+    relTol = 1.0e-03;
+    radTol = 1.0e-05;
+    tempTol = 1.0e-03;
+    presTol = 1.0e-3;
+    massFracTol = 1.0e-06;
+    bathGasTol = 1.0e-05;
+    mdotTol = 1.0e-10;
 
 
     /*Get the maximum Temperature*/
-    for (size_t i =1;i <= data->npts;i++){
-        if(T(i) > maxT){
+    for (size_t i = 1; i <= data->npts; i++) {
+        if (T(i) > maxT) {
             maxT = T(i);
         }
     }
 
     /*reset the tolerance when maxT > initialTemperature +deltaT*/
-    if(maxT >= (data->initialTemperature + deltaT)){
+    if (maxT >= (data->initialTemperature + deltaT)) {
         data->relativeTolerance = relTol;
 
-        for(size_t i =1; i<=data->npts; i++){
-            atolT(i) = tempTol; 
-            atolR(i) = radTol ; 
-            atolP(i) = presTol ;
-            atolMdot(i) = mdotTol ; 
-            
-            for(size_t k =1; k<= data->nsp; k++){
-                if(k!=data->k_bath){
-                    atolY(i,k) = massFracTol;
-                }else{
-                    atolY(i,k) = bathGasTol;
+        for (size_t i = 1; i <= data->npts; i++) {
+            atolT(i) = tempTol;
+            atolR(i) = radTol;
+            atolP(i) = presTol;
+            atolMdot(i) = mdotTol;
+
+            for (size_t k = 1; k <= data->nsp; k++) {
+                if (k != data->k_bath) {
+                    atolY(i, k) = massFracTol;
+                } else {
+                    atolY(i, k) = bathGasTol;
                 }
             }
         }
@@ -1931,145 +2846,444 @@ void resetTolerance(UserData data, N_Vector* y,N_Vector* atolv)
 
 }
 
-void getReactions(UserData data,N_Vector* y,FILE* output){
+void getReactions(UserData data, N_Vector *y, FILE *output) {
     double Tmax;
-    double* ydata; 
+    double *ydata;
     //double deltaT = 400.0;
     //int i = 0;
     size_t nRxns;
     int index;
     nRxns = data->gas->nReactions();
     //DEBUG
-    printf("Total Number of Rxns:%zu \n",nRxns);
-    double fwdROP[nRxns],revROP[nRxns],netROP[nRxns];
-    std::string* rxnArr = new std::string[nRxns];
+    printf("Total Number of Rxns:%zu \n", nRxns);
+    double fwdROP[nRxns], revROP[nRxns], netROP[nRxns];
+    std::string *rxnArr = new std::string[nRxns];
     ydata = N_VGetArrayPointer_OpenMP(*y);
-    Tmax = maxTemperature(ydata,data->nt,data->nvar,data->npts);
+    Tmax = maxTemperature(ydata, data->nt, data->nvar, data->npts);
     //get the rxns' equation array
-    for(size_t ii=0;ii<nRxns;ii++){
-        rxnArr[ii]= data->gas->reactionString(ii);
+    for (size_t ii = 0; ii < nRxns; ii++) {
+        rxnArr[ii] = data->gas->reactionString(ii);
     }
     printf("Printing Rxns Rate Of Progress Data......\n");
-    if(Tmax >= (data->initialTemperature+data->deltaT)){
-        index = maxTemperatureIndex(ydata,data->nt,data->nvar,data->npts); 
-        setGas(data,ydata,index);
+    if (Tmax >= (data->initialTemperature + data->deltaT)) {
+        index = maxTemperatureIndex(ydata, data->nt, data->nvar, data->npts);
+        setGas(data, ydata, index);
         /*Get forward/reverse/net rate of progress of rxns*/
         data->gas->getRevRatesOfProgress(revROP);
         data->gas->getFwdRatesOfProgress(fwdROP);
         data->gas->getNetRatesOfProgress(netROP);
-	    for(size_t j=0 ; j<nRxns; j++){
-            fprintf(output,"%30s\t",rxnArr[j].c_str());
-            fprintf(output,"%15.9e\t%15.9e\t%15.9e\t\n",fwdROP[j],revROP[j],netROP[j]);
-	    }
-	    fprintf(output, "\n");
+        for (size_t j = 0; j < nRxns; j++) {
+            fprintf(output, "%30s\t", rxnArr[j].c_str());
+            fprintf(output, "%15.9e\t%15.9e\t%15.9e\t\n", fwdROP[j], revROP[j], netROP[j]);
+        }
+        fprintf(output, "\n");
         fclose(output);
-     }
-     delete[] rxnArr;
+    }
+    delete[] rxnArr;
 }
 
