Add the function:parseDropSpec for both droplet composition and droplet mole fractions

CMakeLists.txt

@@ -17,6 +17,7 @@ set(IDA_INCLUDES ${IDA_DIR}/include)
 set(GSL_INCLUDES /usr/include/gsl)
 set(COOLPROP_INCLUDES ${COOLPROP_DIR}/include)
 set(FMT_INCLUDES ${FMT_DIR}/include)
+set(EIGEN_INCLUDES /backup/weiye/eigen-3.4.0)
 
 # Search for source files
 aux_source_directory(${PROJECT_SOURCE_DIR}/src SRC_LIST)
@@ -32,7 +33,7 @@ target_link_libraries(DropletCombustion
 
 # Include directories
 target_include_directories(DropletCombustion
-    PRIVATE ${PROJECT_SOURCE_DIR}/include ${CANTERA_INCLUDES} ${IDA_INCLUDES} ${GSL_INCLUDES} ${COOLPROP_INCLUDES} ${FMT_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)

build/CMakeCache.txt

@@ -1,5 +1,5 @@
 # This is the CMakeCache file.
-# For build in directory: /backup/weiye/src_binary_droplet/build
+# For build in directory: /backup/weiye/src_binary_droplet_COPY/build
 # It was generated by CMake: /usr/bin/cmake
 # You can edit this file to change values found and used by cmake.
 # If you do not want to change any of the values, simply exit the editor.
@@ -210,10 +210,10 @@ CMAKE_STRIP:FILEPATH=/usr/bin/strip
 CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE
 
 //Value Computed by CMake
-demo_BINARY_DIR:STATIC=/backup/weiye/src_binary_droplet/build
+demo_BINARY_DIR:STATIC=/backup/weiye/src_binary_droplet_COPY/build
 
 //Value Computed by CMake
-demo_SOURCE_DIR:STATIC=/backup/weiye/src_binary_droplet
+demo_SOURCE_DIR:STATIC=/backup/weiye/src_binary_droplet_COPY
 
 
 ########################
@@ -225,7 +225,7 @@ CMAKE_ADDR2LINE-ADVANCED:INTERNAL=1
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 CMAKE_AR-ADVANCED:INTERNAL=1
 //This is the directory where this CMakeCache.txt was created
-CMAKE_CACHEFILE_DIR:INTERNAL=/backup/weiye/src_binary_droplet/build
+CMAKE_CACHEFILE_DIR:INTERNAL=/backup/weiye/src_binary_droplet_COPY/build
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 CMAKE_CACHE_MAJOR_VERSION:INTERNAL=3
 //Minor version of cmake used to create the current loaded cache
@@ -302,7 +302,7 @@ CMAKE_GENERATOR_PLATFORM:INTERNAL=
 CMAKE_GENERATOR_TOOLSET:INTERNAL=
 //Source directory with the top level CMakeLists.txt file for this
 // project
-CMAKE_HOME_DIRECTORY:INTERNAL=/backup/weiye/src_binary_droplet
+CMAKE_HOME_DIRECTORY:INTERNAL=/backup/weiye/src_binary_droplet_COPY
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-set(CMAKE_RELATIVE_PATH_TOP_BINARY "/backup/weiye/src_binary_droplet/build")
+set(CMAKE_RELATIVE_PATH_TOP_SOURCE "/backup/weiye/src_binary_droplet_COPY")
+set(CMAKE_RELATIVE_PATH_TOP_BINARY "/backup/weiye/src_binary_droplet_COPY/build")
 
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     arg [-pie] ==> ignore
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-    arg [cmTC_cffc1] ==> ignore
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 Determining if the CXX compiler works passed with the following output:
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-Run Build Command(s):/usr/bin/make cmTC_23945/fast && /usr/bin/make -f CMakeFiles/cmTC_23945.dir/build.make CMakeFiles/cmTC_23945.dir/build
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-make[1]: Leaving directory '/backup/weiye/src_binary_droplet/build/CMakeFiles/CMakeTmp'
+Run Build Command(s):/usr/bin/make cmTC_9ab69/fast && /usr/bin/make -f CMakeFiles/cmTC_9ab69.dir/build.make CMakeFiles/cmTC_9ab69.dir/build
+make[1]: Entering directory '/backup/weiye/src_binary_droplet_COPY/build/CMakeFiles/CMakeTmp'
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+Linking CXX executable cmTC_9ab69
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 Detecting CXX compiler ABI info compiled with the following output:
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+Change Dir: /backup/weiye/src_binary_droplet_COPY/build/CMakeFiles/CMakeTmp
 