-void getSpecies(UserData data,N_Vector* y,FILE* output){
+void getSpecies(UserData data, N_Vector *y, FILE *output) {
     double Tmax;
-    double* ydata; 
+    double *ydata;
     int index;
-    double fwdROP[data->nsp],revROP[data->nsp],netROP[data->nsp];
-    std::string* spArr = new std::string[data->nsp];
+    double fwdROP[data->nsp], revROP[data->nsp], netROP[data->nsp];
+    std::string *spArr = new std::string[data->nsp];
     ydata = N_VGetArrayPointer_OpenMP(*y);
-    Tmax = maxTemperature(ydata,data->nt,data->nvar,data->npts);
+    Tmax = maxTemperature(ydata, data->nt, data->nvar, data->npts);
     //get the species name array
-    for(size_t ii=0;ii<data->nsp;ii++){
-        spArr[ii]= data->gas->speciesName(ii);
+    for (size_t ii = 0; ii < data->nsp; ii++) {
+        spArr[ii] = data->gas->speciesName(ii);
     }
     printf("Printing Species Rate of Production/Destruction Data......\n");
-    if(Tmax>=(data->initialTemperature+data->deltaT)){
-        index = maxTemperatureIndex(ydata,data->nt,data->nvar,data->npts); 
-        setGas(data,ydata,index);
+    if (Tmax >= (data->initialTemperature + data->deltaT)) {
+        index = maxTemperatureIndex(ydata, data->nt, data->nvar, data->npts);
+        setGas(data, ydata, index);
         /*Get forward/reverse/net rate of progress of rxns*/
         data->gas->getDestructionRates(revROP);
         data->gas->getCreationRates(fwdROP);
         data->gas->getNetProductionRates(netROP);
         /*Print data to the pertinent output file*/
-	    for(size_t j=0 ; j<data->nsp; j++){
-            fprintf(output,"%15s\t",spArr[j].c_str());
-            fprintf(output,"%15.9e\t%15.9e\t%15.9e\t\n",fwdROP[j],revROP[j],netROP[j]);
-	    }
-	    fprintf(output, "\n");
+        for (size_t j = 0; j < data->nsp; j++) {
+            fprintf(output, "%15s\t", spArr[j].c_str());
+            fprintf(output, "%15.9e\t%15.9e\t%15.9e\t\n", fwdROP[j], revROP[j], netROP[j]);
+        }
+        fprintf(output, "\n");
         fclose(output);
     }
     delete[] spArr;
 }
-//rho : density of liquid phase
-double getLiquidRho(double dropMole[],double temp,double pres){
-     std::vector<std::string> fluids; 
-     fluids.push_back("Propane"); 
-     fluids.push_back("n-Heptane");
-     
-     std::vector<double> Temperature(1,temp),Pressure(1,pres);
-     std::vector<std::string> outputs;
-     outputs.push_back("D"); 
-
-	 std::vector<double> moles;
-	 moles.push_back(dropMole[0]);
-	 moles.push_back(dropMole[1]);
-     double density = CoolProp::PropsSImulti(outputs,"T",Temperature,"P",Pressure,"",fluids,moles)[0][0]; //Unit:kg/m^3
-
-     return density;
+
+//
+////rho : density of liquid phase
+//double getLiquidRho(double dropMole[],double temp,double pres){
+//     std::vector<std::string> fluids;
+//     fluids.push_back("Propane");
+//     fluids.push_back("n-Heptane");
+//
+//     std::vector<double> Temperature(1,temp),Pressure(1,pres);
+//     std::vector<std::string> outputs;
+//     outputs.push_back("D");
+//
+//	 std::vector<double> moles;
+//	 moles.push_back(dropMole[0]);
+//	 moles.push_back(dropMole[1]);
+//     double density = CoolProp::PropsSImulti(outputs,"T",Temperature,"P",Pressure,"",fluids,moles)[0][0]; //Unit:kg/m^3
+//
+//     return density;
+//}
+
+////Cp,l : specific heat capacity at constant pressure of liquid phase
+//double getLiquidCp(double dropMole[],double temp,double pres){
+//     std::vector<std::string> fluids;
+//     fluids.push_back("Propane");
+//     fluids.push_back("n-Heptane");
+//
+//     std::vector<double> Temperature(1,temp),Pressure(1,pres);
+//     std::vector<std::string> outputs;
+//     outputs.push_back("CPMASS");
+//
+//	 std::vector<double> moles;
+//	 moles.push_back(dropMole[0]);
+//	 moles.push_back(dropMole[1]);
+//     double cp = CoolProp::PropsSImulti(outputs,"T",Temperature,"P",Pressure,"",fluids,moles)[0][0]; //Unit:J/(kg*K)
+//
+//     return cp;
+//}
+
+////Hv : heat of vaporization of liquid phase at constant pressure
+//double getLiquidHv(double dropMole[],double temp,double pres){
+//     std::vector<std::string> fluids;
+//     fluids.push_back("Propane");
+//     fluids.push_back("n-Heptane");
+//
+//     std::vector<double> Temperature(1,temp),Pressure(1,pres);
+//     std::vector<std::string> outputs;
+//     outputs.push_back("H");
+//
+//	 std::vector<double> moles;
+//	 moles.push_back(dropMole[0]);
+//	 moles.push_back(dropMole[1]);
+//
+//	 std::vector<double> state1(1,1.0);
+//	 std::vector<double> state2(1,0.0);
+//
+//     double H_V = CoolProp::PropsSImulti(outputs,"P",Pressure,"Q",state1,"",fluids,moles)[0][0]; //Unit:J/kg
+//     double H_L = CoolProp::PropsSImulti(outputs,"P",Pressure,"Q",state2,"",fluids,moles)[0][0]; //Unit:J/kg
+//     double delta_H = H_V - H_L;
+//
+//     return delta_H;
+//}
+
+////MaxT : maximum allowed tempereture of liquid phase
+////Also the boiling point of more volitile component
+//double getLiquidMaxT(double dropMole[],double pres){
+//     std::vector<std::string> fluids;
+//     fluids.push_back("Propane");
+//     //fluids.push_back("n-Heptane");
+//
+//     std::vector<double> Pressure(1,pres);
+//     std::vector<std::string> outputs;
+//     outputs.push_back("T");
+//
+//	double temperature = CoolProp::PropsSI(outputs[0], "P", Pressure[0],"Q",1.0,fluids[0]);
+//
+//    return temperature;
+//}
+
+/*function overloading for single and bi-component*/
+/*calculate the liquid phase density based on droplet type and T,P,X(Y)*/
+/*single component case*/
+double getLiquidDensity(const double temp, const double pres, const std::vector<std::string> &composition) {
+    std::vector<double> Temperature(1, temp), Pressure(1, pres);
+
+    double density = CoolProp::PropsSI("D", "T", Temperature[0], "P", Pressure[0], composition[0]); //Unit:kg/m^3
+    return density;
+}
+
+/*binary component case*/
+double getLiquidDensity(const double temp, const double pres, std::vector<std::string> &composition,
+                        const std::vector<double> &mole) {
+    std::vector<double> Temperature(1, temp), Pressure(1, pres);
+    std::vector<std::string> outputs;
+    outputs.push_back("D");
+
+    double density = CoolProp::PropsSImulti(outputs, "T", Temperature, "P", Pressure, "", composition,
+                                            mole)[0][0]; //Unit:kg/m^3
+    return density;
+}
+
+double getLiquidCond(const double temp, const double pres, const std::vector<std::string> &composition) {
+    std::vector<double> Temperature(1, temp), Pressure(1, pres);
+    double k = CoolProp::PropsSI("conductivity", "T", Temperature[0], "P", Pressure[0], composition[0]);
+    return k;  //Unit:W/m/K (kg*m/s^3/K)
+}
+
+/*binary component case*/
+double getLiquidCond(const double temp, const double pres, std::vector<std::string> &composition,
+                     const std::vector<double> &mole) {
+    std::vector<double> Temperature(1, temp), Pressure(1, pres);
+    std::vector<std::string> outputs;
+    outputs.push_back("conductivity");
+
+    double k = CoolProp::PropsSImulti(outputs, "T", Temperature, "P", Pressure, "", composition,
+                                      mole)[0][0];
+    return k; //Unit:W/m/K (kg*m/s^3/K)
+}
+
+/*Cpb:total liquid phase specific heat capacity at constant pressure*/
+double getLiquidCpb(const double temp,const double pres, const std::vector<std::string>& composition){
+    std::vector<double> Temperature(1, temp), Pressure(1, pres);
+    double k = CoolProp::PropsSI("Cpmass", "T", Temperature[0], "P", Pressure[0], composition[0]); //Unit:kg/m^3
+    return k;  //unit:J/kg/K
+}
+
+/*binary component case*/
+double getLiquidCpb(const double temp, const double pres, const std::vector<std::string> &composition,
+                    const std::vector<double> &mole) {
+    std::vector<double> Temperature(1, temp), Pressure(1, pres);
+    std::vector<std::string> outputs;
+    outputs.push_back("Cpmass");
+
+    double k = CoolProp::PropsSImulti(outputs, "T", Temperature, "P", Pressure, "", composition,
+                                      mole)[0][0]; //Unit:kg/m^3
+    return k; //unit:J/kg/K
+}
+
+/*get Cp vector for binary componet droplet*/
+std::vector<double> getLiquidCp(const double temp, const double pres, const std::vector<std::string> &composition){
+    std::vector<double> k ;
+    double k_temp;
+    std::vector<double> Temperature(1, temp), Pressure(1, pres);
+    for(auto & species : composition){
+        k_temp = CoolProp::PropsSI("Cpmass", "T", Temperature[0], "P", Pressure[0], species);
+        k.push_back(k_temp) ;
+    }
+    return k;
+}
+
+
+/*get gas phase thermal conductivity*/
+double getGasCond(UserData data, double *ydata, size_t gridPoint) {
+    double k;
+    setGas(data, ydata, gridPoint);
+    k = data->trmix->thermalConductivity();
+    return k; //unit:W/(m*K)
+}
+
+/*latent heat of vaporizaiton*/
+/*unit: J/kg*/
+std::vector<double> getLiquidVH(const double pres, const int dropType) {
+    double H, H_V, H_L;
+    std::vector<double> vapheat;
+    std::vector<std::string> fluids;
+    std::vector<double> Pressure(1, pres);
+
+    fluids = components(dropType);
+
+    if (dropType == 0) {
+//        fluids.push_back("nHeptane");
+        H_V = CoolProp::PropsSI("H", "P", Pressure[0], "Q", 1, fluids[0]);
+        H_L = CoolProp::PropsSI("H", "P", Pressure[0], "Q", 0, fluids[0]);
+        H = H_V - H_L;
+        vapheat.push_back(H);
+    } else {
+        for (size_t i = 0; i < fluids.size(); i++) {
+            H_V = CoolProp::PropsSI("H", "P", Pressure[0], "Q", 1, fluids[i]);
+            H_L = CoolProp::PropsSI("H", "P", Pressure[0], "Q", 0, fluids[i]);
+            H = H_V - H_L;
+            vapheat.push_back(H);
+        }
+    }
+    return vapheat;  //unit:J/kg
+}
+
+/*convert mass fraction to mole fraction*/
+/*size of both arrays should be identical*/
+void mass2mole(const std::vector<double> &mass, std::vector<double> &mole, UserData data) {
+    mole.reserve(mass.size());
+    double sum = 0.0;
+    double x_temp;
+    for (size_t i = 0; i < data->dropMole.size(); i++) {
+        sum = sum + mass[i] / data->MW[i];
+    }
+
+    x_temp = mass[0] / (data->MW[0] * sum);
+    mole.push_back(x_temp);
+    mole.push_back(ONE - x_temp);
 }
 