-Run Build Command(s):/usr/bin/make cmTC_6e8aa/fast && /usr/bin/make -f CMakeFiles/cmTC_6e8aa.dir/build.make CMakeFiles/cmTC_6e8aa.dir/build
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+make[1]: Entering directory '/backup/weiye/src_binary_droplet_COPY/build/CMakeFiles/CMakeTmp'
+Building CXX object CMakeFiles/cmTC_cdefd.dir/CMakeCXXCompilerABI.cpp.o
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+CMakeFiles/DropletCombustion.dir/src/residue.cpp.o: /backup/weiye/eigen-3.4.0/Eigen/src/plugins/ReshapedMethods.h
 CMakeFiles/DropletCombustion.dir/src/residue.cpp.o: /backup/weiye/fmt/include/fmt/core.h
 CMakeFiles/DropletCombustion.dir/src/residue.cpp.o: /backup/weiye/fmt/include/fmt/format-inl.h
 CMakeFiles/DropletCombustion.dir/src/residue.cpp.o: /backup/weiye/fmt/include/fmt/format.h

build/CMakeFiles/DropletCombustion.dir/flags.make

@@ -6,5 +6,5 @@ CXX_FLAGS =   -std=gnu++11
 
 CXX_DEFINES = 
 
-CXX_INCLUDES = -I/backup/weiye/src_binary_droplet/include -I/opt/scientific/cantera-2.4_gnu_blas/include -I/opt/scientific/sundials-3.1.1_intel_mkl/include -I/usr/include/gsl -I/backup/weiye/CoolProp/include -I/backup/weiye/fmt/include 
+CXX_INCLUDES = -I/backup/weiye/src_binary_droplet_COPY/include -I/opt/scientific/cantera-2.4_gnu_blas/include -I/opt/scientific/sundials-3.1.1_intel_mkl/include -I/usr/include/gsl -I/backup/weiye/CoolProp/include -I/backup/weiye/fmt/include -I/backup/weiye/eigen-3.4.0 
 

build/CMakeFiles/Makefile2

@@ -44,10 +44,10 @@ RM = /usr/bin/cmake -E remove -f
 EQUALS = =
 
 # The top-level source directory on which CMake was run.
-CMAKE_SOURCE_DIR = /backup/weiye/src_binary_droplet
+CMAKE_SOURCE_DIR = /backup/weiye/src_binary_droplet_COPY
 
 # The top-level build directory on which CMake was run.
-CMAKE_BINARY_DIR = /backup/weiye/src_binary_droplet/build
+CMAKE_BINARY_DIR = /backup/weiye/src_binary_droplet_COPY/build
 
 #=============================================================================
 # Directory level rules for the build root directory
@@ -74,14 +74,14 @@ clean: CMakeFiles/DropletCombustion.dir/clean
 CMakeFiles/DropletCombustion.dir/all:
 	$(MAKE) -f CMakeFiles/DropletCombustion.dir/build.make CMakeFiles/DropletCombustion.dir/depend
 	$(MAKE) -f CMakeFiles/DropletCombustion.dir/build.make CMakeFiles/DropletCombustion.dir/build
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --progress-dir=/backup/weiye/src_binary_droplet/build/CMakeFiles --progress-num=1,2,3,4,5,6,7 "Built target DropletCombustion"
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --progress-dir=/backup/weiye/src_binary_droplet_COPY/build/CMakeFiles --progress-num=1,2,3,4,5,6,7 "Built target DropletCombustion"
 .PHONY : CMakeFiles/DropletCombustion.dir/all
 
 # Build rule for subdir invocation for target.
 CMakeFiles/DropletCombustion.dir/rule: cmake_check_build_system
-	$(CMAKE_COMMAND) -E cmake_progress_start /backup/weiye/src_binary_droplet/build/CMakeFiles 7
+	$(CMAKE_COMMAND) -E cmake_progress_start /backup/weiye/src_binary_droplet_COPY/build/CMakeFiles 7
 	$(MAKE) -f CMakeFiles/Makefile2 CMakeFiles/DropletCombustion.dir/all
-	$(CMAKE_COMMAND) -E cmake_progress_start /backup/weiye/src_binary_droplet/build/CMakeFiles 0
+	$(CMAKE_COMMAND) -E cmake_progress_start /backup/weiye/src_binary_droplet_COPY/build/CMakeFiles 0
 .PHONY : CMakeFiles/DropletCombustion.dir/rule
 
 # Convenience name for target.

build/CMakeFiles/TargetDirectories.txt

@@ -1,3 +1,3 @@
-/backup/weiye/src_binary_droplet/build/CMakeFiles/rebuild_cache.dir
-/backup/weiye/src_binary_droplet/build/CMakeFiles/DropletCombustion.dir
-/backup/weiye/src_binary_droplet/build/CMakeFiles/edit_cache.dir
+/backup/weiye/src_binary_droplet_COPY/build/CMakeFiles/rebuild_cache.dir
+/backup/weiye/src_binary_droplet_COPY/build/CMakeFiles/DropletCombustion.dir
+/backup/weiye/src_binary_droplet_COPY/build/CMakeFiles/edit_cache.dir

build/Makefile

@@ -48,10 +48,10 @@ RM = /usr/bin/cmake -E remove -f
 EQUALS = =
 
 # The top-level source directory on which CMake was run.
-CMAKE_SOURCE_DIR = /backup/weiye/src_binary_droplet
+CMAKE_SOURCE_DIR = /backup/weiye/src_binary_droplet_COPY
 