-//Cp,l : specific heat capacity at constant pressure of liquid phase
-double getLiquidCp(double dropMole[],double temp,double pres){
-     std::vector<std::string> fluids; 
-     fluids.push_back("Propane"); 
-     fluids.push_back("n-Heptane");
-     
-     std::vector<double> Temperature(1,temp),Pressure(1,pres);
-     std::vector<std::string> outputs;
-     outputs.push_back("CPMASS"); 
-
-	 std::vector<double> moles;
-	 moles.push_back(dropMole[0]);
-	 moles.push_back(dropMole[1]);
-     double cp = CoolProp::PropsSImulti(outputs,"T",Temperature,"P",Pressure,"",fluids,moles)[0][0]; //Unit:J/(kg*K)
-
-     return cp;
+/*liquid mass diffusivity D for binary component case*/
+double getLiquidmassdiff(UserData data, double *ydata, size_t gridPoint, const double temp) {
+    std::vector<double> V_ = {75.86, 162.34}; //molar volume at normal boiling point, unit: cm^3/mol
+    std::vector<double> visc_, mole_, mass_, D_inf_;
+    double visc_temp, D, Dinf_temp;
+    std::vector<std::string> composition = components(data->dropType);
+
+    for (size_t i = 0; i < data->dropMole.size(); i++) {
+        visc_temp = 1000.0 * CoolProp::PropsSI("V", "T", temp, "Q", 0, composition[i]);  //unit: mPa*s
+        visc_.push_back(visc_temp);
+    }
+    mole_ = getLiquidmolevec(data, ydata, gridPoint);
+
+    for (size_t i = 0; i < data->dropMole.size(); i++) {
+        if (i == 0) {
+            Dinf_temp = 9.89e-8 * temp * pow(visc_[1], -0.907) * pow(V_[0], -0.45) * pow(V_[1], 0.265);
+            D_inf_.push_back(Dinf_temp);
+        } else {
+            Dinf_temp = 9.89e-8 * temp * pow(visc_[0], -0.907) * pow(V_[1], -0.45) * pow(V_[0], 0.265);
+            D_inf_.push_back(Dinf_temp);
+        }
+    }
+
+    D = mole_[1] * D_inf_[0] + mole_[0] * D_inf_[1]; //unit:cm^2/s
+    return (D / 10000); //unit:m^2/s
 }
 
-//Hv : heat of vaporization of liquid phase at constant pressure
-double getLiquidHv(double dropMole[],double temp,double pres){
-     std::vector<std::string> fluids; 
-     fluids.push_back("Propane"); 
-     fluids.push_back("n-Heptane");
-     
-     std::vector<double> Temperature(1,temp),Pressure(1,pres);
-     std::vector<std::string> outputs;
-     outputs.push_back("H"); 
+//double dropletmass(UserData data,double* ydata){
+//    double mass = 0.0 ;
+//    double rho,rhop;
+//    if (data->dropType==0){
+//            for (size_t i = data->l_npts-1; i>=1 ; i--) {
+//                std::vector<std::string> str;
+//                str.push_back("nHeptane");
+//                rho = getLiquidDensity(T(i), P(i), str);
+//                rhop = getLiquidDensity(T(i + 1), P(i + 1), str);
+//                mass = mass + (R(i + 1) - R(i)) * (rho * calc_area(R(i), &data->metric) +
+//                                                           rhop * calc_area(R(i + 1), &data->metric)) / TWO;
+//            }
+//    }else if(data->dropType==1){
+//            for (size_t i = data->l_npts-1; i>=1 ; i--){
+//                std::vector<std::string> str;
+//                std::vector<double> massFrac,massFracp,moleFrac,moleFracp;
+//                str.push_back("propane");
+//                str.push_back("nHeptane");
+//                for (size_t j = 0; j < data->dropMole.size(); j++){
+//                    massFrac.push_back(Y(i,data->k_drop[j]));
+//                    massFracp.push_back(Y(i+1,data->k_drop[j]));
+//                }
+//                /*convert mass fraction to mole fraction*/
+//                mass2mole(massFrac,moleFrac,data);
+//                mass2mole(massFracp,moleFracp,data);
+//                rho = getLiquidDensity(T(i),P(i),str,moleFrac);
+//                rhop = getLiquidDensity(T(i+1),P(i+1),str,moleFracp);
+//                mass =  mass +(R(i+1)-R(i))*(rho*calc_area(R(i),&data->metric)+rhop*calc_area(R(i+1),&data->metric))/TWO;
+//        }
+//    }
+//    return mass ;
+//}
+
+
+// List of fluid components per dropType
+std::vector<std::string> components(int dropType) {
+    if (dropType == 0) {
+        return {"nHeptane"};
+    } else if (dropType == 1) {
+        return {"propane", "nHeptane"};
+    }
+    return {};
+}
+
+/*calculat droplet mass*/
+double dropletmass(UserData data, double *ydata) {
+    double mass = 0.0;
+    double rho, rhop;
+
+    for (size_t i = data->l_npts - 1; i >= 1; i--) {
+        std::vector<std::string> composition = components(data->dropType);
+
+        if (data->dropType == 0) {
+            rho = getLiquidDensity(T(i), P(i), composition);
+            rhop = getLiquidDensity(T(i + 1), P(i + 1), composition);
 