 # The top-level build directory on which CMake was run.
-CMAKE_BINARY_DIR = /backup/weiye/src_binary_droplet/build
+CMAKE_BINARY_DIR = /backup/weiye/src_binary_droplet_COPY/build
 
 #=============================================================================
 # Targets provided globally by CMake.
@@ -80,9 +80,9 @@ edit_cache/fast: edit_cache
 
 # The main all target
 all: cmake_check_build_system
-	$(CMAKE_COMMAND) -E cmake_progress_start /backup/weiye/src_binary_droplet/build/CMakeFiles /backup/weiye/src_binary_droplet/build/CMakeFiles/progress.marks
+	$(CMAKE_COMMAND) -E cmake_progress_start /backup/weiye/src_binary_droplet_COPY/build/CMakeFiles /backup/weiye/src_binary_droplet_COPY/build/CMakeFiles/progress.marks
 	$(MAKE) -f CMakeFiles/Makefile2 all
-	$(CMAKE_COMMAND) -E cmake_progress_start /backup/weiye/src_binary_droplet/build/CMakeFiles 0
+	$(CMAKE_COMMAND) -E cmake_progress_start /backup/weiye/src_binary_droplet_COPY/build/CMakeFiles 0
 .PHONY : all
 
 # The main clean target

build/cmake_install.cmake

@@ -1,4 +1,4 @@
-# Install script for directory: /backup/weiye/src_binary_droplet
+# Install script for directory: /backup/weiye/src_binary_droplet_COPY
 
 # Set the install prefix
 if(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -45,5 +45,5 @@ endif()
 
 string(REPLACE ";" "\n" CMAKE_INSTALL_MANIFEST_CONTENT
        "${CMAKE_INSTALL_MANIFEST_FILES}")
-file(WRITE "/backup/weiye/src_binary_droplet/build/${CMAKE_INSTALL_MANIFEST}"
+file(WRITE "/backup/weiye/src_binary_droplet_COPY/build/${CMAKE_INSTALL_MANIFEST}"
      "${CMAKE_INSTALL_MANIFEST_CONTENT}")

include/UserData.h

@@ -6,6 +6,8 @@
 
 #include "gridRoutines.h"
 #include <string>
+#include <Eigen/Dense>
+#include <vector>
 
 #ifndef USER_DEF
 #define USER_DEF
@@ -16,16 +18,31 @@ typedef struct UserDataTag{
 	/*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];
+    //double dropMole[2];
+
     /* Droplet species density at given initialTemperature*/
-    double dropDens[2];
-    /* Droplet species mass fractions*/
-    double dropMassFrac[2];
-    double dropRho; 
+    //double dropDens[2];
+
+    
+    //double dropRho; 
+
+	/* Classfication of droplet type : */
+	/* dropType = 0 : single component droplet */
+	/* dropType = 1 : binary components droplet */
+	/* 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<std::string> dropSpec;
+	std::vector<double> dropMole; 
+    //char dropSpec[2][10] = {"propane","n-heptane"};
+
+	/* Droplet species mole fractions */
+    //double dropMoleFrac[2];
+	
 	/*Length of the domain (in meters):*/			  
 	double domainLength;	  
 	/*Initial Droplet Radius (in meters)*/
@@ -219,3 +236,5 @@ void setSaneDefaults(UserData data);
 void freeUserData(UserData data);
 #endif
 
+void getGamma(const double mole[],double gamma[]) ;
+

include/parse.h

@@ -1,15 +1,18 @@
 #ifndef PRINT_DEF
 #define PRINT_DEF
 #include <string.h>	//for strings
-#include <stdio.h>	//for printf,scanf
+#include <stdio.h>	//for printf,scanf (library for C)
 #include <stdlib.h>	//for atoi, atof
-#include <string>
+#include <string>   //C++ header for string
 #include <cstring>
 #include <iostream>
 #include <stdexcept>
 #endif
 
-#ifndef PARSE_DEF
+#include <vector>
+#include <sstream>
+
+#ifndef PARSE_DEF	```
 #define PARSE_DEF
 #define MAXBUFLEN 200
 
@@ -27,6 +30,13 @@ template<typename T>
 int parseArray(FILE* input, const char* keyword, const size_t bufLen,
 		const size_t arrLen, T y[]);
 