-	 std::vector<double> moles;
-	 moles.push_back(dropMole[0]);
-	 moles.push_back(dropMole[1]);
+        } else if (data->dropType == 1) {
+            std::vector<double> moleFrac, moleFracp;
+            moleFrac = getLiquidmolevec(data, ydata, i);
+            moleFracp = getLiquidmolevec(data, ydata, i);
 
-	 std::vector<double> state1(1,1.0);
-	 std::vector<double> state2(1,0.0); 
+            rho = getLiquidDensity(T(i), P(i), composition, moleFrac);
+            rhop = getLiquidDensity(T(i + 1), P(i + 1), composition, moleFracp);
+        }
 
-     double H_V = CoolProp::PropsSImulti(outputs,"P",Pressure,"Q",state1,"",fluids,moles)[0][0]; //Unit:J/kg
-     double H_L = CoolProp::PropsSImulti(outputs,"P",Pressure,"Q",state2,"",fluids,moles)[0][0]; //Unit:J/kg
-     double delta_H = H_V - H_L;
+        double area = calc_area(R(i), &data->metric);
+        double areap = calc_area(R(i + 1), &data->metric);
+        mass += (R(i + 1) - R(i)) * (rho * area + rhop * areap) / TWO;
+    }
+    return mass;
+}
 
-     return delta_H;
+std::vector<double> getLiquidmassvec(UserData data, double *ydata, int gridPoint) {
+    std::vector<double> mass_;
+    mass_.push_back(Y(gridPoint, data->k_drop[0]));
+    mass_.push_back(Y(gridPoint, data->k_drop[1]));
+    return mass_;
 }
 
-//MaxT : maximum allowed tempereture of liquid phase
-//Also the boiling point of more volitile component
-double getLiquidMaxT(double dropMole[],double pres){
-     std::vector<std::string> fluids; 
-     fluids.push_back("Propane"); 
-     //fluids.push_back("n-Heptane");
-     
-     std::vector<double> Pressure(1,pres);
-     std::vector<std::string> outputs;
-     outputs.push_back("T"); 
-	 
-	double temperature = CoolProp::PropsSI(outputs[0], "P", Pressure[0],"Q",1.0,fluids[0]);
-	
-    return temperature;
+std::vector<double> getLiquidmolevec(UserData data, double *ydata, int gridPoint) {
+    std::vector<double> mass_, mole_;
+    mass_ = getLiquidmassvec(data, ydata, gridPoint);
+    mass2mole(mass_, mole_, data);
+    return mole_;
 }
 
+/*return droplet species vapor pressure at interface, unit:Pa*/
+std::vector<double> getVapPressure(UserData data, double* ydata,int gridPoint,const std::vector<double> mole_){
+    std::vector<double> vapPres;
+    vapPres.reserve(mole_.size()) ;
+    std::vector<double> gamma_;
+    getGamma(mole_,gamma_) ;
+    //propane
+    double p1 = 1.0e5 * pow(10, 4.53678 - (1149.36 / (T(gridPoint) + 24.906))) * mole_[0] *
+                gamma_[0];
+    //heptane
+    double p2 = 1.0e5 * pow(10, 4.02832 - (1268.636 / (T(gridPoint) - 56.199))) * mole_[1] *
+                gamma_[1];
+    vapPres.push_back(p1);
+    vapPres.push_back(p2);
+    return vapPres;
+}
+
+void printIddata(UserData data, double *iddata) {
+    FILE *file;
+    file = fopen("id.dat", "w");
+    fprintf(file, "%15s\t%15s\t", "Rid", "Tid");
+    for (size_t k = 1; k <= data->nsp; k++) {
+        fprintf(file, "%15s\t", data->gas->speciesName(k - 1).c_str());
+    }
+    fprintf(file, "%15s\t", "Pid");
+    fprintf(file, "%15s\n", "Mdotid");
+
+    for (size_t i = 1; i <= data->npts; i++) {
+        fprintf(file, "%15lu\t", (size_t) Rid(i));
+        fprintf(file, "%15lu\t", (size_t) Tid(i));
+        for (size_t k = 1; k <= data->nsp; k++) {
+            fprintf(file, "%15lu\t", (size_t) Yid(i, k));
+        }
+        fprintf(file, "%15lu\t", (size_t) Pid(i));
+        fprintf(file, "%15lu\n", (size_t) Mdotid(i));
+    }
+
+    fclose(file);
+}
+
+void printPsidata(UserData data, double* psidata) {
+    FILE *file;
+    file = fopen("psi.dat", "w");
+//    fprintf(file, "%15s\t%15s\t", "Rid", "Tid");
+    for (size_t j = 1; j <= data->npts; j++) {
+        fprintf(file, "%lu\t", j);
+    }
+    fprintf(file, "\n");
+
+    for (size_t j = 1; j <= data->npts; j++) {
+//        fprintf(file, "%15lu\t", (size_t) Rid(i));
+//        fprintf(file, "%15lu\t", (size_t) Tid(i));
+//        for (size_t k = 1; k <= data->nsp; k++) {
+//            fprintf(file, "%15lu\t", (size_t) Yid(i, k));
+//        }
+//        fprintf(file, "%15lu\t", (size_t) Pid(i));
+//        fprintf(file, "%15lu\n", (size_t) Mdotid(i));
+        fprintf(file,"%15.6e\t", psi(j));
+    }
+    fprintf(file, "\n");
+    fclose(file);
+}
\ No newline at end of file
diff --git a/timing.h b/timing.h
deleted file mode 100644
index b65b3d3..0000000
--- a/timing.h
+++ /dev/null
@@ -1,2 +0,0 @@
-double get_wall_time();
-double get_cpu_time();
diff --git a/timing.hpp b/timing.hpp
deleted file mode 100644
index e07e3eb..0000000
--- a/timing.hpp
+++ /dev/null
@@ -1,45 +0,0 @@
-//  Windows
-#ifdef _WIN32
-#include <Windows.h>
-double get_wall_time(){
-    LARGE_INTEGER time,freq;
-    if (!QueryPerformanceFrequency(&freq)){
-        //  Handle error
-        return 0;
-    }
-    if (!QueryPerformanceCounter(&time)){
-        //  Handle error
-        return 0;
-    }
-    return (double)time.QuadPart / freq.QuadPart;
-}
-double get_cpu_time(){
-    FILETIME a,b,c,d;
-    if (GetProcessTimes(GetCurrentProcess(),&a,&b,&c,&d) != 0){
-        //  Returns total user time.
-        //  Can be tweaked to include kernel times as well.
-        return
-            (double)(d.dwLowDateTime |
-            ((unsigned long long)d.dwHighDateTime << 32)) * 0.0000001;
-    }else{
-        //  Handle error
-        return 0;
-    }
-}
-
-//  Posix/Linux
-#else
-#include <time.h>
-#include <sys/time.h>
-double get_wall_time(){
-    struct timeval time;
-    if (gettimeofday(&time,NULL)){
-        //  Handle error
-        return 0;
-    }
-    return (double)time.tv_sec + (double)time.tv_usec * .000001;
-}
-double get_cpu_time(){
-    return (double)clock() / CLOCKS_PER_SEC;
-}
-#endif