+
+template<typename T> 
+int parseDropSpec(FILE* input, const char* keyword, const size_t bufLen,int* dropType, std::vector<T>& dropPara);
+
+template<> 
+int parseDropSpec<std::string>(FILE* input, const char* keyword, const size_t bufLen,int* dropType, std::vector<std::string>& dropPara);
+
 int parseDrop(FILE* input, const char* keyword,char dropSpec[][10],double dropMole[],const size_t bufLen);
 
 #include "parse.hpp"

include/parse.hpp

@@ -73,3 +73,53 @@ int parseArray(FILE* input, const char* keyword, const size_t bufLen,
 	rewind(input);
 	return(-1);
 }
+
+
+/* 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);
+}
+
+/* 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);
+

src/UserData.cpp

@@ -120,18 +120,44 @@ UserData allocateUserData(FILE *input){
 		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");
+	ier=parseNumber<int>(input,"dropType",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");
 		return(NULL);
 	}
 
-	ier=parseNumber<double>(input, "dPdt"		, MAXBUFLEN, &data->dPdt);
+	ier=parseDropSpec<double>(input,"dropletMole",MAXBUFLEN,&data->dropType,dropMole);
+	if(ier== -1){
+		printf("include correct format for droplet mole fraction!\n");
+		printf("single composition droplet: dropletMole:1.00\n");
+		printf("binary composition droplet: dropletMole:0.3,0.7\n");
+		return(NULL);
+	}
+
+	ier=parseDropSpec<std::string>(input,"dropletComposition",MAXBUFLEN,&data->dropType,dropSpec);
+	if(ier== -1){
+		printf("include correct format for droplet composition!\n");
+		printf("single composition droplet: dropletComposition:n-heptane\n");
+		printf("binary composition droplet: dropletComposition:propane,n-heptane\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);
+	ier=parseNumber<double>(input, "Rg", MAXBUFLEN, &data->Rg);
 	if(data->Rg < 0.0){
 		printf("Rg must be greater than 0");
 		return(NULL);
@@ -352,8 +378,8 @@ UserData allocateUserData(FILE *input){
 	//	return(NULL);
 	//}
 
-    ier=parseDrop(input,"dropletComposition",data->dropSpec,data->dropMole,MAXBUFLEN);
-    ier=parseDrop(input,"dropletDensity",data->dropSpec,data->dropDens,MAXBUFLEN);
+    //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);
@@ -364,9 +390,25 @@ UserData allocateUserData(FILE *input){
     
 
 	ier=parseNumber<double>(input, "PCAD", MAXBUFLEN, &data->PCAD);
+	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);
+	}
     ier=parseNumber<int>(input,"JJRG", MAXBUFLEN, &data->JJRG);
+	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);
+	}
 	
     data->nr=0;
 	//data->np=data->nr+1;
@@ -385,21 +427,26 @@ UserData allocateUserData(FILE *input){
         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];
-    }
+    // 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;
 
+	/* 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]) ;
+
 	if(!data->adaptiveGrid){
 		data->uniformGrid = new double [data->npts];
 		data->neq=data->nvar*data->npts;
@@ -415,12 +462,6 @@ UserData allocateUserData(FILE *input){
 		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;
 	}
@@ -497,3 +538,38 @@ void setSaneDefaults(UserData data){
     data->deltaT=200.0;
 }
 
+
+void getGamma(const double mole[],double gamma[]){
+    /* 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(int 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(int 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(int i=0; i<v_.size(); i++){
+        gamma[i] = gammaC_[i] ;
+    }
+
+}

src/main.cpp

@@ -398,7 +398,7 @@ int main(){
             }
 
             /*Floor small value to zero*/
-            floorSmallValue(data, &y);
+            //floorSmallValue(data, &y);
 
 			if(count%data->nSaves==0 && !data->writeEveryRegrid){
 				printSpaceTimeOutput(tNow, &y, data->output, data);

src/parse.cpp

@@ -19,7 +19,14 @@ void getFromString (const char* buf, char* n){
 	printf("%s\n",n);
 }
 
-/*Extract droplet species and mole fractions*/
+std::string getFromString(const char* buf){
+    std::string n(buf);
+    printf("%s\n",n.c_str()); 
+    return 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];
@@ -77,3 +84,47 @@ int parseDrop(FILE* input, const char* keyword,char dropSpec[][10],double dropMo
 	rewind(input);
 	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);
+}

src/residue.cpp

@@ -1194,8 +1194,9 @@ int residue(double t, N_Vector y, N_Vector ydot, N_Vector res, void *user_data){
     /*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] ;    //unit:Pa,Helgeson and Sage,1967,Propane
-    p_i[1] = 1.0e5*pow(10,4.02832-(1268.636/(T(1)-56.199)))*data->dropMole[0] ;    //unit:Pa,n-Heptane
+    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